From ae7652a15de401d85d5493514056353bd03f86c9 Mon Sep 17 00:00:00 2001 From: mmp Date: Tue, 25 Oct 2022 17:24:21 +0100 Subject: [PATCH] [add] nextstrain metadata --- constants/software_names.py | 7 +- datasets/forms.py | 22 +- .../migrations/0012_auto_20221025_1626.py | 21 ++ datasets/models.py | 29 +- datasets/urls.py | 2 +- datasets/views.py | 26 +- managing_files/forms.py | 4 + managing_files/views.py | 4 + .../dataset_files/Nextstrain_metadata.tsv | 10 + .../insa_flu_dataset_output_nextstrain.csv | 2 +- .../insa_flu_dataset_output_nextstrain_2.csv | 2 +- .../nextstrain_metadata_input.tsv | 6 + ...v => out_nextstrain_metadata_expected.tsv} | 12 +- .../out_nextstrain_metadata_expected_2.tsv | 6 + .../project_5000/main_result/Sample_list.csv | 12 +- .../datasets/datasets_consensus_show.html | 7 +- ...sets_upload_description_file_metadata.html | 2 +- .../datasets/datasets_upload_metadata.html | 3 +- .../tests_collect_dataset_extra_data.py | 299 +++++++++++++++++- tests_insaflu/tests_data_columns.py | 24 ++ tests_insaflu/tests_parse_files_nextstrain.py | 63 ++++ utils/collect_dataset_data.py | 37 ++- utils/data_columns.py | 87 ++++- utils/parse_in_files_nextstrain.py | 262 +++++++++++++++ utils/utils.py | 15 +- 25 files changed, 881 insertions(+), 83 deletions(-) create mode 100644 datasets/migrations/0012_auto_20221025_1626.py create mode 100644 static/tests/dataset_files/Nextstrain_metadata.tsv create mode 100755 static/tests/dataset_files/nextstrain_metadata_input.tsv rename static/tests/dataset_files/{out_nextstrain_metadata.tsv => out_nextstrain_metadata_expected.tsv} (66%) create mode 100755 static/tests/dataset_files/out_nextstrain_metadata_expected_2.tsv create mode 100644 tests_insaflu/tests_parse_files_nextstrain.py create mode 100644 utils/parse_in_files_nextstrain.py diff --git a/constants/software_names.py b/constants/software_names.py index b544880f..517dbe1d 100644 --- a/constants/software_names.py +++ b/constants/software_names.py @@ -347,23 +347,24 @@ class SoftwareNames(object): SOFTWARE_NEXTSTRAIN = os.path.join(settings.DIR_SOFTWARE, "nextstrain/nextstrain.sh") SOFTWARE_NEXTSTRAIN_MPX = os.path.join(settings.DIR_SOFTWARE, "nextstrain/nextstrain_mpx.sh") SOFTWARE_NEXTSTRAIN_BUILDS_BASE = os.path.join(settings.DIR_SOFTWARE, "nextstrain/") + + ### Several types of builds for NEXTSTRAIN SOFTWARE_NEXTSTRAIN_BUILDS_generic = "generic" SOFTWARE_NEXTSTRAIN_BUILDS_ncov = "ncov" + SOFTWARE_NEXTSTRAIN_BUILDS_mpx = "mpx" SOFTWARE_NEXTSTRAIN_BUILDS_flu_h3n2_12y = "flu_h3n2_12y" SOFTWARE_NEXTSTRAIN_BUILDS_flu_h1n1pdm_12y = "flu_h1n1pdm_12y" SOFTWARE_NEXTSTRAIN_BUILDS_flu_vic_12y = "flu_vic_12y" SOFTWARE_NEXTSTRAIN_BUILDS_flu_yam_12y = "flu_yam_12y" - SOFTWARE_NEXTSTRAIN_BUILDS_flu = [ + SOFTWARE_NEXTSTRAIN_BUILDS_flu = [ SOFTWARE_NEXTSTRAIN_BUILDS_flu_h3n2_12y, SOFTWARE_NEXTSTRAIN_BUILDS_flu_h1n1pdm_12y, SOFTWARE_NEXTSTRAIN_BUILDS_flu_vic_12y, SOFTWARE_NEXTSTRAIN_BUILDS_flu_yam_12y ] - SOFTWARE_NEXTSTRAIN_BUILDS_mpx = "mpx" - SOFTWARE_NEXTSTRAIN_BUILDS = [ SOFTWARE_NEXTSTRAIN_BUILDS_generic, SOFTWARE_NEXTSTRAIN_BUILDS_ncov, diff --git a/datasets/forms.py b/datasets/forms.py