fix: SKFP-1115 remove some problematic cavatica metadata (#4022)

kids-first · May 29, 2024 · b378394 · b378394
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commit b378394
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Showing 2 changed files with 14 additions and 15 deletions.
diff --git a/src/store/passport/metadata.ts b/src/store/passport/metadata.ts
@@ -31,24 +31,23 @@ const extractParticipantMetaData = (participants: any[]) => {
   return {
     // Removed temporarily due to bug
     // case_id: joinUniquely(participants.map((x) => x.participant_id)),
-    external_participant_ids: joinUniquely(participants.map((x) => x.external_id)),
-    proband: joinUniquely(participants.map((x) => `${x.participant_id}: ${x.is_proband}`)),
-    // Removed temporarily due to bug
     // ethnicity: joinUniquely(participants.map((x) => x.ethnicity)),
     // gender: joinUniquely(participants.map((x) => x.sex)),
     // race: joinUniquely(participants.map((x) => x.race)),
+    // diagnosis_source_text: joinUniquely(diagnosis.map((d) => d.source_text)),
+    // diagnosis_mondo: joinUniquely(diagnosis.map((d) => d.mondo_display_term)),
+    // diagnosis_ncit: joinUniquely(diagnosis.map((d) => d.ncit_id_diagnosis)),
+    // observed_phenotype_hpo: joinUniquely(phenotype.map((p) => p.hpo_phenotype_observed)),
+    // not_observed_phenotype_hpo: joinUniquely(phenotype.map((p) => p.hpo_phenotype_not_observed)),
+    // observed_phenotype_source_text: joinUniquely(phenotype.map((p) => p.source_text)),
+    external_participant_ids: joinUniquely(participants.map((x) => x.external_id)),
+    proband: joinUniquely(participants.map((x) => `${x.participant_id}: ${x.is_proband}`)),
     age_at_participant_diagnosis: joinUniquely(diagnosis.map((d) => d.age_at_event_days)),
     age_at_vital_status: joinUniquely(outcomes.map((o) => o.age_at_event_days.value)),
     age_at_observed_phenotype: joinUniquely(phenotype.map((p) => p.age_at_event_days)),
-    diagnosis_mondo: joinUniquely(diagnosis.map((d) => d.mondo_display_term)),
-    diagnosis_ncit: joinUniquely(diagnosis.map((d) => d.ncit_id_diagnosis)),
-    diagnosis_source_text: joinUniquely(diagnosis.map((d) => d.source_text)),
     family_id: joinUniquely(participants.map((x) => x.families_id)),
     family_composition: joinUniquely(participants.map((x) => x.family_type)),
     family_role: joinUniquely(relation.map((r) => r.role)),
-    observed_phenotype_hpo: joinUniquely(phenotype.map((p) => p.hpo_phenotype_observed)),
-    not_observed_phenotype_hpo: joinUniquely(phenotype.map((p) => p.hpo_phenotype_not_observed)),
-    observed_phenotype_source_text: joinUniquely(phenotype.map((p) => p.source_text)),
     vital_status: joinUniquely(outcomes.map((o) => o.vital_status)),
   };
 };

diff --git a/src/store/passport/thunks.test.ts b/src/store/passport/thunks.test.ts
@@ -305,18 +305,18 @@ describe(`${extractMetadata.name}()`, () => {
       // ethnicity: 'Not Hispanic or Latino',
       // gender: 'female',
       // race: 'White',
+      // observed_phenotype_hpo: 'hpo_phenotype_observed',
+      // not_observed_phenotype_hpo: 'hpo_phenotype_not_observed',
+      // observed_phenotype_source_text: 'mySourceText',
+      // diagnosis_source_text: 'Neuroblastoma',
+      // diagnosis_mondo: 'neuroblastoma (MONDO:0005072)',
+      // diagnosis_ncit: 'NCIT:C3270',
       age_at_participant_diagnosis: '174',
       age_at_vital_status: '3137',
       age_at_observed_phenotype: '31231',
-      diagnosis_mondo: 'neuroblastoma (MONDO:0005072)',
-      diagnosis_ncit: 'NCIT:C3270',
-      diagnosis_source_text: 'Neuroblastoma',
       family_id: 'FM_5ED41H3V',
       family_composition: 'trio',
       family_role: 'mother,father,proband',
-      observed_phenotype_hpo: 'hpo_phenotype_observed',
-      not_observed_phenotype_hpo: 'hpo_phenotype_not_observed',
-      observed_phenotype_source_text: 'mySourceText',
       vital_status: 'Alive',
       sample_id: '595495',
       sample_type: 'DNA',