💥 clean legacy stuff

kids-first · Jun 14, 2024 · 4dec9bb · 4dec9bb
1 parent 6a0e250
commit 4dec9bb
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Showing 16 changed files with 167 additions and 837 deletions.
diff --git a/.env schema b/.env schema
@@ -14,9 +14,6 @@ KEYCLOAK_URL=
 KEYCLOAK_REALM=
 KEYCLOAK_CLIENT=
 
-# Riff 
-RIFF_URL=
-
 # Users-API
 USERS_API_URL=
 

diff --git a/src/env.ts b/src/env.ts
@@ -27,5 +27,4 @@ export const KEYCLOAK_URL = process.env.KEYCLOAK_URL || 'https://kf-keycloak-qa.
 export const KEYCLOAK_REALM = process.env.KEYCLOAK_REALM || 'kidsfirstdrc';
 export const KEYCLOAK_CLIENT = process.env.KEYCLOAK_CLIENT || 'kidsfirst-apis';
 
-export const RIFF_URL = process.env.RIFF_URL || 'https://riff-qa.kf-strides.org';
 export const USERS_API_URL = process.env.USERS_API_URL || 'https://users-api-qa.373997854230.d3b.io';
diff --git a/src/reports/biospecimen-data/configKf.ts b/src/reports/biospecimen-data/configKf.ts
@@ -1,51 +1,51 @@
+import { esBiospecimenIndex } from '../../env';
 import { QueryConfig, ReportConfig, SheetConfig } from '../types';
 
 const biospecimens: SheetConfig = {
     sheetName: 'Biospecimens',
-    root: 'biospecimens',
+    root: null,
     columns: [
-        { field: 'kf_id' },
-        { field: 'external_id' },
-        { field: 'biospecimens.kf_id' },
-        { field: 'biospecimens.external_sample_id' },
-        { field: 'biospecimens.external_aliquot_id' },
-        { field: 'biospecimens.age_at_event_days' },
-        { field: 'biospecimens.composition' },
-        { field: 'biospecimens.analyte_type' },
-        { field: 'biospecimens.concentration_mg_per_ml' },
-        { field: 'biospecimens.volume_ul' },
-        { field: 'biospecimens.shipment_date' },
-        { field: 'biospecimens.shipment_origin' },
-        { field: 'biospecimens.sequencing_center_id' },
-        { field: 'biospecimens.consent_type' },
-        { field: 'biospecimens.dbgap_consent_code' },
-        { field: 'biospecimens.method_of_sample_procurement' },
-        { field: 'biospecimens.source_text_tumor_descriptor' },
-        { field: 'biospecimens.ncit_id_anatomical_site' },
-        { field: 'biospecimens.ncit_id_tissue_type' },
-        { field: 'biospecimens.source_text_anatomical_site' },
-        { field: 'biospecimens.source_text_tissue_type' },
-        { field: 'biospecimens.uberon_id_anatomical_site' },
-        { field: 'biospecimens.spatial_descriptor' },
+        { field: 'participant.participant_id', header: 'Participant ID' },
+        { field: 'participant.external_id', header: 'External Participant ID' },
+        { field: 'collection_sample_id', header: 'Collection ID' },
+        { field: 'external_collection_sample_id', header: 'External Collection ID' },
+        { field: 'collection_sample_type', header: 'Collection Sample Type' },
+        { field: 'sample_id', header: 'Sample ID' },
+        { field: 'external_sample_id', header: 'External Sample ID' },
+        { field: 'sample_type', header: 'Sample Type' },
+        { field: 'parent_sample_id', header: 'Parent Sample ID' },
+        { field: 'parent_sample_type', header: 'Parent Sample Type' },
+        { field: 'study.study_code', header: 'Study Code' },
+        { field: 'age_at_biospecimen_collection', header: 'Age at Biospecimen Collection (Days)' },
+        { field: 'status', header: 'Sample Availability' },
+        { field: 'volume', header: 'Volume' },
+        { field: 'volume_unit', header: 'Volume Unit' },
+        { field: 'collection_method_of_sample_procurement', header: 'Method of Sample Procurement' },
+        { field: 'diagnoses.mondo_display_term', header: 'Histological Diagnosis (MONDO)' },
+        { field: 'diagnoses.diagnosis_ncit', header: 'Histological Diagnosis (NCIT)' },
+        { field: 'diagnoses.source_text', header: 'Histological Diagnosis (Source Text)' },
+        { field: 'diagnoses.source_text_tumor_location', header: 'Tumor Location (Source Text)' },
+        //FIXME { field: '', header: 'Tumor Descriptor (Source Text)' },
+        { field: 'collection_ncit_anatomy_site_id', header: 'Anatomical Site (NCIT)' },
+        { field: 'collection_anatomy_site', header: 'Anatomical Site (Source Text)' },
+        // TODO: Add this back when it's ready { field: 'ncit_id_tissue_type', header: 'Tissue Type (NCIT)' },
+        // TODO: Add this back when it's ready { field: 'tissue_type_source_text', header: 'Tissue Type (Source Text)' },
+        { field: 'consent_type', header: 'Consent Type' },
+        { field: 'dbgap_consent_code', header: 'dbGaP Consent Code' },
+        { field: 'files.sequencing_experiment.sequencing_center_id', header: 'Sequencing Center ID' },
     ],
     sort: [
-        // TODO : SORT BY biospecimens.kf_id
         {
-            'biospecimens.kf_id': {
-                order: 'asc',
-            },
-        },
-        {
-            kf_id: {
+            'participant.participant_id': {
                 order: 'asc',
             },
         },
     ],
 };
 
 const queryConfigs: QueryConfig = {
-    indexName: 'participant',
-    alias: 'participant_centric',
+    indexName: 'biospecimen',
+    alias: esBiospecimenIndex,
 };
 
 const sheetConfigs: SheetConfig[] = [biospecimens];

diff --git a/src/reports/biospecimen-data/configKfNext.ts b/src/reports/biospecimen-data/configKfNext.ts
diff --git a/src/reports/biospecimen-data/index.ts b/src/reports/biospecimen-data/index.ts
@@ -10,20 +10,17 @@ import generateReport from '../generateReport';
 import { ProjectType } from '../types';
 import configInclude from './configInclude';
 import configKf from './configKf';
-import configKfNext from './configKfNext';
 
 const biospecimenDataReport = async (req: Request, res: Response): Promise<void> => {
     console.time('biospecimen-data');
 
-    const { sqon, projectId, filename = null, isKfNext = false } = req.body;
+    const { sqon, projectId, filename = null } = req.body;
     const userId = req['kauth']?.grant?.access_token?.content?.sub;
     const accessToken = req.headers.authorization;
 
     const p = PROJECT.toLowerCase().trim();
     let reportConfig;
-    if (isKfNext) {
-        reportConfig = configKfNext;
-    } else if (p === ProjectType.include) {
+    if (p === ProjectType.include) {
         reportConfig = configInclude;
     } else if (p === ProjectType.kidsFirst) {
         reportConfig = configKf;