kids-first · evans-g-crsj · Jul 24, 2024 · Jul 24, 2024 · Jul 24, 2024
diff --git a/src/env.ts b/src/env.ts
@@ -17,11 +17,8 @@ export const ES_QUERY_MAX_SIZE: number = Number(process.env.ES_QUERY_MAX_SIZE) |
 // Project
 export const PROJECT: string = process.env.PROJECT || 'kids-first';
 
-export const esFileIndex = process.env.ES_FILE_INDEX || 'file_centric';
 export const esFileAlias = process.env.ES_FILE_ALIAS || 'file';
 
-export const esBiospecimenIndex = process.env.ES_BIOSPECIMEN_INDEX || 'biospecimen_centric';
-
 // Keycloak configs
 export const KEYCLOAK_URL = process.env.KEYCLOAK_URL || 'https://kf-keycloak-qa.kf-strides.org/auth';
 export const KEYCLOAK_REALM = process.env.KEYCLOAK_REALM || 'kidsfirstdrc';

diff --git a/src/esVars.ts b/src/esVars.ts
@@ -0,0 +1,2 @@
+export const esFileIndex = 'file_centric';
+export const esBiospecimenIndex = 'biospecimen_centric';
diff --git a/src/reports/biospecimen-data/configInclude.ts b/src/reports/biospecimen-data/configInclude.ts
@@ -1,4 +1,4 @@
-import { esBiospecimenIndex } from '../../env';
+import { esBiospecimenIndex } from '../../esVars';
 import { QueryConfig, ReportConfig, SheetConfig } from '../types';
 
 const biospecimens: SheetConfig = {

diff --git a/src/reports/biospecimen-data/configKf.ts b/src/reports/biospecimen-data/configKf.ts
@@ -1,4 +1,4 @@
-import { esBiospecimenIndex } from '../../env';
+import { esBiospecimenIndex } from '../../esVars';
 import { QueryConfig, ReportConfig, SheetConfig } from '../types';
 
 const biospecimens: SheetConfig = {
@@ -22,14 +22,11 @@ const biospecimens: SheetConfig = {
         { 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.ncit_display_term', 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_ncit_anatomy_site', 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' },

diff --git a/src/reports/biospecimen-request/configInclude.ts b/src/reports/biospecimen-request/configInclude.ts
@@ -1,4 +1,4 @@
-import { esBiospecimenIndex } from '../../env';
+import { esBiospecimenIndex } from '../../esVars';
 import { BioRequestConfig, QueryConfig, ReportConfig, SheetConfig } from '../types';
 
 const contact: SheetConfig = {

diff --git a/src/reports/biospecimen-request/configKf.ts b/src/reports/biospecimen-request/configKf.ts
@@ -1,4 +1,4 @@
-import { esBiospecimenIndex } from '../../env';
+import { esBiospecimenIndex } from '../../esVars';
 import { BioRequestConfig, QueryConfig, ReportConfig, SheetConfig } from '../types';
 
 const contact: SheetConfig = {
@@ -41,10 +41,10 @@ const generateStudyTab: (study_code: string) => SheetConfig = (study_code) =>
             { 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.ncit_display_term', header: 'Histological Diagnosis (NCIT)' },
             { field: 'diagnoses.source_text', header: 'Histological Diagnosis (Source Text)' },
             { field: 'diagnoses.source_text_tumor_location', header: 'Tumor Location (Source Text)' },
-            { field: 'collection_ncit_anatomy_site_id', header: 'Anatomical Site (NCIT)' },
+            { field: 'collection_ncit_anatomy_site', header: 'Anatomical Site (NCIT)' },
             { field: 'collection_anatomy_site', header: 'Anatomical Site (Source Text)' },
         ],
         sort: [
@@ -90,10 +90,10 @@ const wantedFields = [
     'volume_unit',
     'collection_method_of_sample_procurement',
     'diagnoses.mondo_display_term',
-    'diagnoses.diagnosis_ncit',
+    'diagnoses.ncit_display_term',
     'diagnoses.source_text',
     'diagnoses.source_text_tumor_location',
-    'collection_ncit_anatomy_site_id',
+    'collection_ncit_anatomy_site',
     'collection_anatomy_site',
 ];
 

