@zenalexa/unicli 0.218.1 → 0.220.0

package/dist/adapters/pubmed/articles.js

@@ -0,0 +1,385 @@
+/**
+ * @owner   src/adapters/pubmed/articles.ts
+ * @does    Register agent-facing PubMed search, article, author, citation, and related-article commands.
+ * @needs   NCBI E-utilities API, TypeScript adapter loader, PMID/query validation.
+ * @feeds   surface coverage ledger, biomedical literature command surface, agent-readable PubMed rows.
+ * @breaks  NCBI E-utilities envelope drift, weak PMID validation, or silent empty rows hide literature lookup failures.
+ */
+import { DOMParser } from "@xmldom/xmldom";
+import { cli, Strategy } from "../../registry.js";
+const EUTILS_BASE = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils";
+const SUMMARY_COLUMNS = [
+    "rank",
+    "pmid",
+    "title",
+    "authors",
+    "journal",
+    "year",
+    "article_type",
+    "doi",
+    "url",
+];
+const RELATED_COLUMNS = [...SUMMARY_COLUMNS.slice(0, 7), "score", "doi", "url"];
+function stringField(value) {
+    return typeof value === "string" ? value : "";
+}
+function cleanText(value) {
+    return stringField(value)
+        .replace(/&/g, "&")
+        .replace(/&lt;/g, "<")
+        .replace(/&gt;/g, ">")
+        .replace(/&quot;/g, '"')
+        .replace(/&apos;/g, "'")
+        .replace(/&#39;/g, "'")
+        .replace(/\s+/g, " ")
+        .trim();
+}
+export function requirePubMedText(value, label) {
+    const text = String(value ?? "").trim();
+    if (!text)
+        throw new Error(`pubmed ${label} cannot be empty.`);
+    return text;
+}
+export function requirePmid(value, label = "pmid") {
+    const pmid = requirePubMedText(value, label);
+    if (!/^\d+$/.test(pmid))
+        throw new Error(`pubmed ${label} must be a numeric PMID.`);
+    return pmid;
+}
+export function requirePubMedLimit(value, fallback = 20, max = 100) {
+    if (value === undefined || value === null || value === "")
+        return fallback;
+    const n = Number(value);
+    if (!Number.isInteger(n) || n < 1 || n > max) {
+        throw new Error(`pubmed limit must be an integer in [1, ${max}]. Got: ${String(value)}`);
+    }
+    return n;
+}
+function requireChoice(value, choices, label, fallback) {
+    const text = String(value ?? fallback).trim();
+    if (!choices.includes(text))
+        throw new Error(`pubmed ${label} must be one of: ${choices.join(", ")}.`);
+    return text;
+}
+function year(value) {
+    return stringField(value).match(/\d{4}/)?.[0] ?? "";
+}
+function buildUrl(tool, params, retmode = "json") {
+    const search = new URLSearchParams();
+    search.set("db", "pubmed");
+    search.set("retmode", retmode);
+    if (process.env.NCBI_API_KEY)
+        search.set("api_key", process.env.NCBI_API_KEY);
+    if (process.env.NCBI_EMAIL)
+        search.set("email", process.env.NCBI_EMAIL);
+    for (const [key, value] of Object.entries(params)) {
+        if (value !== undefined && value !== null && value !== "")
+            search.set(key, String(value));
+    }
+    return `${EUTILS_BASE}/${tool}.fcgi?${search.toString()}`;
+}
+async function eutilsFetch(tool, params, retmode = "json") {
+    const response = await fetch(buildUrl(tool, params, retmode), {
+        headers: { "User-Agent": "unicli (https://github.com/olo-dot-io/Uni-CLI)" },
+    });
+    if (!response.ok)
+        throw new Error(`PubMed ${tool} returned HTTP ${response.status}.`);
+    if (retmode === "xml")
+        return response.text();
+    const json = (await response.json());
+    if (json.error)
+        throw new Error(`PubMed ${tool} returned an error: ${String(json.error)}`);
+    return json;
+}
+function authorNames(authors, max = 3) {
+    if (!Array.isArray(authors))
+        return "";
+    const names = authors
+        .map((author) => stringField(author.name) ||
+        stringField(author.collectivename) ||
+        [author.lastname, author.initials]
+            .map(stringField)
+            .filter(Boolean)
+            .join(" "))
+        .filter(Boolean);
+    const shown = names.slice(0, max);
+    if (names.length > max)
+        shown.push("et al.");
+    return shown.join(", ");
+}
+function doi(articleIds) {
+    return stringField(Array.isArray(articleIds)
+        ? articleIds.find((id) => stringField(id.idtype).toLowerCase() === "doi")
+            ?.value
+        : "");
+}
+function articleType(types) {
+    const values = Array.isArray(types)
+        ? types.map(stringField).filter(Boolean)
+        : [];
+    return (values.find((type) => type === "Review") ?? values[0] ?? "Journal Article");
+}
+export function mapPubMedSummaryRows(summaries, pmids) {
+    return pmids.flatMap((pmid, index) => {
+        const summary = summaries.find((item) => stringField(item.uid) === pmid);
+        if (!summary)
+            return [];
+        return [
+            {
+                rank: index + 1,
