diff --git a/.rubocop.yml b/.rubocop.yml new file mode 100644 index 00000000..132c1191 --- /dev/null +++ b/.rubocop.yml @@ -0,0 +1,2 @@ +Metrics/LineLength: + Max: 120 \ No newline at end of file diff --git a/Capfile b/Capfile index ef82ed7d..b20936e7 100644 --- a/Capfile +++ b/Capfile @@ -1,3 +1,5 @@ +# frozen_string_literal: true + # Load DSL and Setup Up Stages require 'capistrano/setup' require 'capistrano/deploy' @@ -17,4 +19,4 @@ require 'capistrano/sidekiq/monit' require 'whenever/capistrano' # Loads custom tasks from `lib/capistrano/tasks' if you have any defined. -Dir.glob('lib/capistrano/tasks/*.rake').each { |r| import r } \ No newline at end of file +Dir.glob('lib/capistrano/tasks/*.rake').each { |r| import r } diff --git a/GBOLapp/vendor/plugins/bioruby/generators/bioruby/bioruby_generator.rb b/GBOLapp/vendor/plugins/bioruby/generators/bioruby/bioruby_generator.rb index 0896bd7b..e28adcd1 100644 --- a/GBOLapp/vendor/plugins/bioruby/generators/bioruby/bioruby_generator.rb +++ b/GBOLapp/vendor/plugins/bioruby/generators/bioruby/bioruby_generator.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class BiorubyGenerator < Rails::Generator::Base def manifest record do |m| @@ -26,4 +28,3 @@ def manifest end end end - diff --git a/GBOLapp/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_helper.rb b/GBOLapp/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_helper.rb index 9905406e..9d973794 100644 --- a/GBOLapp/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_helper.rb +++ b/GBOLapp/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_helper.rb @@ -1,9 +1,10 @@ -module BiorubyHelper +# frozen_string_literal: true +module BiorubyHelper include Bio::Shell def project_workdir - if Bio::Shell.cache[:savedir].match(/\.bioruby$/) + if Bio::Shell.cache[:savedir] =~ /\.bioruby$/ Bio::Shell.cache[:workdir] else Bio::Shell.cache[:savedir] @@ -15,13 +16,13 @@ def have_results end def local_variables - eval("local_variables", Bio::Shell.cache[:binding]) - + eval('local_variables', Bio::Shell.cache[:binding]) - BiorubyController::HIDE_VARIABLES end def render_log(page) - page.insert_html :top, :logs, :partial => "log" - page.replace_html "variables", :partial => "variables" + page.insert_html :top, :logs, partial: 'log' + page.replace_html 'variables', partial: 'variables' page.hide "methods_#{@number}" page.hide "classes_#{@number}" page.hide "modules_#{@number}" @@ -31,17 +32,15 @@ def reference_link(class_or_module) name = class_or_module.to_s case name when /Bio::(.+)/ - path = $1.split('::').join('/') + path = Regexp.last_match(1).split('::').join('/') url = "http://bioruby.org/rdoc/classes/Bio/#{path}.html" when /Chem::(.+)/ - path = $1.split('::').join('/') + path = Regexp.last_match(1).split('::').join('/') url = "http://chemruby.org/rdoc/classes/Chem/#{path}.html" else path = name.split('::').join('/') url = "http://www.ruby-doc.org/core/classes/#{path}.html" end - return "#{name}" + "#{name}" end - end - diff --git a/Gemfile b/Gemfile index 7f0af0bd..92aa00b2 100644 --- a/Gemfile +++ b/Gemfile @@ -1,3 +1,5 @@ +# frozen_string_literal: true + source 'https://rubygems.org' ruby '2.3.3' @@ -12,9 +14,9 @@ gem 'pg_search' gem 'puma', '~> 3.0' gem 'redis', '~> 3.0' # Use Redis adapter to run Action Cable in production gem 'sidekiq' -gem 'sidekiq-limit_fetch' gem 'sidekiq-client-cli' -gem 'sinatra', :require => false # Needed to monitor sidekiq jobs +gem 'sidekiq-limit_fetch' +gem 'sinatra', require: false # Needed to monitor sidekiq jobs # Asset pipeline gem 'coffee-rails', '~> 4.2' # Use CoffeeScript for .coffee assets and views @@ -32,12 +34,12 @@ gem 'aws-sdk' gem 'paperclip' # Javascript +gem 'bootstrap-multiselect_rails' # multi select boxes using bootstrap gem 'chosen-rails' # Javascript select boxes gem 'jquery-datatables-rails', github: 'rweng/jquery-datatables-rails' gem 'jquery-fileupload-rails' gem 'jquery-turbolinks' gem 'select2-rails' # Integrate Select2 Javascript library -gem 'bootstrap-multiselect_rails' # multi select boxes using bootstrap gem 'bcrypt', '~> 3.1.7', platforms: :ruby gem 'bio' # BioRuby @@ -51,14 +53,14 @@ gem 'roo-xls' # Handle excel files gem 'rubyzip' # Handle zip files gem 'simple_form' gem 'slim' # TODO: Used anywhere? -gem 'sprockets-rails', :require => 'sprockets/railtie' +gem 'sprockets-rails', require: 'sprockets/railtie' # gem 'turbolinks' # Turbolinks makes navigating your web application faster TODO: Does not work unless first changes to js code, in particular data-tables (see http://guides.rubyonrails.org/working_with_javascript_in_rails.html#turbolinks) gem 'whenever', require: false # Runs scheduled jobs via cron gem 'will_paginate', '> 3.0' # TODO: Really needed? gem 'will_paginate-bootstrap' # TODO: Really needed? # Windows does not include zoneinfo files, so bundle the tzinfo-data gem -gem 'tzinfo-data', platforms: [:mingw, :mswin, :x64_mingw, :jruby] +gem 'tzinfo-data', platforms: %i[mingw mswin x64_mingw jruby] group :development do gem 'capistrano', require: false diff --git a/Rakefile b/Rakefile index e85f9139..488c551f 100644 --- a/Rakefile +++ b/Rakefile @@ -1,3 +1,5 @@ +# frozen_string_literal: true + # Add your own tasks in files placed in lib/tasks ending in .rake, # for example lib/tasks/capistrano.rake, and they will automatically be available to Rake. diff --git a/app/controllers/application_controller.rb b/app/controllers/application_controller.rb index 5dd28135..65209822 100644 --- a/app/controllers/application_controller.rb +++ b/app/controllers/application_controller.rb @@ -1,11 +1,13 @@ +# frozen_string_literal: true + class ApplicationController < ActionController::Base - check_authorization :unless => :devise_controller? + check_authorization unless: :devise_controller? # Prevent CSRF attacks by raising an exception. # For APIs, you may want to use :null_session instead. protect_from_forgery with: :exception - rescue_from CanCan::AccessDenied do |exception| + rescue_from CanCan::AccessDenied do |_exception| redirect_back(fallback_location: root_url, alert: 'You are not authorized to access this page or perform this action.') end end diff --git a/app/controllers/concerns/project_concern.rb b/app/controllers/concerns/project_concern.rb index 4057740e..98d9a84d 100644 --- a/app/controllers/concerns/project_concern.rb +++ b/app/controllers/concerns/project_concern.rb @@ -1,7 +1,9 @@ +# frozen_string_literal: true + module ProjectConcern extend ActiveSupport::Concern def current_project_id - user_signed_in? ? current_user.default_project_id : Project.where('name like ?', "All%").first.id + user_signed_in? ? current_user.default_project_id : Project.where('name like ?', 'All%').first.id end -end \ No newline at end of file +end diff --git a/app/controllers/contig_searches_controller.rb b/app/controllers/contig_searches_controller.rb index 06abb64b..c4b6e4a5 100644 --- a/app/controllers/contig_searches_controller.rb +++ b/app/controllers/contig_searches_controller.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class ContigSearchesController < ApplicationController load_and_authorize_resource @@ -15,8 +17,8 @@ def new def create @contig_search = ContigSearch.create!(contig_search_params) - @contig_search.update(:user_id => current_user.id) - @contig_search.update(:project_id => current_user.default_project_id) + @contig_search.update(user_id: current_user.id) + @contig_search.update(project_id: current_user.default_project_id) redirect_to @contig_search end @@ -51,7 +53,7 @@ def delete_all def export_as_pde @contig_search = ContigSearch.find(params[:contig_search_id]) file_name = @contig_search.title.empty? ? "contig_search_#{@contig_search.created_at}" : @contig_search.title - send_data(ContigSearch.pde(@contig_search.contigs.includes(:partial_cons, isolate: [individual: :species]), add_reads: false), :filename => "#{file_name}.pde", :type => "application/txt") + send_data(ContigSearch.pde(@contig_search.contigs.includes(:partial_cons, isolate: [individual: :species]), add_reads: false), filename: "#{file_name}.pde", type: 'application/txt') end # TODO: Unfinished feature @@ -68,6 +70,7 @@ def export_as_pde # end private + # Never trust parameters from the scary internet, only allow the white list through. def contig_search_params params.require(:contig_search).permit(:title, :assembled, :has_warnings, :family, :marker, :max_age, :max_update, :min_age, :min_update, :name, :order, :species, :specimen, :verified, :verified_by, :project_id, :search_result_archive) diff --git a/app/controllers/contigs_controller.rb b/app/controllers/contigs_controller.rb index 6bc5c71d..2a26cb94 100644 --- a/app/controllers/contigs_controller.rb +++ b/app/controllers/contigs_controller.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class ContigsController < ApplicationController include ProjectConcern @@ -5,8 +7,8 @@ class ContigsController < ApplicationController skip_before_action :verify_authenticity_token - before_action :set_contig, only: [:verify_next, :verify, :pde, :fasta, :fasta_trimmed, :fasta_raw, :overlap, :overlap_background, :show, :edit,\ - :update, :destroy] + before_action :set_contig, only: %i[verify_next verify pde fasta fasta_trimmed fasta_raw overlap overlap_background show edit + update destroy] # GET /contigs # GET /contigs.json @@ -32,8 +34,8 @@ def externally_verified end def filter - @contigs = Contig.in_project(current_project_id).order(:name).where("name ilike ?", "%#{params[:term]}%").limit(100) - size = Contig.in_project(current_project_id).order(:name).where("name ilike ?", "%#{params[:term]}%").size + @contigs = Contig.in_project(current_project_id).order(:name).where('name ilike ?', "%#{params[:term]}%").limit(100) + size = Contig.in_project(current_project_id).order(:name).where('name ilike ?', "%#{params[:term]}%").size if size > 100 message = "and #{size} more..." @@ -45,8 +47,7 @@ def filter # GET /contigs/1 # GET /contigs/1.json - def show - end + def show; end # GET /contigs/new def new @@ -54,8 +55,7 @@ def new end # GET /contigs/1/edit - def edit - end + def edit; end # POST /contigs # POST /contigs.json @@ -79,10 +79,10 @@ def create def update respond_to do |format| if @contig.update(contig_params) - format.html { + format.html do Issue.create(title: "Contig updated by #{current_user.name}", contig_id: @contig.id) redirect_back(fallback_location: edit_contig_path(@contig), notice: 'Contig was successfully updated.') - } + end format.json { render :show, status: :ok, location: @contig } else format.html { render :edit } @@ -107,7 +107,7 @@ def compare_contigs CompareContigs.perform_async(contig_names) - send_data("Comparison started as background process, may take a minute or so. View results under http://gbol5.de/analysis_output\n", filename: "msg.txt", type: "application/txt") + send_data("Comparison started as background process, may take a minute or so. View results under http://gbol5.de/analysis_output\n", filename: 'msg.txt', type: 'application/txt') end def analysis_output @@ -116,7 +116,6 @@ def analysis_output # for overwriting with externally edited / verified contigs in fas format (via .pde) def change_via_script - filename = params[:filename] fastastring = params[:fastastring] @@ -134,23 +133,20 @@ def change_via_script contig.assembled = true contig.verified = true - contig.verified_by = 8 #User.first.id #unclear who did external verification, but won't be displayed anyway if imported + contig.verified_by = 8 # User.first.id #unclear who did external verification, but won't be displayed anyway if imported contig.verified_at = Time.zone.now # destroy all current partial_cons contig.partial_cons.destroy_all - #create a single new partial_con to be overwritten by imported stuff + # create a single new partial_con to be overwritten by imported stuff new_partial_con = contig.partial_cons.create - # get aligned read sequences - fas_seqs = fastastring.split(">") - + fas_seqs = fastastring.split('>') fas_seqs[1..-1].each do |fs| - pair = fs.split("\n") # overwrite single reads (aligned - / manually corrected version (?) ) (> that do match general read pattern; use the exactly matching read or generate new) @@ -167,7 +163,7 @@ def change_via_script primer_read.aligned_seq = pair[1] - #cannot use aligned qualities since not existing when imported from external alignment: + # cannot use aligned qualities since not existing when imported from external alignment: primer_read.aligned_qualities = primer_read.qualities primer_read.overwritten = true @@ -175,7 +171,7 @@ def change_via_script primer_read.used_for_con = true primer_read.assembled = true - # todo: adjust trimmedReadStart etc. based on ???? in aligned_seq (though this is not technically correct due to alignemnt of ??? with gappy stretches in other reads) + # TODO: adjust trimmedReadStart etc. based on ???? in aligned_seq (though this is not technically correct due to alignemnt of ??? with gappy stretches in other reads) if primer_read.trimmedReadStart.nil? primer_read.trimmedReadStart = 1 @@ -197,15 +193,14 @@ def change_via_script # generate marker sequence ms = MarkerSequence.find_or_create_by(name: contig.name) - ms.sequence = pair[1].gsub('-','') - ms.sequence = ms.sequence.gsub('?','') + ms.sequence = pair[1].delete('-') + ms.sequence = ms.sequence.delete('?') ms.contigs << contig ms.marker = contig.marker ms.isolate = contig.isolate ms.save end - end new_partial_con.save @@ -216,17 +211,16 @@ def change_via_script output = "No match found.\n" end - send_data(output, filename: "#{filename}.txt", type: "application/txt") - + send_data(output, filename: "#{filename}.txt", type: 'application/txt') end def identify_primer_read(read_name) - primer_read = PrimerRead.where("name ILIKE ?", "#{read_name}.scf").first + primer_read = PrimerRead.where('name ILIKE ?', "#{read_name}.scf").first if primer_read return primer_read else - primer_read = PrimerRead.where("name ILIKE ?", "#{read_name}.ab1").first + primer_read = PrimerRead.where('name ILIKE ?', "#{read_name}.ab1").first if primer_read return primer_read else @@ -234,14 +228,14 @@ def identify_primer_read(read_name) end end - return nil + nil end def identify_contig(c) contig_name = c[0...-4] - #match found? - contig = Contig.in_project(current_project_id).where("name ILIKE ?", contig_name).first + # match found? + contig = Contig.in_project(current_project_id).where('name ILIKE ?', contig_name).first if contig return contig if contig @@ -256,22 +250,19 @@ def identify_contig(c) isolate_name = m[1] begin primer_names = m[2] - primer_name = primer_names.split("_").last - primer = Primer.where("name ILIKE ?", primer_name).first + primer_name = primer_names.split('_').last + primer = Primer.where('name ILIKE ?', primer_name).first if primer marker = primer.marker if marker true_marker_name = marker.name true_contig_name = isolate_name + "_#{true_marker_name}" - contig = Contig.in_project(current_project_id).where("name ILIKE ?", true_contig_name).first - if contig - return contig - end + contig = Contig.in_project(current_project_id).where('name ILIKE ?', true_contig_name).first + return contig if contig end end - rescue + rescue StandardError end - else end end end @@ -287,23 +278,23 @@ def assemble_all end def verify - if @contig.verified_by or @contig.verified + if @contig.verified_by || @contig.verified @contig.update(verified_by: nil, verified_at: nil, verified: false) - redirect_to edit_contig_path, notice: "Set to non-verified." + redirect_to edit_contig_path, notice: 'Set to non-verified.' else @contig.update(verified_by: current_user.id, verified_at: Time.now, assembled: true, verified: true) # generate / update marker sequence ms = MarkerSequence.find_or_create_by(name: @contig.name) partial_cons = @contig.partial_cons.first - ms.sequence = partial_cons.aligned_sequence.gsub('-','') - ms.sequence = ms.sequence.gsub('?','') + ms.sequence = partial_cons.aligned_sequence.delete('-') + ms.sequence = ms.sequence.delete('?') ms.contigs << @contig ms.marker = @contig.marker ms.isolate = @contig.isolate ms.save - redirect_to edit_contig_path, notice: "Verified & linked marker sequence updated." + redirect_to edit_contig_path, notice: 'Verified & linked marker sequence updated.' end end @@ -314,8 +305,8 @@ def verify_next # generate marker sequence ms = MarkerSequence.find_or_create_by(name: @contig.name) partial_cons = @contig.partial_cons.first - ms.sequence = partial_cons.aligned_sequence.gsub('-','') - ms.sequence = ms.sequence.gsub('?','') + ms.sequence = partial_cons.aligned_sequence.delete('-') + ms.sequence = ms.sequence.delete('?') ms.contigs << @contig ms.marker = @contig.marker ms.isolate = @contig.isolate @@ -346,22 +337,22 @@ def overlap_background def pde pde = Contig.pde([@contig], add_reads: true) - send_data(pde, filename: "#{@contig.name}.pde", type: "application/txt") + send_data(pde, filename: "#{@contig.name}.pde", type: 'application/txt') end def fasta fasta = Contig.fasta([@contig], mode: 'assembled') - send_data(fasta, filename: "#{@contig.name}.fas", type: "application/txt") + send_data(fasta, filename: "#{@contig.name}.fas", type: 'application/txt') end def fasta_trimmed fasta = Contig.fasta([@contig], mode: 'trimmed') - send_data(fasta, filename: "#{@contig.name}_trimmed.fas", type: "application/txt") + send_data(fasta, filename: "#{@contig.name}_trimmed.fas", type: 'application/txt') end def fasta_raw fasta = Contig.fasta([@contig], mode: 'raw') - send_data(fasta, filename: "#{@contig.name}_raw.fas", type: "application/txt") + send_data(fasta, filename: "#{@contig.name}_raw.fas", type: 'application/txt') end # TODO: Not used anywhere yet, talk to Susi about her needs for this export @@ -373,7 +364,7 @@ def fastq fastq = Contig.fastq(contigs.where(verified: true, imported: false), use_mira) - send_data(fastq, filename: "contigs.fastq", type: "application/txt") + send_data(fastq, filename: 'contigs.fastq', type: 'application/txt') end # Is used by API endpoint to compare sequences to PacBio data @@ -386,16 +377,15 @@ def as_fasq contig_names_array = contig_names.split - fasq_str = +"" + fasq_str = +'' not_included_str = +"\n\n\n--------------------------------------------------------------------\n\n\n" contig_names_array.map do |contig_name| - contig_name += "_#{marker}" # mk case insensitive - contig = Contig.in_project(current_project_id).where("name ILIKE ?", contig_name).first + contig = Contig.in_project(current_project_id).where('name ILIKE ?', contig_name).first # ignore if not verified if contig @@ -406,7 +396,7 @@ def as_fasq begin fasq = contig.as_fasq(mira) fasq_str += fasq - rescue + rescue StandardError not_included_str += "#{contig_name}: Unknown issue.\n" end end @@ -418,7 +408,7 @@ def as_fasq end end - send_data(fasq_str + not_included_str, :filename => "fasq.txt", :type => "application/txt") + send_data(fasq_str + not_included_str, filename: 'fasq.txt', type: 'application/txt') end private @@ -429,14 +419,14 @@ def set_contig end # Never trust parameters from the scary internet, only allow the white list through. - #TODO mira and marker only used by fastq export - #TODO contig_names is only used by contig compare feature - #TODO filename and fastastring are only used by change via script action - #TODO: isolate_name used in form for contig, but cant that be done via id? + # TODO mira and marker only used by fastq export + # TODO contig_names is only used by contig compare feature + # TODO filename and fastastring are only used by change via script action + # TODO: isolate_name used in form for contig, but cant that be done via id? def contig_params params.require(:contig).permit(:mira, :marker, :overlap_length, :allowed_mismatch_percent, :imported, :contig_names, :filename, :fastastring, :comment, :assembled, :name, :consensus, :marker_id, :isolate_id, :marker_sequence_id, :term, :isolate_name, :verified, project_ids: []) end -end \ No newline at end of file +end diff --git a/app/controllers/families_controller.rb b/app/controllers/families_controller.rb index 018fc47a..c3485c1e 100644 --- a/app/controllers/families_controller.rb +++ b/app/controllers/families_controller.rb @@ -1,9 +1,11 @@ +# frozen_string_literal: true + class FamiliesController < ApplicationController include ProjectConcern load_and_authorize_resource - before_action :set_family, only: [:show, :edit, :update, :destroy] + before_action :set_family, only: %i[show edit update destroy] # GET /families # GET /families.json @@ -14,7 +16,7 @@ def index end def filter - @families = Family.in_project(current_project_id).order(:name).where("families.name ilike ?", "%#{params[:term]}%") + @families = Family.in_project(current_project_id).order(:name).where('families.name ilike ?', "%#{params[:term]}%") render json: @families.map(&:name) end @@ -27,8 +29,7 @@ def show_species # GET /families/1 # GET /families/1.json - def show - end + def show; end # GET /families/new def new @@ -36,8 +37,7 @@ def new end # GET /families/1/edit - def edit - end + def edit; end # POST /families # POST /families.json @@ -89,6 +89,6 @@ def set_family # Never trust parameters from the scary internet, only allow the white list through. def family_params - params.require(:family).permit(:name, :author, :order_id, :term, :project_ids => []) + params.require(:family).permit(:name, :author, :order_id, :term, project_ids: []) end end diff --git a/app/controllers/freezers_controller.rb b/app/controllers/freezers_controller.rb index 2a594385..d551529c 100644 --- a/app/controllers/freezers_controller.rb +++ b/app/controllers/freezers_controller.rb @@ -1,9 +1,11 @@ +# frozen_string_literal: true + class FreezersController < ApplicationController include ProjectConcern load_and_authorize_resource - before_action :set_freezer, only: [:show, :edit, :update, :destroy] + before_action :set_freezer, only: %i[show edit update destroy] # GET /freezers # GET /freezers.json @@ -16,8 +18,7 @@ def index # GET /freezers/1 # GET /freezers/1.json - def show - end + def show; end # GET /freezers/new def new @@ -25,8 +26,7 @@ def new end # GET /freezers/1/edit - def edit - end + def edit; end # POST /freezers # POST /freezers.json @@ -78,6 +78,6 @@ def set_freezer # Never trust parameters from the scary internet, only allow the white list through. def freezer_params - params.require(:freezer).permit(:freezercode, :lab_id, :project_ids => []) + params.require(:freezer).permit(:freezercode, :lab_id, project_ids: []) end end diff --git a/app/controllers/higher_order_taxons_controller.rb b/app/controllers/higher_order_taxons_controller.rb index e1bf726c..5ea44e4c 100644 --- a/app/controllers/higher_order_taxons_controller.rb +++ b/app/controllers/higher_order_taxons_controller.rb @@ -1,9 +1,11 @@ +# frozen_string_literal: true + class HigherOrderTaxonsController < ApplicationController include ProjectConcern load_and_authorize_resource - before_action :set_higher_order_taxon, only: [:show, :edit, :update, :destroy] + before_action :set_higher_order_taxon, only: %i[show edit update destroy] # GET /higher_order_taxons # GET /higher_order_taxons.json @@ -20,8 +22,7 @@ def show_species # GET /higher_order_taxons/1 # GET /higher_order_taxons/1.json - def show - end + def show; end # GET /higher_order_taxons/new def new @@ -29,8 +30,7 @@ def new end # GET /higher_order_taxons/1/edit - def edit - end + def edit; end # POST /higher_order_taxons # POST /higher_order_taxons.json @@ -82,6 +82,6 @@ def set_higher_order_taxon # Never trust parameters from the scary internet, only allow the white list through. def higher_order_taxon_params - params.require(:higher_order_taxon).permit(:position, :name, :german_name,:marker_ids => [], :project_ids => []) + params.require(:higher_order_taxon).permit(:position, :name, :german_name, marker_ids: [], project_ids: []) end end diff --git a/app/controllers/home_controller.rb b/app/controllers/home_controller.rb index d307bd2e..f17de7a2 100644 --- a/app/controllers/home_controller.rb +++ b/app/controllers/home_controller.rb @@ -1,5 +1,6 @@ -class HomeController < ApplicationController +# frozen_string_literal: true +class HomeController < ApplicationController def overview authorize! :overview, :home end @@ -19,12 +20,7 @@ def privacy_policy authorize! :privacy_policy, :home end - def help - - end - - def contact - - end + def help; end + def contact; end end diff --git a/app/controllers/individual_searches_controller.rb b/app/controllers/individual_searches_controller.rb index 7e718a17..162c512a 100644 --- a/app/controllers/individual_searches_controller.rb +++ b/app/controllers/individual_searches_controller.rb @@ -1,7 +1,9 @@ +# frozen_string_literal: true + class IndividualSearchesController < ApplicationController load_and_authorize_resource - before_action :set_individual_search, only: [:show, :edit, :update, :destroy] + before_action :set_individual_search, only: %i[show edit update destroy] def index respond_to do |format| @@ -24,8 +26,8 @@ def new def create @individual_search = IndividualSearch.new(individual_search_params) - @individual_search.update(:user_id => current_user.id) - @individual_search.update(:project_id => current_user.default_project_id) + @individual_search.update(user_id: current_user.id) + @individual_search.update(project_id: current_user.default_project_id) respond_to do |format| if @individual_search.save diff --git a/app/controllers/individuals_controller.rb b/app/controllers/individuals_controller.rb index 61ec69b8..73de43a6 100644 --- a/app/controllers/individuals_controller.rb +++ b/app/controllers/individuals_controller.rb @@ -1,9 +1,11 @@ +# frozen_string_literal: true + class IndividualsController < ApplicationController include ProjectConcern load_and_authorize_resource - before_action :set_individual, :only => [:show, :edit, :update, :destroy] + before_action :set_individual, only: %i[show edit update destroy] def index respond_to do |format| @@ -24,20 +26,19 @@ def xls def problematic_specimens # Liste aller Bundesländer to check 'state_province' against: - @states = %w(Baden-Württemberg Bayern Berlin Brandenburg Bremen Hamburg Hessen Mecklenburg-Vorpommern Niedersachsen Nordrhein-Westfalen Rheinland-Pfalz Saarland Sachsen Sachsen-Anhalt Schleswig-Holstein Thüringen) + @states = %w[Baden-Württemberg Bayern Berlin Brandenburg Bremen Hamburg Hessen Mecklenburg-Vorpommern Niedersachsen Nordrhein-Westfalen Rheinland-Pfalz Saarland Sachsen Sachsen-Anhalt Schleswig-Holstein Thüringen] @individuals = [] Individual.in_project(current_project_id).each do |i| - if i.country == "Germany" + if i.country == 'Germany' @individuals.push(i) unless @states.include? i.state_province end end - end def filter - @individuals = Individual.where("individuals.specimen_id ilike ?", "%#{params[:term]}%").in_project(current_project_id).limit(100) - size = Individual.where("individuals.specimen_id ilike ?", "%#{params[:term]}%").in_project(current_project_id).size + @individuals = Individual.where('individuals.specimen_id ilike ?', "%#{params[:term]}%").in_project(current_project_id).limit(100) + size = Individual.where('individuals.specimen_id ilike ?', "%#{params[:term]}%").in_project(current_project_id).size if size > 100 message = "and #{size} more..." @@ -49,8 +50,7 @@ def filter # GET /individuals/1 # GET /individuals/1.json - def show - end + def show; end # GET /individuals/new def new @@ -58,8 +58,7 @@ def new end # GET /individuals/1/edit - def edit - end + def edit; end # POST /individuals # POST /individuals.json @@ -137,6 +136,6 @@ def individual_params :comments, :species_id, :species_name, - :project_ids => []) + project_ids: []) end -end \ No newline at end of file +end diff --git a/app/controllers/isolates_controller.rb b/app/controllers/isolates_controller.rb index b885ca10..b077df51 100644 --- a/app/controllers/isolates_controller.rb +++ b/app/controllers/isolates_controller.rb @@ -1,9 +1,11 @@ +# frozen_string_literal: true + class IsolatesController < ApplicationController include ProjectConcern load_and_authorize_resource - before_action :set_isolate, only: [:show, :edit, :update, :destroy] + before_action :set_isolate, only: %i[show edit update destroy] def index respond_to do |format| @@ -12,8 +14,7 @@ def index end end - def duplicates - end + def duplicates; end def no_specimen respond_to do |format| @@ -33,15 +34,13 @@ def import redirect_to isolates_path, notice: 'Imported.' end - def show - end + def show; end def new @isolate = Isolate.new end - def edit - end + def edit; end def create @isolate = Isolate.new(isolate_params) @@ -87,11 +86,11 @@ def set_isolate # Never trust parameters from the scary internet, only allow the white list through. def isolate_params - params.require(:isolate).permit(:comment_orig, :comment_copy, :micronic_tube_id_copy, :micronic_tube_id_orig, :concentration_copy, :concentration_orig, :well_pos_micronic_plate_copy, :well_pos_micronic_plate_orig, :micronic_plate_id_copy,:micronic_plate_id_orig, :isolation_date, :lab_id_copy, :lab_id_orig, :user_id, :well_pos_plant_plate, :lab_nr, :micronic_tube_id, :well_pos_micronic_plate, :concentration, + params.require(:isolate).permit(:comment_orig, :comment_copy, :micronic_tube_id_copy, :micronic_tube_id_orig, :concentration_copy, :concentration_orig, :well_pos_micronic_plate_copy, :well_pos_micronic_plate_orig, :micronic_plate_id_copy, :micronic_plate_id_orig, :isolation_date, :lab_id_copy, :lab_id_orig, :user_id, :well_pos_plant_plate, :lab_nr, :micronic_tube_id, :well_pos_micronic_plate, :concentration, :tissue_id, :micronic_plate_id, :plant_plate_id, :term, :file, :individual_name, :query, - :project_ids => []) + project_ids: []) end end diff --git a/app/controllers/issues_controller.rb b/app/controllers/issues_controller.rb index 4db092c2..dc1d453d 100644 --- a/app/controllers/issues_controller.rb +++ b/app/controllers/issues_controller.rb @@ -1,9 +1,11 @@ +# frozen_string_literal: true + class IssuesController < ApplicationController include ProjectConcern load_and_authorize_resource - before_action :set_issue, only: [:show, :edit, :update, :destroy] + before_action :set_issue, only: %i[show edit update destroy] # GET /issues # GET /issues.json @@ -16,8 +18,7 @@ def index # GET /issues/1 # GET /issues/1.json - def show - end + def show; end # GET /issues/new def new @@ -25,8 +26,7 @@ def new end # GET /issues/1/edit - def edit - end + def edit; end # POST /issues # POST /issues.json @@ -78,6 +78,6 @@ def set_issue # Never trust parameters from the scary internet, only allow the white list through. def issue_params - params.require(:issue).permit(:title, :description, :project_ids => []) + params.require(:issue).permit(:title, :description, project_ids: []) end end diff --git a/app/controllers/lab_racks_controller.rb b/app/controllers/lab_racks_controller.rb index fd1af01b..1036f3a1 100644 --- a/app/controllers/lab_racks_controller.rb +++ b/app/controllers/lab_racks_controller.rb @@ -1,23 +1,24 @@ +# frozen_string_literal: true + class LabRacksController < ApplicationController include ProjectConcern load_and_authorize_resource - before_action :set_lab_rack, only: [:show, :edit, :update, :destroy] + before_action :set_lab_rack, only: %i[show edit update destroy] # GET /lab_racks # GET /lab_racks.json def index respond_to do |format| format.html - format.json { render json: LabRackDatatable.new(view_context, current_project_id)} + format.json { render json: LabRackDatatable.new(view_context, current_project_id) } end end # GET /lab_racks/1 # GET /lab_racks/1.json - def show - end + def show; end # GET /lab_racks/new def new @@ -25,8 +26,7 @@ def new end # GET /lab_racks/1/edit - def edit - end + def edit; end # POST /lab_racks # POST /lab_racks.json @@ -78,6 +78,6 @@ def set_lab_rack # Never trust parameters from the scary internet, only allow the white list through. def lab_rack_params - params.require(:lab_rack).permit(:shelf, :rack_position, :rackcode, :freezer_id, :project_ids => []) + params.require(:lab_rack).permit(:shelf, :rack_position, :rackcode, :freezer_id, project_ids: []) end end diff --git a/app/controllers/labs_controller.rb b/app/controllers/labs_controller.rb index d2415cc1..4febd0bf 100644 --- a/app/controllers/labs_controller.rb +++ b/app/controllers/labs_controller.rb @@ -1,9 +1,11 @@ +# frozen_string_literal: true + class LabsController < ApplicationController include ProjectConcern load_and_authorize_resource - before_action :set_lab, only: [:show, :edit, :update, :destroy] + before_action :set_lab, only: %i[show edit update destroy] # GET /labs # GET /labs.json @@ -13,8 +15,7 @@ def index # GET /labs/1 # GET /labs/1.json - def show - end + def show; end # GET /labs/new def new @@ -22,8 +23,7 @@ def new end # GET /labs/1/edit - def edit - end + def edit; end # POST /labs # POST /labs.json @@ -75,6 +75,6 @@ def set_lab # Never trust parameters from the scary internet, only allow the white list through. def lab_params - params.require(:lab).permit(:labcode, :project_ids => []) + params.require(:lab).permit(:labcode, project_ids: []) end end diff --git a/app/controllers/marker_sequence_searches_controller.rb b/app/controllers/marker_sequence_searches_controller.rb index 9702d2f2..762b44b0 100644 --- a/app/controllers/marker_sequence_searches_controller.rb +++ b/app/controllers/marker_sequence_searches_controller.rb @@ -1,7 +1,9 @@ +# frozen_string_literal: true + class MarkerSequenceSearchesController < ApplicationController load_and_authorize_resource - before_action :set_marker_sequence_search, only: [:export_as_fasta, :export_as_pde] + before_action :set_marker_sequence_search, only: %i[export_as_fasta export_as_pde] def index respond_to do |format| @@ -18,8 +20,8 @@ def create @marker_sequence_search = MarkerSequenceSearch.create!(marker_sequence_search_params) if user_signed_in? - @marker_sequence_search.update(:user_id => current_user.id) - @marker_sequence_search.update(:project_id => current_user.default_project_id) + @marker_sequence_search.update(user_id: current_user.id) + @marker_sequence_search.update(project_id: current_user.default_project_id) end redirect_to @marker_sequence_search @@ -45,12 +47,12 @@ def destroy def export_as_fasta file_name = @marker_sequence_search.title.empty? ? "marker_sequence_search_#{@marker_sequence_search.created_at}" : @marker_sequence_search.title - send_data(MarkerSequenceSearch.fasta(@marker_sequence_search.marker_sequences, metadata: true), :filename => "#{file_name}.fasta", :type => "application/txt") + send_data(MarkerSequenceSearch.fasta(@marker_sequence_search.marker_sequences, metadata: true), filename: "#{file_name}.fasta", type: 'application/txt') end def export_as_pde file_name = @marker_sequence_search.title.empty? ? "marker_sequence_search_#{@marker_sequence_search.created_at}" : @marker_sequence_search.title - send_data(MarkerSequenceSearch.pde(@marker_sequence_search.marker_sequences, {}), :filename => "#{file_name}.pde", :type => "application/txt") + send_data(MarkerSequenceSearch.pde(@marker_sequence_search.marker_sequences, {}), filename: "#{file_name}.pde", type: 'application/txt') end private diff --git a/app/controllers/marker_sequences_controller.rb b/app/controllers/marker_sequences_controller.rb index 5e53ae5b..d569d431 100644 --- a/app/controllers/marker_sequences_controller.rb +++ b/app/controllers/marker_sequences_controller.rb @@ -1,18 +1,19 @@ +# frozen_string_literal: true + class MarkerSequencesController < ApplicationController include ProjectConcern load_and_authorize_resource - before_action :set_marker_sequence, only: [:show, :edit, :update, :destroy] + before_action :set_marker_sequence, only: %i[show edit update destroy] # GET /marker_sequences # GET /marker_sequences.json def index respond_to do |format| format.html - format.json { render json: MarkerSequenceDatatable.new(view_context, current_project_id)} + format.json { render json: MarkerSequenceDatatable.new(view_context, current_project_id) } end - end def filter @@ -29,8 +30,7 @@ def filter # GET /marker_sequences/1 # GET /marker_sequences/1.json - def show - end + def show; end # GET /marker_sequences/new def new @@ -38,8 +38,7 @@ def new end # GET /marker_sequences/1/edit - def edit - end + def edit; end # POST /marker_sequences # POST /marker_sequences.json @@ -65,15 +64,11 @@ def create # PATCH/PUT /marker_sequences/1 # PATCH/PUT /marker_sequences/1.json def update - @marker_sequence.update(marker_sequence_params) - if @marker_sequence.name.empty? - @marker_sequence.generate_name - end + @marker_sequence.generate_name if @marker_sequence.name.empty? redirect_to edit_marker_sequence_path(@marker_sequence), notice: 'Marker sequence was successfully updated.' - end # DELETE /marker_sequences/1 @@ -87,13 +82,14 @@ def destroy end private + # Use callbacks to share common setup or constraints between actions. def set_marker_sequence - @marker_sequence = MarkerSequence.includes(:isolate => :individual).find(params[:id]) + @marker_sequence = MarkerSequence.includes(isolate: :individual).find(params[:id]) end # Never trust parameters from the scary internet, only allow the white list through. def marker_sequence_params - params.require(:marker_sequence).permit(:genbank, :name, :sequence, :isolate_id, :marker_id, :contig_id, :isolate_lab_nr, :reference, :project_ids => []) + params.require(:marker_sequence).permit(:genbank, :name, :sequence, :isolate_id, :marker_id, :contig_id, :isolate_lab_nr, :reference, project_ids: []) end end diff --git a/app/controllers/markers_controller.rb b/app/controllers/markers_controller.rb index 4dbce8f2..d0379fc6 100644 --- a/app/controllers/markers_controller.rb +++ b/app/controllers/markers_controller.rb @@ -1,9 +1,11 @@ +# frozen_string_literal: true + class MarkersController < ApplicationController include ProjectConcern load_and_authorize_resource - before_action :set_marker, only: [:show, :edit, :update, :destroy] + before_action :set_marker, only: %i[show edit update destroy] # GET /markers # GET /markers.json @@ -13,8 +15,7 @@ def index # GET /markers/1 # GET /markers/1.json - def show - end + def show; end # GET /markers/new def new @@ -22,8 +23,7 @@ def new end # GET /markers/1/edit - def edit - end + def edit; end # POST /markers # POST /markers.json @@ -67,13 +67,14 @@ def destroy end private - # Use callbacks to share common setup or constraints between actions. - def set_marker - @marker = Marker.find(params[:id]) - end - # Never trust parameters from the scary internet, only allow the white list through. - def marker_params - params.require(:marker).permit(:alt_name, :is_gbol, :expected_reads, :name, :sequence, :accession, :higher_order_taxon_ids => [], :project_ids => []) - end + # Use callbacks to share common setup or constraints between actions. + def set_marker + @marker = Marker.find(params[:id]) + end + + # Never trust parameters from the scary internet, only allow the white list through. + def marker_params + params.require(:marker).permit(:alt_name, :is_gbol, :expected_reads, :name, :sequence, :accession, higher_order_taxon_ids: [], project_ids: []) + end end diff --git a/app/controllers/micronic_plates_controller.rb b/app/controllers/micronic_plates_controller.rb index 3debf538..298d1cc1 100644 --- a/app/controllers/micronic_plates_controller.rb +++ b/app/controllers/micronic_plates_controller.rb @@ -1,23 +1,24 @@ +# frozen_string_literal: true + class MicronicPlatesController < ApplicationController include ProjectConcern load_and_authorize_resource - before_action :set_micronic_plate, only: [:show, :edit, :update, :destroy] + before_action :set_micronic_plate, only: %i[show edit update destroy] # GET /micronic_plates # GET /micronic_plates.json def index respond_to do |format| format.html - format.json { render json: MicronicPlateDatatable.new(view_context, current_project_id)} + format.json { render json: MicronicPlateDatatable.new(view_context, current_project_id) } end end # GET /micronic_plates/1 # GET /micronic_plates/1.json - def show - end + def show; end # GET /micronic_plates/new def new @@ -25,8 +26,7 @@ def new end # GET /micronic_plates/1/edit - def edit - end + def edit; end # POST /micronic_plates # POST /micronic_plates.json @@ -78,6 +78,6 @@ def set_micronic_plate # Never trust parameters from the scary internet, only allow the white list through. def micronic_plate_params - params.require(:micronic_plate).permit(:location_in_rack, :micronic_plate_id, :name, :project_ids => []) + params.require(:micronic_plate).permit(:location_in_rack, :micronic_plate_id, :name, project_ids: []) end end diff --git a/app/controllers/mislabel_analyses_controller.rb b/app/controllers/mislabel_analyses_controller.rb index e43fd914..9972ba3b 100644 --- a/app/controllers/mislabel_analyses_controller.rb +++ b/app/controllers/mislabel_analyses_controller.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class MislabelAnalysesController < ApplicationController load_and_authorize_resource @@ -40,7 +42,7 @@ def import redirect_to mislabel_analyses_path, alert: 'Please select a SATIVA output file (*.mis) to import results.' else results = File.new(params[:file].path) - title = File.basename(file.original_filename, ".mis") + title = File.basename(file.original_filename, '.mis') @mislabel_analysis = MislabelAnalysis.import(results, title) redirect_to mislabel_analysis_path(@mislabel_analysis), notice: 'Imported analysis output. Possibly mislabeled sequences have been marked.' diff --git a/app/controllers/mislabels_controller.rb b/app/controllers/mislabels_controller.rb index 90e7d398..a5db36c4 100644 --- a/app/controllers/mislabels_controller.rb +++ b/app/controllers/mislabels_controller.rb @@ -1,14 +1,16 @@ +# frozen_string_literal: true + class MislabelsController < ApplicationController load_and_authorize_resource before_action :set_mislabel, only: :solve def solve - if @mislabel.solved_by or @mislabel.solved - redirect_back(fallback_location: marker_sequences_path, warning: "Mislabel warning was already marked as solved.") + if @mislabel.solved_by || @mislabel.solved + redirect_back(fallback_location: marker_sequences_path, warning: 'Mislabel warning was already marked as solved.') else - @mislabel.update(:solved_by => current_user.id, :solved_at => Time.now, :solved => true) - redirect_back(fallback_location: marker_sequences_path, notice: "Mislabel warning marked as solved.") + @mislabel.update(solved_by: current_user.id, solved_at: Time.now, solved: true) + redirect_back(fallback_location: marker_sequences_path, notice: 'Mislabel warning marked as solved.') end end diff --git a/app/controllers/orders_controller.rb b/app/controllers/orders_controller.rb index 4b6d6b85..d9c47fd1 100644 --- a/app/controllers/orders_controller.rb +++ b/app/controllers/orders_controller.rb @@ -1,9 +1,11 @@ +# frozen_string_literal: true + class OrdersController < ApplicationController include ProjectConcern load_and_authorize_resource - before_action :set_order, only: [:show, :edit, :update, :destroy] + before_action :set_order, only: %i[show edit update destroy] # GET /orders # GET /orders.json @@ -13,8 +15,7 @@ def index # GET /orders/1 # GET /orders/1.json - def show - end + def show; end # GET /orders/new def new @@ -22,8 +23,7 @@ def new end # GET /orders/1/edit - def edit - end + def edit; end # POST /orders # POST /orders.json @@ -75,6 +75,6 @@ def set_order # Never trust parameters from the scary internet, only allow the white list through. def order_params - params.require(:order).permit(:name, :author, :higher_order_taxon_id, :project_ids => []) + params.require(:order).permit(:name, :author, :higher_order_taxon_id, project_ids: []) end end diff --git a/app/controllers/overview_diagram_controller.rb b/app/controllers/overview_diagram_controller.rb index 420950b8..d8fc13ed 100644 --- a/app/controllers/overview_diagram_controller.rb +++ b/app/controllers/overview_diagram_controller.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class OverviewDiagramController < ApplicationController include ProjectConcern diff --git a/app/controllers/partial_cons_controller.rb b/app/controllers/partial_cons_controller.rb index f81184fb..d8e20b8f 100644 --- a/app/controllers/partial_cons_controller.rb +++ b/app/controllers/partial_cons_controller.rb @@ -1,21 +1,23 @@ +# frozen_string_literal: true + class PartialConsController < ApplicationController load_and_authorize_resource - before_action :set_partial_con, only: [:show_page, :show_position] + before_action :set_partial_con, only: %i[show_page show_position] def show_page respond_to do |format| - format.json { - render :json => @partial_con.to_json_for_page(params[:page], params[:width_in_bases]) - } + format.json do + render json: @partial_con.to_json_for_page(params[:page], params[:width_in_bases]) + end end end def show_position respond_to do |format| - format.json { - render :json => @partial_con.to_json_for_position(params[:position], params[:width_in_bases]) - } + format.json do + render json: @partial_con.to_json_for_position(params[:position], params[:width_in_bases]) + end end end diff --git a/app/controllers/plant_plates_controller.rb b/app/controllers/plant_plates_controller.rb index 7c67b0fa..30fdb4d5 100644 --- a/app/controllers/plant_plates_controller.rb +++ b/app/controllers/plant_plates_controller.rb @@ -1,23 +1,24 @@ +# frozen_string_literal: true + class PlantPlatesController < ApplicationController include ProjectConcern load_and_authorize_resource - before_action :set_plant_plate, only: [:show, :edit, :update, :destroy] + before_action :set_plant_plate, only: %i[show edit update destroy] # GET /plant_plates # GET /plant_plates.json def index respond_to do |format| format.html - format.json { render json: PlantPlateDatatable.new(view_context, current_project_id)} + format.json { render json: PlantPlateDatatable.new(view_context, current_project_id) } end end # GET /plant_plates/1 # GET /plant_plates/1.json - def show - end + def show; end # GET /plant_plates/new def new @@ -25,8 +26,7 @@ def new end # GET /plant_plates/1/edit - def edit - end + def edit; end # POST /plant_plates # POST /plant_plates.json @@ -78,6 +78,6 @@ def set_plant_plate # Never trust parameters from the scary internet, only allow the white list through. def plant_plate_params - params.require(:plant_plate).permit(:name, :how_many, :project_ids => []) + params.require(:plant_plate).permit(:name, :how_many, project_ids: []) end end diff --git a/app/controllers/primer_pos_on_genomes_controller.rb b/app/controllers/primer_pos_on_genomes_controller.rb index 188e4b9d..b01b7642 100644 --- a/app/controllers/primer_pos_on_genomes_controller.rb +++ b/app/controllers/primer_pos_on_genomes_controller.rb @@ -1,7 +1,9 @@ +# frozen_string_literal: true + class PrimerPosOnGenomesController < ApplicationController load_and_authorize_resource - before_action :set_primer_pos_on_genome, only: [:show, :edit, :update, :destroy] + before_action :set_primer_pos_on_genome, only: %i[show edit update destroy] # GET /primer_pos_on_genomes # GET /primer_pos_on_genomes.json @@ -11,8 +13,7 @@ def index # GET /primer_pos_on_genomes/1 # GET /primer_pos_on_genomes/1.json - def show - end + def show; end # GET /primer_pos_on_genomes/new def new @@ -20,8 +21,7 @@ def new end # GET /primer_pos_on_genomes/1/edit - def edit - end + def edit; end # POST /primer_pos_on_genomes # POST /primer_pos_on_genomes.json @@ -64,13 +64,14 @@ def destroy end private - # Use callbacks to share common setup or constraints between actions. - def set_primer_pos_on_genome - @primer_pos_on_genome = PrimerPosOnGenome.find(params[:id]) - end - # Never trust parameters from the scary internet, only allow the white list through. - def primer_pos_on_genome_params - params.require(:primer_pos_on_genome).permit(:note, :position) - end + # Use callbacks to share common setup or constraints between actions. + def set_primer_pos_on_genome + @primer_pos_on_genome = PrimerPosOnGenome.find(params[:id]) + end + + # Never trust parameters from the scary internet, only allow the white list through. + def primer_pos_on_genome_params + params.require(:primer_pos_on_genome).permit(:note, :position) + end end diff --git a/app/controllers/primer_reads_controller.rb b/app/controllers/primer_reads_controller.rb index 8280494c..757924dc 100644 --- a/app/controllers/primer_reads_controller.rb +++ b/app/controllers/primer_reads_controller.rb @@ -1,39 +1,40 @@ +# frozen_string_literal: true + class PrimerReadsController < ApplicationController include ProjectConcern load_and_authorize_resource - skip_authorize_resource only: [:change_base, :change_left_clip, :change_right_clip] - skip_authorization_check only: [:change_base, :change_left_clip, :change_right_clip] + skip_authorize_resource only: %i[change_base change_left_clip change_right_clip] + skip_authorization_check only: %i[change_base change_left_clip change_right_clip] - before_action :set_primer_read, only: [:go_to_pos, :do_not_use_for_assembly, :use_for_assembly, :change_left_clip, :change_right_clip, :edit, :fasta, :reverse, :restore, :assign, :trim, :show, :update, :change_base, :destroy] + before_action :set_primer_read, only: %i[go_to_pos do_not_use_for_assembly use_for_assembly change_left_clip change_right_clip edit fasta reverse restore assign trim show update change_base destroy] # GET /primer_reads # GET /primer_reads.json def index respond_to do |format| format.html - format.json { render json: PrimerReadDatatable.new(view_context, '', current_project_id)} + format.json { render json: PrimerReadDatatable.new(view_context, '', current_project_id) } end end def duplicates respond_to do |format| format.html - format.json { render json: PrimerReadDatatable.new(view_context, 'duplicates', current_project_id)} + format.json { render json: PrimerReadDatatable.new(view_context, 'duplicates', current_project_id) } end end def reads_without_contigs respond_to do |format| format.html - format.json { render json: PrimerReadDatatable.new(view_context, 'no_contig', current_project_id)} + format.json { render json: PrimerReadDatatable.new(view_context, 'no_contig', current_project_id) } end end # GET /primer_reads/1 # GET /primer_reads/1.json - def show - end + def show; end # GET /primer_reads/new def new @@ -42,7 +43,7 @@ def new # GET /primer_reads/1/edit def edit - #@primer_read = PrimerRead.includes(:primer, :contig).find(params[:id]) #TODO Add select statement here to initially NOT load chromatogram? + # @primer_read = PrimerRead.includes(:primer, :contig).find(params[:id]) #TODO Add select statement here to initially NOT load chromatogram? end # POST /primer_reads @@ -53,8 +54,8 @@ def create if @primer_read.save PherogramProcessing.perform_async(@primer_read.id) - @primer_read.update(:sequence => '') if @primer_read.sequence.nil? - @primer_read.update(:name => @primer_read.name + '_duplicate') if (PrimerRead.where(name: @primer_read.name).size > 1) + @primer_read.update(sequence: '') if @primer_read.sequence.nil? + @primer_read.update(name: @primer_read.name + '_duplicate') if PrimerRead.where(name: @primer_read.name).size > 1 end end @@ -83,28 +84,28 @@ def destroy end def do_not_use_for_assembly - @primer_read.update(:used_for_con => false, :assembled => false) + @primer_read.update(used_for_con: false, assembled: false) if @primer_read.contig - if @primer_read.contig.primer_reads.where(:used_for_con => true).count <= 4 + if @primer_read.contig.primer_reads.where(used_for_con: true).count <= 4 @primer_read.contig.auto_overlap - msg='Assembly finished.' + msg = 'Assembly finished.' else ContigAssembly.perform_async(@primer_read.contig.id) - msg='Assembly started in background.' + msg = 'Assembly started in background.' end end redirect_back(fallback_location: primer_reads_path, notice: msg) end def use_for_assembly - @primer_read.update(:used_for_con => true) + @primer_read.update(used_for_con: true) if @primer_read.contig - if @primer_read.contig.primer_reads.where(:used_for_con => true).count <= 4 + if @primer_read.contig.primer_reads.where(used_for_con: true).count <= 4 @primer_read.contig.auto_overlap - msg='Assembly finished.' + msg = 'Assembly finished.' else ContigAssembly.perform_async(@primer_read.contig.id) - msg='Assembly started in background.' + msg = 'Assembly started in background.' end end redirect_back(fallback_location: primer_reads_path, notice: msg) @@ -129,7 +130,6 @@ def assign else redirect_to edit_primer_read_path, notice: msg_hash[:msg] end - end def reverse @@ -137,10 +137,10 @@ def reverse redirect_to edit_primer_read_path, alert: 'Already reversed.' else begin - @primer_read.update(:reverse => true) + @primer_read.update(reverse: true) @primer_read.auto_trim(true) redirect_to edit_primer_read_path, notice: 'Reversed.' - rescue + rescue StandardError redirect_to edit_primer_read_path, alert: 'Could not reverse' end end @@ -149,11 +149,11 @@ def reverse def restore if @primer_read.reverse begin - @primer_read.update(:reverse => false) + @primer_read.update(reverse: false) @primer_read.auto_trim(true) redirect_to edit_primer_read_path, notice: 'Restored non-reversed state.' - rescue + rescue StandardError redirect_to edit_primer_read_path, alert: 'Could not restore.' end else @@ -173,7 +173,7 @@ def change_base # If insertions needed: handle inserting new elements in qualities etc. arrays if base.length > 1 - insertions_needed = base.length-1 + insertions_needed = base.length - 1 qualities = @primer_read.qualities insertions_needed.times do @@ -185,9 +185,9 @@ def change_base # Compute new indices based on existing neighbors: left_index = peak_indices[pos] - right_index = peak_indices[pos+1] - distance = right_index-left_index - x_increment = (distance/base.length) + right_index = peak_indices[pos + 1] + distance = right_index - left_index + x_increment = (distance / base.length) x = left_index insertions_needed.times do @@ -198,7 +198,7 @@ def change_base # In all cases (replacement, insertion & deletion) insert string: sequence[pos] = base - @primer_read.update(:sequence => sequence) + @primer_read.update(sequence: sequence) head :ok else head :unauthorized @@ -207,7 +207,7 @@ def change_base def change_left_clip if can? :change_left_clip, @primer_read - @primer_read.update(:trimmedReadStart => params[:position].to_i) + @primer_read.update(trimmedReadStart: params[:position].to_i) head :ok else head :unauthorized @@ -216,7 +216,7 @@ def change_left_clip def change_right_clip if can? :change_right_clip, @primer_read - @primer_read.update(:trimmedReadEnd => params[:position].to_i) + @primer_read.update(trimmedReadEnd: params[:position].to_i) head :ok else head :unauthorized @@ -229,16 +229,16 @@ def import end def fasta - str=">#{@primer_read.name} \n#{@primer_read.trimmed_seq}" + str = ">#{@primer_read.name} \n#{@primer_read.trimmed_seq}" # send_data str - send_data(str, :filename => "#{@primer_read.name}.fas", :type => "application/txt") + send_data(str, filename: "#{@primer_read.name}.fas", type: 'application/txt') end private # Use callbacks to share common setup or constraints between actions. def set_primer_read - @primer_read = PrimerRead.includes(:contig => { :isolate => :individual }).find(params[:id]) + @primer_read = PrimerRead.includes(contig: { isolate: :individual }).find(params[:id]) end # Never trust parameters from the scary internet, only allow the white list through. @@ -247,6 +247,6 @@ def primer_read_params :used_for_con, :file, :name, :sequence, :pherogram_url, :chromatogram, :primer_id, :contig_id, :contig_name, :isolate_id, :chromatograms, :trimmedReadEnd, :trimmedReadStart, :min_quality_score, :count_in_window, :window_size, - :position, :base, :project_ids => []) + :position, :base, project_ids: []) end -end \ No newline at end of file +end diff --git a/app/controllers/primers_controller.rb b/app/controllers/primers_controller.rb index 1a59cea7..ceba06e9 100644 --- a/app/controllers/primers_controller.rb +++ b/app/controllers/primers_controller.rb @@ -1,9 +1,11 @@ +# frozen_string_literal: true + class PrimersController < ApplicationController include ProjectConcern load_and_authorize_resource - before_action :set_primer, only: [:show, :edit, :update, :destroy] + before_action :set_primer, only: %i[show edit update destroy] # GET /primers # GET /primers.json @@ -21,8 +23,7 @@ def import # GET /primers/1 # GET /primers/1.json - def show - end + def show; end # GET /primers/new def new @@ -30,8 +31,7 @@ def new end # GET /primers/1/edit - def edit - end + def edit; end # POST /primers # POST /primers.json @@ -75,13 +75,14 @@ def destroy end private - # Use callbacks to share common setup or constraints between actions. - def set_primer - @primer = Primer.find(params[:id]) - end - # Never trust parameters from the scary internet, only allow the white list through. - def primer_params - params.require(:primer).permit(:alt_name, :position, :file, :name, :sequence, :reverse, :marker_id, :project_ids => []) - end + # Use callbacks to share common setup or constraints between actions. + def set_primer + @primer = Primer.find(params[:id]) + end + + # Never trust parameters from the scary internet, only allow the white list through. + def primer_params + params.require(:primer).permit(:alt_name, :position, :file, :name, :sequence, :reverse, :marker_id, project_ids: []) + end end diff --git a/app/controllers/projects_controller.rb b/app/controllers/projects_controller.rb index f673164a..aac6e67a 100644 --- a/app/controllers/projects_controller.rb +++ b/app/controllers/projects_controller.rb @@ -1,22 +1,23 @@ +# frozen_string_literal: true + class ProjectsController < ApplicationController load_and_authorize_resource - before_action :set_project, only: [:show, :edit, :update, :destroy] + before_action :set_project, only: %i[show edit update destroy] # GET /projects # GET /projects.json def index - if user_signed_in? - @projects = current_user.admin? ? Project.all : current_user.projects - else - @projects = [] - end + @projects = if user_signed_in? + current_user.admin? ? Project.all : current_user.projects + else + [] + end end # GET /projects/1 # GET /projects/1.json - def show - end + def show; end # GET /projects/new def new @@ -24,8 +25,7 @@ def new end # GET /projects/1/edit - def edit - end + def edit; end # POST /projects # POST /projects.json @@ -87,6 +87,7 @@ def add_to_taxa end private + # Use callbacks to share common setup or constraints between actions. def set_project @project = Project.find(params[:id]) @@ -94,6 +95,6 @@ def set_project # Never trust parameters from the scary internet, only allow the white list through. def project_params - params.require(:project).permit(:name, :description, :start, :due, :user_ids => []) + params.require(:project).permit(:name, :description, :start, :due, user_ids: []) end end diff --git a/app/controllers/registrations_controller.rb b/app/controllers/registrations_controller.rb index 76c8f539..783f448b 100644 --- a/app/controllers/registrations_controller.rb +++ b/app/controllers/registrations_controller.rb @@ -1,9 +1,10 @@ +# frozen_string_literal: true + class RegistrationsController < Devise::RegistrationsController before_action :update_sanitized_params, if: :devise_controller? def update_sanitized_params - devise_parameter_sanitizer.permit(:sign_up) {|u| u.permit(:name, :email, :password, :password_confirmation)} - devise_parameter_sanitizer.permit(:account_update) {|u| u.permit(:name, :email, :password, :password_confirmation, :current_password)} + devise_parameter_sanitizer.permit(:sign_up) { |u| u.permit(:name, :email, :password, :password_confirmation) } + devise_parameter_sanitizer.permit(:account_update) { |u| u.permit(:name, :email, :password, :password_confirmation, :current_password) } end - end diff --git a/app/controllers/responsibilities_controller.rb b/app/controllers/responsibilities_controller.rb index 55b7c07f..05f9c3ca 100644 --- a/app/controllers/responsibilities_controller.rb +++ b/app/controllers/responsibilities_controller.