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Update the release page to use the new release count webservice
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@tcezard
tcezard committed Jul 3, 2024
1 parent 65fff37 commit bc993c9
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Showing 3 changed files with 67 additions and 63 deletions.
13 changes: 10 additions & 3 deletions Gruntfile.js
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Original file line number Diff line number Diff line change
Expand Up @@ -63,7 +63,8 @@ module.exports = function (grunt) {
'EVA_RELEASE_HOST' : "wwwint.ebi.ac.uk/eva/webservices/release",
'EVA_ACCESSIONING_HOST': 'wwwint.ebi.ac.uk/eva/webservices/identifiers',
'EVA_VCF_DUMPER_HOST': 'wwwint.ebi.ac.uk/eva/webservices/vcf-dumper',
'EVA_VERSION': 'v1'
'EVA_VERSION': 'v1',
'EVA_STAT_VERSION': 'v2'
}
}
},
Expand All @@ -78,7 +79,8 @@ module.exports = function (grunt) {
'EVA_RELEASE_HOST' : "wwwdev.ebi.ac.uk/eva/webservices/release",
'EVA_ACCESSIONING_HOST': 'wwwdev.ebi.ac.uk/eva/webservices/identifiers',
'EVA_VCF_DUMPER_HOST': 'wwwdev.ebi.ac.uk/eva/webservices/vcf-dumper',
'EVA_VERSION': 'v1'
'EVA_VERSION': 'v1',
'EVA_STAT_VERSION': 'v2'
}
}
},
Expand All @@ -93,7 +95,8 @@ module.exports = function (grunt) {
'EVA_RELEASE_HOST' : "www.ebi.ac.uk/eva/webservices/release",
'EVA_ACCESSIONING_HOST': 'www.ebi.ac.uk/eva/webservices/identifiers',
'EVA_VCF_DUMPER_HOST': 'www.ebi.ac.uk/eva/webservices/vcf-dumper',
'EVA_VERSION': 'v1'
'EVA_VERSION': 'v1',
'EVA_STAT_VERSION': 'v2'
}
}
}
Expand Down Expand Up @@ -137,6 +140,10 @@ module.exports = function (grunt) {
{
match: 'EVA_VERSION',
replacement: '<%= grunt.config.get("EVA_VERSION") %>'
},
{
match: 'EVA_STAT_VERSION',
replacement: '<%= grunt.config.get("EVA_STAT_VERSION") %>'
}
]
},
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1 change: 1 addition & 0 deletions src/js/eva-manager-config.js
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Original file line number Diff line number Diff line change
Expand Up @@ -29,6 +29,7 @@ EVA_VCF_DUMPER_HOST = "https:" + "//@@EVA_VCF_DUMPER_HOST";
DBSNP_VERSION = '@@DBSNP_VERSION';
DGVA_VERSION = '@@DGVA_VERSION';
EVA_VERSION = '@@EVA_VERSION';
EVA_STAT_VERSION = '@@EVA_STAT_VERSION';

var EvaManager = {
host: EVA_HOST,
Expand Down
116 changes: 56 additions & 60 deletions src/js/rs-release/rs-release.js
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Original file line number Diff line number Diff line change
Expand Up @@ -33,10 +33,10 @@ EvaRsRelease.prototype = {
}

this.draw(this.createContent(releaseVersion))
$("#rs-release-table").tablesorter({ sortList: [[2,1]] });
$("#rs-release-table-new-data").tablesorter({ sortList: [[2,1]] });
$("#rs-release-table").tablesorter({ sortList: [[4,1]] }); // Sort by Current RS
$("#rs-release-table-new-data").tablesorter({ sortList: [[3,1]] }); // Sort by new Current RS
$("#rs-release-table-by-assembly").tablesorter({ sortList: [[3,1]] });
$("#rs-release-table-by-assembly-new-data").tablesorter({ sortList: [[3,1]] });
$("#rs-release-table-by-assembly-new-data").tablesorter({ sortList: [[2,1]] }); // Sort by new Current RS
$(document).foundation();
},

