case interpreter browser settings added #236

opencb · Jul 13, 2021 · d120a47 · d120a47
1 parent e2775bb
commit d120a47
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Showing 5 changed files with 47 additions and 3 deletions.
diff --git a/lib/jsorolla b/lib/jsorolla
diff --git a/src/conf/variant-interpreter-browser-cancer.settings.js b/src/conf/variant-interpreter-browser-cancer.settings.js
@@ -0,0 +1,19 @@
+const variantInterpreterBrowserCancerSettings = {
+    menu: {
+        // add all filters and let variant-interpreter-browser-cancer handle the visibility based on callers
+    },
+    table: {
+        // merge criterium: spread operator
+        toolbar: {
+            showColumns: true,
+            showExport: false,
+            showDownload: true
+            // columns list will be added in grid components based on settings.table.columns
+        },
+        // merge criterium: uses this array as filter for internal 1D/2D array. It handles row/col span
+        // columns: ["id"]
+    },
+    // merge criterium: uses this array as filter for internal 1D array.
+    detail: []
+
+};
diff --git a/src/conf/variant-interpreter-browser-rd.settings.js b/src/conf/variant-interpreter-browser-rd.settings.js
@@ -67,6 +67,6 @@ const variantInterpreterBrowserRdSettings = {
         columns: ["id", "gene", "type", "consequenceType", "zygosity", "evidences", "VCF_Data", "frequencies", "clinicalInfo", "interpretation", "review", "actions"]
     },
     // merge criterium: uses this array as filter for internal 1D array.
-    detail: ["annotationSummary", "annotationConsType"]
+    detail: ["annotationSummary", "annotationConsType", "annotationPropFreq", "annotationClinical", "fileMetrics", "cohortStats", "samples", "beacon"]
 
 };
diff --git a/src/conf/variant-interpreter.settings.js b/src/conf/variant-interpreter.settings.js
@@ -0,0 +1,24 @@
+const variantInterpreterSettings = {
+    tools: [
+        {
+            id: "select"
+        },
+        {
+            id: "qc",
+            tabs: ["overview", "sampleVariantStats", /*"cancerQCPlots",*/ "somaticVariantStats", "germlineVariantStats", /*"geneCoverage"*/]
+        },
+        /*{
+            id: "methods"
+        },*/
+        {
+            id: "variant-browser"
+        },
+        /*{
+            id: "review"
+        },
+        {
+            id: "report"
+        }*/
+    ]
+    // add QC config
+};
diff --git a/src/index.html b/src/index.html
@@ -60,9 +60,10 @@
     <script defer src="conf/opencga-clinical-analysis-browser.config.js"></script>
     <script defer src="conf/opencga-clinical-analysis-view.settings.js"></script>
     <script defer src="conf/opencga-sample-browser.config.js"></script>
-    <script defer src="conf/variant-interpreter.config.js"></script>
     <script defer src="conf/opencga-clinical-review-cases.settings.js"></script>
+    <script defer src="conf/variant-interpreter.settings.js"></script>
     <script defer src="conf/variant-interpreter-browser-rd.settings.js"></script>
+    <script defer src="conf/variant-interpreter-browser-cancer.settings.js"></script>
     <script defer src="conf/opencga-variant-browser.settings.js"></script>
     <!--    <script src="../lib/jsorolla/src/core/webcomponents/opencga/panels_example.js"></script>-->
     <script src="conf/tools.js"></script>
+2 −2		src/core/clients/rest-response.js
+156 −57		src/core/utilsNew.js
+18 −17		src/core/webcomponents/clinical/opencga-clinical-analysis-grid.js
+10 −1		src/core/webcomponents/clinical/opencga-clinical-analysis-view.js
+20 −5		src/core/webcomponents/clinical/opencga-clinical-review-cases.js
+2 −2		src/core/webcomponents/commons/filters/section-filter.js
+1 −1		src/core/webcomponents/commons/filters/select-field-filter-autocomplete.js
+191 −0		src/core/webcomponents/commons/filters/select-token-filter2.js
+1 −1		src/core/webcomponents/commons/filters/text-field-filter.js
+6 −5		src/core/webcomponents/commons/opencb-grid-toolbar.js
+33 −31		src/core/webcomponents/commons/view/data-form.js
+4 −0		src/core/webcomponents/sample/sample-browser-filter.js
+1 −4		src/core/webcomponents/sample/sample-cancer-variant-stats-browser.js
+1 −4		src/core/webcomponents/sample/sample-qc-signature-view.js
+1 −5		src/core/webcomponents/sample/sample-variant-stats-browser.js
+1 −4		src/core/webcomponents/sample/sample-variant-stats-view.js
+8 −8		src/core/webcomponents/user/opencga-projects.js
+34 −8		src/core/webcomponents/variant/interpretation/variant-interpreter-browser-cancer.js
+20 −13		src/core/webcomponents/variant/interpretation/variant-interpreter-browser-rd.js
+1 −0		src/core/webcomponents/variant/interpretation/variant-interpreter-browser.js
+40 −15		src/core/webcomponents/variant/interpretation/variant-interpreter-grid.js
+2 −2		src/core/webcomponents/variant/interpretation/variant-interpreter-qc-gene-coverage-stats.js
+16 −19		src/core/webcomponents/variant/interpretation/variant-interpreter-qc-variant-stats.js
+97 −66		src/core/webcomponents/variant/interpretation/variant-interpreter-qc.js
+14 −6		src/core/webcomponents/variant/interpretation/variant-interpreter.js
+1 −1		src/core/webcomponents/variant/opencga-variant-filter.js
+13 −2		src/core/webcomponents/variant/variant-browser-grid.js
+32 −6		src/core/webcomponents/variant/variant-browser.js