+                pmid,
+                title: cleanText(summary.title),
+                authors: authorNames(summary.authors),
+                journal: stringField(summary.source),
+                year: year(summary.pubdate),
+                article_type: articleType(summary.pubtype ?? []),
+                doi: doi(summary.articleids),
+                url: `https://pubmed.ncbi.nlm.nih.gov/${pmid}/`,
+            },
+        ];
+    });
+}
+function childText(root, tagName) {
+    return cleanText(root.getElementsByTagName(tagName)[0]?.textContent ?? "");
+}
+function elementTexts(root, tagName) {
+    const nodes = root.getElementsByTagName(tagName);
+    return Array.from({ length: nodes.length }, (_, index) => nodes.item(index))
+        .filter((node) => node !== null)
+        .map((node) => cleanText(node.textContent ?? ""));
+}
+function firstElement(root, tagName) {
+    return root.getElementsByTagName(tagName)[0] ?? null;
+}
+export function mapPubMedArticleRows(xml, pmid, fullAbstract = false) {
+    const document = new DOMParser().parseFromString(xml, "text/xml");
+    const title = childText(document, "ArticleTitle");
+    if (!title)
+        throw new Error(`pubmed article ${pmid} did not include a title.`);
+    const abstract = elementTexts(document, "AbstractText").join(" ");
+    const shownAbstract = fullAbstract || abstract.length <= 500
+        ? abstract
+        : `${abstract.slice(0, 497)}...`;
+    const doiValue = Array.from({ length: document.getElementsByTagName("ArticleId").length }, (_, index) => document.getElementsByTagName("ArticleId").item(index))
+        .filter((node) => node !== null)
+        .find((node) => node.getAttribute("IdType")?.toLowerCase() === "doi")
+        ?.textContent?.trim() ?? "";
+    const authorNodes = document.getElementsByTagName("Author");
+    const authors = Array.from({ length: authorNodes.length }, (_, index) => authorNodes.item(index))
+        .filter((author) => author !== null)
+        .map((author) => [childText(author, "LastName"), childText(author, "Initials")]
+        .filter(Boolean)
+        .join(" "))
+        .filter(Boolean)
+        .join(", ");
+    const journal = firstElement(document, "Journal");
+    const pubDate = firstElement(document, "PubDate");
+    return [
+        { field: "PMID", value: pmid },
+        { field: "Title", value: title },
+        { field: "Authors", value: authors },
+        { field: "Journal", value: journal ? childText(journal, "Title") : "" },
+        { field: "Year", value: pubDate ? childText(pubDate, "Year") : "" },
+        {
+            field: "Date",
+            value: pubDate ? cleanText(pubDate.textContent ?? "") : "",
+        },
+        {
+            field: "Article Type",
+            value: elementTexts(document, "PublicationType")[0] ?? null,
+        },
+        { field: "Language", value: childText(document, "Language") },
+        { field: "DOI", value: doiValue || null },
+        { field: "Abstract", value: shownAbstract || null },
+        { field: "URL", value: `https://pubmed.ncbi.nlm.nih.gov/${pmid}/` },
+    ];
+}
+async function fetchSummaryRows(pmids, label) {
+    const json = (await eutilsFetch("esummary", { id: pmids.join(",") }));
+    const result = json.result ?? {};
+    const summaries = pmids
+        .map((pmid) => result[pmid])
+        .filter((item) => !!item && typeof item === "object");
+    const rows = mapPubMedSummaryRows(summaries, pmids);
+    if (rows.length === 0)
+        throw new Error(`${label} returned no summary rows.`);
+    return rows;
+}
+cli({
+    site: "pubmed",
+    name: "search",
+    description: "Search PubMed articles",
+    domain: "pubmed.ncbi.nlm.nih.gov",
+    strategy: Strategy.PUBLIC,
+    args: [
+        {
+            name: "query",
+            type: "str",
+            required: true,
+            positional: true,
+            description: "Search query",
+        },
+        { name: "limit", type: "int", default: 20, description: "Max results" },
+    ],
+    columns: SUMMARY_COLUMNS,
+    func: async (_page, kwargs) => {
+        const query = requirePubMedText(kwargs.query, "query");
+        const limit = requirePubMedLimit(kwargs.limit);
+        const json = (await eutilsFetch("esearch", {
+            term: query,
+            retmax: limit,
+            sort: "",
+        }));
+        const pmids = Array.isArray(json.esearchresult?.idlist)
+            ? json.esearchresult.idlist
+            : [];
+        if (pmids.length === 0)
+            throw new Error(`No PubMed articles matched "${query}".`);
+        return fetchSummaryRows(pmids, "pubmed search");
+    },
+});
+cli({
+    site: "pubmed",
+    name: "article",
+    description: "Get detailed information for a PubMed article by PMID",
+    domain: "pubmed.ncbi.nlm.nih.gov",
+    strategy: Strategy.PUBLIC,
