fix: refactor file write

src/reports/biospecimen-request/generateBiospecimenRequestFiles.ts

@@ -2,8 +2,8 @@ import { buildQuery } from '@arranger/middleware';
 import { Client } from '@elastic/elasticsearch';
 import xl from 'excel4node';
 import noop from 'lodash/noop';
-import { env } from 'process';
 
+import { ES_PAGESIZE } from '../../env';
 import { getExtendedConfigs, getNestedFields } from '../../utils/arrangerUtils';
 import { executeSearchAfterQuery } from '../../utils/esUtils';
 import ExtendedReportConfigs from '../../utils/extendedReportConfigs';
@@ -15,7 +15,8 @@ import generateTxtFile from '../utils/generateTxtFile';
 import { addConditionAvailableInSqon } from '../utils/getAvailableBiospecimensFromSqon';
 
 // eslint-disable-next-line max-len
-const cbtn_instructions_mock = 'To request biospecimens from CBTN, please use the request form (https://airtable.com/apperYvVD82ti3021/pagdArwI0TxJQpiVW/form). General inquiries can be directed to [email protected].';
+const cbtn_instructions_mock =
+    'To request biospecimens from CBTN, please use the request form (https://airtable.com/apperYvVD82ti3021/pagdArwI0TxJQpiVW/form). General inquiries can be directed to [email protected].';
 
 /**
  * Generate and write locally.
@@ -90,7 +91,7 @@ export default async function generateFiles(
                 }
             },
             onFinish: noop,
-            pageSize: Number(env.ES_PAGESIZE),
+            pageSize: ES_PAGESIZE,
         });
     } catch (err) {
         console.error(`Error while fetching the data for biospecimen request`);

src/reports/file-manifest/index.ts

@@ -42,15 +42,11 @@ const fileManifestReport = async (req: Request, res: Response): Promise<void> =>
             wantedFields,
         );
         const fileIds = files?.map((f) => f.file_id);
-        console.log('OriginalFileIds: ', fileIds);
         const newFileIds = withFamily ? await getFamilyIds(esClient, fileIds) : fileIds;
-        console.log('New unique file ids: ', newFileIds.length);
-
         const filesInfos = await getInfosByConfig(esClient, reportConfig, newFileIds, 'file_id', esFileIndex);
-        console.log('filesInfos: ', filesInfos.length);
 
         const path = `/tmp/${filename}.tsv`;
-        await generateTsvReport(filesInfos, path, reportConfig);
+        generateTsvReport(filesInfos, path, reportConfig);
 
         res.setHeader('Content-Disposition', `attachment; filename="${filename}.tsv"`);
         res.sendFile(path);

src/reports/generateReport.ts

@@ -4,9 +4,10 @@ import { Client } from '@elastic/elasticsearch';
 import xl from 'excel4node';
 import { Response } from 'express';
 import flattenDeep from 'lodash/flattenDeep';
+import noop from 'lodash/noop';
 import uniq from 'lodash/uniq';
 
-import * as env from '../env';
+import { ES_PAGESIZE } from '../env';
 import {
     findValueInField,
     generateColumnsForProperty,
@@ -149,8 +150,8 @@ export default async function generateReport(
                             wrapper.rowIndex += 1;
                         });
                     },
-                    onFinish: () => {},
-                    pageSize: env.ES_PAGESIZE,
+                    onFinish: noop,
+                    pageSize: ES_PAGESIZE,
                 });
                 console.timeEnd(`executeSearchAfterQuery ${sheetConfig.sheetName}`);
             } catch (err) {

src/reports/utils/generateExcelReport.ts

@@ -3,9 +3,10 @@ import { Client } from '@elastic/elasticsearch';
 import xl from 'excel4node';
 import { Response } from 'express';
 import flattenDeep from 'lodash/flattenDeep';
+import noop from 'lodash/noop';
 import uniq from 'lodash/uniq';
 
-import * as env from '../../env';
+import { ES_PAGESIZE } from '../../env';
 import {
     findValueInField,
     generateColumnsForProperty,
@@ -148,8 +149,8 @@ export default async function generateExcelReport(
                             wrapper.rowIndex += 1;
                         });
                     },
-                    onFinish: () => {},
-                    pageSize: env.ES_PAGESIZE,
+                    onFinish: noop,
+                    pageSize: ES_PAGESIZE,
                 });
                 console.timeEnd(`executeSearchAfterQuery ${sheetConfig.sheetName}`);
             } catch (err) {

src/reports/utils/generateTsvReport.ts

@@ -2,15 +2,15 @@ import fs from 'fs';
 
 import { SheetConfig } from '../types';
 
