@inflexa-ai/harness 0.1.1 → 0.3.0

package/dist/tools/bio/search-ctx-exposure.js

@@ -1,176 +0,0 @@
-/**
- * searchCtxExposure — look up chemical exposure data from EPA's CTX
- * Exposure APIs.
- */
-import { ok } from "neverthrow";
-import { z } from "zod";
-import { defineTool } from "../define-tool.js";
-import { apiFetchValidated, describeApiError } from "../lib/api-utils.js";
-import { EPA_CCTE_BASE, getEpaCcteHeaders } from "../lib/toxcast-config.js";
-// The chemical-search endpoint returns rows the code reads `[0].dtxsid` from
-// after a length guard, so `dtxsid` stays required — a row missing it is a
-// contract break surfaced as `invalid_response`, not a silent `undefined`.
-const CtxChemicalSearchRowSchema = z.object({
-    dtxsid: z.string(),
-});
-// SEEM exposure-prediction wire shape (endpoint returns a single object or an
-// array). `probabilityPesticde` is the API's own misspelling, read as a
-// fallback before the corrected `probabilityPesticide`, so both stay modeled.
-const RawSeemPredictionSchema = z.object({
-    dtxsid: z.string().optional(),
-    productionVolume: z.number().nullable().optional(),
-    units: z.string().nullable().optional(),
-    probabilityDietary: z.number().nullable().optional(),
-    probabilityResidential: z.number().nullable().optional(),
-    probabilityPesticde: z.number().nullable().optional(),
-    probabilityPesticide: z.number().nullable().optional(),
-    probabilityIndustrial: z.number().nullable().optional(),
-});
-const RawHttkRowSchema = z.object({
-    parameter: z.string().nullable().optional(),
-    measured: z.number().nullable().optional(),
-    predicted: z.number().nullable().optional(),
-    units: z.string().nullable().optional(),
-    model: z.string().nullable().optional(),
-    species: z.string().nullable().optional(),
-    reference: z.string().nullable().optional(),
-});
-const RawFunctionalUseRowSchema = z.object({
-    functioncategory: z.string().nullable().optional(),
-    reportedfunction: z.string().nullable().optional(),
-    doctitle: z.string().nullable().optional(),
-});
-const RawProductDataRowSchema = z.object({
-    productname: z.string().nullable().optional(),
-    gencat: z.string().nullable().optional(),
-    prodfam: z.string().nullable().optional(),
-    prodtype: z.string().nullable().optional(),
-    centralweightfraction: z.number().nullable().optional(),
-    weightfractiontype: z.string().nullable().optional(),
-});
-export function createSearchCtxExposureTool(deps) {
-    return defineTool({
-        id: "search_ctx_exposure",
-        description: "Look up chemical exposure data from EPA's CTX Exposure APIs. Returns: " +
-            "SEEM general exposure predictions (estimated daily intake, exposure pathway probabilities), " +
-            "HTTK toxicokinetic parameters (Css, clearance, volume of distribution, protein binding), " +
-            "functional use categories, and product composition data. " +
-            "Use for exposure-based safety margin calculations (comparing ToxCast bioactivity AC50 " +
-            "against predicted human exposure), IVIVE context, and exposure pathway characterization. " +
-            "Requires EPA_CCTE_API_KEY environment variable.",
-        inputSchema: z.object({
-            query: z.string().describe("Chemical identifier: DTXSID (e.g. DTXSID7020182), CASRN (e.g. 80-05-7), " + "or chemical name (e.g. bisphenol A)"),
-            dataType: z
-                .enum(["seem", "httk", "functional-use", "product-data", "all"])
-                .default("all")
-                .describe("'seem' for SEEM exposure predictions, " +
-                "'httk' for toxicokinetic parameters, " +
-                "'functional-use' for chemical use categories, " +
-                "'product-data' for consumer product composition, " +
-                "'all' for combined results"),
-            limit: z.number().int().min(1).max(100).default(25).describe("Max results per category (for functional-use and product-data)"),
-        }),
-        execute: async ({ query, dataType = "all", limit = 25 }) => {
-            const headers = getEpaCcteHeaders(deps.apiKey);
-            const resolved = await resolveDtxsid(query, headers);
-            // "No chemical found" is an expected outcome — a data variant, not an error.
