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56 lines
2.4 KiB
JavaScript
56 lines
2.4 KiB
JavaScript
import { cli, Strategy } from '@jackwener/opencli/registry';
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import { CommandExecutionError, EmptyResultError } from '@jackwener/opencli/errors';
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import { eutilsFetch, parseArticleXml, requirePmid, truncateText } from './utils.js';
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cli({
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site: 'pubmed',
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name: 'article',
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aliases: ['paper', 'read'],
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access: 'read',
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description: 'Get detailed information for a PubMed article by PMID',
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domain: 'pubmed.ncbi.nlm.nih.gov',
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strategy: Strategy.PUBLIC,
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browser: false,
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defaultFormat: 'plain',
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args: [
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{ name: 'pmid', positional: true, required: true, help: 'PubMed ID, e.g. 37780221' },
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{ name: 'full-abstract', type: 'boolean', default: false, help: 'Do not truncate the abstract in table output' },
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],
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columns: ['pmid', 'title', 'authors', 'journal', 'year', 'date', 'article_type', 'language', 'doi', 'pmc', 'affiliations', 'grants', 'mesh_terms', 'keywords', 'abstract', 'url'],
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func: async (args) => {
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const pmid = requirePmid(args.pmid);
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const xml = await eutilsFetch('efetch', {
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id: pmid,
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rettype: 'abstract',
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}, { retmode: 'xml', label: 'pubmed article' });
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const article = parseArticleXml(xml, pmid);
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if (!article) {
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throw new EmptyResultError('pubmed article', `No article found for PMID ${pmid}.`);
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}
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if (!article.title) {
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throw new CommandExecutionError(`pubmed article ${pmid} did not include a title`, 'PubMed EFetch response shape may have changed.');
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}
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const abstract = args['full-abstract'] ? article.abstract : truncateText(article.abstract, 500);
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return [
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{
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pmid: article.pmid,
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title: article.title,
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authors: article.authors.join(', '),
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journal: article.journal,
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year: article.year,
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date: article.date || null,
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article_type: article.article_type,
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language: article.language || null,
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doi: article.doi || null,
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pmc: article.pmc || null,
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affiliations: article.affiliations || null,
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grants: article.grants || null,
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mesh_terms: article.mesh_terms || null,
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keywords: article.keywords || null,
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abstract: abstract || null,
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url: article.url,
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},
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];
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},
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});
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