-const generateTsvReport = async (data: { key: string }[], path: string, config: SheetConfig): Promise<void> => {
+const generateTsvReport = (data: { key: string }[], path: string, config: SheetConfig): void => {
     let tsvContent = config.columns.map((c) => c.header).join('\t') + '\n';
 
     for (const row of data) {
         const values = config.columns.map((c) => row[`${c.field}${c.fieldExtraSuffix || ''}`]);
         tsvContent += values.join('\t') + '\n';
     }
 
-    await fs.writeFileSync(path, tsvContent);
+    fs.writeFileSync(path, tsvContent);
 };
 
 export default generateTsvReport;

src/reports/utils/getFamilyIds.ts

@@ -1,7 +1,7 @@
 import { Client } from '@elastic/elasticsearch';
-import { env } from 'process';
+import noop from 'lodash/noop';
 
-import { ES_QUERY_MAX_SIZE, esFileIndex } from '../../env';
+import { ES_PAGESIZE, ES_QUERY_MAX_SIZE, esFileIndex } from '../../env';
 import { executeSearch, executeSearchAfterQuery } from '../../utils/esUtils';
 
 interface IFileInfo {
@@ -21,10 +21,8 @@ const getFilesInfo = async (fileIds: string[], es: Client): Promise<IFileInfo[]>
         onPageFetched: (pageHits) => {
             sources.push(...pageHits);
         },
-        onFinish: (total) => {
-            console.log(`Finished fetching all pages in getFilesInfo. Total hits: ${total}`);
-        },
-        pageSize: Number(env.ES_PAGESIZE),
+        onFinish: noop,
+        pageSize: ES_PAGESIZE,
     });
 
     const filesInfos = [];
@@ -91,9 +89,7 @@ const getFilesIdsMatched = async (filesInfos: IFileInfo[], es: Client): Promise<
  */
 const getFamilyIds = async (es: Client, fileIds: string[]): Promise<string[]> => {
     const filesInfos = await getFilesInfo(fileIds, es);
-    console.log('filesInfos: ', filesInfos.length);
     const filesIdsMatched = await getFilesIdsMatched(filesInfos, es);
-    console.log('filesIdsMatched: ', filesIdsMatched.length);
 
     return [...new Set([...fileIds, ...filesIdsMatched])];
 };

src/reports/utils/getFilesFromSqon.ts

@@ -1,8 +1,8 @@
 import { buildQuery } from '@arranger/middleware';
 import { Client } from '@elastic/elasticsearch';
-import { env } from 'process';
+import noop from 'lodash/noop';
 
-import { esFileAlias, esFileIndex } from '../../env';
+import { ES_PAGESIZE, esFileAlias, esFileIndex } from '../../env';
 import { getExtendedConfigs, getNestedFields } from '../../utils/arrangerUtils';
 import { executeSearchAfterQuery } from '../../utils/esUtils';
 import { Sqon } from '../../utils/setsTypes';
@@ -40,10 +40,8 @@ const getFilesFromSqon = async (
         onPageFetched: (pageHits) => {
             results.push(...pageHits);
         },
-        onFinish: (total) => {
-            console.log(`Finished fetching all pages in getFilesFromSqon. Total hits: ${total}`);
-        },
-        pageSize: Number(env.ES_PAGESIZE),
+        onFinish: noop,
+        pageSize: ES_PAGESIZE,
     });
 
     return results;

src/reports/utils/getInfosByConfig.ts

@@ -1,7 +1,8 @@
 import { Client } from '@elastic/elasticsearch';
 import get from 'lodash/get';
-import { env } from 'process';
+import noop from 'lodash/noop';
 
+import { ES_PAGESIZE } from '../../env';
 import { executeSearchAfterQuery } from '../../utils/esUtils';
 import { SheetConfig } from '../types';
 
@@ -34,10 +35,8 @@ const getInfosByConfig = async (
         onPageFetched: (pageHits) => {
             sources.push(...pageHits);
         },
-        onFinish: (total) => {
-            console.log(`Finished fetching all pages in getInfosByConfig. Total hits: ${total}`);
-        },
-        pageSize: Number(env.ES_PAGESIZE),
+        onFinish: noop,
+        pageSize: ES_PAGESIZE,
     });
 
     return (sources as any).map((source) =>