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59 lines
2.4 KiB
JavaScript
59 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 {
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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: 'review',
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access: 'read',
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description: 'Search PubMed review articles with a review preset',
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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: 'Review topic query, e.g. "immunotherapy"' },
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{ name: 'limit', type: 'int', default: 20, help: 'Max results (1-100)' },
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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: 'has-abstract', type: 'boolean', default: false, help: 'Only include articles with abstracts' },
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{ name: 'sort', default: 'date', choices: ['date', 'relevance'], help: 'Sort by date or relevance' },
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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, ['date', 'relevance'], 'sort', 'date');
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const searchQuery = buildSearchQuery(query, {
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yearFrom,
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yearTo,
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articleType: 'Review',
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hasAbstract: args['has-abstract'],
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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: sort === 'date' ? 'pub_date' : '',
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}, { label: 'pubmed review' });
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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 review 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 review', `No review articles matched "${query}".`);
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}
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return fetchSummaryRows(pmids, 'pubmed review summary');
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},
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});
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