Merge branch 'release-2.12.x' into TASK-5674

opencb · Apr 4, 2024 · 6605204 · 6605204
2 parents f3b1147 + 06a5c68
commit 6605204
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Showing 13 changed files with 153 additions and 181 deletions.
diff --git a/src/core/bioinfo/bioinfo-utils.js b/src/core/bioinfo/bioinfo-utils.js
@@ -34,6 +34,23 @@ export default class BioinfoUtils {
         });
     }
 
+    static getIdName(id, name) {
+        let text = "";
+        if (name) {
+            text = name;
+        }
+
+        if (id) {
+            if (name) {
+                text += ` (${id})`;
+            } else {
+                text = id;
+            }
+        }
+
+        return text;
+    }
+
     // Generate Variant ID in Varsome format
     // https://varsome.com/how-do-i-create-link-varsome/
     static getVariantInVarsomeFormat(variantId) {
@@ -255,7 +272,7 @@ export default class BioinfoUtils {
 
     static getOboLink(ontologyId) {
         const ontologyShort = ontologyId.replace(":", "_");
-        return `http://purl.obolibrary.org/obo/${ontologyShort}`;
+        return `https://purl.obolibrary.org/obo/${ontologyShort}`;
     }
 
     static getHpoLink(hpoTerm) {

diff --git a/src/webcomponents/clinical/clinical-analysis-grid.js b/src/webcomponents/clinical/clinical-analysis-grid.js
@@ -695,11 +695,10 @@ export default class ClinicalAnalysisGrid extends LitElement {
                 events: {
                     "click a": this.onActionClick.bind(this)
                 },
-                visible: !this._config.columns?.hidden?.includes("actions"),
+                visible: this.gridCommons.isColumnVisible("actions"),
             });
         }
 
-        // _columns = UtilsNew.mergeTable(_columns, this._config.columns || this._config.hiddenColumns, !!this._config.hiddenColumns);
         this._columns = this.gridCommons.addColumnsFromExtensions(this._columns, this.COMPONENT_ID);
         return this._columns;
     }

diff --git a/src/webcomponents/cohort/cohort-grid.js b/src/webcomponents/cohort/cohort-grid.js
@@ -336,7 +336,7 @@ export default class CohortGrid extends LitElement {
                 events: {
                     "click a": this.onActionClick.bind(this),
                 },
-                visible: !this._config.columns?.hidden?.includes("actions"),
+                visible: this.gridCommons.isColumnVisible("actions"),
             });
         }
 

diff --git a/src/webcomponents/commons/filters/sample-genotype-filter.js b/src/webcomponents/commons/filters/sample-genotype-filter.js
@@ -85,17 +85,20 @@ export default class SampleGenotypeFilter extends LitElement {
                     id: "0/1", name: "HET"
                 },
                 {
-                    id: "1/1", name: "HOM ALT"
+                    id: "1/1", name: "HOM_ALT"
                 },
                 {
                     separator: true
                 },
                 {
-                    id: "./.", name: "Missing"
+                    id: "1/2", name: "BIALLELIC (1/2)"
                 },
-                {
-                    id: "NA", name: "NA"
-                }
+                // {
+                //     id: "./.", name: "Missing"
+                // },
+                // {
+                //     id: "NA", name: "NA"
+                // }
             ]
         };
     }

diff --git a/src/webcomponents/disease-panel/disease-panel-grid.js b/src/webcomponents/disease-panel/disease-panel-grid.js
@@ -473,7 +473,7 @@ export default class DiseasePanelGrid extends LitElement {
                 events: {
                     "click a": this.onActionClick.bind(this),
                 },
-                visible: !this._config.columns?.hidden?.includes("actions"),
+                visible: this.gridCommons.isColumnVisible("actions"),
             });
         }
 

diff --git a/src/webcomponents/family/family-grid.js b/src/webcomponents/family/family-grid.js
@@ -185,19 +185,27 @@ export default class FamilyGrid extends LitElement {
                         ...this.query
                     };
 
+                    // Calculate the number of cases to fetch
+                    const casesLimit = this.table?.bootstrapTable("getOptions")?.pageSize || this._config.pageSize || 10;
+
                     // Store the current filters
                     this.lastFilters = {...this.filters};
                     this.opencgaSession.opencgaClient.families()
                         .search(this.filters)
                         .then(familyResponse => {
                             // Fetch Clinical Analysis ID per Family in 1 single query
-                            const familyIds = familyResponse.responses[0].results.map(family => family.id).join(",");
+                            const familyIds = familyResponse.responses[0].results
+                                .map(family => family.id)
+                                .join(",");
+
                             if (familyIds) {
-                                this.opencgaSession.opencgaClient.clinical()
+                                this.opencgaSession.opencgaClient
+                                    .clinical()
                                     .search({
                                         family: familyIds,
                                         study: this.opencgaSession.study.fqn,
-                                        include: "id,proband.id,family.members,family.id"
+                                        include: "id,proband.id,family.members,family.id",
+                                        limit: casesLimit * 10
                                     })
                                     .then(caseResponse => {
                                         familyResponse.getResults().forEach(family => {
@@ -541,11 +549,10 @@ export default class FamilyGrid extends LitElement {
                 events: {
                     "click a": this.onActionClick.bind(this)
                 },
-                visible: !this._config.columns?.hidden?.includes("actions")
+                visible: this.gridCommons.isColumnVisible("actions")
             });
         }
 
