Merge branch 'release-2.12.x' into TASK-5864

opencb · Apr 14, 2024 · a4f70f0 · a4f70f0
2 parents 5d85521 + dcec92f
commit a4f70f0
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Showing 4 changed files with 51 additions and 50 deletions.
diff --git a/src/core/bioinfo/bioinfo-utils.js b/src/core/bioinfo/bioinfo-utils.js
@@ -258,7 +258,7 @@ export default class BioinfoUtils {
                 case "SO":
                     return this.getSequenceOntologyLink(ontologyTermId);
                 case "OMIM":
-                    return this.getOmimOntologyLink(id);
+                    return this.getOmimLink(id);
                 case "ORPHA":
                     return this.getOrphanetLink(id);
                 case "MONDO":
@@ -281,15 +281,11 @@ export default class BioinfoUtils {
         return `https://hpo.jax.org/app/browse/term/${hpoTerm}`;
     }
 
-    static getOmimLink(omimEntry) {
-        return `https://www.omim.org/entry/${omimEntry}`;
-    }
-
     static getSequenceOntologyLink(soTerm) {
         return `http://www.sequenceontology.org/browser/current_svn/term/${soTerm}`;
     }
 
-    static getOmimOntologyLink(soTerm) {
+    static getOmimLink(soTerm) {
         return `https://omim.org/entry/${soTerm}"`;
     }
 

diff --git a/src/webcomponents/clinical/clinical-analysis-view.js b/src/webcomponents/clinical/clinical-analysis-view.js
@@ -367,7 +367,7 @@ export default class ClinicalAnalysisView extends LitElement {
                                 template: "${disorder.name} (${disorder.id})",
                                 link: {
                                     "disorder.id": id => id.startsWith("OMIM:") ?
-                                        BioinfoUtils.getOmimOntologyLink(id) :
+                                        BioinfoUtils.getOmimLink(id) :
                                         "",
                                 },
                             },

diff --git a/src/webcomponents/variant/variant-browser-filter.js b/src/webcomponents/variant/variant-browser-filter.js
@@ -14,7 +14,7 @@
  * limitations under the License.
  */
 
-import {LitElement, html} from "lit";
+import {html, LitElement, nothing} from "lit";
 import UtilsNew from "../../core/utils-new.js";
 import "../commons/filters/cadd-filter.js";
 import "../commons/filters/biotype-filter.js";
@@ -340,17 +340,22 @@ export default class VariantBrowserFilter extends LitElement {
                 case "study":
                     content = html`
                         <study-filter
+                            .value="${this.preparedQuery.study}"
                             .opencgaSession="${this.opencgaSession}"
                             @filterChange="${e => this.onFilterChange("study", e.detail.value)}">
                         </study-filter>`;
                     break;
                 case "sample":
+                    const multiStudySelected = this.preparedQuery?.study?.split(",")?.length > 1;
                     content = html`
-                        <catalog-search-autocomplete
+                        ${multiStudySelected ? html`
+                            <div class="alert alert-warning" role="alert">You cannot select samples with more than one study</div>
+                        ` : nothing}
+                        <catalog-search-autocomplete title=${multiStudySelected ? "You cannot select samples with more than one study" : null}
                             .value="${this.preparedQuery.sample}"
                             .opencgaSession="${this.opencgaSession}"
                             .resource="${"SAMPLE"}"
-                            .config="${{multiple: true, maxItems: 3}}"
+                            .config="${{multiple: true, maxItems: 3, disabled: multiStudySelected}}"
                             @filterChange="${e => this.onFilterChange("sample", e.detail.value)}">
                         </catalog-search-autocomplete>`;
                     break;

