Merge pull request #202 from CBIIT/cds_velsera_hotfix

Cds velsera hotfix
CBIIT · Jun 11, 2024 · 11d723c · 11d723c
2 parents 4756c09 + 1fee2e9
commit 11d723c
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Showing 2 changed files with 22 additions and 27 deletions.
diff --git a/src/bento/fileCentricCartWorkflowData.js b/src/bento/fileCentricCartWorkflowData.js
@@ -112,8 +112,8 @@ export const myFilesPageData = {
 
 
 export const manifestData = {
-  keysToInclude: ['file_id', 'file_name', 'subject_id', 'md5sum', 'associated_file', 'associated_drs_uri', 'associated_md5sum', 'study_acronym', 'phs_accession', 'sample_id', 'accesses', 'file_type', 'gender', 'race', 'primary_diagnosis', 'is_tumor', 'analyte_type', 'organ_or_tissue', 'study_data_type', 'library_strategy', 'image_modality', 'experimental_strategy', 'library_layouts', 'license', 'file_size'],
-  header: ['drs_uri', 'name', 'Participant ID', 'Md5sum', 'Associated File', 'Associated File DRS URI', 'Associated File md5sum', 'Study Name', 'Accession', 'Sample Id', 'Study Access', 'File Type', 'Gender', 'Race', 'Primary Diagnosis', 'Sample Tumor Status', 'Analyte Type', 'Organ or Tissue', 'Study Data Type', 'Library Strategy', ' Image Modality', 'Experimental Strategy', 'Library Layout', 'License', 'File Size (in bytes)', 'User Comments'],
+  keysToInclude: ['file_id', 'file_name', 'subject_id', 'md5sum', 'associated_file', 'associated_drs_uri', 'associated_md5sum', 'study_acronym', 'phs_accession', 'sample_id', 'accesses', 'file_type', 'gender', 'race', 'primary_diagnoses', 'is_tumor', 'analyte_type', 'organ_or_tissue', 'study_data_type', 'library_strategy', 'image_modality', 'experimental_strategy', 'library_layouts', 'license', 'file_size'],
+  header: ['drs_uri', 'name', 'Participant ID', 'Md5sum', 'Associated File', 'Associated File DRS URI', 'Associated File md5sum', 'Study Name', 'Accession', 'Sample Id', 'Study Access', 'File Type', 'Gender', 'Race', 'Primary Diagnoses', 'Sample Tumor Status', 'Analyte Type', 'Organ or Tissue', 'Study Data Type', 'Library Strategy', 'Image Modality', 'Experimental Strategy', 'Library Layout', 'License', 'File Size (in bytes)', 'User Comments'],
 };
 
 // --------------- GraphQL query - Retrieve selected cases info --------------

diff --git a/src/pages/cart/customComponent/exportButton/exportButton.js b/src/pages/cart/customComponent/exportButton/exportButton.js
@@ -5,6 +5,7 @@ import { Paper, Popper, Button, ClickAwayListener, Grow, MenuItem, MenuList, wit
 import { noop } from 'lodash';
 import { useQuery } from '@apollo/client';
 import { MY_CART_MANIFEST_QUERY } from '../../../../bento/tableDownloadCSV'
+import { manifestData } from '../../../../bento/fileCentricCartWorkflowData'
 import arrowDownPng from './assets/arrowDown.png';
 import cgcIcon from './assets/cgc.svg';
 import { getManifestData } from './util/TableService';
@@ -69,31 +70,25 @@ const ExportButtonView = (props,) => {
         if (!data) {
           return null;
         }
-        const processedStoreManifestPayload = data.filesInList.map((el) => ({
-            file_name: el ? el.file_name : undefined,
-            file_size: el ? el.file_size : undefined,
-            file_id: el ? el.file_id : undefined,
-            file_type: el ? el.file_type : undefined,
-            md5sum: el ? el.md5sum : undefined,
-            experimental_strategy: el ? el.experimental_strategy : undefined,
-            study_acronym: el ? el.study_acronym : undefined,
-            phs_accession: el ? el.phs_accession : undefined,
-            study_data_type: el ? el.study_data_type : undefined,
-            accesses: el ? el.accesses : undefined,
-            image_modality: el ? el.image_modality : undefined,
-            organ_or_tissue: el ? el.organ_or_tissue : undefined,
-            license: el ? el.license : undefined,
-            library_layouts: el ? el.library_layouts : undefined,
-            library_strategy: el ? el.library_strategy : undefined,
-            subject_id: el ? el.subject_id : undefined,
-            gender: el ? el.gender : undefined,
-            race: el ? el.race : undefined,
-            primary_diagnoses: el ? el.primary_diagnoses : undefined,
-            sample_id: el ? el.sample_id : undefined,
-            analyte_type: el ? el.analyte_type : undefined,
-            is_tumor: el ? el.is_tumor : undefined,
-          }));
-
+        const appendString = 'drs://nci-crdc.datacommons.io/'
+        const processedStoreManifestPayload = data.filesInList.map((el) => {
+          const obj = {}
+          for (let i = 0; i < manifestData.keysToInclude.length; i++) {
+            if (manifestData.keysToInclude[i] === 'file_id') {
+              obj[manifestData.header[i]] = el && el[manifestData.keysToInclude[i]] ? 
+                appendString + el[manifestData.keysToInclude[i]] 
+                : 
+                "";
+            }
+            else {
+              obj[manifestData.header[i]] = el && el[manifestData.keysToInclude[i]] ? 
+              el[manifestData.keysToInclude[i]] 
+              : 
+              "";
+            }
+          }
+          return obj;
+          });
         return processedStoreManifestPayload;
     };