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class ResponsibilitiesController < ApplicationController load_and_authorize_resource @@ -5,15 +7,13 @@ def index @responsibilities = Responsibility.all end - def show - end + def show; end def new @responsibility = Responsibility.new end - def edit - end + def edit; end def create @responsibility = Responsibility.new(responsibility_params) @@ -50,6 +50,7 @@ def destroy end private + # Never trust parameters from the scary internet, only allow the white list through. def responsibility_params params.require(:responsibility).permit(:name, :description) diff --git a/app/controllers/shelves_controller.rb b/app/controllers/shelves_controller.rb index f3211531..727cec79 100644 --- a/app/controllers/shelves_controller.rb +++ b/app/controllers/shelves_controller.rb @@ -1,9 +1,11 @@ +# frozen_string_literal: true + class ShelvesController < ApplicationController include ProjectConcern load_and_authorize_resource - before_action :set_shelf, only: [:show, :edit, :update, :destroy] + before_action :set_shelf, only: %i[show edit update destroy] # GET /shelves # GET /shelves.json @@ -13,8 +15,7 @@ def index # GET /shelves/1 # GET /shelves/1.json - def show - end + def show; end # GET /shelves/new def new @@ -22,8 +23,7 @@ def new end # GET /shelves/1/edit - def edit - end + def edit; end # POST /shelves # POST /shelves.json @@ -75,6 +75,6 @@ def set_shelf # Never trust parameters from the scary internet, only allow the white list through. def shelf_params - params.require(:shelf).permit(:name, :project_ids => []) + params.require(:shelf).permit(:name, project_ids: []) end end diff --git a/app/controllers/species_controller.rb b/app/controllers/species_controller.rb index a7915e0f..a77fc5c9 100644 --- a/app/controllers/species_controller.rb +++ b/app/controllers/species_controller.rb @@ -1,10 +1,12 @@ +# frozen_string_literal: true + # noinspection RubyArgCount class SpeciesController < ApplicationController include ProjectConcern load_and_authorize_resource - before_action :set_species, only: [:show, :edit, :update, :destroy] + before_action :set_species, only: %i[show edit update destroy] def create_xls SpeciesExport.perform_async(current_project_id) @@ -28,8 +30,8 @@ def index end def filter - @species = Species.where("composed_name ILIKE ?", "%#{params[:term]}%").in_project(current_project_id).order(:composed_name).limit(100) - size = Species.where("composed_name ILIKE ?", "%#{params[:term]}%").in_project(current_project_id).order(:composed_name).size + @species = Species.where('composed_name ILIKE ?', "%#{params[:term]}%").in_project(current_project_id).order(:composed_name).limit(100) + size = Species.where('composed_name ILIKE ?', "%#{params[:term]}%").in_project(current_project_id).order(:composed_name).size if size > 100 render json: @species.map(&:composed_name).push("and #{size} more...") @@ -81,18 +83,16 @@ def get_ant def collect_and_send_species(ht) str = '' - @species = Species.joins(:family => { :order => :higher_order_taxon }).where(orders: { higher_order_taxon_id: ht.id }).in_project(current_project_id).each do |s| + @species = Species.joins(family: { order: :higher_order_taxon }).where(orders: { higher_order_taxon_id: ht.id }).in_project(current_project_id).each do |s| str += s.id.to_s + "\t" + s.name_for_display + "\n" end - send_data(str, :filename => "#{ht.name}.txt", :type => "application/txt") + send_data(str, filename: "#{ht.name}.txt", type: 'application/txt') end - # GET /species/1 # GET /species/1.json - def show - end + def show; end # GET /species/new def new @@ -100,8 +100,7 @@ def new end # GET /species/1/edit - def edit - end + def edit; end # POST /species # POST /species.json @@ -111,8 +110,8 @@ def create respond_to do |format| if @species.save - @species.update(:species_component => @species.get_species_component) - @species.update(:composed_name => @species.full_name) + @species.update(species_component: @species.get_species_component) + @species.update(composed_name: @species.full_name) format.html { redirect_to species_index_path, notice: 'Species was successfully created.' } format.json { render :show, status: :created, location: @species } else @@ -127,12 +126,12 @@ def create def update respond_to do |format| if @species.update(species_params) - @species.update(:species_component => @species.get_species_component) - @species.update(:composed_name=>@species.full_name) - format.html { - Issue.create(:title => "#{@species.name_for_display} updated by #{current_user.name}") + @species.update(species_component: @species.get_species_component) + @species.update(composed_name: @species.full_name) + format.html do + Issue.create(title: "#{@species.name_for_display} updated by #{current_user.name}") redirect_to species_index_path, notice: 'Species was successfully updated.' - } + end format.json { render :show, status: :ok, location: @species } else format.html { render :edit } @@ -161,6 +160,6 @@ def set_species # Never trust parameters from the scary internet, only allow the white list through. def species_params params.require(:species).permit(:term, :originalFileName, :file, :infraspecific, :comment, :author_infra, :family_name, :family_id, - :author, :genus_name, :species_epithet, :composed_name, :project_ids => []) + :author, :genus_name, :species_epithet, :composed_name, project_ids: []) end -end \ No newline at end of file +end diff --git a/app/controllers/tissues_controller.rb b/app/controllers/tissues_controller.rb index ecac20e9..dd502405 100644 --- a/app/controllers/tissues_controller.rb +++ b/app/controllers/tissues_controller.rb @@ -1,6 +1,8 @@ +# frozen_string_literal: true + class TissuesController < ApplicationController load_and_authorize_resource - before_action :set_tissue, only: [:show, :edit, :update, :destroy] + before_action :set_tissue, only: %i[show edit update destroy] # GET /tissues # GET /tissues.json @@ -10,8 +12,7 @@ def index # GET /tissues/1 # GET /tissues/1.json - def show - end + def show; end # GET /tissues/new def new @@ -19,8 +20,7 @@ def new end # GET /tissues/1/edit - def edit - end + def edit; end # POST /tissues # POST /tissues.json @@ -63,13 +63,14 @@ def destroy end private - # Use callbacks to share common setup or constraints between actions. - def set_tissue - @tissue = Tissue.find(params[:id]) - end - # Never trust parameters from the scary internet, only allow the white list through. - def tissue_params - params.require(:tissue).permit(:name) - end + # Use callbacks to share common setup or constraints between actions. + def set_tissue + @tissue = Tissue.find(params[:id]) + end + + # Never trust parameters from the scary internet, only allow the white list through. + def tissue_params + params.require(:tissue).permit(:name) + end end diff --git a/app/controllers/txt_uploaders_controller.rb b/app/controllers/txt_uploaders_controller.rb index d3ce1e6f..39aed8c8 100644 --- a/app/controllers/txt_uploaders_controller.rb +++ b/app/controllers/txt_uploaders_controller.rb @@ -1,5 +1,7 @@ +# frozen_string_literal: true + class TxtUploadersController < ApplicationController - before_action :set_txt_uploader, only: [:show, :edit, :update, :destroy] + before_action :set_txt_uploader, only: %i[show edit update destroy] # GET /txt_uploaders # GET /txt_uploaders.json @@ -9,8 +11,7 @@ def index # GET /txt_uploaders/1 # GET /txt_uploaders/1.json - def show - end + def show; end # GET /txt_uploaders/new def new @@ -18,8 +19,7 @@ def new end # GET /txt_uploaders/1/edit - def edit - end + def edit; end # POST /txt_uploaders # POST /txt_uploaders.json @@ -62,13 +62,14 @@ def destroy end private - # Use callbacks to share common setup or constraints between actions. - def set_txt_uploader - @txt_uploader = TxtUploader.find(params[:id]) - end - # Never trust parameters from the scary internet, only allow the white list through. - def txt_uploader_params - params[:txt_uploader] - end + # Use callbacks to share common setup or constraints between actions. + def set_txt_uploader + @txt_uploader = TxtUploader.find(params[:id]) + end + + # Never trust parameters from the scary internet, only allow the white list through. + def txt_uploader_params + params[:txt_uploader] + end end diff --git a/app/controllers/users_controller.rb b/app/controllers/users_controller.rb index 4f8fffab..e55b3e4b 100644 --- a/app/controllers/users_controller.rb +++ b/app/controllers/users_controller.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class UsersController < ApplicationController load_and_authorize_resource @@ -27,7 +29,7 @@ def edit def update @user = User.find(params[:id]) - puts "ATTENTION" + puts 'ATTENTION' puts params[:id], current_user.id if @user.admin? && !current_user.admin? @@ -65,7 +67,8 @@ def home end private + def user_params - params.require(:user).permit(:name, :email, :password, :password_confirmation, :role, :lab_id, :default_project_id, :project_ids => [], :responsibility_ids => []) + params.require(:user).permit(:name, :email, :password, :password_confirmation, :role, :lab_id, :default_project_id, project_ids: [], responsibility_ids: []) end end diff --git a/app/models/ability.rb b/app/models/ability.rb index 272fc711..be666f65 100644 --- a/app/models/ability.rb +++ b/app/models/ability.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class Ability include CanCan::Ability @@ -30,17 +32,17 @@ def initialize(user) # https://github.com/CanCanCommunity/cancancan/wiki/Defining-Abilities # Permissions for every user, even if not logged in - can [:edit, :index, :filter, :change_via_script, :compare_contigs, :as_fasq], Contig - can [:edit, :index, :filter, :show_species], Family - can [:edit, :index, :show_species], HigherOrderTaxon - can [:about, :overview, :impressum, :privacy_policy], :home - can [:edit, :index, :filter, :xls], Individual - can [:edit, :index, :filter], Isolate + can %i[edit index filter change_via_script compare_contigs as_fasq], Contig + can %i[edit index filter show_species], Family + can %i[edit index show_species], HigherOrderTaxon + can %i[about overview impressum privacy_policy], :home + can %i[edit index filter xls], Individual + can %i[edit index filter], Isolate can [:filter], MarkerSequence - can [:edit, :index, :filter], Order + can %i[edit index filter], Order can :manage, PartialCon - can [:edit, :index], PrimerRead - can [:edit, :index, :filter, :show_individuals, :xls], Species + can %i[edit index], PrimerRead + can %i[edit index filter show_individuals xls], Species can :manage, TxtUploader can :manage, :overview_diagram @@ -51,15 +53,15 @@ def initialize(user) cannot :manage, User cannot :manage, Project cannot :manage, Responsibility - cannot [:create, :destroy], MislabelAnalysis - cannot [:create, :destroy], Mislabel + cannot %i[create destroy], MislabelAnalysis + cannot %i[create destroy], Mislabel - can [:read, :search_taxa, :add_to_taxa], Project, id: user.project_ids + can %i[read search_taxa add_to_taxa], Project, id: user.project_ids # Additional permissions for guests if user.guest? - cannot [:change_base, :change_left_clip, :change_right_clip], PrimerRead - cannot [:create, :update, :destroy], :all + cannot %i[change_base change_left_clip change_right_clip], PrimerRead + cannot %i[create update destroy], :all can :edit, :all end @@ -71,10 +73,10 @@ def initialize(user) can :manage, MislabelAnalysis can :manage, Mislabel - cannot [:create, :update, :destroy], User, role: 'admin' if user.supervisor? + cannot %i[create update destroy], User, role: 'admin' if user.supervisor? end - can [:home, :show, :edit, :update, :destroy], User, id: user.id # User can see and edit own profile + can %i[home show edit update destroy], User, id: user.id # User can see and edit own profile cannot :manage, ContigSearch can :create, ContigSearch @@ -84,15 +86,15 @@ def initialize(user) can :create, MarkerSequenceSearch can :manage, MarkerSequenceSearch, user_id: user.id # Users can only edit their own searches - if user.responsibilities.exists?(:name => "lab") # Restrictions for users in project "lab" - cannot [:create, :update, :destroy], [Family, Species, Individual, Division, Order, TaxonomicClass, HigherOrderTaxon] + if user.responsibilities.exists?(name: 'lab') # Restrictions for users in project "lab" + cannot %i[create update destroy], [Family, Species, Individual, Division, Order, TaxonomicClass, HigherOrderTaxon] can :edit, [Family, Species, Individual, Division, Order, TaxonomicClass, HigherOrderTaxon] - elsif user.responsibilities.exists?(:name => 'taxonomy') # Restrictions for users in project "taxonomy" - cannot [:create, :update, :destroy], [Alignment, Contig, Freezer, Isolate, Issue, Lab, LabRack, Marker, - MarkerSequence, MicronicPlate, PartialCon, PlantPlate, Primer, PrimerRead, Shelf, Tissue] + elsif user.responsibilities.exists?(name: 'taxonomy') # Restrictions for users in project "taxonomy" + cannot %i[create update destroy], [Alignment, Contig, Freezer, Isolate, Issue, Lab, LabRack, Marker, + MarkerSequence, MicronicPlate, PartialCon, PlantPlate, Primer, PrimerRead, Shelf, Tissue] can :edit, [Alignment, Contig, Freezer, Isolate, Issue, Lab, LabRack, Marker, MarkerSequence, MicronicPlate, PartialCon, PlantPlate, Primer, PrimerRead, Shelf, Tissue] - cannot [:change_base, :change_left_clip, :change_right_clip], PrimerRead + cannot %i[change_base change_left_clip change_right_clip], PrimerRead cannot :manage, ContigSearch cannot :manage, MarkerSequenceSearch end diff --git a/app/models/application_record.rb b/app/models/application_record.rb index 10a4cba8..71fbba5b 100644 --- a/app/models/application_record.rb +++ b/app/models/application_record.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class ApplicationRecord < ActiveRecord::Base self.abstract_class = true end diff --git a/app/models/concerns/export.rb b/app/models/concerns/export.rb index 3cb70f94..716826b0 100644 --- a/app/models/concerns/export.rb +++ b/app/models/concerns/export.rb @@ -96,7 +96,7 @@ def fastq(contigs, use_mira) def pde_contigs(contigs, add_reads) contigs.each do |contig| species = contig.try(:isolate).try(:individual).try(:species)&.composed_name - contig_name = species.blank? ? contig.name : [contig.name, species.gsub(' ', '_')].join('_') + contig_name = species.blank? ? contig.name : [contig.name, species.tr(' ', '_')].join('_') contig.partial_cons.each do |partial_con| aligned_sequence = partial_con.aligned_sequence.nil? ? '' : partial_con.aligned_sequence @@ -109,20 +109,20 @@ def pde_contigs(contigs, add_reads) next unless add_reads # Add unassembled reads: - contig.primer_reads.not_assembled.each { |read| add_primer_read_to_pde(read, false) } if (contig.primer_reads.not_assembled.count > 0) + contig.primer_reads.not_assembled.each { |read| add_primer_read_to_pde(read, false) } if contig.primer_reads.not_assembled.count > 0 - contig.primer_reads.not_used_for_assembly.each { |read| add_primer_read_to_pde(read, false) } if (contig.primer_reads.not_used_for_assembly.count > 0) + contig.primer_reads.not_used_for_assembly.each { |read| add_primer_read_to_pde(read, false) } if contig.primer_reads.not_used_for_assembly.count > 0 - contig.primer_reads.not_trimmed.each { |read| add_primer_read_to_pde(read, false) } if (contig.primer_reads.not_trimmed.count > 0) + contig.primer_reads.not_trimmed.each { |read| add_primer_read_to_pde(read, false) } if contig.primer_reads.not_trimmed.count > 0 - contig.primer_reads.unprocessed.each { |read| add_primer_read_to_pde(read, false) } if (contig.primer_reads.unprocessed.count > 0) + contig.primer_reads.unprocessed.each { |read| add_primer_read_to_pde(read, false) } if contig.primer_reads.unprocessed.count > 0 end end def pde_marker_sequences(marker_sequences) marker_sequences.each do |marker_sequence| species = marker_sequence.try(:isolate).try(:individual).try(:species)&.composed_name - name = species.blank? ? marker_sequence.name : [marker_sequence.name, species.gsub(' ', '_')].join('_') + name = species.blank? ? marker_sequence.name : [marker_sequence.name, species.tr(' ', '_')].join('_') add_sequence_to_pde(name, species, routes.edit_marker_sequence_url(marker_sequence, url_options), marker_sequence.sequence, false) end @@ -144,12 +144,12 @@ def fasta_contigs(contigs, mode) add_sequence_to_fasta(name, partial_con.aligned_sequence) end when 'trimmed' - used_reads = contig.primer_reads.where("used_for_con = ? AND assembled = ?", true, true).order('position') + used_reads = contig.primer_reads.where('used_for_con = ? AND assembled = ?', true, true).order('position') used_reads.each do |read| add_sequence_to_fasta(read.name, read.trimmed_seq) end when 'raw' - used_reads = contig.primer_reads.where("used_for_con = ? AND assembled = ?", true, true).order('position') + used_reads = contig.primer_reads.where('used_for_con = ? AND assembled = ?', true, true).order('position') used_reads.each do |read| add_sequence_to_fasta(read.name, read.sequence) end @@ -185,7 +185,7 @@ def url_options end def add_sequence_to_pde(name, species, url, sequence, is_primer_read) - sequence = sequence ? sequence : '' + sequence ||= '' @pde_header += ""\ "#{name}" @@ -234,11 +234,10 @@ def add_sequence_to_fastq(contig, use_mira) qualities_to_use = use_mira ? partial_con.mira_consensus_qualities : partial_con.aligned_qualities qualities_to_use.each do |q| - if q > 0 - consensus += raw_cons[count] - qualities += (q + 33).chr - count += 1 - end + next unless q > 0 + consensus += raw_cons[count] + qualities += (q + 33).chr + count += 1 end # Return empty string in case that sequence and qualities do not have the same length diff --git a/app/models/concerns/import.rb b/app/models/concerns/import.rb index fcb9ee4c..ab4d7c97 100644 --- a/app/models/concerns/import.rb +++ b/app/models/concerns/import.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + module Import extend ActiveSupport::Concern @@ -59,7 +61,7 @@ def search_dna_bank(id_string, individual = nil) latitude = unit.at_xpath('//abcd21:LatitudeDecimal').content higher_taxon_rank = unit.at_xpath('//abcd21:HigherTaxonRank').content higher_taxon_name = unit.at_xpath('//abcd21:HigherTaxonName').content - rescue + rescue StandardError puts 'Could not read ABCD.' end @@ -71,36 +73,36 @@ def search_dna_bank(id_string, individual = nil) puts "ID: #{individual.id}" puts "Specimen ID: #{specimen_unit_id}" - individual.update(:specimen_id => specimen_unit_id) + individual.update(specimen_id: specimen_unit_id) if unit_id puts "DNABank number: #{unit_id}" - individual.update(:DNA_bank_id => unit_id) + individual.update(DNA_bank_id: unit_id) end if collector puts "Collector: #{collector.strip}" - individual.update(:collector => collector.strip) + individual.update(collector: collector.strip) end if locality puts "Locality: #{locality}" - individual.update(:locality => locality) + individual.update(locality: locality) end if longitude puts "Longitude: #{longitude}" - individual.update(:longitude => longitude) + individual.update(longitude: longitude) end if latitude puts "Latitude: #{latitude}" - individual.update(:latitude => latitude) + individual.update(latitude: latitude) end if herbarium puts "Herbarium: #{herbarium}" - individual.update(:herbarium => herbarium) + individual.update(herbarium: herbarium) end if full_name @@ -117,33 +119,33 @@ def search_dna_bank(id_string, individual = nil) species = individual.species if species.nil? - species = Species.find_or_create_by(:species_component => species_component) - species.update(:genus_name => genus) - species.update(:species_epithet => species_epithet) - species.update(:composed_name => species.full_name) + species = Species.find_or_create_by(species_component: species_component) + species.update(genus_name: genus) + species.update(species_epithet: species_epithet) + species.update(composed_name: species.full_name) if higher_taxon_rank == 'familia' - if higher_taxon_name.capitalize == 'Labiatae' + if higher_taxon_name.capitalize == 'Labiatae' higher_taxon_name = 'Lamiaceae' end - family = Family.find_or_create_by(:name => higher_taxon_name.capitalize) + family = Family.find_or_create_by(name: higher_taxon_name.capitalize) puts "Family: #{higher_taxon_name}" - species.update(:family => family) + species.update(family: family) end - individual.update(:species => species) + individual.update(species: species) end end end - isolate = Isolate.where(:lab_nr => id_string).first - isolate&.update(:individual => individual) + isolate = Isolate.where(lab_nr: id_string).first + isolate&.update(individual: individual) end puts 'Done.' individual end -end \ No newline at end of file +end diff --git a/app/models/concerns/project_record.rb b/app/models/concerns/project_record.rb index 34d447bc..cdb3834a 100644 --- a/app/models/concerns/project_record.rb +++ b/app/models/concerns/project_record.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + # Contains methods used by records with associated projects module ProjectRecord extend ActiveSupport::Concern @@ -11,7 +13,7 @@ module ProjectRecord # Adds the given project as well as the general project if not already added def add_project(project_id) project = Project.find(project_id) - project_all = Project.where('name like ?', "All%").first + project_all = Project.where('name like ?', 'All%').first projects << project unless projects.include?(project) projects << project_all unless projects.include?(project_all) @@ -27,4 +29,4 @@ def in_project(project_id) joins(:projects).where(projects: { id: project_id }).distinct end end -end \ No newline at end of file +end diff --git a/app/models/contig.rb b/app/models/contig.rb index dbba031f..5737a977 100644 --- a/app/models/contig.rb +++ b/app/models/contig.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + # noinspection RubyStringKeysInHashInspection class Contig < ApplicationRecord include Export @@ -30,9 +32,9 @@ class Contig < ApplicationRecord def self.spp_in_higher_order_taxon(higher_order_taxon_id) # TODO: (how to) includes spp. etc (on top of individual) - contigs = Contig.select("species_id").includes(:isolate => :individual).joins(:isolate => {:individual => {:species => {:family => {:order => :higher_order_taxon}}}}).where(orders: {higher_order_taxon_id: higher_order_taxon_id}) - contigs_s = Contig.select("species_component").includes(:isolate => :individual).joins(:isolate => {:individual => {:species => {:family => {:order => :higher_order_taxon}}}}).where(orders: {higher_order_taxon_id: higher_order_taxon_id}) - contigs_i = Contig.select("individual_id").includes(:isolate => :individual).joins(:isolate => {:individual => {:species => {:family => {:order => :higher_order_taxon}}}}).where(orders: {higher_order_taxon_id: higher_order_taxon_id}) + contigs = Contig.select('species_id').includes(isolate: :individual).joins(isolate: { individual: { species: { family: { order: :higher_order_taxon } } } }).where(orders: { higher_order_taxon_id: higher_order_taxon_id }) + contigs_s = Contig.select('species_component').includes(isolate: :individual).joins(isolate: { individual: { species: { family: { order: :higher_order_taxon } } } }).where(orders: { higher_order_taxon_id: higher_order_taxon_id }) + contigs_i = Contig.select('individual_id').includes(isolate: :individual).joins(isolate: { individual: { species: { family: { order: :higher_order_taxon } } } }).where(orders: { higher_order_taxon_id: higher_order_taxon_id }) [contigs.count, contigs_s.distinct.count, contigs.distinct.count, contigs_i.distinct.count] end @@ -45,7 +47,7 @@ def isolate_name=(name) if name == '' self.isolate = nil else - self.isolate = Isolate.find_or_create_by(:lab_nr => name) if name.present? + self.isolate = Isolate.find_or_create_by(lab_nr: name) if name.present? end end @@ -57,16 +59,16 @@ def marker_sequence_name=(name) if name == '' self.marker_sequence = nil else - self.marker_sequence = MarkerSequence.find_or_create_by(:name => name) if name.present? + self.marker_sequence = MarkerSequence.find_or_create_by(name: name) if name.present? end end def generate_name - if self.marker.present? && self.isolate.present? - self.name = "#{self.isolate.lab_nr}_#{self.marker.name}" - else - self.name = '' - end + self.name = if marker.present? && isolate.present? + "#{isolate.lab_nr}_#{marker.name}" + else + '' + end end def mda(width, height) @@ -74,23 +76,21 @@ def mda(width, height) end def degapped_consensus - self.consensus.gsub('-', '') + consensus.delete('-') end def as_fasq(mira) use_mira = false - if mira == "1" or mira == 1 - use_mira = true - end + use_mira = true if (mira == '1') || (mira == 1) # restrict to cases with partial_cons count == 1 - if self.partial_cons.count > 1 or self.partial_cons.count < 1 - puts "Must have 1 partial_cons." + if (partial_cons.count > 1) || (partial_cons.count < 1) + puts 'Must have 1 partial_cons.' return end - pc = self.partial_cons.first + pc = partial_cons.first # compute coverage used_nucleotides_count = 0 @@ -102,7 +102,7 @@ def as_fasq(mira) coverage = (used_nucleotides_count.to_f / pc.aligned_sequence.length) # header - fasq_str = "@#{self.name} | #{sprintf '%.2f', coverage}" + fasq_str = "@#{name} | #{format '%.2f', coverage}" # seq raw_cons = pc.aligned_sequence @@ -114,21 +114,20 @@ def as_fasq(mira) ctr = 0 - if use_mira - qualities_to_use = pc.aligned_qualities - else - qualities_to_use = pc.mira_consensus_qualities - end + qualities_to_use = if use_mira + pc.aligned_qualities + else + pc.mira_consensus_qualities + end qualities_to_use.each do |q| - if q > 0 - cons_seq += raw_cons[ctr] - qual_str += (q + 33).chr - ctr += 1 - end + next unless q > 0 + cons_seq += raw_cons[ctr] + qual_str += (q + 33).chr + ctr += 1 end - #check that seq + qual have same length -> for externally verified this needs not be true + # check that seq + qual have same length -> for externally verified this needs not be true unless cons_seq.length == qual_str.length puts "Error: seq (#{seq_no_gaps.length}) + qual (#{ctr}) do not have same length" return @@ -136,65 +135,63 @@ def as_fasq(mira) "#{fasq_str}\n#{cons_seq}\n+\n#{qual_str}\n" end - - def auto_overlap - self.partial_cons.destroy_all + def auto_overlap + partial_cons.destroy_all msg = nil - self.primer_reads.use_for_assembly.update_all(:assembled => false) + primer_reads.use_for_assembly.update_all(assembled: false) - remaining_reads = Array.new(self.primer_reads.use_for_assembly) #creates local Array to mess around without affecting db + remaining_reads = Array.new(primer_reads.use_for_assembly) # creates local Array to mess around without affecting db - #test how many + # test how many if remaining_reads.size > 10 - # todo: arbitrary, change. + # TODO: arbitrary, change. msg = 'Currently no more than 10 reads allowed for assembly.' return elsif remaining_reads.size == 1 - single_read = self.primer_reads.use_for_assembly.first + single_read = primer_reads.use_for_assembly.first single_read.get_aligned_peak_indices - pc = PartialCon.create(:aligned_sequence => single_read.trimmed_and_cleaned_seq, :aligned_qualities => single_read.trimmed_quals, :contig_id => self.id) + pc = PartialCon.create(aligned_sequence: single_read.trimmed_and_cleaned_seq, aligned_qualities: single_read.trimmed_quals, contig_id: id) single_read.aligned_qualities = single_read.trimmed_quals single_read.aligned_seq = single_read.trimmed_and_cleaned_seq single_read.assembled = true single_read.save pc.primer_reads << single_read - self.partial_cons << pc - ms = MarkerSequence.find_or_create_by(:name => self.name, :sequence => single_read.trimmed_and_cleaned_seq) + partial_cons << pc + ms = MarkerSequence.find_or_create_by(name: name, sequence: single_read.trimmed_and_cleaned_seq) ms.contigs << self - ms.marker = self.marker - ms.isolate = self.isolate - ms.projects = self.projects + ms.marker = marker + ms.isolate = isolate + ms.projects = projects ms.save self.marker_sequence = ms return - elsif remaining_reads.size == 0 + elsif remaining_reads.empty? msg = 'Need at least 1 read for creating consensus sequence.' return end - #test if trimmed_Seq + # test if trimmed_Seq - starting_read = remaining_reads.delete_at(0) #Deletes the element at the specified index, returning that element, or nil if the index is out of range. + starting_read = remaining_reads.delete_at(0) # Deletes the element at the specified index, returning that element, or nil if the index is out of range. assembled_reads = [starting_read] # successfully overlapped reads - growing_consensus = {:reads => [{:read => starting_read, - :aligned_seq => starting_read.trimmed_and_cleaned_seq, - :aligned_qualities => starting_read.trimmed_quals}], - :consensus => starting_read.trimmed_and_cleaned_seq, - :consensus_qualities => starting_read.trimmed_quals} + growing_consensus = { reads: [{ read: starting_read, + aligned_seq: starting_read.trimmed_and_cleaned_seq, + aligned_qualities: starting_read.trimmed_quals }], + consensus: starting_read.trimmed_and_cleaned_seq, + consensus_qualities: starting_read.trimmed_quals } - partial_contigs = Array.new #contains singleton reads and successful overlaps (sub-contigs) that + partial_contigs = [] # contains singleton reads and successful overlaps (sub-contigs) that # themselves are isolated (including the single & final contig if everything could be overlapped) # format: partial_contigs.push({:reads => assembled_reads, :consensus => growing_consensus }) - assemble(growing_consensus, assembled_reads, partial_contigs, remaining_reads) # -----> ASSEMBLY <------ @@ -202,21 +199,20 @@ def auto_overlap current_largest_partial_contig = 0 current_largest_partial_contig_seq = nil - #clean previously stored partial_cons: - self.partial_cons.destroy_all + # clean previously stored partial_cons: + partial_cons.destroy_all - height = 0 #count needed lines for pde dimensions + height = 0 # count needed lines for pde dimensions max_width = 0 - block_seqs = [] #collect sequences for block, later fill with '?' up to max_width + block_seqs = [] # collect sequences for block, later fill with '?' up to max_width partial_contigs.each do |partial_contig| - - #single partial_contig: ({:reads => assembled_reads, :consensus => growing_consensus}) + # single partial_contig: ({:reads => assembled_reads, :consensus => growing_consensus}) if partial_contig[:reads].size > 1 # something where 2 or more primers overlapped: - #growing_consensus = {:reads => [{:read => starting_read, :aligned_seq => starting_read.trimmed_and_cleaned_seq}], + # growing_consensus = {:reads => [{:read => starting_read, :aligned_seq => starting_read.trimmed_and_cleaned_seq}], # :consensus => starting_read.trimmed_and_cleaned_seq } if partial_contig[:reads].size > current_largest_partial_contig @@ -226,45 +222,41 @@ def auto_overlap growing_consensus = partial_contig[:consensus] - pc = PartialCon.create(:aligned_sequence => growing_consensus[:consensus], :aligned_qualities => growing_consensus[:consensus_qualities]) + pc = PartialCon.create(aligned_sequence: growing_consensus[:consensus], aligned_qualities: growing_consensus[:consensus_qualities]) growing_consensus[:reads].each do |aligned_read| - - #get original primer_read from db: + # get original primer_read from db: pr = PrimerRead.find(aligned_read[:read].id) - pr.update(:aligned_seq => aligned_read[:aligned_seq], :assembled => true, :aligned_qualities => aligned_read[:aligned_qualities]) + pr.update(aligned_seq: aligned_read[:aligned_seq], assembled: true, aligned_qualities: aligned_read[:aligned_qualities]) pr.get_aligned_peak_indices # <-- uses aligned_qualities to populate aligned_peak_indices array. Needed in new variant of d3.js contig slize pc.primer_reads << pr - end - self.partial_cons << pc + partial_cons << pc else # singleton end - end # set to "assembled" & create MarkerSequence if applicable - if current_largest_partial_contig >= self.marker.expected_reads - self.update(:assembled => true) + if current_largest_partial_contig >= marker.expected_reads + update(assembled: true) - ms = MarkerSequence.find_or_create_by(:name => self.name, :sequence => current_largest_partial_contig_seq.gsub('-','')) + ms = MarkerSequence.find_or_create_by(name: name, sequence: current_largest_partial_contig_seq.delete('-')) ms.contigs << self - ms.marker = self.marker - ms.isolate = self.isolate - ms.projects = self.projects + ms.marker = marker + ms.isolate = isolate + ms.projects = projects ms.save end if msg - Issue.create(:title => msg, :contig_id => self.id) + Issue.create(title: msg, contig_id: id) self.assembled = false end - end # Recursive assembly function @@ -273,62 +265,57 @@ def assemble(growing_consensus, assembled_reads, partial_contigs, remaining_read none_overlapped = true remaining_reads.each do |read| - aligned_seqs = overlap(growing_consensus, read.trimmed_and_cleaned_seq, read.trimmed_quals) - if aligned_seqs # if one overlaps - - none_overlapped = false + next unless aligned_seqs # if one overlaps - # only in case overlap worked copy the adjusted_aligned sequences that are returned from "overlap" over to growing_consensus: - (0...aligned_seqs[:adjusted_prev_aligned_reads].size).each { |i| - growing_consensus[:reads][i][:aligned_seq] = aligned_seqs[:adjusted_prev_aligned_reads][i] - growing_consensus[:reads][i][:aligned_qualities] = aligned_seqs[:adjusted_prev_aligned_qualities][i] - } + none_overlapped = false - growing_consensus[:reads].push({:read => read, - :aligned_seq => aligned_seqs[:read_seq], - :aligned_qualities => aligned_seqs[:read_qal]}) + # only in case overlap worked copy the adjusted_aligned sequences that are returned from "overlap" over to growing_consensus: + (0...aligned_seqs[:adjusted_prev_aligned_reads].size).each do |i| + growing_consensus[:reads][i][:aligned_seq] = aligned_seqs[:adjusted_prev_aligned_reads][i] + growing_consensus[:reads][i][:aligned_qualities] = aligned_seqs[:adjusted_prev_aligned_qualities][i] + end + growing_consensus[:reads].push(read: read, + aligned_seq: aligned_seqs[:read_seq], + aligned_qualities: aligned_seqs[:read_qal]) - # move it into assembled_reads - overlapped_read = remaining_reads.delete(read) - assembled_reads.push(overlapped_read) + # move it into assembled_reads + overlapped_read = remaining_reads.delete(read) + assembled_reads.push(overlapped_read) - r = compute_consensus(aligned_seqs[:growing_cons_seq], + r = compute_consensus(aligned_seqs[:growing_cons_seq], aligned_seqs[:growing_consensus_qualities], aligned_seqs[:read_seq], aligned_seqs[:read_qal]) - growing_consensus[:consensus] = r.first - growing_consensus[:consensus_qualities] = r.last - - # break loop through remaining_reads - break - - end + growing_consensus[:consensus] = r.first + growing_consensus[:consensus_qualities] = r.last + # break loop through remaining_reads + break end # if none overlaps, if none_overlapped # move assembled_reads into partial_contigs_and_singleton_reads - partial_contigs.push({:reads => assembled_reads, :consensus => growing_consensus}) + partial_contigs.push(reads: assembled_reads, consensus: growing_consensus) # move first of remaining_reads into growing_consensus & assembled_reads # ( just as during initializing prior to first function call) new_starting_read = remaining_reads.delete_at(0) - if new_starting_read #catch case when new aligned_read could not be pruned + if new_starting_read # catch case when new aligned_read could not be pruned growing_assembled_reads_reset = [new_starting_read] - growing_consensus_reset = {:reads => [{:read => new_starting_read, - :aligned_seq => new_starting_read.trimmed_and_cleaned_seq, - :aligned_qualities => new_starting_read.trimmed_quals}], - :consensus => new_starting_read.trimmed_and_cleaned_seq, :consensus_qualities => new_starting_read.trimmed_quals} + growing_consensus_reset = { reads: [{ read: new_starting_read, + aligned_seq: new_starting_read.trimmed_and_cleaned_seq, + aligned_qualities: new_starting_read.trimmed_quals }], + consensus: new_starting_read.trimmed_and_cleaned_seq, consensus_qualities: new_starting_read.trimmed_quals } assemble(growing_consensus_reset, growing_assembled_reads_reset, partial_contigs, remaining_reads) end @@ -338,7 +325,6 @@ def assemble(growing_consensus, assembled_reads, partial_contigs, remaining_read assemble(growing_consensus, assembled_reads, partial_contigs, remaining_reads) end - end # Perform Needleman-Wunsch-based overlapping: @@ -346,8 +332,8 @@ def overlap(growing_cons_hash, read, qualities) growing_consensus = growing_cons_hash[:consensus] growing_consensus_qualities = growing_cons_hash[:consensus_qualities] - previously_aligned_reads = Array.new - previously_aligned_qualities = Array.new + previously_aligned_reads = [] + previously_aligned_qualities = [] growing_cons_hash[:reads].each do |curr_read| previously_aligned_reads.push(curr_read[:aligned_seq]) @@ -391,8 +377,7 @@ def overlap(growing_cons_hash, read, qualities) '-G' => -1, '-C' => -1, '-T' => -1, - '--' => 1, - } + '--' => 1 } rows = read.length + 1 cols = growing_consensus.length + 1 @@ -406,14 +391,14 @@ def overlap(growing_cons_hash, read, qualities) for i in 0...rows do a[i][0] = 0 end for j in 0...cols do a[0][j] = 0 end - (1...rows).each { |i| - (1...cols).each { |j| - choice1 = a[i - 1][j - 1] + s[(read[i - 1] + growing_consensus[j - 1]).upcase] #match - choice2 = a[i - 1][j] + gap #insert - choice3 = a[i][j - 1] + gap #delete + (1...rows).each do |i| + (1...cols).each do |j| + choice1 = a[i - 1][j - 1] + s[(read[i - 1] + growing_consensus[j - 1]).upcase] # match + choice2 = a[i - 1][j] + gap # insert + choice3 = a[i][j - 1] + gap # delete a[i][j] = [choice1, choice2, choice3].max - } - } + end + end aligned_read_seq = '' # -> aligned_read aligned_read_qual = [] @@ -421,21 +406,20 @@ def overlap(growing_cons_hash, read, qualities) aligned_cons_seq = '' # -> growing_consensus aligned_cons_qual = [] - adjusted_prev_aligned_reads = Array.new - adjusted_prev_aligned_qualities = Array.new + adjusted_prev_aligned_reads = [] + adjusted_prev_aligned_qualities = [] - (0...previously_aligned_reads.size).each { |_| + (0...previously_aligned_reads.size).each do |_| new_seq = '' adjusted_prev_aligned_reads.push(new_seq) adjusted_prev_aligned_qualities.push([]) - } - + end # for classic Needleman-Wunsch: - #start from lowermost rightmost cell + # start from lowermost rightmost cell - #for overlap: + # for overlap: # the best score is now in A(m, j) such that A(m, j) = max_k,l(A(k,n),A(m,l)) and the alignment itself can be # obtained by tracing back from A(m, j) to A(0, 0) as before. @@ -449,9 +433,9 @@ def overlap(growing_cons_hash, read, qualities) while i > 0 if a[i][j] > bestscore - bestscore = a[i][j] - bestscore_i = i - bestscore_j = j + bestscore = a[i][j] + bestscore_i = i + bestscore_j = j end i -= 1 end @@ -461,9 +445,9 @@ def overlap(growing_cons_hash, read, qualities) while j > 0 if a[i][j] > bestscore - bestscore = a[i][j] - bestscore_i = i - bestscore_j = j + bestscore = a[i][j] + bestscore_i = i + bestscore_j = j end j -= 1 end @@ -473,89 +457,88 @@ def overlap(growing_cons_hash, read, qualities) i = read.length j = growing_consensus.length - #add 5' extending gaps... + # add 5' extending gaps... while i > bestscore_i aligned_read_seq = read[i - 1].chr + aligned_read_seq aligned_read_qual.unshift(qualities[i - 1]) - aligned_cons_seq = aligned_cons_seq + '-' + aligned_cons_seq += '-' aligned_cons_qual.push(-1) # -1 ~ '-' # mirror everything that's done to aligned_cons_seq in all previously aligned_seqs: for k in 0...adjusted_prev_aligned_reads.size do - adjusted_prev_aligned_reads[k] = adjusted_prev_aligned_reads[k] + '-' - adjusted_prev_aligned_qualities[k].push(-1) + adjusted_prev_aligned_reads[k] = adjusted_prev_aligned_reads[k] + '-' + adjusted_prev_aligned_qualities[k].push(-1) end i -= 1 end - while j > bestscore_j - aligned_read_seq = aligned_read_seq + '-' + aligned_read_seq += '-' aligned_read_qual.push(-1) aligned_cons_seq = growing_consensus[j - 1].chr + aligned_cons_seq aligned_cons_qual.unshift(growing_consensus_qualities[j - 1]) for k in 0...adjusted_prev_aligned_reads.size do - adjusted_prev_aligned_reads[k] = previously_aligned_reads[k][j - 1].chr + adjusted_prev_aligned_reads[k] - adjusted_prev_aligned_qualities[k].unshift(previously_aligned_qualities[k][j - 1]) + adjusted_prev_aligned_reads[k] = previously_aligned_reads[k][j - 1].chr + adjusted_prev_aligned_reads[k] + adjusted_prev_aligned_qualities[k].unshift(previously_aligned_qualities[k][j - 1]) end j -= 1 end - #tracing back... + # tracing back... i = bestscore_i j = bestscore_j - while i > 0 and j > 0 + while (i > 0) && (j > 0) score = a[i][j] score_diag = a[i - 1][j - 1] score_up = a[i][j - 1] score_left = a[i - 1][j] - if score == score_diag + s[read[i - 1].chr + growing_consensus[j - 1].chr] #match - aligned_read_seq = read[i - 1].chr + aligned_read_seq - aligned_read_qual.unshift(qualities[i - 1]) - aligned_cons_seq = growing_consensus[j - 1].chr + aligned_cons_seq - aligned_cons_qual.unshift(growing_consensus_qualities[j - 1]) - - for k in 0...adjusted_prev_aligned_reads.size do - adjusted_prev_aligned_reads[k] = previously_aligned_reads[k][j - 1].chr + adjusted_prev_aligned_reads[k] - adjusted_prev_aligned_qualities[k].unshift(previously_aligned_qualities[k][j - 1]) - end + if score == score_diag + s[read[i - 1].chr + growing_consensus[j - 1].chr] # match + aligned_read_seq = read[i - 1].chr + aligned_read_seq + aligned_read_qual.unshift(qualities[i - 1]) + aligned_cons_seq = growing_consensus[j - 1].chr + aligned_cons_seq + aligned_cons_qual.unshift(growing_consensus_qualities[j - 1]) + + for k in 0...adjusted_prev_aligned_reads.size do + adjusted_prev_aligned_reads[k] = previously_aligned_reads[k][j - 1].chr + adjusted_prev_aligned_reads[k] + adjusted_prev_aligned_qualities[k].unshift(previously_aligned_qualities[k][j - 1]) + end - i -= 1 - j -= 1 - elsif score == score_left + gap #insert - aligned_read_seq = read[i - 1].chr + aligned_read_seq - aligned_read_qual.unshift(qualities[i - 1]) - aligned_cons_seq = '-' + aligned_cons_seq - aligned_cons_qual.unshift(-1) + i -= 1 + j -= 1 + elsif score == score_left + gap # insert + aligned_read_seq = read[i - 1].chr + aligned_read_seq + aligned_read_qual.unshift(qualities[i - 1]) + aligned_cons_seq = '-' + aligned_cons_seq + aligned_cons_qual.unshift(-1) + + for k in 0...adjusted_prev_aligned_reads.size do + adjusted_prev_aligned_reads[k] = '-' + adjusted_prev_aligned_reads[k] + adjusted_prev_aligned_qualities[k].unshift(-1) + end - for k in 0...adjusted_prev_aligned_reads.size do - adjusted_prev_aligned_reads[k] = '-' + adjusted_prev_aligned_reads[k] - adjusted_prev_aligned_qualities[k].unshift(-1) - end + i -= 1 + elsif score == score_up + gap # delete + aligned_read_seq = '-' + aligned_read_seq + aligned_read_qual.unshift(-1) + aligned_cons_seq = growing_consensus[j - 1].chr + aligned_cons_seq + aligned_cons_qual.unshift(growing_consensus_qualities[j - 1]) - i -= 1 - elsif score == score_up + gap #delete - aligned_read_seq = '-' + aligned_read_seq - aligned_read_qual.unshift(-1) - aligned_cons_seq = growing_consensus[j - 1].chr + aligned_cons_seq - aligned_cons_qual.unshift(growing_consensus_qualities[j - 1]) - - for k in 0...adjusted_prev_aligned_reads.size do - adjusted_prev_aligned_reads[k] = previously_aligned_reads[k][j - 1].chr + adjusted_prev_aligned_reads[k] - adjusted_prev_aligned_qualities[k].unshift(previously_aligned_qualities[k][j - 1]) - end + for k in 0...adjusted_prev_aligned_reads.size do + adjusted_prev_aligned_reads[k] = previously_aligned_reads[k][j - 1].chr + adjusted_prev_aligned_reads[k] + adjusted_prev_aligned_qualities[k].unshift(previously_aligned_qualities[k][j - 1]) + end - j -= 1 + j -= 1 end end - #add 3' extending gaps... + # add 3' extending gaps... while i > 0 aligned_read_seq = read[i - 1].chr + aligned_read_seq aligned_read_qual.unshift(qualities[i - 1]) @@ -564,8 +547,8 @@ def overlap(growing_cons_hash, read, qualities) # mirror everything that's done to aligned_cons_seq in all previously aligned_seqs: for k in 0...adjusted_prev_aligned_reads.size do - adjusted_prev_aligned_reads[k] = '-' + adjusted_prev_aligned_reads[k] - adjusted_prev_aligned_qualities[k].unshift(-1) + adjusted_prev_aligned_reads[k] = '-' + adjusted_prev_aligned_reads[k] + adjusted_prev_aligned_qualities[k].unshift(-1) end i -= 1 @@ -579,8 +562,8 @@ def overlap(growing_cons_hash, read, qualities) # mirror everything that's done to aligned_cons_seq in all previously aligned_seqs: for k in 0...adjusted_prev_aligned_reads.size do - adjusted_prev_aligned_reads[k] = previously_aligned_reads[k][j - 1].chr + adjusted_prev_aligned_reads[k] - adjusted_prev_aligned_qualities[k].unshift(previously_aligned_qualities[k][j - 1]) + adjusted_prev_aligned_reads[k] = previously_aligned_reads[k][j - 1].chr + adjusted_prev_aligned_reads[k] + adjusted_prev_aligned_qualities[k].unshift(previously_aligned_qualities[k][j - 1]) end j -= 1 @@ -589,18 +572,17 @@ def overlap(growing_cons_hash, read, qualities) msg = '' msg_type = 1 - aligned_seqs = {:growing_cons_seq => aligned_cons_seq, - :growing_consensus_qualities => aligned_cons_qual, + aligned_seqs = { growing_cons_seq: aligned_cons_seq, + growing_consensus_qualities: aligned_cons_qual, - :read_seq => aligned_read_seq, - :read_qal => aligned_read_qual, + read_seq: aligned_read_seq, + read_qal: aligned_read_qual, - :adjusted_prev_aligned_reads => adjusted_prev_aligned_reads, - :adjusted_prev_aligned_qualities => adjusted_prev_aligned_qualities, + adjusted_prev_aligned_reads: adjusted_prev_aligned_reads, + adjusted_prev_aligned_qualities: adjusted_prev_aligned_qualities, - :message => msg, - :message_type => msg_type - } + message: msg, + message_type: msg_type } # puts "growing_cons_seq:" # puts aligned_seqs[:growing_cons_seq] @@ -612,45 +594,44 @@ def overlap(growing_cons_hash, read, qualities) diffs = 0 valids = 0 - conflicting_positions = Array.new - - (0...aligned_seqs[:growing_cons_seq].length).each { |m| + conflicting_positions = [] - if aligned_seqs[:growing_cons_seq][m] == '-' or aligned_seqs[:read_seq][m] == '-' - next + (0...aligned_seqs[:growing_cons_seq].length).each do |m| + if (aligned_seqs[:growing_cons_seq][m] == '-') || (aligned_seqs[:read_seq][m] == '-') + next else - valids += 1 + valids += 1 end if aligned_seqs[:growing_cons_seq][m] != aligned_seqs[:read_seq][m] - diffs += 1 - conflicting_positions << m + diffs += 1 + conflicting_positions << m end - } + end perc = (diffs.to_f / valids) - if perc <= self.allowed_mismatch_percent / 100.0 + if perc <= allowed_mismatch_percent / 100.0 # wenn zu wenig overlap: - if valids < self.overlap_length - #return nil - nil + if valids < overlap_length + # return nil + nil else - #return alignment: - aligned_seqs[:message] = perc - aligned_seqs + # return alignment: + aligned_seqs[:message] = perc + aligned_seqs end else - #return nil + # return nil nil end end def not_assembled - self.primer_reads.not_assembled.as_json + primer_reads.not_assembled.as_json end def compute_consensus(seq1, qual1, seq2, qual2) @@ -659,34 +640,20 @@ def compute_consensus(seq1, qual1, seq2, qual2) for i in 0...seq1.length - unless qual1[i] == -1 or qual2[i] == -1 + if (qual1[i] == -1) || (qual2[i] == -1) - if qual1[i] > qual2[i] - consensus_qal.push(qual1[i]) - consensus_seq += seq1[i] - else - consensus_qal.push(qual2[i]) - consensus_seq += seq2[i] - end - - else - - if qual1[i] == -1 and qual2[i] == -1 + if (qual1[i] == -1) && (qual2[i] == -1) consensus_qal.push(-1) consensus_seq += '-' else if qual1[i] == -1 - #if further gap adjacent, it's most likely end of trimmed_seq --> qual2/seq2 win + # if further gap adjacent, it's most likely end of trimmed_seq --> qual2/seq2 win trimmed_end = false if i > 0 - if qual1[i - 1] == -1 or qual1[i + 1] == -1 - trimmed_end = true - end + trimmed_end = true if (qual1[i - 1] == -1) || (qual1[i + 1] == -1) else - if qual1[i + 1] == -1 - trimmed_end = true - end + trimmed_end = true if qual1[i + 1] == -1 end if trimmed_end @@ -696,13 +663,13 @@ def compute_consensus(seq1, qual1, seq2, qual2) else - #get surrounding base qualities + # get surrounding base qualities - if i > 0 - neighboring_qual1 = qual1[i - 1] - else - neighboring_qual1 = qual1[i + 1] - end + neighboring_qual1 = if i > 0 + qual1[i - 1] + else + qual1[i + 1] + end if neighboring_qual1 > qual2[i] consensus_seq += '-' @@ -715,16 +682,12 @@ def compute_consensus(seq1, qual1, seq2, qual2) elsif qual2[i] == -1 - #if further gap adjacent, it's most likely end of trimmed_seq --> qual1/seq1 win + # if further gap adjacent, it's most likely end of trimmed_seq --> qual1/seq1 win trimmed_end = false if i > 0 - if qual2[i - 1] == -1 or qual2[i + 1] == -1 - trimmed_end = true - end + trimmed_end = true if (qual2[i - 1] == -1) || (qual2[i + 1] == -1) else - if qual2[i + 1] == -1 - trimmed_end = true - end + trimmed_end = true if qual2[i + 1] == -1 end if trimmed_end @@ -734,12 +697,12 @@ def compute_consensus(seq1, qual1, seq2, qual2) else - #get surrounding base qualities - if i > 0 - neighboring_qual2 = qual2[i - 1] - else - neighboring_qual2 = qual2[i + 1] - end + # get surrounding base qualities + neighboring_qual2 = if i > 0 + qual2[i - 1] + else + qual2[i + 1] + end if neighboring_qual2 > qual1[i] consensus_seq += '-' @@ -754,16 +717,20 @@ def compute_consensus(seq1, qual1, seq2, qual2) end - end + else + if qual1[i] > qual2[i] + consensus_qal.push(qual1[i]) + consensus_seq += seq1[i] + else + consensus_qal.push(qual2[i]) + consensus_seq += seq2[i] + end + + end end [consensus_seq, consensus_qal] - - end end - - - diff --git a/app/models/contig_search.rb b/app/models/contig_search.rb index 7dffb683..f00b8f31 100644 --- a/app/models/contig_search.rb +++ b/app/models/contig_search.rb @@ -1,10 +1,12 @@ +# frozen_string_literal: true + class ContigSearch < ApplicationRecord include Export belongs_to :user belongs_to :project - enum has_warnings: [:both, :yes, :no] + enum has_warnings: %i[both yes no] # TODO: Unfinished feature # has_attached_file :search_result_archive, @@ -24,40 +26,40 @@ def contigs def find_contigs contigs = Contig.in_project(user.default_project_id).order(:name) - contigs = contigs.where("contigs.name ilike ?", "%#{name}%") if name.present? + contigs = contigs.where('contigs.name ilike ?', "%#{name}%") if name.present? if assembled != 'both' - contigs = contigs.assembled if (assembled == 'assembled') - contigs = contigs.not_assembled if (assembled == 'unassembled') + contigs = contigs.assembled if assembled == 'assembled' + contigs = contigs.not_assembled if assembled == 'unassembled' end if verified != 'both' - contigs = contigs.verified if (verified == 'verified') - contigs = contigs.where(verified: false) if (verified == 'unverified') + contigs = contigs.verified if verified == 'verified' + contigs = contigs.where(verified: false) if verified == 'unverified' end if has_warnings != 'both' - contigs = contigs.with_warnings if (has_warnings == 'yes') - contigs = contigs.where.not(id: Contig.with_warnings.pluck(:id)) if (has_warnings == 'no') + contigs = contigs.with_warnings if has_warnings == 'yes' + contigs = contigs.where.not(id: Contig.with_warnings.pluck(:id)) if has_warnings == 'no' end - contigs = contigs.joins(:marker).where("markers.name ilike ?", "%#{marker}%") if marker.present? + contigs = contigs.joins(:marker).where('markers.name ilike ?', "%#{marker}%") if marker.present? - contigs = contigs.joins(isolate: { individual: { species: { family: :order } } }).where("orders.name ilike ?", "%#{order}%") if order.present? + contigs = contigs.joins(isolate: { individual: { species: { family: :order } } }).where('orders.name ilike ?', "%#{order}%") if order.present? - contigs = contigs.joins(isolate: { individual: { species: :family } }).where("families.name ilike ?", "%#{family}%") if family.present? + contigs = contigs.joins(isolate: { individual: { species: :family } }).where('families.name ilike ?', "%#{family}%") if family.present? - contigs = contigs.joins(isolate: { individual: :species }).where("species.composed_name ilike ?", "%#{species}%") if species.present? + contigs = contigs.joins(isolate: { individual: :species }).where('species.composed_name ilike ?', "%#{species}%") if species.present? - contigs = contigs.joins(isolate: :individual).where("individuals.specimen_id ilike ?", "%#{specimen}%") if specimen.present? + contigs = contigs.joins(isolate: :individual).where('individuals.specimen_id ilike ?', "%#{specimen}%") if specimen.present? - contigs = contigs.where("contigs.verified_by = ?", User.find_by_name(verified_by)&.id) if verified_by.present? + contigs = contigs.where('contigs.verified_by = ?', User.find_by_name(verified_by)&.id) if verified_by.present? - contigs = contigs.where("contigs.created_at >= ?", min_age.midnight) if min_age.present? - contigs = contigs.where("contigs.created_at <= ?", max_age.end_of_day) if max_age.present? + contigs = contigs.where('contigs.created_at >= ?', min_age.midnight) if min_age.present? + contigs = contigs.where('contigs.created_at <= ?', max_age.end_of_day) if max_age.present? - contigs = contigs.where("contigs.updated_at >= ?", min_update.midnight) if min_update.present? - contigs = contigs.where("contigs.updated_at <= ?", max_update.end_of_day) if max_update.present? + contigs = contigs.where('contigs.updated_at >= ?', min_update.midnight) if min_update.present? + contigs = contigs.where('contigs.updated_at <= ?', max_update.end_of_day) if max_update.present? contigs end diff --git a/app/models/division.rb b/app/models/division.rb index 52677dfa..c7a1154a 100644 --- a/app/models/division.rb +++ b/app/models/division.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class Division < ApplicationRecord has_many :subdivisions end diff --git a/app/models/family.rb b/app/models/family.rb index cd7ebc02..cd4cc7c8 100644 --- a/app/models/family.rb +++ b/app/models/family.rb @@ -1,8 +1,10 @@ +# frozen_string_literal: true + class Family < ApplicationRecord include ProjectRecord include PgSearch - multisearchable :against => :name + multisearchable against: :name has_many :species belongs_to :order diff --git a/app/models/freezer.rb b/app/models/freezer.rb index 3c6e8595..c51cbf8f 100644 --- a/app/models/freezer.rb +++ b/app/models/freezer.