index e6284829..1bc6a730 100644 --- a/datasets/forms.py +++ b/datasets/forms.py @@ -18,7 +18,7 @@ from constants.constants import Constants from utils.software import Software from Bio import SeqIO -from utils.parse_in_files import ParseInFiles +from utils.parse_in_files_nextstrain import ParseNextStrainFiles class AddReferencesDatasetForm(forms.ModelForm): """ @@ -286,15 +286,15 @@ def __init__(self, *args, **kwargs): self.helper = FormHelper() self.helper.form_method = 'POST' self.helper.layout = Layout( - HTML('

'), - HTML('
' + \ - dataset_name.get_global_file_by_dataset_web(Dataset.DATASET_FILE_NAME_RESULT_NEXTSTRAIN_CSV) + \ - " Last metadata file 'csv' for '{}'
".format( - dataset_name.name)), +# HTML('

'), +# HTML('
' + \ +# dataset_name.get_global_file_by_dataset_web(Dataset.DATASET_FILE_NAME_RESULT_NEXTSTRAIN_CSV) + \ +# " Last metadata file 'csv' for '{}' dataset
".format( +# dataset_name.name)), HTML('

'), HTML('
' + \ dataset_name.get_global_file_by_dataset_web(Dataset.DATASET_FILE_NAME_RESULT_NEXTSTRAIN_TSV) + \ - " Last metadata file 'tsv' for '{}'
".format( + " Last metadata file 'tsv' for '{}' dataset.".format( dataset_name.name)), HTML('

'), Div('path_name', css_class="col-lm-3"), @@ -310,6 +310,7 @@ def clean(self): """ Clean all """ + software = Software() cleaned_data = super(DatastesUploadDescriptionMetadataForm, self).clean() ### get path name @@ -320,11 +321,12 @@ def clean(self): temp_file_name.write(path_name.file.read()) temp_file_name.flush() temp_file_name.close() + software.dos_2_unix(temp_file_name.name) - parse_in_files = ParseInFiles() + parse_in_files = ParseNextStrainFiles() b_test_char_encoding = True - parse_in_files.parse_sample_files(temp_file_name.name, self.request.user, b_test_char_encoding,\ - ParseInFiles.STATE_READ_metadata_only_detect_errors_and_chech_samples) + parse_in_files.parse_nextstrain_files(temp_file_name.name, self.request.user, b_test_char_encoding,\ + ParseNextStrainFiles.STATE_READ_metadata_only_detect_errors_and_chech_nexttrain) os.unlink(temp_file_name.name) if (parse_in_files.get_errors().has_errors()): diff --git a/datasets/migrations/0012_auto_20221025_1626.py b/datasets/migrations/0012_auto_20221025_1626.py new file mode 100644 index 00000000..c448ae93 --- /dev/null +++ b/datasets/migrations/0012_auto_20221025_1626.py @@ -0,0 +1,21 @@ +# -*- coding: utf-8 -*- +# Generated by Django 1.11.18 on 2022-10-25 16:26 +from __future__ import unicode_literals + +from django.db import migrations, models +import django.db.models.deletion + + +class Migration(migrations.Migration): + + dependencies = [ + ('datasets', '0011_dataset_number_passed_sequences'), + ] + + operations = [ + migrations.AlterField( + model_name='uploadfiles', + name='type_file', + field=models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, related_name='upload_metadata_files', to='datasets.MetaKey'), + ), + ] diff --git a/datasets/models.py b/datasets/models.py index 5cd109d9..39281f60 100644 --- a/datasets/models.py +++ b/datasets/models.py @@ -5,7 +5,7 @@ from django.conf import settings from django.utils.safestring import