Fix detection of rna_seq molecular profile

Former-commit-id: 093264a3978bda42d97308ca67befcb5d9bf7cc9
thehyve · Jan 12, 2022 · 51a1f80 · 51a1f80
1 parent 503158b
commit 51a1f80
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Showing 3 changed files with 56 additions and 25 deletions.
diff --git a/src/pages/patientView/clinicalInformation/PatientViewPageStore.ts b/src/pages/patientView/clinicalInformation/PatientViewPageStore.ts
@@ -1310,7 +1310,11 @@ export class PatientViewPageStore {
         {
             await: () => [this.molecularProfilesInStudy],
             invoke: async () =>
-                findMrnaRankMolecularProfileId(this.molecularProfilesInStudy),
+                findMrnaRankMolecularProfileId(
+                    this.molecularProfilesInStudy.result!.map(
+                        p => p.molecularProfileId
+                    )
+                ),
         },
         null
     );

diff --git a/src/shared/lib/StoreUtils.spec.ts b/src/shared/lib/StoreUtils.spec.ts
@@ -7,6 +7,7 @@ import {
     fetchStudiesForSamplesWithoutCancerTypeClinicalData,
     filterAndAnnotateMolecularData,
     filterAndAnnotateMutations,
+    findMrnaRankMolecularProfileId,
     findSamplesWithoutCancerTypeClinicalData,
     generateMutationIdByEvent,
     generateMutationIdByGeneAndProteinChangeAndEvent,
@@ -1470,4 +1471,47 @@ describe('StoreUtils', () => {
             );
         });
     });
+
+    describe('findMrnaRankMolecularProfileId', () => {
+        it('requires `rna_seq` in profile name', () => {
+            const list = [
+                'ucec_tcga_pub_rppa',
+                'ucec_tcga_pub_rppa_Zscores',
+                'ucec_tcga_pub_gistic',
+                'ucec_tcga_pub_linear_CNA',
+                'ucec_tcga_pub_mutations',
+                'ucec_tcga_pub_methylation_hm27',
+                'ucec_tcga_pub_mrna',
+                'ucec_tcga_pub_mrna_median_Zscores',
+                ',ucec_tcga_pub_mrna_median_all_sample_Zscores',
+                'ucec_tcga_pub_rna_seq_v2_mrna',
+                'ucec_tcga_pub_rna_seq_v2_mrna_median_Zscores',
+                'ucec_tcga_pub_rna_seq_v2_mrna_median_all_sample_Zscores',
+            ];
+
+            assert.equal(
+                findMrnaRankMolecularProfileId(list),
+                'ucec_tcga_pub_rna_seq_v2_mrna_median_Zscores'
+            );
+        });
+
+        it('does not match rppa profiles', () => {
+            const list = [
+                'brca_tcga_pub_rppa',
+                'brca_tcga_pub_rppa_Zscores',
+                'brca_tcga_pub_gistic',
+                'brca_tcga_pub_mrna',
+                'brca_tcga_pub_mrna_median_Zscores',
+                'brca_tcga_pub_linear_CNA',
+                'brca_tcga_pub_methylation_hm27',
+                'brca_tcga_pub_mutations',
+                'brca_tcga_pub_mirna',
+                'brca_tcga_pub_mirna_median_Zscores',
+                'brca_tcga_pub_mrna_merged_median_Zscores',
+                'brca_tcga_pub_mrna_median_all_sample_Zscores',
+            ];
+
+            assert.equal(findMrnaRankMolecularProfileId(list), null);
+        });
+    });
 });
diff --git a/src/shared/lib/StoreUtils.ts b/src/shared/lib/StoreUtils.ts
@@ -1109,33 +1109,16 @@ export function findUncalledMutationMolecularProfileId(
 }
 
 export function findMrnaRankMolecularProfileId(
-    molecularProfilesInStudy: MobxPromise<MolecularProfile[]>
+    molecularProfilesInStudy: string[]
 ) {
-    if (!molecularProfilesInStudy.result) {
-        return null;
-    }
-
-    const regex1 = /^.+rna_seq.*_zscores$/; // We prefer profiles that look like this
-    const regex2 = /^.*_zscores$/; // If none of the above are available, we'll look for ones like this
-    const preferredProfile:
-        | MolecularProfile
-        | undefined = molecularProfilesInStudy.result.find(
-        (gp: MolecularProfile) =>
-            regex1.test(gp.molecularProfileId.toLowerCase())
+    const regex1 = /^.+rna_seq.*_zscores$/i; // We prefer profiles that look like this
+    const preferredProfileId:
+        | string
+        | undefined = molecularProfilesInStudy.find(profileId =>
+        regex1.test(profileId)
     );
 
-    if (preferredProfile) {
-        return preferredProfile.molecularProfileId;
-    } else {
-        const fallbackProfile:
-            | MolecularProfile
-            | undefined = molecularProfilesInStudy.result.find(
-            (gp: MolecularProfile) =>
-                regex2.test(gp.molecularProfileId.toLowerCase())
-        );
-
-        return fallbackProfile ? fallbackProfile.molecularProfileId : null;
-    }
+    return preferredProfileId || null;
 }
 
 export function generateUniqueSampleKeyToTumorTypeMap(