🔧 Fix todo en env.ts and removed is_harmnonized in study mocks

kids-first · Jul 16, 2024 · b34d72e · b34d72e
1 parent e79070e
commit b34d72e
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Showing 3 changed files with 13 additions and 31 deletions.
diff --git a/admin/findClinicalIndicesUsage.mjs b/admin/findClinicalIndicesUsage.mjs
@@ -42,7 +42,7 @@ const unaliasedClinicalIndicesWithCreationDate = makeReleaseToCreationDate(clini
 
 // Make sure that no aliased index contains previously found unaliased releases.
 const unaliasedReleases = unaliasedClinicalIndicesWithCreationDate.map(x => x.release);
-assert(clinicalAliases.every(x => !unaliasedReleases.includes(`re_${x.index.split('re_')[1]}`)));
+assert(clinicalAliases.every(x => !unaliasedReleases.includes(`re_${x.index.split('re_')[1]}`)), 'more than one releases aliased was detected');
 
 console.log(`===== Not Aliased (pattern:re_*)`);
 

diff --git a/admin/mockStudies.mjs b/admin/mockStudies.mjs
@@ -97,7 +97,6 @@ export const mockStudies = [
         date_collection_start_year: '2016',
         institutions: ['Linda Crnic Institute for Down Syndrome'],
         investigator_names: ['Joaquin M. Espinosa'],
-        is_harmonized: true,
         study_code: 'HTP',
     },
     {
@@ -153,7 +152,6 @@ export const mockStudies = [
         date_collection_start_year: '',
         institutions: ['Baylor College Of Medicine'],
         investigator_names: ['Phillip J. Lupo'],
-        is_harmonized: true,
         study_code: 'DS-COG-ALL',
     },
     {
@@ -209,7 +207,6 @@ export const mockStudies = [
         date_collection_start_year: '',
         institutions: ['Emory University School of Medicine'],
         investigator_names: ['Stephanie Sherman'],
-        is_harmonized: true,
         study_code: 'DS360-CHD',
     },
     {
@@ -265,7 +262,6 @@ export const mockStudies = [
         date_collection_start_year: '',
         institutions: ["Cincinnati Children's Hospital Medical Center"],
         investigator_names: ['Eileen C. King'],
-        is_harmonized: true,
         study_code: 'DS-PCGC',
     },
     {
@@ -344,7 +340,6 @@ export const mockStudies = [
         date_collection_start_year: '',
         institutions: ["Children's Hospital of Philadelphia"],
         investigator_names: ['Hakon Hakonarson'],
-        is_harmonized: true,
         study_code: 'X01-Hakonarson',
     },
     {
@@ -400,7 +395,6 @@ export const mockStudies = [
         date_collection_start_year: '',
         institutions: ['University of Oxford'],
         investigator_names: ['Adam de Smith'],
-        is_harmonized: true,
         study_code: 'X01-deSmith',
     },
     {
@@ -409,7 +403,6 @@ export const mockStudies = [
         date_collection_start_year: '2018',
         institutions: ['Benaroya Research Institute'],
         investigator_names: ['Jane Buckner'],
-        is_harmonized: true,
         study_code: 'BRI-DSR',
     },
     {
@@ -418,7 +411,6 @@ export const mockStudies = [
         date_collection_start_year: '',
         institutions: ['Linda Crnic Institute for Down Syndrome'],
         investigator_names: ['Joaquin Espinosa'],
-        is_harmonized: true,
         study_code: 'DS-NEXUS',
     },
     {
@@ -427,7 +419,6 @@ export const mockStudies = [
         date_collection_start_year: '',
         institutions: ['Geisinger Health System'],
         investigator_names: ['Christa Martin'],
-        is_harmonized: true,
         study_code: 'DS-Sleep',
     },
     {
@@ -460,7 +451,6 @@ export const mockStudies = [
         date_collection_start_year: '2013',
         institutions: ['Eunice Kennedy Shriver National Institute of Child Health and Human Development'],
         investigator_names: ['Sujata Bardhan'],
-        is_harmonized: true,
         study_code: 'DSC',
     },
     {
@@ -469,7 +459,6 @@ export const mockStudies = [
         date_collection_start_year: '',
         institutions: ['University of Pittsburgh'],
         investigator_names: ['Bradley T. Christian', 'Benjamin L. Handen', 'Elizabeth Head', 'Mark Mapstone'],
-        is_harmonized: true,
         study_code: 'ABC-DS',
     },
 ];
@@ -570,9 +559,6 @@ const sSchema = {
                 type: 'string',
             },
         },
-        is_harmonized: {
-            type: 'boolean',
-        },
         investigator_names: {
             type: 'array',
             items: {

