diff --git a/lib/jsorolla b/lib/jsorolla index 6b5c62588..fed62514e 160000 --- a/lib/jsorolla +++ b/lib/jsorolla @@ -1 +1 @@ -Subproject commit 6b5c625884d9c51c20b025a1897113a1f93fdadf +Subproject commit fed62514e9686be7aa1a712b033b6d8eef305815 diff --git a/package.json b/package.json index d0acaa53c..d425b461a 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "iva", - "version": "1.0.0-rc3", + "version": "1.0.0-rc4", "description": "IVA description", "repository": { "type": "git", @@ -36,7 +36,7 @@ "crypto-js": "~3.1.9-1", "eonasdan-bootstrap-datetimepicker": "~4.17.43", "file-saver": "~1.3.2", - "font-awesome": "*", + "@fortawesome/fontawesome-free": "^5.6.0", "highcharts": "~4.2.7", "jquery": "~2.2.4", "jquery.json-viewer": "^1.1.0", diff --git a/src/conf/config.js b/src/conf/config.js index d7cc3e177..7d4933da5 100644 --- a/src/conf/config.js +++ b/src/conf/config.js @@ -77,7 +77,7 @@ const opencga = { const application = { title: "IVA", - version: "v1.0.0-rc3", + version: "v1.0.0-rc4", logo: "img/opencb-logo.png", // The order, title and nested submenus are respected menu: [ @@ -91,6 +91,11 @@ const application = { title: "Aggregation Stats", visibility: "public", }, + { + id: "clinicalAnalysisPortal", + title: "Interpretation Portal", + visibility: "public", + }, { id: "beacon", title: "Beacon", @@ -99,22 +104,8 @@ const application = { { id: "case", title: "Clinical", - visibility: "public", + visibility: "none", submenu: [ - { - id: "clinicalAnalysisPortal", - title: "Interpretation Portal", - visibility: "public", - }, - { - id: "interpretation", - title: "Variant Interpreter", - visibility: "public", - }, - { - separator: true, - visibility: "public", - }, { id: "clinical", title: "Clinical (Old)", @@ -124,7 +115,7 @@ const application = { }, { id: "genomeBrowser", - title: "Genome Browser (Beta)", + title: "Genome Browser", visibility: "public" }, { @@ -185,9 +176,14 @@ const application = { category: true, visibility: "public", }, + { + id: "interpretation", + title: "Variant Interpreter", + visibility: "public", + }, { id: "tiering", - title: "Tiering (Genomics England)", + title: "OpenCGA Tiering (Based on GEL Tiering)", visibility: "public", }, { @@ -223,7 +219,7 @@ const application = { }, { id: "catalog", - title: "Catalog (New!)", + title: "Catalog Metadata", visibility: "public", submenu: [ { @@ -283,7 +279,7 @@ const application = { visible: true, }, settings: { - visibility: "public", + visible: false, }, about: { dropdown: true, @@ -367,12 +363,16 @@ const populationFrequencies = { common: "#0000ff", unobserved: "black" }, + tooltip: `1000 Genomes Only considers variants whose observed allelic frequency in the 1000 genomes phase 3 database + is below (or above) the defined value. Genome-wide allelic frequencies were obtained from more than 2.500 genomes.

+ gnomAD Genomes Only considers variants whose observed allelic frequency in the gnomAD Genomes database is + below (or above) the defined value. Frequencies were calculated from about 15,000 unrelated individuals`, studies: [ { id: "1kG_phase3", title: "1000 Genomes", - tooltip: "Only considers variants whose observed allelic frequency in the 1000 genomes phase 3 database is below (or above) " + - "the defined value. Genome-wide allelic frequencies were obtained from more than 2.500 genomes.", + // tooltip: "Only considers variants whose observed allelic frequency in the 1000 genomes phase 3 database is below (or above) " + + // "the defined value. Genome-wide allelic frequencies were obtained from more than 2.500 genomes.", populations: [ { id: "ALL", title: "All populations [ALL]", @@ -397,8 +397,8 @@ const populationFrequencies = { { id: "GNOMAD_GENOMES", title: "gnomAD Genomes", - tooltip: "Only considers variants whose observed allelic frequency in the gnomAD Genomes database is below (or above) the " + - "defined value. Frequencies were calculated from about 15,000 unrelated individuals.", + // tooltip: "Only considers variants whose observed allelic frequency in the gnomAD Genomes database is below (or above) the " + + // "defined value. Frequencies were calculated