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class Freezer < ApplicationRecord include ProjectRecord diff --git a/app/models/higher_order_taxon.rb b/app/models/higher_order_taxon.rb index 6f9b9e0c..ebd5f5d3 100644 --- a/app/models/higher_order_taxon.rb +++ b/app/models/higher_order_taxon.rb @@ -1,11 +1,13 @@ +# frozen_string_literal: true + class HigherOrderTaxon < ApplicationRecord include ProjectRecord include PgSearch - multisearchable :against => :name + multisearchable against: :name has_many :orders - has_many :families, :through => :orders + has_many :families, through: :orders has_and_belongs_to_many :markers validates_presence_of :name diff --git a/app/models/individual.rb b/app/models/individual.rb index 27a6d6fe..d78868c5 100644 --- a/app/models/individual.rb +++ b/app/models/individual.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class Individual < ApplicationRecord include ProjectRecord include PgSearch @@ -5,13 +7,13 @@ class Individual < ApplicationRecord has_many :isolates belongs_to :species - pg_search_scope :quick_search, against: [:specimen_id, :herbarium, :collector, :collection_nr] + pg_search_scope :quick_search, against: %i[specimen_id herbarium collector collection_nr] - scope :without_species, -> { where(:species => nil) } + scope :without_species, -> { where(species: nil) } scope :without_isolates, -> { left_outer_joins(:isolates).select(:id).group(:id).having('count(isolates.id) = 0') } scope :no_species_isolates, -> { without_species.left_outer_joins(:isolates).select(:id).group(:id).having('count(isolates.id) = 0') } - scope :bad_longitude, -> { where('individuals.longitude_original NOT SIMILAR TO ?', '[0-9]{1,}\.{0,}[0-9]{0,}')} - scope :bad_latitude, -> { where('individuals.latitude_original NOT SIMILAR TO ?', '[0-9]{1,}\.{0,}[0-9]{0,}')} + scope :bad_longitude, -> { where('individuals.longitude_original NOT SIMILAR TO ?', '[0-9]{1,}\.{0,}[0-9]{0,}') } + scope :bad_latitude, -> { where('individuals.latitude_original NOT SIMILAR TO ?', '[0-9]{1,}\.{0,}[0-9]{0,}') } scope :bad_location, -> { bad_latitude.or(Individual.bad_longitude) } def self.to_csv(options = {}) @@ -25,8 +27,8 @@ def self.to_csv(options = {}) end def self.spp_in_higher_order_taxon(higher_order_taxon_id) - individuals = Individual.select("species_id").joins(:species => {:family => {:order => :higher_order_taxon}}).where(orders: {higher_order_taxon_id: higher_order_taxon_id}) - individuals_s = Individual.select("species_component").joins(:species => {:family => {:order => :higher_order_taxon}}).where(orders: {higher_order_taxon_id: higher_order_taxon_id}) + individuals = Individual.select('species_id').joins(species: { family: { order: :higher_order_taxon } }).where(orders: { higher_order_taxon_id: higher_order_taxon_id }) + individuals_s = Individual.select('species_component').joins(species: { family: { order: :higher_order_taxon } }).where(orders: { higher_order_taxon_id: higher_order_taxon_id }) [individuals.count, individuals_s.distinct.count, individuals.distinct.count] end @@ -38,31 +40,31 @@ def species_name=(name) if name == '' self.species = nil else - self.species = Species.find_or_create_by(:composed_name => name) if name.present? + self.species = Species.find_or_create_by(composed_name: name) if name.present? end end def habitat_for_display - if self.habitat.present? and self.habitat.length > 60 - "#{self.habitat[0..30]...self.habitat[-30..-1]}" + if habitat.present? && (habitat.length > 60) + (habitat[0..30]...habitat[-30..-1]).to_s else - self.habitat + habitat end end def locality_for_display - if self.locality.present? and self.locality.length > 60 - "#{self.locality[0..30]...self.locality[-30..-1]}" + if locality.present? && (locality.length > 60) + (locality[0..30]...locality[-30..-1]).to_s else - self.locality + locality end end def comments_for_display - if self.comments.present? and self.comments.length > 60 - "#{self.comments[0..30]...self.comments[-30..-1]}" + if comments.present? && (comments.length > 60) + (comments[0..30]...comments[-30..-1]).to_s else - self.comments + comments end end end diff --git a/app/models/individual_search.rb b/app/models/individual_search.rb index 9f914b03..92b6738c 100644 --- a/app/models/individual_search.rb +++ b/app/models/individual_search.rb @@ -1,10 +1,12 @@ +# frozen_string_literal: true + class IndividualSearch < ApplicationRecord belongs_to :user belongs_to :project - enum has_issue: [:all_issue, :issues, :no_issues] - enum has_species: [:all_species, :species, :no_species] - enum has_problematic_location: [:all_location, :bad_location, :location_okay] + enum has_issue: %i[all_issue issues no_issues] + enum has_species: %i[all_species species no_species] + enum has_problematic_location: %i[all_location bad_location location_okay] def individuals @individuals ||= find_individuals @@ -15,30 +17,30 @@ def individuals def find_individuals individuals = Individual.in_project(project_id).order(:specimen_id) - individuals = individuals.where("individuals.specimen_id ilike ?", "%#{specimen_id}%") if specimen_id.present? + individuals = individuals.where('individuals.specimen_id ilike ?', "%#{specimen_id}%") if specimen_id.present? - individuals = individuals.where("individuals.DNA_bank_id ilike ?", "%#{self.DNA_bank_id}%") if self.DNA_bank_id.present? + individuals = individuals.where('individuals.DNA_bank_id ilike ?', "%#{self.DNA_bank_id}%") if self.DNA_bank_id.present? if has_problematic_location != 'all_location' - individuals = individuals.bad_location if (has_problematic_location == 'bad_location') - individuals = individuals.where.not(id: Individual.bad_location.pluck(:id)) if (has_problematic_location == 'location_okay') + individuals = individuals.bad_location if has_problematic_location == 'bad_location' + individuals = individuals.where.not(id: Individual.bad_location.pluck(:id)) if has_problematic_location == 'location_okay' end if has_issue != 'all_issue' - individuals = individuals.where(has_issue: true) if (has_issue == 'issues') - individuals = individuals.where(has_issue: nil).or(individuals.where(has_issue: false)) if (has_issue == 'no_issues') + individuals = individuals.where(has_issue: true) if has_issue == 'issues' + individuals = individuals.where(has_issue: nil).or(individuals.where(has_issue: false)) if has_issue == 'no_issues' end if has_species != 'all_species' - individuals = individuals.joins(:species) if (has_species == 'species') - individuals = individuals.without_species if (has_species == 'no_species') + individuals = individuals.joins(:species) if has_species == 'species' + individuals = individuals.without_species if has_species == 'no_species' end - individuals = individuals.joins(species: { family: :order }).where("orders.name ilike ?", "%#{order}%") if order.present? + individuals = individuals.joins(species: { family: :order }).where('orders.name ilike ?', "%#{order}%") if order.present? - individuals = individuals.joins(species: :family).where("families.name ilike ?", "%#{family}%") if family.present? + individuals = individuals.joins(species: :family).where('families.name ilike ?', "%#{family}%") if family.present? - individuals = individuals.joins(:species).where("species.composed_name ilike ?", "%#{species}%") if species.present? + individuals = individuals.joins(:species).where('species.composed_name ilike ?', "%#{species}%") if species.present? individuals end diff --git a/app/models/isolate.rb b/app/models/isolate.rb index 5ed62f49..8c59d98a 100644 --- a/app/models/isolate.rb +++ b/app/models/isolate.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class Isolate < ApplicationRecord extend Import include ProjectRecord @@ -14,12 +16,12 @@ class Isolate < ApplicationRecord before_create :assign_specimen scope :recent, -> { where('isolates.updated_at > ?', 1.hours.ago) } - scope :no_controls, -> { where(:negative_control => false) } + scope :no_controls, -> { where(negative_control: false) } def self.spp_in_higher_order_taxon(higher_order_taxon_id) - isolates = Isolate.select(:species_id).includes(:individual).joins(:individual => {:species => {:family => {:order => :higher_order_taxon}}}).where(orders: {higher_order_taxon_id: higher_order_taxon_id}) - isolates_s = Isolate.select(:species_component).includes(:individual).joins(:individual => {:species => {:family => {:order => :higher_order_taxon}}}).where(orders: {higher_order_taxon_id: higher_order_taxon_id}) - isolates_i = Isolate.select(:individual_id).joins(:individual => {:species => {:family => {:order => :higher_order_taxon}}}).where(orders: {higher_order_taxon_id: higher_order_taxon_id}) + isolates = Isolate.select(:species_id).includes(:individual).joins(individual: { species: { family: { order: :higher_order_taxon } } }).where(orders: { higher_order_taxon_id: higher_order_taxon_id }) + isolates_s = Isolate.select(:species_component).includes(:individual).joins(individual: { species: { family: { order: :higher_order_taxon } } }).where(orders: { higher_order_taxon_id: higher_order_taxon_id }) + isolates_i = Isolate.select(:individual_id).joins(individual: { species: { family: { order: :higher_order_taxon } } }).where(orders: { higher_order_taxon_id: higher_order_taxon_id }) [isolates.size, isolates_s.distinct.count, isolates.distinct.count, isolates_i.distinct.count] end @@ -35,10 +37,10 @@ def self.import(file, project_id) lab_nr = row['GBoL Isolation No.'] lab_nr ||= row['DNA Bank No'] - isolate = Isolate.where("lab_nr ILIKE ?", lab_nr).first - isolate ||= Isolate.new(:lab_nr => lab_nr) + isolate = Isolate.where('lab_nr ILIKE ?', lab_nr).first + isolate ||= Isolate.new(lab_nr: lab_nr) - plant_plate = PlantPlate.find_or_create_by(:name => row['GBoL5 Tissue Plate No.'].to_i.to_s) + plant_plate = PlantPlate.find_or_create_by(name: row['GBoL5 Tissue Plate No.'].to_i.to_s) isolate.plant_plate = plant_plate isolate.well_pos_plant_plate = row['G5o Well'] @@ -54,36 +56,35 @@ def self.import(file, project_id) isolate.save! individual = row['Voucher ID'] - if individual - individual = Individual.find_or_create_by(specimen_id: individual) # Assign to existing or new individual - - individual.collector = row['Collector'] - individual.herbarium = row['Herbarium'] - individual.country = row['Country'] - individual.state_province = row['State/Province'] - individual.locality = row['Locality'] - individual.latitude = row['Latitude'] - individual.longitude = row['Longitude'] - individual.latitude_original = row['Latitude (original)'] - individual.longitude_original = row['Longitude (original)'] - individual.elevation = row['Elevation'] - individual.exposition = row['Exposition'] - individual.habitat = row['Habitat'] - individual.substrate = row['Substrate'] - individual.life_form = row['Life form'] - individual.collection_nr = row['Collection number'] - individual.collection_date = row['Date'] - individual.determination = row['Determination'] - individual.revision = row['Revision'] - individual.confirmation = row['Confirmation'] - individual.comments = row['Comments'] - - individual.add_project(project_id) - - individual.save! - - isolate.update(individual_id: individual.id) - end + next unless individual + individual = Individual.find_or_create_by(specimen_id: individual) # Assign to existing or new individual + + individual.collector = row['Collector'] + individual.herbarium = row['Herbarium'] + individual.country = row['Country'] + individual.state_province = row['State/Province'] + individual.locality = row['Locality'] + individual.latitude = row['Latitude'] + individual.longitude = row['Longitude'] + individual.latitude_original = row['Latitude (original)'] + individual.longitude_original = row['Longitude (original)'] + individual.elevation = row['Elevation'] + individual.exposition = row['Exposition'] + individual.habitat = row['Habitat'] + individual.substrate = row['Substrate'] + individual.life_form = row['Life form'] + individual.collection_nr = row['Collection number'] + individual.collection_date = row['Date'] + individual.determination = row['Determination'] + individual.revision = row['Revision'] + individual.confirmation = row['Confirmation'] + individual.comments = row['Comments'] + + individual.add_project(project_id) + + individual.save! + + isolate.update(individual_id: individual.id) # species_id = row['GBoL5_TaxID'].to_i # begin @@ -109,7 +110,7 @@ def individual_name=(name) if name == '' self.individual = nil else - self.individual = Individual.find_or_create_by(:specimen_id => name) if name.present? + self.individual = Individual.find_or_create_by(specimen_id: name) if name.present? end end end diff --git a/app/models/issue.rb b/app/models/issue.rb index ebce0491..b0597e2e 100644 --- a/app/models/issue.rb +++ b/app/models/issue.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class Issue < ApplicationRecord include ProjectRecord diff --git a/app/models/lab.rb b/app/models/lab.rb index a21e41f3..33b4aba4 100644 --- a/app/models/lab.rb +++ b/app/models/lab.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class Lab < ApplicationRecord include ProjectRecord diff --git a/app/models/lab_rack.rb b/app/models/lab_rack.rb index 34448a4d..17c7d429 100644 --- a/app/models/lab_rack.rb +++ b/app/models/lab_rack.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class LabRack < ApplicationRecord include ProjectRecord diff --git a/app/models/marker.rb b/app/models/marker.rb index 9d7e9c70..38ae874b 100644 --- a/app/models/marker.rb +++ b/app/models/marker.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class Marker < ApplicationRecord include ProjectRecord @@ -12,18 +14,10 @@ class Marker < ApplicationRecord scope :gbol_marker, -> { in_project(Project.find_by_name('GBOL5')) } def spp_in_higher_order_taxon(higher_order_taxon_id) - ms = MarkerSequence.select("species_id").includes(:isolate => :individual).joins(:isolate => - { :individual => - { :species => - { :family => - { :order => :higher_order_taxon }}}}). - where(orders: { higher_order_taxon_id: higher_order_taxon_id }, marker_sequences: { marker_id: self.id }) - ms_i = MarkerSequence.select("individual_id").includes(:isolate => :individual).joins(:isolate => - {:individual => - {:species => - {:family => - {:order => :higher_order_taxon}}}}). - where(orders: { higher_order_taxon_id: higher_order_taxon_id }, marker_sequences: { marker_id: self.id }) + ms = MarkerSequence.select('species_id').includes(isolate: :individual).joins(isolate: { individual: { species: { family: { order: :higher_order_taxon } } } }) + .where(orders: { higher_order_taxon_id: higher_order_taxon_id }, marker_sequences: { marker_id: id }) + ms_i = MarkerSequence.select('individual_id').includes(isolate: :individual).joins(isolate: { individual: { species: { family: { order: :higher_order_taxon } } } }) + .where(orders: { higher_order_taxon_id: higher_order_taxon_id }, marker_sequences: { marker_id: id }) [ms.count, ms.distinct.count, ms_i.distinct.count] end diff --git a/app/models/marker_sequence.rb b/app/models/marker_sequence.rb index f41b9482..0e39927a 100644 --- a/app/models/marker_sequence.rb +++ b/app/models/marker_sequence.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class MarkerSequence < ApplicationRecord include ProjectRecord @@ -13,17 +15,17 @@ class MarkerSequence < ApplicationRecord scope :with_warnings, -> { joins(:mislabels).where(mislabels: { solved: false }) } def self.spp_in_higher_order_taxon(higher_order_taxon_id) - ms = MarkerSequence.select("species_id").includes(:isolate => :individual).joins(:isolate => {:individual => {:species => {:family => {:order => :higher_order_taxon}}}}).where(orders: {higher_order_taxon_id: higher_order_taxon_id}) - ms_s = MarkerSequence.select("species_component").includes(:isolate => :individual).joins(:isolate => {:individual => {:species => {:family => {:order => :higher_order_taxon}}}}).where(orders: {higher_order_taxon_id: higher_order_taxon_id}) - ms_i = MarkerSequence.select("individual_id").includes(:isolate => :individual).joins(:isolate => {:individual => {:species => {:family => {:order => :higher_order_taxon}}}}).where(orders: {higher_order_taxon_id: higher_order_taxon_id}) + ms = MarkerSequence.select('species_id').includes(isolate: :individual).joins(isolate: { individual: { species: { family: { order: :higher_order_taxon } } } }).where(orders: { higher_order_taxon_id: higher_order_taxon_id }) + ms_s = MarkerSequence.select('species_component').includes(isolate: :individual).joins(isolate: { individual: { species: { family: { order: :higher_order_taxon } } } }).where(orders: { higher_order_taxon_id: higher_order_taxon_id }) + ms_i = MarkerSequence.select('individual_id').includes(isolate: :individual).joins(isolate: { individual: { species: { family: { order: :higher_order_taxon } } } }).where(orders: { higher_order_taxon_id: higher_order_taxon_id }) [ms.count, ms_s.distinct.count, ms.distinct.count, ms_i.distinct.count] end def generate_name - if self.marker.present? and self.isolate.present? - self.update(:name => "#{self.isolate.lab_nr}_#{self.marker.name}") + if marker.present? && isolate.present? + update(name: "#{isolate.lab_nr}_#{marker.name}") else - self.update(:name=>'') + update(name: '') end end @@ -35,11 +37,11 @@ def isolate_lab_nr=(lab_nr) if lab_nr == '' self.isolate = nil else - self.isolate = Isolate.find_or_create_by(:lab_nr => lab_nr) if lab_nr.present? + self.isolate = Isolate.find_or_create_by(lab_nr: lab_nr) if lab_nr.present? end end def has_unsolved_mislabels - !mislabels.where(:solved => false).blank? + !mislabels.where(solved: false).blank? end end diff --git a/app/models/marker_sequence_search.rb b/app/models/marker_sequence_search.rb index e8e97dc2..3c4b2f87 100644 --- a/app/models/marker_sequence_search.rb +++ b/app/models/marker_sequence_search.rb @@ -6,7 +6,7 @@ class MarkerSequenceSearch < ApplicationRecord belongs_to :user belongs_to :project - enum has_warnings: [:both, :yes, :no] + enum has_warnings: %i[both yes no] def marker_sequences @marker_sequences ||= find_marker_sequences @@ -42,42 +42,42 @@ def taxon_file(include_singletons) def find_marker_sequences marker_sequences = MarkerSequence.in_project(project_id).order(:name) - marker_sequences = marker_sequences.where("marker_sequences.name ilike ?", "%#{name}%") if name.present? + marker_sequences = marker_sequences.where('marker_sequences.name ilike ?', "%#{name}%") if name.present? if verified != 'both' - marker_sequences = marker_sequences.verified if (verified == 'verified') - marker_sequences = marker_sequences.not_verified if (verified == 'unverified') + marker_sequences = marker_sequences.verified if verified == 'verified' + marker_sequences = marker_sequences.not_verified if verified == 'unverified' end marker_sequences = marker_sequences.has_species if has_species.present? if has_warnings != 'both' - marker_sequences = marker_sequences.with_warnings if (has_warnings == 'yes') - marker_sequences = marker_sequences.where.not(id: MarkerSequence.with_warnings.pluck(:id)) if (has_warnings == 'no') + marker_sequences = marker_sequences.with_warnings if has_warnings == 'yes' + marker_sequences = marker_sequences.where.not(id: MarkerSequence.with_warnings.pluck(:id)) if has_warnings == 'no' end - marker_sequences = marker_sequences.joins(:marker).where("markers.name ilike ?", "%#{marker}%") if marker.present? + marker_sequences = marker_sequences.joins(:marker).where('markers.name ilike ?', "%#{marker}%") if marker.present? - marker_sequences = marker_sequences.joins(isolate: {individual: {species: {family: {order: :higher_order_taxon}}}}).where("higher_order_taxa.name ilike ?", "%#{higher_order_taxon}%") if higher_order_taxon.present? + marker_sequences = marker_sequences.joins(isolate: { individual: { species: { family: { order: :higher_order_taxon } } } }).where('higher_order_taxa.name ilike ?', "%#{higher_order_taxon}%") if higher_order_taxon.present? - marker_sequences = marker_sequences.joins(isolate: {individual: {species: {family: :order}}}).where("orders.name ilike ?", "%#{order}%") if order.present? + marker_sequences = marker_sequences.joins(isolate: { individual: { species: { family: :order } } }).where('orders.name ilike ?', "%#{order}%") if order.present? - marker_sequences = marker_sequences.joins(isolate: {individual: {species: :family}}).where("families.name ilike ?", "%#{family}%") if family.present? + marker_sequences = marker_sequences.joins(isolate: { individual: { species: :family } }).where('families.name ilike ?', "%#{family}%") if family.present? - marker_sequences = marker_sequences.joins(isolate: {individual: :species }).where("species.composed_name ilike ?", "%#{species}%") if species.present? + marker_sequences = marker_sequences.joins(isolate: { individual: :species }).where('species.composed_name ilike ?', "%#{species}%") if species.present? - marker_sequences = marker_sequences.joins(isolate: :individual).where("individuals.specimen_id ilike ?", "%#{specimen}%") if specimen.present? + marker_sequences = marker_sequences.joins(isolate: :individual).where('individuals.specimen_id ilike ?', "%#{specimen}%") if specimen.present? - marker_sequences = marker_sequences.joins(:contigs).where("contigs.verified_by = ?", User.find_by_name(verified_by)&.id) if verified_by.present? + marker_sequences = marker_sequences.joins(:contigs).where('contigs.verified_by = ?', User.find_by_name(verified_by)&.id) if verified_by.present? - marker_sequences = marker_sequences.where("length(marker_sequences.sequence) >= ?", min_length) if min_length.present? - marker_sequences = marker_sequences.where("length(marker_sequences.sequence) <= ?", max_length) if max_length.present? + marker_sequences = marker_sequences.where('length(marker_sequences.sequence) >= ?', min_length) if min_length.present? + marker_sequences = marker_sequences.where('length(marker_sequences.sequence) <= ?', max_length) if max_length.present? - marker_sequences = marker_sequences.where("marker_sequences.created_at >= ?", min_age.midnight) if min_age.present? - marker_sequences = marker_sequences.where("marker_sequences.created_at <= ?", max_age.end_of_day) if max_age.present? + marker_sequences = marker_sequences.where('marker_sequences.created_at >= ?', min_age.midnight) if min_age.present? + marker_sequences = marker_sequences.where('marker_sequences.created_at <= ?', max_age.end_of_day) if max_age.present? - marker_sequences = marker_sequences.where("marker_sequences.updated_at >= ?", min_update.midnight) if min_update.present? - marker_sequences = marker_sequences.where("marker_sequences.updated_at <= ?", max_update.end_of_day) if max_update.present? + marker_sequences = marker_sequences.where('marker_sequences.updated_at >= ?', min_update.midnight) if min_update.present? + marker_sequences = marker_sequences.where('marker_sequences.updated_at <= ?', max_update.end_of_day) if max_update.present? marker_sequences end diff --git a/app/models/micronic_plate.rb b/app/models/micronic_plate.rb index 5f376957..546f6f59 100644 --- a/app/models/micronic_plate.rb +++ b/app/models/micronic_plate.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class MicronicPlate < ApplicationRecord include ProjectRecord diff --git a/app/models/mislabel.rb b/app/models/mislabel.rb index 83f4af57..fe729564 100644 --- a/app/models/mislabel.rb +++ b/app/models/mislabel.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class Mislabel < ApplicationRecord belongs_to :mislabel_analysis belongs_to :marker_sequence diff --git a/app/models/mislabel_analysis.rb b/app/models/mislabel_analysis.rb index ee7339f3..98e0c94d 100644 --- a/app/models/mislabel_analysis.rb +++ b/app/models/mislabel_analysis.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class MislabelAnalysis < ApplicationRecord belongs_to :marker has_many :mislabels, dependent: :destroy diff --git a/app/models/order.rb b/app/models/order.rb index 75ddae73..50ff1a77 100644 --- a/app/models/order.rb +++ b/app/models/order.rb @@ -1,11 +1,13 @@ +# frozen_string_literal: true + class Order < ApplicationRecord include ProjectRecord include PgSearch - multisearchable :against => :name + multisearchable against: :name has_many :families - has_many :species, :through => :families + has_many :species, through: :families belongs_to :higher_order_taxon belongs_to :taxonomic_class diff --git a/app/models/overview_all_taxa.rb b/app/models/overview_all_taxa.rb index d93f6fed..77452688 100644 --- a/app/models/overview_all_taxa.rb +++ b/app/models/overview_all_taxa.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class OverviewAllTaxa < ApplicationRecord include ProjectRecord diff --git a/app/models/overview_finished_taxa.rb b/app/models/overview_finished_taxa.rb index b2ffff5a..c0ef6216 100644 --- a/app/models/overview_finished_taxa.rb +++ b/app/models/overview_finished_taxa.rb @@ -1,10 +1,12 @@ +# frozen_string_literal: true + class OverviewFinishedTaxa < ApplicationRecord include ProjectRecord def self.finished_taxa_json(current_project_id, marker_id) root = { :name => 'root', 'children' => [] } taxa = HigherOrderTaxon.in_project(current_project_id).includes(orders: [:families]).order(:position) - marker_sequence_cnts = MarkerSequence.in_project(current_project_id).joins(isolate: [individual: [species: :family]]).where(:marker => marker_id).order('families.name').group('families.name').count + marker_sequence_cnts = MarkerSequence.in_project(current_project_id).joins(isolate: [individual: [species: :family]]).where(marker: marker_id).order('families.name').group('families.name').count i = 0 taxa.each do |taxon| diff --git a/app/models/partial_con.rb b/app/models/partial_con.rb index 34849dc7..5c6e3743 100644 --- a/app/models/partial_con.rb +++ b/app/models/partial_con.rb @@ -1,34 +1,33 @@ +# frozen_string_literal: true + class PartialCon < ApplicationRecord belongs_to :contig, counter_cache: true has_many :primer_reads def mira_consensus_qualities - group_probs_all_pos=[] + group_probs_all_pos = [] # for each position: (0...aligned_sequence.length).each do |i| - unless aligned_qualities[i] < 0 #cases with gap in consensus, -1 or -10 - #get group probabilities for consensus character: - group_prob=0 - ctr=0 - primer_reads.each do |r| - if ctr>1 - break - end - - if r.aligned_seq[i]==aligned_sequence[i] - group_prob += r.aligned_qualities[i] - end - - ctr+=1 + next if aligned_qualities[i] < 0 # cases with gap in consensus, -1 or -10 + # get group probabilities for consensus character: + group_prob = 0 + ctr = 0 + primer_reads.each do |r| + break if ctr > 1 + + if r.aligned_seq[i] == aligned_sequence[i] + group_prob += r.aligned_qualities[i] end - if group_prob > 93 - group_probs_all_pos << 93 - else - group_probs_all_pos << group_prob - end + ctr += 1 end + + group_probs_all_pos << if group_prob > 93 + 93 + else + group_prob + end end group_probs_all_pos @@ -38,8 +37,8 @@ def test_name puts id end - def as_json(options={}) - super(:include => [:primer_reads]) + def as_json(_options = {}) + super(include: [:primer_reads]) end def to_json_for_page(page, width_in_bases) @@ -57,17 +56,17 @@ def to_json_for_page(page, width_in_bases) end_pos = alignment_length - 1 if end_pos > alignment_length { - :page => page.as_json, - :aligned_sequence => aligned_sequence[start_pos..end_pos].as_json, + page: page.as_json, + aligned_sequence: aligned_sequence[start_pos..end_pos].as_json, # :aligned_qualities => self.aligned_qualities[start_pos..end_pos].as_json, - :start_pos => start_pos.as_json, - :end_pos => end_pos.as_json, - :primer_reads => primer_reads.map { |pr| pr.slice_to_json(start_pos, end_pos) } + start_pos: start_pos.as_json, + end_pos: end_pos.as_json, + primer_reads: primer_reads.map { |pr| pr.slice_to_json(start_pos, end_pos) } } end def to_json_for_position(position_string, width_in_bases) - alignment_length = self.aligned_qualities.blank? ? self.aligned_sequence.length : self.aligned_qualities.length # Most externally edited contigs do not have the aligned qualities array + alignment_length = aligned_qualities.blank? ? aligned_sequence.length : aligned_qualities.length # Most externally edited contigs do not have the aligned qualities array start_pos = position_string.to_i start_pos = 0 if start_pos < 0 @@ -79,12 +78,12 @@ def to_json_for_position(position_string, width_in_bases) page = (start_pos / alignment_length).to_i { - :page => page.as_json, - :aligned_sequence => self.aligned_sequence[start_pos..end_pos].as_json, + page: page.as_json, + aligned_sequence: aligned_sequence[start_pos..end_pos].as_json, # :aligned_qualities => self.aligned_qualities[start_pos..end_pos].as_json, - :start_pos => start_pos.as_json, - :end_pos => end_pos.as_json, - :primer_reads => self.primer_reads.map { |pr| pr.slice_to_json(start_pos, end_pos) } + start_pos: start_pos.as_json, + end_pos: end_pos.as_json, + primer_reads: primer_reads.map { |pr| pr.slice_to_json(start_pos, end_pos) } } end end diff --git a/app/models/plant_plate.rb b/app/models/plant_plate.rb index b690a237..fbdf5f65 100644 --- a/app/models/plant_plate.rb +++ b/app/models/plant_plate.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class PlantPlate < ApplicationRecord include ProjectRecord diff --git a/app/models/primer.rb b/app/models/primer.rb index b314acaf..97cbec18 100644 --- a/app/models/primer.rb +++ b/app/models/primer.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class Primer < ApplicationRecord extend Import include ProjectRecord @@ -15,13 +17,13 @@ def self.import(file, project_id) (2..spreadsheet.last_row).each do |i| row = Hash[[header, spreadsheet.row(i)].transpose] - valid_keys = ['alt_name', 'sequence', 'author', 'name', 'tm', 'target_group'] # Only direct attributes; associations are extra: + valid_keys = %w[alt_name sequence author name tm target_group] # Only direct attributes; associations are extra: # Update existing spp or create new primer = find_or_create_by(name: row['name']) # Add marker or assign to existing: - marker = Marker.find_or_create_by(:name => row['marker']) + marker = Marker.find_or_create_by(name: row['marker']) marker.add_project_and_save(project_id) primer.marker_id = marker.id diff --git a/app/models/primer_pos_on_genome.rb b/app/models/primer_pos_on_genome.rb index 28f364bd..b818fbef 100644 --- a/app/models/primer_pos_on_genome.rb +++ b/app/models/primer_pos_on_genome.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class PrimerPosOnGenome < ApplicationRecord belongs_to :primer belongs_to :species diff --git a/app/models/primer_read.rb b/app/models/primer_read.rb index 15c7e933..5fa6b8fd 100644 --- a/app/models/primer_read.rb +++ b/app/models/primer_read.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class PrimerRead < ApplicationRecord include ProjectRecord @@ -7,30 +9,30 @@ class PrimerRead < ApplicationRecord has_many :issues, dependent: :destroy has_attached_file :chromatogram, - :default_url => '/chromatograms/primer_read.scf' + default_url: '/chromatograms/primer_read.scf' # Do_not_validate_attachment_file_type :chromatogram # Validate content type - validates_attachment_content_type :chromatogram, :content_type => /\Aapplication\/octet-stream/ + validates_attachment_content_type :chromatogram, content_type: /\Aapplication\/octet-stream/ # Validate filename - validates_attachment_file_name :chromatogram, :matches => [/scf\Z/, /ab1\Z/] + validates_attachment_file_name :chromatogram, matches: [/scf\Z/, /ab1\Z/] before_create :default_name - scope :assembled, -> { use_for_assembly.where(:assembled => true) } - scope :not_assembled, -> { use_for_assembly.where(:assembled => false) } + scope :assembled, -> { use_for_assembly.where(assembled: true) } + scope :not_assembled, -> { use_for_assembly.where(assembled: false) } - scope :use_for_assembly, -> { trimmed.where(:used_for_con => true) } - scope :not_used_for_assembly, -> { trimmed.where(:used_for_con => false) } + scope :use_for_assembly, -> { trimmed.where(used_for_con: true) } + scope :not_used_for_assembly, -> { trimmed.where(used_for_con: false) } - scope :trimmed, -> { where.not(:trimmedReadStart => nil) } - scope :not_trimmed, -> { where(:trimmedReadStart => nil) } + scope :trimmed, -> { where.not(trimmedReadStart: nil) } + scope :not_trimmed, -> { where(trimmedReadStart: nil) } - scope :processed, -> { where(:processed => true) } - scope :unprocessed, -> { where(:processed => false) } - scope :contig_not_verified, -> { joins(:contig).where(:contigs => {:verified => false, :verified_by => nil}) } + scope :processed, -> { where(processed: true) } + scope :unprocessed, -> { where(processed: false) } + scope :contig_not_verified, -> { joins(:contig).where(contigs: { verified: false, verified_by: nil }) } validates_attachment_presence :chromatogram @@ -39,7 +41,7 @@ def self.in_higher_order_taxon(higher_order_taxon_id) HigherOrderTaxon.find(higher_order_taxon_id).orders.each do |ord| ord.families.each do |fam| - fam.species.each do |sp| + fam.species.each do |sp| sp.individuals.each do |ind| ind.isolates.each do |iso| iso.contigs.each do |con| @@ -55,87 +57,84 @@ def self.in_higher_order_taxon(higher_order_taxon_id) end def file_name_id - self.name.gsub('.', "_#{self.id}.") + name.gsub('.', "_#{id}.") end def slice_to_json(start_pos, end_pos) # get trace position corresponding to first / last aligned_peaks index that exists and is not -1: - start_pos_trace=start_pos - end_pos_trace=end_pos + start_pos_trace = start_pos + end_pos_trace = end_pos - xstart=self.aligned_peak_indices[start_pos_trace] + xstart = aligned_peak_indices[start_pos_trace] while xstart == -1 - start_pos_trace+=1 - xstart=self.aligned_peak_indices[start_pos_trace] + start_pos_trace += 1 + xstart = aligned_peak_indices[start_pos_trace] end # does aligned_peaks index exist? - if self.aligned_peak_indices[end_pos_trace] - xend=self.aligned_peak_indices[end_pos_trace] - #else use last: + if aligned_peak_indices[end_pos_trace] + xend = aligned_peak_indices[end_pos_trace] + # else use last: else - end_pos_trace=self.aligned_peak_indices.count-1 - xend=self.aligned_peak_indices[end_pos_trace] + end_pos_trace = aligned_peak_indices.count - 1 + xend = aligned_peak_indices[end_pos_trace] end # find first that isnt -1: - while xend == -1 and end_pos_trace > 0 - end_pos_trace-=1 - xend=self.aligned_peak_indices[end_pos_trace] + while (xend == -1) && (end_pos_trace > 0) + end_pos_trace -= 1 + xend = aligned_peak_indices[end_pos_trace] end # create hash with x-pos as key, ya, yc, … as value - traces=Hash.new + traces = {} - if xstart and xend #account for situations where nothing from this read is seen in respective contig slice/page: + if xstart && xend # account for situations where nothing from this read is seen in respective contig slice/page: - xstart-=10 - xend+=10 + xstart -= 10 + xend += 10 (xstart..xend).each do |x| traces[x] = { - :ay => self.atrace[x], - :cy => self.ctrace[x], - :gy => self.gtrace[x], - :ty => self.ttrace[x] + ay: atrace[x], + cy: ctrace[x], + gy: gtrace[x], + ty: ttrace[x] } end end # get position in original, non-trimmed, non-aligned primer read: - # return json { - :id => self.id.as_json, - :name => self.name.as_json, - :aligned_seq => self.aligned_seq[start_pos..end_pos].as_json, - :aligned_qualities => self.aligned_qualities[start_pos..end_pos].as_json, - :traces => traces.as_json, - :aligned_peak_indices => self.aligned_peak_indices[start_pos..end_pos].as_json, - :trimmedReadStart => self.trimmedReadStart.as_json, - :trimmedReadEnd => self.trimmedReadEnd.as_json, - :original_positions => self.original_positions[start_pos..end_pos].as_json + id: id.as_json, + name: name.as_json, + aligned_seq: aligned_seq[start_pos..end_pos].as_json, + aligned_qualities: aligned_qualities[start_pos..end_pos].as_json, + traces: traces.as_json, + aligned_peak_indices: aligned_peak_indices[start_pos..end_pos].as_json, + trimmedReadStart: trimmedReadStart.as_json, + trimmedReadEnd: trimmedReadEnd.as_json, + original_positions: original_positions[start_pos..end_pos].as_json } end def original_positions - original_positions=Array.new + original_positions = [] - i=self.trimmedReadStart - - self.aligned_qualities.each do |aq| + i = trimmedReadStart + aligned_qualities.each do |aq| if aq == -1 original_positions << -1 else original_positions << i - i+=1 + i += 1 end - end original_positions @@ -149,28 +148,28 @@ def contig_name=(name) if name == '' self.contig = nil else - self.contig = Contig.find_or_create_by(:name => name) if name.present? + self.contig = Contig.find_or_create_by(name: name) if name.present? end end def seq_for_display - "#{self.sequence[0..30]...self.sequence[-30..-1]}" if self.sequence.present? + (sequence[0..30]...sequence[-30..-1]).to_s if sequence.present? end def trimmed_seq_for_display - "#{self.sequence[self.trimmedReadStart..self.trimmedReadStart+30]...self.sequence[self.trimmedReadEnd-30..self.trimmedReadEnd]}" if self.sequence.present? + (sequence[trimmedReadStart..trimmedReadStart + 30]...sequence[trimmedReadEnd - 30..trimmedReadEnd]).to_s if sequence.present? end def name_for_display - if self.name.length > 25 - "#{self.name[0..11]...self.name[-11..-5]}" + if name.length > 25 + (name[0..11]...name[-11..-5]).to_s else - "#{self.name[0..-5]}" + name[0..-5].to_s end end def default_name - self.name ||= self.chromatogram.original_filename + self.name ||= chromatogram.original_filename end def auto_assign @@ -184,16 +183,16 @@ def auto_assign if name_components primer_name = name_components[3] name_variants_t7 = %w[T7promoter T7 T7-1] # T7 is always forward - name_variants_m13 = %w[M13R-pUC M13-RP M13-RP-1] #M13R-pU + name_variants_m13 = %w[M13R-pUC M13-RP M13-RP-1] # M13R-pU - #logic if T7promoter or M13R-pUC.scf: + # logic if T7promoter or M13R-pUC.scf: if name_variants_t7.include? primer_name rgx = /^_([A-Za-z0-9]+)_([A-Za-z0-9]+)$/ matches = name_components[2].match(rgx) # --> uv2 primer_name = matches[1] - primer = Primer.where("primers.name ILIKE ?", "#{primer_name}").first - primer ||= Primer.where("primers.alt_name ILIKE ?", "#{primer_name}").first + primer = Primer.where('primers.name ILIKE ?', primer_name.to_s).first + primer ||= Primer.where('primers.alt_name ILIKE ?', primer_name.to_s).first if primer primer_name = matches[2] if primer.reverse @@ -206,8 +205,8 @@ def auto_assign matches = name_components[2].match(rgx) # --> 4 primer_name = matches[2] # --> uv4 - primer = Primer.where("primers.name ILIKE ?", "#{primer_name}").first - primer ||= Primer.where("primers.alt_name ILIKE ?", "#{primer_name}").first + primer = Primer.where('primers.name ILIKE ?', primer_name.to_s).first + primer ||= Primer.where('primers.alt_name ILIKE ?', primer_name.to_s).first if primer primer_name = matches[1] unless primer.reverse @@ -215,20 +214,18 @@ def auto_assign output_message = "Cannot find primer with name #{primer_name}." create_issue = true end - else - # Leave primer_name as is end # Find & assign primer - primer = Primer.where("primers.name ILIKE ?", "#{primer_name}").first - primer ||= Primer.where("primers.alt_name ILIKE ?", "#{primer_name}").first + primer = Primer.where('primers.name ILIKE ?', primer_name.to_s).first + primer ||= Primer.where('primers.alt_name ILIKE ?', primer_name.to_s).first puts primer.name - puts "STOP" + puts 'STOP' if primer - self.update(:primer_id => primer.id, :reverse => primer.reverse) + update(primer_id: primer.id, reverse: primer.reverse) # find marker that primer belongs to marker = primer.marker @@ -245,32 +242,32 @@ def auto_assign isolate_component = "#{db_number_name_components[1]} #{db_number_name_components[2]}" # DNABank number end - isolate = Isolate.where("isolates.lab_nr ILIKE ?", isolate_component.to_s).first - isolate ||= Isolate.where("isolates.dna_bank_id ILIKE ?", isolate_component.to_s).first - isolate ||= Isolate.create(:lab_nr => isolate_component) + isolate = Isolate.where('isolates.lab_nr ILIKE ?', isolate_component.to_s).first + isolate ||= Isolate.where('isolates.dna_bank_id ILIKE ?', isolate_component.to_s).first + isolate ||= Isolate.create(lab_nr: isolate_component) if db_number_name_components - isolate.update(:dna_bank_id => isolate_component) + isolate.update(dna_bank_id: isolate_component) end - self.update(:isolate_id => isolate.id) + update(isolate_id: isolate.id) # Figure out which contig to assign to - matching_contig = Contig.where("contigs.marker_id = ? AND contigs.isolate_id = ?", marker.id, isolate.id).first + matching_contig = Contig.where('contigs.marker_id = ? AND contigs.isolate_id = ?', marker.id, isolate.id).first if matching_contig self.contig = matching_contig - self.save + save output_message = "Assigned to contig #{matching_contig.name}." else # Create new contig, auto assign to primer, copy, auto-name - contig = Contig.new(:marker_id => marker.id, :isolate_id => isolate.id, :assembled => false) - contig.projects = self.projects + contig = Contig.new(marker_id: marker.id, isolate_id: isolate.id, assembled: false) + contig.projects = projects contig.generate_name contig.save self.contig = contig - self.save + save output_message = "Created contig #{contig.name} and assigned primer read to it." end @@ -288,175 +285,165 @@ def auto_assign end if create_issue - i = Issue.create(:title => output_message, :primer_read_id => self.id) + i = Issue.create(title: output_message, primer_read_id: id) else # Everything worked - self.contig.update(:assembled => false, :assembly_tried => false) + self.contig.update(assembled: false, assembly_tried: false) end - { :msg => output_message, :create_issue => create_issue } + { msg: output_message, create_issue: create_issue } end def get_position_in_marker(p) # get position in marker - pp=nil + pp = nil - if self.trimmed_seq - if self.reverse - pp= p.position-self.trimmed_seq.length - else - pp= p.position - end + if trimmed_seq + pp = if reverse + p.position - trimmed_seq.length + else + p.position + end end pp end def auto_trim(write_to_db) - msg=nil + msg = nil create_issue = false # Get local copy from s3 - dest = Tempfile.new(self.chromatogram_file_name) + dest = Tempfile.new(chromatogram_file_name) dest.binmode - self.chromatogram.copy_to_local_file(:original, dest.path) + chromatogram.copy_to_local_file(:original, dest.path) begin chromatogram_ff1 = nil p = /\.ab1$/ - if self.chromatogram_file_name.match(p) - chromatogram_ff1 = Bio::Abif.open(dest.path) - else - chromatogram_ff1 = Bio::Scf.open(dest.path) - end + chromatogram_ff1 = if chromatogram_file_name.match(p) + Bio::Abif.open(dest.path) + else + Bio::Scf.open(dest.path) + end chromatogram1 = chromatogram_ff1.next_entry - if self.reverse - chromatogram1.complement!() - end + chromatogram1.complement! if reverse sequence = chromatogram1.sequence.upcase - #copy chromatogram over into db - if self.sequence.nil? or write_to_db - self.update(:sequence => sequence) - self.update(:base_count => sequence.length) + # copy chromatogram over into db + if self.sequence.nil? || write_to_db + update(sequence: sequence) + update(base_count: sequence.length) end - if self.qualities.nil? or write_to_db - self.update(:qualities => chromatogram1.qualities) + if qualities.nil? || write_to_db + update(qualities: chromatogram1.qualities) end - if self.atrace.nil? or write_to_db - self.update(:atrace => chromatogram1.atrace) - self.update(:ctrace => chromatogram1.ctrace) - self.update(:gtrace => chromatogram1.gtrace) - self.update(:ttrace => chromatogram1.ttrace) - self.update(:peak_indices => chromatogram1.peak_indices) + if atrace.nil? || write_to_db + update(atrace: chromatogram1.atrace) + update(ctrace: chromatogram1.ctrace) + update(gtrace: chromatogram1.gtrace) + update(ttrace: chromatogram1.ttrace) + update(peak_indices: chromatogram1.peak_indices) end - se = Array.new + se = [] - se = self.trim_seq(chromatogram1.qualities, self.min_quality_score, self.window_size, self.count_in_window) + se = trim_seq(chromatogram1.qualities, min_quality_score, window_size, count_in_window) - #se = self.trim_seq_inverse(chromatogram1.qualities) + # se = self.trim_seq_inverse(chromatogram1.qualities) if se - if se[0]>=se[1] # trimming has not found any stretch of bases > min_score - msg='Quality too low - no stretch of readable bases found.' - create_issue=true - self.update(:used_for_con => false) + if se[0] >= se[1] # trimming has not found any stretch of bases > min_score + msg = 'Quality too low - no stretch of readable bases found.' + create_issue = true + update(used_for_con: false) elsif se[2] > 0.6 - msg="Quality too low - #{(se[2]*100).round}% low-quality base calls in trimmed sequence." - create_issue=true + msg = "Quality too low - #{(se[2] * 100).round}% low-quality base calls in trimmed sequence." + create_issue = true - self.update(:used_for_con => false) + update(used_for_con: false) else # everything works: - self.update(:trimmedReadStart => se[0]+1, :trimmedReadEnd => se[1]+1, :used_for_con => true) + update(trimmedReadStart: se[0] + 1, trimmedReadEnd: se[1] + 1, used_for_con: true) #:position => self.get_position_in_marker(self.primer) - msg='Sequence trimmed.' + msg = 'Sequence trimmed.' end else - msg='Quality too low - no stretch of readable bases found.' - create_issue=true - self.update(:used_for_con => false) + msg = 'Quality too low - no stretch of readable bases found.' + create_issue = true + update(used_for_con: false) end - rescue - msg='Sequence could not be trimmed - no scf/ab1 file or no quality scores?' + rescue StandardError + msg = 'Sequence could not be trimmed - no scf/ab1 file or no quality scores?' create_issue = true - self.update(:used_for_con => false) + update(used_for_con: false) end if create_issue - i=Issue.create(:title => msg, :primer_read_id => self.id) - self.update(:used_for_con=>false) + i = Issue.create(title: msg, primer_read_id: id) + update(used_for_con: false) end - {:msg => msg, :create_issue => create_issue} - + { msg: msg, create_issue: create_issue } end def trimmed_seq - if trimmedReadStart.nil? or trimmedReadEnd.nil? + if trimmedReadStart.nil? || trimmedReadEnd.nil? nil else if trimmedReadEnd > trimmedReadStart - self.sequence[(self.trimmedReadStart-1)..(self.trimmedReadEnd-1)] if self.sequence.present? - #cleaned_sequence = raw_sequence.gsub('-', '') # in case basecalls in pherogram have already '-' - as in some crappy seq. I got from BN - else - nil + sequence[(trimmedReadStart - 1)..(trimmedReadEnd - 1)] if sequence.present? + # cleaned_sequence = raw_sequence.gsub('-', '') # in case basecalls in pherogram have already '-' - as in some crappy seq. I got from BN end end end def trimmed_quals - if trimmedReadStart.nil? or trimmedReadEnd.nil? + if trimmedReadStart.nil? || trimmedReadEnd.nil? nil else if trimmedReadEnd > trimmedReadStart - self.qualities[(self.trimmedReadStart-1)..(self.trimmedReadEnd-1)] if self.qualities.present? - else - nil + qualities[(trimmedReadStart - 1)..(trimmedReadEnd - 1)] if qualities.present? end end end def trimmed_and_cleaned_seq - self.trimmed_seq.upcase.gsub /[^ACTGN-]+/, 'N' + trimmed_seq.upcase.gsub /[^ACTGN-]+/, 'N' end def get_aligned_peak_indices + if trimmedReadStart - if self.trimmedReadStart - - aligned_peak_indices = Array.new + aligned_peak_indices = [] - pi=self.trimmedReadStart-2 + pi = trimmedReadStart - 2 - if self.aligned_qualities + if aligned_qualities - self.aligned_qualities.each do |aq| - if aq==-1 + aligned_qualities.each do |aq| + if aq == -1 aligned_peak_indices << -1 else - aligned_peak_indices << self.peak_indices[pi] - pi+=1 + aligned_peak_indices << peak_indices[pi] + pi += 1 end end - self.update_columns(aligned_peak_indices: aligned_peak_indices) + update_columns(aligned_peak_indices: aligned_peak_indices) end end - end - - #deactivated cause even worse than original + # deactivated cause even worse than original # def trim_seq_inverse(qualities) # # #settings @@ -612,93 +599,79 @@ def get_aligned_peak_indices # # end - # old version def trim_seq(qualities, min_quality_score, t, c) - trimmed_read_start = 0 trimmed_read_end = qualities.length # --- find readstart: - for i in 0..qualities.length-t - #extract window of size t + for i in 0..qualities.length - t + # extract window of size t - count=0 + count = 0 - for k in i...i+t - if qualities[k]>=min_quality_score - count += 1 - end + for k in i...i + t + count += 1 if qualities[k] >= min_quality_score end - if count>=c + if count >= c trimmed_read_start = i break end end - #fine-tune: if bad bases are at beginning of last window, cut further until current base's score >= min_qual: + # fine-tune: if bad bases are at beginning of last window, cut further until current base's score >= min_qual: - ctr=trimmed_read_start + ctr = trimmed_read_start - for a in ctr..ctr+t - if qualities[a]>=min_quality_score + for a in ctr..ctr + t + if qualities[a] >= min_quality_score trimmed_read_start = a break end end - # --- find readend: - i =qualities.length + i = qualities.length while i > 0 - #extract window of size t + # extract window of size t # k=i - count=0 + count = 0 - for k in i-t...i - if qualities[k]>=min_quality_score - count += 1 - end + for k in i - t...i + count += 1 if qualities[k] >= min_quality_score end - if count>=c + if count >= c trimmed_read_end = i break end - i-=1 + i -= 1 end - #fine-tune: if bad bases are at beginning of last window, go back until current base's score >= min_qual: + # fine-tune: if bad bases are at beginning of last window, go back until current base's score >= min_qual: - while i > trimmed_read_end-t - if qualities[i]>=min_quality_score - break - end - i-=1 + while i > trimmed_read_end - t + break if qualities[i] >= min_quality_score + i -= 1 end trimmed_read_end = i - #check if xy% < min_score: - ctr_bad=0 - ctr_total=0 + # check if xy% < min_score: + ctr_bad = 0 + ctr_total = 0 for j in trimmed_read_start...trimmed_read_end - if qualities[j] :composed_name + multisearchable against: :composed_name has_many :individuals has_many :primer_pos_on_genomes belongs_to :family def self.spp_in_higher_order_taxon(higher_order_taxon_id) - spp = Species.select(:species_component).joins(:family => {:order => :higher_order_taxon}).where(orders: {higher_order_taxon_id: higher_order_taxon_id}) - subspp = Species.select(:id).joins(:family => {:order => :higher_order_taxon}).where(orders: {higher_order_taxon_id: higher_order_taxon_id}) + spp = Species.select(:species_component).joins(family: { order: :higher_order_taxon }).where(orders: { higher_order_taxon_id: higher_order_taxon_id }) + subspp = Species.select(:id).joins(family: { order: :higher_order_taxon }).where(orders: { higher_order_taxon_id: higher_order_taxon_id }) [spp.distinct.count, subspp.count] end @@ -72,26 +74,26 @@ def self.import_species(file, valid_keys, project_id) def self.import_stuttgart(file, project_id) # Only direct attributes; associations are extra - valid_keys = ['genus_name', - 'species_epithet', - 'id', - 'author', - 'author_infra', - 'infraspecific', - 'comment', - 'german_name'] + valid_keys = %w[genus_name + species_epithet + id + author + author_infra + infraspecific + comment + german_name] import_species(file, valid_keys, project_id) end def self.import_berlin(file, project_id) - valid_keys = ['genus_name', - 'species_epithet', - 'id', - 'author', - 'infraspecific', - 'author_infra', - 'comment'] # Only direct attributes; associations are extra + valid_keys = %w[genus_name + species_epithet + id + author + infraspecific + author_infra + comment] # Only direct attributes; associations are extra import_species(file, valid_keys, project_id) end @@ -104,43 +106,42 @@ def self.import_gbolII(file) (2..spreadsheet.last_row).each do |i| row = Hash[[header, spreadsheet.row(i)].transpose] - if (row['GBOL 1 oder 2?'].include? 'GBOL2') || (row['GBOL 1 oder 2?'].include? 'Nachtrag') # Only add new species - # Add family or assign to existing: - family = Family.find_or_create_by(:name => row['Familie (sensu APG)']) - - # Add order or assign to existing - order = Order.find_or_create_by(:name => row['Ordnung (sensu APG)']) - family.update(:order_id => order.id) - - full_name = row['Arten/Unterarten'] - components = full_name.split(' ') - - species = Species.find_or_create_by(:composed_name => full_name) - - species.update(:family => family) - species.update(:genus_name => components.first) - - case components.size - when 2 - species.update(:species_epithet => components[1]) - when 3 - if components[1] == 'x' - species_ep = components[1] + ' ' + components.last - species.update(:species_epithet => species_ep) - else - species.update(:species_epithet => components[1], :infraspecific => components.last) - end - when 4 - if components[2] == 'subsp.' - species.update(:species_epithet => components[1], :infraspecific => components.last) - else - infraspecific = components[2] + ' ' + components.last - species.update(:species_epithet => components[1], :infraspecific => infraspecific) - end - end + next unless (row['GBOL 1 oder 2?'].include? 'GBOL2') || (row['GBOL 1 oder 2?'].include? 'Nachtrag') # Only add new species + # Add family or assign to existing: + family = Family.find_or_create_by(name: row['Familie (sensu APG)']) + + # Add order or assign to existing + order = Order.find_or_create_by(name: row['Ordnung (sensu APG)']) + family.update(order_id: order.id) + + full_name = row['Arten/Unterarten'] + components = full_name.split(' ') + + species = Species.find_or_create_by(composed_name: full_name) + + species.update(family: family) + species.update(genus_name: components.first) - species.update(:species_component => species.get_species_component) + case components.size + when 2 + species.update(species_epithet: components[1]) + when 3 + if components[1] == 'x' + species_ep = components[1] + ' ' + components.last + species.update(species_epithet: species_ep) + else + species.update(species_epithet: components[1], infraspecific: components.last) + end + when 4 + if components[2] == 'subsp.' + species.update(species_epithet: components[1], infraspecific: components.last) + else + infraspecific = components[2] + ' ' + components.last + species.update(species_epithet: components[1], infraspecific: infraspecific) + end end + + species.update(species_component: species.get_species_component) end end @@ -150,24 +151,18 @@ def self.import_stuttgart_set_class(file) header = spreadsheet.row(1) (2..spreadsheet.last_row).each do |i| - row = Hash[[header, spreadsheet.row(i)].transpose] order = Order.find_by_name(row['order']) - if order - taxonomic_class = TaxonomicClass.find_or_create_by(:name => row['class']) - - if taxonomic_class - order.update(:taxonomic_class_id => taxonomic_class.id) - subdivision = Subdivision.find_or_create_by(:name => row['subdivision']) + next unless order + taxonomic_class = TaxonomicClass.find_or_create_by(name: row['class']) - if subdivision - taxonomic_class.update(:subdivision_id => subdivision.id) - end - end - end + next unless taxonomic_class + order.update(taxonomic_class_id: taxonomic_class.id) + subdivision = Subdivision.find_or_create_by(name: row['subdivision']) + taxonomic_class.update(subdivision_id: subdivision.id) if subdivision end end @@ -194,6 +189,6 @@ def family_name end def family_name=(name) - self.family = Family.find_or_create_by(:name => name) if name.present? + self.family = Family.find_or_create_by(name: name) if name.present? end end diff --git a/app/models/species_exporter.rb b/app/models/species_exporter.rb index cb0312dd..afb4b0c3 100644 --- a/app/models/species_exporter.rb +++ b/app/models/species_exporter.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + # Write SPECIMENS & STATUS to Excel-XML (xls) for use by ZFMK for their "Portal / db : bolgermany.de " class SpeciesExporter < ApplicationRecord has_attached_file :species_export, @@ -15,7 +17,7 @@ def create_species_export(project_id) file_to_upload.close self.species_export = File.open('species_export.xls') - self.save! + save! end def xml_string(project_id) diff --git a/app/models/specimen_exporter.rb b/app/models/specimen_exporter.rb index d3bcabc9..856e4757 100644 --- a/app/models/specimen_exporter.rb +++ b/app/models/specimen_exporter.