@inflexa-ai/harness 0.13.0 → 0.14.1

package/dist/tools/bio/search-gwas-catalog.js

@@ -1,172 +0,0 @@
-/**
- * searchGwasCatalog — search NHGRI-EBI GWAS Catalog for SNP-trait associations.
- *
- * Public REST API, no key required. Three search modes:
- *   - 'gene' — gene-trait associations (via SNP-by-gene lookup, then assocs)
- *   - 'trait' — trait-gene associations (via EFO trait search, then assocs)
- *   - 'variant' — direct rsID lookup
- */
-import { ok } from "neverthrow";
-import { z } from "zod";
-import { defineTool } from "../define-tool.js";
-import { apiFetchValidated, describeApiError } from "../lib/api-utils.js";
-import { GWAS_BASE, GWAS_HEADERS } from "../lib/gwas-catalog-config.js";
-// GWAS Catalog raw wire shapes (HAL+JSON), validated at the fetch boundary.
-// Every field is optional because the API omits absent values; leaf strings
-// that the API can return as an explicit `null` are `.nullable()`.
-const RawGwasStudySchema = z.object({
-    accessionId: z.string().optional(),
-    pubmedId: z.string().optional(),
-    initialSampleSize: z.string().optional(),
-});
-// `_snpRsId` is not on the wire — the 'gene' search path assigns it after
-// parsing (`a._snpRsId = snp.rsId`), so it stays a writable optional field.
-const RawGwasAssociationSchema = z.object({
-    _snpRsId: z.string().optional(),
-    loci: z
-        .array(z.object({
-        strongestRiskAlleles: z.array(z.object({ riskAlleleName: z.string().nullable().optional() })).optional(),
-        authorReportedGenes: z.array(z.object({ geneName: z.string().nullable().optional() })).optional(),
-    }))
-        .optional(),
-    efoTraits: z.array(z.object({ trait: z.string().nullable().optional() })).optional(),
-    study: RawGwasStudySchema.optional(),
-    pvalueMantissa: z.number().optional(),
-    pvalueExponent: z.number().optional(),
-    riskFrequency: z.string().optional(),
-    orPerCopyNum: z.number().nullable().optional(),
-    betaNum: z.number().nullable().optional(),
-    range: z.string().optional(),
-});
-const GwasEmbeddedSchema = z.object({
-    _embedded: z.object({ associations: z.array(RawGwasAssociationSchema).optional() }).optional(),
-    page: z.object({ totalElements: z.number().optional() }).optional(),
-});
-const GwasTraitSearchResponseSchema = z.object({
-    _embedded: z
-        .object({
-        efoTraits: z.array(z.object({ _links: z.object({ self: z.object({ href: z.string().optional() }).optional() }).optional() })).optional(),
-    })
-        .optional(),
-});
-const GwasSnpSearchResponseSchema = z.object({
-    _embedded: z
-        .object({
-        singleNucleotidePolymorphisms: z
-            .array(z.object({
-            rsId: z.string().optional(),
-            _links: z.object({ associations: z.object({ href: z.string().optional() }).optional() }).optional(),
-        }))
-            .optional(),
-    })
-        .optional(),
-});
-function mapAssociation(a) {
-    const loci = a.loci ?? [];
-    const riskAlleles = loci.flatMap((l) => l.strongestRiskAlleles?.map((ra) => String(ra.riskAlleleName ?? "")) ?? []);
-    const genes = loci.flatMap((l) => l.authorReportedGenes?.map((g) => String(g.geneName ?? "")) ?? []);
-    const traits = (a.efoTraits ?? []).map((t) => String(t.trait ?? ""));
-    const study = a.study ?? {};
-    const pMantissa = a.pvalueMantissa ?? 0;
-    const pExponent = a.pvalueExponent ?? 0;
-    return {
-        rsId: String(a._snpRsId ?? riskAlleles[0]?.split("-")[0] ?? ""),
-        pValue: pMantissa * Math.pow(10, pExponent),
-        pValueMantissa: pMantissa,
-        pValueExponent: pExponent,
-        riskAllele: riskAlleles.join(", "),
-        riskFrequency: String(a.riskFrequency ?? ""),
-        orBeta: (a.orPerCopyNum ?? a.betaNum ?? null),
-        ci: String(a.range ?? ""),
-        trait: traits.join("; "),
-        mappedGenes: [...new Set(genes)],
-        studyAccession: String(study.accessionId ?? ""),
-        pubmedId: String(study.pubmedId ?? ""),
-        sampleSize: String(study.initialSampleSize ?? ""),
-    };
-}
-export const searchGwasCatalogTool = defineTool({
-    id: "search_gwas_catalog",
-    description: "Search the NHGRI-EBI GWAS Catalog for genome-wide association study results. " +