-            if (!resolved)
-                return ok({ found: false, query });
-            const { dtxsid } = resolved;
-            const result = { found: true, dtxsid };
-            const fetchers = [];
-            if (dataType === "seem" || dataType === "all") {
-                fetchers.push(fetchSeem(dtxsid, headers).then((v) => {
-                    result.seem = v;
-                }));
-            }
-            if (dataType === "httk" || dataType === "all") {
-                fetchers.push(fetchHttk(dtxsid, headers).then((v) => {
-                    result.httk = v;
-                }));
-            }
-            if (dataType === "functional-use" || dataType === "all") {
-                fetchers.push(fetchFunctionalUse(dtxsid, headers, limit).then((v) => {
-                    result.functionalUse = v;
-                }));
-            }
-            if (dataType === "product-data" || dataType === "all") {
-                fetchers.push(fetchProductData(dtxsid, headers, limit).then((v) => {
-                    result.productData = v;
-                }));
-            }
-            await Promise.all(fetchers);
-            return ok(result);
-        },
-    });
-}
-async function resolveDtxsid(query, headers) {
-    if (query.startsWith("DTXSID")) {
-        return { dtxsid: query };
-    }
-    const url = `${EPA_CCTE_BASE}/chemical/search/equal/${encodeURIComponent(query)}`;
-    const res = await apiFetchValidated(url, z.array(CtxChemicalSearchRowSchema), { headers });
-    if (res.isErr())
-        throw new Error(describeApiError(res.error));
-    if (!res.value?.length)
-        return null;
-    return { dtxsid: res.value[0].dtxsid };
-}
-async function fetchSeem(dtxsid, headers) {
-    const url = `${EPA_CCTE_BASE}/exposure/seem/general/search/by-dtxsid/${dtxsid}`;
-    const res = await apiFetchValidated(url, z.union([RawSeemPredictionSchema, z.array(RawSeemPredictionSchema)]), { headers });
-    if (res.isErr() || !res.value)
-        return undefined;
-    const d = Array.isArray(res.value) ? res.value[0] : res.value;
-    if (!d)
-        return undefined;
-    return {
-        dtxsid: d.dtxsid ?? dtxsid,
-        productionVolume: d.productionVolume ?? null,
-        units: d.units ?? "",
-        probabilityDietary: d.probabilityDietary ?? null,
-        probabilityResidential: d.probabilityResidential ?? null,
-        probabilityPesticide: d.probabilityPesticde ?? d.probabilityPesticide ?? null,
-        probabilityIndustrial: d.probabilityIndustrial ?? null,
-    };
-}
-async function fetchHttk(dtxsid, headers) {
-    const url = `${EPA_CCTE_BASE}/exposure/httk/search/by-dtxsid/${dtxsid}`;
-    const res = await apiFetchValidated(url, z.array(RawHttkRowSchema), { headers });
-    if (res.isErr() || !Array.isArray(res.value))
-        return [];
-    return res.value.map((r) => ({
-        parameter: r.parameter ?? "",
-        measured: r.measured ?? null,
-        predicted: r.predicted ?? null,
-        units: r.units ?? "",
-        model: r.model ?? "",
-        species: r.species ?? "",
-        reference: r.reference ?? "",
-    }));
-}
-async function fetchFunctionalUse(dtxsid, headers, limit) {
-    const url = `${EPA_CCTE_BASE}/exposure/functional-use/search/by-dtxsid/${dtxsid}`;
-    const res = await apiFetchValidated(url, z.array(RawFunctionalUseRowSchema), { headers });
-    if (res.isErr() || !Array.isArray(res.value))
-        return [];
-    return res.value.slice(0, limit).map((r) => ({
-        functionCategory: r.functioncategory ?? "",
-        reportedFunction: r.reportedfunction ?? "",
-        docTitle: r.doctitle ?? "",
-    }));
-}
-async function fetchProductData(dtxsid, headers, limit) {
-    const url = `${EPA_CCTE_BASE}/exposure/product-data/search/by-dtxsid/${dtxsid}`;
-    const res = await apiFetchValidated(url, z.array(RawProductDataRowSchema), { headers });
-    if (res.isErr() || !Array.isArray(res.value))
-        return [];
-    return res.value.slice(0, limit).map((r) => ({
-        productName: r.productname ?? "",
-        generalCategory: r.gencat ?? "",
-        productFamily: r.prodfam ?? "",
-        productType: r.prodtype ?? "",
-        centralWeightFraction: r.centralweightfraction ?? null,
-        weightFractionType: r.weightfractiontype ?? "",
-    }));
-}