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + # Write SPECIMENS & STATUS to Excel-XML (xls) for use by ZFMK for their "Portal / db : bolgermany.de " class SpecimenExporter < ApplicationRecord include ActionView::Helpers @@ -16,15 +18,15 @@ def create_specimen_export(project_id) file_to_upload.close self.specimen_export = File.open('specimens_export.xls') - self.save! + save! end def xml_string(project_id) markers = Marker.gbol_marker @states = %w[Baden-Württemberg Bayern Berlin Brandenburg Bremen Hamburg - Hessen Mecklenburg-Vorpommern Niedersachsen Nordrhein-Westfalen - Rheinland-Pfalz Saarland Sachsen Sachsen-Anhalt Schleswig-Holstein + Hessen Mecklenburg-Vorpommern Niedersachsen Nordrhein-Westfalen + Rheinland-Pfalz Saarland Sachsen Sachsen-Anhalt Schleswig-Holstein Thüringen] @header_cells = ['GBOL5 specimen ID', @@ -67,15 +69,14 @@ def xml_string(project_id) builder = Nokogiri::XML::Builder.new do |xml| xml.comment("Generated by gbol5.de web app on #{Time.zone.now}") - xml.Workbook('xmlns'=>'urn:schemas-microsoft-com:office:spreadsheet', - 'xmlns:o'=>'urn:schemas-microsoft-com:office:office', - 'xmlns:x'=>'urn:schemas-microsoft-com:office:excel', - 'xmlns:ss'=>'urn:schemas-microsoft-com:office:spreadsheet', - 'xmlns:html'=>'https://www.w3.org/TR/REC-html40') do - xml.Worksheet('ss:Name'=>'Sheet1') do + xml.Workbook('xmlns' => 'urn:schemas-microsoft-com:office:spreadsheet', + 'xmlns:o' => 'urn:schemas-microsoft-com:office:office', + 'xmlns:x' => 'urn:schemas-microsoft-com:office:excel', + 'xmlns:ss' => 'urn:schemas-microsoft-com:office:spreadsheet', + 'xmlns:html' => 'https://www.w3.org/TR/REC-html40') do + xml.Worksheet('ss:Name' => 'Sheet1') do xml.Table do xml.Row do - @header_cells.each do |o| xml.Cell do xml.Data('ss:Type' => 'String') do @@ -83,11 +84,10 @@ def xml_string(project_id) end end end - end # Individuals in current project - Individual.includes(isolates: [contigs: [:marker_sequence, :marker, :isolate]], species: :family).in_project(project_id).find_each do |individual| + Individual.includes(isolates: [contigs: %i[marker_sequence marker isolate]], species: :family).in_project(project_id).find_each do |individual| xml.Row do # GBOL5 specimen ID xml.Cell do @@ -228,8 +228,7 @@ def xml_string(project_id) # Bundesland xml.Cell do xml.Data('ss:Type' => 'String') do - - if individual.country == 'Germany' or individual.country == 'Deutschland' + if (individual.country == 'Germany') || (individual.country == 'Deutschland') # tests first if is a Bundesland; outputs nothing if other crap was entered in this field: if @states.include? individual.state_province @@ -269,14 +268,14 @@ def xml_string(project_id) # Breitengrad xml.Cell do xml.Data('ss:Type' => 'String') do - xml.text(number_with_precision(individual.latitude, precision:5)) + xml.text(number_with_precision(individual.latitude, precision: 5)) end end # Längengrad xml.Cell do xml.Data('ss:Type' => 'String') do - xml.text(number_with_precision(individual.longitude, precision:5)) + xml.text(number_with_precision(individual.longitude, precision: 5)) end end @@ -334,18 +333,15 @@ def xml_string(project_id) individual.try(:isolates).each do |iso| markers.each do |current_marker| - current_contig = iso.try(:contigs).includes(marker_sequence: :contigs).where(marker_id: current_marker.id).first current_marker_sequence = current_contig&.marker_sequence current_ms_sequence = current_marker_sequence&.sequence - if current_ms_sequence - longest_sequences[current_marker.id] ||= current_marker_sequence - if current_ms_sequence.length > longest_sequences[current_marker.id].sequence.length - longest_sequences[current_marker.id] = current_marker_sequence - end + next unless current_ms_sequence + longest_sequences[current_marker.id] ||= current_marker_sequence + if current_ms_sequence.length > longest_sequences[current_marker.id].sequence.length + longest_sequences[current_marker.id] = current_marker_sequence end - end end @@ -358,7 +354,7 @@ def xml_string(project_id) xml.Data('ss:Type' => 'String') do current_contig_id = current_sequence&.contigs&.first&.id if current_contig_id - xml.text("gbol5.de/contigs/#{current_contig_id}/edit") #edit_contig_path(current_sequence.contigs.first) + xml.text("gbol5.de/contigs/#{current_contig_id}/edit") # edit_contig_path(current_sequence.contigs.first) end end end @@ -366,9 +362,7 @@ def xml_string(project_id) # Markersequenz xml.Cell do xml.Data('ss:Type' => 'String') do - if current_ms - xml.text(current_ms) - end + xml.text(current_ms) if current_ms end end @@ -390,4 +384,4 @@ def xml_string(project_id) builder.to_xml end -end \ No newline at end of file +end diff --git a/app/models/subdivision.rb b/app/models/subdivision.rb index 201241ea..1f4c662a 100644 --- a/app/models/subdivision.rb +++ b/app/models/subdivision.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class Subdivision < ApplicationRecord has_many :taxonomic_classes belongs_to :division diff --git a/app/models/taxonomic_class.rb b/app/models/taxonomic_class.rb index 811ef71f..bc04a0ba 100644 --- a/app/models/taxonomic_class.rb +++ b/app/models/taxonomic_class.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class TaxonomicClass < ApplicationRecord belongs_to :subdivision has_many :orders diff --git a/app/models/tissue.rb b/app/models/tissue.rb index 1dad5405..dd956905 100644 --- a/app/models/tissue.rb +++ b/app/models/tissue.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class Tissue < ApplicationRecord has_many :isolates diff --git a/app/models/txt_uploader.rb b/app/models/txt_uploader.rb index 12f8cbbe..5a31109b 100644 --- a/app/models/txt_uploader.rb +++ b/app/models/txt_uploader.rb @@ -1,21 +1,22 @@ -class TxtUploader < ApplicationRecord +# frozen_string_literal: true +class TxtUploader < ApplicationRecord has_attached_file :uploaded_file, - :path => "/output.txt" + path: '/output.txt' # Validate content type - validates_attachment_content_type :uploaded_file, :content_type => /\Atext\/plain/ + validates_attachment_content_type :uploaded_file, content_type: /\Atext\/plain/ # Validate filename - validates_attachment_file_name :uploaded_file, :matches => [/txt\Z/] + validates_attachment_file_name :uploaded_file, matches: [/txt\Z/] def create_uploaded_file(text) - file_to_upload = File.open("output.txt", "w") + file_to_upload = File.open('output.txt', 'w') file_to_upload.write(text) file_to_upload.close - self.uploaded_file = File.open("output.txt") - self.save! + self.uploaded_file = File.open('output.txt') + save! end end diff --git a/app/models/user.rb b/app/models/user.rb index 356a59fb..f70dcb32 100644 --- a/app/models/user.rb +++ b/app/models/user.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class User < ApplicationRecord include ProjectRecord @@ -17,9 +19,9 @@ class User < ApplicationRecord before_save :default_project - enum role: [:guest, :user, :supervisor, :admin] + enum role: %i[guest user supervisor admin] def default_project self.default_project_id ||= projects&.first&.id end -end \ No newline at end of file +end diff --git a/app/views/contigs/index.json.jbuilder b/app/views/contigs/index.json.jbuilder index e2dc5b86..e6562a0e 100644 --- a/app/views/contigs/index.json.jbuilder +++ b/app/views/contigs/index.json.jbuilder @@ -1,3 +1,5 @@ +# frozen_string_literal: true + json.array!(@contigs) do |contig| json.extract! contig, :id, :name, :consensus json.url contig_url(contig, format: :json) diff --git a/app/views/contigs/show.json.jbuilder b/app/views/contigs/show.json.jbuilder index 62a7853a..4ac40877 100644 --- a/app/views/contigs/show.json.jbuilder +++ b/app/views/contigs/show.json.jbuilder @@ -1 +1,3 @@ +# frozen_string_literal: true + json.extract! @contig, :id, :name, :consensus, :created_at, :updated_at diff --git a/app/views/families/index.json.jbuilder b/app/views/families/index.json.jbuilder index 9eea844f..eaea640d 100644 --- a/app/views/families/index.json.jbuilder +++ b/app/views/families/index.json.jbuilder @@ -1,3 +1,5 @@ +# frozen_string_literal: true + json.array!(@families) do |family| json.extract! family, :id, :name, :author json.url family_url(family, format: :json) diff --git a/app/views/families/show.json.jbuilder b/app/views/families/show.json.jbuilder index e18940b7..63c04bdf 100644 --- a/app/views/families/show.json.jbuilder +++ b/app/views/families/show.json.jbuilder @@ -1 +1,3 @@ +# frozen_string_literal: true + json.extract! @family, :id, :name, :author, :created_at, :updated_at diff --git a/app/views/freezers/index.json.jbuilder b/app/views/freezers/index.json.jbuilder index 0f59e848..0bc24547 100644 --- a/app/views/freezers/index.json.jbuilder +++ b/app/views/freezers/index.json.jbuilder @@ -1,3 +1,5 @@ +# frozen_string_literal: true + json.array!(@freezers) do |freezer| json.extract! freezer, :id, :freezercode json.url freezer_url(freezer, format: :json) diff --git a/app/views/freezers/show.json.jbuilder b/app/views/freezers/show.json.jbuilder index dca9a8b3..f026725b 100644 --- a/app/views/freezers/show.json.jbuilder +++ b/app/views/freezers/show.json.jbuilder @@ -1 +1,3 @@ +# frozen_string_literal: true + json.extract! @freezer, :id, :freezercode, :created_at, :updated_at diff --git a/app/views/higher_order_taxons/index.json.jbuilder b/app/views/higher_order_taxons/index.json.jbuilder index 7e688779..15e90a1d 100644 --- a/app/views/higher_order_taxons/index.json.jbuilder +++ b/app/views/higher_order_taxons/index.json.jbuilder @@ -1,3 +1,5 @@ +# frozen_string_literal: true + json.array!(@higher_order_taxons) do |higher_order_taxon| json.extract! higher_order_taxon, :id, :name json.url higher_order_taxon_url(higher_order_taxon, format: :json) diff --git a/app/views/higher_order_taxons/show.json.jbuilder b/app/views/higher_order_taxons/show.json.jbuilder index 46a97555..79366c64 100644 --- a/app/views/higher_order_taxons/show.json.jbuilder +++ b/app/views/higher_order_taxons/show.json.jbuilder @@ -1 +1,3 @@ +# frozen_string_literal: true + json.extract! @higher_order_taxon, :id, :name, :created_at, :updated_at diff --git a/app/views/individuals/index.json.jbuilder b/app/views/individuals/index.json.jbuilder index 25be9eaa..e8c51fa8 100644 --- a/app/views/individuals/index.json.jbuilder +++ b/app/views/individuals/index.json.jbuilder @@ -1,3 +1,5 @@ +# frozen_string_literal: true + json.array!(@individuals) do |individual| json.extract! individual, :id, :specimen_id, :DNA_bank_id, :collector json.url individual_url(individual, format: :json) diff --git a/app/views/individuals/show.json.jbuilder b/app/views/individuals/show.json.jbuilder index 51d21fde..50ca9d13 100644 --- a/app/views/individuals/show.json.jbuilder +++ b/app/views/individuals/show.json.jbuilder @@ -1 +1,3 @@ +# frozen_string_literal: true + json.extract! @individual, :id, :specimen_id, :DNA_bank_id, :collector, :created_at, :updated_at diff --git a/app/views/isolates/index.json.jbuilder b/app/views/isolates/index.json.jbuilder index 0af21fa9..2176482c 100644 --- a/app/views/isolates/index.json.jbuilder +++ b/app/views/isolates/index.json.jbuilder @@ -1,3 +1,5 @@ +# frozen_string_literal: true + json.array!(@isolates) do |copy| json.extract! copy, :id, :well_pos_plant_plate, :lab_nr, :micronic_tube_id, :well_pos_micronic_plate, :concentration json.url copy_url(copy, format: :json) diff --git a/app/views/isolates/show.json.jbuilder b/app/views/isolates/show.json.jbuilder index 3e14735d..1b51a9c0 100644 --- a/app/views/isolates/show.json.jbuilder +++ b/app/views/isolates/show.json.jbuilder @@ -1 +1,3 @@ +# frozen_string_literal: true + json.extract! @isolate, :id, :well_pos_plant_plate, :lab_nr, :micronic_tube_id, :well_pos_micronic_plate, :concentration, :created_at, :updated_at diff --git a/app/views/issues/index.json.jbuilder b/app/views/issues/index.json.jbuilder index ceab77bf..f361db2d 100644 --- a/app/views/issues/index.json.jbuilder +++ b/app/views/issues/index.json.jbuilder @@ -1,3 +1,5 @@ +# frozen_string_literal: true + json.array!(@issues) do |issue| json.extract! issue, :id, :title, :description json.url issue_url(issue, format: :json) diff --git a/app/views/issues/show.json.jbuilder b/app/views/issues/show.json.jbuilder index a1ff8b89..99dccf9f 100644 --- a/app/views/issues/show.json.jbuilder +++ b/app/views/issues/show.json.jbuilder @@ -1 +1,3 @@ +# frozen_string_literal: true + json.extract! @issue, :id, :title, :description, :created_at, :updated_at diff --git a/app/views/lab_racks/index.json.jbuilder b/app/views/lab_racks/index.json.jbuilder index 21bbc9aa..f9609134 100644 --- a/app/views/lab_racks/index.json.jbuilder +++ b/app/views/lab_racks/index.json.jbuilder @@ -1,3 +1,5 @@ +# frozen_string_literal: true + json.array!(@lab_racks) do |lab_rack| json.extract! lab_rack, :id, :rackcode json.url lab_rack_url(lab_rack, format: :json) diff --git a/app/views/lab_racks/show.json.jbuilder b/app/views/lab_racks/show.json.jbuilder index 06b10ba8..aaf4944e 100644 --- a/app/views/lab_racks/show.json.jbuilder +++ b/app/views/lab_racks/show.json.jbuilder @@ -1 +1,3 @@ +# frozen_string_literal: true + json.extract! @lab_rack, :id, :rackcode, :created_at, :updated_at diff --git a/app/views/labs/index.json.jbuilder b/app/views/labs/index.json.jbuilder index 2b1071eb..9571aca3 100644 --- a/app/views/labs/index.json.jbuilder +++ b/app/views/labs/index.json.jbuilder @@ -1,3 +1,5 @@ +# frozen_string_literal: true + json.array!(@labs) do |lab| json.extract! lab, :id, :labcode json.url lab_url(lab, format: :json) diff --git a/app/views/labs/show.json.jbuilder b/app/views/labs/show.json.jbuilder index d55a3675..b1b5b3b5 100644 --- a/app/views/labs/show.json.jbuilder +++ b/app/views/labs/show.json.jbuilder @@ -1 +1,3 @@ +# frozen_string_literal: true + json.extract! @lab, :id, :labcode, :created_at, :updated_at diff --git a/app/views/marker_sequences/index.json.jbuilder b/app/views/marker_sequences/index.json.jbuilder index 35ec3845..93a6bb09 100644 --- a/app/views/marker_sequences/index.json.jbuilder +++ b/app/views/marker_sequences/index.json.jbuilder @@ -1,3 +1,5 @@ +# frozen_string_literal: true + json.array!(@marker_sequences) do |marker_sequence| json.extract! marker_sequence, :id, :name, :sequence json.url marker_sequence_url(marker_sequence, format: :json) diff --git a/app/views/marker_sequences/show.json.jbuilder b/app/views/marker_sequences/show.json.jbuilder index 09f3f5f6..65e1509d 100644 --- a/app/views/marker_sequences/show.json.jbuilder +++ b/app/views/marker_sequences/show.json.jbuilder @@ -1 +1,3 @@ +# frozen_string_literal: true + json.extract! @marker_sequence, :id, :name, :sequence, :created_at, :updated_at diff --git a/app/views/markers/index.json.jbuilder b/app/views/markers/index.json.jbuilder index 1ca0abdd..a3f6bc11 100644 --- a/app/views/markers/index.json.jbuilder +++ b/app/views/markers/index.json.jbuilder @@ -1,3 +1,5 @@ +# frozen_string_literal: true + json.array!(@markers) do |marker| json.extract! marker, :id, :name, :sequence, :accession json.url marker_url(marker, format: :json) diff --git a/app/views/markers/show.json.jbuilder b/app/views/markers/show.json.jbuilder index 5aa1da68..9c9f4137 100644 --- a/app/views/markers/show.json.jbuilder +++ b/app/views/markers/show.json.jbuilder @@ -1 +1,3 @@ +# frozen_string_literal: true + json.extract! @marker, :id, :name, :sequence, :accession, :created_at, :updated_at diff --git a/app/views/micronic_plates/index.json.jbuilder b/app/views/micronic_plates/index.json.jbuilder index 2cb64676..ec567cb9 100644 --- a/app/views/micronic_plates/index.json.jbuilder +++ b/app/views/micronic_plates/index.json.jbuilder @@ -1,3 +1,5 @@ +# frozen_string_literal: true + json.array!(@micronic_plates) do |micronic_plate| json.extract! micronic_plate, :id, :micronic_plate_id, :name json.url micronic_plate_url(micronic_plate, format: :json) diff --git a/app/views/micronic_plates/show.json.jbuilder b/app/views/micronic_plates/show.json.jbuilder index 0ed82b62..6ee5d175 100644 --- a/app/views/micronic_plates/show.json.jbuilder +++ b/app/views/micronic_plates/show.json.jbuilder @@ -1 +1,3 @@ +# frozen_string_literal: true + json.extract! @micronic_plate, :id, :micronic_plate_id, :name, :created_at, :updated_at diff --git a/app/views/orders/index.json.jbuilder b/app/views/orders/index.json.jbuilder index e81672fe..51345067 100644 --- a/app/views/orders/index.json.jbuilder +++ b/app/views/orders/index.json.jbuilder @@ -1,3 +1,5 @@ +# frozen_string_literal: true + json.array!(@orders) do |order| json.extract! order, :id, :name, :author json.url order_url(order, format: :json) diff --git a/app/views/orders/show.json.jbuilder b/app/views/orders/show.json.jbuilder index 5971c423..f182a27f 100644 --- a/app/views/orders/show.json.jbuilder +++ b/app/views/orders/show.json.jbuilder @@ -1 +1,3 @@ +# frozen_string_literal: true + json.extract! @order, :id, :name, :author, :created_at, :updated_at diff --git a/app/views/plant_plates/index.json.jbuilder b/app/views/plant_plates/index.json.jbuilder index 06781cc1..5a981341 100644 --- a/app/views/plant_plates/index.json.jbuilder +++ b/app/views/plant_plates/index.json.jbuilder @@ -1,3 +1,5 @@ +# frozen_string_literal: true + json.array!(@plant_plates) do |plant_plate| json.extract! plant_plate, :id, :name, :how_many json.url plant_plate_url(plant_plate, format: :json) diff --git a/app/views/plant_plates/show.json.jbuilder b/app/views/plant_plates/show.json.jbuilder index 97d6ca4f..bd1c048e 100644 --- a/app/views/plant_plates/show.json.jbuilder +++ b/app/views/plant_plates/show.json.jbuilder @@ -1 +1,3 @@ +# frozen_string_literal: true + json.extract! @plant_plate, :id, :name, :how_many, :created_at, :updated_at diff --git a/app/views/primer_pos_on_genomes/index.json.jbuilder b/app/views/primer_pos_on_genomes/index.json.jbuilder index f0c89d2c..9248fbd2 100644 --- a/app/views/primer_pos_on_genomes/index.json.jbuilder +++ b/app/views/primer_pos_on_genomes/index.json.jbuilder @@ -1,3 +1,5 @@ +# frozen_string_literal: true + json.array!(@primer_pos_on_genomes) do |primer_pos_on_genome| json.extract! primer_pos_on_genome, :id, :note, :position json.url primer_pos_on_genome_url(primer_pos_on_genome, format: :json) diff --git a/app/views/primer_pos_on_genomes/show.json.jbuilder b/app/views/primer_pos_on_genomes/show.json.jbuilder index bfcf22f0..b7098efa 100644 --- a/app/views/primer_pos_on_genomes/show.json.jbuilder +++ b/app/views/primer_pos_on_genomes/show.json.jbuilder @@ -1 +1,3 @@ +# frozen_string_literal: true + json.extract! @primer_pos_on_genome, :id, :note, :position, :created_at, :updated_at diff --git a/app/views/primer_reads/index.json.jbuilder b/app/views/primer_reads/index.json.jbuilder index e5784c3e..9e53caea 100644 --- a/app/views/primer_reads/index.json.jbuilder +++ b/app/views/primer_reads/index.json.jbuilder @@ -1,3 +1,5 @@ +# frozen_string_literal: true + json.array!(@primer_reads) do |primer_read| json.extract! primer_read, :id, :name, :sequence, :pherogram_url json.url primer_read_url(primer_read, format: :json) diff --git a/app/views/primer_reads/show.json.jbuilder b/app/views/primer_reads/show.json.jbuilder index 86c6f37b..f476cf47 100644 --- a/app/views/primer_reads/show.json.jbuilder +++ b/app/views/primer_reads/show.json.jbuilder @@ -1 +1,3 @@ +# frozen_string_literal: true + json.extract! @primer_read, :id, :name, :sequence, :pherogram_url, :created_at, :updated_at diff --git a/app/views/primers/index.json.jbuilder b/app/views/primers/index.json.jbuilder index 1d9a88e9..29dadeed 100644 --- a/app/views/primers/index.json.jbuilder +++ b/app/views/primers/index.json.jbuilder @@ -1,3 +1,5 @@ +# frozen_string_literal: true + json.array!(@primers) do |primer| json.extract! primer, :id, :name, :sequence, :reverse json.url primer_url(primer, format: :json) diff --git a/app/views/primers/show.json.jbuilder b/app/views/primers/show.json.jbuilder index 2dc72640..2528aefb 100644 --- a/app/views/primers/show.json.jbuilder +++ b/app/views/primers/show.json.jbuilder @@ -1 +1,3 @@ +# frozen_string_literal: true + json.extract! @primer, :id, :name, :sequence, :reverse, :created_at, :updated_at diff --git a/app/views/projects/index.json.jbuilder b/app/views/projects/index.json.jbuilder index 5c99b6cb..d598b5f3 100644 --- a/app/views/projects/index.json.jbuilder +++ b/app/views/projects/index.json.jbuilder @@ -1,3 +1,5 @@ +# frozen_string_literal: true + json.array!(@projects) do |project| json.extract! project, :id, :name, :description, :start, :due json.url project_url(project, format: :json) diff --git a/app/views/projects/show.json.jbuilder b/app/views/projects/show.json.jbuilder index e2eccac4..b2a264e6 100644 --- a/app/views/projects/show.json.jbuilder +++ b/app/views/projects/show.json.jbuilder @@ -1 +1,3 @@ +# frozen_string_literal: true + json.extract! @project, :id, :name, :description, :start, :due, :created_at, :updated_at diff --git a/app/views/shelves/index.json.jbuilder b/app/views/shelves/index.json.jbuilder index a5cbb32a..25d597ec 100644 --- a/app/views/shelves/index.json.jbuilder +++ b/app/views/shelves/index.json.jbuilder @@ -1,3 +1,5 @@ +# frozen_string_literal: true + json.array!(@shelves) do |shelf| json.extract! shelf, :id, :name json.url shelf_url(shelf, format: :json) diff --git a/app/views/shelves/show.json.jbuilder b/app/views/shelves/show.json.jbuilder index 3bd2d99e..0de1cc8b 100644 --- a/app/views/shelves/show.json.jbuilder +++ b/app/views/shelves/show.json.jbuilder @@ -1 +1,3 @@ +# frozen_string_literal: true + json.extract! @shelf, :id, :name, :created_at, :updated_at diff --git a/app/views/species/index.json.jbuilder b/app/views/species/index.json.jbuilder index 8dea39fd..6c362d17 100644 --- a/app/views/species/index.json.jbuilder +++ b/app/views/species/index.json.jbuilder @@ -1,3 +1,5 @@ +# frozen_string_literal: true + json.array!(@species) do |species| json.extract! species, :id, :author, :genus_name, :species_epithet json.url species_url(species, format: :json) diff --git a/app/views/species/show.json.jbuilder b/app/views/species/show.json.jbuilder index c4b5a20f..3825e2ac 100644 --- a/app/views/species/show.json.jbuilder +++ b/app/views/species/show.json.jbuilder @@ -1 +1,3 @@ +# frozen_string_literal: true + json.extract! @species, :id, :author, :genus_name, :species_epithet, :created_at, :updated_at diff --git a/app/views/tissues/index.json.jbuilder b/app/views/tissues/index.json.jbuilder index aae81277..c0b473ec 100644 --- a/app/views/tissues/index.json.jbuilder +++ b/app/views/tissues/index.json.jbuilder @@ -1,3 +1,5 @@ +# frozen_string_literal: true + json.array!(@tissues) do |tissue| json.extract! tissue, :id, :name json.url tissue_url(tissue, format: :json) diff --git a/app/views/tissues/show.json.jbuilder b/app/views/tissues/show.json.jbuilder index eb781faf..19260f4d 100644 --- a/app/views/tissues/show.json.jbuilder +++ b/app/views/tissues/show.json.jbuilder @@ -1 +1,3 @@ +# frozen_string_literal: true + json.extract! @tissue, :id, :name, :created_at, :updated_at diff --git a/app/views/txt_uploaders/index.json.jbuilder b/app/views/txt_uploaders/index.json.jbuilder index 1f5005f4..bcfd3f08 100644 --- a/app/views/txt_uploaders/index.json.jbuilder +++ b/app/views/txt_uploaders/index.json.jbuilder @@ -1,3 +1,5 @@ +# frozen_string_literal: true + json.array!(@txt_uploaders) do |txt_uploader| json.extract! txt_uploader, :id json.url txt_uploader_url(txt_uploader, format: :json) diff --git a/app/views/txt_uploaders/show.json.jbuilder b/app/views/txt_uploaders/show.json.jbuilder index d7851c51..2be5cc84 100644 --- a/app/views/txt_uploaders/show.json.jbuilder +++ b/app/views/txt_uploaders/show.json.jbuilder @@ -1 +1,3 @@ +# frozen_string_literal: true + json.extract! @txt_uploader, :id, :created_at, :updated_at diff --git a/config.ru b/config.ru index 5bc2a619..61c04e13 100644 --- a/config.ru +++ b/config.ru @@ -1,4 +1,6 @@ +# frozen_string_literal: true + # This file is used by Rack-based servers to start the application. -require ::File.expand_path('../config/environment', __FILE__) +require ::File.expand_path('../config/environment', __FILE__) run Rails.application diff --git a/config/application.rb b/config/application.rb index f5f7f2f2..50efef84 100644 --- a/config/application.rb +++ b/config/application.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + require_relative 'boot' require 'csv' @@ -9,7 +11,6 @@ module GBOLapp class Application < Rails::Application - config.generators do |g| g.test_framework :minitest end diff --git a/config/boot.rb b/config/boot.rb index 30f5120d..30e594e2 100644 --- a/config/boot.rb +++ b/config/boot.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + ENV['BUNDLE_GEMFILE'] ||= File.expand_path('../Gemfile', __dir__) require 'bundler/setup' # Set up gems listed in the Gemfile. diff --git a/config/deploy.rb b/config/deploy.rb index 87f22d78..a4fe484a 100644 --- a/config/deploy.rb +++ b/config/deploy.rb @@ -1,5 +1,7 @@ +# frozen_string_literal: true + # Change these -server '46.101.149.34', port: 1694, roles: [:web, :app, :db], primary: true +server '46.101.149.34', port: 1694, roles: %i[web app db], primary: true set :repo_url, 'ssh://Sarah_Wiechers@bitbucket.org/kai42/gbol5.git' set :application, 'gbol5' @@ -8,7 +10,7 @@ set :puma_workers, 2 # Always deploy currently checked out branch -set :branch, $1 if `git branch` =~ /\* (\S+)\s/m +set :branch, Regexp.last_match(1) if `git branch` =~ /\* (\S+)\s/m # Rbenv setup set :whenever_environment, fetch(:stage) @@ -35,11 +37,11 @@ set :puma_user, fetch(:user) # Set key location to 'C:/Users/Sarah/.ssh/id_rsa' when deploying from windows -set :ssh_options, { port: 1694, forward_agent: true, user: fetch(:user), keys: %w(/home/sarah/.ssh/id_rsa) } +set :ssh_options, port: 1694, forward_agent: true, user: fetch(:user), keys: %w[/home/sarah/.ssh/id_rsa] # Sidekiq setup -set :sidekiq_log => File.join(release_path, 'log', 'sidekiq.log') -set :sidekiq_config => File.join(shared_path, 'config', 'sidekiq.yml') +set sidekiq_log: File.join(release_path, 'log', 'sidekiq.log') +set sidekiq_config: File.join(shared_path, 'config', 'sidekiq.yml') ## Defaults: # set :scm, :git @@ -65,12 +67,12 @@ end namespace :deploy do - desc "Make sure local git is in sync with remote." + desc 'Make sure local git is in sync with remote.' task :check_revision do on roles(:app) do unless `git rev-parse HEAD` == `git rev-parse origin/#{fetch(:branch)}` - puts "WARNING: HEAD is not the same as origin/master" - puts "Run `git push` to sync changes." + puts 'WARNING: HEAD is not the same as origin/master' + puts 'Run `git push` to sync changes.' exit end end @@ -99,14 +101,14 @@ before 'deploy:assets:precompile', :symlink_config_files -desc "Link shared files" +desc 'Link shared files' task :symlink_config_files do symlinks = { - "#{shared_path}/config/database.yml" => "#{release_path}/config/database.yml", - "#{shared_path}/config/local_env.yml" => "#{release_path}/config/local_env.yml" + "#{shared_path}/config/database.yml" => "#{release_path}/config/database.yml", + "#{shared_path}/config/local_env.yml" => "#{release_path}/config/local_env.yml" } on roles(:app) do - execute symlinks.map{|from, to| "ln -nfs #{from} #{to}"}.join(" && ") + execute symlinks.map { |from, to| "ln -nfs #{from} #{to}" }.join(' && ') end -end \ No newline at end of file +end diff --git a/config/deploy/production.rb b/config/deploy/production.rb index 4bb7a714..b84cc032 100644 --- a/config/deploy/production.rb +++ b/config/deploy/production.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + # server-based syntax # ====================== # Defines a single server with a list of roles and multiple properties. @@ -7,8 +9,6 @@ # server "example.com", user: "deploy", roles: %w{app web}, other_property: :other_value # server "db.example.com", user: "deploy", roles: %w{db} - - # role-based syntax # ================== @@ -21,8 +21,6 @@ # role :web, %w{user1@primary.com user2@additional.com}, other_property: :other_value # role :db, %w{deploy@example.com} - - # Configuration # ============= # You can set any configuration variable like in config/deploy.rb @@ -31,8 +29,6 @@ # http://capistranorb.com/documentation/getting-started/configuration/ # Feel free to add new variables to customise your setup. - - # Custom SSH Options # ================== # You may pass any option but keep in mind that net/ssh understands a diff --git a/config/deploy/staging.rb b/config/deploy/staging.rb index 4bb7a714..b84cc032 100644 --- a/config/deploy/staging.rb +++ b/config/deploy/staging.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + # server-based syntax # ====================== # Defines a single server with a list of roles and multiple properties. @@ -7,8 +9,6 @@ # server "example.com", user: "deploy", roles: %w{app web}, other_property: :other_value # server "db.example.com", user: "deploy", roles: %w{db} - - # role-based syntax # ================== @@ -21,8 +21,6 @@ # role :web, %w{user1@primary.com user2@additional.com}, other_property: :other_value # role :db, %w{deploy@example.com} - - # Configuration # ============= # You can set any configuration variable like in config/deploy.rb @@ -31,8 +29,6 @@ # http://capistranorb.com/documentation/getting-started/configuration/ # Feel free to add new variables to customise your setup. - - # Custom SSH Options # ================== # You may pass any option but keep in mind that net/ssh understands a diff --git a/config/environment.rb b/config/environment.rb index 426333bb..d5abe558 100644 --- a/config/environment.rb +++ b/config/environment.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + # Load the Rails application. require_relative 'application' diff --git a/config/environments/development.rb b/config/environments/development.rb index ad106a61..e704e2ea 100644 --- a/config/environments/development.rb +++ b/config/environments/development.rb @@ -1,8 +1,10 @@ +# frozen_string_literal: true + Rails.application.configure do # for devise - config.action_mailer.default_url_options = { :host => 'localhost:3000' } + config.action_mailer.default_url_options = { host: 'localhost:3000' } config.action_mailer.delivery_method = :smtp - config.action_mailer.smtp_settings = {:address => 'localhost', :port => 1025} + config.action_mailer.smtp_settings = { address: 'localhost', port: 1025 } # Settings specified here will take precedence over those in config/application.rb. @@ -70,6 +72,6 @@ end config.paperclip_defaults = { - :storage => 'filesystem' + storage: 'filesystem' } end diff --git a/config/environments/production.rb b/config/environments/production.rb index 8f1df812..da1b510a 100644 --- a/config/environments/production.rb +++ b/config/environments/production.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + Rails.application.configure do # Settings specified here will take precedence over those in config/application.rb. @@ -33,9 +35,11 @@ # Load environment variables config.before_configuration do env_file = File.join(Rails.root, 'config', 'local_env.yml') - YAML.load(File.open(env_file)).each do |key, value| - ENV[key.to_s] = value - end if File.exists?(env_file) + if File.exist?(env_file) + YAML.safe_load(File.open(env_file)).each do |key, value| + ENV[key.to_s] = value + end + end end # Enable serving of images, stylesheets, and JavaScripts from an asset server. @@ -58,7 +62,7 @@ config.log_level = :info # Prepend all log lines with the following tags. - config.log_tags = [ :request_id ] + config.log_tags = [:request_id] # Use a different cache store in production. # config.cache_store = :mem_cache_store @@ -72,11 +76,11 @@ config.action_mailer.default_url_options = { host: 'gbol5.de' } config.action_mailer.delivery_method = :smtp config.action_mailer.smtp_settings = { - :address => '127.0.0.1', - :port => 25, - :domain => 'gbol5.de', - :tls => false, - :enable_starttls_auto => false, + address: '127.0.0.1', + port: 25, + domain: 'gbol5.de', + tls: false, + enable_starttls_auto: false } # Ignore bad email addresses and do not raise email delivery errors. @@ -110,15 +114,15 @@ config.secret_key_base = '<%= ENV["SECRET_KEY_BASE"] %>' config.paperclip_defaults = { - :storage => :s3, - :url =>':s3_domain_url', - :path => '/:class/:attachment/:id_partition/:style/:filename', - :s3_credentials => { - :bucket => ENV['S3_BUCKET_NAME'], - :access_key_id => ENV['AWS_ACCESS_KEY_ID'], - :secret_access_key => ENV['AWS_SECRET_ACCESS_KEY'], - :s3_region => ENV['S3_REGION'], - :preserve_files => true - }, + storage: :s3, + url: ':s3_domain_url', + path: '/:class/:attachment/:id_partition/:style/:filename', + s3_credentials: { + bucket: ENV['S3_BUCKET_NAME'], + access_key_id: ENV['AWS_ACCESS_KEY_ID'], + secret_access_key: ENV['AWS_SECRET_ACCESS_KEY'], + s3_region: ENV['S3_REGION'], + preserve_files: true + } } end diff --git a/config/environments/test.rb b/config/environments/test.rb index 666724af..f45fd458 100644 --- a/config/environments/test.rb +++ b/config/environments/test.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + Rails.application.configure do # for devise config.action_mailer.default_url_options = { host: 'localhost', port: 3000 } @@ -50,5 +52,4 @@ Rails.application.configure do config.active_support.test_order = :sorted end - end diff --git a/config/initializers/assets.rb b/config/initializers/assets.rb index 01ef3e66..678efe9f 100644 --- a/config/initializers/assets.rb +++ b/config/initializers/assets.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + # Be sure to restart your server when you modify this file. # Version of your assets, change this if you want to expire all your assets. diff --git a/config/initializers/backtrace_silencers.rb b/config/initializers/backtrace_silencers.rb index 59385cdf..4b63f289 100644 --- a/config/initializers/backtrace_silencers.rb +++ b/config/initializers/backtrace_silencers.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + # Be sure to restart your server when you modify this file. # You can add backtrace silencers for libraries that you're using but don't wish to see in your backtraces. diff --git a/config/initializers/cookies_serializer.rb b/config/initializers/cookies_serializer.rb index 5a6a32d3..ee8dff9c 100644 --- a/config/initializers/cookies_serializer.rb +++ b/config/initializers/cookies_serializer.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + # Be sure to restart your server when you modify this file. # Specify a serializer for the signed and encrypted cookie jars. diff --git a/config/initializers/devise.rb b/config/initializers/devise.rb index 06e6924b..6492f73d 100644 --- a/config/initializers/devise.rb +++ b/config/initializers/devise.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + # Use this hook to configure devise mailer, warden hooks and so forth. # Many of these configuration options can be set straight in your model. Devise.setup do |config| @@ -8,7 +10,6 @@ config.secret_key = '422ed9a725773e72abb68813a794ffcc0659a7426fc1687bac085b61b10b1a0ac2a4440799d0e085b1baa622ed3a7d501931b96caaadcc4133021e94cb540c80' - # ==> Mailer Configuration # Configure the e-mail address which will be shown in Devise::Mailer, # note that it will be overwritten if you use your own mailer class @@ -44,12 +45,12 @@ # Configure which authentication keys should be case-insensitive. # These keys will be downcased upon creating or modifying a user and when used # to authenticate or find a user. Default is :email. - config.case_insensitive_keys = [ :email ] + config.case_insensitive_keys = [:email] # Configure which authentication keys should have whitespace stripped. # These keys will have whitespace before and after removed upon creating or # modifying a user and when used to authenticate or find a user. Default is :email. - config.strip_whitespace_keys = [ :email ] + config.strip_whitespace_keys = [:email] # Tell if authentication through request.params is enabled. True by default. # It can be set to an array that will enable params authentication only for the diff --git a/config/initializers/filter_parameter_logging.rb b/config/initializers/filter_parameter_logging.rb index f24a2166..52f05587 100644 --- a/config/initializers/filter_parameter_logging.rb +++ b/config/initializers/filter_parameter_logging.rb @@ -1,4 +1,6 @@ +# frozen_string_literal: true + # Be sure to restart your server when you modify this file. # Configure sensitive parameters which will be filtered from the log file. -Rails.application.config.filter_parameters += [:password, :user_name, :user_id] +Rails.application.config.filter_parameters += %i[password user_name user_id] diff --git a/config/initializers/inflections.rb b/config/initializers/inflections.rb index a245e208..123a9e36 100644 --- a/config/initializers/inflections.rb +++ b/config/initializers/inflections.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + # Be sure to restart your server when you modify this file. # Add new inflection rules using the following format. Inflections @@ -5,16 +7,16 @@ # locales as you wish. All of these examples are active by default: ActiveSupport::Inflector.inflections(:en) do |inflect| -# inflect.plural /^(ox)$/i, '\1en' -# inflect.singular /^(ox)en/i, '\1' -# inflect.irregular 'person', 'people' -# inflect.uncountable %w( fish sheep ) - inflect.uncountable %w( species ) - inflect.irregular 'syntaxon', 'syntaxa' - inflect.irregular 'higher_order_taxon', 'higher_order_taxa' - inflect.irregular 'HigherOrderTaxon', 'HigherOrderTaxa' - inflect.irregular 'genus', 'genera' - inflect.uncountable %w( subspecies ) + # inflect.plural /^(ox)$/i, '\1en' + # inflect.singular /^(ox)en/i, '\1' + # inflect.irregular 'person', 'people' + # inflect.uncountable %w( fish sheep ) + inflect.uncountable %w[species] + inflect.irregular 'syntaxon', 'syntaxa' + inflect.irregular 'higher_order_taxon', 'higher_order_taxa' + inflect.irregular 'HigherOrderTaxon', 'HigherOrderTaxa' + inflect.irregular 'genus', 'genera' + inflect.uncountable %w[subspecies] end # These inflection rules are supported but not enabled by default: diff --git a/config/initializers/mime_types.rb b/config/initializers/mime_types.rb index 212d2fe0..5aaebc7b 100644 --- a/config/initializers/mime_types.rb +++ b/config/initializers/mime_types.rb @@ -1,7 +1,9 @@ +# frozen_string_literal: true + # Be sure to restart your server when you modify this file. # Add new mime types for use in respond_to blocks: # Mime::Type.register "text/richtext", :rtf -Mime::Type.register "application/xls", :xls -Mime::Type.register "application/xml ", :abc +Mime::Type.register 'application/xls', :xls +Mime::Type.register 'application/xml ', :abc diff --git a/config/initializers/paperclip.rb b/config/initializers/paperclip.rb index 152ff87c..b68e8a9a 100644 --- a/config/initializers/paperclip.rb +++ b/config/initializers/paperclip.rb @@ -1,5 +1,7 @@ +# frozen_string_literal: true + Paperclip.options[:content_type_mappings] = { - :scf => "application/octet-stream", - :ab1 => "application/octet-stream" - # :xls => "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet" -} \ No newline at end of file + scf: 'application/octet-stream', + ab1: 'application/octet-stream' + # :xls => "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet" +} diff --git a/config/initializers/pg_search.rb b/config/initializers/pg_search.rb index 7c8e5fd3..63b10e8a 100644 --- a/config/initializers/pg_search.rb +++ b/config/initializers/pg_search.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + PgSearch.multisearch_options = { - :using => { :tsearch => { :prefix => true }, :trigram => {} } -} \ No newline at end of file + using: { tsearch: { prefix: true }, trigram: {} } +} diff --git a/config/initializers/redis.rb b/config/initializers/redis.rb index 746171f5..6f03e3a5 100644 --- a/config/initializers/redis.rb +++ b/config/initializers/redis.rb @@ -1,2 +1,4 @@ +# frozen_string_literal: true + # uri = URI.parse(ENV["REDISTOGO_URL"]) -# REDIS = Redis.new(:url => ENV['REDISTOGO_URL']) \ No newline at end of file +# REDIS = Redis.new(:url => ENV['REDISTOGO_URL']) diff --git a/config/initializers/session_store.rb b/config/initializers/session_store.rb index 1865c681..e7b0fab1 100644 --- a/config/initializers/session_store.rb +++ b/config/initializers/session_store.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + # Be sure to restart your server when you modify this file. Rails.application.config.session_store :cookie_store, key: '_gbo_lapp_session' diff --git a/config/initializers/simple_form.rb b/config/initializers/simple_form.rb index 6986de98..29665f56 100644 --- a/config/initializers/simple_form.rb +++ b/config/initializers/simple_form.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + # Use this setup block to configure all options available in SimpleForm. SimpleForm.setup do |config| # Wrappers are used by the form builder to generate a @@ -6,7 +8,7 @@ # stack. The options given below are used to wrap the # whole input. config.wrappers :default, class: :input, - hint_class: :field_with_hint, error_class: :field_with_errors do |b| + hint_class: :field_with_hint, error_class: :field_with_errors do |b| ## Extensions enabled by default # Any of these extensions can be disabled for a # given input by passing: `f.input EXTENSION_NAME => false`. diff --git a/config/initializers/simple_form_bootstrap.rb b/config/initializers/simple_form_bootstrap.rb index ad4ca74c..140a8ecd 100644 --- a/config/initializers/simple_form_bootstrap.rb +++ b/config/initializers/simple_form_bootstrap.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + # Use this setup block to configure all options available in SimpleForm. SimpleForm.setup do |config| config.wrappers :bootstrap, tag: 'div', class: 'control-group', error_class: 'error' do |b| @@ -11,7 +13,7 @@ end end - config.wrappers :prepend, tag: 'div', class: "control-group", error_class: 'error' do |b| + config.wrappers :prepend, tag: 'div', class: 'control-group', error_class: 'error' do |b| b.use :html5 b.use :placeholder b.use :label @@ -24,7 +26,7 @@ end end - config.wrappers :append, tag: 'div', class: "control-group", error_class: 'error' do |b| + config.wrappers :append, tag: 'div', class: 'control-group', error_class: 'error' do |b| b.use :html5 b.use :placeholder b.use :label diff --git a/config/initializers/wrap_parameters.rb b/config/initializers/wrap_parameters.rb index bbfc3961..2f3c0db4 100644 --- a/config/initializers/wrap_parameters.rb +++ b/config/initializers/wrap_parameters.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + # Be sure to restart your server when you modify this file. # This file contains settings for ActionController::ParamsWrapper which diff --git a/config/puma.rb b/config/puma.rb index 15e8ac3e..a508ed35 100644 --- a/config/puma.rb +++ b/config/puma.rb @@ -1,21 +1,23 @@ +# frozen_string_literal: true + # Puma can serve each request in a thread from an internal thread pool. # The `threads` method setting takes two numbers: a minimum and maximum. # Any libraries that use thread pools should be configured to match # the maximum value specified for Puma. Default is set to 5 threads for minimum # and maximum; this matches the default thread size of Active Record. # -threads_count = ENV.fetch("RAILS_MAX_THREADS") { 5 } +threads_count = ENV.fetch('RAILS_MAX_THREADS') { 5 } threads threads_count, threads_count rackup DefaultRackup # Specifies the `port` that Puma will listen on to receive requests; default is 3000. # -port ENV.fetch("PORT") { 3000 } +port ENV.fetch('PORT') { 3000 } # Specifies the `environment` that Puma will run in. # -environment ENV.fetch("RAILS_ENV") { "development" } +environment ENV.fetch('RAILS_ENV') { 'development' } # Specifies the number of `workers` to boot in clustered mode. # Workers are forked webserver processes. If using threads and workers together @@ -54,4 +56,4 @@ end # Allow puma to be restarted by `rails restart` command. -plugin :tmp_restart \ No newline at end of file +plugin :tmp_restart diff --git a/config/routes.rb b/config/routes.rb index a58dcb58..a7097c4d 100644 --- a/config/routes.rb +++ b/config/routes.rb @@ -1,6 +1,7 @@ -GBOLapp::Application.routes.draw do +# frozen_string_literal: true - root :to => "home#about" +GBOLapp::Application.routes.draw do + root to: 'home#about' match 'help', to: 'home#help', via: 'get' match 'about', to: 'home#about', via: 'get' @@ -10,11 +11,11 @@ match 'overview', to: 'home#overview', via: 'get' get 'overview_diagram/index' - get 'overview_diagram/all_species', :defaults => { :format => 'json' } - get 'overview_diagram/finished_species_trnlf', :defaults => { :format => 'json' } - get 'overview_diagram/finished_species_its', :defaults => { :format => 'json' } - get 'overview_diagram/finished_species_rpl16', :defaults => { :format => 'json' } - get 'overview_diagram/finished_species_trnk_matk', :defaults => { :format => 'json' } + get 'overview_diagram/all_species', defaults: { format: 'json' } + get 'overview_diagram/finished_species_trnlf', defaults: { format: 'json' } + get 'overview_diagram/finished_species_its', defaults: { format: 'json' } + get 'overview_diagram/finished_species_rpl16', defaults: { format: 'json' } + get 'overview_diagram/finished_species_trnk_matk', defaults: { format: 'json' } get 'specimens_xls', action: :xls, controller: 'individuals' get 'specimens_create_xls', action: :create_xls, controller: 'individuals' @@ -24,8 +25,8 @@ get 'analysis_output', action: :analysis_output, controller: 'contigs' get 'reads_without_contigs', action: :reads_without_contigs, controller: 'primer_reads' - get 'partial_cons/:id/:page/:width_in_bases', action: :show_page, controller: 'partial_cons', :defaults => { :format => 'json' } - get 'partial_cons_pos/:id/:position/:width_in_bases', action: :show_position, controller: 'partial_cons', :defaults => { :format => 'json' } + get 'partial_cons/:id/:page/:width_in_bases', action: :show_page, controller: 'partial_cons', defaults: { format: 'json' } + get 'partial_cons_pos/:id/:position/:width_in_bases', action: :show_position, controller: 'partial_cons', defaults: { format: 'json' } get 'primer_reads/:id/edit/:pos', action: :go_to_pos, controller: 'primer_reads' @@ -44,7 +45,6 @@ resources :individual_searches resources :contigs do - collection do get 'show_need_verify' get 'caryophyllales_need_verification' @@ -73,7 +73,6 @@ get 'overlap' get 'overlap_background' end - end resources :individuals do @@ -204,18 +203,18 @@ resources :responsibilities - #hack: avoid malicious users to directly type in the sign-up route - #later: use authorization system to + # HACK: avoid malicious users to directly type in the sign-up route + # later: use authorization system to devise_scope :user do - get "/users/sign_up", :to => "home#about" + get '/users/sign_up', to: 'home#about' end - devise_for :users, :controllers => {:registrations => "registrations"}, path_names: {sign_in: "login", sign_out: "logout"} + devise_for :users, controllers: { registrations: 'registrations' }, path_names: { sign_in: 'login', sign_out: 'logout' } devise_scope :users do get '/login' => 'devise/sessions#new' get '/logout' => 'devise/sessions#destroy' end - resources :users, :controller => 'users' do + resources :users, controller: 'users' do member do get 'home' end @@ -226,4 +225,4 @@ require 'sidekiq/web' mount Sidekiq::Web => '/sidekiq' -end \ No newline at end of file +end diff --git a/config/schedule.rb b/config/schedule.rb index 4afc3242..b81d3191 100644 --- a/config/schedule.rb +++ b/config/schedule.rb @@ -1,32 +1,34 @@ +# frozen_string_literal: true + set :output, "#{path}/log/cron.log" # Whenever config if defined? rbenv_root - job_type :rake, %{cd :path && :environment_variable=:environment :rbenv_root/bin/rbenv exec bundle exec rake :task --silent :output} - job_type :runner, %{cd :path && :rbenv_root/bin/rbenv exec bundle exec rails runner -e :environment ':task' :output} - job_type :script, %{cd :path && :environment_variable=:environment :rbenv_root/bin/rbenv exec bundle exec script/:task :output} + job_type :rake, %(cd :path && :environment_variable=:environment :rbenv_root/bin/rbenv exec bundle exec rake :task --silent :output) + job_type :runner, %(cd :path && :rbenv_root/bin/rbenv exec bundle exec rails runner -e :environment ':task' :output) + job_type :script, %(cd :path && :environment_variable=:environment :rbenv_root/bin/rbenv exec bundle exec script/:task :output) end -every 1.day, :at => '23:30 am' do - rake "data:create_xls" # Create Specimen.xls file from current database +every 1.day, at: '23:30 am' do + rake 'data:create_xls' # Create Specimen.xls file from current database end -every 1.day, :at => '0:30 am' do - rake "data:remove_old_searches" # Delete all untitled contig searches older than a month +every 1.day, at: '0:30 am' do + rake 'data:remove_old_searches' # Delete all untitled contig searches older than a month end -every 1.day, :at => '21:00 am' do - rake "data:check_new_marker_sequences" # Checks amount of new/updated sequences and runs SATIVA analysis if necessary +every 1.day, at: '21:00 am' do + rake 'data:check_new_marker_sequences' # Checks amount of new/updated sequences and runs SATIVA analysis if necessary end -every 1.day, :at => '5:00 am' do - rake "data:download_sativa_results" # Downloads any available SATIVA results +every 1.day, at: '5:00 am' do + rake 'data:download_sativa_results' # Downloads any available SATIVA results end -every 1.day, :at => '5:10 am' do - rake "data:flag_specimen" # Places a warning on specimens with multiple sequences that have issues +every 1.day, at: '5:10 am' do + rake 'data:flag_specimen' # Places a warning on specimens with multiple sequences that have issues end -every 1.day, :at => '5:15 am' do - rake "data:unflag_specimen" # Removes warnings from specimens with less than two sequences that have issues -end \ No newline at end of file +every 1.day, at: '5:15 am' do + rake 'data:unflag_specimen' # Removes warnings from specimens with less than two sequences that have issues +end diff --git a/db/migrate/20140427145700_devise_create_users.rb b/db/migrate/20140427145700_devise_create_users.rb index cf497c27..620b04c3 100644 --- a/db/migrate/20140427145700_devise_create_users.rb +++ b/db/migrate/20140427145700_devise_create_users.rb @@ -1,9 +1,11 @@ +# frozen_string_literal: true + class DeviseCreateUsers < ActiveRecord::Migration def change create_table(:users) do |t| ## Database authenticatable - t.string :email, null: false, default: "" - t.string :encrypted_password, null: false, default: "" + t.string :email, null: false, default: '' + t.string :encrypted_password, null: false, default: '' ## Recoverable t.string :reset_password_token @@ -30,7 +32,6 @@ def change # t.string :unlock_token # Only if unlock strategy is :email or :both # t.datetime :locked_at - t.timestamps end diff --git a/db/migrate/20140427145702_add_name_to_users.rb b/db/migrate/20140427145702_add_name_to_users.rb index bac750eb..f6e6bef4 100644 --- a/db/migrate/20140427145702_add_name_to_users.rb +++ b/db/migrate/20140427145702_add_name_to_users.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddNameToUsers < ActiveRecord::Migration def change add_column :users, :name, :string diff --git a/db/migrate/20140427170957_create_contigs.rb b/db/migrate/20140427170957_create_contigs.rb index 81c734cb..23b36e94 100644 --- a/db/migrate/20140427170957_create_contigs.rb +++ b/db/migrate/20140427170957_create_contigs.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class CreateContigs < ActiveRecord::Migration def change create_table :contigs do |t| diff --git a/db/migrate/20140427171206_create_families.rb b/db/migrate/20140427171206_create_families.rb index 7cce5b66..c175392b 100644 --- a/db/migrate/20140427171206_create_families.rb +++ b/db/migrate/20140427171206_create_families.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class CreateFamilies < ActiveRecord::Migration def change create_table :families do |t| diff --git a/db/migrate/20140427171750_create_copies.rb b/db/migrate/20140427171750_create_copies.rb index 02a2e978..950553a9 100644 --- a/db/migrate/20140427171750_create_copies.rb +++ b/db/migrate/20140427171750_create_copies.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class CreateCopies < ActiveRecord::Migration def change create_table :copies do |t| diff --git a/db/migrate/20140427171848_create_markers.rb b/db/migrate/20140427171848_create_markers.rb index 4185f8ef..64dba680 100644 --- a/db/migrate/20140427171848_create_markers.rb +++ b/db/migrate/20140427171848_create_markers.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class CreateMarkers < ActiveRecord::Migration def change create_table :markers do |t| diff --git a/db/migrate/20140427171933_create_micronic_plates.rb b/db/migrate/20140427171933_create_micronic_plates.rb index 25b3f4d2..b15e550c 100644 --- a/db/migrate/20140427171933_create_micronic_plates.rb +++ b/db/migrate/20140427171933_create_micronic_plates.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class CreateMicronicPlates < ActiveRecord::Migration def change create_table :micronic_plates do |t| diff --git a/db/migrate/20140427172024_create_plant_plates.rb b/db/migrate/20140427172024_create_plant_plates.rb index 2ca6bfda..a3bdfb6a 100644 --- a/db/migrate/20140427172024_create_plant_plates.rb +++ b/db/migrate/20140427172024_create_plant_plates.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class CreatePlantPlates < ActiveRecord::Migration def change create_table :plant_plates do |t| diff --git a/db/migrate/20140427172121_create_primer_reads.rb b/db/migrate/20140427172121_create_primer_reads.rb index 8f9809fb..7e2c181d 100644 --- a/db/migrate/20140427172121_create_primer_reads.rb +++ b/db/migrate/20140427172121_create_primer_reads.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class CreatePrimerReads < ActiveRecord::Migration def change create_table :primer_reads do |t| diff --git a/db/migrate/20140427172201_create_primers.rb b/db/migrate/20140427172201_create_primers.rb index 28c23db4..cfccb8b2 100644 --- a/db/migrate/20140427172201_create_primers.rb +++ b/db/migrate/20140427172201_create_primers.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class CreatePrimers < ActiveRecord::Migration def change create_table :primers do |t| diff --git a/db/migrate/20140427172301_create_statuses.rb b/db/migrate/20140427172301_create_statuses.rb index f6c0e156..2489d53d 100644 --- a/db/migrate/20140427172301_create_statuses.rb +++ b/db/migrate/20140427172301_create_statuses.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class CreateStatuses < ActiveRecord::Migration def change create_table :statuses do |t| diff --git a/db/migrate/20140427172324_create_tissues.rb b/db/migrate/20140427172324_create_tissues.rb index 027ac8d0..a2ddd262 100644 --- a/db/migrate/20140427172324_create_tissues.rb +++ b/db/migrate/20140427172324_create_tissues.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class CreateTissues < ActiveRecord::Migration def change create_table :tissues do |t| diff --git a/db/migrate/20140427175033_create_individuals.rb b/db/migrate/20140427175033_create_individuals.rb index 27e9485f..c305b3b7 100644 --- a/db/migrate/20140427175033_create_individuals.rb +++ b/db/migrate/20140427175033_create_individuals.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class CreateIndividuals < ActiveRecord::Migration def change create_table :individuals do |t| diff --git a/db/migrate/20140504191737_create_orders.rb b/db/migrate/20140504191737_create_orders.rb index ef944c8d..599c89b2 100644 --- a/db/migrate/20140504191737_create_orders.rb +++ b/db/migrate/20140504191737_create_orders.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class CreateOrders < ActiveRecord::Migration def change create_table :orders do |t| diff --git a/db/migrate/20140505202236_create_marker_sequences.rb b/db/migrate/20140505202236_create_marker_sequences.rb index b677a3f5..91a66af6 100644 --- a/db/migrate/20140505202236_create_marker_sequences.rb +++ b/db/migrate/20140505202236_create_marker_sequences.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class CreateMarkerSequences < ActiveRecord::Migration def change create_table :marker_sequences do |t| diff --git a/db/migrate/20140507193213_add_genbank_to_marker_sequences.rb b/db/migrate/20140507193213_add_genbank_to_marker_sequences.rb index 417a1cd8..8a6460d1 100644 --- a/db/migrate/20140507193213_add_genbank_to_marker_sequences.rb +++ b/db/migrate/20140507193213_add_genbank_to_marker_sequences.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddGenbankToMarkerSequences < ActiveRecord::Migration def change add_column :marker_sequences, :genbank, :string diff --git a/db/migrate/20140507194029_create_lab_racks.rb b/db/migrate/20140507194029_create_lab_racks.rb index 552451b6..570fadbf 100644 --- a/db/migrate/20140507194029_create_lab_racks.rb +++ b/db/migrate/20140507194029_create_lab_racks.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class CreateLabRacks < ActiveRecord::Migration def change create_table :lab_racks do |t| diff --git a/db/migrate/20140507194056_create_freezers.rb b/db/migrate/20140507194056_create_freezers.rb index 5b20ae20..cfd51ee8 100644 --- a/db/migrate/20140507194056_create_freezers.rb +++ b/db/migrate/20140507194056_create_freezers.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class CreateFreezers < ActiveRecord::Migration def change create_table :freezers do |t| diff --git a/db/migrate/20140507194116_create_labs.rb b/db/migrate/20140507194116_create_labs.rb index 365eb117..cae876fd 100644 --- a/db/migrate/20140507194116_create_labs.rb +++ b/db/migrate/20140507194116_create_labs.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class CreateLabs < ActiveRecord::Migration def change create_table :labs do |t| diff --git a/db/migrate/20140507195652_remove_sequence_from_marker_sequences.rb b/db/migrate/20140507195652_remove_sequence_from_marker_sequences.rb index 64a982f0..c3e026d5 100644 --- a/db/migrate/20140507195652_remove_sequence_from_marker_sequences.rb +++ b/db/migrate/20140507195652_remove_sequence_from_marker_sequences.