npm - @djmima/pubmed-mcp - Versions diffs - 1.0.0 → 1.0.1 - Mend

@djmima/pubmed-mcp 1.0.0 → 1.0.1

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Files changed (12) hide show

package/CHANGELOG.md +28 -0
package/README.md +804 -793
package/dist/cli/commands.js +114 -114
package/dist/cli/run.js +31 -31
package/dist/pubmed/client.d.ts.map +1 -1
package/dist/pubmed/client.js +8 -4
package/dist/pubmed/client.js.map +1 -1
package/dist/utils/xml.d.ts.map +1 -1
package/dist/utils/xml.js +2 -1
package/dist/utils/xml.js.map +1 -1
package/package.json +3 -2
package/skills/pubmed-cli/SKILL.md +79 -79

package/dist/cli/commands.js CHANGED Viewed

@@ -37,32 +37,32 @@ const search = {
         'date-to': { type: 'string' },
         datetype: { type: 'string' },
     },
-    help: `Usage: pubmed search <query> [options]
-       pubmed search - [options]      (read the query from stdin)
-Search PubMed. Prints PMIDs with total_count, query_translation, warnings,
-and errors (same JSON as the search_articles MCP tool).
-Options:
-  --max-results <n>   PMIDs to return, 1-10000 (default 20)
-  --retstart <n>      Offset of the first PMID, for paging (default 0)
-  --sort <order>      relevance | pub_date | author | journal_name
-  --field <field>     Restrict untagged terms to one field:
-                      title | tiab | mesh | author | journal | affiliation
-  --date-from <date>  Start date: YYYY, YYYY/MM, or YYYY/MM/DD
-  --date-to <date>    End date, same formats (either bound may be omitted)
-  --datetype <type>   pdat = publication date (default) | edat = Entrez date |
-                      mdat = modification date
-PubMed maps untagged terms through Automatic Term Mapping (ATM). Before
-concluding that a low or zero total_count means no literature exists, check
-query_translation, warnings, and errors. To search several words in one
-field, tag each term; when a quoted phrase is not indexed, use a proximity
-search such as "drug resistance"[tiab:~0].
-Example:
-  pubmed search "TP53[tiab] AND myelodysplastic syndromes[mh]" --max-results 200 -o search.json
-  jq '{total_count, query_translation, warnings, errors}' search.json
+    help: `Usage: pubmed search <query> [options]
+       pubmed search - [options]      (read the query from stdin)
+Search PubMed. Prints PMIDs with total_count, query_translation, warnings,
+and errors (same JSON as the search_articles MCP tool).
+Options:
+  --max-results <n>   PMIDs to return, 1-10000 (default 20)
+  --retstart <n>      Offset of the first PMID, for paging (default 0)
+  --sort <order>      relevance | pub_date | author | journal_name
+  --field <field>     Restrict untagged terms to one field:
+                      title | tiab | mesh | author | journal | affiliation
+  --date-from <date>  Start date: YYYY, YYYY/MM, or YYYY/MM/DD
+  --date-to <date>    End date, same formats (either bound may be omitted)
+  --datetype <type>   pdat = publication date (default) | edat = Entrez date |
+                      mdat = modification date
+PubMed maps untagged terms through Automatic Term Mapping (ATM). Before
+concluding that a low or zero total_count means no literature exists, check
+query_translation, warnings, and errors. To search several words in one
+field, tag each term; when a quoted phrase is not indexed, use a proximity
+search such as "drug resistance"[tiab:~0].
+Example:
+  pubmed search "TP53[tiab] AND myelodysplastic syndromes[mh]" --max-results 200 -o search.json
+  jq '{total_count, query_translation, warnings, errors}' search.json
 `,
     async execute(input, client) {
         // A query read from stdin may span several lines.
@@ -94,24 +94,24 @@ const metadata = {
         authors: { type: 'string' },
         affiliations: { type: 'string' },
     },
-    help: `Usage: pubmed metadata <pmid>... | - [options]
-Get title, abstract, authors, journal, publication date, MeSH terms,
-keywords, and article types (same JSON as get_article_metadata).
-Lists longer than ${MAX_METADATA_PMIDS} PMIDs are fetched in batches and merged.
-Options:
-  --authors <mode>       all (default) | first_last | first | none
-                         author_count always gives the full number of authors
-  --affiliations <bool>  false (default) | true: include the affiliations of
-                         the returned authors
-Records are large (abstracts, and with --affiliations also affiliations): save
-them with -o and extract the fields you need with jq.
-Example:
-  jq -r '.pmids[]' search.json | pubmed metadata - --authors first_last -o meta.json