mark_safe from django.contrib.auth.models import User -from managing_files.models import ProjectSample, Reference, MetaKey, user_directory_path +from managing_files.models import ProjectSample, Reference, user_directory_path from fluwebvirus.formatChecker import ContentTypeRestrictedFileField from constants.constants import Constants, TypePath, FileExtensions # Create your models here. @@ -295,6 +295,17 @@ def get_project_name(self): if not self.project_sample is None: return self.project_sample.project.name return "" +class MetaKey(models.Model): + """ + Has meta tags to put values, for example, quality in the files, or samples + """ + name = models.CharField(max_length=200, db_index=True, blank=True, null=True) + def __str__(self): + return self.name + + class Meta: + ordering = ['name', ] + class UploadFiles(models.Model): """ @@ -328,6 +339,9 @@ class UploadFiles(models.Model): dataset = models.ForeignKey(Dataset, related_name='dataset_upload_metadata_file', blank=True, null=True, on_delete=models.CASCADE) description = models.TextField(default="") ## has a json result.ProcessResults instance with errors or successes + ## constants + constants = Constants() + class Meta: ordering = ['-creation_date'] @@ -353,20 +367,9 @@ def get_metadata_fasta_web(self): if (os.path.exists(out_file)): return mark_safe(' {}'.format(self.get_path_to_file(\ TypePath.MEDIA_URL), os.path.basename(self.get_path_to_file(TypePath.MEDIA_ROOT)), - self.constants.short_name(self.name, Constants.SHORT_NAME_LENGTH))) + self.constants.short_name(self.file_name, Constants.SHORT_NAME_LENGTH))) return 'File not available.' -class MetaKey(models.Model): - """ - Has meta tags to put values, for example, quality in the files, or samples - """ - name = models.CharField(max_length=200, db_index=True, blank=True, null=True) - def __str__(self): - return self.name - - class Meta: - ordering = ['name', ] - class MetaKeyDataset(models.Model): """ Relation ManyToMany in diff --git a/datasets/urls.py b/datasets/urls.py index 3431a07b..78e7b892 100644 --- a/datasets/urls.py +++ b/datasets/urls.py @@ -13,7 +13,7 @@ url(r'(?P\d+)/show_dataset_settings$', views.DatasetsSettingsView.as_view(), name='dataset-settings'), url(r'(?P\d+)/dataset_update_metadata$', views.UpdateMetadataDataset.as_view(), name='dataset-update-metadata'), ## upload new matadata to replace the exist - url(r'(?P\d+)/dataset_update_metadata_file$', views.AddSingleMetadataDatasetFile.as_view(), name='dataset-add-single-csv-file-metadata'), ## upload new matadata to replace the exist + url(r'(?P\d+)/dataset_update_metadata_file$', views.AddSingleMetadataDatasetFile.as_view(), name='dataset-add-single-file-metadata'), ## upload new matadata to replace the exist url(r'^ajax/remove_dataset$', ajax_views.remove_dataset, name='remove_dataset'), ## remove a dataset url(r'^ajax/add_dataset_name$', ajax_views.add_dataset_name, name='add_dataset_name'), ## add a dataset diff --git a/datasets/views.py b/datasets/views.py index 9db856db..00196bfc 100644 --- a/datasets/views.py +++ b/datasets/views.py @@ -5,11 +5,11 @@ from braces.views import