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class RemoveSequenceFromMarkerSequences < ActiveRecord::Migration def change remove_column :marker_sequences, :sequence, :string diff --git a/db/migrate/20140507195841_add_sequence_to_marker_sequences.rb b/db/migrate/20140507195841_add_sequence_to_marker_sequences.rb index 92d57bc4..3865a304 100644 --- a/db/migrate/20140507195841_add_sequence_to_marker_sequences.rb +++ b/db/migrate/20140507195841_add_sequence_to_marker_sequences.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddSequenceToMarkerSequences < ActiveRecord::Migration def change add_column :marker_sequences, :sequence, :string diff --git a/db/migrate/20140507195937_remove_sequence_from_markers.rb b/db/migrate/20140507195937_remove_sequence_from_markers.rb index d96b1f6d..e22a666a 100644 --- a/db/migrate/20140507195937_remove_sequence_from_markers.rb +++ b/db/migrate/20140507195937_remove_sequence_from_markers.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class RemoveSequenceFromMarkers < ActiveRecord::Migration def change remove_column :markers, :sequence, :text diff --git a/db/migrate/20140507200016_remove_accession_from_markers.rb b/db/migrate/20140507200016_remove_accession_from_markers.rb index cca94d01..eda50305 100644 --- a/db/migrate/20140507200016_remove_accession_from_markers.rb +++ b/db/migrate/20140507200016_remove_accession_from_markers.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class RemoveAccessionFromMarkers < ActiveRecord::Migration def change remove_column :markers, :accession, :string diff --git a/db/migrate/20140507200544_remove_seqe_from_marker_sequences.rb b/db/migrate/20140507200544_remove_seqe_from_marker_sequences.rb index 8b99b43a..6e52554f 100644 --- a/db/migrate/20140507200544_remove_seqe_from_marker_sequences.rb +++ b/db/migrate/20140507200544_remove_seqe_from_marker_sequences.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class RemoveSeqeFromMarkerSequences < ActiveRecord::Migration def change remove_column :marker_sequences, :sequence, :string diff --git a/db/migrate/20140507200617_add_seq_to_marker_sequences.rb b/db/migrate/20140507200617_add_seq_to_marker_sequences.rb index a060e229..8615cdb3 100644 --- a/db/migrate/20140507200617_add_seq_to_marker_sequences.rb +++ b/db/migrate/20140507200617_add_seq_to_marker_sequences.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddSeqToMarkerSequences < ActiveRecord::Migration def change add_column :marker_sequences, :sequence, :text diff --git a/db/migrate/20140509145138_create_shelves.rb b/db/migrate/20140509145138_create_shelves.rb index 92234a1d..b3ec3084 100644 --- a/db/migrate/20140509145138_create_shelves.rb +++ b/db/migrate/20140509145138_create_shelves.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class CreateShelves < ActiveRecord::Migration def change create_table :shelves do |t| diff --git a/db/migrate/20140510135015_create_projects.rb b/db/migrate/20140510135015_create_projects.rb index e466a13d..5bd14967 100644 --- a/db/migrate/20140510135015_create_projects.rb +++ b/db/migrate/20140510135015_create_projects.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class CreateProjects < ActiveRecord::Migration def change create_table :projects do |t| diff --git a/db/migrate/20140510135301_create_alignments.rb b/db/migrate/20140510135301_create_alignments.rb index 2a0bcef3..5987c6cb 100644 --- a/db/migrate/20140510135301_create_alignments.rb +++ b/db/migrate/20140510135301_create_alignments.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class CreateAlignments < ActiveRecord::Migration def change create_table :alignments do |t| diff --git a/db/migrate/20140510143055_create_primer_pos_on_genomes.rb b/db/migrate/20140510143055_create_primer_pos_on_genomes.rb index 90848ba4..37f47cac 100644 --- a/db/migrate/20140510143055_create_primer_pos_on_genomes.rb +++ b/db/migrate/20140510143055_create_primer_pos_on_genomes.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class CreatePrimerPosOnGenomes < ActiveRecord::Migration def change create_table :primer_pos_on_genomes do |t| diff --git a/db/migrate/20140510144847_add_projects_users_table.rb b/db/migrate/20140510144847_add_projects_users_table.rb index 27c6bec5..6150274c 100644 --- a/db/migrate/20140510144847_add_projects_users_table.rb +++ b/db/migrate/20140510144847_add_projects_users_table.rb @@ -1,7 +1,8 @@ -class AddProjUsersTable < ActiveRecord::Migration +# frozen_string_literal: true +class AddProjUsersTable < ActiveRecord::Migration def change - create_table :projects_users, :id => false do |t| + create_table :projects_users, id: false do |t| t.references :project t.references :user end @@ -10,4 +11,4 @@ def change def self.down drop_table :projects_users end -end \ No newline at end of file +end diff --git a/db/migrate/20140510151628_add_pr_us_table.rb b/db/migrate/20140510151628_add_pr_us_table.rb index 3924d0fe..aaa815e3 100644 --- a/db/migrate/20140510151628_add_pr_us_table.rb +++ b/db/migrate/20140510151628_add_pr_us_table.rb @@ -1,6 +1,8 @@ +# frozen_string_literal: true + class AddPrUsTable < ActiveRecord::Migration def change - create_table :projects_users, :id => false do |t| + create_table :projects_users, id: false do |t| t.references :project t.references :user end diff --git a/db/migrate/20140510163102_add_silica_gel_to_individuals.rb b/db/migrate/20140510163102_add_silica_gel_to_individuals.rb index 17b099e2..d8407f06 100644 --- a/db/migrate/20140510163102_add_silica_gel_to_individuals.rb +++ b/db/migrate/20140510163102_add_silica_gel_to_individuals.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddSilicaGelToIndividuals < ActiveRecord::Migration def change add_column :individuals, :silica_gel, :boolean diff --git a/db/migrate/20140510163211_add_collected_to_individuals.rb b/db/migrate/20140510163211_add_collected_to_individuals.rb index 8171a068..2f6cfb1b 100644 --- a/db/migrate/20140510163211_add_collected_to_individuals.rb +++ b/db/migrate/20140510163211_add_collected_to_individuals.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddCollectedToIndividuals < ActiveRecord::Migration def change add_column :individuals, :collected, :date diff --git a/db/migrate/20140510174836_add_notes_to_primers.rb b/db/migrate/20140510174836_add_notes_to_primers.rb index 9cbd6c07..4e914faa 100644 --- a/db/migrate/20140510174836_add_notes_to_primers.rb +++ b/db/migrate/20140510174836_add_notes_to_primers.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddNotesToPrimers < ActiveRecord::Migration def change add_column :primers, :notes, :text diff --git a/db/migrate/20140510175052_create_higher_order_taxons.rb b/db/migrate/20140510175052_create_higher_order_taxons.rb index 0b68a165..867adae7 100644 --- a/db/migrate/20140510175052_create_higher_order_taxons.rb +++ b/db/migrate/20140510175052_create_higher_order_taxons.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class CreateHigherOrderTaxons < ActiveRecord::Migration def change create_table :higher_order_taxons do |t| diff --git a/db/migrate/20140510175410_add_location_in_rack_to_plant_plate.rb b/db/migrate/20140510175410_add_location_in_rack_to_plant_plate.rb index c3947e3c..13587e6f 100644 --- a/db/migrate/20140510175410_add_location_in_rack_to_plant_plate.rb +++ b/db/migrate/20140510175410_add_location_in_rack_to_plant_plate.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddLocationInRackToPlantPlate < ActiveRecord::Migration def change add_column :plant_plates, :location_in_rack, :string diff --git a/db/migrate/20140510175437_add_location_in_rack_to_micronic_plate.rb b/db/migrate/20140510175437_add_location_in_rack_to_micronic_plate.rb index d6399ce8..e9f01eb7 100644 --- a/db/migrate/20140510175437_add_location_in_rack_to_micronic_plate.rb +++ b/db/migrate/20140510175437_add_location_in_rack_to_micronic_plate.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddLocationInRackToMicronicPlate < ActiveRecord::Migration def change add_column :micronic_plates, :location_in_rack, :string diff --git a/db/migrate/20140510175842_add_is_copy_to_copy.rb b/db/migrate/20140510175842_add_is_copy_to_copy.rb index a770526e..825f4247 100644 --- a/db/migrate/20140510175842_add_is_copy_to_copy.rb +++ b/db/migrate/20140510175842_add_is_copy_to_copy.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddIsCopyToCopy < ActiveRecord::Migration def change add_column :copies, :isCopy, :boolean diff --git a/db/migrate/20140510181511_drop_spec_epi.rb b/db/migrate/20140510181511_drop_spec_epi.rb index ff565a32..ac4ff069 100644 --- a/db/migrate/20140510181511_drop_spec_epi.rb +++ b/db/migrate/20140510181511_drop_spec_epi.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class DropSpecEpi < ActiveRecord::Migration def change drop_table :species_epithets diff --git a/db/migrate/20140510181759_remove_species_epithet_from_species.rb b/db/migrate/20140510181759_remove_species_epithet_from_species.rb index ddd415be..cf789924 100644 --- a/db/migrate/20140510181759_remove_species_epithet_from_species.rb +++ b/db/migrate/20140510181759_remove_species_epithet_from_species.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class RemoveSpeciesEpithetFromSpecies < ActiveRecord::Migration def change remove_column :species, :species_epithet, :string diff --git a/db/migrate/20140510181829_remove_author_from_species.rb b/db/migrate/20140510181829_remove_author_from_species.rb index ed86374a..2434be4c 100644 --- a/db/migrate/20140510181829_remove_author_from_species.rb +++ b/db/migrate/20140510181829_remove_author_from_species.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class RemoveAuthorFromSpecies < ActiveRecord::Migration def change remove_column :species, :author, :string diff --git a/db/migrate/20140510182038_add_published_to_species.rb b/db/migrate/20140510182038_add_published_to_species.rb index 3fbb9899..13dc732e 100644 --- a/db/migrate/20140510182038_add_published_to_species.rb +++ b/db/migrate/20140510182038_add_published_to_species.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddPublishedToSpecies < ActiveRecord::Migration def change add_column :species, :published, :date diff --git a/db/migrate/20140510182641_drop_table_species_eptithets.rb b/db/migrate/20140510182641_drop_table_species_eptithets.rb index fc4ac682..64ed0587 100644 --- a/db/migrate/20140510182641_drop_table_species_eptithets.rb +++ b/db/migrate/20140510182641_drop_table_species_eptithets.rb @@ -1,6 +1,7 @@ +# frozen_string_literal: true + class DropTableSpeciesEptithets < ActiveRecord::Migration def change drop_table :species_eptithets - end end diff --git a/db/migrate/20140511124759_create_issues.rb b/db/migrate/20140511124759_create_issues.rb index f4295c72..9c4a2366 100644 --- a/db/migrate/20140511124759_create_issues.rb +++ b/db/migrate/20140511124759_create_issues.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class CreateIssues < ActiveRecord::Migration def change create_table :issues do |t| diff --git a/db/migrate/20140530114118_add_chromatogram_to_primer_read.rb b/db/migrate/20140530114118_add_chromatogram_to_primer_read.rb index 9eb21a67..457b9b35 100644 --- a/db/migrate/20140530114118_add_chromatogram_to_primer_read.rb +++ b/db/migrate/20140530114118_add_chromatogram_to_primer_read.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddChromatogramToPrimerRead < ActiveRecord::Migration def self.up add_attachment :primer_reads, :chromatogram diff --git a/db/migrate/20140530151411_add_primer_id_to_primer_reads.rb b/db/migrate/20140530151411_add_primer_id_to_primer_reads.rb index f03c6cab..87fc710d 100644 --- a/db/migrate/20140530151411_add_primer_id_to_primer_reads.rb +++ b/db/migrate/20140530151411_add_primer_id_to_primer_reads.rb @@ -1,7 +1,7 @@ +# frozen_string_literal: true + class AddPrimerIdToPrimerReads < ActiveRecord::Migration def change - - add_column :primer_reads, :primer_id, :integer - + add_column :primer_reads, :primer_id, :integer end end diff --git a/db/migrate/20140530153116_add_copy_id_to_primer_reads.rb b/db/migrate/20140530153116_add_copy_id_to_primer_reads.rb index 3b3b47fd..920cb4dc 100644 --- a/db/migrate/20140530153116_add_copy_id_to_primer_reads.rb +++ b/db/migrate/20140530153116_add_copy_id_to_primer_reads.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddCopyIdToPrimerReads < ActiveRecord::Migration def change add_column :primer_reads, :copy_id, :integer diff --git a/db/migrate/20140530154334_add_author_id_to_species.rb b/db/migrate/20140530154334_add_author_id_to_species.rb index 7e328b3d..059b9463 100644 --- a/db/migrate/20140530154334_add_author_id_to_species.rb +++ b/db/migrate/20140530154334_add_author_id_to_species.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddAuthorIdToSpecies < ActiveRecord::Migration def change add_column :species, :author_id, :integer diff --git a/db/migrate/20140530161425_add_genus_id_to_species.rb b/db/migrate/20140530161425_add_genus_id_to_species.rb index 95a88434..b8ac0387 100644 --- a/db/migrate/20140530161425_add_genus_id_to_species.rb +++ b/db/migrate/20140530161425_add_genus_id_to_species.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddGenusIdToSpecies < ActiveRecord::Migration def change add_column :species, :genus_id, :integer diff --git a/db/migrate/20140530161534_add_epithet_id_to_species.rb b/db/migrate/20140530161534_add_epithet_id_to_species.rb index cfaff9f0..3432be6b 100644 --- a/db/migrate/20140530161534_add_epithet_id_to_species.rb +++ b/db/migrate/20140530161534_add_epithet_id_to_species.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddEpithetIdToSpecies < ActiveRecord::Migration def change add_column :species, :epithet_id, :integer diff --git a/db/migrate/20140530161733_add_family_id_to_genus.rb b/db/migrate/20140530161733_add_family_id_to_genus.rb index e9d4f98f..f46bcdc9 100644 --- a/db/migrate/20140530161733_add_family_id_to_genus.rb +++ b/db/migrate/20140530161733_add_family_id_to_genus.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddFamilyIdToGenus < ActiveRecord::Migration def change add_column :gens, :family_id, :integer diff --git a/db/migrate/20140530161912_add_marker_id_to_primer.rb b/db/migrate/20140530161912_add_marker_id_to_primer.rb index b62c6b51..3db5f276 100644 --- a/db/migrate/20140530161912_add_marker_id_to_primer.rb +++ b/db/migrate/20140530161912_add_marker_id_to_primer.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddMarkerIdToPrimer < ActiveRecord::Migration def change add_column :primers, :marker_id, :integer diff --git a/db/migrate/20140530172425_change_species_id_names.rb b/db/migrate/20140530172425_change_species_id_names.rb index 65ee4f93..88887c04 100644 --- a/db/migrate/20140530172425_change_species_id_names.rb +++ b/db/migrate/20140530172425_change_species_id_names.rb @@ -1,8 +1,8 @@ +# frozen_string_literal: true + class ChangeSpeciesIdNames < ActiveRecord::Migration def change - - rename_column :species, :epithet_id, :species_epithet_id - rename_column :species, :genus_id, :gen_id - + rename_column :species, :epithet_id, :species_epithet_id + rename_column :species, :genus_id, :gen_id end end diff --git a/db/migrate/20140530175330_rename_higher_order_id.rb b/db/migrate/20140530175330_rename_higher_order_id.rb index 8ca20b60..a7155f5b 100644 --- a/db/migrate/20140530175330_rename_higher_order_id.rb +++ b/db/migrate/20140530175330_rename_higher_order_id.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class RenameHigherOrderId < ActiveRecord::Migration def change rename_column :orders, :higher_order_id, :higher_order_taxon_id diff --git a/db/migrate/20140530192237_remove_lab_nr_from_copies.rb b/db/migrate/20140530192237_remove_lab_nr_from_copies.rb index 50c6a854..ec166b7a 100644 --- a/db/migrate/20140530192237_remove_lab_nr_from_copies.rb +++ b/db/migrate/20140530192237_remove_lab_nr_from_copies.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class RemoveLabNrFromCopies < ActiveRecord::Migration def change remove_column :copies, :lab_nr, :integer diff --git a/db/migrate/20140530193440_rename_marker_seq_id.rb b/db/migrate/20140530193440_rename_marker_seq_id.rb index 2b203598..efcab851 100644 --- a/db/migrate/20140530193440_rename_marker_seq_id.rb +++ b/db/migrate/20140530193440_rename_marker_seq_id.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class RenameMarkerSeqId < ActiveRecord::Migration def change rename_column :contigs, :marker_seq_id, :marker_sequence_id diff --git a/db/migrate/20140611123927_add_trimmed_to_primer_read.rb b/db/migrate/20140611123927_add_trimmed_to_primer_read.rb index e9db62e9..c216bbd2 100644 --- a/db/migrate/20140611123927_add_trimmed_to_primer_read.rb +++ b/db/migrate/20140611123927_add_trimmed_to_primer_read.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddTrimmedToPrimerRead < ActiveRecord::Migration def change add_column :primer_reads, :trimmedReadEnd, :integer diff --git a/db/migrate/20140611125718_add_qualities.rb b/db/migrate/20140611125718_add_qualities.rb index a9edfe38..892d6fe1 100644 --- a/db/migrate/20140611125718_add_qualities.rb +++ b/db/migrate/20140611125718_add_qualities.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddQualities < ActiveRecord::Migration def change add_column :primer_reads, :qualities, :integer, array: true diff --git a/db/migrate/20140628084625_add_labcode_to_primers.rb b/db/migrate/20140628084625_add_labcode_to_primers.rb index 496efd1b..8b2bca71 100644 --- a/db/migrate/20140628084625_add_labcode_to_primers.rb +++ b/db/migrate/20140628084625_add_labcode_to_primers.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddLabcodeToPrimers < ActiveRecord::Migration def change add_column :primers, :labcode, :string diff --git a/db/migrate/20140629173725_add_copy_id_to_contigs.rb b/db/migrate/20140629173725_add_copy_id_to_contigs.rb index a9b60e7f..4a3cc479 100644 --- a/db/migrate/20140629173725_add_copy_id_to_contigs.rb +++ b/db/migrate/20140629173725_add_copy_id_to_contigs.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddCopyIdToContigs < ActiveRecord::Migration def change add_column :contigs, :copy_id, :integer diff --git a/db/migrate/20140629173952_add_marker_id_to_contigs.rb b/db/migrate/20140629173952_add_marker_id_to_contigs.rb index 9fa5f951..d4cf1858 100644 --- a/db/migrate/20140629173952_add_marker_id_to_contigs.rb +++ b/db/migrate/20140629173952_add_marker_id_to_contigs.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddMarkerIdToContigs < ActiveRecord::Migration def change add_column :contigs, :marker_id, :integer diff --git a/db/migrate/20140701183233_add_primer_read_id_to_issues.rb b/db/migrate/20140701183233_add_primer_read_id_to_issues.rb index 5973f3ec..244811c4 100644 --- a/db/migrate/20140701183233_add_primer_read_id_to_issues.rb +++ b/db/migrate/20140701183233_add_primer_read_id_to_issues.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddPrimerReadIdToIssues < ActiveRecord::Migration def change add_column :issues, :primer_read_id, :integer diff --git a/db/migrate/20140703164632_add_reverse_to_primer_reads.rb b/db/migrate/20140703164632_add_reverse_to_primer_reads.rb index 25830852..7416ed5f 100644 --- a/db/migrate/20140703164632_add_reverse_to_primer_reads.rb +++ b/db/migrate/20140703164632_add_reverse_to_primer_reads.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddReverseToPrimerReads < ActiveRecord::Migration def change add_column :primer_reads, :reverse, :boolean diff --git a/db/migrate/20140704191315_add_aligned_seq_to_primer_read.rb b/db/migrate/20140704191315_add_aligned_seq_to_primer_read.rb index ab0d0d80..aea1fd57 100644 --- a/db/migrate/20140704191315_add_aligned_seq_to_primer_read.rb +++ b/db/migrate/20140704191315_add_aligned_seq_to_primer_read.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddAlignedSeqToPrimerRead < ActiveRecord::Migration def change add_column :primer_reads, :aligned_seq, :string diff --git a/db/migrate/20140704191354_add_used_for_con_to_primer_read.rb b/db/migrate/20140704191354_add_used_for_con_to_primer_read.rb index 80624f18..a231ecee 100644 --- a/db/migrate/20140704191354_add_used_for_con_to_primer_read.rb +++ b/db/migrate/20140704191354_add_used_for_con_to_primer_read.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddUsedForConToPrimerRead < ActiveRecord::Migration def change add_column :primer_reads, :used_for_con, :boolean diff --git a/db/migrate/20140705130422_change_type.rb b/db/migrate/20140705130422_change_type.rb index f1ac7f77..4b1fbe96 100644 --- a/db/migrate/20140705130422_change_type.rb +++ b/db/migrate/20140705130422_change_type.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class ChangeType < ActiveRecord::Migration def change change_column(:primer_reads, :aligned_seq, :text) diff --git a/db/migrate/20140706140552_add_contig_id_to_issue.rb b/db/migrate/20140706140552_add_contig_id_to_issue.rb index 2cd74c48..02c8edb9 100644 --- a/db/migrate/20140706140552_add_contig_id_to_issue.rb +++ b/db/migrate/20140706140552_add_contig_id_to_issue.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddContigIdToIssue < ActiveRecord::Migration def change add_column :issues, :contig_id, :integer diff --git a/db/migrate/20140706182145_add_quality_string_to_primer_reads.rb b/db/migrate/20140706182145_add_quality_string_to_primer_reads.rb index 6ec95989..441fd0ae 100644 --- a/db/migrate/20140706182145_add_quality_string_to_primer_reads.rb +++ b/db/migrate/20140706182145_add_quality_string_to_primer_reads.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddQualityStringToPrimerReads < ActiveRecord::Migration def change add_column :primer_reads, :quality_string, :text diff --git a/db/migrate/20140711115017_remove_gen_id_from_species.rb b/db/migrate/20140711115017_remove_gen_id_from_species.rb index 501af530..fb03ddd0 100644 --- a/db/migrate/20140711115017_remove_gen_id_from_species.rb +++ b/db/migrate/20140711115017_remove_gen_id_from_species.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class RemoveGenIdFromSpecies < ActiveRecord::Migration def change remove_column :species, :gen_id, :integer diff --git a/db/migrate/20140711115143_remove_sp_epi_from_species.rb b/db/migrate/20140711115143_remove_sp_epi_from_species.rb index b3670367..8c716461 100644 --- a/db/migrate/20140711115143_remove_sp_epi_from_species.rb +++ b/db/migrate/20140711115143_remove_sp_epi_from_species.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class RemoveSpEpiFromSpecies < ActiveRecord::Migration def change remove_column :species, :species_epithet_id, :integer diff --git a/db/migrate/20140711115248_remove_author_id_from_species.rb b/db/migrate/20140711115248_remove_author_id_from_species.rb index 64ac2386..6ec44ea8 100644 --- a/db/migrate/20140711115248_remove_author_id_from_species.rb +++ b/db/migrate/20140711115248_remove_author_id_from_species.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class RemoveAuthorIdFromSpecies < ActiveRecord::Migration def change remove_column :species, :author_id, :integer diff --git a/db/migrate/20140711115330_remove_published_from_species.rb b/db/migrate/20140711115330_remove_published_from_species.rb index f9d37fb0..45a4aa41 100644 --- a/db/migrate/20140711115330_remove_published_from_species.rb +++ b/db/migrate/20140711115330_remove_published_from_species.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class RemovePublishedFromSpecies < ActiveRecord::Migration def change remove_column :species, :published, :date diff --git a/db/migrate/20140711115522_add_genus_name_to_species.rb b/db/migrate/20140711115522_add_genus_name_to_species.rb index 0c452b72..ef1e811b 100644 --- a/db/migrate/20140711115522_add_genus_name_to_species.rb +++ b/db/migrate/20140711115522_add_genus_name_to_species.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddGenusNameToSpecies < ActiveRecord::Migration def change add_column :species, :genus_name, :string diff --git a/db/migrate/20140711115558_add_species_epithet_to_species.rb b/db/migrate/20140711115558_add_species_epithet_to_species.rb index 478a060d..f3bbd553 100644 --- a/db/migrate/20140711115558_add_species_epithet_to_species.rb +++ b/db/migrate/20140711115558_add_species_epithet_to_species.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddSpeciesEpithetToSpecies < ActiveRecord::Migration def change add_column :species, :species_epithet, :string diff --git a/db/migrate/20140711115635_add_author_to_species.rb b/db/migrate/20140711115635_add_author_to_species.rb index c98fdc8c..cf8fe23b 100644 --- a/db/migrate/20140711115635_add_author_to_species.rb +++ b/db/migrate/20140711115635_add_author_to_species.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddAuthorToSpecies < ActiveRecord::Migration def change add_column :species, :author, :string diff --git a/db/migrate/20140711115737_add_family_id_to_species.rb b/db/migrate/20140711115737_add_family_id_to_species.rb index c79a31f3..d2ccaa81 100644 --- a/db/migrate/20140711115737_add_family_id_to_species.rb +++ b/db/migrate/20140711115737_add_family_id_to_species.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddFamilyIdToSpecies < ActiveRecord::Migration def change add_column :species, :family_id, :integer diff --git a/db/migrate/20140711121015_drop_gens_etc.rb b/db/migrate/20140711121015_drop_gens_etc.rb index b0c89e22..80f08951 100644 --- a/db/migrate/20140711121015_drop_gens_etc.rb +++ b/db/migrate/20140711121015_drop_gens_etc.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class DropGensEtc < ActiveRecord::Migration def change drop_table :gens diff --git a/db/migrate/20140711155739_create_species.rb b/db/migrate/20140711155739_create_species.rb index a73b32b6..80bd3197 100644 --- a/db/migrate/20140711155739_create_species.rb +++ b/db/migrate/20140711155739_create_species.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class CreateSpecies < ActiveRecord::Migration def change create_table :species do |t| diff --git a/db/migrate/20140711163837_add_family_to_species.rb b/db/migrate/20140711163837_add_family_to_species.rb index 13bf76b9..fb6a0913 100644 --- a/db/migrate/20140711163837_add_family_to_species.rb +++ b/db/migrate/20140711163837_add_family_to_species.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddFamilyToSpecies < ActiveRecord::Migration def change add_column :species, :family_id, :integer diff --git a/db/migrate/20140711193809_add_infra_to_species.rb b/db/migrate/20140711193809_add_infra_to_species.rb index b3ea7f70..49ae473f 100644 --- a/db/migrate/20140711193809_add_infra_to_species.rb +++ b/db/migrate/20140711193809_add_infra_to_species.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddInfraToSpecies < ActiveRecord::Migration def change add_column :species, :infraspecific, :string diff --git a/db/migrate/20140711193842_add_comment_to_species.rb b/db/migrate/20140711193842_add_comment_to_species.rb index f4cc391c..0bf44ed6 100644 --- a/db/migrate/20140711193842_add_comment_to_species.rb +++ b/db/migrate/20140711193842_add_comment_to_species.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddCommentToSpecies < ActiveRecord::Migration def change add_column :species, :comment, :text diff --git a/db/migrate/20140711194227_add_german_to_species.rb b/db/migrate/20140711194227_add_german_to_species.rb index 81236be2..c415fcd1 100644 --- a/db/migrate/20140711194227_add_german_to_species.rb +++ b/db/migrate/20140711194227_add_german_to_species.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddGermanToSpecies < ActiveRecord::Migration def change add_column :species, :german_name, :string diff --git a/db/migrate/20140711201249_add_infraauthor_to_species.rb b/db/migrate/20140711201249_add_infraauthor_to_species.rb index 7b878d74..15582d59 100644 --- a/db/migrate/20140711201249_add_infraauthor_to_species.rb +++ b/db/migrate/20140711201249_add_infraauthor_to_species.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddInfraauthorToSpecies < ActiveRecord::Migration def change add_column :species, :author_infra, :string diff --git a/db/migrate/20140711205359_add_germa_to_higher_order_taxons.rb b/db/migrate/20140711205359_add_germa_to_higher_order_taxons.rb index 3073813c..d64031e7 100644 --- a/db/migrate/20140711205359_add_germa_to_higher_order_taxons.rb +++ b/db/migrate/20140711205359_add_germa_to_higher_order_taxons.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddGermaToHigherOrderTaxons < ActiveRecord::Migration def change add_column :higher_order_taxons, :german_name, :string diff --git a/db/migrate/20140712202023_create_delayed_jobs.rb b/db/migrate/20140712202023_create_delayed_jobs.rb index ec0dd93c..e9e32d0f 100644 --- a/db/migrate/20140712202023_create_delayed_jobs.rb +++ b/db/migrate/20140712202023_create_delayed_jobs.rb @@ -1,9 +1,11 @@ +# frozen_string_literal: true + class CreateDelayedJobs < ActiveRecord::Migration def self.up - create_table :delayed_jobs, :force => true do |table| - table.integer :priority, :default => 0, :null => false # Allows some jobs to jump to the front of the queue - table.integer :attempts, :default => 0, :null => false # Provides for retries, but still fail eventually. - table.text :handler, :null => false # YAML-encoded string of the object that will do work + create_table :delayed_jobs, force: true do |table| + table.integer :priority, default: 0, null: false # Allows some jobs to jump to the front of the queue + table.integer :attempts, default: 0, null: false # Provides for retries, but still fail eventually. + table.text :handler, null: false # YAML-encoded string of the object that will do work table.text :last_error # reason for last failure (See Note below) table.datetime :run_at # When to run. Could be Time.zone.now for immediately, or sometime in the future. table.datetime :locked_at # Set when a client is working on this object @@ -13,7 +15,7 @@ def self.up table.timestamps end - add_index :delayed_jobs, [:priority, :run_at], :name => 'delayed_jobs_priority' + add_index :delayed_jobs, %i[priority run_at], name: 'delayed_jobs_priority' end def self.down diff --git a/db/migrate/20140713183721_add_contig_id_to_statuses.rb b/db/migrate/20140713183721_add_contig_id_to_statuses.rb index 792048f3..e820c0b2 100644 --- a/db/migrate/20140713183721_add_contig_id_to_statuses.rb +++ b/db/migrate/20140713183721_add_contig_id_to_statuses.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddContigIdToStatuses < ActiveRecord::Migration def change add_column :statuses, :contig_id, :integer diff --git a/db/migrate/20140713184925_add_assembled_to_contigs.rb b/db/migrate/20140713184925_add_assembled_to_contigs.rb index 26b49220..6b3933a3 100644 --- a/db/migrate/20140713184925_add_assembled_to_contigs.rb +++ b/db/migrate/20140713184925_add_assembled_to_contigs.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddAssembledToContigs < ActiveRecord::Migration def change add_column :contigs, :assembled, :boolean diff --git a/db/migrate/20140716134550_add_position_to_primer_reads.rb b/db/migrate/20140716134550_add_position_to_primer_reads.rb index 8292be6b..1e840773 100644 --- a/db/migrate/20140716134550_add_position_to_primer_reads.rb +++ b/db/migrate/20140716134550_add_position_to_primer_reads.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddPositionToPrimerReads < ActiveRecord::Migration def change add_column :primer_reads, :position, :integer diff --git a/db/migrate/20140716162344_add_assembled_to_primer_reads.rb b/db/migrate/20140716162344_add_assembled_to_primer_reads.rb index 1a820932..c5474f04 100644 --- a/db/migrate/20140716162344_add_assembled_to_primer_reads.rb +++ b/db/migrate/20140716162344_add_assembled_to_primer_reads.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddAssembledToPrimerReads < ActiveRecord::Migration def change add_column :primer_reads, :assembled, :boolean diff --git a/db/migrate/20140716201705_add_author_to_primers.rb b/db/migrate/20140716201705_add_author_to_primers.rb index 8a628711..9ae58d47 100644 --- a/db/migrate/20140716201705_add_author_to_primers.rb +++ b/db/migrate/20140716201705_add_author_to_primers.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddAuthorToPrimers < ActiveRecord::Migration def change add_column :primers, :author, :string diff --git a/db/migrate/20140716201746_add_alt_name_to_primers.rb b/db/migrate/20140716201746_add_alt_name_to_primers.rb index 0d9e006e..3e985fbc 100644 --- a/db/migrate/20140716201746_add_alt_name_to_primers.rb +++ b/db/migrate/20140716201746_add_alt_name_to_primers.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddAltNameToPrimers < ActiveRecord::Migration def change add_column :primers, :alt_name, :string diff --git a/db/migrate/20140716201820_add_target_group_to_primers.rb b/db/migrate/20140716201820_add_target_group_to_primers.rb index a3b5ccef..36f695ef 100644 --- a/db/migrate/20140716201820_add_target_group_to_primers.rb +++ b/db/migrate/20140716201820_add_target_group_to_primers.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddTargetGroupToPrimers < ActiveRecord::Migration def change add_column :primers, :target_group, :string diff --git a/db/migrate/20140716203939_add_tm_to_primers.rb b/db/migrate/20140716203939_add_tm_to_primers.rb index 136419da..91985ade 100644 --- a/db/migrate/20140716203939_add_tm_to_primers.rb +++ b/db/migrate/20140716203939_add_tm_to_primers.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddTmToPrimers < ActiveRecord::Migration def change add_column :primers, :tm, :string diff --git a/db/migrate/20140717115622_add_overlaps_to_contigs.rb b/db/migrate/20140717115622_add_overlaps_to_contigs.rb index 3b661d3f..5b1620c4 100644 --- a/db/migrate/20140717115622_add_overlaps_to_contigs.rb +++ b/db/migrate/20140717115622_add_overlaps_to_contigs.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddOverlapsToContigs < ActiveRecord::Migration def change add_column :contigs, :overlaps, :integer diff --git a/db/migrate/20140717120009_add_expected_reads_to_markers.rb b/db/migrate/20140717120009_add_expected_reads_to_markers.rb index b22a145b..a022963b 100644 --- a/db/migrate/20140717120009_add_expected_reads_to_markers.rb +++ b/db/migrate/20140717120009_add_expected_reads_to_markers.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddExpectedReadsToMarkers < ActiveRecord::Migration def change add_column :markers, :expected_reads, :integer diff --git a/db/migrate/20140717135209_add_partial_cons1_to_contigs.rb b/db/migrate/20140717135209_add_partial_cons1_to_contigs.rb index 58d27f2a..c9132e58 100644 --- a/db/migrate/20140717135209_add_partial_cons1_to_contigs.rb +++ b/db/migrate/20140717135209_add_partial_cons1_to_contigs.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddPartialCons1ToContigs < ActiveRecord::Migration def change add_column :contigs, :partial_cons1, :text diff --git a/db/migrate/20140717135233_add_partial_cons2_to_contigs.rb b/db/migrate/20140717135233_add_partial_cons2_to_contigs.rb index 57baa1bc..27589fb9 100644 --- a/db/migrate/20140717135233_add_partial_cons2_to_contigs.rb +++ b/db/migrate/20140717135233_add_partial_cons2_to_contigs.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddPartialCons2ToContigs < ActiveRecord::Migration def change add_column :contigs, :partial_cons2, :text diff --git a/db/migrate/20140717173827_add_assembly_tried_to_contigs.rb b/db/migrate/20140717173827_add_assembly_tried_to_contigs.rb index 68d6b64d..f1cf2ba2 100644 --- a/db/migrate/20140717173827_add_assembly_tried_to_contigs.rb +++ b/db/migrate/20140717173827_add_assembly_tried_to_contigs.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddAssemblyTriedToContigs < ActiveRecord::Migration def change add_column :contigs, :assembly_tried, :boolean diff --git a/db/migrate/20140718112955_add_position_to_primers.rb b/db/migrate/20140718112955_add_position_to_primers.rb index 9f966ca6..70e76d9e 100644 --- a/db/migrate/20140718112955_add_position_to_primers.rb +++ b/db/migrate/20140718112955_add_position_to_primers.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddPositionToPrimers < ActiveRecord::Migration def change add_column :primers, :position, :integer diff --git a/db/migrate/20140911131412_add_synonym_to_species.rb b/db/migrate/20140911131412_add_synonym_to_species.rb index 54d131b7..f9267067 100644 --- a/db/migrate/20140911131412_add_synonym_to_species.rb +++ b/db/migrate/20140911131412_add_synonym_to_species.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddSynonymToSpecies < ActiveRecord::Migration def change add_column :species, :synonym, :string diff --git a/db/migrate/20140921155154_add_gbol_to_markers.rb b/db/migrate/20140921155154_add_gbol_to_markers.rb index cd288718..ee3e1287 100644 --- a/db/migrate/20140921155154_add_gbol_to_markers.rb +++ b/db/migrate/20140921155154_add_gbol_to_markers.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddGbolToMarkers < ActiveRecord::Migration def change add_column :markers, :is_gbol, :boolean diff --git a/db/migrate/20140923152840_add_aligned_cons_to_contigs.rb b/db/migrate/20140923152840_add_aligned_cons_to_contigs.rb index 7817286d..557999be 100644 --- a/db/migrate/20140923152840_add_aligned_cons_to_contigs.rb +++ b/db/migrate/20140923152840_add_aligned_cons_to_contigs.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddAlignedConsToContigs < ActiveRecord::Migration def change add_column :contigs, :aligned_cons, :string diff --git a/db/migrate/20140924170203_create_partial_cons.rb b/db/migrate/20140924170203_create_partial_cons.rb index 2f462dd2..50e01899 100644 --- a/db/migrate/20140924170203_create_partial_cons.rb +++ b/db/migrate/20140924170203_create_partial_cons.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class CreatePartialCons < ActiveRecord::Migration def change create_table :partial_cons do |t| diff --git a/db/migrate/20140924170931_add_column.rb b/db/migrate/20140924170931_add_column.rb index 25bc9b56..d5440f09 100644 --- a/db/migrate/20140924170931_add_column.rb +++ b/db/migrate/20140924170931_add_column.rb @@ -1,5 +1,5 @@ -class AddColumn < ActiveRecord::Migration - def change +# frozen_string_literal: true - end +class AddColumn < ActiveRecord::Migration + def change; end end diff --git a/db/migrate/20140924171250_add_contig_id_to_partial_cons.rb b/db/migrate/20140924171250_add_contig_id_to_partial_cons.rb index 9274e24e..0fc480f0 100644 --- a/db/migrate/20140924171250_add_contig_id_to_partial_cons.rb +++ b/db/migrate/20140924171250_add_contig_id_to_partial_cons.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddContigIdToPartialCons < ActiveRecord::Migration def change add_column :partial_cons, :contig_id, :integer diff --git a/db/migrate/20140924171424_add_partial_con_id_to_primer_read.rb b/db/migrate/20140924171424_add_partial_con_id_to_primer_read.rb index 4ef20ccd..3f1840f3 100644 --- a/db/migrate/20140924171424_add_partial_con_id_to_primer_read.rb +++ b/db/migrate/20140924171424_add_partial_con_id_to_primer_read.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddPartialConIdToPrimerRead < ActiveRecord::Migration def change add_column :primer_reads, :partial_con_id, :integer diff --git a/db/migrate/20140924173029_change_partial_cons_type.rb b/db/migrate/20140924173029_change_partial_cons_type.rb index 772d8045..1dfae845 100644 --- a/db/migrate/20140924173029_change_partial_cons_type.rb +++ b/db/migrate/20140924173029_change_partial_cons_type.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class ChangePartialConsType < ActiveRecord::Migration def change change_column :partial_cons, :aligned_sequence, :text diff --git a/db/migrate/20140925105938_pde.rb b/db/migrate/20140925105938_pde.rb index 471666d8..4c9d4884 100644 --- a/db/migrate/20140925105938_pde.rb +++ b/db/migrate/20140925105938_pde.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class Pde < ActiveRecord::Migration def change add_column :contigs, :pde, :text diff --git a/db/migrate/20140926160225_rename_copy_to_isolate.rb b/db/migrate/20140926160225_rename_copy_to_isolate.rb index 5ce33f25..217480ff 100644 --- a/db/migrate/20140926160225_rename_copy_to_isolate.rb +++ b/db/migrate/20140926160225_rename_copy_to_isolate.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class RenameCopyToIsolate < ActiveRecord::Migration def change rename_table :copies, :isolates diff --git a/db/migrate/20140926163501_add_gbol_isolation_nr_to_isolates.rb b/db/migrate/20140926163501_add_gbol_isolation_nr_to_isolates.rb index 68568f72..f6c8bfe0 100644 --- a/db/migrate/20140926163501_add_gbol_isolation_nr_to_isolates.rb +++ b/db/migrate/20140926163501_add_gbol_isolation_nr_to_isolates.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddGbolIsolationNrToIsolates < ActiveRecord::Migration def change add_column :isolates, :gbol_isolation_nr, :string diff --git a/db/migrate/20140926163549_add_herbarium_to_individuals.rb b/db/migrate/20140926163549_add_herbarium_to_individuals.rb index 97f38170..bc9c43ee 100644 --- a/db/migrate/20140926163549_add_herbarium_to_individuals.rb +++ b/db/migrate/20140926163549_add_herbarium_to_individuals.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddHerbariumToIndividuals < ActiveRecord::Migration def change add_column :individuals, :herbarium, :string diff --git a/db/migrate/20140928114133_rename_copy_id.rb b/db/migrate/20140928114133_rename_copy_id.rb index 47eff859..020ba864 100644 --- a/db/migrate/20140928114133_rename_copy_id.rb +++ b/db/migrate/20140928114133_rename_copy_id.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class RenameCopyId < ActiveRecord::Migration def change rename_column :contigs, :copy_id, :isolate_id diff --git a/db/migrate/20140928124921_add_composed_name_to_species.rb b/db/migrate/20140928124921_add_composed_name_to_species.rb index cf7a8254..70a42129 100644 --- a/db/migrate/20140928124921_add_composed_name_to_species.rb +++ b/db/migrate/20140928124921_add_composed_name_to_species.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddComposedNameToSpecies < ActiveRecord::Migration def change add_column :species, :composed_name, :string diff --git a/db/migrate/20140928164126_add_individual_id_to_isolates.rb b/db/migrate/20140928164126_add_individual_id_to_isolates.rb index fe818bef..65c90e54 100644 --- a/db/migrate/20140928164126_add_individual_id_to_isolates.rb +++ b/db/migrate/20140928164126_add_individual_id_to_isolates.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddIndividualIdToIsolates < ActiveRecord::Migration def change add_column :isolates, :individual_id, :integer diff --git a/db/migrate/20140928203437_change_tube_id_type.rb b/db/migrate/20140928203437_change_tube_id_type.rb index 3027f469..9928b59f 100644 --- a/db/migrate/20140928203437_change_tube_id_type.rb +++ b/db/migrate/20140928203437_change_tube_id_type.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class ChangeTubeIdType < ActiveRecord::Migration def change change_column :isolates, :micronic_tube_id, :string diff --git a/db/migrate/20140929134322_rename_higher.rb b/db/migrate/20140929134322_rename_higher.rb index 01bfbea3..da897c64 100644 --- a/db/migrate/20140929134322_rename_higher.rb +++ b/db/migrate/20140929134322_rename_higher.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class RenameHigher < ActiveRecord::Migration def change rename_table :higher_order_taxons, :higher_order_taxa diff --git a/db/migrate/20140929195137_add_aligned_qualities_to_primer_reads.rb b/db/migrate/20140929195137_add_aligned_qualities_to_primer_reads.rb index e7e810f1..f89ef2c4 100644 --- a/db/migrate/20140929195137_add_aligned_qualities_to_primer_reads.rb +++ b/db/migrate/20140929195137_add_aligned_qualities_to_primer_reads.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddAlignedQualitiesToPrimerReads < ActiveRecord::Migration def change add_column :primer_reads, :aligned_qualities, :integer, array: true diff --git a/db/migrate/20140929201548_add_aligned_qualities_to_partial_con.rb b/db/migrate/20140929201548_add_aligned_qualities_to_partial_con.rb index 79a485ac..1618eeed 100644 --- a/db/migrate/20140929201548_add_aligned_qualities_to_partial_con.rb +++ b/db/migrate/20140929201548_add_aligned_qualities_to_partial_con.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddAlignedQualitiesToPartialCon < ActiveRecord::Migration def change add_column :partial_cons, :aligned_qualities, :integer, array: true diff --git a/db/migrate/20141002132544_rename_copy.rb b/db/migrate/20141002132544_rename_copy.rb index 2226a2eb..6f77fa13 100644 --- a/db/migrate/20141002132544_rename_copy.rb +++ b/db/migrate/20141002132544_rename_copy.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class RenameCopy < ActiveRecord::Migration def change rename_column :marker_sequences, :copy_id, :isolate_id diff --git a/db/migrate/20141002133841_add_marker_id_to_marker_sequences.rb b/db/migrate/20141002133841_add_marker_id_to_marker_sequences.rb index 103f0ce7..61eeb55a 100644 --- a/db/migrate/20141002133841_add_marker_id_to_marker_sequences.rb +++ b/db/migrate/20141002133841_add_marker_id_to_marker_sequences.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddMarkerIdToMarkerSequences < ActiveRecord::Migration def change add_column :marker_sequences, :marker_id, :integer diff --git a/db/migrate/20141002202251_add_settings.rb b/db/migrate/20141002202251_add_settings.rb index ed3ab6ff..5b4c19f3 100644 --- a/db/migrate/20141002202251_add_settings.rb +++ b/db/migrate/20141002202251_add_settings.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddSettings < ActiveRecord::Migration def change add_column :primer_reads, :window_size, :integer diff --git a/db/migrate/20141002202721_set_defaults.rb b/db/migrate/20141002202721_set_defaults.rb index 0dbe10af..54fb15cd 100644 --- a/db/migrate/20141002202721_set_defaults.rb +++ b/db/migrate/20141002202721_set_defaults.rb @@ -1,7 +1,9 @@ +# frozen_string_literal: true + class SetDefaults < ActiveRecord::Migration def change - change_column :primer_reads, :window_size, :integer, :default => 10 - change_column :primer_reads, :count_in_window, :integer, :default => 8 - change_column :primer_reads, :min_quality_score, :integer, :default => 30 + change_column :primer_reads, :window_size, :integer, default: 10 + change_column :primer_reads, :count_in_window, :integer, default: 8 + change_column :primer_reads, :min_quality_score, :integer, default: 30 end end diff --git a/db/migrate/20141003111508_add_traces.rb b/db/migrate/20141003111508_add_traces.rb index cb8a51be..bd61c06b 100644 --- a/db/migrate/20141003111508_add_traces.rb +++ b/db/migrate/20141003111508_add_traces.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddTraces < ActiveRecord::Migration def change add_column :primer_reads, :atrace, :integer, array: true diff --git a/db/migrate/20141003125433_rename_c_id.rb b/db/migrate/20141003125433_rename_c_id.rb index b8d6a66b..7b38946e 100644 --- a/db/migrate/20141003125433_rename_c_id.rb +++ b/db/migrate/20141003125433_rename_c_id.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class RenameCId < ActiveRecord::Migration def change rename_column :primer_reads, :copy_id, :isolate_id diff --git a/db/migrate/20141008133438_add_pos.rb b/db/migrate/20141008133438_add_pos.rb index d5795419..7be2e474 100644 --- a/db/migrate/20141008133438_add_pos.rb +++ b/db/migrate/20141008133438_add_pos.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddPos < ActiveRecord::Migration def change add_column :higher_order_taxa, :position, :integer diff --git a/db/migrate/20141008144017_add_dnabank.rb b/db/migrate/20141008144017_add_dnabank.rb index b4ca6fdd..45880e17 100644 --- a/db/migrate/20141008144017_add_dnabank.rb +++ b/db/migrate/20141008144017_add_dnabank.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddDnabank < ActiveRecord::Migration def change add_column :isolates, :DNA_bank_id, :string diff --git a/db/migrate/20141008162119_reanme.rb b/db/migrate/20141008162119_reanme.rb index 615cc044..ba5fd399 100644 --- a/db/migrate/20141008162119_reanme.rb +++ b/db/migrate/20141008162119_reanme.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class Reanme < ActiveRecord::Migration def change rename_column :isolates, :DNA_bank_id, :dna_bank_id diff --git a/db/migrate/20141008185051_rm_gblol_nr.rb b/db/migrate/20141008185051_rm_gblol_nr.rb index 8d86b614..3fa32b41 100644 --- a/db/migrate/20141008185051_rm_gblol_nr.rb +++ b/db/migrate/20141008185051_rm_gblol_nr.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class RmGblolNr < ActiveRecord::Migration def change remove_column :isolates, :gbol_isolation_nr diff --git a/db/migrate/20141008191217_change_lab_nr_type.rb b/db/migrate/20141008191217_change_lab_nr_type.rb index 0f085b29..8eced61d 100644 --- a/db/migrate/20141008191217_change_lab_nr_type.rb +++ b/db/migrate/20141008191217_change_lab_nr_type.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class ChangeLabNrType < ActiveRecord::Migration def change change_column :isolates, :lab_nr, :string diff --git a/db/migrate/20150129141612_add_primary_key_isolates.rb b/db/migrate/20150129141612_add_primary_key_isolates.rb index 5a42c5ca..bc36ba97 100644 --- a/db/migrate/20150129141612_add_primary_key_isolates.rb +++ b/db/migrate/20150129141612_add_primary_key_isolates.rb @@ -1,5 +1,7 @@ +# frozen_string_literal: true + class AddPrimaryKeyIsolates < ActiveRecord::Migration def change - execute "ALTER TABLE isolates ADD PRIMARY KEY (id);" + execute 'ALTER TABLE isolates ADD PRIMARY KEY (id);' end end diff --git a/db/migrate/20150211200426_add_processed_to_primer_reads.rb b/db/migrate/20150211200426_add_processed_to_primer_reads.rb index fda99e05..2fa3fe74 100644 --- a/db/migrate/20150211200426_add_processed_to_primer_reads.rb +++ b/db/migrate/20150211200426_add_processed_to_primer_reads.rb @@ -1,5 +1,7 @@ +# frozen_string_literal: true + class AddProcessedToPrimerReads < ActiveRecord::Migration def change - add_column :primer_reads, :processed, :boolean, :default => false + add_column :primer_reads, :processed, :boolean, default: false end end diff --git a/db/migrate/20150227173532_create_higher_order_taxa_markers_join_table.rb b/db/migrate/20150227173532_create_higher_order_taxa_markers_join_table.rb index f0ef9082..567447e5 100644 --- a/db/migrate/20150227173532_create_higher_order_taxa_markers_join_table.rb +++ b/db/migrate/20150227173532_create_higher_order_taxa_markers_join_table.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class CreateHigherOrderTaxaMarkersJoinTable < ActiveRecord::Migration def change create_table :higher_order_taxa_markers, id: false do |t| diff --git a/db/migrate/20150228182800_add_species_component_to_species.rb b/db/migrate/20150228182800_add_species_component_to_species.rb index 40a2e91c..0c56661b 100644 --- a/db/migrate/20150228182800_add_species_component_to_species.rb +++ b/db/migrate/20150228182800_add_species_component_to_species.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddSpeciesComponentToSpecies < ActiveRecord::Migration def change add_column :species, :species_component, :string diff --git a/db/migrate/20150301190309_add_base_count_to_primer_reads.rb b/db/migrate/20150301190309_add_base_count_to_primer_reads.rb index daadfb4c..7836470f 100644 --- a/db/migrate/20150301190309_add_base_count_to_primer_reads.rb +++ b/db/migrate/20150301190309_add_base_count_to_primer_reads.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddBaseCountToPrimerReads < ActiveRecord::Migration def change add_column :primer_reads, :base_count, :integer diff --git a/db/migrate/20150302001516_add_negative_control_to_isolates.rb b/db/migrate/20150302001516_add_negative_control_to_isolates.rb index b86ab58b..12a22a4e 100644 --- a/db/migrate/20150302001516_add_negative_control_to_isolates.rb +++ b/db/migrate/20150302001516_add_negative_control_to_isolates.rb @@ -1,5 +1,7 @@ +# frozen_string_literal: true + class AddNegativeControlToIsolates < ActiveRecord::Migration def change - add_column :isolates, :negative_control, :boolean, :default => false + add_column :isolates, :negative_control, :boolean, default: false end end diff --git a/db/migrate/20150305175028_add_verified_to_contigs.rb b/db/migrate/20150305175028_add_verified_to_contigs.rb index 4fcd6520..134977f9 100644 --- a/db/migrate/20150305175028_add_verified_to_contigs.rb +++ b/db/migrate/20150305175028_add_verified_to_contigs.rb @@ -1,5 +1,7 @@ +# frozen_string_literal: true + class AddVerifiedToContigs < ActiveRecord::Migration def change - add_column :contigs, :verified, :boolean, :default => false + add_column :contigs, :verified, :boolean, default: false end end diff --git a/db/migrate/20150308202429_add_verified_by_to_contigs.rb b/db/migrate/20150308202429_add_verified_by_to_contigs.rb index 33c3415d..8e3d7800 100644 --- a/db/migrate/20150308202429_add_verified_by_to_contigs.rb +++ b/db/migrate/20150308202429_add_verified_by_to_contigs.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddVerifiedByToContigs < ActiveRecord::Migration def change add_column :contigs, :verified_by, :integer diff --git a/db/migrate/20150704192029_create_xml_uploaders.rb b/db/migrate/20150704192029_create_xml_uploaders.rb index 3bc140b9..9c59fda1 100644 --- a/db/migrate/20150704192029_create_xml_uploaders.rb +++ b/db/migrate/20150704192029_create_xml_uploaders.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class CreateXmlUploaders < ActiveRecord::Migration def change create_table :xml_uploaders do |t| diff --git a/db/migrate/20150719172520_habtm_individuals_projects.rb b/db/migrate/20150719172520_habtm_individuals_projects.rb index 4c92a06e..d5c9d284 100644 --- a/db/migrate/20150719172520_habtm_individuals_projects.rb +++ b/db/migrate/20150719172520_habtm_individuals_projects.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class HabtmIndividualsProjects < ActiveRecord::Migration def change create_table :individuals_projects, id: false do |t| @@ -5,4 +7,4 @@ def change t.integer :project_id end end -end \ No newline at end of file +end diff --git a/db/migrate/20150719194029_add_projects_species.rb b/db/migrate/20150719194029_add_projects_species.rb index 8a929033..02b192b3 100644 --- a/db/migrate/20150719194029_add_projects_species.rb +++ b/db/migrate/20150719194029_add_projects_species.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddProjectsSpecies < ActiveRecord::Migration def change create_table :projects_species, id: false do |t| diff --git a/db/migrate/20150719195650_contigs_projects.rb b/db/migrate/20150719195650_contigs_projects.rb index 17543c22..a272b39f 100644 --- a/db/migrate/20150719195650_contigs_projects.rb +++ b/db/migrate/20150719195650_contigs_projects.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class ContigsProjects < ActiveRecord::Migration def change create_table :contigs_projects, id: false do |t| diff --git a/db/migrate/20150719195755_families_projects.rb b/db/migrate/20150719195755_families_projects.rb index 445912de..2b74c1db 100644 --- a/db/migrate/20150719195755_families_projects.rb +++ b/db/migrate/20150719195755_families_projects.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class FamiliesProjects < ActiveRecord::Migration def change create_table :families_projects, id: false do |t| diff --git a/db/migrate/20150719195821_orders_projects.rb b/db/migrate/20150719195821_orders_projects.rb index 023b7627..827483df 100644 --- a/db/migrate/20150719195821_orders_projects.rb +++ b/db/migrate/20150719195821_orders_projects.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class OrdersProjects < ActiveRecord::Migration def change create_table :orders_projects, id: false do |t| @@ -5,5 +7,4 @@ def change t.integer :project_id end end - end diff --git a/db/migrate/20150719195851_higher_order_taxa_projects.rb b/db/migrate/20150719195851_higher_order_taxa_projects.rb index c7557853..27efc6c0 100644 --- a/db/migrate/20150719195851_higher_order_taxa_projects.rb +++ b/db/migrate/20150719195851_higher_order_taxa_projects.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class HigherOrderTaxaProjects < ActiveRecord::Migration def change create_table :higher_order_taxa_projects, id: false do |t| diff --git a/db/migrate/20150719195926_isolates_projects.rb b/db/migrate/20150719195926_isolates_projects.rb index e1323427..9077f6ba 100644 --- a/db/migrate/20150719195926_isolates_projects.rb +++ b/db/migrate/20150719195926_isolates_projects.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class IsolatesProjects < ActiveRecord::Migration def change create_table :isolates_projects, id: false do |t| diff --git a/db/migrate/20150719200002_primer_reads_projects.rb b/db/migrate/20150719200002_primer_reads_projects.rb index 7f98d228..27905b19 100644 --- a/db/migrate/20150719200002_primer_reads_projects.rb +++ b/db/migrate/20150719200002_primer_reads_projects.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class PrimerReadsProjects < ActiveRecord::Migration def change create_table :primer_reads_projects, id: false do |t| diff --git a/db/migrate/20150719200028_issues_projects.rb b/db/migrate/20150719200028_issues_projects.rb index 2503207c..e05abc72 100644 --- a/db/migrate/20150719200028_issues_projects.rb +++ b/db/migrate/20150719200028_issues_projects.