diff --git a/src/env.ts b/src/env.ts
@@ -2,10 +2,7 @@ import dotenv from 'dotenv';
 
 dotenv.config();
 
-//TODO DELETE in confs //export const PROJECT_KIDSFIRST = 'KidsFirst';
-//TODO DELETE in confs //export const PROJECT_INCLUDE = 'Include';
 
-//TODO DELETE in confs //export const project = process.env.PROJECT || PROJECT_KIDSFIRST;
 export const port = process.env.PORT || 5050;
 
 export const keycloakURL = process.env.KEYCLOAK_URL || 'https://kf-keycloak-qa.kf-strides.org/auth';
@@ -28,20 +25,19 @@ export const maxNOfGenomicFeatureSuggestions = process.env.MAX_NUMBER_OF_GF_SUGG
 export const indexNameGeneFeatureSuggestion = process.env.GENES_SUGGESTIONS_INDEX_NAME;
 export const indexNameVariantFeatureSuggestion = process.env.VARIANTS_SUGGESTIONS_INDEX_NAME;
 
-//TODO DELETE in confs //export const riffURL = process.env.RIFF_URL || 'https://riff-qa.kf-strides.org';
+
 export const userApiURL = process.env.USER_API_URL || 'https://include-users-api-qa.373997854230.d3b.io';
-//TODO DELETE in confs //export const sendUpdateToSqs = process.env.SEND_UPDATE_TO_SQS !== 'false';
-//TODO DELETE in confs //export const sqsQueueUrl = process.env.SQS_QUEUE_URL || '';
+
 export const maxSetContentSize: number = Number.parseInt(process.env.MAX_SET_CONTENT_SIZE) || 100000;
-//TODO change default values
-export const idKey = process.env.ID_KEY || 'kf_id';
-export const fileIdKey = process.env.FILE_ID_KEY || 'kf_id';
-export const studyIdKey = process.env.STUDY_ID_KEY || 'kf_id';
-export const participantIdKey = process.env.PARTICIPANT_ID_KEY || 'kf_id';
-export const biospecimenIdKey = process.env.BIOSPECIMEN_ID_KEY || 'kf_id';
-export const familyIdKey = process.env.FAMILY_ID_KEY || 'family_id';
-export const participantKey = process.env.TO_PARTICIPANT_ID_KEY || 'kf_id';
-export const participantFileKey = process.env.TO_PARTICIPANT_FILE_ID_KEY || 'kf_id';
-export const participantBiospecimenKey = process.env.TO_PARTICIPANT_BIOSPECIMEN_ID_KEY || 'kf_id';
+
+export const idKey = process.env.ID_KEY || 'fhir_id';
+export const fileIdKey = process.env.FILE_ID_KEY || 'file_id';
+export const studyIdKey = process.env.STUDY_ID_KEY || 'study_id';
+export const participantIdKey = process.env.PARTICIPANT_ID_KEY || 'participant_id';
+export const biospecimenIdKey = process.env.BIOSPECIMEN_ID_KEY || 'sample_id';
+export const familyIdKey = process.env.FAMILY_ID_KEY || 'family.family_id';
+export const participantKey = process.env.TO_PARTICIPANT_ID_KEY || 'fhir_id';
+export const participantFileKey = process.env.TO_PARTICIPANT_FILE_ID_KEY || 'files.fhir_id';
+export const participantBiospecimenKey = process.env.TO_PARTICIPANT_BIOSPECIMEN_ID_KEY || 'files.biospecimens.fhir_id';
 
 export const cacheTTL: number = Number.parseInt(process.env.CACHE_TTL_SEC) || 3600;