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feat(pubmed): add workflow presets and richer article metadata #1778

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276 changes: 274 additions & 2 deletions cli-manifest.json
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Original file line number Diff line number Diff line change
Expand Up @@ -20595,9 +20595,24 @@
}
],
"columns": [
"field",
"value"
"pmid",
"title",
"authors",
"journal",
"year",
"date",
"article_type",
"language",
"doi",
"pmc",
"affiliations",
"grants",
"mesh_terms",
"keywords",
"abstract",
"url"
],
"defaultFormat": "plain",
"type": "js",
"modulePath": "pubmed/article.js",
"sourceFile": "pubmed/article.js"
Expand Down Expand Up @@ -20732,6 +20747,194 @@
"modulePath": "pubmed/citations.js",
"sourceFile": "pubmed/citations.js"
},
{
"site": "pubmed",
"name": "clinical-trial",
"description": "Search PubMed clinical trials with a trial-study preset",
"access": "read",
"domain": "pubmed.ncbi.nlm.nih.gov",
"strategy": "public",
"browser": false,
"args": [
{
"name": "query",
"type": "str",
"required": true,
"positional": true,
"help": "Clinical topic query, e.g. \"breast cancer\""
},
{
"name": "limit",
"type": "int",
"default": 20,
"required": false,
"help": "Max results (1-100)"
},
{
"name": "year-from",
"type": "int",
"required": false,
"help": "Filter publication year from"
},
{
"name": "year-to",
"type": "int",
"required": false,
"help": "Filter publication year to"
},
{
"name": "free-full-text",
"type": "boolean",
"default": false,
"required": false,
"help": "Only include free full text articles"
},
{
"name": "sort",
"type": "str",
"default": "date",
"required": false,
"help": "Sort by date or relevance",
"choices": [
"date",
"relevance"
]
}
],
"columns": [
"rank",
"pmid",
"title",
"authors",
"journal",
"year",
"article_type",
"doi",
"url"
],
"type": "js",
"modulePath": "pubmed/clinical-trial.js",
"sourceFile": "pubmed/clinical-trial.js"
},
{
"site": "pubmed",
"name": "journal",
"description": "Search PubMed articles by journal name",
"access": "read",
"domain": "pubmed.ncbi.nlm.nih.gov",
"strategy": "public",
"browser": false,
"args": [
{
"name": "journal",
"type": "str",
"required": true,
"positional": true,
"help": "Journal name, e.g. \"Nature\" or \"The Lancet\""
},
{
"name": "limit",
"type": "int",
"default": 20,
"required": false,
"help": "Max results (1-100)"
},
{
"name": "year-from",
"type": "int",
"required": false,
"help": "Filter publication year from"
},
{
"name": "year-to",
"type": "int",
"required": false,
"help": "Filter publication year to"
},
{
"name": "sort",
"type": "str",
"default": "relevance",
"required": false,
"help": "Sort by relevance or date",
"choices": [
"relevance",
"date"
]
}
],
"columns": [
"rank",
"pmid",
"title",
"authors",
"journal",
"year",
"article_type",
"doi",
"url"
],
"type": "js",
"modulePath": "pubmed/journal.js",
"sourceFile": "pubmed/journal.js"
},
{
"site": "pubmed",
"name": "mesh",
"description": "Search PubMed articles by MeSH term",
"access": "read",
"domain": "pubmed.ncbi.nlm.nih.gov",
"strategy": "public",
"browser": false,
"args": [
{
"name": "term",
"type": "str",
"required": true,
"positional": true,
"help": "MeSH term, e.g. \"Neoplasms\" or \"Machine Learning\""
},
{
"name": "limit",
"type": "int",
"default": 20,
"required": false,
"help": "Max results (1-100)"
},
{
"name": "major",
"type": "boolean",
"default": false,
"required": false,
"help": "Only include articles where this is a major MeSH topic"
},
{
"name": "sort",
"type": "str",
"default": "relevance",
"required": false,
"help": "Sort by relevance or date",
"choices": [
"relevance",
"date"
]
}
],
"columns": [