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class IssuesProjects < ActiveRecord::Migration def change create_table :issues_projects, id: false do |t| diff --git a/db/migrate/20150719200053_labs_projects.rb b/db/migrate/20150719200053_labs_projects.rb index f50ffe22..22954642 100644 --- a/db/migrate/20150719200053_labs_projects.rb +++ b/db/migrate/20150719200053_labs_projects.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class LabsProjects < ActiveRecord::Migration def change create_table :labs_projects, id: false do |t| diff --git a/db/migrate/20160502113129_add_comment_to_primer_reads.rb b/db/migrate/20160502113129_add_comment_to_primer_reads.rb index dbcce39f..a0a8efab 100644 --- a/db/migrate/20160502113129_add_comment_to_primer_reads.rb +++ b/db/migrate/20160502113129_add_comment_to_primer_reads.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddCommentToPrimerReads < ActiveRecord::Migration def change add_column :primer_reads, :comment, :string diff --git a/db/migrate/20160502113154_add_comment_to_contigs.rb b/db/migrate/20160502113154_add_comment_to_contigs.rb index cf1aa3d2..cd556644 100644 --- a/db/migrate/20160502113154_add_comment_to_contigs.rb +++ b/db/migrate/20160502113154_add_comment_to_contigs.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddCommentToContigs < ActiveRecord::Migration def change add_column :contigs, :comment, :string diff --git a/db/migrate/20160502144910_add_alt_name_to_markers.rb b/db/migrate/20160502144910_add_alt_name_to_markers.rb index 53ccb5bf..c34a5802 100644 --- a/db/migrate/20160502144910_add_alt_name_to_markers.rb +++ b/db/migrate/20160502144910_add_alt_name_to_markers.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddAltNameToMarkers < ActiveRecord::Migration def change add_column :markers, :alt_name, :string diff --git a/db/migrate/20160505161255_create_txt_uploaders.rb b/db/migrate/20160505161255_create_txt_uploaders.rb index fd8ebecb..132fa509 100644 --- a/db/migrate/20160505161255_create_txt_uploaders.rb +++ b/db/migrate/20160505161255_create_txt_uploaders.rb @@ -1,7 +1,8 @@ +# frozen_string_literal: true + class CreateTxtUploaders < ActiveRecord::Migration def change create_table :txt_uploaders do |t| - t.timestamps null: false end end diff --git a/db/migrate/20160505163022_add_filename_to_txt_uploaders.rb b/db/migrate/20160505163022_add_filename_to_txt_uploaders.rb index e0d0c09e..ccc6b558 100644 --- a/db/migrate/20160505163022_add_filename_to_txt_uploaders.rb +++ b/db/migrate/20160505163022_add_filename_to_txt_uploaders.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddFilenameToTxtUploaders < ActiveRecord::Migration def change add_column :txt_uploaders, :file_name, :string diff --git a/db/migrate/20160505163634_add_attachment_uploaded_file_to_txt_uploaders.rb b/db/migrate/20160505163634_add_attachment_uploaded_file_to_txt_uploaders.rb index a9ba8257..a38d06d3 100644 --- a/db/migrate/20160505163634_add_attachment_uploaded_file_to_txt_uploaders.rb +++ b/db/migrate/20160505163634_add_attachment_uploaded_file_to_txt_uploaders.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddAttachmentUploadedFileToTxtUploaders < ActiveRecord::Migration def self.up change_table :txt_uploaders do |t| diff --git a/db/migrate/20160505163813_remove_file_name_from_txt_uploaders.rb b/db/migrate/20160505163813_remove_file_name_from_txt_uploaders.rb index edb0a77e..9cee5750 100644 --- a/db/migrate/20160505163813_remove_file_name_from_txt_uploaders.rb +++ b/db/migrate/20160505163813_remove_file_name_from_txt_uploaders.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class RemoveFileNameFromTxtUploaders < ActiveRecord::Migration def change remove_column :txt_uploaders, :file_name diff --git a/db/migrate/20160507111437_rename_latitude.rb b/db/migrate/20160507111437_rename_latitude.rb index d962076c..41f3a760 100644 --- a/db/migrate/20160507111437_rename_latitude.rb +++ b/db/migrate/20160507111437_rename_latitude.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class RenameLatitude < ActiveRecord::Migration def change rename_column :individuals, :latitude, :latitude_original diff --git a/db/migrate/20160507112312_add_latitude_to_individuals.rb b/db/migrate/20160507112312_add_latitude_to_individuals.rb index c3f02745..f00f4293 100644 --- a/db/migrate/20160507112312_add_latitude_to_individuals.rb +++ b/db/migrate/20160507112312_add_latitude_to_individuals.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddLatitudeToIndividuals < ActiveRecord::Migration def change add_column :individuals, :latitude, :decimal diff --git a/db/migrate/20160508134633_add_imported_to_contigs.rb b/db/migrate/20160508134633_add_imported_to_contigs.rb index 780874fb..7e94ea14 100644 --- a/db/migrate/20160508134633_add_imported_to_contigs.rb +++ b/db/migrate/20160508134633_add_imported_to_contigs.rb @@ -1,5 +1,7 @@ +# frozen_string_literal: true + class AddImportedToContigs < ActiveRecord::Migration def change - add_column :contigs, :imported, :boolean, :default => false + add_column :contigs, :imported, :boolean, default: false end end diff --git a/db/migrate/20160508150233_add_overwritten_to_primer_reads.rb b/db/migrate/20160508150233_add_overwritten_to_primer_reads.rb index d7c651d7..c6116a4a 100644 --- a/db/migrate/20160508150233_add_overwritten_to_primer_reads.rb +++ b/db/migrate/20160508150233_add_overwritten_to_primer_reads.rb @@ -1,5 +1,7 @@ +# frozen_string_literal: true + class AddOverwrittenToPrimerReads < ActiveRecord::Migration def change - add_column :primer_reads, :overwritten, :boolean, :default => false + add_column :primer_reads, :overwritten, :boolean, default: false end end diff --git a/db/migrate/20160509194717_add_copy_attributes_to_isolates.rb b/db/migrate/20160509194717_add_copy_attributes_to_isolates.rb index d2cfbfc9..8630507d 100644 --- a/db/migrate/20160509194717_add_copy_attributes_to_isolates.rb +++ b/db/migrate/20160509194717_add_copy_attributes_to_isolates.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddCopyAttributesToIsolates < ActiveRecord::Migration def change add_column :isolates, :lab_id_orig, :integer diff --git a/db/migrate/20160509200511_add_user_to_isolates.rb b/db/migrate/20160509200511_add_user_to_isolates.rb index fe7d7418..1eb6bad2 100644 --- a/db/migrate/20160509200511_add_user_to_isolates.rb +++ b/db/migrate/20160509200511_add_user_to_isolates.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddUserToIsolates < ActiveRecord::Migration def change add_column :isolates, :user_id, :integer diff --git a/db/migrate/20160510123450_add_lab_rack_id_to_micronic_plates.rb b/db/migrate/20160510123450_add_lab_rack_id_to_micronic_plates.rb index 9c2c1487..f8a2e1a2 100644 --- a/db/migrate/20160510123450_add_lab_rack_id_to_micronic_plates.rb +++ b/db/migrate/20160510123450_add_lab_rack_id_to_micronic_plates.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddLabRackIdToMicronicPlates < ActiveRecord::Migration def change add_column :micronic_plates, :lab_rack_id, :integer diff --git a/db/migrate/20160510125555_add_rack_position_to_lab_racks.rb b/db/migrate/20160510125555_add_rack_position_to_lab_racks.rb index 013482bc..1c53b426 100644 --- a/db/migrate/20160510125555_add_rack_position_to_lab_racks.rb +++ b/db/migrate/20160510125555_add_rack_position_to_lab_racks.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddRackPositionToLabRacks < ActiveRecord::Migration def change add_column :lab_racks, :rack_position, :string diff --git a/db/migrate/20160510161111_add_shelf_to_lab_rack.rb b/db/migrate/20160510161111_add_shelf_to_lab_rack.rb index 5304eab1..a3338ac2 100644 --- a/db/migrate/20160510161111_add_shelf_to_lab_rack.rb +++ b/db/migrate/20160510161111_add_shelf_to_lab_rack.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddShelfToLabRack < ActiveRecord::Migration def change add_column :lab_racks, :shelf, :string diff --git a/db/migrate/20160511191823_change_precision_of_concentration.rb b/db/migrate/20160511191823_change_precision_of_concentration.rb index a34acd65..5189b056 100644 --- a/db/migrate/20160511191823_change_precision_of_concentration.rb +++ b/db/migrate/20160511191823_change_precision_of_concentration.rb @@ -1,6 +1,8 @@ +# frozen_string_literal: true + class ChangePrecisionOfConcentration < ActiveRecord::Migration def change - change_column :isolates, :concentration_orig, :decimal, :precision => 15, :scale => 2 - change_column :isolates, :concentration_copy, :decimal, :precision => 15, :scale => 2 + change_column :isolates, :concentration_orig, :decimal, precision: 15, scale: 2 + change_column :isolates, :concentration_copy, :decimal, precision: 15, scale: 2 end end diff --git a/db/migrate/20160529123449_add_partial_cons_count_to_contigs.rb b/db/migrate/20160529123449_add_partial_cons_count_to_contigs.rb index ac330fc9..9963bb0b 100644 --- a/db/migrate/20160529123449_add_partial_cons_count_to_contigs.rb +++ b/db/migrate/20160529123449_add_partial_cons_count_to_contigs.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddPartialConsCountToContigs < ActiveRecord::Migration def change add_column :contigs, :partial_cons_count, :integer diff --git a/db/migrate/20160603084804_add_aligned_peak_indices_to_primer_reads.rb b/db/migrate/20160603084804_add_aligned_peak_indices_to_primer_reads.rb index 0fd4f807..150ce397 100644 --- a/db/migrate/20160603084804_add_aligned_peak_indices_to_primer_reads.rb +++ b/db/migrate/20160603084804_add_aligned_peak_indices_to_primer_reads.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddAlignedPeakIndicesToPrimerReads < ActiveRecord::Migration def change add_column :primer_reads, :aligned_peak_indices, :integer, array: true diff --git a/db/migrate/20160607140007_create_species_xml_uploaders.rb b/db/migrate/20160607140007_create_species_xml_uploaders.rb index 1008a8a3..245cf293 100644 --- a/db/migrate/20160607140007_create_species_xml_uploaders.rb +++ b/db/migrate/20160607140007_create_species_xml_uploaders.rb @@ -1,7 +1,8 @@ +# frozen_string_literal: true + class CreateSpeciesXmlUploaders < ActiveRecord::Migration def change create_table :species_xml_uploaders do |t| - t.timestamps null: false end end diff --git a/db/migrate/20160607140336_add_attachment_uploaded_file_to_species_xml_uploaders.rb b/db/migrate/20160607140336_add_attachment_uploaded_file_to_species_xml_uploaders.rb index fd8f6ed9..53bc8b01 100644 --- a/db/migrate/20160607140336_add_attachment_uploaded_file_to_species_xml_uploaders.rb +++ b/db/migrate/20160607140336_add_attachment_uploaded_file_to_species_xml_uploaders.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddAttachmentUploadedFileToSpeciesXmlUploaders < ActiveRecord::Migration def self.up change_table :species_xml_uploaders do |t| diff --git a/db/migrate/20160609122522_create_divisions.rb b/db/migrate/20160609122522_create_divisions.rb index f6892a1e..5cb5f781 100644 --- a/db/migrate/20160609122522_create_divisions.rb +++ b/db/migrate/20160609122522_create_divisions.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class CreateDivisions < ActiveRecord::Migration def change create_table :divisions do |t| diff --git a/db/migrate/20160609122800_create_subdivisions.rb b/db/migrate/20160609122800_create_subdivisions.rb index 96ad778f..b9b1b65c 100644 --- a/db/migrate/20160609122800_create_subdivisions.rb +++ b/db/migrate/20160609122800_create_subdivisions.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class CreateSubdivisions < ActiveRecord::Migration def change create_table :subdivisions do |t| diff --git a/db/migrate/20160609122903_create_taxonomic_classes.rb b/db/migrate/20160609122903_create_taxonomic_classes.rb index 9e487514..ec723035 100644 --- a/db/migrate/20160609122903_create_taxonomic_classes.rb +++ b/db/migrate/20160609122903_create_taxonomic_classes.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class CreateTaxonomicClasses < ActiveRecord::Migration def change create_table :taxonomic_classes do |t| diff --git a/db/migrate/20160609130939_add_class_id_to_orders.rb b/db/migrate/20160609130939_add_class_id_to_orders.rb index d8fe1730..63882b0c 100644 --- a/db/migrate/20160609130939_add_class_id_to_orders.rb +++ b/db/migrate/20160609130939_add_class_id_to_orders.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddClassIdToOrders < ActiveRecord::Migration def change add_column :orders, :taxonomic_class_id, :integer diff --git a/db/migrate/20160609131329_add_subdivision_id_to_taxonomic_classes.rb b/db/migrate/20160609131329_add_subdivision_id_to_taxonomic_classes.rb index 285cd5dc..2d3a1bb2 100644 --- a/db/migrate/20160609131329_add_subdivision_id_to_taxonomic_classes.rb +++ b/db/migrate/20160609131329_add_subdivision_id_to_taxonomic_classes.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddSubdivisionIdToTaxonomicClasses < ActiveRecord::Migration def change add_column :taxonomic_classes, :subdivision_id, :integer diff --git a/db/migrate/20160609133011_add_position_to_subdivisions.rb b/db/migrate/20160609133011_add_position_to_subdivisions.rb index 8ee1072b..affd38c7 100644 --- a/db/migrate/20160609133011_add_position_to_subdivisions.rb +++ b/db/migrate/20160609133011_add_position_to_subdivisions.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddPositionToSubdivisions < ActiveRecord::Migration def change add_column :subdivisions, :position, :integer diff --git a/db/migrate/20160627170221_add_overlap_length_to_contigs.rb b/db/migrate/20160627170221_add_overlap_length_to_contigs.rb index f5ad3424..567355e0 100644 --- a/db/migrate/20160627170221_add_overlap_length_to_contigs.rb +++ b/db/migrate/20160627170221_add_overlap_length_to_contigs.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddOverlapLengthToContigs < ActiveRecord::Migration def change add_column :contigs, :overlap_length, :integer, default: 15 diff --git a/db/migrate/20160905163301_add_comment_to_isolate.rb b/db/migrate/20160905163301_add_comment_to_isolate.rb index fb038224..4cc51a54 100644 --- a/db/migrate/20160905163301_add_comment_to_isolate.rb +++ b/db/migrate/20160905163301_add_comment_to_isolate.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddCommentToIsolate < ActiveRecord::Migration def change add_column :isolates, :comment_orig, :text diff --git a/db/migrate/20170619101312_create_contig_pde_uploader.rb b/db/migrate/20170619101312_create_contig_pde_uploader.rb index 1f8bb187..a33542f8 100644 --- a/db/migrate/20170619101312_create_contig_pde_uploader.rb +++ b/db/migrate/20170619101312_create_contig_pde_uploader.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class CreateContigPdeUploader < ActiveRecord::Migration[5.0] def change create_table :contig_pde_uploaders do |t| diff --git a/db/migrate/20170620124842_remove_pde_from_contigs.rb b/db/migrate/20170620124842_remove_pde_from_contigs.rb index e5338d45..73b8581e 100644 --- a/db/migrate/20170620124842_remove_pde_from_contigs.rb +++ b/db/migrate/20170620124842_remove_pde_from_contigs.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class RemovePdeFromContigs < ActiveRecord::Migration[5.0] def up remove_column :contigs, :pde, :text diff --git a/db/migrate/20170920100203_add_reference_to_marker_sequence.rb b/db/migrate/20170920100203_add_reference_to_marker_sequence.rb index 94890399..47345cb7 100644 --- a/db/migrate/20170920100203_add_reference_to_marker_sequence.rb +++ b/db/migrate/20170920100203_add_reference_to_marker_sequence.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddReferenceToMarkerSequence < ActiveRecord::Migration[5.0] def up add_column :marker_sequences, :reference, :string diff --git a/db/migrate/20170922091324_change_precision_of_location_data.rb b/db/migrate/20170922091324_change_precision_of_location_data.rb index 3909a156..7e87f1f2 100644 --- a/db/migrate/20170922091324_change_precision_of_location_data.rb +++ b/db/migrate/20170922091324_change_precision_of_location_data.rb @@ -1,7 +1,9 @@ +# frozen_string_literal: true + class ChangePrecisionOfLocationData < ActiveRecord::Migration[5.0] def up - change_column :individuals, :latitude, :decimal, :precision => 15, :scale => 6 - change_column :individuals, :longitude, :decimal, :precision => 15, :scale => 6 + change_column :individuals, :latitude, :decimal, precision: 15, scale: 6 + change_column :individuals, :longitude, :decimal, precision: 15, scale: 6 end def down diff --git a/db/migrate/20171018120345_create_contig_searches.rb b/db/migrate/20171018120345_create_contig_searches.rb index 66f76af9..383e2a62 100644 --- a/db/migrate/20171018120345_create_contig_searches.rb +++ b/db/migrate/20171018120345_create_contig_searches.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class CreateContigSearches < ActiveRecord::Migration[5.0] def up create_table :contig_searches do |t| diff --git a/db/migrate/20171018133939_change_types_in_contig_search.rb b/db/migrate/20171018133939_change_types_in_contig_search.rb index bcf8a8f9..997e2e77 100644 --- a/db/migrate/20171018133939_change_types_in_contig_search.rb +++ b/db/migrate/20171018133939_change_types_in_contig_search.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class ChangeTypesInContigSearch < ActiveRecord::Migration[5.0] def self.up remove_column :contig_searches, :min_age diff --git a/db/migrate/20171018142430_add_attributes_to_contig_search.rb b/db/migrate/20171018142430_add_attributes_to_contig_search.rb index 285b7604..c83c01fd 100644 --- a/db/migrate/20171018142430_add_attributes_to_contig_search.rb +++ b/db/migrate/20171018142430_add_attributes_to_contig_search.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddAttributesToContigSearch < ActiveRecord::Migration[5.0] def up add_column :contig_searches, :unassembled, :boolean diff --git a/db/migrate/20171027123414_change_types_in_contig_search_to_date.rb b/db/migrate/20171027123414_change_types_in_contig_search_to_date.rb index a61d5a5f..1b620f50 100644 --- a/db/migrate/20171027123414_change_types_in_contig_search_to_date.rb +++ b/db/migrate/20171027123414_change_types_in_contig_search_to_date.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class ChangeTypesInContigSearchToDate < ActiveRecord::Migration[5.0] def self.up change_column :contig_searches, :min_age, :date diff --git a/db/migrate/20171102131258_change_booleans_in_contig_search.rb b/db/migrate/20171102131258_change_booleans_in_contig_search.rb index 3edefc2d..26b41891 100644 --- a/db/migrate/20171102131258_change_booleans_in_contig_search.rb +++ b/db/migrate/20171102131258_change_booleans_in_contig_search.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class ChangeBooleansInContigSearch < ActiveRecord::Migration[5.0] def up change_column :contig_searches, :assembled, :string diff --git a/db/migrate/20171107114403_change_id_attributes_in_contig_search.rb b/db/migrate/20171107114403_change_id_attributes_in_contig_search.rb index a30a74e9..2ff9f62b 100644 --- a/db/migrate/20171107114403_change_id_attributes_in_contig_search.rb +++ b/db/migrate/20171107114403_change_id_attributes_in_contig_search.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class ChangeIdAttributesInContigSearch < ActiveRecord::Migration[5.0] def up rename_column :contig_searches, :order_id, :order diff --git a/db/migrate/20171107143211_add_title_to_contig_search.rb b/db/migrate/20171107143211_add_title_to_contig_search.rb index 4bf56b0d..e3a4af11 100644 --- a/db/migrate/20171107143211_add_title_to_contig_search.rb +++ b/db/migrate/20171107143211_add_title_to_contig_search.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddTitleToContigSearch < ActiveRecord::Migration[5.0] def up add_column :contig_searches, :title, :string diff --git a/db/migrate/20171204141837_create_overview_all_taxa_matviews.rb b/db/migrate/20171204141837_create_overview_all_taxa_matviews.rb index 8be6a5e5..be539a1a 100644 --- a/db/migrate/20171204141837_create_overview_all_taxa_matviews.rb +++ b/db/migrate/20171204141837_create_overview_all_taxa_matviews.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class CreateOverviewAllTaxaMatviews < ActiveRecord::Migration[5.0] def change create_view :overview_all_taxa_matviews, materialized: true diff --git a/db/migrate/20171207133553_update_overview_all_taxa_matviews_to_version_2.rb b/db/migrate/20171207133553_update_overview_all_taxa_matviews_to_version_2.rb index 5eceec72..e8f99a53 100644 --- a/db/migrate/20171207133553_update_overview_all_taxa_matviews_to_version_2.rb +++ b/db/migrate/20171207133553_update_overview_all_taxa_matviews_to_version_2.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class UpdateOverviewAllTaxaMatviewsToVersion2 < ActiveRecord::Migration[5.0] def change update_view :overview_all_taxa_matviews, version: 2, revert_to_version: 1, materialized: true diff --git a/db/migrate/20171213104138_update_overview_all_taxa_matviews_to_version_3.rb b/db/migrate/20171213104138_update_overview_all_taxa_matviews_to_version_3.rb index fae4703e..8b768303 100644 --- a/db/migrate/20171213104138_update_overview_all_taxa_matviews_to_version_3.rb +++ b/db/migrate/20171213104138_update_overview_all_taxa_matviews_to_version_3.rb @@ -1,8 +1,10 @@ +# frozen_string_literal: true + class UpdateOverviewAllTaxaMatviewsToVersion3 < ActiveRecord::Migration[5.0] def change update_view :overview_all_taxa_matviews, - version: 3, - revert_to_version: 2, - materialized: true + version: 3, + revert_to_version: 2, + materialized: true end end diff --git a/db/migrate/20171213141704_create_overview_finished_taxa_matviews.rb b/db/migrate/20171213141704_create_overview_finished_taxa_matviews.rb index 44d2cfc3..db81aba5 100644 --- a/db/migrate/20171213141704_create_overview_finished_taxa_matviews.rb +++ b/db/migrate/20171213141704_create_overview_finished_taxa_matviews.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class CreateOverviewFinishedTaxaMatviews < ActiveRecord::Migration[5.0] def change create_view :overview_finished_taxa_matviews, materialized: true diff --git a/db/migrate/20180111122659_update_overview_all_taxa_matviews_to_version_4.rb b/db/migrate/20180111122659_update_overview_all_taxa_matviews_to_version_4.rb index c0e6362f..866a7f17 100644 --- a/db/migrate/20180111122659_update_overview_all_taxa_matviews_to_version_4.rb +++ b/db/migrate/20180111122659_update_overview_all_taxa_matviews_to_version_4.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class UpdateOverviewAllTaxaMatviewsToVersion4 < ActiveRecord::Migration[5.0] def change update_view :overview_all_taxa_matviews, diff --git a/db/migrate/20180111123732_update_overview_finished_taxa_matviews_to_version_2.rb b/db/migrate/20180111123732_update_overview_finished_taxa_matviews_to_version_2.rb index 6f16d4b6..b81b98d9 100644 --- a/db/migrate/20180111123732_update_overview_finished_taxa_matviews_to_version_2.rb +++ b/db/migrate/20180111123732_update_overview_finished_taxa_matviews_to_version_2.rb @@ -1,8 +1,10 @@ +# frozen_string_literal: true + class UpdateOverviewFinishedTaxaMatviewsToVersion2 < ActiveRecord::Migration[5.0] def change update_view :overview_finished_taxa_matviews, - version: 2, - revert_to_version: 1, - materialized: true + version: 2, + revert_to_version: 1, + materialized: true end end diff --git a/db/migrate/20180111125140_update_overview_finished_taxa_matviews_to_version_3.rb b/db/migrate/20180111125140_update_overview_finished_taxa_matviews_to_version_3.rb index 905e4dfb..a1cb3d95 100644 --- a/db/migrate/20180111125140_update_overview_finished_taxa_matviews_to_version_3.rb +++ b/db/migrate/20180111125140_update_overview_finished_taxa_matviews_to_version_3.rb @@ -1,8 +1,10 @@ +# frozen_string_literal: true + class UpdateOverviewFinishedTaxaMatviewsToVersion3 < ActiveRecord::Migration[5.0] def change update_view :overview_finished_taxa_matviews, - version: 3, - revert_to_version: 2, - materialized: true + version: 3, + revert_to_version: 2, + materialized: true end end diff --git a/db/migrate/20180112101532_update_overview_finished_taxa_matviews_to_version_4.rb b/db/migrate/20180112101532_update_overview_finished_taxa_matviews_to_version_4.rb index ffe2e14e..834d8327 100644 --- a/db/migrate/20180112101532_update_overview_finished_taxa_matviews_to_version_4.rb +++ b/db/migrate/20180112101532_update_overview_finished_taxa_matviews_to_version_4.rb @@ -1,8 +1,10 @@ +# frozen_string_literal: true + class UpdateOverviewFinishedTaxaMatviewsToVersion4 < ActiveRecord::Migration[5.0] def change update_view :overview_finished_taxa_matviews, - version: 4, - revert_to_version: 3, - materialized: true + version: 4, + revert_to_version: 3, + materialized: true end end diff --git a/db/migrate/20180115103305_update_overview_finished_taxa_matviews_to_version_5.rb b/db/migrate/20180115103305_update_overview_finished_taxa_matviews_to_version_5.rb index 9a60dc0d..02611cbd 100644 --- a/db/migrate/20180115103305_update_overview_finished_taxa_matviews_to_version_5.rb +++ b/db/migrate/20180115103305_update_overview_finished_taxa_matviews_to_version_5.rb @@ -1,8 +1,10 @@ +# frozen_string_literal: true + class UpdateOverviewFinishedTaxaMatviewsToVersion5 < ActiveRecord::Migration[5.0] def change update_view :overview_finished_taxa_matviews, - version: 5, - revert_to_version: 4, - materialized: true + version: 5, + revert_to_version: 4, + materialized: true end end diff --git a/db/migrate/20180117150033_add_roles_to_users.rb b/db/migrate/20180117150033_add_roles_to_users.rb index 44814e22..7a65dfc2 100644 --- a/db/migrate/20180117150033_add_roles_to_users.rb +++ b/db/migrate/20180117150033_add_roles_to_users.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddRolesToUsers < ActiveRecord::Migration[5.0] def change add_column :users, :admin, :boolean diff --git a/db/migrate/20180122164030_add_supervisor_to_user.rb b/db/migrate/20180122164030_add_supervisor_to_user.rb index 7afb74b1..6c5913a7 100644 --- a/db/migrate/20180122164030_add_supervisor_to_user.rb +++ b/db/migrate/20180122164030_add_supervisor_to_user.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddSupervisorToUser < ActiveRecord::Migration[5.0] def change add_column :users, :supervisor, :boolean diff --git a/db/migrate/20180124130027_add_lab_id_to_user.rb b/db/migrate/20180124130027_add_lab_id_to_user.rb index c24ad3ac..2d7992ff 100644 --- a/db/migrate/20180124130027_add_lab_id_to_user.rb +++ b/db/migrate/20180124130027_add_lab_id_to_user.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddLabIdToUser < ActiveRecord::Migration[5.0] def change add_column :users, :lab_id, :integer diff --git a/db/migrate/20180124133256_add_user_id_to_contig_search.rb b/db/migrate/20180124133256_add_user_id_to_contig_search.rb index 1f769883..11c149ef 100644 --- a/db/migrate/20180124133256_add_user_id_to_contig_search.rb +++ b/db/migrate/20180124133256_add_user_id_to_contig_search.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddUserIdToContigSearch < ActiveRecord::Migration[5.0] def change add_column :contig_searches, :user_id, :integer diff --git a/db/migrate/20180320143645_create_marker_sequence_searches.rb b/db/migrate/20180320143645_create_marker_sequence_searches.rb index e2209a32..71339be7 100644 --- a/db/migrate/20180320143645_create_marker_sequence_searches.rb +++ b/db/migrate/20180320143645_create_marker_sequence_searches.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class CreateMarkerSequenceSearches < ActiveRecord::Migration[5.0] def change create_table :marker_sequence_searches do |t| diff --git a/db/migrate/20180321102252_add_attributes_to_marker_sequence_search.rb b/db/migrate/20180321102252_add_attributes_to_marker_sequence_search.rb index b807b3f7..69dad1d2 100644 --- a/db/migrate/20180321102252_add_attributes_to_marker_sequence_search.rb +++ b/db/migrate/20180321102252_add_attributes_to_marker_sequence_search.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddAttributesToMarkerSequenceSearch < ActiveRecord::Migration[5.0] def up add_column :marker_sequence_searches, :user_id, :integer diff --git a/db/migrate/20180323103303_change_datatype_marker_sequence_search_marker.rb b/db/migrate/20180323103303_change_datatype_marker_sequence_search_marker.rb index 2936d882..0aa76c9e 100644 --- a/db/migrate/20180323103303_change_datatype_marker_sequence_search_marker.rb +++ b/db/migrate/20180323103303_change_datatype_marker_sequence_search_marker.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class ChangeDatatypeMarkerSequenceSearchMarker < ActiveRecord::Migration[5.0] def up change_column :marker_sequence_searches, :marker, :string diff --git a/db/migrate/20180411081530_update_overview_finished_taxa_matviews_to_version_6.rb b/db/migrate/20180411081530_update_overview_finished_taxa_matviews_to_version_6.rb index 0a67f25a..bd99c77c 100644 --- a/db/migrate/20180411081530_update_overview_finished_taxa_matviews_to_version_6.rb +++ b/db/migrate/20180411081530_update_overview_finished_taxa_matviews_to_version_6.rb @@ -1,8 +1,10 @@ +# frozen_string_literal: true + class UpdateOverviewFinishedTaxaMatviewsToVersion6 < ActiveRecord::Migration[5.0] def change update_view :overview_finished_taxa_matviews, - version: 6, - revert_to_version: 5, - materialized: true + version: 6, + revert_to_version: 5, + materialized: true end end diff --git a/db/migrate/20180416072622_create_responsibilities.rb b/db/migrate/20180416072622_create_responsibilities.rb index b1bc5163..6e636854 100644 --- a/db/migrate/20180416072622_create_responsibilities.rb +++ b/db/migrate/20180416072622_create_responsibilities.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class CreateResponsibilities < ActiveRecord::Migration[5.0] def change create_table :responsibilities do |t| diff --git a/db/migrate/20180416075103_create_join_table_responsibility_user.rb b/db/migrate/20180416075103_create_join_table_responsibility_user.rb index b3de2705..8afd3ac4 100644 --- a/db/migrate/20180416075103_create_join_table_responsibility_user.rb +++ b/db/migrate/20180416075103_create_join_table_responsibility_user.rb @@ -1,7 +1,9 @@ +# frozen_string_literal: true + class CreateJoinTableResponsibilityUser < ActiveRecord::Migration[5.0] def change create_join_table :responsibilities, :users do |t| - t.index [:responsibility_id, :user_id] + t.index %i[responsibility_id user_id] end end end diff --git a/db/migrate/20180416093136_add_role_to_user.rb b/db/migrate/20180416093136_add_role_to_user.rb index ae75f4fd..111cdb42 100644 --- a/db/migrate/20180416093136_add_role_to_user.rb +++ b/db/migrate/20180416093136_add_role_to_user.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddRoleToUser < ActiveRecord::Migration[5.0] def change add_column :users, :role, :integer diff --git a/db/migrate/20180416093403_remove_unused_attributes_from_user.rb b/db/migrate/20180416093403_remove_unused_attributes_from_user.rb index 2722a85c..f5e80135 100644 --- a/db/migrate/20180416093403_remove_unused_attributes_from_user.rb +++ b/db/migrate/20180416093403_remove_unused_attributes_from_user.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class RemoveUnusedAttributesFromUser < ActiveRecord::Migration[5.0] def change remove_column :users, :admin diff --git a/db/migrate/20180416123308_create_join_table_primer_project.rb b/db/migrate/20180416123308_create_join_table_primer_project.rb index f989f917..73c4a0dd 100644 --- a/db/migrate/20180416123308_create_join_table_primer_project.rb +++ b/db/migrate/20180416123308_create_join_table_primer_project.rb @@ -1,7 +1,9 @@ +# frozen_string_literal: true + class CreateJoinTablePrimerProject < ActiveRecord::Migration[5.0] def change create_join_table :primers, :projects do |t| - t.index [:primer_id, :project_id] + t.index %i[primer_id project_id] end end end diff --git a/db/migrate/20180416123337_create_join_table_marker_project.rb b/db/migrate/20180416123337_create_join_table_marker_project.rb index 97c4a1ac..f40f6c3d 100644 --- a/db/migrate/20180416123337_create_join_table_marker_project.rb +++ b/db/migrate/20180416123337_create_join_table_marker_project.rb @@ -1,7 +1,9 @@ +# frozen_string_literal: true + class CreateJoinTableMarkerProject < ActiveRecord::Migration[5.0] def change create_join_table :markers, :projects do |t| - t.index [:marker_id, :project_id] + t.index %i[marker_id project_id] end end end diff --git a/db/migrate/20180416123357_create_join_table_marker_sequence_project.rb b/db/migrate/20180416123357_create_join_table_marker_sequence_project.rb index 91815381..dad9309e 100644 --- a/db/migrate/20180416123357_create_join_table_marker_sequence_project.rb +++ b/db/migrate/20180416123357_create_join_table_marker_sequence_project.rb @@ -1,7 +1,9 @@ +# frozen_string_literal: true + class CreateJoinTableMarkerSequenceProject < ActiveRecord::Migration[5.0] def change create_join_table :marker_sequences, :projects do |t| - t.index [:marker_sequence_id, :project_id], name: 'index_marker_sequences_projects' + t.index %i[marker_sequence_id project_id], name: 'index_marker_sequences_projects' end end end diff --git a/db/migrate/20180416125519_add_default_project_to_user.rb b/db/migrate/20180416125519_add_default_project_to_user.rb index 465dee18..d1da9012 100644 --- a/db/migrate/20180416125519_add_default_project_to_user.rb +++ b/db/migrate/20180416125519_add_default_project_to_user.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddDefaultProjectToUser < ActiveRecord::Migration[5.0] def change add_column :users, :default_project_id, :integer diff --git a/db/migrate/20180418071549_create_join_table_freezer_project.rb b/db/migrate/20180418071549_create_join_table_freezer_project.rb index c80818de..24557b5b 100644 --- a/db/migrate/20180418071549_create_join_table_freezer_project.rb +++ b/db/migrate/20180418071549_create_join_table_freezer_project.rb @@ -1,7 +1,9 @@ +# frozen_string_literal: true + class CreateJoinTableFreezerProject < ActiveRecord::Migration[5.0] def change create_join_table :freezers, :projects do |t| - t.index [:freezer_id, :project_id] + t.index %i[freezer_id project_id] end end end diff --git a/db/migrate/20180418071616_create_join_table_lab_rack_project.rb b/db/migrate/20180418071616_create_join_table_lab_rack_project.rb index 9811f572..f8ce1977 100644 --- a/db/migrate/20180418071616_create_join_table_lab_rack_project.rb +++ b/db/migrate/20180418071616_create_join_table_lab_rack_project.rb @@ -1,7 +1,9 @@ +# frozen_string_literal: true + class CreateJoinTableLabRackProject < ActiveRecord::Migration[5.0] def change create_join_table :lab_racks, :projects do |t| - t.index [:lab_rack_id, :project_id] + t.index %i[lab_rack_id project_id] end end end diff --git a/db/migrate/20180418071641_create_join_table_micronic_plate_project.rb b/db/migrate/20180418071641_create_join_table_micronic_plate_project.rb index 9b83dc60..69d32071 100644 --- a/db/migrate/20180418071641_create_join_table_micronic_plate_project.rb +++ b/db/migrate/20180418071641_create_join_table_micronic_plate_project.rb @@ -1,7 +1,9 @@ +# frozen_string_literal: true + class CreateJoinTableMicronicPlateProject < ActiveRecord::Migration[5.0] def change create_join_table :micronic_plates, :projects do |t| - t.index [:micronic_plate_id, :project_id], name: 'index_micronic_plates_projects' + t.index %i[micronic_plate_id project_id], name: 'index_micronic_plates_projects' end end end diff --git a/db/migrate/20180418071707_create_join_table_plant_plate_project.rb b/db/migrate/20180418071707_create_join_table_plant_plate_project.rb index b12967f8..cf02b58b 100644 --- a/db/migrate/20180418071707_create_join_table_plant_plate_project.rb +++ b/db/migrate/20180418071707_create_join_table_plant_plate_project.rb @@ -1,7 +1,9 @@ +# frozen_string_literal: true + class CreateJoinTablePlantPlateProject < ActiveRecord::Migration[5.0] def change create_join_table :plant_plates, :projects do |t| - t.index [:plant_plate_id, :project_id] + t.index %i[plant_plate_id project_id] end end end diff --git a/db/migrate/20180418085911_add_lab_rack_to_plant_plate.rb b/db/migrate/20180418085911_add_lab_rack_to_plant_plate.rb index 8d312bc8..596c412b 100644 --- a/db/migrate/20180418085911_add_lab_rack_to_plant_plate.rb +++ b/db/migrate/20180418085911_add_lab_rack_to_plant_plate.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddLabRackToPlantPlate < ActiveRecord::Migration[5.0] def change add_reference :plant_plates, :lab_rack, foreign_key: true diff --git a/db/migrate/20180418142452_create_join_table_project_shelf.rb b/db/migrate/20180418142452_create_join_table_project_shelf.rb index 14a8bcd3..289d99bf 100644 --- a/db/migrate/20180418142452_create_join_table_project_shelf.rb +++ b/db/migrate/20180418142452_create_join_table_project_shelf.rb @@ -1,7 +1,9 @@ +# frozen_string_literal: true + class CreateJoinTableProjectShelf < ActiveRecord::Migration[5.0] def change create_join_table :projects, :shelves do |t| - t.index [:project_id, :shelf_id] + t.index %i[project_id shelf_id] end end end diff --git a/db/migrate/20180418142950_add_freezer_to_shelf.rb b/db/migrate/20180418142950_add_freezer_to_shelf.rb index 649fca00..baf8a9ae 100644 --- a/db/migrate/20180418142950_add_freezer_to_shelf.rb +++ b/db/migrate/20180418142950_add_freezer_to_shelf.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddFreezerToShelf < ActiveRecord::Migration[5.0] def change add_reference :shelves, :freezer, foreign_key: true diff --git a/db/migrate/20180424090248_add_project_to_contig_search.rb b/db/migrate/20180424090248_add_project_to_contig_search.rb index 493af9af..861bf865 100644 --- a/db/migrate/20180424090248_add_project_to_contig_search.rb +++ b/db/migrate/20180424090248_add_project_to_contig_search.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddProjectToContigSearch < ActiveRecord::Migration[5.0] def change add_reference :contig_searches, :project, foreign_key: true diff --git a/db/migrate/20180424090325_add_project_to_marker_sequence_search.rb b/db/migrate/20180424090325_add_project_to_marker_sequence_search.rb index ba304ca6..7337a842 100644 --- a/db/migrate/20180424090325_add_project_to_marker_sequence_search.rb +++ b/db/migrate/20180424090325_add_project_to_marker_sequence_search.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddProjectToMarkerSequenceSearch < ActiveRecord::Migration[5.0] def change add_reference :marker_sequence_searches, :project, foreign_key: true diff --git a/db/migrate/20180516123145_add_attachment_search_result_archive_to_contig_searches.rb b/db/migrate/20180516123145_add_attachment_search_result_archive_to_contig_searches.rb index 399f3d5c..a3385b8b 100644 --- a/db/migrate/20180516123145_add_attachment_search_result_archive_to_contig_searches.rb +++ b/db/migrate/20180516123145_add_attachment_search_result_archive_to_contig_searches.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddAttachmentSearchResultArchiveToContigSearches < ActiveRecord::Migration[5.0] def self.up change_table :contig_searches do |t| diff --git a/db/migrate/20180518091457_create_pg_search_documents.rb b/db/migrate/20180518091457_create_pg_search_documents.rb index 64a491e1..b03e6069 100644 --- a/db/migrate/20180518091457_create_pg_search_documents.rb +++ b/db/migrate/20180518091457_create_pg_search_documents.rb @@ -1,16 +1,18 @@ +# frozen_string_literal: true + class CreatePgSearchDocuments < ActiveRecord::Migration[5.0] def self.up - say_with_time("Creating table for pg_search multisearch") do + say_with_time('Creating table for pg_search multisearch') do create_table :pg_search_documents do |t| t.text :content - t.belongs_to :searchable, :polymorphic => true, :index => true + t.belongs_to :searchable, polymorphic: true, index: true t.timestamps null: false end end end def self.down - say_with_time("Dropping table for pg_search multisearch") do + say_with_time('Dropping table for pg_search multisearch') do drop_table :pg_search_documents end end diff --git a/db/migrate/20180518095542_add_pg_trgm_extension_to_db.rb b/db/migrate/20180518095542_add_pg_trgm_extension_to_db.rb index 2ad7e7de..eb000a70 100644 --- a/db/migrate/20180518095542_add_pg_trgm_extension_to_db.rb +++ b/db/migrate/20180518095542_add_pg_trgm_extension_to_db.rb @@ -1,5 +1,7 @@ +# frozen_string_literal: true + class AddPgTrgmExtensionToDb < ActiveRecord::Migration[5.0] def change - execute "create extension pg_trgm;" + execute 'create extension pg_trgm;' end end diff --git a/db/migrate/20180528142049_drop_overview_all_taxa_matview_to_overview_all_taxa.rb b/db/migrate/20180528142049_drop_overview_all_taxa_matview_to_overview_all_taxa.rb index f90e138a..fedc3ac4 100644 --- a/db/migrate/20180528142049_drop_overview_all_taxa_matview_to_overview_all_taxa.rb +++ b/db/migrate/20180528142049_drop_overview_all_taxa_matview_to_overview_all_taxa.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class DropOverviewAllTaxaMatviewToOverviewAllTaxa < ActiveRecord::Migration[5.0] def change drop_view :overview_all_taxa_matviews, materialized: true diff --git a/db/migrate/20180528143409_drop_overview_finished_taxa_matview.rb b/db/migrate/20180528143409_drop_overview_finished_taxa_matview.rb index 3c0354c4..74c72949 100644 --- a/db/migrate/20180528143409_drop_overview_finished_taxa_matview.rb +++ b/db/migrate/20180528143409_drop_overview_finished_taxa_matview.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class DropOverviewFinishedTaxaMatview < ActiveRecord::Migration[5.0] def change drop_view :overview_finished_taxa_matviews, materialized: true diff --git a/db/migrate/20180607132126_add_has_species_to_marker_sequence_searches.rb b/db/migrate/20180607132126_add_has_species_to_marker_sequence_searches.rb index da9aebe2..4aad948c 100644 --- a/db/migrate/20180607132126_add_has_species_to_marker_sequence_searches.rb +++ b/db/migrate/20180607132126_add_has_species_to_marker_sequence_searches.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddHasSpeciesToMarkerSequenceSearches < ActiveRecord::Migration[5.0] def change add_column :marker_sequence_searches, :has_species, :boolean diff --git a/db/migrate/20180608122922_add_higher_order_taxon_to_marker_sequence_search.rb b/db/migrate/20180608122922_add_higher_order_taxon_to_marker_sequence_search.rb index 3a11644f..3a80a2f8 100644 --- a/db/migrate/20180608122922_add_higher_order_taxon_to_marker_sequence_search.rb +++ b/db/migrate/20180608122922_add_higher_order_taxon_to_marker_sequence_search.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddHigherOrderTaxonToMarkerSequenceSearch < ActiveRecord::Migration[5.0] def change add_column :marker_sequence_searches, :higher_order_taxon, :string diff --git a/db/migrate/20180615090349_create_mislabel_analyses.rb b/db/migrate/20180615090349_create_mislabel_analyses.rb index cce91567..8dc9d243 100644 --- a/db/migrate/20180615090349_create_mislabel_analyses.rb +++ b/db/migrate/20180615090349_create_mislabel_analyses.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class CreateMislabelAnalyses < ActiveRecord::Migration[5.0] def change create_table :mislabel_analyses do |t| diff --git a/db/migrate/20180615090753_create_mislabels.rb b/db/migrate/20180615090753_create_mislabels.rb index 63648754..b9ad1d51 100644 --- a/db/migrate/20180615090753_create_mislabels.rb +++ b/db/migrate/20180615090753_create_mislabels.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class CreateMislabels < ActiveRecord::Migration[5.0] def change create_table :mislabels do |t| diff --git a/db/migrate/20180615091448_create_join_table_marker_sequences_mislabel_analyses.rb b/db/migrate/20180615091448_create_join_table_marker_sequences_mislabel_analyses.rb index 1c0a89f4..37861023 100644 --- a/db/migrate/20180615091448_create_join_table_marker_sequences_mislabel_analyses.rb +++ b/db/migrate/20180615091448_create_join_table_marker_sequences_mislabel_analyses.rb @@ -1,7 +1,9 @@ +# frozen_string_literal: true + class CreateJoinTableMarkerSequencesMislabelAnalyses < ActiveRecord::Migration[5.0] def change create_join_table :marker_sequences, :mislabel_analyses do |t| - t.index [:marker_sequence_id, :mislabel_analysis_id], name: 'index_marker_sequences_mislabel_analyses' + t.index %i[marker_sequence_id mislabel_analysis_id], name: 'index_marker_sequences_mislabel_analyses' end end end diff --git a/db/migrate/20180615091603_add_mislabels_to_marker_sequences.rb b/db/migrate/20180615091603_add_mislabels_to_marker_sequences.rb index 190a7eab..c05ada45 100644 --- a/db/migrate/20180615091603_add_mislabels_to_marker_sequences.rb +++ b/db/migrate/20180615091603_add_mislabels_to_marker_sequences.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddMislabelsToMarkerSequences < ActiveRecord::Migration[5.0] def change add_reference :mislabels, :marker_sequence, foreign_key: true diff --git a/db/migrate/20180621112511_add_solved_to_mislabels.rb b/db/migrate/20180621112511_add_solved_to_mislabels.rb index 2663f258..7d34de73 100644 --- a/db/migrate/20180621112511_add_solved_to_mislabels.rb +++ b/db/migrate/20180621112511_add_solved_to_mislabels.rb @@ -1,6 +1,8 @@ +# frozen_string_literal: true + class AddSolvedToMislabels < ActiveRecord::Migration[5.0] def change - add_column :mislabels, :solved, :boolean, :default => false + add_column :mislabels, :solved, :boolean, default: false add_column :mislabels, :solved_by, :integer add_column :mislabels, :solved_at, :datetime end diff --git a/db/migrate/20180621122934_add_has_warnings_to_marker_sequence_search.rb b/db/migrate/20180621122934_add_has_warnings_to_marker_sequence_search.rb index b6a18d24..992dba96 100644 --- a/db/migrate/20180621122934_add_has_warnings_to_marker_sequence_search.rb +++ b/db/migrate/20180621122934_add_has_warnings_to_marker_sequence_search.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddHasWarningsToMarkerSequenceSearch < ActiveRecord::Migration[5.0] def change add_column :marker_sequence_searches, :has_warnings, :integer diff --git a/db/migrate/20180622121926_add_has_warnings_to_contig_search.rb b/db/migrate/20180622121926_add_has_warnings_to_contig_search.rb index f83cd88c..948b8e3b 100644 --- a/db/migrate/20180622121926_add_has_warnings_to_contig_search.rb +++ b/db/migrate/20180622121926_add_has_warnings_to_contig_search.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddHasWarningsToContigSearch < ActiveRecord::Migration[5.0] def change add_column :contig_searches, :has_warnings, :integer diff --git a/db/migrate/20180628115013_add_attributes_to_mislabel_analysis.rb b/db/migrate/20180628115013_add_attributes_to_mislabel_analysis.rb index 1e273a77..53361969 100644 --- a/db/migrate/20180628115013_add_attributes_to_mislabel_analysis.rb +++ b/db/migrate/20180628115013_add_attributes_to_mislabel_analysis.rb @@ -1,6 +1,8 @@ +# frozen_string_literal: true + class AddAttributesToMislabelAnalysis < ActiveRecord::Migration[5.0] def change - add_column :mislabel_analyses, :automatic, :boolean, :default => false + add_column :mislabel_analyses, :automatic, :boolean, default: false add_reference :mislabel_analyses, :marker, foreign_key: true end end diff --git a/db/migrate/20180629094941_add_total_seq_number_to_mislabel_analysis.rb b/db/migrate/20180629094941_add_total_seq_number_to_mislabel_analysis.rb index 016ebea1..a26908ee 100644 --- a/db/migrate/20180629094941_add_total_seq_number_to_mislabel_analysis.rb +++ b/db/migrate/20180629094941_add_total_seq_number_to_mislabel_analysis.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddTotalSeqNumberToMislabelAnalysis < ActiveRecord::Migration[5.0] def change add_column :mislabel_analyses, :total_seq_number, :integer diff --git a/db/migrate/20180629112840_add_has_issue_to_individuals.rb b/db/migrate/20180629112840_add_has_issue_to_individuals.rb index 91f9f24d..a15ab51d 100644 --- a/db/migrate/20180629112840_add_has_issue_to_individuals.rb +++ b/db/migrate/20180629112840_add_has_issue_to_individuals.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddHasIssueToIndividuals < ActiveRecord::Migration[5.0] def change add_column :individuals, :has_issue, :boolean diff --git a/db/migrate/20180629120118_create_individual_searches.rb b/db/migrate/20180629120118_create_individual_searches.rb index b49131fd..86e37cdd 100644 --- a/db/migrate/20180629120118_create_individual_searches.rb +++ b/db/migrate/20180629120118_create_individual_searches.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class CreateIndividualSearches < ActiveRecord::Migration[5.0] def change create_table :individual_searches do |t| diff --git a/db/migrate/20180629122812_change_attributes_of_individual_search.rb b/db/migrate/20180629122812_change_attributes_of_individual_search.rb index ddb0f80c..4c8be34c 100644 --- a/db/migrate/20180629122812_change_attributes_of_individual_search.rb +++ b/db/migrate/20180629122812_change_attributes_of_individual_search.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class ChangeAttributesOfIndividualSearch < ActiveRecord::Migration[5.0] def change add_reference :individual_searches, :project, foreign_key: true diff --git a/db/migrate/20180629124238_change_has_species_of_individual_search.rb b/db/migrate/20180629124238_change_has_species_of_individual_search.rb index 049f5d30..577484cc 100644 --- a/db/migrate/20180629124238_change_has_species_of_individual_search.rb +++ b/db/migrate/20180629124238_change_has_species_of_individual_search.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class ChangeHasSpeciesOfIndividualSearch < ActiveRecord::Migration[5.0] def change change_column :individual_searches, :has_species, 'integer USING CAST(has_issue AS integer)' diff --git a/db/migrate/20180718141806_add_checksum_to_primer_reads.rb b/db/migrate/20180718141806_add_checksum_to_primer_reads.rb index cc7014c1..3d1bd619 100644 --- a/db/migrate/20180718141806_add_checksum_to_primer_reads.rb +++ b/db/migrate/20180718141806_add_checksum_to_primer_reads.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddChecksumToPrimerReads < ActiveRecord::Migration[5.0] def change add_column :primer_reads, :chromatogram_fingerprint, :string diff --git a/db/migrate/20180921081203_add_update_and_creation_constraints_to_ms_search.rb b/db/migrate/20180921081203_add_update_and_creation_constraints_to_ms_search.rb index b1fa36bc..ff4275da 100644 --- a/db/migrate/20180921081203_add_update_and_creation_constraints_to_ms_search.rb +++ b/db/migrate/20180921081203_add_update_and_creation_constraints_to_ms_search.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddUpdateAndCreationConstraintsToMsSearch < ActiveRecord::Migration[5.0] def change add_column :marker_sequence_searches, :min_age, :date diff --git a/db/migrate/20181010123611_add_verified_by_to_contig_search.rb b/db/migrate/20181010123611_add_verified_by_to_contig_search.rb index f846b9c3..94291abf 100644 --- a/db/migrate/20181010123611_add_verified_by_to_contig_search.rb +++ b/db/migrate/20181010123611_add_verified_by_to_contig_search.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddVerifiedByToContigSearch < ActiveRecord::Migration[5.0] def change add_column :contig_searches, :verified_by, :string diff --git a/db/migrate/20181010124944_add_verified_by_to_marker_sequence_search.rb b/db/migrate/20181010124944_add_verified_by_to_marker_sequence_search.rb index ae7947d4..1d058fc9 100644 --- a/db/migrate/20181010124944_add_verified_by_to_marker_sequence_search.rb +++ b/db/migrate/20181010124944_add_verified_by_to_marker_sequence_search.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class AddVerifiedByToMarkerSequenceSearch < ActiveRecord::Migration[5.0] def change add_column :marker_sequence_searches, :verified_by, :string diff --git a/db/migrate/20181016135130_drop_alignments.rb b/db/migrate/20181016135130_drop_alignments.rb index b625ec03..b23d72ba 100644 --- a/db/migrate/20181016135130_drop_alignments.rb +++ b/db/migrate/20181016135130_drop_alignments.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class DropAlignments < ActiveRecord::Migration[5.0] def up drop_table :alignments diff --git a/db/migrate/20181016154851_drop_status.rb b/db/migrate/20181016154851_drop_status.rb index 7abf129a..ce545c48 100644 --- a/db/migrate/20181016154851_drop_status.rb +++ b/db/migrate/20181016154851_drop_status.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class DropStatus < ActiveRecord::Migration[5.0] def up drop_table :statuses diff --git a/db/migrate/20181017083633_rename_xml_uploader.rb b/db/migrate/20181017083633_rename_xml_uploader.rb index 7312f96d..fe4fce8a 100644 --- a/db/migrate/20181017083633_rename_xml_uploader.rb +++ b/db/migrate/20181017083633_rename_xml_uploader.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class RenameXmlUploader < ActiveRecord::Migration[5.0] def self.up rename_table :xml_uploaders, :specimen_exporters diff --git a/db/migrate/20181017084242_rename_species_xml_uploader.rb b/db/migrate/20181017084242_rename_species_xml_uploader.rb index 1d8d722d..ce9e8a11 100644 --- a/db/migrate/20181017084242_rename_species_xml_uploader.rb +++ b/db/migrate/20181017084242_rename_species_xml_uploader.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class RenameSpeciesXmlUploader < ActiveRecord::Migration[5.0] def self.up rename_table :species_xml_uploaders, :species_exporters diff --git a/db/migrate/20181017085059_rename_exporter_uploaded_file.rb b/db/migrate/20181017085059_rename_exporter_uploaded_file.rb index 894ae603..24ffec26 100644 --- a/db/migrate/20181017085059_rename_exporter_uploaded_file.rb +++ b/db/migrate/20181017085059_rename_exporter_uploaded_file.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class RenameExporterUploadedFile < ActiveRecord::Migration[5.0] def self.rename_attachment(table, old, new) attachment_columns = [['file_name', :string], ['content_type', :string], ['file_size', :integer], ['updated_at', :datetime]] diff --git a/db/migrate/20181018093520_remove_partial_cons_text_columns_from_contigs.rb b/db/migrate/20181018093520_remove_partial_cons_text_columns_from_contigs.rb index e3b4c727..aa9df11b 100644 --- a/db/migrate/20181018093520_remove_partial_cons_text_columns_from_contigs.rb +++ b/db/migrate/20181018093520_remove_partial_cons_text_columns_from_contigs.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class RemovePartialConsTextColumnsFromContigs < ActiveRecord::Migration[5.0] def change remove_column :contigs, :partial_cons1, :text diff --git a/db/migrate/20181018094614_remove_unused_columns_from_contigs.rb b/db/migrate/20181018094614_remove_unused_columns_from_contigs.rb index c3de5962..05a0370b 100644 --- a/db/migrate/20181018094614_remove_unused_columns_from_contigs.rb +++ b/db/migrate/20181018094614_remove_unused_columns_from_contigs.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + class RemoveUnusedColumnsFromContigs < ActiveRecord::Migration[5.0] def change remove_column :contigs, :aligned_cons, :string diff --git a/db/schema.rb b/db/schema.rb index f065dfc0..4127cddc 100644 --- a/db/schema.rb +++ b/db/schema.