diff --git a/src/webcomponents/variant/variant-grid-formatter.js b/src/webcomponents/variant/variant-grid-formatter.js
@@ -1190,28 +1190,59 @@ export default class VariantGridFormatter {
                         </div>
                         <div>
                             ${
-                    hotspot.variants
-                        .map(variant => `
-                                    <span
-                                        class="help-block"
-                                        style="margin: 5px 1px">${AMINOACID_CODE[hotspot.aminoacidReference]}${hotspot.aminoacidPosition}${AMINOACID_CODE[variant.aminoacidAlternate]}: ${variant.count} sample(s)
-                                    </span>`)
-                        .join("")
-                }
+                                hotspot.variants
+                                    .map(variant => `
+                                        <span
+                                            class="help-block"
+                                            style="margin: 5px 1px">${AMINOACID_CODE[hotspot.aminoacidReference]}${hotspot.aminoacidPosition}${AMINOACID_CODE[variant.aminoacidAlternate]}: ${variant.count} sample(s)
+                                        </span>`)
+                                    .join("")
+                            }
                         </div>
                     </div>`;
             }
 
             if (cancerHotspotsHtml.size > 0) {
                 return `
-                     <a class="hotspots-tooltip" tooltip-title='Info' tooltip-text='${tooltipText}' tooltip-position-at="left bottom" tooltip-position-my="right top">
+                    <a class="hotspots-tooltip" tooltip-title='Info' tooltip-text='${tooltipText}' tooltip-position-at="left bottom" tooltip-position-my="right top">
                         <span style="color: green">${cancerHotspotsHtml.size} ${cancerHotspotsHtml.size === 1 ? "variant" : "variants"}</span>
                     </a>`;
             }
         }
         return "<span title='No clinical records found for this variant'><i class='fa fa-times' style='color: gray'></i></span>";
     }
 
+    static clinicalOmimFormatter(value, row) {
+        const entries = (row?.annotation?.geneTraitAssociation || [])
+            .filter(item => (item?.id || "").startsWith("OMIM:"))
+            .map(item => item.id.replace("OMIM:", ""));
+
+        if (entries?.length > 0) {
+            const uniqueEntries = new Set(entries);
+            const entriesLinks = Array.from(uniqueEntries)
+                .map(entry => {
+                    return `
+                        <div style="">
+                            <a href="${BioinfoUtils.getOmimLink(entry)}" target="_blank">${entry}</a>
+                        </div>
+                    `;
+                });
+            const tooltipText = entriesLinks.join("");
+
+            return `
+                <a class="omim-tooltip" tooltip-title='Info' tooltip-text='${tooltipText}' tooltip-position-at="left bottom" tooltip-position-my="right top">
+                    <span style='color:green;'>${uniqueEntries.size}<br>${uniqueEntries.size === 1 ? "entry" : "entries"}</span>
+                </a>
+            `;
+        } else {
+            return `
+                <span title='No clinical records found for this variant'>
+                    <i class='fa fa-times' style='color: gray'></i>
+                </span>
+            `;
+        }
+    }
+
     static clinicalTableDetail(value, row, index) {
         const clinvar = [];
         const cosmic = [];
@@ -1517,35 +1548,4 @@ export default class VariantGridFormatter {
         return "-";
     }
 
-
-    static clinicalOmimFormatter(value, row) {
-        const entries = (row?.annotation?.geneTraitAssociation || [])
-            .filter(item => (item?.id || "").startsWith("OMIM:"))
-            .map(item => item.id.replace("OMIM:", ""));
-
-        if (entries.length > 0) {
-            const uniqueEntries = new Set(entries);
-            const entriesLinks = Array.from(uniqueEntries).map(entry => {
-                return `
-                    <div style="">
-                        <a href="${BioinfoUtils.getOmimLink(entry)}" target="_blank">${entry}</a>
-                    </div>
-                `;
-            });
-            const tooltipText = entriesLinks.join("");
-
-            return `
-                <a class="hotspots-tooltip" tooltip-title='Info' tooltip-text='${tooltipText}' tooltip-position-at="left bottom" tooltip-position-my="right top">
-                    <span style='color:green;'>${uniqueEntries.size}<br>${uniqueEntries.size === 1 ? "entry" : "entries"}</span>
-                </a>
-            `;
-        } else {
-            return `
-                <span title='No clinical records found for this variant'>
-                    <i class='fa fa-times' style='color: gray'></i>
-                </span>
-            `;
-        }
-    }
-
 }