from about 15,000 unrelated individuals.", populations: [ { id: "ALL", title: "gnomAD [ALL]", diff --git a/src/conf/tools.js b/src/conf/tools.js index c90f5edc2..ddab97209 100644 --- a/src/conf/tools.js +++ b/src/conf/tools.js @@ -17,6 +17,7 @@ /** * Created by imedina on 05/06/17. */ + const filterMenu = { searchButtonText: "Search", tooltip: { @@ -77,7 +78,7 @@ const filterMenu = { }, { id: "biotype", - title: "Biotype", + title: "Gene Biotype", biotypes: [ "3prime_overlapping_ncrna", "IG_C_gene", "IG_C_pseudogene", "IG_D_gene", "IG_J_gene", "IG_J_pseudogene", "IG_V_gene", "IG_V_pseudogene", "Mt_rRNA", "Mt_tRNA", "TR_C_gene", "TR_D_gene", "TR_J_gene", "TR_J_pseudogene", @@ -104,13 +105,8 @@ const filterMenu = { { id: "populationFrequency", title: "Select Population Frequency", - tooltip: "1000 Genomes only considers variants whose observed allelic frequency in the 1000 Genomes " + - "Phase 3 project is below (or above) the defined value. Allele frequencies were obtained from about 2,500 samples." + - "
ExAC only considers variants whose observed allelic frequency in the The Exome Aggregation " + - "Consortium (ExAC) database is below (or above) the defined value. ExAC covers only exomic positions. " + - "The frequencies were obtained using more than 60.000 exomes." + - "
ESP56500 only considers variants whose observed allelic frequency in the Exome Variant Server " + - "(ESP6500) database is below (or above) the defined value. ESP6500 covers only exomic positions from about 6000 exomes" + tooltip: populationFrequencies.tooltip, + showSetAll: true } ] }, @@ -247,7 +243,7 @@ const tools = { examples: [ { name: "Example BRCA2", - active: true, + active: false, query: { gene: "BRCA2", conservation: "phylop<0.001" @@ -304,13 +300,13 @@ const tools = { { id: "network", component: "reactome-variant-network", - title: "Gene network" + title: "Reactome Pathways" }, - { - id: "template", - component: "opencga-variant-detail-template", - title: "Template" - } + // { + // id: "template", + // component: "opencga-variant-detail-template", + // title: "Template" + // } ] }, interpretation: { @@ -318,7 +314,20 @@ const tools = { active: false, filter: { menu: interpreterMenu, + lof: ["transcript_ablation", "splice_acceptor_variant", "splice_donor_variant", "stop_gained", "frameshift_variant", + "stop_lost", "start_lost", "transcript_amplification", "inframe_insertion", "inframe_deletion"], examples: [ + { + name: "Default (protein and missense)", + active: true, + query: { + biotype: "protein_coding", + // alternate_frequency: "1kG_phase3:ALL<0.001;GNOMAD_GENOMES:ALL<0.001", + ct: "transcript_ablation,splice_acceptor_variant,splice_donor_variant,stop_gained," + + "frameshift_variant,stop_lost,start_lost,transcript_amplification,inframe_insertion,inframe_deletion," + + "missense_variant", + } + }, { name: "Tiering (AR)", active: false, @@ -345,19 +354,6 @@ const tools = { "SO:0001821,SO:0001822,SO:0001583,SO:0001630,SO:0001626" } }, - { - name: "Clinical Interpretation", - active: true, - query: { - region: "1", - biotype: "protein_coding", - alternate_frequency: "1kG_phase3:ALL<0.001;GNOMAD_GENOMES:ALL<0.001", - ct: "transcript_ablation,splice_acceptor_variant,splice_donor_variant,stop_gained," + - "frameshift_variant,stop_lost,start_lost,transcript_amplification,inframe_insertion,inframe_deletion," + - "missense_variant", - // genotype: "NA12877:0/1;NA12878:0/1;NA12879:0/1,1/1" - } - }, { name: "Stickler syndrome", query: { @@ -403,11 +399,11 @@ const tools = { // "lovd", "hgmd", "icgc", "sahgp" // ] }, - { - id: "template", - component: "opencga-variant-detail-template", - title: "Template" - } + // { + // id: "template", + // component: "opencga-variant-detail-template", + // title: "Template" + // } ], css: { style: "font-size: 12px" diff --git a/src/index.html b/src/index.html index fea6f19cb..07ffc1f39 100644 --- a/src/index.html +++ b/src/index.html @@ -85,7 +85,8 @@ - + + diff --git a/src/iva-app.html b/src/iva-app.html index b35800c15..777d48ead 100644 --- a/src/iva-app.html +++ b/src/iva-app.html @@ -40,13 +40,13 @@ - - - - + + + + - + @@ -82,8 +82,8 @@
-
-