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Merged in remove_old_taxonomy branch.
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@SarahW91
SarahW91 committed Jul 16, 2021
1 parent 296368c commit 34a3834
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Showing 84 changed files with 995 additions and 3,597 deletions.
4 changes: 3 additions & 1 deletion Capfile
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Original file line number Diff line number Diff line change
Expand Up @@ -12,10 +12,12 @@ require 'capistrano/rbenv'

require 'capistrano/puma'
install_plugin Capistrano::Puma
install_plugin Capistrano::Puma::Systemd
install_plugin Capistrano::Puma::Monit

require 'capistrano/sidekiq'
require 'capistrano/sidekiq/monit'
install_plugin Capistrano::Sidekiq
install_plugin Capistrano::Sidekiq::Monit

require 'whenever/capistrano'

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361 changes: 361 additions & 0 deletions app/assets/javascripts/datatable_initialisation.js
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@@ -0,0 +1,361 @@
jQuery(function() {
// FREEZERS
$('#freezers').DataTable( {
bProcessing: true,
bServerSide: true,
sAjaxSource: $('#freezers').data('source'),
"columnDefs": [
{ "orderable": false, "targets": 3 }
],
"order": [ 2, 'desc' ]
} );

//HERBARIA
$('#herbaria').DataTable( {
bProcessing: true,
bServerSide: true,
sAjaxSource: $('#herbaria').data('source'),
"columnDefs": [
{ "orderable": false, "targets": 3 }
],
"order": [1, 'asc']
} );

// ISOLATES
$('#isolates').DataTable( {
bProcessing: true,
bServerSide: true,
sAjaxSource: $('#isolates').data('source'),
"columnDefs": [
{ "orderable": false, "targets": 5 }
],
"order": [ 4, 'desc' ]
} );

$('#isolates_no_specimen').DataTable( {
bProcessing: true,
bServerSide: true,
sAjaxSource: $('#isolates_no_specimen').data('source'),
"columnDefs": [
{ "orderable": false, "targets": 5 }
],
"order": [ 0, 'asc' ]
} );

$('#isolates_duplicates').DataTable( {
bProcessing: true,
bServerSide: true,
sAjaxSource: $('#isolates_duplicates').data('source'),
"columnDefs": [
{ "orderable": false, "targets": 5 }
],
"order": [ 0, 'desc' ]
} );

// LAB RACKS
$('#lab_racks').DataTable( {
bProcessing: true,
bServerSide: true,
sAjaxSource: $('#lab_racks').data('source'),
"columnDefs": [
{ "orderable": false, "targets": 5 }
],
"order": [ 0, 'desc' ]
} );

// MARKERS
$('#markers').DataTable( {
"columnDefs": [
{ "orderable": false, "targets": 2 }
],
"order": [ 7, 'desc' ]
} );

// MICRONIC PLATES
$('#micronic_plates').DataTable( {
bProcessing: true,
bServerSide: true,
sAjaxSource: $('#micronic_plates').data('source'),
"columnDefs": [
{ "orderable": false, "targets": 6 }
],
"order": [ 5, 'desc' ]
} );

// PLANT PLATES
$('#plant_plates').DataTable( {
bProcessing: true,
bServerSide: true,
sAjaxSource: $('#plant_plates').data('source'),
"columnDefs": [
{ "orderable": false, "targets": 2 }
],
"order": [ 1, 'desc' ]
} );

// PRIMERS
$('#primers').DataTable( {
"order": [ 4, 'desc' ],
"columnDefs": [
{ "orderable": false, "targets": 5 }
]
} );

// USERS
$('#users').DataTable( {
"columnDefs": [
{ "orderable": false, "targets": 3 },
{ "orderable": false, "targets": 7 }
]
} );

// CLUSTERS
$('#clusters').DataTable( {
bProcessing: true,
bServerSide: true,
sAjaxSource: $('#clusters').data('source'),
"columnDefs": [
{ "orderable": false, "targets": 5 }
],
"order": [ 4, 'desc' ]
} );

// CONTIG SEARCHES
$('#contig_searches').dataTable( {
bProcessing: true,
bServerSide: true,
sAjaxSource: $('#contig_searches').data('source'),
"columnDefs": [{
"targets": 3,
"orderable": false
}],
"order": [ 2, 'desc' ]
} );

$('#contig_search_results').dataTable( {
bProcessing: true,
bServerSide: true,
sAjaxSource: $('#contig_search_results').data('source'),
"columnDefs": [{
"targets": [1, 2, 5],
"orderable": false
}],
"order": [ 0, 'asc' ]
} );

// CONTIGS
$('#contigs').DataTable( {
bProcessing: true,
bServerSide: true,
sAjaxSource: $('#contigs').data('source'),
"columnDefs": [
{ "orderable": false, "targets": 5 }
],
"order": [ 4, 'desc' ]
} );

$('#contigs-duplicates').DataTable( {
bProcessing: true,
bServerSide: true,
sAjaxSource: $('#contigs-duplicates').data('source'),
"columnDefs": [
{ "orderable": false, "targets": 5 }
],
"order": [ 0, 'asc' ]
} );