Expand Down Expand Up @@ -126,7 +126,7 @@ EvaRsRelease.prototype = {
var releaseData;
EvaManager.get({
host:EVA_RELEASE_HOST,
version: EVA_VERSION,
version: EVA_STAT_VERSION,
category: 'stats',
resource: 'per-species',
params: {releaseVersion: releaseVersion},
Expand All @@ -143,10 +143,11 @@ EvaRsRelease.prototype = {
var table = '<table id="rs-release-table" class="responsive-table hover tablesorter table-fixed">' +
'<thead>' +
'<tr>' +
'<th>Download link</th>' +
'<th>Scientific name</th>' +
'<th>Taxonomy ID</th>' +
'<th>Assemblies</th>' +
'<th><div title="RS IDs that can be browsed on the EVA websites">Current RS <i class="icon icon-generic" data-icon="i"></div></th>' +
'<th><div title="RS IDs that are resolved to multiple location on the genome">Multi-mapped RS <i class="icon icon-generic" data-icon="i"></div></th>' +
'<th><div title="RS IDs that should NOT be used because they are merged into another active RS">Merged RS <i class="icon icon-generic" data-icon="i"></div></th>' +
'<th><div title="RS IDs that should NOT be used since these RS IDs were deprecated">Deprecated RS <i class="icon icon-generic" data-icon="i"></div></th>' +
'<th><div title="RS IDs that should NOT be used because they have been merged into a deprecated RS">Merged Deprecated RS <i class="icon icon-generic" data-icon="i"></div></th>' +
Expand All @@ -156,14 +157,19 @@ EvaRsRelease.prototype = {
'<tbody>';

_.each(releaseData, function (species) {
releaseLink = '<a target="_blank" href="' + species.releaseLink + '">' + species.scientificName + '</a>';
releaseLink = '<a target="_blank" href="' + species.releaseLink + '">FTP link</a>';
taxonomyLink = '<a target="_blank" href="' + species.taxonomyLink + '">' + species.taxonomyId + '</a>';

AssemblyLinks = _.chain(species.assemblyAccessions)
.filter(function(assemblyAccession){return assemblyAccession !== "Unmapped"})
.map(function(assemblyAccession){
return '<a target="_blank" href="https://www.ebi.ac.uk/ena/browser/view/' + assemblyAccession + '">' + assemblyAccession + '</a>';})
.value().join(', ');
table += '<tr>' +
'<td><span class="rs-release-scientific-name">' + releaseLink + '</span></td>' +
'<td>' + releaseLink + '</span></td>' +
'<td><span class="rs-release-scientific-name">' + species.scientificName + '</span></td>' +
'<td><span class="rs-release-tax-id">' + taxonomyLink + '</span></td>' +
'<td><span class="rs-release-assembly-accession">' + AssemblyLinks + '</span></td>' +
'<td class="numerical-column-right-align"><span class="rs-release-current-rs">' + species.currentRs.toLocaleString() + '</span></td>' +
'<td class="numerical-column-right-align"><span class="rs-release-current-rs">' + species.multiMappedRs.toLocaleString() + '</span></td>' +
'<td class="numerical-column-right-align"><span class="rs-release-current-rs">' + species.mergedRs.toLocaleString() + '</span></td>' +
'<td class="numerical-column-right-align"><span class="rs-release-current-rs">' + species.deprecatedRs.toLocaleString() + '</span></td>' +
'<td class="numerical-column-right-align"><span class="rs-release-current-rs">' + species.mergedDeprecatedRs.toLocaleString() + '</span></td>' +
Expand All @@ -179,7 +185,7 @@ EvaRsRelease.prototype = {
var releaseData;
EvaManager.get({
host:EVA_RELEASE_HOST,
version: EVA_VERSION,
version: EVA_STAT_VERSION,
category: 'stats',
resource: 'per-assembly/new',
params: {releaseVersion: releaseVersion},
Expand All @@ -193,35 +199,29 @@ EvaRsRelease.prototype = {
}
});

var table = '<table id="rs-release-table-by-assembly" class="responsive-table hover tablesorter table-fixed">' +
var table = '<table id="rs-release-table-by-assembly-new-data" class="responsive-table hover tablesorter table-fixed">' +
'<thead>' +
'<tr>' +
'<th>Scientific name</th>' +
'<th>Taxonomy ID</th>' +
'<th>Download link</th>' +
'<th>Assembly accession</th>' +
'<th><div title="RS IDs that were clustered in the current release">New Current RS <i class="icon icon-generic" data-icon="i"></div></th>' +
'<th><div title="RS IDs that were issued for remapped variants">Remapped clustered <i class="icon icon-generic" data-icon="i"></div></th>' +
'<th><div title="RS IDs that were created for new variants">Newly clustered <i class="icon icon-generic" data-icon="i"></div></th>' +
'<th><div title="RS IDs that should NOT be used because they are merged into another active RS">Merged RS <i class="icon icon-generic" data-icon="i"></div></th>' +
'<th><div title="RS IDs that were split into multiple active RS due to remapping">Split RS <i class="icon icon-generic" data-icon="i"></div></th>' +
'<th><div title="RS IDs that were added in the current release">New Current RS<i class="icon icon-generic" data-icon="i"></div></th>' +
'</tr>' +
'</thead>' +
'<tbody>';

_.each(releaseData, function (species) {
releaseLink = '<a target="_blank" href="' + species.releaseLink + '">' + species.scientificName + '</a>';
taxonomyLink = '<a target="_blank" href="' + species.taxonomyLink + '">' + species.taxonomyId + '</a>';
assemblyLink = '<a target="_blank" href="' + species.releaseLink + '">' + species.assemblyAccession + '</a>';

