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Greatkaijackwener
Greatkai
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jackwener
authored
feat(pubmed): revive public eutils adapter (#819)
Co-authored-by: jackwener <jakevingoo@gmail.com> Co-authored-by: Greatkai <4587517+Greatkai@users.noreply.github.com>
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‎README.zh-CN.md‎

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| **devto** | `top` `tag` `user` | 公开 |
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| **dictionary** | `search` `synonyms` `examples` | 公开 |
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| **arxiv** | `search` `paper` | 公开 |
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| **pubmed** | `search` `article` `author` `citations` `related` | 公开 |
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| **openreview** | `search` `venue` `paper` `reviews` | 公开 |
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| **paperreview** | `submit` `review` `feedback` | 公开 |
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| **wikipedia** | `search` `summary` `random` `trending` | 公开 |

‎cli-manifest.json‎

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"modulePath": "producthunt/today.js",
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"sourceFile": "producthunt/today.js"
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},
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{
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"site": "pubmed",
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"name": "article",
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"aliases": [
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"paper",
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"read"
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],
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"description": "Get detailed information for a PubMed article by PMID",
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"access": "read",
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"domain": "pubmed.ncbi.nlm.nih.gov",
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"strategy": "public",
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"browser": false,
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"args": [
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{
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"name": "pmid",
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"type": "str",
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"required": true,
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"positional": true,
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"help": "PubMed ID, e.g. 37780221"
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},
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{
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"name": "full-abstract",
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"type": "boolean",
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"default": false,
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"required": false,
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"help": "Do not truncate the abstract in table output"
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}
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],
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"columns": [
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"field",
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"value"
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],
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"type": "js",
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"modulePath": "pubmed/article.js",
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"sourceFile": "pubmed/article.js"
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},
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{
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"site": "pubmed",
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"name": "author",
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"description": "Search PubMed articles by author name and optional affiliation",
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"access": "read",
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"domain": "pubmed.ncbi.nlm.nih.gov",
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"strategy": "public",
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"browser": false,
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"args": [
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{
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"name": "name",
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"type": "str",
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"required": true,
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"positional": true,
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"help": "Author name, e.g. \"Smith J\""
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},
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{
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"name": "limit",
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"type": "int",
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"default": 20,
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"required": false,
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"help": "Max results (1-100)"
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},
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{
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"name": "affiliation",
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"type": "str",
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"required": false,
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"help": "Filter by author affiliation"
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},
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{
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"name": "position",
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"type": "str",
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"default": "any",
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"required": false,
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"help": "Author position: any, first, or last",
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"choices": [
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"any",
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"first",
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"last"
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]
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},
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{
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"name": "year-from",
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"type": "int",
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"required": false,
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"help": "Filter publication year from"
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},
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{
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"name": "year-to",
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"type": "int",
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"required": false,
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"help": "Filter publication year to"
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},
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{
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"name": "sort",
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"type": "str",
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"default": "date",
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"required": false,
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"help": "Sort by date or relevance",
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"choices": [
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"date",
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"relevance"
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]
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}
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],
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"columns": [
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"rank",
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"pmid",
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"title",
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"authors",
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"journal",
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"year",
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"article_type",
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"doi",
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"url"
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],
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"type": "js",
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"modulePath": "pubmed/author.js",
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"sourceFile": "pubmed/author.js"
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},
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{
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"site": "pubmed",
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"name": "citations",
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"description": "Get PubMed citation relationships for an article",
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"access": "read",
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"domain": "pubmed.ncbi.nlm.nih.gov",
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"strategy": "public",
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"browser": false,
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"args": [
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{
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"name": "pmid",
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"type": "str",
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"required": true,
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"positional": true,
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"help": "PubMed ID, e.g. 37780221"
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},
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{
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"name": "direction",
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"type": "str",
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"default": "citedby",
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"required": false,
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"help": "citedby or references",
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"choices": [
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"citedby",
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"references"
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]
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},
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{
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"name": "limit",
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"type": "int",
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"default": 20,
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"required": false,
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"help": "Max results (1-100)"
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}
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],
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"columns": [
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"rank",
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"pmid",
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"title",
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"authors",
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"journal",
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"year",
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"article_type",
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"doi",
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"url"
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],
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"type": "js",
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"modulePath": "pubmed/citations.js",
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"sourceFile": "pubmed/citations.js"
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},
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{
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"site": "pubmed",