-        // _columns = UtilsNew.mergeTable(_columns, this._config.columns || this._config.hiddenColumns, !!this._config.hiddenColumns);
         this._columns = this.gridCommons.addColumnsFromExtensions(this._columns, this.COMPONENT_ID);
         return this._columns;
     }

diff --git a/src/webcomponents/file/file-grid.js b/src/webcomponents/file/file-grid.js
@@ -430,7 +430,7 @@ export default class OpencgaFileGrid extends LitElement {
                 events: {
                     "click a": this.onActionClick.bind(this)
                 },
-                visible: !this._config.columns?.hidden?.includes("actions")
+                visible: this.gridCommons.isColumnVisible("actions")
             });
         }
 

diff --git a/src/webcomponents/individual/individual-grid.js b/src/webcomponents/individual/individual-grid.js
@@ -189,19 +189,28 @@ export default class IndividualGrid extends LitElement {
                         ...this.query
                     };
 
+                    // Calculate the number of cases to fetch
+                    const casesLimit = this.table?.bootstrapTable("getOptions")?.pageSize || this._config.pageSize || 10;
+
                     // Store the current filters
                     this.lastFilters = {...this.filters};
                     this.opencgaSession.opencgaClient.individuals()
                         .search(this.filters)
                         .then(individualResponse => {
                             // Fetch Clinical Analysis ID per individual in 1 single query
-                            const individualIds = individualResponse.getResults().map(individual => individual.id).filter(Boolean).join(",");
+                            const individualIds = individualResponse.getResults()
+                                .map(individual => individual.id)
+                                .filter(Boolean)
+                                .join(",");
+
                             if (individualIds) {
-                                this.opencgaSession.opencgaClient.clinical()
+                                this.opencgaSession.opencgaClient
+                                    .clinical()
                                     .search({
                                         individual: individualIds,
                                         study: this.opencgaSession.study.fqn,
-                                        include: "id,proband.id,family.members"
+                                        include: "id,proband.id,family.members",
+                                        limit: casesLimit * 10
                                     })
                                     .then(caseResponse => {
                                         individualResponse.getResults().forEach(individual => {
@@ -589,11 +598,10 @@ export default class IndividualGrid extends LitElement {
                 events: {
                     "click a": this.onActionClick.bind(this),
                 },
-                visible: !this._config.columns?.hidden?.includes("actions"),
+                visible: this.gridCommons.isColumnVisible("actions"),
             });
         }
 
-        // _columns = UtilsNew.mergeTable(_columns, this._config.columns || this._config.hiddenColumns, !!this._config.hiddenColumns);
         this._columns = this.gridCommons.addColumnsFromExtensions(this._columns, this.COMPONENT_ID);
         return this._columns;
     }

diff --git a/src/webcomponents/job/job-grid.js b/src/webcomponents/job/job-grid.js
@@ -568,7 +568,7 @@ export default class JobGrid extends LitElement {
                 events: {
                     "click a": this.onActionClick.bind(this),
                 },
-                visible: !this._config.columns?.hidden?.includes("actions"),
+                visible: this.gridCommons.isColumnVisible("actions"),
             });
         }
 

diff --git a/src/webcomponents/sample/sample-grid.js b/src/webcomponents/sample/sample-grid.js
@@ -188,6 +188,9 @@ export default class SampleGrid extends LitElement {
                         ...this.query
                     };
 
+                    // Calculate the number of cases to fetch
+                    const casesLimit = this.table?.bootstrapTable("getOptions")?.pageSize || this._config.pageSize || 10;
+
                     // Store the current filters
                     this.lastFilters = {...this.filters};
                     this.opencgaSession.opencgaClient.samples()
@@ -196,14 +199,18 @@ export default class SampleGrid extends LitElement {
                             // Fetch clinical analysis to display the Case ID
                             const individualIds = sampleResponse.getResults()
                                 .map(sample => sample.individualId)
-                                .filter(Boolean).join(",");
+                                .filter(Boolean)
+                                .join(",");
+
                             if (individualIds) {
-                                this.opencgaSession.opencgaClient.clinical()
+                                this.opencgaSession.opencgaClient
+                                    .clinical()
                                     .search(
                                         {
                                             individual: individualIds,
                                             study: this.opencgaSession.study.fqn,
-                                            include: "id,proband.id,family.members"
+                                            include: "id,proband.id,family.members",
+                                            limit: casesLimit * 10
                                         })
                                     .then(caseResponse => {
                                         sampleResponse.getResults().forEach(sample => {
@@ -463,11 +470,10 @@ export default class SampleGrid extends LitElement {
                 events: {
                     "click a": this.onActionClick.bind(this)
                 },
-                visible: !this._config.columns?.hidden?.includes("actions")
+                visible: this.gridCommons.isColumnVisible("actions")
             });
         }
 
-        // _columns = UtilsNew.mergeTable(_columns, this._config.columns || this._config.hiddenColumns, !!this._config.hiddenColumns);
         this._columns = this.gridCommons.addColumnsFromExtensions(this._columns, this.COMPONENT_ID);
         return this._columns;
     }