opencb · jmjuanes · Nov 10, 2025 · Jun 5, 2025 · Jun 5, 2025 · Jun 5, 2025
diff --git a/cypress/e2e/iva/cohort-browser-grid.cy.js b/cypress/e2e/iva/cohort-browser-grid.cy.js
@@ -101,7 +101,7 @@ context("Cohort Browser Grid", () => {
         });
 
         it("should allow to hide columns in the grid", () => {
-            const columns = ["Cohort ID", "Creation Date"];
+            const columns = ["Cohort", "Creation Date"];
 
             cy.get("@cohort-grid")
                 .find("thead th")

diff --git a/cypress/e2e/iva/variant-browser-grid.cy.js b/cypress/e2e/iva/variant-browser-grid.cy.js
@@ -270,9 +270,8 @@ context("Variant Browser Grid", () => {
                 const externalLinks = [
                     ["Decipher", "https://www.deciphergenomics.org/sequence-variant/"],
                     ["Varsome", "https://varsome.com/variant/"],
-                    ["CellBase v5.2", "https://ws.zettagenomics.com/cellbase/webservices/rest/v5.2"],
-                    ["CellBase v5.8", "https://ws.zettagenomics.com/cellbase/webservices/rest/v5.8"],
-                    ["Ensembl Genome Browser", "http://ensembl.org/Homo_sapiens/Location/View"],
+                    ["CellBase", "https://ws.zettagenomics.com/cellbase/webservices/rest"],
+                    ["Ensembl Genome Browser", "https://www.ensembl.org/Homo_sapiens/Location/View"],
                     ["UCSC Genome Browser", "https://genome.ucsc.edu/cgi-bin/hgTracks"],
                 ];
 

diff --git a/src/core/bioinfo/bioinfo-utils.js b/src/core/bioinfo/bioinfo-utils.js
@@ -16,6 +16,14 @@
 
 export default class BioinfoUtils {
 
+    static isHuman(species) {
+        return ["hsapiens", "homo_sapiens", "homosapiens", "human"].includes(species.toLowerCase());
+    }
+
+    static getEnsemblHost(assembly = "GRCh38") {
+        return (assembly.toLowerCase() === "grch37") ? "https://grch37.ensembl.org" : "https://www.ensembl.org";
+    }
+
     static sort(consequenceTypes, field) {
         consequenceTypes.sort((a, b) => {
             if (field(a) === "" && field(b) !== "") {
@@ -62,16 +70,21 @@ export default class BioinfoUtils {
         return "https://www.genenames.org/tools/search/#!/all?query=" + geneName;
     }
 
-    static getEnsemblLink(featureId, type = "gene", assembly = "GRCh38") {
-        const ensemblHost = assembly.toUpperCase() === "GRCH38" ? "www.ensembl.org" : "grch37.ensembl.org";
+    // Note: currently only human and mouse are supported
+    static getEnsemblLink(featureId, type = "gene", species = "hsapiens", assembly = "GRCh38") {
+        const ensemblHost = BioinfoUtils.getEnsemblHost(assembly);
+        const ensemblSpecies = BioinfoUtils.isHuman(species) ? "Homo_sapiens" : "Mus_musculus";
         switch (type.toUpperCase()) {
             case "GENE":
-                return `https://${ensemblHost}/Homo_sapiens/Gene/Summary?db=core;g=${featureId}`;
+                return `${ensemblHost}/${ensemblSpecies}/Gene/Summary?db=core;g=${featureId}`;
             case "TRANSCRIPT":
-                return `https://${ensemblHost}/Homo_sapiens/Transcript/Summary?db=core;t=${featureId}`;
+                return `${ensemblHost}/${ensemblSpecies}/Transcript/Summary?db=core;t=${featureId}`;
             case "VARIANT":
             case "VARIATION":
-                return `https://${ensemblHost}/Homo_sapiens/Variation/Explore?vdb=variation;v=${featureId}`;
+                return `${ensemblHost}/${ensemblSpecies}/Variation/Explore?vdb=variation;v=${featureId}`;
+            case "LOCATION":
+            case "BROWSER":
+                return `${ensemblHost}/${ensemblSpecies}/Location/View?r=${featureId}`;
         }
         return "";
     }
@@ -92,28 +105,23 @@ export default class BioinfoUtils {
         return "https://www.ncbi.nlm.nih.gov/clinvar/variation/" + variantId;
     }
 