package/dist/tools/bio/search-ctx-hazard.d.ts

@@ -1,111 +0,0 @@
-/**
- * searchCtxHazard — search EPA CTX Hazard APIs (ToxValDB, ToxRefDB) for
- * toxicological hazard data on a chemical.
- */
-import { z } from "zod";
-declare const ToxValSchema: z.ZodPipe<z.ZodObject<{
-    source: z.ZodOptional<z.ZodNullable<z.ZodString>>;
-    toxvalType: z.ZodOptional<z.ZodNullable<z.ZodString>>;
-    toxvalNumeric: z.ZodOptional<z.ZodUnknown>;
-    toxvalUnits: z.ZodOptional<z.ZodNullable<z.ZodString>>;
-    studyType: z.ZodOptional<z.ZodNullable<z.ZodString>>;
-    studyDurationClass: z.ZodOptional<z.ZodNullable<z.ZodString>>;
-    speciesCommon: z.ZodOptional<z.ZodNullable<z.ZodString>>;
-    exposureRoute: z.ZodOptional<z.ZodNullable<z.ZodString>>;
-    toxicologicalEffect: z.ZodOptional<z.ZodNullable<z.ZodString>>;
-    riskAssessmentClass: z.ZodOptional<z.ZodNullable<z.ZodString>>;
-    humanEco: z.ZodOptional<z.ZodNullable<z.ZodString>>;
-    year: z.ZodOptional<z.ZodUnknown>;
-    quality: z.ZodOptional<z.ZodNullable<z.ZodString>>;
-}, z.core.$strip>, z.ZodTransform<{
-    source: string;
-    toxvalType: string;
-    toxvalNumeric: number | null;
-    toxvalUnits: string;
-    studyType: string;
-    studyDurationClass: string;
-    species: string;
-    exposureRoute: string;
-    toxicologicalEffect: string;
-    riskAssessmentClass: string;
-    humanEco: string;
-    year: number | null;
-    quality: string;
-}, {
-    source?: string | null | undefined;
-    toxvalType?: string | null | undefined;
-    toxvalNumeric?: unknown;
-    toxvalUnits?: string | null | undefined;
-    studyType?: string | null | undefined;
-    studyDurationClass?: string | null | undefined;
-    speciesCommon?: string | null | undefined;
-    exposureRoute?: string | null | undefined;
-    toxicologicalEffect?: string | null | undefined;
-    riskAssessmentClass?: string | null | undefined;
-    humanEco?: string | null | undefined;
-    year?: unknown;
-    quality?: string | null | undefined;
-}>>;
-type ToxValEntry = z.infer<typeof ToxValSchema>;
-declare const GenetoxSchema: z.ZodPipe<z.ZodObject<{
-    source: z.ZodOptional<z.ZodNullable<z.ZodString>>;
-    assayCategory: z.ZodOptional<z.ZodNullable<z.ZodString>>;
-    assayType: z.ZodOptional<z.ZodNullable<z.ZodString>>;
-    metabolicActivation: z.ZodOptional<z.ZodNullable<z.ZodString>>;
-    species: z.ZodOptional<z.ZodNullable<z.ZodString>>;
-    overallResult: z.ZodOptional<z.ZodNullable<z.ZodString>>;
-    year: z.ZodOptional<z.ZodUnknown>;
-}, z.core.$strip>, z.ZodTransform<{
-    source: string;
-    assayCategory: string;
-    assayType: string;
-    metabolicActivation: string;
-    species: string;
-    overallResult: string;
-    year: number | null;
-}, {
-    source?: string | null | undefined;
-    assayCategory?: string | null | undefined;
-    assayType?: string | null | undefined;
-    metabolicActivation?: string | null | undefined;
-    species?: string | null | undefined;
-    overallResult?: string | null | undefined;
-    year?: unknown;
-}>>;
-type GenetoxSummary = z.infer<typeof GenetoxSchema>;
-declare const CancerSchema: z.ZodPipe<z.ZodObject<{
-    source: z.ZodOptional<z.ZodNullable<z.ZodString>>;
-    classification: z.ZodOptional<z.ZodNullable<z.ZodString>>;
-    cancerClassification: z.ZodOptional<z.ZodNullable<z.ZodString>>;
-    url: z.ZodOptional<z.ZodNullable<z.ZodString>>;
-}, z.core.$strip>, z.ZodTransform<{
-    source: string;
-    classification: string;
-    url: string;
-}, {
-    source?: string | null | undefined;
-    classification?: string | null | undefined;
-    cancerClassification?: string | null | undefined;
-    url?: string | null | undefined;
-}>>;
-type CancerSummary = z.infer<typeof CancerSchema>;
-interface CtxHazardOutput {
-    found: true;
-    dtxsid: string;
-    preferredName: string;
-    toxval?: ToxValEntry[];
-    genetox?: GenetoxSummary[];
-    cancer?: CancerSummary[];
-}
-type CtxHazardResult = {
-    found: false;
-    query: string;
-} | CtxHazardOutput;
-export declare function createSearchCtxHazardTool(deps: {
-    apiKey: string;
-}): import("../define-tool.js").Tool<{
-    query: string;
-    dataType: "toxval" | "genetox" | "cancer" | "all";
-    limit: number;
-}, CtxHazardResult>;
-export {};