diff --git a/src/reports/clinical-data/configInclude.ts b/src/reports/clinical-data/configInclude.ts
@@ -77,7 +77,7 @@ const diagnoses: SheetConfig = {
     columns: [
         { field: 'participant_id', header: 'Participant ID' },
         { field: 'external_id', header: 'External Participant ID' },
-        { field: 'diagnosis.mondo_id_diagnosis', header: ' Diagnosis (MONDO)' },
+        { field: 'diagnosis.mondo_display_term', header: ' Diagnosis (MONDO)' },
         { field: 'diagnosis.source_text', header: 'Condition (Source Text)' },
         {
             field: 'diagnosis.age_at_event_days',

diff --git a/src/reports/clinical-data/configKf.ts b/src/reports/clinical-data/configKf.ts
@@ -70,18 +70,11 @@ const diagnoses: SheetConfig = {
         { field: 'external_id', header: 'External Participant ID' },
         { field: 'families_id', header: 'Family ID' },
         { field: 'is_proband', header: 'Proband' },
-        //TODO { field: '?', header: 'Diagnosis Category' },
-
         { field: 'diagnosis.mondo_display_term', header: 'Diagnosis (MONDO)' },
-
         {
             field: 'diagnosis.ncit_display_term',
-            additionalFields: ['diagnosis.ncit_code'],
             header: 'Diagnosis (NCIT)',
-            transform: (displayTerm: string, row: { diagnosis: { ncit_code: string } }) =>
-                displayTerm || row?.diagnosis?.ncit_code || '',
         },
-
         { field: 'diagnosis.source_text', header: 'Diagnosis (Source Text)' },
         { field: 'diagnosis.age_at_event_days', header: 'Age at Diagnosis (Days)' },
         { field: 'diagnosis.source_text_tumor_location', header: 'Tumor Location (Source Text)' },
@@ -113,7 +106,7 @@ const familyRelationship: SheetConfig = {
 
 export const queryConfigs: QueryConfig = {
     indexName: 'participant',
-    alias: 'next_participant_centric',
+    alias: 'participant_centric',
 };
 
 export const sheetConfigs: SheetConfig[] = [participants, phenotypes, diagnoses, familyRelationship];

diff --git a/src/reports/family-clinical-data/configInclude.ts b/src/reports/family-clinical-data/configInclude.ts
@@ -99,7 +99,7 @@ const diagnoses: SheetConfig = {
         { field: 'participant_id', header: 'Participant ID' },
         { field: 'external_id', header: 'External Participant ID' },
         { field: 'families_id', header: 'Family ID' },
-        { field: 'diagnosis.mondo_id_diagnosis', header: ' Diagnosis (MONDO)' },
+        { field: 'diagnosis.mondo_display_term', header: ' Diagnosis (MONDO)' },
         { field: 'diagnosis.source_text', header: 'Condition (Source Text)' },
         {
             field: 'diagnosis.age_at_event_days',

diff --git a/src/reports/family-clinical-data/configKf.ts b/src/reports/family-clinical-data/configKf.ts
@@ -90,14 +90,10 @@ const diagnoses: SheetConfig = {
         { field: 'external_id', header: 'External Participant ID' },
         { field: 'families_id', header: 'Family ID' },
         { field: 'is_proband', header: 'Proband' },
-        //TODO { field: '?', header: 'Diagnosis Category' },
         { field: 'diagnosis.mondo_display_term', header: 'Diagnosis (MONDO)' },
         {
             field: 'diagnosis.ncit_display_term',
-            additionalFields: ['diagnosis.ncit_code'],
             header: 'Diagnosis (NCIT)',
-            transform: (displayTerm: string, row: { diagnosis: { ncit_code: string } }) =>
-                displayTerm || row?.diagnosis?.ncit_code || '',
         },
         { field: 'diagnosis.source_text', header: 'Diagnosis (Source Text)' },
         { field: 'diagnosis.age_at_event_days', header: 'Age at Diagnosis (Days)' },
@@ -108,7 +104,7 @@ const diagnoses: SheetConfig = {
 