-    static getUniprotLink(featureId, species = "Homo sapiens") {
-        // return "https://www.uniprot.org/uniprot/?sort=score&query=" + featureId + "+organism:" + species;
-        return "https://www.uniprot.org/uniprot/" + featureId;
+    static getUniprotLink(featureId) {
+        return `https://www.uniprot.org/uniprotkb?query=${featureId}`;
     }
 
-    static getVariantLink(id, location, source, assembly) {
+    static getVariantLink(id, location, source, species = "hsapiens", assembly = "grch38") {
         if (!source) {
             return null;
         }
 
-        // Check for cellbase source
+        // Check for CellBase source
         if (source.toUpperCase().startsWith("CELLBASE_V")) {
             const version = source.toUpperCase().replace("CELLBASE_", "").toLowerCase();
-            return `https://ws.zettagenomics.com/cellbase/webservices/rest/${version}/hsapiens/genomic/variant/${id}/annotation`;
+            return BioinfoUtils.getCellbaseVariantLink(id, "https://ws.zettagenomics.com/cellbase", version, "", "", species, assembly);
         }
 
         if (id?.startsWith("rs")) {
-            if (assembly?.toUpperCase() === "GRCH38") {
-                return `http://ensembl.org/Homo_sapiens/Variation/Explore?vdb=variation;v=${id}`;
-            } else {
-                return `http://grch37.ensembl.org/Homo_sapiens/Variation/Explore?vdb=variation;v=${id}`;
-            }
+            return BioinfoUtils.getEnsemblLink(id, "VARIATION", species, assembly);
         }
 
         if (id?.startsWith("HGNC:")) {
@@ -126,27 +134,20 @@ export default class BioinfoUtils {
 
         switch (source.toUpperCase()) {
             case "DECIPHER":
-                // To make things easier the conversion of OpenCB Variant ID to Decipher ID must happen here
+                // To make things easier, the conversion of OpenCB Variant ID to Decipher ID must happen here
                 const decipherId = id.replace(/:/g, "-");
                 return `https://www.deciphergenomics.org/sequence-variant/${decipherId}`;
             case "ENSEMBL_GENOME_BROWSER":
-                if (assembly?.toUpperCase() === "GRCH38") {
-                    return `http://ensembl.org/Homo_sapiens/Location/View?r=${region}`;
-                } else {
-                    return `http://grch37.ensembl.org/Homo_sapiens/Location/View?r=${region}`;
-                }
+                return BioinfoUtils.getEnsemblLink(region, "BROWSER", species, assembly);
             case "UCSC_GENOME_BROWSER":
-                return `https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&position=chr${region}`;
+                const hg = assembly?.toUpperCase() === "GRCH38" ? "hg38" : "hg19";
+                return `https://genome.ucsc.edu/cgi-bin/hgTracks?db=${hg}&position=chr${region}`;
             case "VARSOME":
-                if (assembly?.toUpperCase() === "GRCH38") {
-                    return `https://varsome.com/variant/hg38/${BioinfoUtils.getVariantInVarsomeFormat(id)}`;
-                } else {
-                    return `https://varsome.com/variant/hg19/${BioinfoUtils.getVariantInVarsomeFormat(id)}`;
-                }
+                return `https://varsome.com/variant/${assembly?.toUpperCase() === "GRCH38" ? "hg38" : "hg19"}/${BioinfoUtils.getVariantInVarsomeFormat(id)}`;
         }
     }
 