LoginRequiredMixin, FormValidMessageMixin from django.conf import settings from constants.software_names import SoftwareNames -from managing_files.models import Reference, Project, ProjectSample, MetaKey +from managing_files.models import Reference, Project, ProjectSample from datasets.forms import ConsensusForm from django.views.generic import ListView from utils.utils import Utils -from datasets.models import Dataset, DatasetConsensus, Consensus, UploadFiles +from datasets.models import Dataset, DatasetConsensus, Consensus, UploadFiles, MetaKey from datasets.tables import DatasetTable, ReferenceTable, ConsensusTable, ProjectTable from datasets.tables import DatasetConsensusTable, AddDatasetFromCvsFileTableMetadata from datasets.forms import AddReferencesDatasetForm, AddConsensusDatasetForm, AddProjectsDatasetForm @@ -30,7 +30,6 @@ from django.db import transaction from Bio import SeqIO from utils.support_django_template import get_link_for_dropdown_item -from utils.process_SGE import ProcessSGE from settings.models import Software as SoftwareSettings from settings.constants_settings import ConstantsSettings from settings.tables import SoftwaresTable @@ -789,6 +788,9 @@ def get_context_data(self, **kwargs): dataset.get_clean_dataset_name(), datetime.datetime.now().strftime(settings.DATE_FORMAT_FOR_SHOW))) context['different_references'] = dataset.get_number_different_references() + context['number_of_consensus'] = dataset.number_of_sequences_from_consensus + context['number_of_references'] = dataset.number_of_sequences_from_references + context['n_consensus_from_projects'] = dataset.number_of_sequences_from_projects context['spinner_url'] = os.path.join("/" + Constants.DIR_STATIC, Constants.DIR_ICONS, Constants.AJAX_LOADING_GIF) context['show_info_main_page'] = ShowInfoMainPage() ## show main information about the institute return context @@ -829,7 +831,8 @@ def get_context_data(self, **kwargs): tag_search = 'search_datasets' query_set = UploadFiles.objects.filter(owner__id=self.request.user.id, is_deleted=False,\ - type_file__name=TypeFile.TYPE_FILE_dataset_file_metadata).order_by('-creation_date') + type_file__name=TypeFile.TYPE_FILE_dataset_file_metadata, is_valid=True, + dataset=dataset).order_by('-creation_date') if (self.request.GET.get(tag_search) != None and self.request.GET.get(tag_search)): query_set = query_set.filter(Q(file_name__icontains=self.request.GET.get(tag_search)) |\ Q(owner__username__icontains=self.request.GET.get(tag_search))) @@ -841,14 +844,11 @@ def get_context_data(self, **kwargs): context['nav_dataset'] = True context['disable_upload_files'] = disable_upload_files - ### test if exists files to process to match with (csv/tsv) file - context['does_not_exists_fastq_files_to_process'] = UploadFiles.objects.filter(owner__id=self.request.user.id, is_deleted=False,\ - type_file__name=TypeFile.TYPE_FILE_sample_file_metadata).order_by('-creation_date').count() == 0 - ### test if can add other csv file count_not_complete = UploadFiles.objects.filter(owner__id=self.request.user.id, is_deleted=False,\ - type_file__name=TypeFile.TYPE_FILE_sample_file_metadata, is_processed=False).count() - if (count_not_complete > 0): + type_file__name=TypeFile.TYPE_FILE_sample_file_metadata, is_processed=False, is_valid=True, + dataset=dataset).count() + if (count_not_complete > 0): context['can_add_other_file'] = "You cannot add other file because there is a file in pipeline." context['disable_upload_files'] = True @@ -916,8 +916,8 @@ def get_context_data(self, **kwargs): context['nav_dataset'] = True context['disable_upload_files'] = disable_upload_files - context['nav_modal'] = True ## short the size of modal window - context['dataset'] = dataset ## dataset in analysis + context['nav_modal'] = True ## short the size of modal window + context['dataset'] = dataset ## dataset in analysis context['show_info_main_page'] = ShowInfoMainPage() ## show main information about the institute return context @@ -933,6 +933,7 @@ def form_valid(self, form): pass utils = Utils() + software = Software() path_name = form.cleaned_data['path_name'] ## create a genbank file @@ -968,6 +969,7 @@ def form_valid(self, form): TypeFile.TYPE_FILE_dataset_file_metadata), upload_files.file_name) sz_file_to = utils.get_unique_file(sz_file_to) ## get unique file name, user can upload files with same name... utils.move_file(os.path.join(getattr(settings, "MEDIA_ROOT", None), upload_files.path_name.name), sz_file_to) + software.dos_2_unix(sz_file_to) upload_files.path_name.name = os.path.join(utils.get_path_upload_file(self.request.user.id,\ TypeFile.TYPE_FILE_dataset_file_metadata), ntpath.basename(sz_file_to)) upload_files.save() diff --git a/managing_files/forms.py b/managing_files/forms.py index ef8e591c..866311ee 100644 --- a/managing_files/forms.py +++ b/managing_files/forms.py @@ -612,6 +612,7 @@ def clean(self): """ Clean all """ + software = Software() cleaned_data = super(SamplesUploadDescriptionForm, self).clean() ### get path name @@ -622,6 +623,7 @@ def clean(self): temp_file_name.write(path_name.file.read()) temp_file_name.flush() temp_file_name.close() + software.dos_2_unix(temp_file_name.name) parse_in_files = ParseInFiles() b_test_char_encoding = True @@ -687,6 +689,7 @@ def clean(self): """ Clean all """ + software = Software() cleaned_data = super(SamplesUploadDescriptionMetadataForm, self).clean() ### get path name @@ -697,6 +700,7 @@ def clean(self): temp_file_name.write(path_name.file.read()) temp_file_name.flush() temp_file_name.close() + software.dos_2_unix(temp_file_name.name) parse_in_files = ParseInFiles() b_test_char_encoding = True diff --git a/managing_files/views.py b/managing_files/views.py index c8b3a156..af338706 100644 --- a/managing_files/views.py +++ b/managing_files/views.py @@ -589,6 +589,7 @@ def form_valid(self, form): pass utils = Utils() + software = Software() path_name = form.cleaned_data['path_name'] ## create a genbank file @@ -620,6 +621,7 @@ def form_valid(self, form): TypeFile.TYPE_FILE_sample_file), upload_files.file_name) sz_file_to = utils.get_unique_file(sz_file_to) ## get unique file name, user can upload files with same name... utils.move_file(os.path.join(getattr(settings, "MEDIA_ROOT", None), upload_files.path_name.name), sz_file_to) + software.dos_2_unix(sz_file_to) upload_files.path_name.name = os.path.join(utils.get_path_upload_file(self.request.user.id,\ TypeFile.TYPE_FILE_sample_file), ntpath.basename(sz_file_to)) upload_files.save() @@ -675,6 +677,7 @@ def form_valid(self, form): pass utils = Utils() + software = Software() path_name = form.cleaned_data['path_name'] ## create a genbank file @@ -706,6 +709,7 @@ def form_valid(self, form): TypeFile.TYPE_FILE_sample_file_metadata), upload_files.file_name) sz_file_to = utils.get_unique_file(sz_file_to) ## get unique file name, user can upload files with same name... utils.move_file(os.path.join(getattr(settings, "MEDIA_ROOT", None), upload_files.path_name.name), sz_file_to) + software.dos_2_unix(sz_file_to) upload_files.path_name.name = os.path.join(utils.get_path_upload_file(self.request.user.id,\ TypeFile.TYPE_FILE_sample_file_metadata), ntpath.basename(sz_file_to)) upload_files.save() diff --git a/static/tests/dataset_files/Nextstrain_metadata.tsv b/static/tests/dataset_files/Nextstrain_metadata.tsv new file mode 100644 index 00000000..ff66bf71 --- /dev/null +++ b/static/tests/dataset_files/Nextstrain_metadata.tsv @@ -0,0 +1,10 @@ +strain date virus region gisaid_epi_isl genbank_accession length segment sex age host vaccine status week latitude longitude type-subtype putative mixed-infection Lineage (Pangolin) classification Lineage Pangolin Scorpio Pangolin +SARS_CoV_2_Wuhan_Hu_1_MN908947 2019-12-26 ncov Asia EPI_ISL_402125 MN908947 29903 genome ? ? ? ? ? ? ? ? ? ? ? ? ? +to_4 2019-12-26 ncov Asia EPI_ISL_406798 LR757998 29866 genome ? ? ? ? ? ? ? ? ? ? ? ? ? +ERR4082026_covid_minion 2022-06-20 ncov Europe ? ? 29903 genome ? ? ? ? ? ? ? Not assigned No B.1.1 ? ? ? +ERR4082025_covid_minion 2022-06-20 ncov Europe ? ? 29905 genome ? ? ? ? ? ? ? Not assigned No B.1 ? ? ? +ERR4569681 2022-06-20 ncov Europe ? ? 29910 genome ? ? ? ? ? ? ? Not assigned No B.1.1.301 ? ? ? +test_covid_4082026 2022-06-20 ncov Europe ? ? 29903 genome ? ? ? ? ? ? ? ? NA (not applicable) ? NA (not applicable) B.1.1 ? +ERR4082027_covid_minion 2022-02-20 ncov Europe ? ? 2d903 genome ? ? ? ? ? ? ? ? NA (not applicable) ? Not assigned B.1.1 ? +ERR4082026_covid_minion_1 2022-06-20 ncov Europe ? ? 29903 genome ? s ? ? ? ? ? ? NA (not applicable) ? Not assigned B.1.1 ? +ERR4082025_covid_minion_1 2022-06-20 ncov Europe ? ? 29903 genome ? 4 ? ? ? ? ? ? NA (not applicable) ? Not assigned B.1.93 ? diff --git a/static/tests/dataset_files/insa_flu_dataset_output_nextstrain.csv b/static/tests/dataset_files/insa_flu_dataset_output_nextstrain.csv index d1fc92b9..236258c4 100755 --- a/static/tests/dataset_files/insa_flu_dataset_output_nextstrain.csv +++ b/static/tests/dataset_files/insa_flu_dataset_output_nextstrain.csv @@ -5,4 +5,4 @@ xpto,2019-12-26,ncov,Europe,?,?,?,genome,?,?,?,a,b,? xpto3,2019-12-21,ncov,Europe,?,?,?,genome,?,?,?,a3,b3,? xpto2,2018-12-21,ncov,Europe,?,?,?,genome,?,?,?,?,a1,b1 xptow2,2015-12-21,ncov,Europe,?,?,?,genome,?,?,?,?,a1,b1 -xptow3,2022-10-19,ncov,Europe,?,?,?,genome,?,?,?,?,a1,b1 +xptow3,DATE_TO_REPLACE,ncov,Europe,?,?,?,genome,?,?,?,?,a1,b1 diff --git a/static/tests/dataset_files/insa_flu_dataset_output_nextstrain_2.csv b/static/tests/dataset_files/insa_flu_dataset_output_nextstrain_2.csv index a4d1806a..24393d96 100755 --- a/static/tests/dataset_files/insa_flu_dataset_output_nextstrain_2.csv +++ b/static/tests/dataset_files/insa_flu_dataset_output_nextstrain_2.csv @@ -5,4 +5,4 @@ xpto,2019-12-26,?,Europe,?,a,b,? xpto3,2019-12-21,?,Europe,?,a3,b3,? xpto2,2018-12-21,?,Europe,?,?,a1,b1 xptow2,2015-12-21,?,Europe,?,?,a1,b1 -xptow3,2022-10-19,?,Europe,?,?,a1,b1 +xptow3,DATE_TO_REPLACE,?,Europe,?,?,a1,b1 diff --git a/static/tests/dataset_files/nextstrain_metadata_input.tsv b/static/tests/dataset_files/nextstrain_metadata_input.tsv new file mode 100755 index 00000000..e421fd8e --- /dev/null +++ b/static/tests/dataset_files/nextstrain_metadata_input.tsv @@ -0,0 +1,6 @@ +strain date genbank_accession region host vaccine status week latitude longitude type-subtype putative mixed-infection xpto new_columns +second_stage_2__test_create_tree 2022-10-24 ? Europe ? ? ? ? ? ? ? ? f +EVA001_S66 2022-10-19 ? Europe ? ? ? ? ? xpto, zpto ? xpto xpto g +EVA002_S52 2022-10-19 ? Europe ? ? ? ? ? xpto, zpto ? xpto xpto h +EVA003_S91 2022-10-24 ? Europe ? ? ? ? ? xpto, zpto ? xpto xpto j +EVA011_S54 2022-10-21 ? Europe ? ? ? ? ? xpto, zpto ? xpto xpto diff --git a/static/tests/dataset_files/out_nextstrain_metadata.tsv b/static/tests/dataset_files/out_nextstrain_metadata_expected.tsv similarity index 66% rename from static/tests/dataset_files/out_nextstrain_metadata.tsv rename to static/tests/dataset_files/out_nextstrain_metadata_expected.tsv index 88129520..b7d1c27d 100755 --- a/static/tests/dataset_files/out_nextstrain_metadata.tsv +++ b/static/tests/dataset_files/out_nextstrain_metadata_expected.tsv @@ -1,6 +1,6 @@ -"strain" "date" "genbank_accession" "region" "host" "vaccine status" "week" "latitude" "longitude" "type-subtype" "putative mixed-infection" "xpto" -"second_stage_2__test_create_tree" "2022-10-19" "?" "Europe" "?" "?" "?" "?" "?" "?" "?" "?" -"EVA001_S66" "2022-10-19" "?" "Europe" "?" "?" "?" "?" "?" "xpto, zpto" "?" "xpto xpto" -"EVA002_S52" "2022-10-19" "?" "Europe" "?" "?" "?" "?" "?" "xpto, zpto" "?" "xpto xpto" -"EVA003_S91" "2022-10-19" "?" "Europe" "?" "?" "?" "?" "?" "xpto, zpto" "?" "xpto xpto" -"EVA011_S54" "2022-10-19" "?" "Europe" "?" "?" "?" "?" "?" "xpto, zpto" "?" "xpto xpto" +"strain" "date" "genbank_accession" "region" "host" "vaccine status" "week" "latitude" "longitude" "type-subtype" "putative mixed-infection" "xpto" +"second_stage_2__test_create_tree" "2022-10-24" "?" "Europe" "?" "?" "?" "?" "?" "?" "?" "?" +"EVA001_S66" "2022-10-19" "?" "Europe" "?" "?" "?" "?" "?" "xpto, zpto" "?" "xpto xpto" +"EVA002_S52" "2022-10-19" "?" "Europe" "?" "?" "?" "?" "?" "xpto, zpto" "?" "xpto xpto" +"EVA003_S91" "2022-10-24" "?" "Europe" "?" "?" "?" "?" "?" "xpto, zpto" "?" "xpto xpto" +"EVA011_S54" "2022-10-21" "?" "Europe" "?" "?" "?" "?" "?" "xpto, zpto" "?" "xpto xpto" diff --git a/static/tests/dataset_files/out_nextstrain_metadata_expected_2.tsv b/static/tests/dataset_files/out_nextstrain_metadata_expected_2.tsv