_.each(releaseData, function (assembly) {
releaseLink = '<a target="_blank" href="' + assembly.releaseLink + '">FTP link</a>';
assemblyLink = '<a target="_blank" href="' + assembly.releaseLink + '">' + assembly.assemblyAccession + '</a>';
scientificNames = '';
taxonomyLinks = _.chain(assembly.taxonomyIds)
.zip(assembly.taxonomyLinks)
.map(function(taxonomyInfo){
return '<a target="_blank" href="' + taxonomyInfo[1] + '">' + taxonomyInfo[0] + '</a>'})
.value().join(', ');
table += '<tr>' +
'<td><span class="rs-release-scientific-name">' + releaseLink + '</span></td>' +
'<td><span class="rs-release-tax-id">' + taxonomyLink + '</span></td>' +
'<td>' + releaseLink + '</td>' +
'<td><span class="rs-release-assembly-accession">' + assemblyLink + '</span></td>' +
'<td class="numerical-column-right-align"><span class="rs-release-current-rs">' + species.newCurrentRs.toLocaleString() + '</span></td>' +
'<td class="numerical-column-right-align"><span class="rs-release-current-rs">' + species.newRemappedCurrentRs.toLocaleString() + '</span></td>' +
'<td class="numerical-column-right-align"><span class="rs-release-current-rs">' + species.newClusteredCurrentRs.toLocaleString() + '</span></td>' +
'<td class="numerical-column-right-align"><span class="rs-release-current-rs">' + species.newMergedRs.toLocaleString() + '</span></td>' +
'<td class="numerical-column-right-align"><span class="rs-release-current-rs">' + species.newSplitRs.toLocaleString() + '</span></td>' +
'<td class="numerical-column-right-align"><span class="rs-release-current-rs">' + assembly.newCurrentRs.toLocaleString() + '</span></td>' +
'</tr>';
})

Expand All @@ -233,7 +233,7 @@ EvaRsRelease.prototype = {
var releaseData;
EvaManager.get({
host:EVA_RELEASE_HOST,
version: EVA_VERSION,
version: EVA_STAT_VERSION,
category: 'stats',
resource: 'per-assembly',
params: {releaseVersion: releaseVersion},
Expand All @@ -247,43 +247,40 @@ EvaRsRelease.prototype = {
}
});

var table = '<table id="rs-release-table-by-assembly-new-data" class="responsive-table hover tablesorter table-fixed">' +
var table = '<table id="rs-release-table-by-assembly" class="responsive-table hover tablesorter table-fixed">' +
'<thead>' +
'<tr>' +
'<th>Scientific name</th>' +
'<th>Taxonomy ID</th>' +
'<th>Download link</th>' +
'<th>Assembly accession</th>' +
'<th>Taxonomy ID</th>' +
'<th><div title="RS IDs that can be browsed on the EVA websites">Current RS <i class="icon icon-generic" data-icon="i"></div></th>' +
'<th><div title="RS IDs that were clustered but the EVA">Clustered Current RS <i class="icon icon-generic" data-icon="i"></div></th>' +
'<th><div title="RS IDs that are resolved to multiple location on the genome">Multi-mapped RS <i class="icon icon-generic" data-icon="i"></div></th>' +
'<th><div title="RS IDs that should NOT be used because they are merged into another active RS">Merged RS <i class="icon icon-generic" data-icon="i"></div></th>' +
'<th><div title="RS IDs that were split into multiple active RS due to remapping">Split RS <i class="icon icon-generic" data-icon="i"></div></th>' +
'<th><div title="RS IDs that should NOT be used since these RS IDs were deprecated">Deprecated RS <i class="icon icon-generic" data-icon="i"></div></th>' +
'<th><div title="RS IDs that should NOT be used because they have been merged into a deprecated RS">Merged Deprecated RS <i class="icon icon-generic" data-icon="i"></div></th>' +
'<th><div title="SS IDs that have been clustered">SS clustered <i class="icon icon-generic" data-icon="i"></div></th>' +
'</tr>' +
'</thead>' +
'<tbody>';

_.each(releaseData, function (species) {
releaseLink = '<a target="_blank" href="' + species.releaseLink + '">' + species.scientificName + '</a>';
taxonomyLink = '<a target="_blank" href="' + species.taxonomyLink + '">' + species.taxonomyId + '</a>';
assemblyLink = '<a target="_blank" href="' + species.releaseLink + '">' + species.assemblyAccession + '</a>';