-  jq -r '.articles[] | [.identifiers.pmid, .publication_date.year, .title] | @tsv' meta.json
+    help: `Usage: pubmed metadata <pmid>... | - [options]
+Get title, abstract, authors, journal, publication date, MeSH terms,
+keywords, and article types (same JSON as get_article_metadata).
+Lists longer than ${MAX_METADATA_PMIDS} PMIDs are fetched in batches and merged.
+Options:
+  --authors <mode>       all (default) | first_last | first | none
+                         author_count always gives the full number of authors
+  --affiliations <bool>  false (default) | true: include the affiliations of
+                         the returned authors
+Records are large (abstracts, and with --affiliations also affiliations): save
+them with -o and extract the fields you need with jq.
+Example:
+  jq -r '.pmids[]' search.json | pubmed metadata - --authors first_last -o meta.json
+  jq -r '.articles[] | [.identifiers.pmid, .publication_date.year, .title] | @tsv' meta.json
 `,
     async execute(input, client) {
         const pmids = await readIds(input, PMID);
@@ -143,25 +143,25 @@ const related = {
         'link-type': { type: 'string' },
         'max-results': { type: 'string' },
     },
-    help: `Usage: pubmed related <pmid>... | - [options]
-Find linked records for each PMID with NCBI ELink (same JSON as
-find_related_articles). Lists longer than ${RELATED_BATCH_SIZE} PMIDs are split into batches.
-Options:
-  --link-type <type>  similar_articles (default)  similar PubMed articles
-                      citing_pmc_articles         PMC articles citing the PMID
-                      linked_gene_records         NCBI Gene records
-                      linked_refseq_proteins      RefSeq protein records
-                      linked_refseq_nucleotides   RefSeq nucleotide records
-  --max-results <n>   Cap on links per source PMID, 1-1000
-citing_pmc_articles returns PMC IDs without the "PMC" prefix; pubmed fulltext
-and pubmed convert --id-type pmcid accept them as they are.
-Example:
-  pubmed related 34265844 --link-type citing_pmc_articles -o citing.json
-  jq -r '.linksets[].linksetdbs[].links[]' citing.json
+    help: `Usage: pubmed related <pmid>... | - [options]
+Find linked records for each PMID with NCBI ELink (same JSON as
+find_related_articles). Lists longer than ${RELATED_BATCH_SIZE} PMIDs are split into batches.
+Options:
+  --link-type <type>  similar_articles (default)  similar PubMed articles
+                      citing_pmc_articles         PMC articles citing the PMID
+                      linked_gene_records         NCBI Gene records
+                      linked_refseq_proteins      RefSeq protein records
+                      linked_refseq_nucleotides   RefSeq nucleotide records
+  --max-results <n>   Cap on links per source PMID, 1-1000
+citing_pmc_articles returns PMC IDs without the "PMC" prefix; pubmed fulltext
+and pubmed convert --id-type pmcid accept them as they are.
+Example:
+  pubmed related 34265844 --link-type citing_pmc_articles -o citing.json
+  jq -r '.linksets[].linksetdbs[].links[]' citing.json
 `,
     async execute(input, client) {
         const pmids = await readIds(input, PMID);
@@ -195,26 +195,26 @@ const citation = {
         key: { type: 'string' },
         input: { type: 'string' },
     },
-    help: `Usage: pubmed citation --journal <name> --year <yyyy> [options]
-       pubmed citation --input <file|->
-Find PMIDs from citation details with NCBI ECitMatch (same JSON as
-lookup_article_by_citation). Unmatched citations have an empty pmid.
-Options:
-  --journal <name>    Journal title or abbreviation, e.g. "N Engl J Med"
-  --year <yyyy>       Publication year
-  --volume <v>        Volume
-  --first-page <p>    First page
-  --author <name>     First author's last name
-  --key <key>         Label echoed back in the result (default 1)
-  --input <file|->    Many citations: a JSON array or JSON Lines of objects
-                      {journal, year, volume, first_page, author, key};
-                      missing keys default to 1, 2, 3, ... Lists longer than
-                      ${MAX_CITATIONS} are split into batches.
-Example:
-  pubmed citation --journal Nature --year 2021 --volume 596 --first-page 583 --author Jumper
+    help: `Usage: pubmed citation --journal <name> --year <yyyy> [options]
+       pubmed citation --input <file|->
+Find PMIDs from citation details with NCBI ECitMatch (same JSON as
+lookup_article_by_citation). Unmatched citations have an empty pmid.
+Options:
+  --journal <name>    Journal title or abbreviation, e.g. "N Engl J Med"
+  --year <yyyy>       Publication year
+  --volume <v>        Volume
+  --first-page <p>    First page
+  --author <name>     First author's last name
+  --key <key>         Label echoed back in the result (default 1)
+  --input <file|->    Many citations: a JSON array or JSON Lines of objects
+                      {journal, year, volume, first_page, author, key};
+                      missing keys default to 1, 2, 3, ... Lists longer than
+                      ${MAX_CITATIONS} are split into batches.
+Example:
+  pubmed citation --journal Nature --year 2021 --volume 596 --first-page 583 --author Jumper
 `,
     async execute(input, client) {
         const citations = (input.values.input !== undefined
@@ -315,14 +315,14 @@ const convert = {
     options: {
         'id-type': { type: 'string' },
     },
-    help: `Usage: pubmed convert <id>... | - [--id-type pmid|pmcid|doi]
-Convert between PMID, PMCID, and DOI with the NCBI PMC ID Converter (same
-JSON as convert_article_ids). All IDs must be of the --id-type given
-(default pmid). Lists longer than ${MAX_CONVERT_IDS} IDs are split into batches.
-Example:
-  pubmed convert 34265844 | jq -r '.records[] | [.pmid, .pmcid // "", .doi // ""] | @tsv'
+    help: `Usage: pubmed convert <id>... | - [--id-type pmid|pmcid|doi]
+Convert between PMID, PMCID, and DOI with the NCBI PMC ID Converter (same
+JSON as convert_article_ids). All IDs must be of the --id-type given
+(default pmid). Lists longer than ${MAX_CONVERT_IDS} IDs are split into batches.
+Example:
+  pubmed convert 34265844 | jq -r '.records[] | [.pmid, .pmcid // "", .doi // ""] | @tsv'
 `,
     async execute(input, client) {
         const idType = input.values['id-type'] ?? 'pmid';
@@ -349,20 +349,20 @@ const fulltext = {
     tool: 'get_full_text_article',
     description: 'Get the full text of PMC open-access articles',
     options: {},
-    help: `Usage: pubmed fulltext <pmcid>... | -
-Get the full text of PMC articles as plain text: all sections, figure and
-table captions, and references (same JSON as get_full_text_article). Only the
-PMC Open Access subset is available; other IDs are listed in errors. Lists
-longer than ${MAX_FULL_TEXT_IDS} PMCIDs are fetched in batches and merged.
-Each article is typically tens of thousands of characters. Save them with -o
-and pull out only the passages you need. Get PMCIDs from PMIDs with pubmed
-convert, or check which PMIDs have full text with pubmed copyright.
-Example:
-  pubmed fulltext PMC8371605 -o full.json
-  jq -r '.articles[0].full_text' full.json | grep -n -i 'confidence'
+    help: `Usage: pubmed fulltext <pmcid>... | -
+Get the full text of PMC articles as plain text: all sections, figure and
+table captions, and references (same JSON as get_full_text_article). Only the
+PMC Open Access subset is available; other IDs are listed in errors. Lists
+longer than ${MAX_FULL_TEXT_IDS} PMCIDs are fetched in batches and merged.
+Each article is typically tens of thousands of characters. Save them with -o
+and pull out only the passages you need. Get PMCIDs from PMIDs with pubmed
+convert, or check which PMIDs have full text with pubmed copyright.
+Example:
+  pubmed fulltext PMC8371605 -o full.json
+  jq -r '.articles[0].full_text' full.json | grep -n -i 'confidence'
 `,
     async execute(input, client) {
         const pmcids = await readIds(input, PMCID);
@@ -387,15 +387,15 @@ const copyright = {
     tool: 'get_copyright_status',
     description: 'Check full-text availability and license',
     options: {},
-    help: `Usage: pubmed copyright <pmid>... | -
-Check whether full text can be retrieved (has_full_text), plus the license,
-copyright statement, and PMC open-access status (same JSON as
-get_copyright_status). Lists longer than ${MAX_COPYRIGHT_PMIDS} PMIDs are split into batches.
-Example:
-  pubmed copyright - < pmids.txt -o rights.json
-  jq -r '.statuses[] | select(.has_full_text) | .pmcid' rights.json | pubmed fulltext - -o full.json
+    help: `Usage: pubmed copyright <pmid>... | -
+Check whether full text can be retrieved (has_full_text), plus the license,
+copyright statement, and PMC open-access status (same JSON as
+get_copyright_status). Lists longer than ${MAX_COPYRIGHT_PMIDS} PMIDs are split into batches.
+Example:
+  pubmed copyright - < pmids.txt -o rights.json
+  jq -r '.statuses[] | select(.has_full_text) | .pmcid' rights.json | pubmed fulltext - -o full.json
 `,
     async execute(input, client) {
         const pmids = await readIds(input, PMID);