-        "Returns SNP associations with traits/diseases, effect sizes, p-values, and mapped genes. " +
-        "Use to find genetic evidence linking genes to phenotypes for target validation or " +
-        "Mendelian randomization support.",
-    inputSchema: z.object({
-        query: z.string().describe("Gene symbol (e.g. PCSK9), trait keyword (e.g. cholesterol), or rsID (e.g. rs11591147)"),
-        searchType: z
-            .enum(["gene", "trait", "variant"])
-            .describe("'gene' for gene-trait associations, 'trait' for trait-gene associations, 'variant' for a specific rsID"),
-        pValueThreshold: z.number().default(5e-8).describe("P-value threshold for genome-wide significance"),
-        limit: z.number().int().min(1).max(100).default(25).describe("Max results to return"),
-    }),
-    execute: async ({ query, searchType, pValueThreshold = 5e-8, limit = 25 }) => {
-        let url;
-        if (searchType === "variant") {
-            const rsId = query.startsWith("rs") ? query : `rs${query}`;
-            url = `${GWAS_BASE}/singleNucleotidePolymorphisms/${rsId}/associations?projection=associationBySnp`;
-        }
-        else if (searchType === "gene") {
-            url = `${GWAS_BASE}/singleNucleotidePolymorphisms/search/findByGene?geneName=${encodeURIComponent(query)}&projection=snpByGene`;
-        }
-        else {
-            url = `${GWAS_BASE}/efoTraits/search/findBySearchQuery?query=${encodeURIComponent(query)}`;
-        }
-        if (searchType === "trait") {
-            const traitRes = await apiFetchValidated(url, GwasTraitSearchResponseSchema, { headers: GWAS_HEADERS });
-            if (traitRes.isErr())
-                throw new Error(describeApiError(traitRes.error));
-            const traits = traitRes.value?._embedded?.efoTraits ?? [];
-            if (traits.length === 0) {
-                return ok({ totalFound: 0, associations: [] });
-            }
-            const traitUri = traits[0]?._links?.self?.href;
-            if (!traitUri) {
-                return ok({ totalFound: 0, associations: [] });
-            }
-            const traitId = traitUri.split("/").pop();
-            url = `${GWAS_BASE}/efoTraits/${traitId}/associations?size=${limit}`;
-        }
-        if (searchType === "gene") {
-            const snpRes = await apiFetchValidated(url, GwasSnpSearchResponseSchema, { headers: GWAS_HEADERS });
-            if (snpRes.isErr())
-                throw new Error(describeApiError(snpRes.error));
-            const snps = snpRes.value?._embedded?.singleNucleotidePolymorphisms ?? [];
-            const allAssocs = [];
-            for (const snp of snps.slice(0, Math.min(limit, 10))) {
-                const assocLink = snp?._links?.associations?.href;
-                if (!assocLink)
-                    continue;
-                const aRes = await apiFetchValidated(assocLink, GwasEmbeddedSchema, {
-                    headers: GWAS_HEADERS,
-                });
-                if (aRes.isOk()) {
-                    for (const a of aRes.value?._embedded?.associations ?? []) {
-                        a._snpRsId = snp.rsId;
-                        allAssocs.push(a);
-                    }
-                }
-                if (allAssocs.length >= limit)
-                    break;
-            }
-            return ok({
-                totalFound: allAssocs.length,
-                associations: allAssocs.slice(0, limit).map(mapAssociation),
-            });
-        }
-        const res = await apiFetchValidated(url, GwasEmbeddedSchema, { headers: GWAS_HEADERS });
-        if (res.isErr())
-            throw new Error(describeApiError(res.error));
-        const rawAssocs = res.value?._embedded?.associations ?? [];
-        const totalFound = res.value?.page?.totalElements ?? rawAssocs.length;
-        const filtered = rawAssocs
-            .filter((a) => {
-            const p = (a.pvalueMantissa ?? 1) * Math.pow(10, a.pvalueExponent ?? 0);
-            return p <= pValueThreshold;
-        })
-            .slice(0, limit);
-        return ok({
-            totalFound,
-            associations: filtered.map(mapAssociation),
-        });
-    },
-});