-    static getGeneLink(geneId, source, assembly = "GRCh38") {
+    static getGeneLink(geneId, source, species = "hsapiens", assembly = "GRCh38") {
         if (!geneId) {
             return null;
         }
@@ -158,15 +159,9 @@ export default class BioinfoUtils {
 
         switch (s.toUpperCase()) {
             case "ENSEMBL":
-                if (assembly.toUpperCase() === "GRCH38") {
-                    return `https://www.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=${geneId}`;
-                } else {
-                    return `https://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=${geneId}`;
-                }
+                return BioinfoUtils.getEnsemblLink(geneId, "GENE", species, assembly);
             case "HGNC":
                 return "https://www.genenames.org/tools/search/#!/all?query=" + geneId;
-            case "LRG":
-                return `https://www.lrg-sequence.org/search/?query=${geneId}`;
             case "DECIPHER":
                 return `https://www.deciphergenomics.org/gene/${geneId}`;
             case "COSMIC":
@@ -200,11 +195,7 @@ export default class BioinfoUtils {
 
         switch (s.toUpperCase()) {
             case "ENSEMBL":
-                if (assembly.toUpperCase() === "GRCH38") {
-                    return `https://www.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=${transcriptId}`;
-                } else {
-                    return `https://grch37.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=${transcriptId}`;
-                }
+                return BioinfoUtils.getEnsemblLink(transcriptId, "TRANSCRIPT", "hsapiens", assembly);
             case "REFSEQ":
                 return `https://www.ncbi.nlm.nih.gov/gene/?term=${transcriptId}`;
         }
@@ -222,7 +213,7 @@ export default class BioinfoUtils {
 
         switch (s.toUpperCase()) {
             case "ENSEMBL":
-                return `http://www.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;p=${proteinId}`;
+                return BioinfoUtils.getEnsemblLink(proteinId, "PROTEIN", "hsapiens", "");
             case "REFSEQ":
                 return `https://www.ncbi.nlm.nih.gov/gene/?term=${proteinId}`;
         }
@@ -304,4 +295,38 @@ export default class BioinfoUtils {
         return `https://www.pharmgkb.org/chemical/${pharmGKBId}`;
     }
 
+    static getCellbaseLink(id, type = "VARIANT", host = "https://ws.zettagenomics.com/cellbase", version = "v5", dataRelease = "", apiKey = "", species = "hsapiens", assembly) {
+        let url = `${host}/webservices/rest/${version}/${species}`;
+        const searchParams = new URLSearchParams();
+
+        // 1. check the resource to generate the correct URL
+        switch (type?.toUpperCase()) {
+            case "VARIANT":
+                url = `${url}/genomic/variant/${id}/annotation`;
+                break;
+        }
+
+        // 2. check if dataRelease is provided
+        if (dataRelease) {
+            searchParams.append("dataRelease", dataRelease);
+        }
+
+        // 3. check if apiKey is provided
+        if (apiKey) {
+            searchParams.append("apiKey", apiKey);
+        }
+
+        // 4. add assembly if provided
+        if (assembly) {
+            searchParams.append("assembly", assembly);
+        }
+
+        return searchParams.size > 0 ? `${url}?${searchParams.toString()}` : url;
+    }
+
+    // alias to getCellbaseLink with type VARIANT
+    static getCellbaseVariantLink(id, host, version, dataRelease, apiKey, species, assembly) {
+        return BioinfoUtils.getCellbaseLink(id, "VARIANT", host, version, dataRelease, apiKey, species, assembly);
+    }
+
 }
diff --git a/src/core/clients/opencga/opencga-client.js b/src/core/clients/opencga/opencga-client.js
@@ -462,10 +462,23 @@ export class OpenCGAClient {
                                                             study: study.fqn,
                                                             internalStatus: "READY,CALCULATING,INVALID",
                                                             exclude: "samples",
-                                                            limit: 100,
+                                                            limit: 250,
                                                         });
+
+                                                    // Sort cohorts alphabetically, but "ALL" first
                                                     study.cohorts = cohortsResponse.responses[0].results
-                                                        .filter(cohort => !cohort.attributes?.IVA?.ignore);
+                                                        .filter(cohort => !cohort.attributes?.IVA?.ignore)
+                                                        // FIXME line above should check cohort.internal instead
+                                                        // .filter(cohort => cohort.internal.index?.status === "READY");
+                                                        .sort((a, b) => {
+                                                            if (a.id === "ALL") {
+                                                                return -1;
+                                                            } else if (b.id === "ALL") {
+                                                                return 1;
+                                                            } else {
+                                                                return a.id.localeCompare(b.id);
+                                                            }
+                                                        });
 
