feat: SJIP-569 fix esClient close at any error and add field in biosp…

…ecimen request report
kids-first · Oct 20, 2023 · 872242e · 872242e
1 parent a3401d0
commit 872242e
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Showing 9 changed files with 10 additions and 9 deletions.
diff --git a/src/errors.ts b/src/errors.ts
@@ -16,9 +16,8 @@ export class ApplicationError extends Error {
     }
 }
 
-export const reportGenerationErrorHandler = (err: any, es: Client): void => {
+export const reportGenerationErrorHandler = (err: any): void => {
     console.error(`An error occurs while generating the report`, err);
-    es && es.close();
     throw new ApplicationError(err.message || err.details || 'An unknown error occurred.', INTERNAL_ERROR_STATUS_CODE);
 };
 

diff --git a/src/reports/biospecimen-data/index.ts b/src/reports/biospecimen-data/index.ts
@@ -39,7 +39,7 @@ const biospecimenDataReport = async (req: Request, res: Response): Promise<void>
         // Generate the report
         await generateReport(esClient, res, projectId, sqon, filename, normalizedConfigs, userId, accessToken);
     } catch (err) {
-        reportGenerationErrorHandler(err, esClient);
+        reportGenerationErrorHandler(err);
     }
 
     console.timeEnd('biospecimen-data');

diff --git a/src/reports/biospecimen-request/biospecimenRequestStats.ts b/src/reports/biospecimen-request/biospecimenRequestStats.ts
@@ -53,7 +53,7 @@ const biospecimenRequestStats = async (req: Request, res: Response): Promise<voi
 
         res.send(biospecimenDatasByStudy);
     } catch (err) {
-        reportGenerationErrorHandler(err, esClient);
+        reportGenerationErrorHandler(err);
     }
 
     console.timeEnd('biospecimenRequestStats');

diff --git a/src/reports/biospecimen-request/config.ts b/src/reports/biospecimen-request/config.ts
@@ -32,6 +32,7 @@ export const generateStudyTab: (study_code: string) => SheetConfig = study_code
             { field: 'collection_sample_id', header: 'INCLUDE Collection ID' },
             { field: 'collection_sample_type', header: 'Collection Sample Type' },
             { field: 'container_id', header: 'Container ID' },
+            { field: 'external_container_id', header: 'External Container ID' },
             { field: 'participant.external_id', header: 'External Participant ID' },
             { field: 'participant.participant_id', header: 'INCLUDE Participant ID' },
             { field: 'study.study_code', header: 'Study Code' },
@@ -65,6 +66,7 @@ export const wantedFields = [
     'collection_sample_id',
     'collection_sample_type',
     'container_id',
+    'external_container_id',
     'participant.external_id',
     'participant.participant_id',
     'study.study_code',

diff --git a/src/reports/biospecimen-request/index.ts b/src/reports/biospecimen-request/index.ts
@@ -67,7 +67,7 @@ const biospecimenRequest = async (req: Request, res: Response, _next: NextFuncti
                 res.sendFile(pathFileZip);
             });
     } catch (err) {
-        reportGenerationErrorHandler(err, esClient);
+        reportGenerationErrorHandler(err);
     } finally {
         console.timeEnd('biospecimenRequest');
     }

diff --git a/src/reports/clinical-data/index.ts b/src/reports/clinical-data/index.ts
@@ -37,7 +37,7 @@ const clinicalDataReport = async (req: Request, res: Response): Promise<void> =>
         // Generate the report
         await generateReport(esClient, res, projectId, sqon, filename, normalizedConfigs, userId, accessToken);
     } catch (err) {
-        reportGenerationErrorHandler(err, esClient);
+        reportGenerationErrorHandler(err);
     }
 
     console.timeEnd('clinical-data');

diff --git a/src/reports/family-clinical-data/index.ts b/src/reports/family-clinical-data/index.ts
@@ -52,7 +52,7 @@ const clinicalDataReport = async (req: Request, res: Response): Promise<void> =>
         // Generate the report
         await generateReport(esClient, res, projectId, familySqon, filename, normalizedConfigs, userId, accessToken);
     } catch (err) {
-        reportGenerationErrorHandler(err, esClient);
+        reportGenerationErrorHandler(err);
     }
 
     console.timeEnd('family-clinical-data');

diff --git a/src/reports/file-manifest/fileManifestStats.ts b/src/reports/file-manifest/fileManifestStats.ts
@@ -52,7 +52,7 @@ const fileManifestStats = async (req: Request, res: Response): Promise<void> =>
 
         res.send(filesInfosData);
     } catch (err) {
-        reportGenerationErrorHandler(err, esClient);
+        reportGenerationErrorHandler(err);
     }
 
     console.timeEnd('getFileManifestStats');

diff --git a/src/reports/file-manifest/index.ts b/src/reports/file-manifest/index.ts
@@ -34,7 +34,7 @@ const fileManifestReport = async (req: Request, res: Response): Promise<void> =>
         res.setHeader('Content-Disposition', `attachment; filename="${filename}.tsv"`);
         res.sendFile(path);
     } catch (err) {
-        reportGenerationErrorHandler(err, esClient);
+        reportGenerationErrorHandler(err);
     }
 
     console.timeEnd('fileManifestReport');