feat(pubmed): add comprehensive PubMed adapter with 5 commands

README.zh-CN.md

@@ -271,6 +271,7 @@ npm link
 | **devto** | `top` `tag` `user` | 公开 |
 | **dictionary** | `search` `synonyms` `examples` | 公开 |
 | **arxiv** | `search` `paper` | 公开 |
+| **pubmed** | `search` `article` `author` `citations` `related` | 公开 |
 | **openreview** | `search` `venue` `paper` `reviews` | 公开 |
 | **paperreview** | `submit` `review` `feedback` | 公开 |
 | **wikipedia** | `search` `summary` `random` `trending` | 公开 |

cli-manifest.json

@@ -15181,6 +15181,329 @@
     "modulePath": "producthunt/today.js",
     "sourceFile": "producthunt/today.js"
   },
+  {
+    "site": "pubmed",
+    "name": "article",
+    "aliases": [
+      "paper",
+      "read"
+    ],
+    "description": "Get detailed information for a PubMed article by PMID",
+    "access": "read",
+    "domain": "pubmed.ncbi.nlm.nih.gov",
+    "strategy": "public",
+    "browser": false,
+    "args": [
+      {
+        "name": "pmid",
+        "type": "str",
+        "required": true,
+        "positional": true,
+        "help": "PubMed ID, e.g. 37780221"
+      },
+      {
+        "name": "full-abstract",
+        "type": "boolean",
+        "default": false,
+        "required": false,
+        "help": "Do not truncate the abstract in table output"
+      }
+    ],
+    "columns": [
+      "field",
+      "value"
+    ],
+    "type": "js",
+    "modulePath": "pubmed/article.js",
+    "sourceFile": "pubmed/article.js"
+  },
+  {
+    "site": "pubmed",
+    "name": "author",
+    "description": "Search PubMed articles by author name and optional affiliation",
+    "access": "read",
+    "domain": "pubmed.ncbi.nlm.nih.gov",
+    "strategy": "public",
+    "browser": false,
+    "args": [
+      {
+        "name": "name",
+        "type": "str",
+        "required": true,
+        "positional": true,
+        "help": "Author name, e.g. \"Smith J\""
+      },
+      {
+        "name": "limit",
+        "type": "int",
+        "default": 20,
+        "required": false,
+        "help": "Max results (1-100)"
+      },
+      {
+        "name": "affiliation",
+        "type": "str",
+        "required": false,
+        "help": "Filter by author affiliation"
+      },
+      {
+        "name": "position",
+        "type": "str",
+        "default": "any",
+        "required": false,
+        "help": "Author position: any, first, or last",
+        "choices": [
+          "any",
+          "first",
+          "last"
+        ]
+      },
+      {
+        "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": "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/author.js",
+    "sourceFile": "pubmed/author.js"
+  },
+  {
+    "site": "pubmed",
+    "name": "citations",
+    "description": "Get PubMed citation relationships for an article",
+    "access": "read",
+    "domain": "pubmed.ncbi.nlm.nih.gov",
+    "strategy": "public",
+    "browser": false,
+    "args": [
+      {
+        "name": "pmid",
+        "type": "str",
+        "required": true,
+        "positional": true,
+        "help": "PubMed ID, e.g. 37780221"
+      },
+      {
+        "name": "direction",
+        "type": "str",
+        "default": "citedby",
+        "required": false,
+        "help": "citedby or references",
+        "choices": [
+          "citedby",
+          "references"
+        ]
+      },
+      {
+        "name": "limit",
+        "type": "int",
+        "default": 20,
+        "required": false,
+        "help": "Max results (1-100)"
+      }
+    ],
+    "columns": [
+      "rank",
+      "pmid",
+      "title",
+      "authors",
+      "journal",
+      "year",
+      "article_type",
+      "doi",
+      "url"
+    ],
+    "type": "js",
+    "modulePath": "pubmed/citations.js",
+    "sourceFile": "pubmed/citations.js"
+  },
+  {
+    "site": "pubmed",
+    "name": "related",
+    "description": "Find articles related to a PubMed article",
+    "access": "read",
+    "domain": "pubmed.ncbi.nlm.nih.gov",
+    "strategy": "public",
+    "browser": false,
+    "args": [
+      {
+        "name": "pmid",
+        "type": "str",
+        "required": true,
+        "positional": true,
+        "help": "PubMed ID, e.g. 37780221"
+      },
+      {
+        "name": "limit",
+        "type": "int",
+        "default": 20,
+        "required": false,
+        "help": "Max results (1-100)"
+      },
+      {
+        "name": "score",
+        "type": "boolean",
+        "default": false,
+        "required": false,
+        "help": "Show similarity scores when available"
+      }
+    ],
+    "columns": [
+      "rank",
+      "pmid",
+      "title",
+      "authors",
+      "journal",
+      "year",
+      "article_type",
+      "score",
+      "doi",
+      "url"
+    ],
+    "type": "js",
+    "modulePath": "pubmed/related.js",
+    "sourceFile": "pubmed/related.js"
+  },
+  {
+    "site": "pubmed",
+    "name": "search",
+    "description": "Search PubMed articles with advanced filters",
+    "access": "read",
+    "domain": "pubmed.ncbi.nlm.nih.gov",
+    "strategy": "public",
+    "browser": false,
+    "args": [
+      {
+        "name": "query",
+        "type": "str",
+        "required": true,
+        "positional": true,
+        "help": "Search query, e.g. \"machine learning cancer\""
+      },
+      {
+        "name": "limit",
+        "type": "int",
+        "default": 20,
+        "required": false,
+        "help": "Max results (1-100)"
+      },
+      {
+        "name": "author",
+        "type": "str",
+        "required": false,
+        "help": "Filter by author name"
+      },
+      {
+        "name": "journal",
+        "type": "str",
+        "required": false,
+        "help": "Filter by journal name"
+      },
+      {
+        "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": "article-type",
+        "type": "str",
+        "required": false,
+        "help": "Filter by publication type, e.g. Review or Clinical Trial"
+      },
+      {
+        "name": "has-abstract",
+        "type": "boolean",
+        "default": false,
+        "required": false,
+        "help": "Only include articles with abstracts"
+      },
+      {
+        "name": "free-full-text",
+        "type": "boolean",
+        "default": false,
+        "required": false,
+        "help": "Only include free full text articles"
+      },
+      {
+        "name": "humans-only",
+        "type": "boolean",
+        "default": false,
+        "required": false,
+        "help": "Only include human studies"
+      },
+      {
+        "name": "english-only",
+        "type": "boolean",
+        "default": false,
+        "required": false,
+        "help": "Only include English articles"
+      },
+      {
+        "name": "sort",
+        "type": "str",
+        "default": "relevance",
+        "required": false,
+        "help": "Sort by relevance, date, author, or journal",
+        "choices": [
+          "relevance",
+          "date",
+          "author",
+          "journal"
+        ]
+      }
+    ],
+    "columns": [
+      "rank",
+      "pmid",
+      "title",
+      "authors",
+      "journal",
+      "year",
+      "article_type",
+      "doi",
+      "url"
+    ],
+    "type": "js",
+    "modulePath": "pubmed/search.js",
+    "sourceFile": "pubmed/search.js"
+  },
   {
     "site": "quark",
     "name": "ls",