package/dist/tools/bio/search-ctx-hazard.js

@@ -1,178 +0,0 @@
-/**
- * searchCtxHazard — search EPA CTX Hazard APIs (ToxValDB, ToxRefDB) for
- * toxicological hazard data on a chemical.
- */
-import { ok } from "neverthrow";
-import { z } from "zod";
-import { defineTool } from "../define-tool.js";
-import { apiFetchValidated, describeApiError } from "../lib/api-utils.js";
-import { EPA_CCTE_BASE, getEpaCcteHeaders } from "../lib/toxcast-config.js";
-// Each schema below both validates one raw CTX hazard row and normalizes it
-// into the curated output shape via `.transform`; `z.infer` is that output
-// type. Every wire field is optional (the API omits absent values); the two
-// numeric fields the API sends as string-or-number stay `z.unknown()` so
-// `toNumberOrNull` can coerce them without the schema rejecting the row.
-const ToxValSchema = z
-    .object({
-    source: z.string().nullable().optional(),
-    toxvalType: z.string().nullable().optional(),
-    toxvalNumeric: z.unknown().optional(),
-    toxvalUnits: z.string().nullable().optional(),
-    studyType: z.string().nullable().optional(),
-    studyDurationClass: z.string().nullable().optional(),
-    speciesCommon: z.string().nullable().optional(),
-    exposureRoute: z.string().nullable().optional(),
-    toxicologicalEffect: z.string().nullable().optional(),
-    riskAssessmentClass: z.string().nullable().optional(),
-    humanEco: z.string().nullable().optional(),
-    year: z.unknown().optional(),
-    quality: z.string().nullable().optional(),
-})
-    .transform((r) => ({
-    source: r.source ?? "",
-    toxvalType: r.toxvalType ?? "",
-    toxvalNumeric: toNumberOrNull(r.toxvalNumeric),
-    toxvalUnits: r.toxvalUnits ?? "",
-    studyType: r.studyType ?? "",
-    studyDurationClass: r.studyDurationClass ?? "",
-    species: r.speciesCommon ?? "",
-    exposureRoute: r.exposureRoute ?? "",
-    toxicologicalEffect: r.toxicologicalEffect ?? "",
-    riskAssessmentClass: r.riskAssessmentClass ?? "",
-    humanEco: r.humanEco ?? "",
-    year: toNumberOrNull(r.year),
-    quality: r.quality ?? "",
-}));
-const GenetoxSchema = z
-    .object({
-    source: z.string().nullable().optional(),
-    assayCategory: z.string().nullable().optional(),
-    assayType: z.string().nullable().optional(),
-    metabolicActivation: z.string().nullable().optional(),
-    species: z.string().nullable().optional(),
-    overallResult: z.string().nullable().optional(),
-    year: z.unknown().optional(),
-})
-    .transform((r) => ({
-    source: r.source ?? "",
-    assayCategory: r.assayCategory ?? "",
-    assayType: r.assayType ?? "",
-    metabolicActivation: r.metabolicActivation ?? "",
-    species: r.species ?? "",
-    overallResult: r.overallResult ?? "",
-    year: toNumberOrNull(r.year),
-}));
-const CancerSchema = z
-    .object({
-    source: z.string().nullable().optional(),
-    classification: z.string().nullable().optional(),
-    cancerClassification: z.string().nullable().optional(),
-    url: z.string().nullable().optional(),
-})
-    .transform((r) => ({
-    source: r.source ?? "",
-    classification: r.classification ?? r.cancerClassification ?? "",
-    url: r.url ?? "",
-}));
-// The chemical-search endpoint returns rows the code reads `dtxsid` from
-// unguarded, so `dtxsid` stays required — a row missing it is a contract break
-// surfaced as `invalid_response`, not a silent `undefined`.
-const CtxChemicalSearchRowSchema = z.object({
-    dtxsid: z.string(),
-    preferredName: z.string().nullable().optional(),
-});
-export function createSearchCtxHazardTool(deps) {
-    return defineTool({
-        id: "search_ctx_hazard",
-        description: "Search EPA CTX Hazard APIs (ToxValDB, ToxRefDB) for toxicological hazard data on a chemical. " +
-            "Returns in-vivo toxicity values (NOAELs, LOAELs, LD50s, BMDs), " +
-            "genetox summaries, and cancer classifications. " +
