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During bulk export skip the files where the conversion is failing #885

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Merged
merged 1 commit into from
Oct 29, 2020
Merged

During bulk export skip the files where the conversion is failing #885

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23 changes: 16 additions & 7 deletions src/server/routes/api/document/export.js
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Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,7 @@ import fetch from 'node-fetch';
import JSZip from 'jszip';
import _ from 'lodash';
import fs from 'fs';
import logger from '../../../logger';

import Document from '../../../../model/document';

Expand All @@ -13,8 +14,8 @@ import { convertDocumentToBiopax,
const DOCUMENT_STATUS_FIELDS = Document.statusFields();
const CHUNK_SIZE = 20;
const EXPORT_TYPES = Object.freeze({
'JS': 'js',
'BP': 'bp',
'JS': 'json',
'BP': 'biopax',
'SBGN': 'sbgn'
});

Expand Down Expand Up @@ -65,7 +66,13 @@ const exportToZip = (baseUrl, zipPath, types) => {
types = Object.keys( typeToConverter );
}

const idToFiles = id => types.map( t => typeToConverter[ t ]( id, baseUrl ) );
const idToFiles = id => types.map( t => {
return typeToConverter[ t ]( id, baseUrl )
.catch( () => {
logger.error(`Error in export: cannot convert the document ${id} into ${t}`);
return null;
} );
} );

let promises = ids.map( idToFiles );
promises = _.flatten( promises );
Expand All @@ -76,11 +83,13 @@ const exportToZip = (baseUrl, zipPath, types) => {
return Promise.all( promises )
.then( contents => {
contents.forEach( ( content, i ) => {
let id = ids[ Math.floor( i / s ) ];
let ext = fileExts[ i % s ];
let fileName = id + ext;
if ( content != null ) {
let id = ids[ Math.floor( i / s ) ];
let ext = fileExts[ i % s ];
let fileName = id + ext;

zip.file( fileName, content );
zip.file( fileName, content );
}
} );
} );
};
Expand Down
4 changes: 3 additions & 1 deletion src/util/document.js
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Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,9 @@ import { checkHTTPStatus } from './fetch';
function convertDocumentToBiopax(docId, baseUrl = '') {
let SERVER_URL = baseUrl + `/api/document/biopax/${docId}`;
let makeRequest = () => fetch(SERVER_URL);
return tryPromise( makeRequest ).then( result => result.text() );
return tryPromise( makeRequest )
.then( checkHTTPStatus )
.then( result => result.text() );
}

function convertDocumentToTxt(docId, baseUrl = '') {
Expand Down