"rank",
"pmid",
"title",
"authors",
"journal",
"year",
"article_type",
"doi",
"url"
],
"type": "js",
"modulePath": "pubmed/mesh.js",
"sourceFile": "pubmed/mesh.js"
},
{
"site": "pubmed",
"name": "related",
Expand Down Expand Up @@ -20779,6 +20982,75 @@
"modulePath": "pubmed/related.js",
"sourceFile": "pubmed/related.js"
},
{
"site": "pubmed",
"name": "review",
"description": "Search PubMed review articles with a review preset",
"access": "read",
"domain": "pubmed.ncbi.nlm.nih.gov",
"strategy": "public",
"browser": false,
"args": [
{
"name": "query",
"type": "str",
"required": true,
"positional": true,
"help": "Review topic query, e.g. \"immunotherapy\""
},
{
"name": "limit",
"type": "int",
"default": 20,
"required": false,
"help": "Max results (1-100)"
},
{
"name": "year-from",
"type": "int",
"required": false,
"help": "Filter publication year from"
},
{
"name": "year-to",
"type": "int",
"required": false,
"help": "Filter publication year to"
},
{
"name": "has-abstract",
"type": "boolean",
"default": false,
"required": false,
"help": "Only include articles with abstracts"
},
{
"name": "sort",
"type": "str",
"default": "date",
"required": false,
"help": "Sort by date or relevance",
"choices": [
"date",
"relevance"
]
}
],
"columns": [
"rank",
"pmid",
"title",
"authors",
"journal",
"year",
"article_type",
"doi",
"url"
],
"type": "js",
"modulePath": "pubmed/review.js",
"sourceFile": "pubmed/review.js"
},
{
"site": "pubmed",
"name": "search",
Expand Down
35 changes: 20 additions & 15 deletions clis/pubmed/article.js
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Original file line number Diff line number Diff line change
Expand Up @@ -11,11 +11,12 @@ cli({
domain: 'pubmed.ncbi.nlm.nih.gov',
strategy: Strategy.PUBLIC,
browser: false,
defaultFormat: 'plain',
args: [
{ name: 'pmid', positional: true, required: true, help: 'PubMed ID, e.g. 37780221' },
{ name: 'full-abstract', type: 'boolean', default: false, help: 'Do not truncate the abstract in table output' },
],
columns: ['field', 'value'],
columns: ['pmid', 'title', 'authors', 'journal', 'year', 'date', 'article_type', 'language', 'doi', 'pmc', 'affiliations', 'grants', 'mesh_terms', 'keywords', 'abstract', 'url'],
func: async (args) => {
const pmid = requirePmid(args.pmid);
const xml = await eutilsFetch('efetch', {
Expand All @@ -31,20 +32,24 @@ cli({
}
const abstract = args['full-abstract'] ? article.abstract : truncateText(article.abstract, 500);
return [
{ field: 'PMID', value: article.pmid },
{ field: 'Title', value: article.title },
{ field: 'Authors', value: article.authors.join(', ') },
{ field: 'Journal', value: article.journal },
{ field: 'Year', value: article.year },
{ field: 'Date', value: article.date },
{ field: 'Article Type', value: article.article_type },
{ field: 'Language', value: article.language },
{ field: 'DOI', value: article.doi || null },
{ field: 'PMC ID', value: article.pmc || null },
{ field: 'MeSH Terms', value: article.mesh_terms || null },
{ field: 'Keywords', value: article.keywords || null },
{ field: 'Abstract', value: abstract || null },
{ field: 'URL', value: article.url },
{
pmid: article.pmid,
title: article.title,
authors: article.authors.join(', '),
journal: article.journal,
year: article.year,
date: article.date || null,
article_type: article.article_type,
language: article.language || null,
doi: article.doi || null,
pmc: article.pmc || null,
affiliations: article.affiliations || null,
grants: article.grants || null,
mesh_terms: article.mesh_terms || null,
keywords: article.keywords || null,
abstract: abstract || null,
url: article.url,
},
];
},
});
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