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In biopax export constantly use citation() and do not set publication field when pmid is missing. #830

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Merged
merged 1 commit into from
Sep 15, 2020
Merged

In biopax export constantly use citation() and do not set publication field when pmid is missing. #830

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15 changes: 9 additions & 6 deletions src/model/document/document.js
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Original file line number Diff line number Diff line change
Expand Up @@ -471,13 +471,16 @@ class Document {

toBiopaxTemplate(){
let interactions = this.toBiopaxIntnTemplates();
let articleData = _.get( this.article(), ['PubmedData', 'ArticleIdList', 0]);
let pubId = articleData.id;
let pubDb = articleData.IdType;
let pathwayName = this.citation().title;
let publication = { id: pubId, db: pubDb };
let citation = this.citation();
let pathwayName = citation.title;
let pmid = citation.pmid;

return { interactions, publication, pathwayName};
let template = { interactions, pathwayName};
if ( pmid ) {
template.publication = { id: pmid, db: 'pubmed' };
}

return template;
}

toSearchTemplates(){
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