Update Genome Nexus API model and reVUE reference to fit new model (#…

…4919) * Update Genome Nexus API model * Update revue reference to fit new model
cBioPortal · Jun 6, 2024 · 2e1a275 · 2e1a275
1 parent 20cf5ad
commit 2e1a275
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Showing 6 changed files with 88 additions and 24 deletions.
diff --git a/packages/genome-nexus-ts-api-client/src/generated/GenomeNexusAPI-docs.json b/packages/genome-nexus-ts-api-client/src/generated/GenomeNexusAPI-docs.json
@@ -3800,6 +3800,18 @@
         }
       }
     },
+    "VueReference": {
+      "type": "object",
+      "properties": {
+        "pubmedId": {
+          "type": "integer",
+          "format": "int32"
+        },
+        "referenceText": {
+          "type": "string"
+        }
+      }
+    },
     "Vues": {
       "type": "object",
       "properties": {
@@ -3824,19 +3836,24 @@
         "hugoGeneSymbol": {
           "type": "string"
         },
-        "pubmedId": {
-          "type": "integer",
-          "format": "int32"
-        },
-        "referenceText": {
+        "mutationOrigin": {
           "type": "string"
         },
+        "references": {
+          "type": "array",
+          "items": {
+            "$ref": "#/definitions/VueReference"
+          }
+        },
         "revisedProteinEffect": {
           "type": "string"
         },
         "revisedVariantClassification": {
           "type": "string"
         },
+        "revisedVariantClassificationStandard": {
+          "type": "string"
+        },
         "transcriptId": {
           "type": "string"
         },

diff --git a/packages/genome-nexus-ts-api-client/src/generated/GenomeNexusAPI.ts b/packages/genome-nexus-ts-api-client/src/generated/GenomeNexusAPI.ts
@@ -1060,6 +1060,12 @@ export type Version = {
 
         'version': string
 
+};
+export type VueReference = {
+    'pubmedId': number
+
+        'referenceText': string
+
 };
 export type Vues = {
     'comment': string
@@ -1076,14 +1082,16 @@ export type Vues = {
 
         'hugoGeneSymbol': string
 
-        'pubmedId': number
+        'mutationOrigin': string
 
-        'referenceText': string
+        'references': Array < VueReference >
 
         'revisedProteinEffect': string
 
         'revisedVariantClassification': string
 
+        'revisedVariantClassificationStandard': string
+
         'transcriptId': string
 
         'variant': string

diff --git a/packages/genome-nexus-ts-api-client/src/generated/GenomeNexusAPIInternal-docs.json b/packages/genome-nexus-ts-api-client/src/generated/GenomeNexusAPIInternal-docs.json
@@ -2370,6 +2370,18 @@
         }
       }
     },
+    "VueReference": {
+      "type": "object",
+      "properties": {
+        "pubmedId": {
+          "type": "integer",
+          "format": "int32"
+        },
+        "referenceText": {
+          "type": "string"
+        }
+      }
+    },
     "Vues": {
       "type": "object",
       "properties": {
@@ -2394,19 +2406,24 @@
         "hugoGeneSymbol": {
           "type": "string"
         },
-        "pubmedId": {
-          "type": "integer",
-          "format": "int32"
-        },
-        "referenceText": {
+        "mutationOrigin": {
           "type": "string"
         },
+        "references": {
+          "type": "array",
+          "items": {
+            "$ref": "#/definitions/VueReference"
+          }
+        },
         "revisedProteinEffect": {
           "type": "string"
         },
         "revisedVariantClassification": {
           "type": "string"
         },
+        "revisedVariantClassificationStandard": {
+          "type": "string"
+        },
         "transcriptId": {
           "type": "string"
         },

diff --git a/packages/genome-nexus-ts-api-client/src/generated/GenomeNexusAPIInternal.ts b/packages/genome-nexus-ts-api-client/src/generated/GenomeNexusAPIInternal.ts
@@ -614,6 +614,12 @@ export type Vcf = {
 
         'ref': string
 
+};
+export type VueReference = {
+    'pubmedId': number
+
+        'referenceText': string
+
 };
 export type Vues = {
     'comment': string
@@ -630,14 +636,16 @@ export type Vues = {
 
         'hugoGeneSymbol': string
 
-        'pubmedId': number
+        'mutationOrigin': string
 
-        'referenceText': string
+        'references': Array < VueReference >
 
         'revisedProteinEffect': string
 
         'revisedVariantClassification': string
 
+        'revisedVariantClassificationStandard': string
+
         'transcriptId': string
 
         'variant': string

diff --git a/packages/react-mutation-mapper/src/component/revue/Revue.tsx b/packages/react-mutation-mapper/src/component/revue/Revue.tsx
@@ -34,15 +34,18 @@ export const RevueTooltipContent: React.FunctionComponent<{
                     </a>
                 }
                 {` (`}
-                {
-                    <a
-                        href={`https://pubmed.ncbi.nlm.nih.gov/${props.vue.pubmedId}/`}
-                        rel="noopener noreferrer"
-                        target="_blank"
-                    >
-                        {props.vue.referenceText}
-                    </a>
-                }
+                {props.vue.references.map((reference, index) => (
+                    <span key={index}>
+                        <a
+                            href={`https://pubmed.ncbi.nlm.nih.gov/${reference.pubmedId}/`}
+                            rel="noopener noreferrer"
+                            target="_blank"
+                        >
+                            {reference.referenceText}
+                        </a>
+                        {index < props.vue.references.length - 1 && ';'}
+                    </span>
+                ))}
                 {`): `}
                 <strong>{props.vue.revisedProteinEffect}</strong>
             </li>

diff --git a/src/shared/components/mutationTable/column/AnnotationColumnFormatter.tsx b/src/shared/components/mutationTable/column/AnnotationColumnFormatter.tsx
@@ -98,7 +98,18 @@ export default class AnnotationColumnFormatter {
             annotationDownloadContent.push(
                 `reVUE: ${
                     annotationData.vue
-                        ? `${annotationData.vue.comment},PubmedId:${annotationData.vue.pubmedId},PredictedEffect:${annotationData.vue.defaultEffect},ExperimentallyValidatedEffect:${annotationData.vue.revisedVariantClassification},RevisedProteinEffect:${annotationData.vue.revisedProteinEffect}`
+                        ? `${
+                              annotationData.vue.comment
+                          },PubmedId:${annotationData.vue.references
+                              .map(reference => reference.pubmedId)
+                              .join(';')},PredictedEffect:${
+                              annotationData.vue.defaultEffect
+                          },ExperimentallyValidatedEffect:${
+                              annotationData.vue
+                                  .revisedVariantClassificationStandard
+                          },RevisedProteinEffect:${
+                              annotationData.vue.revisedProteinEffect
+                          }`
                         : 'no'
                 }`
             );