// INDIVIDUAL SEARCHES
$('#individual_searches').dataTable( {
bProcessing: true,
bServerSide: true,
sAjaxSource: $('#individual_searches').data('source'),
"columnDefs": [{
"orderable": false,
"targets": 3
}],
"order": [ 2, 'desc' ]
} );

$('#individual_search_results').dataTable( {
bProcessing: true,
bServerSide: true,
sAjaxSource: $('#individual_search_results').data('source'),
"columnDefs": [{
"orderable": false,
"targets": [1, 6]
}],
"order": [ 0, 'asc' ]
} );

// INDIVIDUALS
$('#individuals').DataTable( {
bProcessing: true,
bServerSide: true,
sAjaxSource: $('#individuals').data('source'),
"columnDefs": [
{ "orderable": false, "targets": 6 }
],
"order": [5, 'desc']
} );

// ISSUES
$('#issues').dataTable( {
bProcessing: true,
bServerSide: true,
sAjaxSource: $('#issues').data('source'),
"columnDefs": [
{ "orderable": false, "targets": 1 },
{ "orderable": false, "targets": 2 }
],
"order": [ 3, 'desc' ]
} );

// MARKERS SEQUENCE SEARCHES
$('#marker_sequence_searches').dataTable( {
bProcessing: true,
bServerSide: true,
sAjaxSource: $('#marker_sequence_searches').data('source'),
"columnDefs": [{
"orderable": false,
"targets": 3
}],
"order": [ 2, 'desc' ]
} );

$('#marker_sequence_search_results').dataTable( {
bProcessing: true,
bServerSide: true,
sAjaxSource: $('#marker_sequence_search_results').data('source'),
"columnDefs": [{
"orderable": false,
"targets": [1, 3]
}],
"order": [ 0, 'asc' ]
} );

// MARKER SEQUENCES
$('#marker_sequences').DataTable( {
bProcessing: true,
bServerSide: true,
sAjaxSource: $('#marker_sequences').data('source'),
"columnDefs": [
{ "orderable": false, "targets": 3 }
],
"order": [ 2, 'desc' ]
} );

// MISLABEL ANALYSES
$('#mislabel_analyses').dataTable( {
bProcessing: true,
bServerSide: true,
sAjaxSource: $('#mislabel_analyses').data('source'),
"columnDefs": [{
"orderable": false,
"targets": [1, 4]
}],
"order": [3, 'desc']
} );

$('#mislabel_analysis_results').dataTable( {
bProcessing: true,
bServerSide: true,
sAjaxSource: $('#mislabel_analysis_results').data('source'),
"columnDefs": [{
"orderable": false,
"targets": 6
}],
"order": [0, 'asc']
} );

// NGS RUNS
$('#ngs_runs').dataTable( {
bProcessing: true,
bServerSide: true,
sAjaxSource: $('#ngs_runs').data('source'),
"columnDefs": [{
"targets": 2,
"orderable": false
}],
"order": [1, 'desc']
} );

$('#ngs_run_results').dataTable( {
bProcessing: true,
bServerSide: true,
sAjaxSource: $('#ngs_run_results').data('source'),
"sScrollY": document.body.clientHeight * 70 / 100,
"scrollX": true,
scroller: {
loadingIndicator: true,
displayBuffer: 2
},
deferRender: true,
"columnDefs": [{
"targets": 3,
"orderable": false
}],
"order": [0, 'desc']
} );

// PRIMER READS
$('#primer_reads').DataTable( {
bProcessing: true,
bServerSide: true,
sAjaxSource: $('#primer_reads').data('source'),
"columnDefs": [
{ "orderable": false, "targets": 4 }
],
"order": [ 3, 'desc' ]
} );

$('#primer_reads-duplicates').DataTable( {
bProcessing: true,
bServerSide: true,
sAjaxSource: $('#primer_reads-duplicates').data('source'),
"columnDefs": [
{ "orderable": false, "targets": 4 }
],
"order": [ 0, 'asc' ]
} );

$('#reads_without_contigs').DataTable( {
bProcessing: true,
bServerSide: true,
sAjaxSource: $('#reads_without_contigs').data('source'),
"columnDefs": [
{ "orderable": false, "targets": 4 }
],
"order": [ 3, 'desc' ]
} );

// TAXA
$('#associated_individuals').DataTable( {
bProcessing: true,
bServerSide: true,
sAjaxSource: $('#associated_individuals').data('source'),
"columnDefs": [
{ "orderable": false, "targets": 6 }
],
"order": [5, 'desc']
} );

$('#direct_children').DataTable( {
bProcessing: true,
bServerSide: true,
sAjaxSource: $('#direct_children').data('source'),
"columnDefs": [
{ "orderable": false, "targets": 5 }
],
"order": [ 0, 'asc' ]
} );

$('#orphans').DataTable( {
bProcessing: true,
bServerSide: true,
sAjaxSource: $('#orphans').data('source'),
"columnDefs": [
{ "orderable": false, "targets": 5 }
],
"order": [ 0, 'asc' ]
} );
} );
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