package/dist/cli/run.js CHANGED Viewed

@@ -103,10 +103,10 @@ function usageFailure(io, command, message) {
     io.stderr(`pubmed ${command.name}: ${message}\nRun "pubmed ${command.name} --help" for usage.\n`);
     return 2;
 }
-const COMMON_OPTIONS_HELP = `
-Common options:
-  -o, --output <file>  Write the JSON to <file> instead of stdout ("-" = stdout)
-  -h, --help           Show this help
+const COMMON_OPTIONS_HELP = `
+Common options:
+  -o, --output <file>  Write the JSON to <file> instead of stdout ("-" = stdout)
+  -h, --help           Show this help
 `;
 function commandHelp(command) {
     return command.help + COMMON_OPTIONS_HELP;
@@ -115,33 +115,33 @@ function globalHelp() {
     const nameWidth = Math.max(...COMMANDS.map((c) => c.name.length));
     const descriptionWidth = Math.max(...COMMANDS.map((c) => c.description.length));
     const commandList = COMMANDS.map((c) => `  ${c.name.padEnd(nameWidth)}  ${c.description.padEnd(descriptionWidth)}  (${c.tool})`).join('\n');
-    return `Usage: pubmed <command> [options] [arguments]
-Query PubMed and PubMed Central through NCBI E-utilities. Each command runs
-the matching PubMed MCP tool and prints the same JSON, so results can be
-saved to a file and filtered with jq instead of being read in full.
-Commands:
-${commandList}
-Options:
-  -o, --output <file>  Write the JSON to <file> instead of stdout
-  -h, --help           Show help; "pubmed <command> --help" for a command
-IDs are given as arguments separated by spaces or commas, or read from stdin
-with "-". Long lists are split into batches and sent one at a time.
-Environment:
-  NCBI_API_KEY  NCBI API key; raises the rate limit from 3 to 8 requests/s.
-                In a source checkout, also read from its .env file.
-Exit status: 0 on success, 1 when NCBI or a file operation fails, 2 on
-invalid usage.
-Example:
-  pubmed search "TP53 AND myelodysplastic syndromes[mh]" --max-results 100 -o search.json
-  jq -r '.pmids[]' search.json | pubmed metadata - -o meta.json
-  jq -c '.articles[] | {pmid: .identifiers.pmid, title}' meta.json
+    return `Usage: pubmed <command> [options] [arguments]
+Query PubMed and PubMed Central through NCBI E-utilities. Each command runs
+the matching PubMed MCP tool and prints the same JSON, so results can be
+saved to a file and filtered with jq instead of being read in full.
+Commands:
+${commandList}
+Options:
+  -o, --output <file>  Write the JSON to <file> instead of stdout
+  -h, --help           Show help; "pubmed <command> --help" for a command
+IDs are given as arguments separated by spaces or commas, or read from stdin
+with "-". Long lists are split into batches and sent one at a time.
+Environment:
+  NCBI_API_KEY  NCBI API key; raises the rate limit from 3 to 8 requests/s.
+                In a source checkout, also read from its .env file.
+Exit status: 0 on success, 1 when NCBI or a file operation fails, 2 on
+invalid usage.
+Example:
+  pubmed search "TP53 AND myelodysplastic syndromes[mh]" --max-results 100 -o search.json
+  jq -r '.pmids[]' search.json | pubmed metadata - -o meta.json
+  jq -c '.articles[] | {pmid: .identifiers.pmid, title}' meta.json
 `;
 }
 function formatBytes(bytes) {

package/dist/pubmed/client.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/pubmed/client.js CHANGED Viewed

@@ -24,7 +24,13 @@ const HTTPS_AGENT = new https.Agent({
     keepAlive: true,
 });
 const TOOL_NAME = 'pubmed-mcp';
-const TOOL_EMAIL = 'pubmed-mcp@example.com';
+/**
+ * NCBI requires `email` to be the software developer's address, not an end
+ * user's, and registered with NCBI together with `tool`. A forwarding alias,
+ * so the maintainer's own address stays private.
+ * https://www.ncbi.nlm.nih.gov/books/NBK25497/
+ */
+const TOOL_EMAIL = 'pubmed-mcp.github.ointment121@simplelogin.com';
 // ─── Rate limiter ────────────────────────────────────────────────────────────
 class RateLimiter {
     nextSlot = 0;
@@ -215,9 +221,7 @@ export class NcbiClient {
         const response = await this.request('idConvert', () => axios.get(PMC_ID_CONVERTER_URL, {
             httpsAgent: HTTPS_AGENT,
             params: {
-                tool: TOOL_NAME,
-                email: TOOL_EMAIL,
-                ...(this.apiKey ? { api_key: this.apiKey } : {}),
+                ...this.commonParams(),
                 format: 'json',
                 ids: params.ids.join(','),
                 idtype: params.idtype ?? 'pmid',