clis/pubmed/article.js

@@ -0,0 +1,50 @@
+import { cli, Strategy } from '@jackwener/opencli/registry';
+import { CommandExecutionError, EmptyResultError } from '@jackwener/opencli/errors';
+import { eutilsFetch, parseArticleXml, requirePmid, truncateText } from './utils.js';
+
+cli({
+    site: 'pubmed',
+    name: 'article',
+    aliases: ['paper', 'read'],
+    access: 'read',
+    description: 'Get detailed information for a PubMed article by PMID',
+    domain: 'pubmed.ncbi.nlm.nih.gov',
+    strategy: Strategy.PUBLIC,
+    browser: false,
+    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'],
+    func: async (args) => {
+        const pmid = requirePmid(args.pmid);
+        const xml = await eutilsFetch('efetch', {
+            id: pmid,
+            rettype: 'abstract',
+        }, { retmode: 'xml', label: 'pubmed article' });
+        const article = parseArticleXml(xml, pmid);
+        if (!article) {
+            throw new EmptyResultError('pubmed article', `No article found for PMID ${pmid}.`);
+        }
+        if (!article.title) {
+            throw new CommandExecutionError(`pubmed article ${pmid} did not include a title`, 'PubMed EFetch response shape may have changed.');
+        }
+        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 },
+        ];
+    },
+});