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"name": "related",
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"description": "Find articles related to a PubMed article",
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"access": "read",
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"domain": "pubmed.ncbi.nlm.nih.gov",
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"strategy": "public",
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"browser": false,
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"args": [
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{
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"name": "pmid",
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"type": "str",
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"required": true,
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"positional": true,
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"help": "PubMed ID, e.g. 37780221"
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},
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{
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"name": "limit",
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"type": "int",
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"default": 20,
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"required": false,
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"help": "Max results (1-100)"
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},
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{
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"name": "score",
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"type": "boolean",
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"default": false,
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"required": false,
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"help": "Show similarity scores when available"
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}
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],
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"columns": [
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"rank",
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"pmid",
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"title",
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"authors",
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"journal",
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"year",
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"article_type",
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"score",
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"doi",
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"url"
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],
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"type": "js",
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"modulePath": "pubmed/related.js",
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"sourceFile": "pubmed/related.js"
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},
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{
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"site": "pubmed",
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"name": "search",
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"description": "Search PubMed articles with advanced filters",
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"access": "read",
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"domain": "pubmed.ncbi.nlm.nih.gov",
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"strategy": "public",
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"browser": false,
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"args": [
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{
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"name": "query",
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"type": "str",
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"required": true,
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"positional": true,
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"help": "Search query, e.g. \"machine learning cancer\""
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},
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{
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"name": "limit",
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"type": "int",
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"default": 20,
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"required": false,
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"help": "Max results (1-100)"
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},
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{
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"name": "author",
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"type": "str",
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"required": false,
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"help": "Filter by author name"
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},
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{
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"name": "journal",
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"type": "str",
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"required": false,
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"help": "Filter by journal name"
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},
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{
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"name": "year-from",
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"type": "int",
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"required": false,
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"help": "Filter publication year from"
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},
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{
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"name": "year-to",
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"type": "int",
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"required": false,
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"help": "Filter publication year to"
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},
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{
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"name": "article-type",
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"type": "str",
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"required": false,
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"help": "Filter by publication type, e.g. Review or Clinical Trial"
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},
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{
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"name": "has-abstract",
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"type": "boolean",
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"default": false,
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"required": false,
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"help": "Only include articles with abstracts"
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},
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{
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"name": "free-full-text",
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"type": "boolean",
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"default": false,
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"required": false,
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"help": "Only include free full text articles"
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},
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{
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"name": "humans-only",
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"type": "boolean",
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"default": false,
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"required": false,
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"help": "Only include human studies"
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},
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{
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"name": "english-only",
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"type": "boolean",
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"default": false,
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"required": false,
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"help": "Only include English articles"
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},
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{
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"name": "sort",
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"type": "str",
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"default": "relevance",
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"required": false,
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"help": "Sort by relevance, date, author, or journal",
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"choices": [
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"relevance",
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"date",
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"author",
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"journal"
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]
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}
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],
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"columns": [
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"rank",
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"pmid",
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"title",
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"authors",
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"journal",
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"year",
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"article_type",
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"doi",
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"url"
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],
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"type": "js",
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"modulePath": "pubmed/search.js",
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"sourceFile": "pubmed/search.js"
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},
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{
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"site": "quark",
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"name": "ls",

‎clis/pubmed/article.js‎

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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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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: ['field', 'value'],
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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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{ field: 'PMID', value: article.pmid },
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{ field: 'Title', value: article.title },
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{ field: 'Authors', value: article.authors.join(', ') },
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{ field: 'Journal', value: article.journal },
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{ field: 'Year', value: article.year },
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{ field: 'Date', value: article.date },
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{ field: 'Article Type', value: article.article_type },
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{ field: 'Language', value: article.language },
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{ field: 'DOI', value: article.doi || null },
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{ field: 'PMC ID', value: article.pmc || null },
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{ field: 'MeSH Terms', value: article.mesh_terms || null },
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{ field: 'Keywords', value: article.keywords || null },
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{ field: 'Abstract', value: abstract || null },
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{ field: 'URL', value: article.url },
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];
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},
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});

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