                                                     // Keep track of the studies to fetch Disease Panels
                                                     studies.push(study.fqn);

diff --git a/src/sites/iva/conf/browsers.settings.js b/src/sites/iva/conf/browsers.settings.js
@@ -52,7 +52,7 @@ const CATALOG_SETTINGS = {
             // merge criterium: internal sections and filters are used to hydrates the external filters list for each section (which is a list of string). Sections and filter order is respected.
             sections: [
                 {
-                    filters: ["id", "samples", "type", "date", "annotations"]
+                    filters: ["id", "name", "samples", "tags", "date", "annotations"],
                 }
             ],
             // merge criterium: full outer join-like. it adds objects presents in internal array only and in external array only. In case of same id, the external value overwrite the internal.
@@ -71,7 +71,7 @@ const CATALOG_SETTINGS = {
             },
             // merge criterium: uses this array as filter for internal 1D/2D array. It handles row/col span
             // It is supported either columns[] or hiddenColumns[].
-            columns: ["id", "numSamples", "creationDate", "type"]
+            columns: ["id", "name", "tags", "numSamples", "creationDate", "status"],
         },
         // merge criterium: uses this array as filter for internal 1D array.
         details: ["cohort-view", "sample-view", "json-view"]
@@ -181,7 +181,7 @@ const CATALOG_SETTINGS = {
             // merge criterium: internal sections and filters are used to hydrates the external filters list for each section (which is a list of string). Sections and filter order is respected.
             sections: [
                 {
-                    filters: ["id", "tool", "input", "internalStatus", "priority", "tags", "creationDate", "visited"]
+                    filters: ["id", "tool", "input", "internalStatus", "userId", "priority", "tags", "creationDate", "visited"]
                 }
             ],
             // merge criterium: full outer join-like. it adds objects presents in internal array only and in external array only. In case of same id, the external value overwrite the internal.

diff --git a/src/sites/iva/conf/config.js b/src/sites/iva/conf/config.js
@@ -26,7 +26,7 @@ const hosts = [
     },
     {
         id: "reference",
-        url: "https://test.app.zettagenomics.com/task-7706/opencga"
+        url: "https://test.app.zettagenomics.com/task-7733/opencga"
     },
 ];
 
@@ -42,51 +42,21 @@ const opencga = {
         active: false,
         cookie: "JSESSIONID"
     },
+};
 
-    // This forces the following projects to be used instead of the user's project
-    // projects: [
-    //     {
-    //         id: "platinum",
-    //         name: "Platinum",
-    //         alias: "platinum",
-    //         organism: {
-    //             scientificName: "Homo sapiens",
-    //             assembly: "GRCh37"
-    //         },
-    //         studies : [
-    //             {
-    //                 id: "illumina_platinum",
-    //                 name: "Illumina Platinum",
-    //                 alias: "illumina_platinum"
-    //             }
-    //         ]
-    //     }
-    // ],
-
-    // This allows IVA to query a OpenCGA instance being an 'anonymous' user, this means that no login is required.
-    // If 'projects' is empty then all public projects and studies of 'user' will be used.
-    // anonymous: {
-    //     // user: "hgvauser",
-    //     projects: [
-    //         {
-    //             id: "platinum",
-    //             name: "Platinum",
-    //             alias: "platinum",
-    //             organism: {
-    //                 scientificName: "Homo sapiens",
-    //                 assembly: "GRCh37"
-    //             },
-    //             studies : [
-    //                 {
-    //                     id: "illumina_platinum",
-    //                     name: "Illumina Platinum",
-    //                     alias: "illumina_platinum"
-    //                 }
-    //             ]
-    //         }
-    //     ]
-    // },
-    // summary: true,
+const CELLBASE = {
+    supportedVersions: [
+        {
+            host: "https://ws.zettagenomics.com/cellbase",
+            version: "v5.2",
+            dataRelease: 3,
+        },
+        {
+            host: "https://ws.zettagenomics.com/cellbase",
+            version: "v5.8",
+            dataRelease: 7,
+        },
+    ],
 };
 