+    args: [
+        {
+            name: "pmid",
+            type: "str",
+            required: true,
+            positional: true,
+            description: "PubMed ID",
+        },
+        {
+            name: "full-abstract",
+            type: "bool",
+            default: false,
+            description: "Do not truncate abstract",
+        },
+    ],
+    columns: ["field", "value"],
+    func: async (_page, kwargs) => {
+        const pmid = requirePmid(kwargs.pmid);
+        const xml = String(await eutilsFetch("efetch", { id: pmid, rettype: "abstract" }, "xml"));
+        return mapPubMedArticleRows(xml, pmid, kwargs["full-abstract"] === true);
+    },
+});
+cli({
+    site: "pubmed",
+    name: "author",
+    description: "Search PubMed articles by author name",
+    domain: "pubmed.ncbi.nlm.nih.gov",
+    strategy: Strategy.PUBLIC,
+    args: [
+        {
+            name: "name",
+            type: "str",
+            required: true,
+            positional: true,
+            description: "Author name",
+        },
+        { name: "limit", type: "int", default: 20, description: "Max results" },
+    ],
+    columns: SUMMARY_COLUMNS,
+    func: async (_page, kwargs) => {
+        const name = requirePubMedText(kwargs.name, "author");
+        const limit = requirePubMedLimit(kwargs.limit);
+        const json = (await eutilsFetch("esearch", {
+            term: `${name}[au]`,
+            retmax: limit,
+            sort: "pub_date",
+        }));
+        const pmids = Array.isArray(json.esearchresult?.idlist)
+            ? json.esearchresult.idlist
+            : [];
+        if (pmids.length === 0)
+            throw new Error(`No PubMed articles found for author "${name}".`);
+        return fetchSummaryRows(pmids, "pubmed author");
+    },
+});
+cli({
+    site: "pubmed",
+    name: "citations",
+    description: "Get PubMed citation relationships for an article",
+    domain: "pubmed.ncbi.nlm.nih.gov",
+    strategy: Strategy.PUBLIC,
+    args: [
+        {
+            name: "pmid",
+            type: "str",
+            required: true,
+            positional: true,
+            description: "PubMed ID",
+        },
+        {
+            name: "direction",
+            type: "str",
+            default: "citedby",
+            choices: ["citedby", "references"],
+            description: "citedby or references",
+        },
+        { name: "limit", type: "int", default: 20, description: "Max results" },
+    ],
+    columns: SUMMARY_COLUMNS,
+    func: async (_page, kwargs) => {
+        const pmid = requirePmid(kwargs.pmid);
+        const direction = requireChoice(kwargs.direction, ["citedby", "references"], "direction", "citedby");
+        const linkname = direction === "citedby" ? "pubmed_pubmed_citedin" : "pubmed_pubmed_refs";
+        const limit = requirePubMedLimit(kwargs.limit);
+        const json = (await eutilsFetch("elink", {
+            id: pmid,
+            dbfrom: "pubmed",
+            cmd: "neighbor",
+            linkname,
+        }));
+        const links = json.linksets?.[0]?.linksetdbs?.[0]?.links?.map(String).slice(0, limit) ??
+            [];
+        if (links.length === 0)
+            throw new Error(`No ${direction} links found for PMID ${pmid}.`);
+        return fetchSummaryRows(links, "pubmed citations");
+    },
+});
+cli({
+    site: "pubmed",
+    name: "related",
+    description: "Find articles related to a PubMed article",
+    domain: "pubmed.ncbi.nlm.nih.gov",
+    strategy: Strategy.PUBLIC,
+    args: [
+        {
+            name: "pmid",
+            type: "str",
+            required: true,
+            positional: true,
+            description: "PubMed ID",
+        },
+        { name: "limit", type: "int", default: 20, description: "Max results" },
+    ],
+    columns: RELATED_COLUMNS,
+    func: async (_page, kwargs) => {
+        const pmid = requirePmid(kwargs.pmid);
+        const limit = requirePubMedLimit(kwargs.limit);
+        const json = (await eutilsFetch("elink", {
+            id: pmid,
+            dbfrom: "pubmed",
+            cmd: "neighbor_score",
+            linkname: "pubmed_pubmed",
+        }));
+        const links = json.linksets?.[0]?.linksetdbs?.[0]?.links
+            ?.map((link) => typeof link === "string"
+            ? { id: link, score: null }
+            : { id: stringField(link.id), score: Number(link.score) })
+            .filter((link) => link.id && link.id !== pmid)
+            .slice(0, limit) ?? [];
+        if (links.length === 0)
+            throw new Error(`No related articles found for PMID ${pmid}.`);
+        const rows = await fetchSummaryRows(links.map((link) => link.id), "pubmed related");
+        return rows.map((row, index) => ({
+            ...row,
+            score: links[index]?.score ?? null,
+        }));
+    },
+});
+//# sourceMappingURL=articles.js.map

