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Cds velsera hotfix #202

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merged 2 commits into from
Jun 11, 2024
Merged

Cds velsera hotfix #202

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1a64c28
updated mapping, added append string for drs, corrected header
huuaho Jun 11, 2024
1fee2e9
off by 1 error
huuaho Jun 11, 2024
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4 changes: 2 additions & 2 deletions src/bento/fileCentricCartWorkflowData.js
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Original file line number Diff line number Diff line change
Expand Up @@ -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 --------------
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45 changes: 20 additions & 25 deletions src/pages/cart/customComponent/exportButton/exportButton.js
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Original file line number Diff line number Diff line change
Expand Up @@ -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';
Expand Down Expand Up @@ -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;
};

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