package/dist/pubmed/client.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/dist/utils/xml.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"xml.d.ts","sourceRoot":"","sources":["../../src/utils/xml.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAGH,OAAO,KAAK,EAKV,eAAe,EAEf,eAAe,EAEhB,MAAM,oBAAoB,CAAC;AA2G5B;;GAEG;AACH,wBAAgB,oBAAoB,CAAC,GAAG,EAAE,MAAM,GAAG,eAAe,EAAE,CAOnE;AAyID;;GAEG;AACH,wBAAgB,iBAAiB,CAAC,GAAG,EAAE,MAAM,GAAG,eAAe,EAAE,CAOhE;~~AAqJD~~,MAAM,WAAW,aAAa;IAC5B,KAAK,EAAE,MAAM,CAAC;IACd,2DAA2D;IAC3D,YAAY,EAAE,OAAO,CAAC;IACtB,+EAA+E;IAC/E,WAAW,EAAE,OAAO,CAAC;IACrB,iFAAiF;IACjF,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,kBAAkB,CAAC,EAAE,MAAM,CAAC;CAC7B;AAED;;;GAGG;AACH,wBAAgB,iBAAiB,CAAC,GAAG,EAAE,MAAM,GAAG,aAAa,EAAE,CA+B9D;AAWD;;;GAGG;AACH,wBAAgB,WAAW,CAAC,IAAI,EAAE,OAAO,GAAG,MAAM,CA4BjD;AA+CD,wBAAgB,YAAY,CAAC,IAAI,EAAE,MAAM,GAAG,MAAM,CAQjD"}
1	+ {"version":3,"file":"xml.d.ts","sourceRoot":"","sources":["../../src/utils/xml.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAGH,OAAO,KAAK,EAKV,eAAe,EAEf,eAAe,EAEhB,MAAM,oBAAoB,CAAC;AA2G5B;;GAEG;AACH,wBAAgB,oBAAoB,CAAC,GAAG,EAAE,MAAM,GAAG,eAAe,EAAE,CAOnE;AAyID;;GAEG;AACH,wBAAgB,iBAAiB,CAAC,GAAG,EAAE,MAAM,GAAG,eAAe,EAAE,CAOhE;AAsJD,MAAM,WAAW,aAAa;IAC5B,KAAK,EAAE,MAAM,CAAC;IACd,2DAA2D;IAC3D,YAAY,EAAE,OAAO,CAAC;IACtB,+EAA+E;IAC/E,WAAW,EAAE,OAAO,CAAC;IACrB,iFAAiF;IACjF,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,kBAAkB,CAAC,EAAE,MAAM,CAAC;CAC7B;AAED;;;GAGG;AACH,wBAAgB,iBAAiB,CAAC,GAAG,EAAE,MAAM,GAAG,aAAa,EAAE,CA+B9D;AAWD;;;GAGG;AACH,wBAAgB,WAAW,CAAC,IAAI,EAAE,OAAO,GAAG,MAAM,CA4BjD;AA+CD,wBAAgB,YAAY,CAAC,IAAI,EAAE,MAAM,GAAG,MAAM,CAQjD"}

package/dist/utils/xml.js CHANGED Viewed

@@ -359,7 +359,8 @@ function extractPmcBackText(back) {
         return '';
     const parts = [];
     const refLists = findNodesByKey(back, 'ref-list');
-    for (const refList of refLists) {
+    for (const node of refLists) {
+        const refList = node;
         const title = extractText(refList?.title);
         if (title)
             parts.push(title);

package/dist/utils/xml.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/package.json CHANGED Viewed

@@ -1,6 +1,6 @@
 {
   "name": "@djmima/pubmed-mcp",
-  "version": "1.0.0",
+  "version": "1.0.1",
   "description": "MCP server providing access to PubMed biomedical literature and citations",
   "license": "MIT",
   "author": "DJ MIMA",
@@ -30,7 +30,8 @@
   },
   "files": [
     "dist",
-    "skills"
+    "skills",
+    "CHANGELOG.md"
   ],
   "scripts": {
     "build": "tsc",