_.chain(releaseData)
.filter(function(releaseData){return releaseData.assemblyAccession !== "Unmapped"})
.each(function (assembly) {
releaseLink = '<a target="_blank" href="' + assembly.releaseLink + '">FTP link</a>';
assemblyLink = '<a target="_blank" href="' + assembly.releaseLink + '">' + assembly.assemblyAccession + '</a>';
taxonomyLinks = _.chain(assembly.taxonomyIds)
.zip(assembly.taxonomyLinks)
.map(function(taxonomyInfo){
return '<a target="_blank" href="' + taxonomyInfo[1] + '">' + taxonomyInfo[0] + '</a>'})
.value().join(', ');
table += '<tr>' +
'<td><span class="rs-release-scientific-name">' + releaseLink + '</span></td>' +
'<td><span class="rs-release-tax-id">' + taxonomyLink + '</span></td>' +
'<td>' + releaseLink + '</td>' +
'<td><span class="rs-release-assembly-accession">' + assemblyLink + '</span></td>' +
'<td class="numerical-column-right-align"><span class="rs-release-current-rs">' + species.currentRs.toLocaleString() + '</span></td>' +
'<td class="numerical-column-right-align"><span class="rs-release-current-rs">' + species.clusteredCurrentRs.toLocaleString() + '</span></td>' +
'<td class="numerical-column-right-align"><span class="rs-release-current-rs">' + species.multiMappedRs.toLocaleString() + '</span></td>' +
'<td class="numerical-column-right-align"><span class="rs-release-current-rs">' + species.mergedRs.toLocaleString() + '</span></td>' +
'<td class="numerical-column-right-align"><span class="rs-release-current-rs">' + species.splitRs.toLocaleString() + '</span></td>' +
'<td class="numerical-column-right-align"><span class="rs-release-current-rs">' + species.deprecatedRs.toLocaleString() + '</span></td>' +
'<td class="numerical-column-right-align"><span class="rs-release-current-rs">' + species.mergedDeprecatedRs.toLocaleString() + '</span></td>' +
'<td class="numerical-column-right-align"><span class="rs-release-current-rs">' + species.ssClustered.toLocaleString() + '</span></td>' +
'<td><span class="rs-release-tax-id">' + taxonomyLinks + '</span></td>' +
'<td class="numerical-column-right-align"><span class="rs-release-current-rs">' + assembly.currentRs.toLocaleString() + '</span></td>' +
'<td class="numerical-column-right-align"><span class="rs-release-current-rs">' + assembly.mergedRs.toLocaleString() + '</span></td>' +
'<td class="numerical-column-right-align"><span class="rs-release-current-rs">' + assembly.deprecatedRs.toLocaleString() + '</span></td>' +
'<td class="numerical-column-right-align"><span class="rs-release-current-rs">' + assembly.mergedDeprecatedRs.toLocaleString() + '</span></td>' +
'</tr>';
})
}).value()

table += '</tbody></table>';
return table;
Expand All @@ -293,7 +290,7 @@ EvaRsRelease.prototype = {
var newDataReleased;
EvaManager.get({
host:EVA_RELEASE_HOST,
version: EVA_VERSION,
version: EVA_STAT_VERSION,
category: 'stats',
resource: 'per-species/new',
params: {releaseVersion: releaseVersion},
Expand All @@ -310,23 +307,22 @@ EvaRsRelease.prototype = {
var table = '<table id="rs-release-table-new-data" class="responsive-table hover tablesorter table-fixed">' +
'<thead>' +
'<tr>' +
'<th>Download link</th>' +
'<th>Scientific name</th>' +
'<th>Taxonomy ID</th>' +
'<th><div title="RS IDs that were created in this release">New RS IDs <i class="icon icon-generic" data-icon="i"></div></th>' +
'<th><div title="SS id that were clustered in this release under an new or existing RS id">New SS IDs Clustered <i class="icon icon-generic" data-icon="i"></div></th>' +
'</tr>' +
'</thead>' +
'<tbody>';

_.each(newDataReleased, function (species) {
releaseLink = '<a target="_blank" href="' + species.releaseLink + '">' + species.scientificName + '</a>';
releaseLink = '<a target="_blank" href="' + species.releaseLink + '">FTP link</a>';
taxonomyLink = '<a target="_blank" href="' + species.taxonomyLink + '">' + species.taxonomyId + '</a>';

table += '<tr>' +
'<td><span class="rs-release-scientific-name">' + releaseLink + '</span></td>' +
'<td>' + releaseLink + '</span></td>' +
'<td><span class="rs-release-scientific-name">' + species.scientificName + '</span></td>' +
'<td><span class="rs-release-tax-id">' + taxonomyLink + '</span></td>' +
'<td class="numerical-column-right-align"><span class="rs-release-current-rs">' + species.newCurrentRs.toLocaleString() + '</span></td>' +
'<td class="numerical-column-right-align"><span class="rs-release-current-rs">' + species.newSsClustered.toLocaleString() + '</span></td>' +
'</tr>';
})

Expand Down

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