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + # This file is auto-generated from the current state of the database. Instead # of editing this file, please use the migrations feature of Active Record to # incrementally modify your database, and then regenerate this schema definition. @@ -10,729 +12,728 @@ # # It's strongly recommended that you check this file into your version control system. -ActiveRecord::Schema.define(version: 20181018094614) do - +ActiveRecord::Schema.define(version: 20_181_018_094_614) do # These are extensions that must be enabled in order to support this database - enable_extension "plpgsql" - enable_extension "pg_stat_statements" - enable_extension "pg_trgm" - - create_table "centroid_sequences", force: :cascade do |t| - t.datetime "created_at", null: false - t.datetime "updated_at", null: false - end - - create_table "clusters", force: :cascade do |t| - t.datetime "created_at", null: false - t.datetime "updated_at", null: false - end - - create_table "contig_pde_uploaders", force: :cascade do |t| - t.string "uploaded_file_file_name" - t.string "uploaded_file_content_type" - t.integer "uploaded_file_file_size" - t.datetime "uploaded_file_updated_at" - t.datetime "created_at", null: false - t.datetime "updated_at", null: false - end - - create_table "contig_searches", force: :cascade do |t| - t.string "species" - t.string "order" - t.string "specimen" - t.string "family" - t.string "verified" - t.string "marker" - t.string "name" - t.string "assembled" - t.datetime "created_at", null: false - t.datetime "updated_at", null: false - t.date "min_age" - t.date "max_age" - t.date "min_update" - t.date "max_update" - t.string "title" - t.integer "user_id" - t.integer "project_id" - t.string "search_result_archive_file_name" - t.string "search_result_archive_content_type" - t.integer "search_result_archive_file_size" - t.datetime "search_result_archive_updated_at" - t.integer "has_warnings" - t.string "verified_by" - t.index ["project_id"], name: "index_contig_searches_on_project_id", using: :btree - end - - create_table "contigs", force: :cascade do |t| - t.string "name", limit: 255 - t.text "consensus" - t.datetime "created_at" - t.datetime "updated_at" - t.integer "marker_sequence_id" - t.integer "isolate_id" - t.integer "marker_id" - t.boolean "assembled" - t.boolean "assembly_tried" - t.text "fas" - t.boolean "verified", default: false - t.integer "verified_by" - t.datetime "verified_at" - t.string "comment" - t.boolean "imported", default: false - t.integer "partial_cons_count" - t.integer "overlap_length", default: 15 - t.integer "allowed_mismatch_percent", default: 5 - end - - create_table "contigs_projects", id: false, force: :cascade do |t| - t.integer "contig_id" - t.integer "project_id" - end - - create_table "copies", force: :cascade do |t| - t.string "well_pos_plant_plate" - t.integer "lab_nr" - t.integer "micronic_tube_id" - t.string "well_pos_micronic_plate" - t.decimal "concentration" - t.datetime "created_at" - t.datetime "updated_at" - end - - create_table "delayed_jobs", force: :cascade do |t| - t.integer "priority", default: 0, null: false - t.integer "attempts", default: 0, null: false - t.text "handler", null: false - t.text "last_error" - t.datetime "run_at" - t.datetime "locked_at" - t.datetime "failed_at" - t.string "locked_by", limit: 255 - t.string "queue", limit: 255 - t.datetime "created_at" - t.datetime "updated_at" - t.index ["priority", "run_at"], name: "delayed_jobs_priority", using: :btree - end - - create_table "divisions", force: :cascade do |t| - t.string "name" - t.datetime "created_at", null: false - t.datetime "updated_at", null: false - end - - create_table "families", force: :cascade do |t| - t.string "name", limit: 255 - t.string "author", limit: 255 - t.datetime "created_at" - t.datetime "updated_at" - t.integer "order_id" - end - - create_table "families_projects", id: false, force: :cascade do |t| - t.integer "family_id" - t.integer "project_id" - end - - create_table "freezers", force: :cascade do |t| - t.string "freezercode", limit: 255 - t.datetime "created_at" - t.datetime "updated_at" - t.integer "lab_id" - end - - create_table "freezers_projects", id: false, force: :cascade do |t| - t.integer "freezer_id", null: false - t.integer "project_id", null: false - t.index ["freezer_id", "project_id"], name: "index_freezers_projects_on_freezer_id_and_project_id", using: :btree - end - - create_table "genera", force: :cascade do |t| - t.string "name", limit: 255 - t.string "author", limit: 255 - t.datetime "created_at" - t.datetime "updated_at" - end - - create_table "helps", force: :cascade do |t| - t.datetime "created_at" - t.datetime "updated_at" - end - - create_table "higher_order_taxa", force: :cascade do |t| - t.string "name", limit: 255 - t.datetime "created_at" - t.datetime "updated_at" - t.string "german_name", limit: 255 - t.integer "position" - end - - create_table "higher_order_taxa_markers", id: false, force: :cascade do |t| - t.integer "higher_order_taxon_id" - t.integer "marker_id" - end - - create_table "higher_order_taxa_projects", id: false, force: :cascade do |t| - t.integer "higher_order_taxon_id" - t.integer "project_id" - end - - create_table "individual_searches", force: :cascade do |t| - t.string "title" - t.integer "has_species" - t.integer "has_problematic_location" - t.integer "has_issue" - t.string "specimen_id" - t.string "DNA_bank_id" - t.string "species" - t.string "family" - t.string "order" - t.datetime "created_at", null: false - t.datetime "updated_at", null: false - t.integer "project_id" - t.integer "user_id" - t.index ["project_id"], name: "index_individual_searches_on_project_id", using: :btree - t.index ["user_id"], name: "index_individual_searches_on_user_id", using: :btree - end - - create_table "individuals", force: :cascade do |t| - t.string "specimen_id", limit: 255 - t.string "DNA_bank_id", limit: 255 - t.string "collector", limit: 255 - t.datetime "created_at" - t.datetime "updated_at" - t.boolean "silica_gel" - t.date "collected" - t.integer "species_id" - t.string "herbarium", limit: 255 - t.string "voucher", limit: 255 - t.string "country", limit: 255 - t.string "state_province", limit: 255 - t.text "locality" - t.string "latitude_original", limit: 255 - t.string "longitude_original", limit: 255 - t.string "elevation", limit: 255 - t.string "exposition", limit: 255 - t.text "habitat" - t.string "substrate", limit: 255 - t.string "life_form", limit: 255 - t.string "collection_nr", limit: 255 - t.string "collection_date", limit: 255 - t.string "determination", limit: 255 - t.string "revision", limit: 255 - t.string "confirmation", limit: 255 - t.text "comments" - t.decimal "latitude", precision: 15, scale: 6 - t.decimal "longitude", precision: 15, scale: 6 - t.boolean "has_issue" - end - - create_table "individuals_projects", id: false, force: :cascade do |t| - t.integer "individual_id" - t.integer "project_id" - end - - create_table "isolates", force: :cascade do |t| - t.string "well_pos_plant_plate", limit: 255 - t.string "micronic_tube_id", limit: 255 - t.string "well_pos_micronic_plate", limit: 255 - t.decimal "concentration" - t.datetime "created_at" - t.datetime "updated_at" - t.boolean "isCopy" - t.integer "tissue_id" - t.integer "micronic_plate_id" - t.integer "plant_plate_id" - t.integer "individual_id" - t.string "dna_bank_id", limit: 255 - t.string "lab_nr", limit: 255 - t.boolean "negative_control", default: false - t.integer "lab_id_orig" - t.integer "lab_id_copy" - t.datetime "isolation_date" - t.integer "micronic_plate_id_orig" - t.integer "micronic_plate_id_copy" - t.string "well_pos_micronic_plate_orig" - t.string "well_pos_micronic_plate_copy" - t.decimal "concentration_orig", precision: 15, scale: 2 - t.decimal "concentration_copy", precision: 15, scale: 2 - t.string "micronic_tube_id_orig" - t.string "micronic_tube_id_copy" - t.integer "user_id" - t.text "comment_orig" - t.text "comment_copy" - end - - create_table "isolates_projects", id: false, force: :cascade do |t| - t.integer "isolate_id" - t.integer "project_id" - end - - create_table "issues", force: :cascade do |t| - t.string "title", limit: 255 - t.text "description" - t.datetime "created_at" - t.datetime "updated_at" - t.integer "primer_read_id" - t.integer "contig_id" - end - - create_table "issues_projects", id: false, force: :cascade do |t| - t.integer "issue_id" - t.integer "project_id" - end - - create_table "lab_racks", force: :cascade do |t| - t.string "rackcode", limit: 255 - t.datetime "created_at" - t.datetime "updated_at" - t.integer "freezer_id" - t.string "rack_position" - t.string "shelf" - end - - create_table "lab_racks_projects", id: false, force: :cascade do |t| - t.integer "lab_rack_id", null: false - t.integer "project_id", null: false - t.index ["lab_rack_id", "project_id"], name: "index_lab_racks_projects_on_lab_rack_id_and_project_id", using: :btree - end - - create_table "labs", force: :cascade do |t| - t.string "labcode", limit: 255 - t.datetime "created_at" - t.datetime "updated_at" - end - - create_table "labs_projects", id: false, force: :cascade do |t| - t.integer "lab_id" - t.integer "project_id" - end - - create_table "marker_sequence_searches", force: :cascade do |t| - t.string "name" - t.string "verified" - t.string "species" - t.string "order" - t.string "specimen" - t.datetime "created_at", null: false - t.datetime "updated_at", null: false - t.integer "user_id" - t.string "title" - t.string "family" - t.string "marker" - t.integer "min_length" - t.integer "max_length" - t.integer "project_id" - t.boolean "has_species" - t.string "higher_order_taxon" - t.integer "has_warnings" - t.date "min_age" - t.date "max_age" - t.date "min_update" - t.date "max_update" - t.string "verified_by" - t.index ["project_id"], name: "index_marker_sequence_searches_on_project_id", using: :btree - end - - create_table "marker_sequences", force: :cascade do |t| - t.string "name", limit: 255 - t.datetime "created_at" - t.datetime "updated_at" - t.string "genbank", limit: 255 - t.text "sequence" - t.integer "isolate_id" - t.integer "marker_id" - t.string "reference" - end - - create_table "marker_sequences_mislabel_analyses", id: false, force: :cascade do |t| - t.integer "marker_sequence_id", null: false - t.integer "mislabel_analysis_id", null: false - t.index ["marker_sequence_id", "mislabel_analysis_id"], name: "index_marker_sequences_mislabel_analyses", using: :btree - end - - create_table "marker_sequences_projects", id: false, force: :cascade do |t| - t.integer "marker_sequence_id", null: false - t.integer "project_id", null: false - t.index ["marker_sequence_id", "project_id"], name: "index_marker_sequences_projects", using: :btree - end - - create_table "markers", force: :cascade do |t| - t.string "name", limit: 255 - t.datetime "created_at" - t.datetime "updated_at" - t.integer "expected_reads" - t.boolean "is_gbol" - t.string "alt_name" - end - - create_table "markers_projects", id: false, force: :cascade do |t| - t.integer "marker_id", null: false - t.integer "project_id", null: false - t.index ["marker_id", "project_id"], name: "index_markers_projects_on_marker_id_and_project_id", using: :btree - end - - create_table "micronic_plates", force: :cascade do |t| - t.string "micronic_plate_id", limit: 255 - t.string "name", limit: 255 - t.datetime "created_at" - t.datetime "updated_at" - t.string "location_in_rack", limit: 255 - t.integer "lab_rack_id" - end - - create_table "micronic_plates_projects", id: false, force: :cascade do |t| - t.integer "micronic_plate_id", null: false - t.integer "project_id", null: false - t.index ["micronic_plate_id", "project_id"], name: "index_micronic_plates_projects", using: :btree - end - - create_table "mislabel_analyses", force: :cascade do |t| - t.string "title" - t.datetime "created_at", null: false - t.datetime "updated_at", null: false - t.boolean "automatic", default: false - t.integer "marker_id" - t.integer "total_seq_number" - t.index ["marker_id"], name: "index_mislabel_analyses_on_marker_id", using: :btree - end - - create_table "mislabels", force: :cascade do |t| - t.string "level" - t.decimal "confidence" - t.string "proposed_label" - t.string "proposed_path" - t.string "path_confidence" - t.integer "mislabel_analysis_id" - t.datetime "created_at", null: false - t.datetime "updated_at", null: false - t.integer "marker_sequence_id" - t.boolean "solved", default: false - t.integer "solved_by" - t.datetime "solved_at" - t.index ["marker_sequence_id"], name: "index_mislabels_on_marker_sequence_id", using: :btree - t.index ["mislabel_analysis_id"], name: "index_mislabels_on_mislabel_analysis_id", using: :btree - end - - create_table "news", force: :cascade do |t| - t.string "title", limit: 255 - t.text "body" - t.datetime "published" - t.datetime "created_at" - t.datetime "updated_at" - end - - create_table "ngs_runs", force: :cascade do |t| - t.integer "quality_threshold" - t.integer "tag_mismates" - t.integer "primer_mismatches" - t.datetime "created_at", null: false - t.datetime "updated_at", null: false - t.string "name" - t.string "fastq_file_name" - t.string "fastq_content_type" - t.integer "fastq_file_size" - t.datetime "fastq_updated_at" - t.integer "higher_order_taxon_id" - t.string "set_tag_map_file_name" - t.string "set_tag_map_content_type" - t.integer "set_tag_map_file_size" - t.datetime "set_tag_map_updated_at" - t.index ["higher_order_taxon_id"], name: "index_ngs_runs_on_higher_order_taxon_id", using: :btree - end - - create_table "ngs_runs_projects", id: false, force: :cascade do |t| - t.integer "ngs_run_id", null: false - t.integer "project_id", null: false - t.index ["ngs_run_id", "project_id"], name: "index_ngs_runs_projects_on_ngs_run_id_and_project_id", using: :btree - end - - create_table "oders", force: :cascade do |t| - t.string "name", limit: 255 - t.string "author", limit: 255 - t.datetime "created_at" - t.datetime "updated_at" - end - - create_table "orders", force: :cascade do |t| - t.string "name", limit: 255 - t.string "author", limit: 255 - t.datetime "created_at" - t.datetime "updated_at" - t.integer "higher_order_taxon_id" - t.integer "taxonomic_class_id" - end - - create_table "orders_projects", id: false, force: :cascade do |t| - t.integer "order_id" - t.integer "project_id" - end - - create_table "partial_cons", force: :cascade do |t| - t.text "sequence" - t.text "aligned_sequence" - t.datetime "created_at" - t.datetime "updated_at" - t.integer "contig_id" - t.integer "aligned_qualities", array: true - end - - create_table "pg_search_documents", force: :cascade do |t| - t.text "content" - t.string "searchable_type" - t.integer "searchable_id" - t.datetime "created_at", null: false - t.datetime "updated_at", null: false - t.index ["searchable_type", "searchable_id"], name: "index_pg_search_documents_on_searchable_type_and_searchable_id", using: :btree - end - - create_table "plant_plates", force: :cascade do |t| - t.string "name", limit: 255 - t.integer "how_many" - t.datetime "created_at" - t.datetime "updated_at" - t.string "location_in_rack", limit: 255 - t.integer "lab_rack_id" - t.index ["lab_rack_id"], name: "index_plant_plates_on_lab_rack_id", using: :btree - end - - create_table "plant_plates_projects", id: false, force: :cascade do |t| - t.integer "plant_plate_id", null: false - t.integer "project_id", null: false - t.index ["plant_plate_id", "project_id"], name: "index_plant_plates_projects_on_plant_plate_id_and_project_id", using: :btree - end - - create_table "primer_pos_on_genomes", force: :cascade do |t| - t.text "note" - t.integer "position" - t.datetime "created_at" - t.datetime "updated_at" - end - - create_table "primer_reads", force: :cascade do |t| - t.string "name", limit: 255 - t.text "sequence" - t.string "pherogram_url", limit: 255 - t.datetime "created_at" - t.datetime "updated_at" - t.string "chromatogram_file_name", limit: 255 - t.string "chromatogram_content_type", limit: 255 - t.integer "chromatogram_file_size" - t.datetime "chromatogram_updated_at" - t.integer "primer_id" - t.integer "isolate_id" - t.integer "contig_id" - t.integer "trimmedReadEnd" - t.integer "trimmedReadStart" - t.integer "qualities", array: true - t.boolean "reverse" - t.text "aligned_seq" - t.boolean "used_for_con" - t.text "quality_string" - t.integer "position" - t.boolean "assembled" - t.integer "partial_con_id" - t.integer "aligned_qualities", array: true - t.integer "window_size", default: 10 - t.integer "count_in_window", default: 8 - t.integer "min_quality_score", default: 30 - t.integer "atrace", array: true - t.integer "ctrace", array: true - t.integer "gtrace", array: true - t.integer "ttrace", array: true - t.integer "peak_indices", array: true - t.boolean "processed", default: false - t.integer "base_count" - t.string "comment" - t.boolean "overwritten", default: false - t.integer "aligned_peak_indices", array: true - t.string "chromatogram_fingerprint" - end - - create_table "primer_reads_projects", id: false, force: :cascade do |t| - t.integer "primer_read_id" - t.integer "project_id" - end - - create_table "primers", force: :cascade do |t| - t.string "name", limit: 255 - t.string "sequence", limit: 255 - t.boolean "reverse" - t.datetime "created_at" - t.datetime "updated_at" - t.text "notes" - t.integer "marker_id" - t.string "labcode", limit: 255 - t.string "author", limit: 255 - t.string "alt_name", limit: 255 - t.string "target_group", limit: 255 - t.string "tm", limit: 255 - t.integer "position" - end - - create_table "primers_projects", id: false, force: :cascade do |t| - t.integer "primer_id", null: false - t.integer "project_id", null: false - t.index ["primer_id", "project_id"], name: "index_primers_projects_on_primer_id_and_project_id", using: :btree - end - - create_table "projects", force: :cascade do |t| - t.string "name", limit: 255 - t.text "description" - t.datetime "start" - t.datetime "due" - t.datetime "created_at" - t.datetime "updated_at" - end - - create_table "projects_shelves", id: false, force: :cascade do |t| - t.integer "project_id", null: false - t.integer "shelf_id", null: false - t.index ["project_id", "shelf_id"], name: "index_projects_shelves_on_project_id_and_shelf_id", using: :btree - end - - create_table "projects_species", id: false, force: :cascade do |t| - t.integer "project_id" - t.integer "species_id" - end - - create_table "projects_tag_primer_maps", id: false, force: :cascade do |t| - t.integer "project_id", null: false - t.integer "tag_primer_map_id", null: false - t.index ["project_id", "tag_primer_map_id"], name: "index_projects_tag_primer_maps", using: :btree - end - - create_table "projects_users", id: false, force: :cascade do |t| - t.integer "project_id" - t.integer "user_id" - end - - create_table "responsibilities", force: :cascade do |t| - t.string "name" - t.text "description" - t.datetime "created_at", null: false - t.datetime "updated_at", null: false - end - - create_table "responsibilities_users", id: false, force: :cascade do |t| - t.integer "responsibility_id", null: false - t.integer "user_id", null: false - t.index ["responsibility_id", "user_id"], name: "index_responsibilities_users_on_responsibility_id_and_user_id", using: :btree - end - - create_table "shelves", force: :cascade do |t| - t.string "name", limit: 255 - t.datetime "created_at" - t.datetime "updated_at" - t.integer "freezer_id" - t.index ["freezer_id"], name: "index_shelves_on_freezer_id", using: :btree - end - - create_table "species", force: :cascade do |t| - t.string "author", limit: 255 - t.string "genus_name", limit: 255 - t.string "species_epithet", limit: 255 - t.datetime "created_at" - t.datetime "updated_at" - t.integer "family_id" - t.string "infraspecific", limit: 255 - t.text "comment" - t.string "german_name", limit: 255 - t.string "author_infra", limit: 255 - t.string "synonym", limit: 255 - t.string "composed_name", limit: 255 - t.string "species_component" - end - - create_table "species_exporters", force: :cascade do |t| - t.datetime "created_at", null: false - t.datetime "updated_at", null: false - t.string "species_export_file_name" - t.string "species_export_content_type" - t.integer "species_export_file_size" - t.datetime "species_export_updated_at" - end - - create_table "specimen_exporters", force: :cascade do |t| - t.string "specimen_export_file_name" - t.string "specimen_export_content_type" - t.integer "specimen_export_file_size" - t.datetime "specimen_export_updated_at" - t.datetime "created_at" - t.datetime "updated_at" - end - - create_table "subdivisions", force: :cascade do |t| - t.string "name" - t.datetime "created_at", null: false - t.datetime "updated_at", null: false - t.integer "position" - t.string "german_name" - end - - create_table "tag_primer_maps", force: :cascade do |t| - t.datetime "created_at", null: false - t.datetime "updated_at", null: false - t.integer "ngs_run_id" - t.string "tag_primer_map_file_name" - t.string "tag_primer_map_content_type" - t.integer "tag_primer_map_file_size" - t.datetime "tag_primer_map_updated_at" - t.string "name" - t.string "tag" - t.index ["ngs_run_id"], name: "index_tag_primer_maps_on_ngs_run_id", using: :btree - end - - create_table "taxonomic_classes", force: :cascade do |t| - t.string "name" - t.datetime "created_at", null: false - t.datetime "updated_at", null: false - t.integer "subdivision_id" - t.string "german_name" - end - - create_table "tissues", force: :cascade do |t| - t.string "name", limit: 255 - t.datetime "created_at" - t.datetime "updated_at" - end - - create_table "txt_uploaders", force: :cascade do |t| - t.datetime "created_at", null: false - t.datetime "updated_at", null: false - t.string "uploaded_file_file_name" - t.string "uploaded_file_content_type" - t.integer "uploaded_file_file_size" - t.datetime "uploaded_file_updated_at" - end - - create_table "users", force: :cascade do |t| - t.string "email", limit: 255, default: "", null: false - t.string "encrypted_password", limit: 255, default: "", null: false - t.string "reset_password_token", limit: 255 - t.datetime "reset_password_sent_at" - t.datetime "remember_created_at" - t.integer "sign_in_count", default: 0, null: false - t.datetime "current_sign_in_at" - t.datetime "last_sign_in_at" - t.string "current_sign_in_ip", limit: 255 - t.string "last_sign_in_ip", limit: 255 - t.datetime "created_at" - t.datetime "updated_at" - t.string "name", limit: 255 - t.integer "lab_id" - t.integer "role" - t.integer "default_project_id" - t.index ["email"], name: "index_users_on_email", unique: true, using: :btree - t.index ["reset_password_token"], name: "index_users_on_reset_password_token", unique: true, using: :btree - end - - add_foreign_key "contig_searches", "projects" - add_foreign_key "individual_searches", "projects" - add_foreign_key "individual_searches", "users" - add_foreign_key "marker_sequence_searches", "projects" - add_foreign_key "mislabel_analyses", "markers" - add_foreign_key "mislabels", "marker_sequences" - add_foreign_key "ngs_runs", "higher_order_taxa" - add_foreign_key "plant_plates", "lab_racks" - add_foreign_key "shelves", "freezers" + enable_extension 'plpgsql' + enable_extension 'pg_stat_statements' + enable_extension 'pg_trgm' + + create_table 'centroid_sequences', force: :cascade do |t| + t.datetime 'created_at', null: false + t.datetime 'updated_at', null: false + end + + create_table 'clusters', force: :cascade do |t| + t.datetime 'created_at', null: false + t.datetime 'updated_at', null: false + end + + create_table 'contig_pde_uploaders', force: :cascade do |t| + t.string 'uploaded_file_file_name' + t.string 'uploaded_file_content_type' + t.integer 'uploaded_file_file_size' + t.datetime 'uploaded_file_updated_at' + t.datetime 'created_at', null: false + t.datetime 'updated_at', null: false + end + + create_table 'contig_searches', force: :cascade do |t| + t.string 'species' + t.string 'order' + t.string 'specimen' + t.string 'family' + t.string 'verified' + t.string 'marker' + t.string 'name' + t.string 'assembled' + t.datetime 'created_at', null: false + t.datetime 'updated_at', null: false + t.date 'min_age' + t.date 'max_age' + t.date 'min_update' + t.date 'max_update' + t.string 'title' + t.integer 'user_id' + t.integer 'project_id' + t.string 'search_result_archive_file_name' + t.string 'search_result_archive_content_type' + t.integer 'search_result_archive_file_size' + t.datetime 'search_result_archive_updated_at' + t.integer 'has_warnings' + t.string 'verified_by' + t.index ['project_id'], name: 'index_contig_searches_on_project_id', using: :btree + end + + create_table 'contigs', force: :cascade do |t| + t.string 'name', limit: 255 + t.text 'consensus' + t.datetime 'created_at' + t.datetime 'updated_at' + t.integer 'marker_sequence_id' + t.integer 'isolate_id' + t.integer 'marker_id' + t.boolean 'assembled' + t.boolean 'assembly_tried' + t.text 'fas' + t.boolean 'verified', default: false + t.integer 'verified_by' + t.datetime 'verified_at' + t.string 'comment' + t.boolean 'imported', default: false + t.integer 'partial_cons_count' + t.integer 'overlap_length', default: 15 + t.integer 'allowed_mismatch_percent', default: 5 + end + + create_table 'contigs_projects', id: false, force: :cascade do |t| + t.integer 'contig_id' + t.integer 'project_id' + end + + create_table 'copies', force: :cascade do |t| + t.string 'well_pos_plant_plate' + t.integer 'lab_nr' + t.integer 'micronic_tube_id' + t.string 'well_pos_micronic_plate' + t.decimal 'concentration' + t.datetime 'created_at' + t.datetime 'updated_at' + end + + create_table 'delayed_jobs', force: :cascade do |t| + t.integer 'priority', default: 0, null: false + t.integer 'attempts', default: 0, null: false + t.text 'handler', null: false + t.text 'last_error' + t.datetime 'run_at' + t.datetime 'locked_at' + t.datetime 'failed_at' + t.string 'locked_by', limit: 255 + t.string 'queue', limit: 255 + t.datetime 'created_at' + t.datetime 'updated_at' + t.index %w[priority run_at], name: 'delayed_jobs_priority', using: :btree + end + + create_table 'divisions', force: :cascade do |t| + t.string 'name' + t.datetime 'created_at', null: false + t.datetime 'updated_at', null: false + end + + create_table 'families', force: :cascade do |t| + t.string 'name', limit: 255 + t.string 'author', limit: 255 + t.datetime 'created_at' + t.datetime 'updated_at' + t.integer 'order_id' + end + + create_table 'families_projects', id: false, force: :cascade do |t| + t.integer 'family_id' + t.integer 'project_id' + end + + create_table 'freezers', force: :cascade do |t| + t.string 'freezercode', limit: 255 + t.datetime 'created_at' + t.datetime 'updated_at' + t.integer 'lab_id' + end + + create_table 'freezers_projects', id: false, force: :cascade do |t| + t.integer 'freezer_id', null: false + t.integer 'project_id', null: false + t.index %w[freezer_id project_id], name: 'index_freezers_projects_on_freezer_id_and_project_id', using: :btree + end + + create_table 'genera', force: :cascade do |t| + t.string 'name', limit: 255 + t.string 'author', limit: 255 + t.datetime 'created_at' + t.datetime 'updated_at' + end + + create_table 'helps', force: :cascade do |t| + t.datetime 'created_at' + t.datetime 'updated_at' + end + + create_table 'higher_order_taxa', force: :cascade do |t| + t.string 'name', limit: 255 + t.datetime 'created_at' + t.datetime 'updated_at' + t.string 'german_name', limit: 255 + t.integer 'position' + end + + create_table 'higher_order_taxa_markers', id: false, force: :cascade do |t| + t.integer 'higher_order_taxon_id' + t.integer 'marker_id' + end + + create_table 'higher_order_taxa_projects', id: false, force: :cascade do |t| + t.integer 'higher_order_taxon_id' + t.integer 'project_id' + end + + create_table 'individual_searches', force: :cascade do |t| + t.string 'title' + t.integer 'has_species' + t.integer 'has_problematic_location' + t.integer 'has_issue' + t.string 'specimen_id' + t.string 'DNA_bank_id' + t.string 'species' + t.string 'family' + t.string 'order' + t.datetime 'created_at', null: false + t.datetime 'updated_at', null: false + t.integer 'project_id' + t.integer 'user_id' + t.index ['project_id'], name: 'index_individual_searches_on_project_id', using: :btree + t.index ['user_id'], name: 'index_individual_searches_on_user_id', using: :btree + end + + create_table 'individuals', force: :cascade do |t| + t.string 'specimen_id', limit: 255 + t.string 'DNA_bank_id', limit: 255 + t.string 'collector', limit: 255 + t.datetime 'created_at' + t.datetime 'updated_at' + t.boolean 'silica_gel' + t.date 'collected' + t.integer 'species_id' + t.string 'herbarium', limit: 255 + t.string 'voucher', limit: 255 + t.string 'country', limit: 255 + t.string 'state_province', limit: 255 + t.text 'locality' + t.string 'latitude_original', limit: 255 + t.string 'longitude_original', limit: 255 + t.string 'elevation', limit: 255 + t.string 'exposition', limit: 255 + t.text 'habitat' + t.string 'substrate', limit: 255 + t.string 'life_form', limit: 255 + t.string 'collection_nr', limit: 255 + t.string 'collection_date', limit: 255 + t.string 'determination', limit: 255 + t.string 'revision', limit: 255 + t.string 'confirmation', limit: 255 + t.text 'comments' + t.decimal 'latitude', precision: 15, scale: 6 + t.decimal 'longitude', precision: 15, scale: 6 + t.boolean 'has_issue' + end + + create_table 'individuals_projects', id: false, force: :cascade do |t| + t.integer 'individual_id' + t.integer 'project_id' + end + + create_table 'isolates', force: :cascade do |t| + t.string 'well_pos_plant_plate', limit: 255 + t.string 'micronic_tube_id', limit: 255 + t.string 'well_pos_micronic_plate', limit: 255 + t.decimal 'concentration' + t.datetime 'created_at' + t.datetime 'updated_at' + t.boolean 'isCopy' + t.integer 'tissue_id' + t.integer 'micronic_plate_id' + t.integer 'plant_plate_id' + t.integer 'individual_id' + t.string 'dna_bank_id', limit: 255 + t.string 'lab_nr', limit: 255 + t.boolean 'negative_control', default: false + t.integer 'lab_id_orig' + t.integer 'lab_id_copy' + t.datetime 'isolation_date' + t.integer 'micronic_plate_id_orig' + t.integer 'micronic_plate_id_copy' + t.string 'well_pos_micronic_plate_orig' + t.string 'well_pos_micronic_plate_copy' + t.decimal 'concentration_orig', precision: 15, scale: 2 + t.decimal 'concentration_copy', precision: 15, scale: 2 + t.string 'micronic_tube_id_orig' + t.string 'micronic_tube_id_copy' + t.integer 'user_id' + t.text 'comment_orig' + t.text 'comment_copy' + end + + create_table 'isolates_projects', id: false, force: :cascade do |t| + t.integer 'isolate_id' + t.integer 'project_id' + end + + create_table 'issues', force: :cascade do |t| + t.string 'title', limit: 255 + t.text 'description' + t.datetime 'created_at' + t.datetime 'updated_at' + t.integer 'primer_read_id' + t.integer 'contig_id' + end + + create_table 'issues_projects', id: false, force: :cascade do |t| + t.integer 'issue_id' + t.integer 'project_id' + end + + create_table 'lab_racks', force: :cascade do |t| + t.string 'rackcode', limit: 255 + t.datetime 'created_at' + t.datetime 'updated_at' + t.integer 'freezer_id' + t.string 'rack_position' + t.string 'shelf' + end + + create_table 'lab_racks_projects', id: false, force: :cascade do |t| + t.integer 'lab_rack_id', null: false + t.integer 'project_id', null: false + t.index %w[lab_rack_id project_id], name: 'index_lab_racks_projects_on_lab_rack_id_and_project_id', using: :btree + end + + create_table 'labs', force: :cascade do |t| + t.string 'labcode', limit: 255 + t.datetime 'created_at' + t.datetime 'updated_at' + end + + create_table 'labs_projects', id: false, force: :cascade do |t| + t.integer 'lab_id' + t.integer 'project_id' + end + + create_table 'marker_sequence_searches', force: :cascade do |t| + t.string 'name' + t.string 'verified' + t.string 'species' + t.string 'order' + t.string 'specimen' + t.datetime 'created_at', null: false + t.datetime 'updated_at', null: false + t.integer 'user_id' + t.string 'title' + t.string 'family' + t.string 'marker' + t.integer 'min_length' + t.integer 'max_length' + t.integer 'project_id' + t.boolean 'has_species' + t.string 'higher_order_taxon' + t.integer 'has_warnings' + t.date 'min_age' + t.date 'max_age' + t.date 'min_update' + t.date 'max_update' + t.string 'verified_by' + t.index ['project_id'], name: 'index_marker_sequence_searches_on_project_id', using: :btree + end + + create_table 'marker_sequences', force: :cascade do |t| + t.string 'name', limit: 255 + t.datetime 'created_at' + t.datetime 'updated_at' + t.string 'genbank', limit: 255 + t.text 'sequence' + t.integer 'isolate_id' + t.integer 'marker_id' + t.string 'reference' + end + + create_table 'marker_sequences_mislabel_analyses', id: false, force: :cascade do |t| + t.integer 'marker_sequence_id', null: false + t.integer 'mislabel_analysis_id', null: false + t.index %w[marker_sequence_id mislabel_analysis_id], name: 'index_marker_sequences_mislabel_analyses', using: :btree + end + + create_table 'marker_sequences_projects', id: false, force: :cascade do |t| + t.integer 'marker_sequence_id', null: false + t.integer 'project_id', null: false + t.index %w[marker_sequence_id project_id], name: 'index_marker_sequences_projects', using: :btree + end + + create_table 'markers', force: :cascade do |t| + t.string 'name', limit: 255 + t.datetime 'created_at' + t.datetime 'updated_at' + t.integer 'expected_reads' + t.boolean 'is_gbol' + t.string 'alt_name' + end + + create_table 'markers_projects', id: false, force: :cascade do |t| + t.integer 'marker_id', null: false + t.integer 'project_id', null: false + t.index %w[marker_id project_id], name: 'index_markers_projects_on_marker_id_and_project_id', using: :btree + end + + create_table 'micronic_plates', force: :cascade do |t| + t.string 'micronic_plate_id', limit: 255 + t.string 'name', limit: 255 + t.datetime 'created_at' + t.datetime 'updated_at' + t.string 'location_in_rack', limit: 255 + t.integer 'lab_rack_id' + end + + create_table 'micronic_plates_projects', id: false, force: :cascade do |t| + t.integer 'micronic_plate_id', null: false + t.integer 'project_id', null: false + t.index %w[micronic_plate_id project_id], name: 'index_micronic_plates_projects', using: :btree + end + + create_table 'mislabel_analyses', force: :cascade do |t| + t.string 'title' + t.datetime 'created_at', null: false + t.datetime 'updated_at', null: false + t.boolean 'automatic', default: false + t.integer 'marker_id' + t.integer 'total_seq_number' + t.index ['marker_id'], name: 'index_mislabel_analyses_on_marker_id', using: :btree + end + + create_table 'mislabels', force: :cascade do |t| + t.string 'level' + t.decimal 'confidence' + t.string 'proposed_label' + t.string 'proposed_path' + t.string 'path_confidence' + t.integer 'mislabel_analysis_id' + t.datetime 'created_at', null: false + t.datetime 'updated_at', null: false + t.integer 'marker_sequence_id' + t.boolean 'solved', default: false + t.integer 'solved_by' + t.datetime 'solved_at' + t.index ['marker_sequence_id'], name: 'index_mislabels_on_marker_sequence_id', using: :btree + t.index ['mislabel_analysis_id'], name: 'index_mislabels_on_mislabel_analysis_id', using: :btree + end + + create_table 'news', force: :cascade do |t| + t.string 'title', limit: 255 + t.text 'body' + t.datetime 'published' + t.datetime 'created_at' + t.datetime 'updated_at' + end + + create_table 'ngs_runs', force: :cascade do |t| + t.integer 'quality_threshold' + t.integer 'tag_mismates' + t.integer 'primer_mismatches' + t.datetime 'created_at', null: false + t.datetime 'updated_at', null: false + t.string 'name' + t.string 'fastq_file_name' + t.string 'fastq_content_type' + t.integer 'fastq_file_size' + t.datetime 'fastq_updated_at' + t.integer 'higher_order_taxon_id' + t.string 'set_tag_map_file_name' + t.string 'set_tag_map_content_type' + t.integer 'set_tag_map_file_size' + t.datetime 'set_tag_map_updated_at' + t.index ['higher_order_taxon_id'], name: 'index_ngs_runs_on_higher_order_taxon_id', using: :btree + end + + create_table 'ngs_runs_projects', id: false, force: :cascade do |t| + t.integer 'ngs_run_id', null: false + t.integer 'project_id', null: false + t.index %w[ngs_run_id project_id], name: 'index_ngs_runs_projects_on_ngs_run_id_and_project_id', using: :btree + end + + create_table 'oders', force: :cascade do |t| + t.string 'name', limit: 255 + t.string 'author', limit: 255 + t.datetime 'created_at' + t.datetime 'updated_at' + end + + create_table 'orders', force: :cascade do |t| + t.string 'name', limit: 255 + t.string 'author', limit: 255 + t.datetime 'created_at' + t.datetime 'updated_at' + t.integer 'higher_order_taxon_id' + t.integer 'taxonomic_class_id' + end + + create_table 'orders_projects', id: false, force: :cascade do |t| + t.integer 'order_id' + t.integer 'project_id' + end + + create_table 'partial_cons', force: :cascade do |t| + t.text 'sequence' + t.text 'aligned_sequence' + t.datetime 'created_at' + t.datetime 'updated_at' + t.integer 'contig_id' + t.integer 'aligned_qualities', array: true + end + + create_table 'pg_search_documents', force: :cascade do |t| + t.text 'content' + t.string 'searchable_type' + t.integer 'searchable_id' + t.datetime 'created_at', null: false + t.datetime 'updated_at', null: false + t.index %w[searchable_type searchable_id], name: 'index_pg_search_documents_on_searchable_type_and_searchable_id', using: :btree + end + + create_table 'plant_plates', force: :cascade do |t| + t.string 'name', limit: 255 + t.integer 'how_many' + t.datetime 'created_at' + t.datetime 'updated_at' + t.string 'location_in_rack', limit: 255 + t.integer 'lab_rack_id' + t.index ['lab_rack_id'], name: 'index_plant_plates_on_lab_rack_id', using: :btree + end + + create_table 'plant_plates_projects', id: false, force: :cascade do |t| + t.integer 'plant_plate_id', null: false + t.integer 'project_id', null: false + t.index %w[plant_plate_id project_id], name: 'index_plant_plates_projects_on_plant_plate_id_and_project_id', using: :btree + end + + create_table 'primer_pos_on_genomes', force: :cascade do |t| + t.text 'note' + t.integer 'position' + t.datetime 'created_at' + t.datetime 'updated_at' + end + + create_table 'primer_reads', force: :cascade do |t| + t.string 'name', limit: 255 + t.text 'sequence' + t.string 'pherogram_url', limit: 255 + t.datetime 'created_at' + t.datetime 'updated_at' + t.string 'chromatogram_file_name', limit: 255 + t.string 'chromatogram_content_type', limit: 255 + t.integer 'chromatogram_file_size' + t.datetime 'chromatogram_updated_at' + t.integer 'primer_id' + t.integer 'isolate_id' + t.integer 'contig_id' + t.integer 'trimmedReadEnd' + t.integer 'trimmedReadStart' + t.integer 'qualities', array: true + t.boolean 'reverse' + t.text 'aligned_seq' + t.boolean 'used_for_con' + t.text 'quality_string' + t.integer 'position' + t.boolean 'assembled' + t.integer 'partial_con_id' + t.integer 'aligned_qualities', array: true + t.integer 'window_size', default: 10 + t.integer 'count_in_window', default: 8 + t.integer 'min_quality_score', default: 30 + t.integer 'atrace', array: true + t.integer 'ctrace', array: true + t.integer 'gtrace', array: true + t.integer 'ttrace', array: true + t.integer 'peak_indices', array: true + t.boolean 'processed', default: false + t.integer 'base_count' + t.string 'comment' + t.boolean 'overwritten', default: false + t.integer 'aligned_peak_indices', array: true + t.string 'chromatogram_fingerprint' + end + + create_table 'primer_reads_projects', id: false, force: :cascade do |t| + t.integer 'primer_read_id' + t.integer 'project_id' + end + + create_table 'primers', force: :cascade do |t| + t.string 'name', limit: 255 + t.string 'sequence', limit: 255 + t.boolean 'reverse' + t.datetime 'created_at' + t.datetime 'updated_at' + t.text 'notes' + t.integer 'marker_id' + t.string 'labcode', limit: 255 + t.string 'author', limit: 255 + t.string 'alt_name', limit: 255 + t.string 'target_group', limit: 255 + t.string 'tm', limit: 255 + t.integer 'position' + end + + create_table 'primers_projects', id: false, force: :cascade do |t| + t.integer 'primer_id', null: false + t.integer 'project_id', null: false + t.index %w[primer_id project_id], name: 'index_primers_projects_on_primer_id_and_project_id', using: :btree + end + + create_table 'projects', force: :cascade do |t| + t.string 'name', limit: 255 + t.text 'description' + t.datetime 'start' + t.datetime 'due' + t.datetime 'created_at' + t.datetime 'updated_at' + end + + create_table 'projects_shelves', id: false, force: :cascade do |t| + t.integer 'project_id', null: false + t.integer 'shelf_id', null: false + t.index %w[project_id shelf_id], name: 'index_projects_shelves_on_project_id_and_shelf_id', using: :btree + end + + create_table 'projects_species', id: false, force: :cascade do |t| + t.integer 'project_id' + t.integer 'species_id' + end + + create_table 'projects_tag_primer_maps', id: false, force: :cascade do |t| + t.integer 'project_id', null: false + t.integer 'tag_primer_map_id', null: false + t.index %w[project_id tag_primer_map_id], name: 'index_projects_tag_primer_maps', using: :btree + end + + create_table 'projects_users', id: false, force: :cascade do |t| + t.integer 'project_id' + t.integer 'user_id' + end + + create_table 'responsibilities', force: :cascade do |t| + t.string 'name' + t.text 'description' + t.datetime 'created_at', null: false + t.datetime 'updated_at', null: false + end + + create_table 'responsibilities_users', id: false, force: :cascade do |t| + t.integer 'responsibility_id', null: false + t.integer 'user_id', null: false + t.index %w[responsibility_id user_id], name: 'index_responsibilities_users_on_responsibility_id_and_user_id', using: :btree + end + + create_table 'shelves', force: :cascade do |t| + t.string 'name', limit: 255 + t.datetime 'created_at' + t.datetime 'updated_at' + t.integer 'freezer_id' + t.index ['freezer_id'], name: 'index_shelves_on_freezer_id', using: :btree + end + + create_table 'species', force: :cascade do |t| + t.string 'author', limit: 255 + t.string 'genus_name', limit: 255 + t.string 'species_epithet', limit: 255 + t.datetime 'created_at' + t.datetime 'updated_at' + t.integer 'family_id' + t.string 'infraspecific', limit: 255 + t.text 'comment' + t.string 'german_name', limit: 255 + t.string 'author_infra', limit: 255 + t.string 'synonym', limit: 255 + t.string 'composed_name', limit: 255 + t.string 'species_component' + end + + create_table 'species_exporters', force: :cascade do |t| + t.datetime 'created_at', null: false + t.datetime 'updated_at', null: false + t.string 'species_export_file_name' + t.string 'species_export_content_type' + t.integer 'species_export_file_size' + t.datetime 'species_export_updated_at' + end + + create_table 'specimen_exporters', force: :cascade do |t| + t.string 'specimen_export_file_name' + t.string 'specimen_export_content_type' + t.integer 'specimen_export_file_size' + t.datetime 'specimen_export_updated_at' + t.datetime 'created_at' + t.datetime 'updated_at' + end + + create_table 'subdivisions', force: :cascade do |t| + t.string 'name' + t.datetime 'created_at', null: false + t.datetime 'updated_at', null: false + t.integer 'position' + t.string 'german_name' + end + + create_table 'tag_primer_maps', force: :cascade do |t| + t.datetime 'created_at', null: false + t.datetime 'updated_at', null: false + t.integer 'ngs_run_id' + t.string 'tag_primer_map_file_name' + t.string 'tag_primer_map_content_type' + t.integer 'tag_primer_map_file_size' + t.datetime 'tag_primer_map_updated_at' + t.string 'name' + t.string 'tag' + t.index ['ngs_run_id'], name: 'index_tag_primer_maps_on_ngs_run_id', using: :btree + end + + create_table 'taxonomic_classes', force: :cascade do |t| + t.string 'name' + t.datetime 'created_at', null: false + t.datetime 'updated_at', null: false + t.integer 'subdivision_id' + t.string 'german_name' + end + + create_table 'tissues', force: :cascade do |t| + t.string 'name', limit: 255 + t.datetime 'created_at' + t.datetime 'updated_at' + end + + create_table 'txt_uploaders', force: :cascade do |t| + t.datetime 'created_at', null: false + t.datetime 'updated_at', null: false + t.string 'uploaded_file_file_name' + t.string 'uploaded_file_content_type' + t.integer 'uploaded_file_file_size' + t.datetime 'uploaded_file_updated_at' + end + + create_table 'users', force: :cascade do |t| + t.string 'email', limit: 255, default: '', null: false + t.string 'encrypted_password', limit: 255, default: '', null: false + t.string 'reset_password_token', limit: 255 + t.datetime 'reset_password_sent_at' + t.datetime 'remember_created_at' + t.integer 'sign_in_count', default: 0, null: false + t.datetime 'current_sign_in_at' + t.datetime 'last_sign_in_at' + t.string 'current_sign_in_ip', limit: 255 + t.string 'last_sign_in_ip', limit: 255 + t.datetime 'created_at' + t.datetime 'updated_at' + t.string 'name', limit: 255 + t.integer 'lab_id' + t.integer 'role' + t.integer 'default_project_id' + t.index ['email'], name: 'index_users_on_email', unique: true, using: :btree + t.index ['reset_password_token'], name: 'index_users_on_reset_password_token', unique: true, using: :btree + end + + add_foreign_key 'contig_searches', 'projects' + add_foreign_key 'individual_searches', 'projects' + add_foreign_key 'individual_searches', 'users' + add_foreign_key 'marker_sequence_searches', 'projects' + add_foreign_key 'mislabel_analyses', 'markers' + add_foreign_key 'mislabels', 'marker_sequences' + add_foreign_key 'ngs_runs', 'higher_order_taxa' + add_foreign_key 'plant_plates', 'lab_racks' + add_foreign_key 'shelves', 'freezers' end diff --git a/db/seeds.rb b/db/seeds.rb index 997068dd..86dc8249 100644 --- a/db/seeds.rb +++ b/db/seeds.rb @@ -1,3 +1,5 @@ +# frozen_string_literal: true + # This file should contain all the record creation needed to seed the database with its default values. # The data can then be loaded with the rake db:seed (or created alongside the db with db:setup). # diff --git a/lib/tasks/add_projects.rake b/lib/tasks/add_projects.rake index e27741bf..27bc679c 100644 --- a/lib/tasks/add_projects.rake +++ b/lib/tasks/add_projects.rake @@ -1,6 +1,8 @@ +# frozen_string_literal: true + namespace :data do desc 'Add general project to all records.' - task :add_general_project => :environment do + task add_general_project: :environment do project = Project.find_or_create_by(name: 'All Records') add_to_join_table(project, Individual.all.select(:id).find_each) @@ -26,9 +28,9 @@ namespace :data do end desc 'Add GBOL5 project to all eligible records.' - task :add_gbol5_project => :environment do + task add_gbol5_project: :environment do project = Project.find_or_create_by(name: 'GBOL5') - gbol_labs = %w(BGBM IEB NEES ZFMK Gießen) + gbol_labs = %w[BGBM IEB NEES ZFMK Gießen] Shelf.update_all(freezer_id: Freezer.first.id) @@ -42,11 +44,11 @@ namespace :data do add_to_join_table(project, User.joins(:lab).merge(Lab.in_project(project.id)).select(:id)) add_to_join_table(project, Marker.where(is_gbol: true).select(:id)) add_to_join_table(project, Primer.joins(:marker).merge(Marker.in_project(project.id)).select(:id)) - add_to_join_table(project, Isolate.where("lab_nr ilike ?", "gbol%").or(Isolate.where("lab_nr ilike ?", "db%")).select(:id).find_each) - add_to_join_table(project, Contig.where("name ilike ?", "gbol%").or(Contig.where("name ilike ?", "db%")).select(:id).find_each) + add_to_join_table(project, Isolate.where('lab_nr ilike ?', 'gbol%').or(Isolate.where('lab_nr ilike ?', 'db%')).select(:id).find_each) + add_to_join_table(project, Contig.where('name ilike ?', 'gbol%').or(Contig.where('name ilike ?', 'db%')).select(:id).find_each) add_to_join_table(project, PrimerRead.joins(:contig).merge(Contig.in_project(project.id).select(:id)).select(:id).find_each) add_to_join_table(project, Issue.joins(:primer_read).merge(PrimerRead.in_project(project.id)).select(:id) + Issue.joins(:contig).merge(Contig.in_project(project.id)).select(:id)) - add_to_join_table(project, MarkerSequence.where("name ilike ?", "gbol%").or(MarkerSequence.where("name ilike ?", "db%")).select(:id)) + add_to_join_table(project, MarkerSequence.where('name ilike ?', 'gbol%').or(MarkerSequence.where('name ilike ?', 'db%')).select(:id)) add_to_join_table(project, Individual.joins(:isolates).merge(Isolate.in_project(project.id)).select(:id).find_each) add_to_join_table(project, Species.all.select(:id).find_each) @@ -56,7 +58,7 @@ namespace :data do end desc 'Add transects project to all eligible records.' - task :add_transects_project => :environment do + task add_transects_project: :environment do project = Project.find_or_create_by(name: '3transects') users = ['Kai Müller', 'Dietmar Quandt', 'Sarah Wiechers'] @@ -76,11 +78,11 @@ namespace :data do add_to_join_table(project, PlantPlate.all.select(:id)) add_to_join_table(project, Marker.all.select(:id)) add_to_join_table(project, Primer.joins(:marker).merge(Marker.in_project(project.id)).select(:id)) - add_to_join_table(project, Isolate.where("lab_nr like ?", "F%").or(Isolate.where("lab_nr like ?", "B%")).select(:id).find_each) - add_to_join_table(project, Contig.where("name like ?", "F%").or(Contig.where("name like ?", "B%")).select(:id).find_each) + add_to_join_table(project, Isolate.where('lab_nr like ?', 'F%').or(Isolate.where('lab_nr like ?', 'B%')).select(:id).find_each) + add_to_join_table(project, Contig.where('name like ?', 'F%').or(Contig.where('name like ?', 'B%')).select(:id).find_each) add_to_join_table(project, PrimerRead.joins(:contig).merge(Contig.in_project(project.id).select(:id)).select(:id).find_each) add_to_join_table(project, Issue.joins(:primer_read).merge(PrimerRead.in_project(project.id)).select(:id) + Issue.joins(:contig).merge(Contig.in_project(project.id)).select(:id)) - add_to_join_table(project, MarkerSequence.where("name like ?", "F%").or(MarkerSequence.where("name like ?", "B%")).select(:id)) + add_to_join_table(project, MarkerSequence.where('name like ?', 'F%').or(MarkerSequence.where('name like ?', 'B%')).select(:id)) end private @@ -91,11 +93,11 @@ namespace :data do if record_class.name.casecmp(Project.name) == -1 # Record name comes first alphabetically table_name = pluralized_name(record_class) + '_' + pluralized_name(Project) values = records.map { |record| "(#{record.id},#{project.id})" }.join(',') - ActiveRecord::Base.connection.execute("INSERT INTO #{table_name} (#{id_string(record_class)}, #{id_string(Project)}) VALUES #{values}") if !values.blank? + ActiveRecord::Base.connection.execute("INSERT INTO #{table_name} (#{id_string(record_class)}, #{id_string(Project)}) VALUES #{values}") unless values.blank? else table_name = pluralized_name(Project) + '_' + pluralized_name(record_class) values = records.map { |record| "(#{project.id},#{record.id})" }.join(',') - ActiveRecord::Base.connection.execute("INSERT INTO #{table_name} (#{id_string(Project)}, #{id_string(record_class)}) VALUES #{values}") if !values.blank? + ActiveRecord::Base.connection.execute("INSERT INTO #{table_name} (#{id_string(Project)}, #{id_string(record_class)}) VALUES #{values}") unless values.blank? end end diff --git a/lib/tasks/base_counts.rake b/lib/tasks/base_counts.rake index d2a0a4a7..89af34a1 100644 --- a/lib/tasks/base_counts.rake +++ b/lib/tasks/base_counts.rake @@ -1,18 +1,17 @@ +# frozen_string_literal: true + namespace :data do desc "fill reads' basecount" - task :base_counts => :environment do - - PrimerRead.where(:base_count => nil).find_each(batch_size: 100) do |p| + task base_counts: :environment do + PrimerRead.where(base_count: nil).find_each(batch_size: 100) do |p| if p.sequence - p.base_count= p.sequence.length + p.base_count = p.sequence.length p.save! puts p.name end end - puts "Done." - + puts 'Done.' end - -end \ No newline at end of file +end diff --git a/lib/tasks/check_consensus_sequences.rake b/lib/tasks/check_consensus_sequences.rake index 4f21548b..c254ea5c 100644 --- a/lib/tasks/check_consensus_sequences.rake +++ b/lib/tasks/check_consensus_sequences.rake @@ -1,7 +1,8 @@ -namespace :data do +# frozen_string_literal: true +namespace :data do desc 'Compare contig consensus sequences and resulting marker sequences. Alert if different.' - task :check_consensus_sequences => :environment do + task check_consensus_sequences: :environment do puts 'Checking contig consensus sequences...' contigs = Contig.gbol.includes(:marker_sequence, :partial_cons).where.not(marker_sequence: nil).select(:id, :name, :marker_sequence_id) @@ -20,11 +21,9 @@ namespace :data do no_sequence << contig.name else # Marker sequences are created from modified aligned_sequence of first partial con after verification - partial_sequence = partial_sequence.gsub('?', '').gsub('-', '') + partial_sequence = partial_sequence.delete('?').delete('-') - if marker_sequence != partial_sequence - alert << contig.name - end + alert << contig.name if marker_sequence != partial_sequence end end end @@ -36,4 +35,4 @@ namespace :data do puts "#{ms_blank.size} contigs had no marker sequence." end -end \ No newline at end of file +end diff --git a/lib/tasks/check_faulty_isolates.rake b/lib/tasks/check_faulty_isolates.rake index 263b4369..5c206db7 100644 --- a/lib/tasks/check_faulty_isolates.rake +++ b/lib/tasks/check_faulty_isolates.rake @@ -1,7 +1,8 @@ -namespace :data do +# frozen_string_literal: true +namespace :data do desc 'Check if faulty isolates in db have primer reads associated' - task :check_faulty_isolates => :environment do + task check_faulty_isolates: :environment do puts 'Starting check for faulty isolates and plates...' plate_names = [*49..51] @@ -9,7 +10,7 @@ namespace :data do plates_count = 0 - plate_names.each do | name | + plate_names.each do |name| plates_count += 1 if PlantPlate.find_by_name(name.to_s) end @@ -29,15 +30,15 @@ namespace :data do present = [] - gbol_numbers.each do | name | - gbol_name = "gbol#{name.to_s}" + gbol_numbers.each do |name| + gbol_name = "gbol#{name}" - isolate = Isolate.where("lab_nr ilike ?", gbol_name).first + isolate = Isolate.where('lab_nr ilike ?', gbol_name).first isolates.add? isolate if isolate present << name if isolate - isolate&.contigs&.each do | contig | + isolate&.contigs&.each do |contig| contigs_cnt += 1 primer_reads.add? isolate if contig&.primer_reads&.size&.nonzero? end @@ -56,9 +57,9 @@ namespace :data do puts 'The same amount of isolates, contigs and marker sequences was found as expected.' end - if primer_reads.size > 0 + unless primer_reads.empty? puts "#{primer_reads.size} isolates with associated primer reads were found:" - primer_reads.each {|isolate| print "#{isolate.lab_nr}, " } + primer_reads.each { |isolate| print "#{isolate.lab_nr}, " } puts "\n\n" end @@ -66,22 +67,22 @@ namespace :data do end desc 'Delete incorrect isolate metadata' - task :delete_incorrect_isolate_metadata => :environment do + task delete_incorrect_isolate_metadata: :environment do 'Starting deletion of incorrect metadata...' # Delete incorrect specimen associations of isolates gbol_numbers = [*4609..4896] gbol_numbers.concat [*5665..7008] - gbol_numbers.each do | name | - gbol_name = "GBoL#{name.to_s}" - isolate = Isolate.where("lab_nr ilike ?", gbol_name) + gbol_numbers.each do |name| + gbol_name = "GBoL#{name}" + isolate = Isolate.where('lab_nr ilike ?', gbol_name) if isolate.size > 1 puts "More than one isolate with the name #{gbol_name} was found." else isolate = isolate.first - isolate&.update(:individual_id => nil) + isolate&.update(individual_id: nil) end end diff --git a/lib/tasks/create_analysis_files.rake b/lib/tasks/create_analysis_files.rake index 5dde5d85..0637ff70 100644 --- a/lib/tasks/create_analysis_files.rake +++ b/lib/tasks/create_analysis_files.rake @@ -1,11 +1,13 @@ +# frozen_string_literal: true + namespace :data do desc 'Create fasta and taxon file from marker sequence search for further analyses.' task :create_analysis_files, [:title] => [:environment] do |_, args| length_minima = { - 'ITS' => 485, - 'rpl16' => 580, - 'trnLF' => 516, - 'trnK-matK' => 1188 + 'ITS' => 485, + 'rpl16' => 580, + 'trnLF' => 516, + 'trnK-matK' => 1188 } title = args[:title] @@ -30,4 +32,4 @@ namespace :data do f.write(search.taxon_file(false)) end end -end \ No newline at end of file +end diff --git a/lib/tasks/create_xls.rake b/lib/tasks/create_xls.rake index ffcf5fc6..c5776b72 100644 --- a/lib/tasks/create_xls.rake +++ b/lib/tasks/create_xls.rake @@ -1,8 +1,8 @@ -namespace :data do +# frozen_string_literal: true +namespace :data do desc 'export specimen info to ZFMK readable xls format' - task :create_xls => :environment do - SpecimenExport.perform_async(Project.where('name ilike ?', "%gbol%").first.id) + task create_xls: :environment do + SpecimenExport.perform_async(Project.where('name ilike ?', '%gbol%').first.id) end - -end \ No newline at end of file +end diff --git a/lib/tasks/cucumber.rake b/lib/tasks/cucumber.rake index 9f53ce49..a4768efd 100644 --- a/lib/tasks/cucumber.rake +++ b/lib/tasks/cucumber.rake @@ -1,65 +1,66 @@ +# frozen_string_literal: true + # IMPORTANT: This file is generated by cucumber-rails - edit at your own peril. # It is recommended to regenerate this file in the future when you upgrade to a # newer version of cucumber-rails. Consider adding your own code to a new file # instead of editing this one. Cucumber will automatically load all features/**/*.rb # files. +unless ARGV.any? { |a| a =~ /^gems/ } # Don't load anything when running the gems:* tasks -unless ARGV.any? {|a| a =~ /^gems/} # Don't load anything when running the gems:* tasks - -vendored_cucumber_bin = Dir["#{Rails.root}/vendor/{gems,plugins}/cucumber*/bin/cucumber"].first -$LOAD_PATH.unshift(File.dirname(vendored_cucumber_bin) + '/../lib') unless vendored_cucumber_bin.nil? + vendored_cucumber_bin = Dir["#{Rails.root}/vendor/{gems,plugins}/cucumber*/bin/cucumber"].first + $LOAD_PATH.unshift(File.dirname(vendored_cucumber_bin) + '/../lib') unless vendored_cucumber_bin.nil? -begin - require 'cucumber/rake/task' + begin + require 'cucumber/rake/task' - namespace :cucumber do - Cucumber::Rake::Task.new({:ok => 'test:prepare'}, 'Run features that should pass') do |t| - t.binary = vendored_cucumber_bin # If nil, the gem's binary is used. - t.fork = true # You may get faster startup if you set this to false - t.profile = 'default' - end + namespace :cucumber do + Cucumber::Rake::Task.new({ ok: 'test:prepare' }, 'Run features that should pass') do |t| + t.binary = vendored_cucumber_bin # If nil, the gem's binary is used. + t.fork = true # You may get faster startup if you set this to false + t.profile = 'default' + end - Cucumber::Rake::Task.new({:wip => 'test:prepare'}, 'Run features that are being worked on') do |t| - t.binary = vendored_cucumber_bin - t.fork = true # You may get faster startup if you set this to false - t.profile = 'wip' - end + Cucumber::Rake::Task.new({ wip: 'test:prepare' }, 'Run features that are being worked on') do |t| + t.binary = vendored_cucumber_bin + t.fork = true # You may get faster startup if you set this to false + t.profile = 'wip' + end - Cucumber::Rake::Task.new({:rerun => 'test:prepare'}, 'Record failing features and run only them if any exist') do |t| - t.binary = vendored_cucumber_bin - t.fork = true # You may get faster startup if you set this to false - t.profile = 'rerun' - end + Cucumber::Rake::Task.new({ rerun: 'test:prepare' }, 'Record failing features and run only them if any exist') do |t| + t.binary = vendored_cucumber_bin + t.fork = true # You may get faster startup if you set this to false + t.profile = 'rerun' + end - desc 'Run all features' - task :all => [:ok, :wip] + desc 'Run all features' + task all: %i[ok wip] - task :statsetup do - require 'rails/code_statistics' - ::STATS_DIRECTORIES << %w(Cucumber\ features features) if File.exist?