package/dist/adapters/pubmed/articles.js.map

@@ -0,0 +1 @@
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package/dist/adapters/pypi/package.d.ts

@@ -0,0 +1,38 @@
+/**
+ * @owner   src/adapters/pypi/package.ts
+ * @does    Register agent-facing PyPI package metadata and download-stat commands.
+ * @needs   Public PyPI JSON API, public pypistats JSON API, TypeScript adapter loader.
+ * @feeds   surface coverage ledger, Python package registry command surface, agent-readable package rows.
+ * @breaks  PyPI/pypistats API drift, weak distribution-name parsing, or silent empty rows hide package lookup failures.
+ */
+interface PyPiInfo {
+    name?: unknown;
+    version?: unknown;
+    summary?: unknown;
+    author?: unknown;
+    author_email?: unknown;
+    license_expression?: unknown;
+    license?: unknown;
+    home_page?: unknown;
+    project_urls?: Record<string, unknown> | null;
+    requires_python?: unknown;
+    keywords?: unknown;
+    package_url?: unknown;
+}
+interface PyPiPackageBody {
+    info?: PyPiInfo;
+    releases?: Record<string, Array<{
+        upload_time?: unknown;
+    }>>;
+}
+interface PyPiDownloadsBody {
+    package?: unknown;
+    data?: unknown;
+}
+export declare function requirePyPiPackageName(value: unknown): string;
+export declare function requirePyPiDownloadsPeriod(value: unknown): "recent" | "overall";
+export declare function mapPyPiPackageRow(body: PyPiPackageBody, requestedName: string): Record<string, unknown>;
+export declare function mapRecentDownloadRows(body: PyPiDownloadsBody, requestedName: string): Array<Record<string, unknown>>;
+export declare function mapOverallDownloadRows(body: PyPiDownloadsBody, requestedName: string): Array<Record<string, unknown>>;
+export {};
+//# sourceMappingURL=package.d.ts.map

package/dist/adapters/pypi/package.d.ts.map

@@ -0,0 +1 @@
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