 const SUITE = {

diff --git a/src/sites/iva/conf/opencga-cohort-browser.settings.js b/src/sites/iva/conf/opencga-cohort-browser.settings.js
@@ -6,7 +6,7 @@ const OPENCGA_COHORT_BROWSER_SETTINGS = {
         // merge criterium: internal sections and filters are used to hydrates the external filters list for each section (which is a list of string). Sections and filter order is respected.
         sections: [
             {
-                filters: ["id", "samples", "type", "date", "annotations"]
+                filters: ["id", "name", "samples", "tags", "date", "annotations"]
             }
         ],
         // merge criterium: full outer join-like. it adds objects presents in internal array only and in external array only. In case of same id, the external value overwrite the internal.
@@ -24,7 +24,7 @@ const OPENCGA_COHORT_BROWSER_SETTINGS = {
         },
         // merge criterium: uses this array as filter for internal 1D/2D array. It handles row/col span
         // It is supported either columns[] or hiddenColumns[].
-        columns: ["id", "numSamples", "creationDate", "type"]
+        columns: ["id", "name", "tags", "numSamples", "creationDate", "status"]
     },
     // merge criterium: uses this array as filter for internal 1D array.
     details: ["cohort-view", "sample-view", "json-view"]

diff --git a/src/sites/iva/conf/opencga-individual-browser.settings.js b/src/sites/iva/conf/opencga-individual-browser.settings.js
@@ -1,10 +1,12 @@
 const OPENCGA_INDIVIDUAL_BROWSER_SETTINGS = {
-    /**
-     *  Full settings
-     */
-
-    // TODO clinical-analysis-grid has no action column here
-
+    // model: {
+    //     disorders: {
+    //         source: "HPO",
+    //     },
+    //     phenotypes: {
+    //         source: "HPO",
+    //     },
+    // },
     menu: {
         // merge criterium: internal sections and filters are used to hydrates the external filters list for each section (which is a list of string). Sections and filter order is respected.
         sections: [
@@ -44,6 +46,4 @@ const OPENCGA_INDIVIDUAL_BROWSER_SETTINGS = {
         //     }
         // ]
     },
-    // merge criterium: uses this array as filter for internal 1D array.
-    details: ["individual-view", "clinical-analysis-grid", "individual-inferred-sex", "individual-mendelian-error", "json-view"]
 };
diff --git a/src/sites/iva/conf/opencga-job-browser.settings.js b/src/sites/iva/conf/opencga-job-browser.settings.js
@@ -6,7 +6,7 @@ const OPENCGA_JOB_BROWSER_SETTINGS = {
         // merge criterium: internal sections and filters are used to hydrates the external filters list for each section (which is a list of string). Sections and filter order is respected.
         sections: [
             {
-                filters: ["id", "tool", "input", "internalStatus", "priority", "tags", "creationDate", "visited"]
+                filters: ["id", "tool", "input", "internalStatus", "userId", "priority", "tags", "creationDate", "visited"]
             }
         ],
         // merge criterium: full outer join-like. it adds objects presents in internal array only and in external array only. In case of same id, the external value overwrite the internal.