-            "Use to assess toxicological hazard profile for safety evaluation. " +
-            "Requires EPA_CCTE_API_KEY environment variable.",
-        inputSchema: z.object({
-            query: z.string().describe("Chemical identifier: DTXSID (e.g. DTXSID7020182), CASRN (e.g. 80-05-7), " + "or chemical name (e.g. bisphenol A)"),
-            dataType: z
-                .enum(["toxval", "genetox", "cancer", "all"])
-                .default("all")
-                .describe("'toxval' for ToxValDB dose-response data (NOAELs, LOAELs, LD50s), " +
-                "'genetox' for genotoxicity summaries, " +
-                "'cancer' for cancer classifications, " +
-                "'all' for combined results"),
-            limit: z.number().int().min(1).max(100).default(30).describe("Max results per category"),
-        }),
-        execute: async ({ query, dataType = "all", limit = 30 }) => {
-            const headers = getEpaCcteHeaders(deps.apiKey);
-            const resolved = await resolveDtxsid(query, headers);
-            // "No chemical found" is an expected outcome — a data variant, not an error.
-            if (!resolved)
-                return ok({ found: false, query });
-            const { dtxsid, preferredName } = resolved;
-            const result = {
-                found: true,
-                dtxsid,
-                preferredName,
-            };
-            const fetchers = [];
-            if (dataType === "toxval" || dataType === "all") {
-                fetchers.push(fetchToxval(dtxsid, headers, limit).then((v) => {
-                    result.toxval = v;
-                }));
-            }
-            if (dataType === "genetox" || dataType === "all") {
-                fetchers.push(fetchGenetox(dtxsid, headers, limit).then((v) => {
-                    result.genetox = v;
-                }));
-            }
-            if (dataType === "cancer" || dataType === "all") {
-                fetchers.push(fetchCancer(dtxsid, headers).then((v) => {
-                    result.cancer = v;
-                }));
-            }
-            await Promise.all(fetchers);
-            return ok(result);
-        },
-    });
-}
-async function resolveDtxsid(query, headers) {
-    if (query.startsWith("DTXSID")) {
-        return { dtxsid: query, preferredName: query };
-    }
-    const url = `${EPA_CCTE_BASE}/chemical/search/equal/${encodeURIComponent(query)}`;
-    const res = await apiFetchValidated(url, z.array(CtxChemicalSearchRowSchema), { headers });
-    if (res.isErr())
-        throw new Error(describeApiError(res.error));
-    if (!res.value?.length)
-        return null;
-    const chem = res.value[0];
-    return {
-        dtxsid: chem.dtxsid,
-        preferredName: chem.preferredName ?? query,
-    };
-}
-async function fetchToxval(dtxsid, headers, limit) {
-    const url = `${EPA_CCTE_BASE}/hazard/toxval/search/by-dtxsid/${dtxsid}`;
-    const res = await apiFetchValidated(url, z.array(ToxValSchema), { headers });
-    if (res.isErr() || !Array.isArray(res.value))
-        return [];
-    return res.value.slice(0, limit);
-}
-function toNumberOrNull(v) {
-    if (v == null || v === "")
-        return null;
-    const n = typeof v === "number" ? v : Number(v);
-    return Number.isFinite(n) ? n : null;
-}
-async function fetchGenetox(dtxsid, headers, limit) {
-    const url = `${EPA_CCTE_BASE}/hazard/genetox/summary/search/by-dtxsid/${dtxsid}`;
-    const res = await apiFetchValidated(url, z.array(GenetoxSchema), { headers });
-    if (res.isErr() || !Array.isArray(res.value))
-        return [];
-    return res.value.slice(0, limit);
-}
-async function fetchCancer(dtxsid, headers) {
-    const url = `${EPA_CCTE_BASE}/hazard/cancer-summary/search/by-dtxsid/${dtxsid}`;
-    const res = await apiFetchValidated(url, z.array(CancerSchema), { headers });
-    if (res.isErr() || !Array.isArray(res.value))
-        return [];
-    return res.value;
-}