package/dist/tools/bio/search-pathway.d.ts

@@ -1,12 +0,0 @@
-/**
- * searchPathway — search biological pathways via KEGG and Reactome.
- */
-export declare const searchPathwayTool: import("../define-tool.js").Tool<{
-    query: string;
-    source: "kegg" | "reactome" | "both";
-    organism: string;
-    includeGenes: boolean;
-    maxResults: number;
-}, {
-    pathways: import("../lib/pathway-client.js").Pathway[];
-}>;

package/dist/tools/bio/search-pathway.js

@@ -1,32 +0,0 @@
-/**
- * searchPathway — search biological pathways via KEGG and Reactome.
- */
-import { ok } from "neverthrow";
-import { z } from "zod";
-import { defineTool } from "../define-tool.js";
-import { searchPathways } from "../lib/pathway-client.js";
-export const searchPathwayTool = defineTool({
-    id: "search_pathway",
-    description: "Search biological pathways in KEGG and/or Reactome databases. " +
-        "Returns pathway IDs, names, URLs, and optionally gene lists. " +
-        "Use source='both' to query both databases in parallel.",
-    inputSchema: z.object({
-        query: z.string().min(1).describe("Pathway search term (e.g. 'apoptosis', 'MAPK signaling')"),
-        source: z.enum(["kegg", "reactome", "both"]).default("both").describe("Which database to search"),
-        organism: z
-            .string()
-            .default("hsa")
-            .describe("KEGG organism code (e.g. 'hsa' for human, 'mmu' for mouse). " + "Automatically mapped to species name for Reactome."),
-        includeGenes: z.boolean().default(false).describe("Whether to fetch gene lists for each pathway (slower)"),
-        maxResults: z.number().int().min(1).max(50).default(10),
-    }),
-    execute: async ({ query, source, organism, includeGenes, maxResults }) => {
-        const pathways = await searchPathways(query, {
-            source,
-            organism,
-            includeGenes,
-            maxResults,
-        });
-        return ok({ pathways });
-    },
-});

package/dist/tools/bio/search-pharmgkb.d.ts

@@ -1,17 +0,0 @@
-/**
- * searchPharmgkb — search PharmGKB for pharmacogenomic clinical annotations.
- */
-export declare const searchPharmgkbTool: import("../define-tool.js").Tool<{
-    query: string;
-    searchType: "drug" | "gene";
-    limit: number;
-}, {
-    annotations: {
-        gene: string;
-        drug: string;
-        phenotype: null;
-        levelOfEvidence: string;
-        guidelineSource: null;
-        summary: null;
-    }[];
-}>;

package/dist/tools/bio/search-pharmgkb.js

@@ -1,52 +0,0 @@
-/**
- * searchPharmgkb — search PharmGKB for pharmacogenomic clinical annotations.
- */
-import { ok } from "neverthrow";
-import { z } from "zod";
-import { defineTool } from "../define-tool.js";
-import { apiFetchValidated, describeApiError } from "../lib/api-utils.js";
-import { PHARMGKB_BASE, PHARMGKB_HEADERS } from "../lib/pharmgkb-config.js";
-// Raw PharmGKB clinicalAnnotation wire shape, validated at the fetch boundary.
-// Every field is optional because the API omits absent values; the mapper in
-// `execute` folds request context (`query`) into its output, so the schema
-// models only the raw wire and the mapping stays where it is.
-const PharmgkbAnnotationSchema = z.object({
-    location: z.object({ genes: z.array(z.object({ symbol: z.string().optional() })).optional() }).optional(),
-    relatedChemicals: z.array(z.object({ name: z.string().optional() })).optional(),
-    levelOfEvidence: z.object({ term: z.string().optional() }).optional(),
-});
-const PharmgkbResponseSchema = z.object({
-    data: z.array(PharmgkbAnnotationSchema).optional(),
-});
-export const searchPharmgkbTool = defineTool({
-    id: "search_pharmgkb",
-    description: "Search PharmGKB clinical annotations for a gene-drug pharmacogenomic link — use it to judge whether a gene affects a drug's metabolism, efficacy, or toxicity. " +
-        "Returns annotations[]: { gene, drug, levelOfEvidence (PharmGKB 1A…4, where 1A is guideline-backed) }. The phenotype, guidelineSource and summary fields are always null " +
-        "in this tool's output — treat levelOfEvidence as the only strength signal and do not attribute CPIC/DPWG guideline text to it. " +
-        "Matching is an exact field filter, not a search: 'CYP2D6' resolves, 'cytochrome P450 2D6' does not. " +
-        "An empty annotations array is valid no-data (no curated PGx link) — do not retry.",
-    inputSchema: z.object({
-        query: z
-            .string()
-            .describe("Exact gene symbol (e.g. 'CYP2D6') when searchType='gene', or exact drug name (e.g. 'tamoxifen') when searchType='drug'. No fuzzy matching."),
-        searchType: z.enum(["gene", "drug"]).describe("'gene' filters PharmGKB on location.genes.symbol; 'drug' filters on relatedChemicals.name."),
-        limit: z.number().int().min(1).max(50).default(20).describe("Max annotations to return (default 20, max 50); applied client-side after the fetch."),
-    }),
-    execute: async ({ query, searchType, limit = 20 }) => {
-        const filter = searchType === "gene" ? `location.genes.symbol=${encodeURIComponent(query)}` : `relatedChemicals.name=${encodeURIComponent(query)}`;
-        const endpoint = `${PHARMGKB_BASE}/clinicalAnnotation?${filter}`;
-        const res = await apiFetchValidated(endpoint, PharmgkbResponseSchema, { headers: PHARMGKB_HEADERS });
-        if (res.isErr())
-            throw new Error(describeApiError(res.error));
-        const data = res.value?.data ?? [];
-        const annotations = data.slice(0, limit).map((ann) => ({
-            gene: ann.location?.genes?.map((g) => g.symbol).join(", ") ?? query,
-            drug: ann.relatedChemicals?.map((c) => c.name).join(", ") ?? "",
-            phenotype: null,
-            levelOfEvidence: ann.levelOfEvidence?.term ?? "Unknown",
-            guidelineSource: null,
-            summary: null,
-        }));
-        return ok({ annotations });
-    },
-});