Merge branch 'release-2.12.x' into TASK-5834

opencb · Apr 4, 2024 · c94f02d · c94f02d
2 parents c6d75cc + 505dba6
commit c94f02d
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Showing 12 changed files with 119 additions and 171 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
@@ -806,11 +806,10 @@ 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
@@ -360,7 +360,7 @@ 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
@@ -502,7 +502,7 @@ 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
@@ -556,11 +556,10 @@ 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
@@ -449,7 +449,7 @@ 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
@@ -622,11 +622,10 @@ 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
@@ -583,7 +583,7 @@ 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
@@ -485,11 +485,10 @@ 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;
     }