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

@@ -1,11 +0,0 @@
-/**
- * searchOpenTargets — query Open Targets Platform for target-disease
- * associations, genetic evidence, tractability, and known drug scores.
- */
-export declare const searchOpenTargetsTool: import("../define-tool.js").Tool<{
-    query: string;
-    searchType: "target" | "disease";
-    limit: number;
-}, {
-    associations: import("../lib/opentargets-client.js").Association[];
-}>;

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

@@ -1,25 +0,0 @@
-/**
- * searchOpenTargets — query Open Targets Platform for target-disease
- * associations, genetic evidence, tractability, and known drug scores.
- */
-import { ok } from "neverthrow";
-import { z } from "zod";
-import { defineTool } from "../define-tool.js";
-import { searchDiseaseAssociations, searchTargetAssociations } from "../lib/opentargets-client.js";
-export const searchOpenTargetsTool = defineTool({
-    id: "search_opentargets",
-    description: "Search Open Targets Platform for target-disease associations, genetic evidence, tractability, and known drug scores. Query by Ensembl gene ID (target mode) or EFO disease ID (disease mode).",
-    inputSchema: z.object({
-        query: z.string().describe("Ensembl gene ID (e.g. ENSG00000141510) or EFO disease ID (e.g. EFO_0000311)"),
-        searchType: z.enum(["target", "disease"]).describe("'target' to find diseases for a gene, 'disease' to find targets for a disease"),
-        limit: z.number().int().min(1).max(100).default(25).describe("Max results to return"),
-    }),
-    execute: async ({ query, searchType, limit = 25 }) => {
-        if (searchType === "target") {
-            const targetInfo = await searchTargetAssociations(query, limit);
-            return ok({ targetInfo, associations: targetInfo?.associations ?? [] });
-        }
-        const associations = await searchDiseaseAssociations(query, limit);
-        return ok({ associations });
-    },
-});

package/dist/tools/bio/search-pubchem-compound.d.ts

@@ -1,26 +0,0 @@
-/**
- * searchPubchemCompound tool — resolve compounds against PubChem's 110M+ database.
- *
- * Supports search by name, SMILES, InChI, InChIKey, or CID.
- * Returns compound identity and computed molecular properties.
- */
-export declare const searchPubchemCompoundTool: import("../define-tool.js").Tool<{
-    query: string;
-    searchBy: "name" | "smiles" | "inchikey" | "cid" | "inchi";
-}, {
-    results: {
-        cid: number;
-        canonicalSmiles: string | null;
-        molecularFormula: string | null;
-        molecularWeight: number | null;
-        iupacName: string | null;
-        inchi: string | null;
-        inchiKey: string | null;
-        xlogp: number | null;
-        tpsa: number | null;
-        hbondDonorCount: number | null;
-        hbondAcceptorCount: number | null;
-        rotatableBondCount: number | null;
-        complexity: number | null;
-    }[];
-}>;