 export const queryConfigs: QueryConfig = {
     indexName: 'participant',
-    alias: 'next_participant_centric',
+    alias: 'participant_centric',
 };
 
 export const sheetConfigs: SheetConfig[] = [participants, phenotypes, diagnoses];

diff --git a/src/reports/file-manifest/index.ts b/src/reports/file-manifest/index.ts
@@ -2,7 +2,7 @@
 import { Request, Response } from 'express';
 
 import EsInstance from '../../ElasticSearchClientInstance';
-import { esFileIndex, PROJECT } from '../../env';
+import { PROJECT } from '../../env';
 import { reportGenerationErrorHandler } from '../../errors';
 import { ProjectType } from '../types';
 import generateTsvReport from '../utils/generateTsvReport';
@@ -11,6 +11,7 @@ import getFilesFromSqon from '../utils/getFilesFromSqon';
 import getInfosByConfig from '../utils/getInfosByConfig';
 import configInclude from './configInclude';
 import configKf from './configKf';
+import { esFileIndex } from '../../esVars';
 
 const fileManifestReport = async (req: Request, res: Response): Promise<void> => {
     console.time('fileManifestReport');

diff --git a/src/reports/utils/getAvailableBiospecimensFromSqon.ts b/src/reports/utils/getAvailableBiospecimensFromSqon.ts
@@ -1,11 +1,12 @@
 import { buildQuery } from '@arranger/middleware';
 import { Client } from '@elastic/elasticsearch';
 
-import { ES_QUERY_MAX_SIZE, esBiospecimenIndex } from '../../env';
+import { ES_QUERY_MAX_SIZE } from '../../env';
 import { getExtendedConfigs, getNestedFields } from '../../utils/arrangerUtils';
 import { executeSearch } from '../../utils/esUtils';
 import { Sqon } from '../../utils/setsTypes';
 import { resolveSetsInSqon } from '../../utils/sqonUtils';
+import { esBiospecimenIndex } from '../../esVars';
 
 /**
  * Retrieve all available biospecimen from a sqon of a list of biospecimen ids.

diff --git a/src/reports/utils/getFamilyIds.ts b/src/reports/utils/getFamilyIds.ts
@@ -1,8 +1,9 @@
 import { Client } from '@elastic/elasticsearch';
 import noop from 'lodash/noop';
 
-import { ES_PAGESIZE, ES_QUERY_MAX_SIZE, esFileIndex } from '../../env';
+import { ES_PAGESIZE, ES_QUERY_MAX_SIZE } from '../../env';
 import { executeSearch, executeSearchAfterQuery } from '../../utils/esUtils';
+import { esFileIndex } from '../../esVars';
 
 interface IFileInfo {
     data_type: string;

diff --git a/src/reports/utils/getFilesFromSqon.ts b/src/reports/utils/getFilesFromSqon.ts
@@ -2,7 +2,8 @@ import { buildQuery } from '@arranger/middleware';
 import { Client } from '@elastic/elasticsearch';
 import noop from 'lodash/noop';
 
-import { ES_PAGESIZE, esFileAlias, esFileIndex } from '../../env';
+import { ES_PAGESIZE, esFileAlias } from '../../env';
+import { esFileIndex } from '../../esVars';
 import { getExtendedConfigs, getNestedFields } from '../../utils/arrangerUtils';
 import { executeSearchAfterQuery } from '../../utils/esUtils';
 import { Sqon } from '../../utils/setsTypes';