new file mode 100755 index 00000000..5b8c1cd4 --- /dev/null +++ b/static/tests/dataset_files/out_nextstrain_metadata_expected_2.tsv @@ -0,0 +1,6 @@ +"strain" "date" "genbank_accession" "region" "host" "vaccine status" "week" "latitude" "longitude" "type-subtype" "putative mixed-infection" "xpto" "new_columns" +"second_stage_2__test_create_tree" "2022-10-24" "?" "Europe" "?" "?" "?" "?" "?" "?" "?" "?" "f" +"EVA001_S66" "2022-10-19" "?" "Europe" "?" "?" "?" "?" "?" "xpto, zpto" "?" "xpto xpto" "g" +"EVA002_S52" "2022-10-19" "?" "Europe" "?" "?" "?" "?" "?" "xpto, zpto" "?" "xpto xpto" "h" +"EVA003_S91" "2022-10-24" "?" "Europe" "?" "?" "?" "?" "?" "xpto, zpto" "?" "xpto xpto" "j" +"EVA011_S54" "2022-10-21" "?" "Europe" "?" "?" "?" "?" "?" "xpto, zpto" "?" "xpto xpto" "?" diff --git a/static/tests/projects/result/user_5000/project_5000/main_result/Sample_list.csv b/static/tests/projects/result/user_5000/project_5000/main_result/Sample_list.csv index c583b79a..4d015077 100644 --- a/static/tests/projects/result/user_5000/project_5000/main_result/Sample_list.csv +++ b/static/tests/projects/result/user_5000/project_5000/main_result/Sample_list.csv @@ -1,6 +1,6 @@ -id,fastq1,fastq2,data set,vaccine status,week,onset date,collection date,lab reception date,latitude,longitude,type-subtype,putative mixed-infection,xpto -second_stage_2_ test_create_tree,,,,,,,,,,,,, -EVA011_S54,EVA011_S54_L001_R1_001.fastq.gz,EVA011_S54_L001_R2_001.fastq.gz,,,,,,,,,"xpto, zpto",,xpto xpto -EVA003_S91,EVA003_S91_L001_R1_001.fastq.gz,EVA003_S91_L001_R2_001.fastq.gz,,,,,,,,,"xpto, zpto",,xpto xpto -EVA002_S52,EVA002_S52_L001_R1_001.fastq.gz,EVA002_S52_L001_R2_001.fastq.gz,,,,,,,,,"xpto, zpto",,xpto xpto -EVA001_S66,EVA001_S66_L001_R1_001.fastq.gz,EVA001_S66_L001_R2_001.fastq.gz,,,,,,,,,"xpto, zpto",,xpto xpto +id,fastq1,fastq2,data set,vaccine status,week,onset date,collection date,lab reception date,latitude,longitude,type-subtype,putative mixed-infection,xpto +second_stage_2_ test_create_tree,,,,,,2022-10-19,2022-10-19,2022-10-19,,,,, +EVA011_S54,EVA011_S54_L001_R1_001.fastq.gz,EVA011_S54_L001_R2_001.fastq.gz,,,,2022-10-20,2022-10-21,2022-10-22,,,"xpto, zpto",,xpto xpto +EVA003_S91,EVA003_S91_L001_R1_001.fastq.gz,EVA003_S91_L001_R2_001.fastq.gz,,,,2022-10-25,2022-10-24,2022-10-23,,,"xpto, zpto",,xpto xpto +EVA002_S52,EVA002_S52_L001_R1_001.fastq.gz,EVA002_S52_L001_R2_001.fastq.gz,,,,2022-10-19,2022-10-19,2022-10-19,,,"xpto, zpto",,xpto xpto +EVA001_S66,EVA001_S66_L001_R1_001.fastq.gz,EVA001_S66_L001_R2_001.fastq.gz,,,,2022-10-19,2022-10-19,2022-10-19,,,"xpto, zpto",,xpto xpto diff --git a/templates/datasets/datasets_consensus_show.html b/templates/datasets/datasets_consensus_show.html index e0a2d3b0..655ed82e 100644 --- a/templates/datasets/datasets_consensus_show.html +++ b/templates/datasets/datasets_consensus_show.html @@ -54,8 +54,7 @@
-
#References: {{ n_references }}
-
#Consensus: {{ n_consensus }}
+
#References: {{ number_of_references }}
#Consensus from projects: {{ n_consensus_from_projects }}
@@ -166,7 +165,7 @@
Metadata for NextStrain @@ -254,7 +253,7 @@
{% endif %} Go back - + Refresh