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76 lines
3.3 KiB
JavaScript
76 lines
3.3 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 {
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SEARCH_COLUMNS,
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buildSearchQuery,
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eutilsFetch,
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fetchSummaryRows,
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requireBoundedInt,
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requireChoice,
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requireText,
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requireYear,
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} from './utils.js';
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cli({
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site: 'pubmed',
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name: 'search',
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access: 'read',
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description: 'Search PubMed articles with advanced filters',
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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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args: [
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{ name: 'query', positional: true, required: true, help: 'Search query, e.g. "machine learning cancer"' },
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{ name: 'limit', type: 'int', default: 20, help: 'Max results (1-100)' },
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{ name: 'author', help: 'Filter by author name' },
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{ name: 'journal', help: 'Filter by journal name' },
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{ name: 'year-from', type: 'int', help: 'Filter publication year from' },
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{ name: 'year-to', type: 'int', help: 'Filter publication year to' },
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{ name: 'article-type', help: 'Filter by publication type, e.g. Review or Clinical Trial' },
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{ name: 'has-abstract', type: 'boolean', default: false, help: 'Only include articles with abstracts' },
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{ name: 'free-full-text', type: 'boolean', default: false, help: 'Only include free full text articles' },
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{ name: 'humans-only', type: 'boolean', default: false, help: 'Only include human studies' },
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{ name: 'english-only', type: 'boolean', default: false, help: 'Only include English articles' },
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{ name: 'sort', default: 'relevance', choices: ['relevance', 'date', 'author', 'journal'], help: 'Sort by relevance, date, author, or journal' },
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],
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columns: SEARCH_COLUMNS,
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func: async (args) => {
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const query = requireText(args.query, 'query');
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const limit = requireBoundedInt(args.limit, 20, 100);
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const yearFrom = requireYear(args['year-from'], 'year-from');
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const yearTo = requireYear(args['year-to'], 'year-to');
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const sort = requireChoice(args.sort, ['relevance', 'date', 'author', 'journal'], 'sort', 'relevance');
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const sortMap = {
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relevance: '',
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date: 'pub_date',
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author: 'Author',
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journal: 'JournalName',
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};
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const searchQuery = buildSearchQuery(query, {
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author: args.author,
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journal: args.journal,
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yearFrom,
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yearTo,
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articleType: args['article-type'],
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hasAbstract: args['has-abstract'],
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hasFullText: args['free-full-text'],
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humanOnly: args['humans-only'],
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englishOnly: args['english-only'],
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});
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const esearch = await eutilsFetch('esearch', {
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term: searchQuery,
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retmax: limit,
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usehistory: 'y',
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sort: sortMap[sort],
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}, { label: 'pubmed search' });
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const pmids = esearch?.esearchresult?.idlist;
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if (!Array.isArray(pmids)) {
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throw new CommandExecutionError('pubmed search did not return an id list', 'PubMed ESearch response shape may have changed.');
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}
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if (pmids.length === 0) {
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throw new EmptyResultError('pubmed search', `No articles matched "${query}".`);
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}
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return fetchSummaryRows(pmids, 'pubmed search summary');
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},
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});
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