Merge branch 'develop'

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",

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: `<strong>1000 Genomes</strong> 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.<br><br>
+              <strong>gnomAD Genomes</strong> 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]",

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: "<strong>1000 Genomes</strong> 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." +
-                    "<br><strong>ExAC</strong> 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." +
-                    "<br><strong>ESP56500</strong> 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"
@@ -304,21 +300,34 @@ 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: {
         title: "Variant Interpreter",
         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"

src/index.html

@@ -85,7 +85,8 @@
     <!-- /build -->
 
     <!-- build:css css/font-awesome.min.css -->
-    <link rel="stylesheet" href="../node_modules/font-awesome/css/font-awesome.min.css">
+    <!--<link rel="stylesheet" href="../node_modules/font-awesome/css/font-awesome.min.css">-->
+    <link rel="stylesheet" href="../node_modules/@fortawesome/fontawesome-free/css/all.min.css">
     <!-- /build -->
 
     <!-- build:css css/jquery.qtip.min.css -->