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 @@