feat: SKFP-848 add file manifest for Include

kids-first · Nov 6, 2023 · b6ace2b · b6ace2b
1 parent de011be
commit b6ace2b
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Showing 3 changed files with 105 additions and 4 deletions.
diff --git a/src/reports/file-manifest/configInclude.ts b/src/reports/file-manifest/configInclude.ts
@@ -0,0 +1,91 @@
+import { formatFileSize } from '../../utils/formatFileSize';
+import { SheetConfig } from '../types';
+
+type BiospecimenData = {
+    family?: { family_id?: string };
+    sample_id?: string;
+    external_sample_id?: string;
+    container_id?: string;
+    external_collection_sample_id?: string;
+};
+type ParticipantsData = {
+    biospecimens: BiospecimenData[];
+}[];
+const processBiospecimens = (participants: ParticipantsData, key: keyof BiospecimenData): string[] =>
+    Array.from(
+        new Set(
+            (participants || [])
+                .map(x => x?.biospecimens || [])
+                // eslint-disable-next-line @typescript-eslint/ban-ts-comment
+                //@ts-ignore
+                .flat()
+                .map(x => x[key])
+                .filter(x => !!x),
+        ),
+    );
+
+const config: SheetConfig = {
+    sheetName: 'Files',
+    root: null,
+    columns: [
+        { field: 'access_urls', header: 'Access URL' },
+        {
+            field: 'file_id',
+            header: 'File ID',
+        },
+        { field: 'file_name', header: 'File Name' },
+        { field: 'size', header: 'File Size', transform: value => formatFileSize(value, { output: 'string' }) },
+        { field: 'data_category', header: 'Data Category' },
+        { field: 'data_type', header: 'Data Type' },
+        { field: 'file_format', header: 'File Format' },
+        { field: 'sequencing_experiment.experiment_strategy', header: 'Experimental Strategy' },
+        { field: 'hashes.md5', header: 'Hash' },
+        { field: 'study.study_name', header: 'Study Name' },
+        { field: 'participants.participant_id', header: 'Participant ID' },
+        {
+            fieldExtraSuffix: '_sample_id',
+            field: 'participants',
+            header: 'Sample ID',
+            transform: participants => processBiospecimens(participants, 'sample_id'),
+        },
+        {
+            fieldExtraSuffix: '_container_id',
+            field: 'participants',
+            header: 'INCLUDE Container ID',
+            transform: participants => processBiospecimens(participants, 'container_id'),
+        },
+        {
+            fieldExtraSuffix: '_down_syndrome_status',
+            field: 'participants',
+            header: 'Down Syndrome Status',
+            transform: participants => (participants || []).map(x => x?.down_syndrome_status ?? ''),
+        },
+        {
+            fieldExtraSuffix: '_family',
+            field: 'participants',
+            header: 'Family ID',
+            transform: participants => (participants || []).map(x => x?.family?.family_id ?? ''),
+        },
+        {
+            fieldExtraSuffix: '_external_id',
+            field: 'participants',
+            header: 'External Participant ID',
+            transform: participants => (participants || []).map(x => x?.external_id ?? ''),
+        },
+        {
+            fieldExtraSuffix: '_external_sample_id',
+            field: 'participants',
+            header: 'External Sample ID',
+            transform: participants => processBiospecimens(participants, 'external_sample_id'),
+        },
+        {
+            fieldExtraSuffix: '_external_collection_sample_id',
+            field: 'participants',
+            header: 'External Collection ID',
+            transform: participants => processBiospecimens(participants, 'external_collection_sample_id'),
+        },
+    ],
+    sort: [{ file_id: { order: 'asc' } }],
+};
+
+export default config;
diff --git a/src/reports/file-manifest/config.ts → src/reports/file-manifest/configKf.ts b/src/reports/file-manifest/config.ts → src/reports/file-manifest/configKf.ts
diff --git a/src/reports/file-manifest/index.ts b/src/reports/file-manifest/index.ts
@@ -7,8 +7,10 @@ import generateTsvReport from '../utils/generateTsvReport';
 import getFamilyIds from '../utils/getFamilyIds';
 import getFilesFromSqon from '../utils/getFilesFromSqon';
 import getInfosByConfig from '../utils/getInfosByConfig';
-import config from './config';
-import { esFileIndex } from '../../env';
+import configKf from './configKf';
+import configInclude from './configInclude';
+import { PROJECT, esFileIndex } from '../../env';
+import { ProjectType } from '../types';
 
 const fileManifestReport = async (req: Request, res: Response): Promise<void> => {
     console.time('fileManifestReport');
@@ -17,6 +19,14 @@ const fileManifestReport = async (req: Request, res: Response): Promise<void> =>
     const userId = req['kauth']?.grant?.access_token?.content?.sub;
     const accessToken = req.headers.authorization;
 
+    let reportConfig;
+    const p = PROJECT.toLowerCase().trim();
+    if (p === ProjectType.include) {
+        reportConfig = configInclude;
+    } else {
+        reportConfig = configKf;
+    }
+
     const wantedFields = ['file_id'];
 
     const esClient = EsInstance.getInstance();
@@ -26,10 +36,10 @@ const fileManifestReport = async (req: Request, res: Response): Promise<void> =>
         const fileIds = files?.map(f => f.file_id);
         const newFileIds = withFamily ? await getFamilyIds(esClient, fileIds) : fileIds;
 
-        const filesInfos = await getInfosByConfig(esClient, config, newFileIds, 'file_id', esFileIndex);
+        const filesInfos = await getInfosByConfig(esClient, reportConfig, newFileIds, 'file_id', esFileIndex);
 
         const path = `/tmp/${filename}.tsv`;
-        await generateTsvReport(filesInfos, path, config);
+        await generateTsvReport(filesInfos, path, reportConfig);
 
         res.setHeader('Content-Disposition', `attachment; filename="${filename}.tsv"`);
         res.sendFile(path);