('features') - ::CodeStatistics::TEST_TYPES << "Cucumber features" if File.exist?('features') + task :statsetup do + require 'rails/code_statistics' + ::STATS_DIRECTORIES << %w[Cucumber\ features features] if File.exist?('features') + ::CodeStatistics::TEST_TYPES << 'Cucumber features' if File.exist?('features') + end end - end - desc 'Alias for cucumber:ok' - task :cucumber => 'cucumber:ok' + desc 'Alias for cucumber:ok' + task cucumber: 'cucumber:ok' - task :default => :cucumber + task default: :cucumber - task :features => :cucumber do - STDERR.puts "*** The 'features' task is deprecated. See rake -T cucumber ***" - end + task features: :cucumber do + STDERR.puts "*** The 'features' task is deprecated. See rake -T cucumber ***" + end - # In case we don't have the generic Rails test:prepare hook, append a no-op task that we can depend upon. - task 'test:prepare' do - end + # In case we don't have the generic Rails test:prepare hook, append a no-op task that we can depend upon. + task 'test:prepare' do + end - task :stats => 'cucumber:statsetup' -rescue LoadError - desc 'cucumber rake task not available (cucumber not installed)' - task :cucumber do - abort 'Cucumber rake task is not available. Be sure to install cucumber as a gem or plugin' + task stats: 'cucumber:statsetup' + rescue LoadError + desc 'cucumber rake task not available (cucumber not installed)' + task :cucumber do + abort 'Cucumber rake task is not available. Be sure to install cucumber as a gem or plugin' + end end -end end diff --git a/lib/tasks/database_operations.rake b/lib/tasks/database_operations.rake index f50085d0..19d0c4d4 100644 --- a/lib/tasks/database_operations.rake +++ b/lib/tasks/database_operations.rake @@ -1,3 +1,5 @@ +# frozen_string_literal: true + require 'net/http' require 'nokogiri' @@ -7,70 +9,68 @@ def get_state(i) matches = i.locality.match(regex) if matches state_component = matches[1] - i.update(:state_province => state_component) + i.update(state_province: state_component) end end end namespace :data do - - desc "Change precision of existing specimen location data records" - task :change_location_data_precision => :environment do + desc 'Change precision of existing specimen location data records' + task change_location_data_precision: :environment do cnt = 0 - puts "Changing location data precision..." + puts 'Changing location data precision...' - Individual.find_each(:batch_size => 50) do |individual| - individual.update(:latitude => individual.latitude&.round(6)) - individual.update(:longitude => individual.longitude&.round(6)) + Individual.find_each(batch_size: 50) do |individual| + individual.update(latitude: individual.latitude&.round(6)) + individual.update(longitude: individual.longitude&.round(6)) cnt += 1 end puts "Done. Changed location data precision for #{cnt} records." end - desc "Create users" - task :create_users => :environment do - @user = User.new(:name => 'Tim Boehnert', :email => 'tim.boehnert@uni-bonn.de', :password => 'HMeWE98qRp3f', :password_confirmation => 'HMeWE98qRp3f') + desc 'Create users' + task create_users: :environment do + @user = User.new(name: 'Tim Boehnert', email: 'tim.boehnert@uni-bonn.de', password: 'HMeWE98qRp3f', password_confirmation: 'HMeWE98qRp3f') @user.save - @user2 = User.new(:name => 'Saskia Schlesak', :email => 'saskia.schlesak@googlemail.com', :password => 'tJ6knF6q3DZX', :password_confirmation => 'tJ6knF6q3DZX') + @user2 = User.new(name: 'Saskia Schlesak', email: 'saskia.schlesak@googlemail.com', password: 'tJ6knF6q3DZX', password_confirmation: 'tJ6knF6q3DZX') @user2.save - @user3 = User.new(:name => 'Gabriele Droege', :email => 'G.Droege@bgbm.org', :password => 'T3HqXUd4zVA2', :password_confirmation => 'T3HqXUd4zVA2') + @user3 = User.new(name: 'Gabriele Droege', email: 'G.Droege@bgbm.org', password: 'T3HqXUd4zVA2', password_confirmation: 'T3HqXUd4zVA2') @user3.save - puts "Done." + puts 'Done.' end - desc "destroy duplicate reads from non-verified contigs" - task :destroy_duplicate_reads => :environment do + desc 'destroy duplicate reads from non-verified contigs' + task destroy_duplicate_reads: :environment do # get list w duplicate reads FROM NON-VERIFIED CONTIGS ONLY a = [] - PrimerRead.select("name").contig_not_verified.each do |i| + PrimerRead.select('name').contig_not_verified.each do |i| a << i.name end - d = a.select{ |e| a.count(e) > 1 }.uniq + d = a.select { |e| a.count(e) > 1 }.uniq # Iterate over duplicate read names: d.each do |duplicate| # Get all members of given duplicate list: # IGNORE THOSE FROM VERIFIED CONTIGS IN THIS DUPLICATE LIST - dups = PrimerRead.contig_not_verified.where(:name => duplicate) + dups = PrimerRead.contig_not_verified.where(name: duplicate) # Get first - first_dup=dups.first + first_dup = dups.first # puts "will keep #{first_dup.name} (#{first_dup.id})" # Get all others - #TODO: scary loop in which arr.elements are deleted (?) - fix! + # TODO: scary loop in which arr.elements are deleted (?) - fix! - (1..dups.count-1).each do |i| - - curr_dup= dups[i] + (1..dups.count - 1).each do |i| + curr_dup = dups[i] # puts "will destroy #{curr_dup.name} (#{curr_dup.id})" @@ -83,55 +83,50 @@ namespace :data do puts 'Done.' end - desc "fix empty state-province from DNABank- import" - task :fix_state_province => :environment do - Individual.where(:state_province => nil).each do |i| + desc 'fix empty state-province from DNABank- import' + task fix_state_province: :environment do + Individual.where(state_province: nil).each do |i| get_state(i) end - Individual.where(:state_province => "").each do |i| + Individual.where(state_province: '').each do |i| get_state(i) end end - #TODO: scary loop in which arr.elements are deleted - fix! + # TODO: scary loop in which arr.elements are deleted - fix! - desc "Merge multiple copies of same contigs into one with all associations & attributes" - task :merge_duplicate_contigs => :environment do + desc 'Merge multiple copies of same contigs into one with all associations & attributes' + task merge_duplicate_contigs: :environment do # get list w duplicates - a=[] - Contig.select("name").each do |i| + a = [] + Contig.select('name').each do |i| a << i.name end - d = a.select{ |e| a.count(e) > 1 }.uniq + d = a.select { |e| a.count(e) > 1 }.uniq # iterate over duplicate lab_nrs: d.each do |duplicate| - - #get all members of given duplicate list: - dups=Contig.where(:name => duplicate).where(:verified_by => nil) + # get all members of given duplicate list: + dups = Contig.where(name: duplicate).where(verified_by: nil) if dups.count > 1 - #get first - first_dup=dups.first + # get first + first_dup = dups.first - #get all others and compare to first - (1..dups.count-1).each do |i| - curr_dup= dups[i] + # get all others and compare to first + (1..dups.count - 1).each do |i| + curr_dup = dups[i] puts "#{curr_dup.name} (#{curr_dup.id}) vs #{first_dup.name} ( #{first_dup.id} ):" - if curr_dup.isolate - first_dup.update(:isolate => curr_dup.isolate) - end + first_dup.update(isolate: curr_dup.isolate) if curr_dup.isolate - if curr_dup.marker - first_dup.update(:marker => curr_dup.marker) - end + first_dup.update(marker: curr_dup.marker) if curr_dup.marker if curr_dup.marker_sequence - first_dup.update(:marker_sequence => curr_dup.marker_sequence) + first_dup.update(marker_sequence: curr_dup.marker_sequence) end if curr_dup.partial_cons.count > 0 @@ -140,53 +135,46 @@ namespace :data do end end - if curr_dup.primer_reads.count >0 + if curr_dup.primer_reads.count > 0 curr_dup.primer_reads.each do |c| first_dup.primer_reads << c end end curr_dup.destroy - end end - puts "" + puts '' end - puts "Done." - + puts 'Done.' end - #TODO: scary loop in which arr.elements are deleted - fix! - desc "Merge multiple copies of same isolate into one with all associations & attributes" - task :merge_duplicate_isolates => :environment do - + # TODO: scary loop in which arr.elements are deleted - fix! + desc 'Merge multiple copies of same isolate into one with all associations & attributes' + task merge_duplicate_isolates: :environment do # get list w duplicates - a=[] - Isolate.select("lab_nr").all.each do |i| + a = [] + Isolate.select('lab_nr').all.each do |i| a << i.lab_nr end - d=a.select{ |e| a.count(e) > 1 }.uniq - + d = a.select { |e| a.count(e) > 1 }.uniq # iterate over duplicate lab_nrs: d.each do |duplicate_isolate| + # get all members of given duplicate list: + dups = Isolate.includes(individual: :species).where(lab_nr: duplicate_isolate) - #get all members of given duplicate list: - dups=Isolate.includes(:individual => :species).where(:lab_nr => duplicate_isolate) - - #get first - first_dup=dups.first + # get first + first_dup = dups.first - #get all others and compare to first - (1..dups.count-1).each do |i| - curr_dup= dups[i] + # get all others and compare to first + (1..dups.count - 1).each do |i| + curr_dup = dups[i] puts "#{curr_dup.lab_nr} (#{curr_dup.id}) vs #{first_dup.lab_nr} ( #{first_dup.id} ):" - if curr_dup.individual - first_dup.update(:individual => curr_dup.individual) - end + first_dup.update(individual: curr_dup.individual) if curr_dup.individual if curr_dup.marker_sequences.count > 0 curr_dup.marker_sequences.each do |m| @@ -194,43 +182,40 @@ namespace :data do end end - if curr_dup.contigs.count >0 + if curr_dup.contigs.count > 0 curr_dup.contigs.each do |c| first_dup.contigs << c end end curr_dup.destroy - end - puts "" + puts '' end - puts "Done." - + puts 'Done.' end desc 'Remove duplicate reads not associated with a contig' - task :remove_duplicate_reads_without_contig => :environment do + task remove_duplicate_reads_without_contig: :environment do puts 'Deleting duplicate primer reads not associated with a contig if one of the pair/group is associated with a contig...' - names_with_multiple = PrimerRead.select(:name).group(:name).having("count(name) > 1").count.keys + names_with_multiple = PrimerRead.select(:name).group(:name).having('count(name) > 1').count.keys primer_reads_cnt = PrimerRead.where(name: names_with_multiple).count delete_cnt = 0 puts "#{primer_reads_cnt} duplicate reads were found." - names_with_multiple.each do | read_name | - duplicates = PrimerRead.where(:name => read_name) + names_with_multiple.each do |read_name| + duplicates = PrimerRead.where(name: read_name) reads_wo_contig = [] - duplicates.each {|d| reads_wo_contig << d if !d.contig } + duplicates.each { |d| reads_wo_contig << d unless d.contig } - if duplicates.size > reads_wo_contig.size && !reads_wo_contig.empty? - reads_wo_contig.each do |read| - delete_cnt += 1 - read.destroy! - end + next unless duplicates.size > reads_wo_contig.size && !reads_wo_contig.empty? + reads_wo_contig.each do |read| + delete_cnt += 1 + read.destroy! end end @@ -238,24 +223,23 @@ namespace :data do end desc 'Remove older ones of a group of duplicate reads' - task :delete_older_duplicate_reads => :environment do + task delete_older_duplicate_reads: :environment do puts 'Deleting the older primer reads of a group of duplicates...' - names_with_multiple = PrimerRead.select(:name).group(:name).having("count(name) > 1").count.keys + names_with_multiple = PrimerRead.select(:name).group(:name).having('count(name) > 1').count.keys primer_reads_cnt = PrimerRead.where(name: names_with_multiple).count delete_cnt = 0 puts "#{primer_reads_cnt} duplicate reads were found." - names_with_multiple.each do | read_name | - if read_name.match('\AF') # Only treat reads starting with an 'F' - duplicates = PrimerRead.where(:name => read_name).order(created_at: :desc) + names_with_multiple.each do |read_name| + next unless read_name.match('\AF') # Only treat reads starting with an 'F' + duplicates = PrimerRead.where(name: read_name).order(created_at: :desc) - # Delete all older reads, keep only newest one - duplicates[1..-1].each do |r| - r.destroy! - delete_cnt += 1 - end + # Delete all older reads, keep only newest one + duplicates[1..-1].each do |r| + r.destroy! + delete_cnt += 1 end end @@ -263,7 +247,7 @@ namespace :data do end desc 'Migrate responsibilities from project to new model responsibilities' - task :migrate_responsibilities => :environment do + task migrate_responsibilities: :environment do Project.all.each do |project| # Create new responsibilities from old project records responsibility = Responsibility.new(name: project.name, description: project.description) @@ -277,7 +261,7 @@ namespace :data do end desc 'Set user roles with new enum attribute' - task :set_user_roles => :environment do + task set_user_roles: :environment do User.update_all(role: 'user') User.find_by_name('Sarah Wiechers').update(role: 'admin') @@ -291,28 +275,27 @@ namespace :data do end desc 'Remove duplicate marker sequences not associated with a contig' - task :remove_duplicate_sequences_without_contig => :environment do + task remove_duplicate_sequences_without_contig: :environment do puts 'Deleting duplicate marker sequences not associated with a contig if one of the pair/group is associated with a contig...' - names_with_multiple = MarkerSequence.select(:name).group(:name).having("count(name) > 1").count.keys + names_with_multiple = MarkerSequence.select(:name).group(:name).having('count(name) > 1').count.keys sequences_count = MarkerSequence.where(name: names_with_multiple).count delete_cnt = 0 puts "#{sequences_count} duplicate sequences were found." names_with_multiple.each do |sequence_name| - duplicates = MarkerSequence.where(:name => sequence_name) + duplicates = MarkerSequence.where(name: sequence_name) sequences_without_contig = [] - duplicates.each { |d| sequences_without_contig << d if d.contigs.size == 0 } + duplicates.each { |d| sequences_without_contig << d if d.contigs.empty? } - if duplicates.size > sequences_without_contig.size && !sequences_without_contig.empty? - sequences_without_contig.each do |sequence| - delete_cnt += 1 - sequence.destroy! - end + next unless duplicates.size > sequences_without_contig.size && !sequences_without_contig.empty? + sequences_without_contig.each do |sequence| + delete_cnt += 1 + sequence.destroy! end end puts "#{delete_cnt} duplicate sequences could be deleted." end -end \ No newline at end of file +end diff --git a/lib/tasks/dna_bank.rake b/lib/tasks/dna_bank.rake index ed80e421..217e83be 100644 --- a/lib/tasks/dna_bank.rake +++ b/lib/tasks/dna_bank.rake @@ -1,18 +1,17 @@ +# frozen_string_literal: true + require 'net/http' require 'nokogiri' namespace :data do - desc 'Get specimen info from DNA-Bank' - task :fetch_DNABank_info => :environment do - #Asterales - list_with_UnitIDs="DB 10140".split("\n") + task fetch_DNABank_info: :environment do + # Asterales + list_with_UnitIDs = 'DB 10140'.split("\n") counter = 1 list_with_UnitIDs.each do |unit_id| - if counter > 1 - break - end + break if counter > 1 service_url = "http://ww3.bgbm.org/biocase/pywrapper.cgi?dsa=DNA_Bank&query=
search
http://www.tdwg.org/schemas/abcd/2.1http://www.tdwg.org/schemas/abcd/2.1#{unit_id}false" @@ -45,14 +44,12 @@ namespace :data do puts specimen_id - if full_name - puts full_name - end + puts full_name if full_name - # todo: altervative base on gbol_nr that now also gets stored in DNA Bank + # TODO: altervative base on gbol_nr that now also gets stored in DNA Bank puts "------------------\n" - rescue + rescue StandardError end counter += 1 @@ -62,69 +59,67 @@ namespace :data do end # not to be used for regular background processes; only for manually crafted queries where DNA-Bank number known and a specific range of DNA-Bank numbers manually entered below: - desc "Get range of DNA-Bank numbers related to GBOL and extract all specimen info and associated isolates (GBOL-Nrs.)" - task :get_all_DNABank => :environment do - - (10000..12350).each do |unit_id| - - service_url="http://ww3.bgbm.org/biocase/pywrapper.cgi?dsa=DNA_Bank&query=
search
http://www.tdwg.org/schemas/abcd/2.1http://www.tdwg.org/schemas/abcd/2.1DB #{unit_id}false" + desc 'Get range of DNA-Bank numbers related to GBOL and extract all specimen info and associated isolates (GBOL-Nrs.)' + task get_all_DNABank: :environment do + (10_000..12_350).each do |unit_id| + service_url = "http://ww3.bgbm.org/biocase/pywrapper.cgi?dsa=DNA_Bank&query=
search
http://www.tdwg.org/schemas/abcd/2.1http://www.tdwg.org/schemas/abcd/2.1DB #{unit_id}false" url = URI.parse(service_url) req = Net::HTTP::Get.new(url.to_s) - res = Net::HTTP.start(url.host, url.port) { |http| + res = Net::HTTP.start(url.host, url.port) do |http| http.request(req) - } + end - doc= Nokogiri::XML(res.body) + doc = Nokogiri::XML(res.body) - full_name=nil - collector=nil - locality=nil - longitude=nil - latitude=nil - specimen_id=nil - herbarium=nil - gbol_nr=nil + full_name = nil + collector = nil + locality = nil + longitude = nil + latitude = nil + specimen_id = nil + herbarium = nil + gbol_nr = nil begin unit = doc.at_xpath('//abcd21:Unit') - specimen_id=unit.at_xpath('//abcd21:UnitAssociation/abcd21:UnitID').content - full_name= unit.at_xpath('//abcd21:FullScientificNameString').content - gbol_nr=unit.at_xpath('//abcd21:sampleDesignation').content - herbarium=unit.at_xpath('//abcd21:SourceInstitutionCode').content - collector= unit.at_xpath('//abcd21:GatheringAgent').content - locality=unit.at_xpath('//abcd21:LocalityText').content - longitude=unit.at_xpath('//abcd21:LongitudeDecimal').content - latitude=unit.at_xpath('//abcd21:LatitudeDecimal').content - rescue + specimen_id = unit.at_xpath('//abcd21:UnitAssociation/abcd21:UnitID').content + full_name = unit.at_xpath('//abcd21:FullScientificNameString').content + gbol_nr = unit.at_xpath('//abcd21:sampleDesignation').content + herbarium = unit.at_xpath('//abcd21:SourceInstitutionCode').content + collector = unit.at_xpath('//abcd21:GatheringAgent').content + locality = unit.at_xpath('//abcd21:LocalityText').content + longitude = unit.at_xpath('//abcd21:LongitudeDecimal').content + latitude = unit.at_xpath('//abcd21:LatitudeDecimal').content + rescue StandardError end puts unit_id puts specimen_id - if specimen_id - individual = Individual.find_or_create_by(:specimen_id => specimen_id) - else - individual = Individual.create(:specimen_id => "") - end + individual = if specimen_id + Individual.find_or_create_by(specimen_id: specimen_id) + else + Individual.create(specimen_id: '') + end - individual.update(:DNA_bank_id => "DB #{unit_id}") unless individual.DNA_bank_id + individual.update(DNA_bank_id: "DB #{unit_id}") unless individual.DNA_bank_id puts collector - individual.update(:collector => collector.strip) if collector + individual.update(collector: collector.strip) if collector puts locality - individual.update(:locality => locality) if locality + individual.update(locality: locality) if locality puts longitude - individual.update(:longitude => longitude) if longitude + individual.update(longitude: longitude) if longitude puts latitude - individual.update(:latitude => latitude) if latiude + individual.update(latitude: latitude) if latiude puts herbarium - individual.update(:herbarium => herbarium) if herbarium + individual.update(herbarium: herbarium) if herbarium if full_name regex = /^(\w+\s+\w+)/ @@ -137,341 +132,287 @@ namespace :data do sp = individual.species if sp.nil? - sp= Species.find_or_create_by(:species_component => species_component) - individual.update(:species=>sp) + sp = Species.find_or_create_by(species_component: species_component) + individual.update(species: sp) end end end - #todo make case insensitive match: - - if gbol_nr - # inconsistent in DNABank: sometimes lowercase, sometimes uppercase o in GBOL: - if gbol_nr[2]=='O' - gbol_nr[2]='o' - end - puts gbol_nr - isolate = Isolate.find_or_create_by(:lab_nr => gbol_nr) - isolate.update(:individual => individual) - end + # TODO: make case insensitive match: + next unless gbol_nr + # inconsistent in DNABank: sometimes lowercase, sometimes uppercase o in GBOL: + gbol_nr[2] = 'o' if gbol_nr[2] == 'O' + puts gbol_nr + isolate = Isolate.find_or_create_by(lab_nr: gbol_nr) + isolate.update(individual: individual) end puts 'Done.' end - desc "Get all GBOL-Nrs that have no specimen assigned and extract all specimen info from DNABank, if corresponding GBOL-Nr exists there." - task :get_DNABank_by_gbol_nr => :environment do - + desc 'Get all GBOL-Nrs that have no specimen assigned and extract all specimen info from DNABank, if corresponding GBOL-Nr exists there.' + task get_DNABank_by_gbol_nr: :environment do # get all gbol-nr where no specimen - Isolate.where(:individual => nil).where('isolates.lab_nr ILIKE ?', "%GBOL%").each do |i| - + Isolate.where(individual: nil).where('isolates.lab_nr ILIKE ?', '%GBOL%').each do |i| # for each number, do a call for GBOL and GBoL versions: - gbol_nr=i.lab_nr + gbol_nr = i.lab_nr - gbol_nr_1=gbol_nr + gbol_nr_1 = gbol_nr - gbol_nrs=[] + gbol_nrs = [] gbol_nrs[0] = gbol_nr_1 - if gbol_nr_1[2]=='O' - gbol_nr_2=gbol_nr_1.clone - gbol_nr_2[2]='o' - gbol_nrs[1]=gbol_nr_2 + if gbol_nr_1[2] == 'O' + gbol_nr_2 = gbol_nr_1.clone + gbol_nr_2[2] = 'o' + gbol_nrs[1] = gbol_nr_2 else - gbol_nr_2=gbol_nr_1.clone - gbol_nr_2[2]='O' - gbol_nrs[1]=gbol_nr_2 + gbol_nr_2 = gbol_nr_1.clone + gbol_nr_2[2] = 'O' + gbol_nrs[1] = gbol_nr_2 end gbol_nrs[1] = gbol_nr_2 gbol_nrs.each do |gbol_nr| - puts "Query for #{gbol_nr}...\n" - service_url="http://ww3.bgbm.org/biocase/pywrapper.cgi?dsa=DNA_Bank&query=
search
http://www.tdwg.org/schemas/abcd/2.1http://www.tdwg.org/schemas/abcd/2.1#{gbol_nr}false" + service_url = "http://ww3.bgbm.org/biocase/pywrapper.cgi?dsa=DNA_Bank&query=
search
http://www.tdwg.org/schemas/abcd/2.1http://www.tdwg.org/schemas/abcd/2.1#{gbol_nr}false" url = URI.parse(service_url) req = Net::HTTP::Get.new(url.to_s) - res = Net::HTTP.start(url.host, url.port) { |http| + res = Net::HTTP.start(url.host, url.port) do |http| http.request(req) - } + end - doc= Nokogiri::XML(res.body) + doc = Nokogiri::XML(res.body) - full_name=nil - collector=nil - locality=nil - longitude=nil - latitude=nil - specimen_id=nil - herbarium=nil + full_name = nil + collector = nil + locality = nil + longitude = nil + latitude = nil + specimen_id = nil + herbarium = nil begin unit = doc.at_xpath('//abcd21:Unit') - unit_id=doc.at_xpath('//abcd21:Unit/abcd21:UnitID').content # = DNA Bank nr - specimen_id=unit.at_xpath('//abcd21:UnitAssociation/abcd21:UnitID').content - full_name= unit.at_xpath('//abcd21:FullScientificNameString').content - herbarium=unit.at_xpath('//abcd21:SourceInstitutionCode').content - collector= unit.at_xpath('//abcd21:GatheringAgent').content - locality=unit.at_xpath('//abcd21:LocalityText').content - longitude=unit.at_xpath('//abcd21:LongitudeDecimal').content - latitude=unit.at_xpath('//abcd21:LatitudeDecimal').content - - rescue - + unit_id = doc.at_xpath('//abcd21:Unit/abcd21:UnitID').content # = DNA Bank nr + specimen_id = unit.at_xpath('//abcd21:UnitAssociation/abcd21:UnitID').content + full_name = unit.at_xpath('//abcd21:FullScientificNameString').content + herbarium = unit.at_xpath('//abcd21:SourceInstitutionCode').content + collector = unit.at_xpath('//abcd21:GatheringAgent').content + locality = unit.at_xpath('//abcd21:LocalityText').content + longitude = unit.at_xpath('//abcd21:LongitudeDecimal').content + latitude = unit.at_xpath('//abcd21:LatitudeDecimal').content + rescue StandardError end - if unit_id - puts unit_id - end + puts unit_id if unit_id - if specimen_id + next unless specimen_id - puts specimen_id + puts specimen_id - individual = Individual.find_or_create_by(:specimen_id => specimen_id) + individual = Individual.find_or_create_by(specimen_id: specimen_id) - if unit_id - puts unit_id - individual.update(:DNA_bank_id => unit_id ) - begin - individual.isolates.each do |iso| - iso.update(:dna_bank_id => unit_id) - end - rescue + if unit_id + puts unit_id + individual.update(DNA_bank_id: unit_id) + begin + individual.isolates.each do |iso| + iso.update(dna_bank_id: unit_id) end + rescue StandardError end + end - puts collector - if collector - individual.update(:collector => collector.strip) - end + puts collector + individual.update(collector: collector.strip) if collector - puts locality - if locality - individual.update(:locality => locality) - end + puts locality + individual.update(locality: locality) if locality - puts longitude - if longitude - individual.update(:longitude => longitude) - end + puts longitude + individual.update(longitude: longitude) if longitude - puts latitude - if latitude - individual.update(:latitude => latitude) - end + puts latitude + individual.update(latitude: latitude) if latitude - puts herbarium - if herbarium - individual.update(:herbarium => herbarium) - end + puts herbarium + individual.update(herbarium: herbarium) if herbarium - if full_name + if full_name - regex = /^(\w+\s+\w+)/ - matches = full_name.match(regex) - if matches - species_component = matches[1] + regex = /^(\w+\s+\w+)/ + matches = full_name.match(regex) + if matches + species_component = matches[1] - puts species_component + puts species_component - sp=individual.species + sp = individual.species - if sp.nil? - sp= Species.find_or_create_by(:species_component => species_component) - individual.update(:species => sp) - end + if sp.nil? + sp = Species.find_or_create_by(species_component: species_component) + individual.update(species: sp) end - end - isolate = Isolate.where(:lab_nr => i.lab_nr).first - - if isolate - isolate.update(:individual => individual) - end + end - break # no need to try alternative "gbol" spelling if already found a match + isolate = Isolate.where(lab_nr: i.lab_nr).first - end + isolate&.update(individual: individual) + break # no need to try alternative "gbol" spelling if already found a match end - end - puts "Done." - + puts 'Done.' end - desc "Get all specimens with as specimen id, try to get an isolate from this specimen with a gbol-nr, and extract all specimen info from DNABank, if corresponding GBOL-Nr exists there." - task :get_DNABank_by_specimen_without_id => :environment do - + desc 'Get all specimens with as specimen id, try to get an isolate from this specimen with a gbol-nr, and extract all specimen info from DNABank, if corresponding GBOL-Nr exists there.' + task get_DNABank_by_specimen_without_id: :environment do # get all gbol-nr where such specimen - Individual.where(:specimen_id => "").each do |individual| - + Individual.where(specimen_id: '').each do |individual| # for each number, do a call for GBOL and GBoL versions: begin - gbol_nr=individual.isolates.first.lab_nr + gbol_nr = individual.isolates.first.lab_nr - gbol_nr_1=gbol_nr + gbol_nr_1 = gbol_nr - gbol_nrs=[] + gbol_nrs = [] gbol_nrs[0] = gbol_nr_1 - - if gbol_nr_1[2]=='O' - gbol_nr_2=gbol_nr_1.clone - gbol_nr_2[2]='o' - gbol_nrs[1]=gbol_nr_2 + if gbol_nr_1[2] == 'O' + gbol_nr_2 = gbol_nr_1.clone + gbol_nr_2[2] = 'o' + gbol_nrs[1] = gbol_nr_2 else - gbol_nr_2=gbol_nr_1.clone - gbol_nr_2[2]='O' - gbol_nrs[1]=gbol_nr_2 + gbol_nr_2 = gbol_nr_1.clone + gbol_nr_2[2] = 'O' + gbol_nrs[1] = gbol_nr_2 end gbol_nrs[1] = gbol_nr_2 gbol_nrs.each do |gbol_nr| - puts "Query for #{gbol_nr}...\n" - service_url="http://ww3.bgbm.org/biocase/pywrapper.cgi?dsa=DNA_Bank&query=
search
http://www.tdwg.org/schemas/abcd/2.1http://www.tdwg.org/schemas/abcd/2.1#{gbol_nr}false" + service_url = "http://ww3.bgbm.org/biocase/pywrapper.cgi?dsa=DNA_Bank&query=
search
http://www.tdwg.org/schemas/abcd/2.1http://www.tdwg.org/schemas/abcd/2.1#{gbol_nr}false" url = URI.parse(service_url) req = Net::HTTP::Get.new(url.to_s) - res = Net::HTTP.start(url.host, url.port) { |http| + res = Net::HTTP.start(url.host, url.port) do |http| http.request(req) - } + end - doc= Nokogiri::XML(res.body) + doc = Nokogiri::XML(res.body) - full_name=nil - collector=nil - locality=nil - longitude=nil - latitude=nil - specimen_id=nil - herbarium=nil + full_name = nil + collector = nil + locality = nil + longitude = nil + latitude = nil + specimen_id = nil + herbarium = nil begin unit = doc.at_xpath('//abcd21:Unit') - unit_id=doc.at_xpath('//abcd21:Unit/abcd21:UnitID').content # = DNA Bank nr - specimen_id=unit.at_xpath('//abcd21:UnitAssociation/abcd21:UnitID').content - full_name= unit.at_xpath('//abcd21:FullScientificNameString').content - herbarium=unit.at_xpath('//abcd21:SourceInstitutionCode').content - collector= unit.at_xpath('//abcd21:GatheringAgent').content - locality=unit.at_xpath('//abcd21:LocalityText').content - longitude=unit.at_xpath('//abcd21:LongitudeDecimal').content - latitude=unit.at_xpath('//abcd21:LatitudeDecimal').content - rescue -# ignored + unit_id = doc.at_xpath('//abcd21:Unit/abcd21:UnitID').content # = DNA Bank nr + specimen_id = unit.at_xpath('//abcd21:UnitAssociation/abcd21:UnitID').content + full_name = unit.at_xpath('//abcd21:FullScientificNameString').content + herbarium = unit.at_xpath('//abcd21:SourceInstitutionCode').content + collector = unit.at_xpath('//abcd21:GatheringAgent').content + locality = unit.at_xpath('//abcd21:LocalityText').content + longitude = unit.at_xpath('//abcd21:LongitudeDecimal').content + latitude = unit.at_xpath('//abcd21:LatitudeDecimal').content + rescue StandardError + # ignored end - if unit_id - puts unit_id - end + puts unit_id if unit_id - if specimen_id + next unless specimen_id - individual.update(:specimen_id => specimen_id) + individual.update(specimen_id: specimen_id) - puts specimen_id + puts specimen_id - if unit_id - puts unit_id - individual.update(:DNA_bank_id => unit_id) - end + if unit_id + puts unit_id + individual.update(DNA_bank_id: unit_id) + end - puts collector - if collector - individual.update(:collector => collector.strip) - end + puts collector + individual.update(collector: collector.strip) if collector - puts locality - if locality - individual.update(:locality => locality) - end + puts locality + individual.update(locality: locality) if locality - puts longitude - if longitude - individual.update(:longitude => longitude) - end + puts longitude + individual.update(longitude: longitude) if longitude - puts latitude - if latitude - individual.update(:latitude => latitude) - end + puts latitude + individual.update(latitude: latitude) if latitude - puts herbarium - if herbarium - individual.update(:herbarium => herbarium) - end + puts herbarium + individual.update(herbarium: herbarium) if herbarium - if full_name + if full_name - regex = /^(\w+\s+\w+)/ - matches = full_name.match(regex) - if matches - species_component = matches[1] + regex = /^(\w+\s+\w+)/ + matches = full_name.match(regex) + if matches + species_component = matches[1] - puts species_component + puts species_component - sp=individual.species + sp = individual.species - if sp.nil? - sp= Species.find_or_create_by(:species_component => species_component) - individual.update(:species => sp) - end + if sp.nil? + sp = Species.find_or_create_by(species_component: species_component) + individual.update(species: sp) end - end - isolate = Isolate.where(:lab_nr => i.lab_nr).first + end - if isolate - isolate.update(:individual => individual) - end + isolate = Isolate.where(lab_nr: i.lab_nr).first - break # no need to try alternative "gbOl" spelling if already found a match - - end + isolate&.update(individual: individual) + break # no need to try alternative "gbOl" spelling if already found a match end - rescue -# ignored + rescue StandardError + # ignored end - end - puts "Done." - + puts 'Done.' end - desc "For given GBOL-Nrs, extract all specimen info from DNABank, if corresponding GBOL-Nr exists there." - task :reset_DNABank_by_gbol_nr => :environment do - + desc 'For given GBOL-Nrs, extract all specimen info from DNABank, if corresponding GBOL-Nr exists there.' + task reset_DNABank_by_gbol_nr: :environment do outputstr = "Isolate ID\tGBOL-Nr (Lab-Nr)\tcurrent DNA-Bank-Nr\tcurrent specimen\tcurrent species\tfuture DNA-Bank-Nr\tfuture specimen\tfuture species\n" - c=Isolate.all.count - ctr=1 + c = Isolate.all.count + ctr = 1 Isolate.all.each do |i| # Isolate.find([11302, 11317, 9986]).each do |i| progress = "#{ctr} / #{c}" + "\r" puts progress - specimen="" - species="" + specimen = '' + species = '' if i.individual - specimen=i.individual.specimen_id - if i.individual.species - species=i.individual.species.species_component - end + specimen = i.individual.specimen_id + species = i.individual.species.species_component if i.individual.species end gbol_nr = i.lab_nr @@ -488,50 +429,49 @@ namespace :data do puts "Query for #{gbol_nr}..." - service_url="http://ww3.bgbm.org/biocase/pywrapper.cgi?dsa=DNA_Bank&query=
search
http://www.tdwg.org/schemas/abcd/2.1http://www.tdwg.org/schemas/abcd/2.1#{gbol_nr}false" + service_url = "http://ww3.bgbm.org/biocase/pywrapper.cgi?dsa=DNA_Bank&query=
search
http://www.tdwg.org/schemas/abcd/2.1http://www.tdwg.org/schemas/abcd/2.1#{gbol_nr}false" url = URI.parse(service_url) req = Net::HTTP::Get.new(url.to_s) - res = Net::HTTP.start(url.host, url.port) { |http| + res = Net::HTTP.start(url.host, url.port) do |http| http.request(req) - } + end doc = Nokogiri::XML(res.body) begin unit = doc.at_xpath('//abcd21:Unit') - unit_id=doc.at_xpath('//abcd21:Unit/abcd21:UnitID').content # = DNA Bank nr - specimen_id=unit.at_xpath('//abcd21:UnitAssociation/abcd21:UnitID').content - full_name= unit.at_xpath('//abcd21:FullScientificNameString').content - herbarium=unit.at_xpath('//abcd21:SourceInstitutionCode').content - collector= unit.at_xpath('//abcd21:GatheringAgent').content - locality=unit.at_xpath('//abcd21:LocalityText').content - longitude=unit.at_xpath('//abcd21:LongitudeDecimal').content - latitude=unit.at_xpath('//abcd21:LatitudeDecimal').content - rescue + unit_id = doc.at_xpath('//abcd21:Unit/abcd21:UnitID').content # = DNA Bank nr + specimen_id = unit.at_xpath('//abcd21:UnitAssociation/abcd21:UnitID').content + full_name = unit.at_xpath('//abcd21:FullScientificNameString').content + herbarium = unit.at_xpath('//abcd21:SourceInstitutionCode').content + collector = unit.at_xpath('//abcd21:GatheringAgent').content + locality = unit.at_xpath('//abcd21:LocalityText').content + longitude = unit.at_xpath('//abcd21:LongitudeDecimal').content + latitude = unit.at_xpath('//abcd21:LatitudeDecimal').content + rescue StandardError # puts "Extraction not possible." end puts if unit_id && i.dna_bank_id - if unit_id.gsub(/\s+/, "") == i.dna_bank_id.gsub(/\s+/, "") - #don't output anything - correction from upcoming DNABank query will not change anything + if unit_id.gsub(/\s+/, '') == i.dna_bank_id.gsub(/\s+/, '') + # don't output anything - correction from upcoming DNABank query will not change anything else - outputstr+= "#{i.id}\t#{i.lab_nr}\t#{i.dna_bank_id}\t#{specimen}\t#{species}\t" - outputstr+= "#{unit_id}\t" #future dna_bank_id + outputstr += "#{i.id}\t#{i.lab_nr}\t#{i.dna_bank_id}\t#{specimen}\t#{species}\t" + outputstr += "#{unit_id}\t" # future dna_bank_id if specimen_id - outputstr+= "#{specimen_id}\t" #future specimen_id - outputstr+= "#{full_name}\n" if full_name + outputstr += "#{specimen_id}\t" # future specimen_id + outputstr += "#{full_name}\n" if full_name end end end - ctr=ctr+1 + ctr += 1 end puts "#{outputstr}\n\nDone." - end -end \ No newline at end of file +end diff --git a/lib/tasks/flag_specimens.rake b/lib/tasks/flag_specimens.rake index 555851e7..c63a9c72 100644 --- a/lib/tasks/flag_specimens.rake +++ b/lib/tasks/flag_specimens.rake @@ -1,12 +1,13 @@ -namespace :data do +# frozen_string_literal: true - task :flag_specimen => :environment do +namespace :data do + task flag_specimen: :environment do individual_ids = Individual.joins(isolates: :marker_sequences).distinct.merge(MarkerSequence.with_warnings).pluck(:id) individuals_with_issues = [] individual_ids.each do |individual_id| sequences = MarkerSequence.joins(isolate: :individual).distinct.with_warnings.where('individuals.id = ?', individual_id) - individuals_with_issues << individual_id if (sequences.size > 1) + individuals_with_issues << individual_id if sequences.size > 1 end individuals_with_issues.each do |individual_id| @@ -14,12 +15,12 @@ namespace :data do end end - task :unflag_specimen => :environment do + task unflag_specimen: :environment do individuals_with_flag = Individual.where(has_issue: true) individuals_with_flag.each do |individual| sequences = MarkerSequence.joins(isolate: :individual).distinct.with_warnings.where('individuals.id = ?', individual.id) - individual.update(has_issue: false) if (sequences.size < 2) + individual.update(has_issue: false) if sequences.size < 2 end end -end \ No newline at end of file +end diff --git a/lib/tasks/get_aligned_peak_indices.rake b/lib/tasks/get_aligned_peak_indices.rake index 5b88968e..c4a13756 100644 --- a/lib/tasks/get_aligned_peak_indices.rake +++ b/lib/tasks/get_aligned_peak_indices.rake @@ -1,22 +1,20 @@ -namespace :data do - - desc "get_aligned_peak_indices" +# frozen_string_literal: true - task :get_aligned_peak_indices => :environment do +namespace :data do + desc 'get_aligned_peak_indices' - total= PrimerRead.use_for_assembly.where(:aligned_peak_indices => nil).count + task get_aligned_peak_indices: :environment do + total = PrimerRead.use_for_assembly.where(aligned_peak_indices: nil).count - ctr=0 - PrimerRead.use_for_assembly.where( :aligned_peak_indices => nil).select(:id, :trimmedReadStart, :aligned_qualities, :aligned_peak_indices, :peak_indices).find_in_batches(batch_size: 100) do |batch| + ctr = 0 + PrimerRead.use_for_assembly.where(aligned_peak_indices: nil).select(:id, :trimmedReadStart, :aligned_qualities, :aligned_peak_indices, :peak_indices).find_in_batches(batch_size: 100) do |batch| batch.each do |pr| - ctr+=1 + ctr += 1 puts "#{ctr} / #{total}" pr.get_aligned_peak_indices end end - puts "Done." - + puts 'Done.' end - -end \ No newline at end of file +end diff --git a/lib/tasks/identification_success.rake b/lib/tasks/identification_success.rake index 73150127..e1ae766f 100644 --- a/lib/tasks/identification_success.rake +++ b/lib/tasks/identification_success.rake @@ -1,7 +1,9 @@ +# frozen_string_literal: true + namespace :data do desc 'Calculate identification success of marker' - task :identification_success, [:marker] => [:environment] do |t, args| + task :identification_success, [:marker] => [:environment] do |_t, args| marker = Marker.find_by_name(args[:marker]) sequences = MarkerSequence.joins(isolate: [individual: :species]) diff --git a/lib/tasks/mark_negative_controls.rake b/lib/tasks/mark_negative_controls.rake index 29bc9e7c..b82f2b69 100644 --- a/lib/tasks/mark_negative_controls.rake +++ b/lib/tasks/mark_negative_controls.rake @@ -1,86 +1,83 @@ +# frozen_string_literal: true + namespace :data do desc "fill reads' basecount" - task :mark_negative_controls => :environment do - - controls=[ - 'GBoL96', - 'GBoL192', - 'GBoL288', - 'GBoL384', - 'GBoL480', - 'GBoL576', - 'GBoL672', - 'GBoL768', - 'GBoL864', - 'GBoL960', - 'GBoL1056', - 'GBoL1152', - 'GBoL1248', - 'GBoL1344', - 'GBoL1440', - 'GBoL1536', - 'GBoL1632', - 'GBoL1728', - 'GBoL1824', - 'GBoL1920', - 'GBoL2016', - 'GBoL2112', - 'GBoL2208', - 'GBoL2304', - 'GBoL2400', - 'GBoL2496', - 'GBoL2592', - 'GBoL2688', - 'GBoL2784', - 'GBoL2880', - 'GBoL2976', - 'GBoL3072', - 'GBoL3168', - 'GBoL3264', - 'GBoL3360', - 'GBoL3456', - 'GBoL3552', - 'GBoL3648', - 'GBoL3744', - 'GBoL3840', - 'GBoL3936', - 'GBoL4032', - 'GBoL4128', - 'GBoL4224', - 'GBoL4320', - 'GBoL4416', - 'GBoL4512', - 'GBoL4608', - 'GBoL4704', - 'GBoL4800', - 'GBoL4896', - 'GBoL4992', - 'GBoL5088', - 'GBoL5184', - 'GBoL5280', - 'GBoL5376', - 'GBoL5472', - 'GBoL5568', - 'GBoL5664', - 'GBoL5760', - 'GBoL5856', - 'GBoL5952', - 'GBoL6048', - 'GBoL6144', - 'GBoL6240', - 'GBoL6336' + task mark_negative_controls: :environment do + controls = %w[ + GBoL96 + GBoL192 + GBoL288 + GBoL384 + GBoL480 + GBoL576 + GBoL672 + GBoL768 + GBoL864 + GBoL960 + GBoL1056 + GBoL1152 + GBoL1248 + GBoL1344 + GBoL1440 + GBoL1536 + GBoL1632 + GBoL1728 + GBoL1824 + GBoL1920 + GBoL2016 + GBoL2112 + GBoL2208 + GBoL2304 + GBoL2400 + GBoL2496 + GBoL2592 + GBoL2688 + GBoL2784 + GBoL2880 + GBoL2976 + GBoL3072 + GBoL3168 + GBoL3264 + GBoL3360 + GBoL3456 + GBoL3552 + GBoL3648 + GBoL3744 + GBoL3840 + GBoL3936 + GBoL4032 + GBoL4128 + GBoL4224 + GBoL4320 + GBoL4416 + GBoL4512 + GBoL4608 + GBoL4704 + GBoL4800 + GBoL4896 + GBoL4992 + GBoL5088 + GBoL5184 + GBoL5280 + GBoL5376 + GBoL5472 + GBoL5568 + GBoL5664 + GBoL5760 + GBoL5856 + GBoL5952 + GBoL6048 + GBoL6144 + GBoL6240 + GBoL6336 ] controls.each do |c| - isolate=Isolate.where(:lab_nr => c).first - if isolate - isolate.update(:negative_control => true) - end + isolate = Isolate.where(lab_nr: c).first + isolate&.update(negative_control: true) end - puts "Done." - + puts 'Done.' end - -end \ No newline at end of file +end diff --git a/lib/tasks/query_contigs_for_isolate_list.rake b/lib/tasks/query_contigs_for_isolate_list.rake index da6c1244..359f25ee 100644 --- a/lib/tasks/query_contigs_for_isolate_list.rake +++ b/lib/tasks/query_contigs_for_isolate_list.rake @@ -1,15 +1,15 @@ +# frozen_string_literal: true + require 'net/http' require 'nokogiri' namespace :data do + desc 'For given GBOL-Nrs, check which contigs exist.' - desc "For given GBOL-Nrs, check which contigs exist." - - task :query_contigs_for_isolate_list => :environment do - + task query_contigs_for_isolate_list: :environment do outputstr = "Isolate ID\tITS\ttrnK-matK\ttrnLF\trpl16\n" - list_with_gbol_nrs="GBoL3457 + list_with_gbol_nrs = "GBoL3457 GBoL3467 GBoL3459 GBoL3474 @@ -60,34 +60,27 @@ GBoL3541 ".split("\n") list_with_gbol_nrs.each do |i| - outputstr += "#{i}\t" - isolate = Isolate.where(:lab_nr => i).first + isolate = Isolate.where(lab_nr: i).first isolate.contigs.each do |c| - - if c.verified_at.nil? - outputstr += "#{c.marker.name} " - else - outputstr += "#{c.marker.name} (verified)" - end + outputstr += if c.verified_at.nil? + "#{c.marker.name} " + else + "#{c.marker.name} (verified)" + end outputstr += "\t" - end - outputstr+="\n" - - + outputstr += "\n" end puts outputstr puts - puts "Done." - + puts 'Done.' end - -end \ No newline at end of file +end diff --git a/lib/tasks/remove_searches.rake b/lib/tasks/remove_searches.rake index 019942d1..440f309c 100644 --- a/lib/tasks/remove_searches.rake +++ b/lib/tasks/remove_searches.rake @@ -1,13 +1,13 @@ -namespace :data do +# frozen_string_literal: true +namespace :data do desc 'Remove untitled contig searches older than a month' - task :remove_old_searches => :environment do - ContigSearch.where("created_at < ?", 1.month.ago).where(title: nil).delete_all + task remove_old_searches: :environment do + ContigSearch.where('created_at < ?', 1.month.ago).where(title: nil).delete_all end desc 'Remove all untitled contig searches' - task :remove_untitled_searches => :environment do + task remove_untitled_searches: :environment do ContigSearch.where(title: nil).delete_all end - -end \ No newline at end of file +end diff --git a/lib/tasks/reupload_chromatograms.rake b/lib/tasks/reupload_chromatograms.rake index 578a989b..220cb3a5 100644 --- a/lib/tasks/reupload_chromatograms.rake +++ b/lib/tasks/reupload_chromatograms.rake @@ -1,9 +1,10 @@ +# frozen_string_literal: true + require 'net/http' namespace :data do - desc 'Delete faulty primer reads and import them again correctly' - task :reimport_chromatograms => :environment do + task reimport_chromatograms: :environment do nil_reads = PrimerRead.where(sequence: nil) # download chromatograms of records without sequence @@ -16,4 +17,4 @@ namespace :data do # destroy all reads without sequence PrimerRead.where(sequence: nil).destroy_all end -end \ No newline at end of file +end diff --git a/lib/tasks/script_runner.rake b/lib/tasks/script_runner.rake index bd7f390d..067e3e62 100644 --- a/lib/tasks/script_runner.rake +++ b/lib/tasks/script_runner.rake @@ -1,13 +1,14 @@ -namespace :data do +# frozen_string_literal: true - task :run_python => :environment do +namespace :data do + task run_python: :environment do file = Rails.root.join('lib', 'sativa_test_files', 'python_test.py') output = `python #{file}` puts output end - desc "Runs a SATIVA mislabel analysis" - task :run_sativa => :environment do + desc 'Runs a SATIVA mislabel analysis' + task run_sativa: :environment do # SATIVA only understands relative file paths and has to be called inside the directory with the analysis data analysis_dir = Rails.root.join('lib', 'sativa_test_files') alignment_file = 'gbol5_caryophyllales_ITS_aligned.fasta' @@ -17,5 +18,4 @@ namespace :data do `python /home/sarah/SATIVA/sativa/sativa.py -s #{alignment_file} -t #{tax_file} -x BOT` end end - -end \ No newline at end of file +end diff --git a/lib/tasks/sequence_quality.rake b/lib/tasks/sequence_quality.rake index 45a291d8..da8f6559 100644 --- a/lib/tasks/sequence_quality.rake +++ b/lib/tasks/sequence_quality.rake @@ -1,7 +1,8 @@ -namespace :data do +# frozen_string_literal: true +namespace :data do desc 'Get information about verified marker sequences (with associated species) and contigs in database' - task :sequence_info_verified => [:environment, :general_info] do + task sequence_info_verified: %i[environment general_info] do marker_sequences = MarkerSequence.gbol.has_species.verified contigs = Contig.gbol.verified.joins(:primer_reads) @@ -9,7 +10,7 @@ namespace :data do end desc 'Get information about all gbol5 marker sequences and contigs in database' - task :sequence_info_gbol => [:environment, :general_info] do + task sequence_info_gbol: %i[environment general_info] do marker_sequences = MarkerSequence.gbol contigs = Contig.joins(:primer_reads).gbol @@ -17,13 +18,13 @@ namespace :data do end desc 'Get general information about gbol5 marker sequences and contigs in database' - task :general_info => :environment do + task general_info: :environment do marker_sequences = MarkerSequence.gbol puts "Number of marker sequences: #{marker_sequences.size}" puts "Number of verified marker sequences in database: #{marker_sequences.verified.size}" puts "Number of verified marker sequences with associated species in database: #{marker_sequences.has_species.verified.length}" puts "Number of marker sequences without associated contigs: #{marker_sequences.includes(:contigs).where(contigs: { id: nil }).size}" - puts "Number of marker sequences without associated isolate: #{marker_sequences.includes(:isolate).where( isolate: nil ).size}" + puts "Number of marker sequences without associated isolate: #{marker_sequences.includes(:isolate).where(isolate: nil).size}" puts '' contigs = Contig.gbol @@ -35,7 +36,7 @@ namespace :data do puts '' end - task :duplicate_sequences => :environment do + task duplicate_sequences: :environment do gbol_sequences = MarkerSequence.gbol ms_with_contig = gbol_sequences.joins(:contigs).distinct @@ -50,10 +51,10 @@ namespace :data do end desc 'Get the number of species with more than 1, 2, 3, 4 or 5 sequences per marker' - task :sequences_per_species => :environment do + task sequences_per_species: :environment do # TODO: Exclude cases where one individual has multiple isolates or one isolate has multiple sequences per marker species = Species.joins(individuals: [isolates: :marker_sequences]).distinct - columns = %w(min_one gt_one gt_two gt_three gt_four gt_five) + columns = %w[min_one gt_one gt_two gt_three gt_four gt_five] its = {} rpl16 = {} trnk_matk = {} @@ -80,7 +81,7 @@ namespace :data do end desc 'Get the number of species with only a single sequence per marker' - task :singletons_per_marker => :environment do + task singletons_per_marker: :environment do species = Species.joins(individuals: [isolates: :marker_sequences]).distinct species_cnt = species.size @@ -97,7 +98,7 @@ namespace :data do end desc 'Get the average number of specimen per species' - task :specimen_per_species => :environment do + task specimen_per_species: :environment do species_cnt = Species.all.size specimen_cnt = Individual.all.size @@ -124,7 +125,7 @@ namespace :data do # MarkerSequence.joins(isolate: [individual: :species]).distinct.order('species.species_component').group('species.species_component').count end - task :get_high_quality_sequences => :environment do + task get_high_quality_sequences: :environment do sequences = MarkerSequence.gbol # Only GBOL5 sequences # sequences = MarkerSequence.gbol.joins(isolate: {individual: {species: {family: :order}}}).where("orders.name ilike ?", "%Caryophyllales%") puts "Number of GBOL5 sequences: #{sequences.size}" @@ -155,7 +156,7 @@ namespace :data do end # Check sequences for stop codons - stop_codons = %w(tag tga taa) + stop_codons = %w[tag tga taa] # sequence = Bio::Sequence::NA.new(MarkerSequence.gbol.first.sequence) # codons = sequence.codon_usage # stop_codons.each { |codon| puts codons[codon] } @@ -169,8 +170,8 @@ namespace :data do def species_count_with_exact_ms_count(species, marker_id, ms_count) species.where(individuals: { isolates: { marker_sequences: { marker: marker_id } } }) - .group(:id) - .having('count(marker_sequences) = ?', ms_count).length + .group(:id) + .having('count(marker_sequences) = ?', ms_count).length end def get_information(marker_sequences, contigs) @@ -189,17 +190,16 @@ namespace :data do if sequences.size.positive? sequence_count[marker.name] = sequences.size sequence_length_avg[marker.name] = sequences.average('length(sequence)').to_f.round(2) - sequence_length_min[marker.name] = sequences.select(:sequence, 'length(sequence)').where.not(:sequence => nil).order('length(sequence) asc').first.sequence.length - sequence_length_max[marker.name] = sequences.select(:sequence, 'length(sequence)').where.not(:sequence => nil).order('length(sequence) desc').first.sequence.length + sequence_length_min[marker.name] = sequences.select(:sequence, 'length(sequence)').where.not(sequence: nil).order('length(sequence) asc').first.sequence.length + sequence_length_max[marker.name] = sequences.select(:sequence, 'length(sequence)').where.not(sequence: nil).order('length(sequence) desc').first.sequence.length end - if contigs_marker.size.positive? - primer_read_counts = contigs_marker.group(:id).count('primer_reads.id') # TODO: only count assembled reads + next unless contigs_marker.size.positive? + primer_read_counts = contigs_marker.group(:id).count('primer_reads.id') # TODO: only count assembled reads - reads_per_contig_avg[marker.name] = (primer_read_counts.values.sum / primer_read_counts.values.size.to_f).round(2) - reads_per_contig_min[marker.name] = primer_read_counts.values.min - reads_per_contig_max[marker.name] = primer_read_counts.values.max - end + reads_per_contig_avg[marker.name] = (primer_read_counts.values.sum / primer_read_counts.values.size.to_f).round(2) + reads_per_contig_min[marker.name] = primer_read_counts.values.min + reads_per_contig_max[marker.name] = primer_read_counts.values.max end puts 'Number of sequences per marker:' @@ -226,7 +226,7 @@ namespace :data do has_ms = false s.individuals.each do |i| i.isolates.each do |iso| - has_ms = iso.marker_sequences.where(:marker_id => marker_id).any? ? true : has_ms + has_ms = iso.marker_sequences.where(marker_id: marker_id).any? ? true : has_ms end end count += 1 if has_ms diff --git a/lib/tasks/ssh.rake b/lib/tasks/ssh.rake index ac3bd827..eeb874f3 100644 --- a/lib/tasks/ssh.rake +++ b/lib/tasks/ssh.rake @@ -1,10 +1,12 @@ +# frozen_string_literal: true + namespace :data do require 'net/ssh' require 'net/scp' require 'net/sftp' desc 'Check how many sequences were created or updated since last analysis and redo analysis if necessary' - task :check_new_marker_sequences => :environment do + task check_new_marker_sequences: :environment do # TODO: Do analyses for all existing projects (except all_records) Marker.gbol_marker.each do |marker| puts "Checking if analysis is necessary for #{marker.name}..." @@ -20,7 +22,7 @@ namespace :data do end desc 'Check if recent SATIVA results exist and download them' - task :download_sativa_results => :environment do + task download_sativa_results: :environment do Marker.gbol_marker.each do |marker| puts "Checking if analysis results exist for #{marker.name}..." @@ -107,4 +109,4 @@ namespace :data do def current_time Time.now.strftime('%H:%M:%S') end -end \ No newline at end of file +end diff --git a/lib/tasks/update_location_data.rake b/lib/tasks/update_location_data.rake index 52adbdeb..cbb34425 100644 --- a/lib/tasks/update_location_data.rake +++ b/lib/tasks/update_location_data.rake @@ -1,11 +1,11 @@ +# frozen_string_literal: true + require 'net/http' require 'nokogiri' - namespace :data do - desc 'Update Specimen Location Data' - task :update_location_data => :environment do + task update_location_data: :environment do spreadsheet = Roo::Excelx.new('/home/sarah/apps/gbol5/current/GBOL_2015_Koordinaten_Korrektur.xlsx') header = spreadsheet.row(1) no_specimen = [] @@ -19,18 +19,18 @@ namespace :data do isolate_lab_nr = row['GBoL Isolation No.'] latitude = row['Latitude (calc.)']&.to_d longitude = row['Longitude (calc.)']&.to_d - specimen = Individual.find_by_id(Isolate.where(:lab_nr => isolate_lab_nr).first&.individual_id) + specimen = Individual.find_by_id(Isolate.where(lab_nr: isolate_lab_nr).first&.individual_id) if specimen if latitude&.nonzero? && specimen.latitude != latitude - specimen.update(:latitude => latitude) - specimen.update(:latitude_original => row['Latitude (calc.)']) + specimen.update(latitude: latitude) + specimen.update(latitude_original: row['Latitude (calc.)']) lat_cnt += 1 end if longitude&.nonzero? && specimen.longitude != longitude - specimen.update(:longitude => longitude) - specimen.update(:longitude_original => row['Longitude (calc.)']) + specimen.update(longitude: longitude) + specimen.update(longitude_original: row['Longitude (calc.)']) long_cnt += 1 end @@ -43,4 +43,4 @@ namespace :data do puts "Done. Updated latitude data for #{lat_cnt} specimen and longitude data for #{long_cnt}."\ "\nNo specimens are assigned to the following #{no_specimen.length} isolates: #{no_specimen}" end -end \ No newline at end of file +end diff --git a/lib/tasks/work_statistics.rake b/lib/tasks/work_statistics.rake index 55d92e15..8cded86a 100644 --- a/lib/tasks/work_statistics.rake +++ b/lib/tasks/work_statistics.rake @@ -1,7 +1,8 @@ -namespace :data do +# frozen_string_literal: true +namespace :data do desc 'Do work statistics for and Lab with ' - task :work_statistics_yearly, [:year, :labcode] => [:environment] do |t, args| + task :work_statistics_yearly, %i[year labcode] => [:environment] do |_t, args| lab_prefixes = { nees: 'gbol', bgbm: 'db' } range = Time.new(args[:year].to_i, 1, 1).all_year @@ -9,17 +10,17 @@ namespace :data do puts prefix - isolates = Isolate.where("lab_nr ilike ?", "#{prefix}%") - .where(:created_at => range) + isolates = Isolate.where('lab_nr ilike ?', "#{prefix}%") + .where(created_at: range) .select(:id, :lab_nr) - contigs = Contig.where("contigs.name ilike ?", "#{prefix}%") + contigs = Contig.where('contigs.name ilike ?', "#{prefix}%") .where(verified_at: range) .select(:id, :name) - reads = PrimerRead.where("primer_reads.name ilike ?", "#{prefix}%") - .where(:created_at => range) + reads = PrimerRead.where('primer_reads.name ilike ?', "#{prefix}%") + .where(created_at: range) .select(:id, :name) - marker_sequences = MarkerSequence.where("marker_sequences.name ilike ?", "#{prefix}%") - .where(:created_at => range) + marker_sequences = MarkerSequence.where('marker_sequences.name ilike ?', "#{prefix}%") + .where(created_at: range) .select(:id, :sequence, :name) puts "Calculating activities for #{range.first.year} in lab #{args[:labcode]}...\n" @@ -57,14 +58,14 @@ namespace :data do end desc 'Do work statistics' - task :work_statistics_total => [:environment] do |t, args| + task work_statistics_total: [:environment] do |_t, _args| gbol_marker = Marker.gbol_marker - puts "Calculating activities in total..." + puts 'Calculating activities in total...' all_isolates_count = Isolate.all.size - isolates_bonn_cnt = Isolate.where("lab_nr ilike ?", "%gbol%").size - isolates_berlin_cnt = Isolate.where("lab_nr ilike ?", "%db%").size + isolates_bonn_cnt = Isolate.where('lab_nr ilike ?', '%gbol%').size + isolates_berlin_cnt = Isolate.where('lab_nr ilike ?', '%db%').size other_isolates_count = all_isolates_count - isolates_bonn_cnt - isolates_berlin_cnt puts "Number of isolates: #{all_isolates_count} (total), #{isolates_bonn_cnt} (Bonn), #{isolates_berlin_cnt} (Berlin), #{other_isolates_count} (not assigned to a lab)" @@ -73,7 +74,7 @@ namespace :data do gbol_marker.each do |marker| sequence_cnt_per_marker[marker.name] = MarkerSequence.where(marker_id: marker.id).size - verified_count_per_marker[marker.name] = Isolate.joins(contigs: :marker).where(contigs: { verified: true , marker_id: marker.id}).count('contigs.id') + verified_count_per_marker[marker.name] = Isolate.joins(contigs: :marker).where(contigs: { verified: true, marker_id: marker.id }).count('contigs.id') end puts "Number of barcode sequences per marker: #{sequence_cnt_per_marker}"