package/dist/tools/bio/search-pubchem-compound.js

@@ -1,110 +0,0 @@
-/**
- * searchPubchemCompound tool — resolve compounds against PubChem's 110M+ database.
- *
- * Supports search by name, SMILES, InChI, InChIKey, or CID.
- * Returns compound identity and computed molecular properties.
- */
-import { ok } from "neverthrow";
-import { z } from "zod";
-import { defineTool } from "../define-tool.js";
-import { apiFetchValidated, describeApiError } from "../lib/api-utils.js";
-import { PUBCHEM_HEADERS as HEADERS, PUBCHEM_BASE } from "../lib/pubchem-config.js";
-const PROPERTY_LIST = [
-    "MolecularFormula",
-    "MolecularWeight",
-    "CanonicalSMILES",
-    "InChI",
-    "InChIKey",
-    "IUPACName",
-    "XLogP",
-    "TPSA",
-    "HBondDonorCount",
-    "HBondAcceptorCount",
-    "RotatableBondCount",
-    "Complexity",
-].join(",");
-// A single schema that both validates and normalizes one PUG-REST property row:
-// the `.object(...)` half is the wire shape (every field optional — PubChem
-// omits absent properties), the `.transform(...)` half maps it to the camelCase
-// `Compound` we return. Parsing IS the validation, and because the transform
-// rides on the schema, `z.infer` below is the OUTPUT type — no separate raw
-// interface or mapper.
-const PugPropertyRowSchema = z
-    .object({
-    CID: z.number().optional(),
-    CanonicalSMILES: z.string().optional(),
-    MolecularFormula: z.string().optional(),
-    // PUG-REST serializes MolecularWeight as a string (e.g. "180.16") to
-    // preserve significant figures; accept both and let the transform's
-    // `Number(...)` normalize it.
-    MolecularWeight: z.union([z.number(), z.string()]).optional(),
-    IUPACName: z.string().optional(),
-    InChI: z.string().optional(),
-    InChIKey: z.string().optional(),
-    XLogP: z.number().optional(),
-    TPSA: z.number().optional(),
-    HBondDonorCount: z.number().optional(),
-    HBondAcceptorCount: z.number().optional(),
-    RotatableBondCount: z.number().optional(),
-    Complexity: z.number().optional(),
-})
-    .transform((raw) => ({
-    cid: raw.CID ?? 0,
-    canonicalSmiles: raw.CanonicalSMILES ?? null,
-    molecularFormula: raw.MolecularFormula ?? null,
-    molecularWeight: raw.MolecularWeight != null ? Number(raw.MolecularWeight) : null,
-    iupacName: raw.IUPACName ?? null,
-    inchi: raw.InChI ?? null,
-    inchiKey: raw.InChIKey ?? null,
-    xlogp: raw.XLogP ?? null,
-    tpsa: raw.TPSA ?? null,
-    hbondDonorCount: raw.HBondDonorCount ?? null,
-    hbondAcceptorCount: raw.HBondAcceptorCount ?? null,
-    rotatableBondCount: raw.RotatableBondCount ?? null,
-    complexity: raw.Complexity ?? null,
-}));
-const PubChemPropertyResponseSchema = z.object({
-    PropertyTable: z.object({ Properties: z.array(PugPropertyRowSchema).optional() }).optional(),
-});
-/** Build the PUG-REST URL path segment for the given search type. */
-function buildNamespace(searchBy, query) {
-    switch (searchBy) {
-        case "name":
-            return `compound/name/${encodeURIComponent(query)}`;
-        case "smiles":
-            return `compound/smiles/${encodeURIComponent(query)}`;
-        case "inchi":
-            return `compound/inchi/${encodeURIComponent(query)}`;
-        case "inchikey":
-            return `compound/inchikey/${encodeURIComponent(query)}`;
-        case "cid":
-            return `compound/cid/${encodeURIComponent(query)}`;
-        default:
-            return `compound/name/${encodeURIComponent(query)}`;
-    }
-}
-export const searchPubchemCompoundTool = defineTool({
-    id: "search_pubchem_compound",
-    description: "Search PubChem for a compound by name, SMILES, InChI, InChIKey, or CID. " +
-        "Returns compound identity (CID, SMILES, InChI, IUPAC name) and computed properties " +
-        "(molecular weight, XLogP, TPSA, HBD, HBA, rotatable bonds, complexity). " +
-        "PubChem covers 110M+ compounds — use when ChEMBL doesn't find the compound.",
-    inputSchema: z.object({
-        query: z.string().min(1).describe("Search term: compound name, SMILES, InChI, InChIKey, or CID"),
-        searchBy: z.enum(["name", "smiles", "inchi", "inchikey", "cid"]).describe("Identifier type for the query"),
-    }),
-    execute: async ({ query, searchBy }) => {
-        const namespace = buildNamespace(searchBy, query);
-        const url = `${PUBCHEM_BASE}/${namespace}/property/${PROPERTY_LIST}/JSON`;
-        const res = await apiFetchValidated(url, PubChemPropertyResponseSchema, { headers: HEADERS });
-        if (res.isErr()) {
-            // PubChem returns 404 when the query matches no compound — expected.
-            if (res.error.type === "http_status" && res.error.status === 404)
-                return ok({ results: [] });
-            throw new Error(describeApiError(res.error));
-        }
-        // Already validated + normalized by PugPropertyRowSchema's transform.
-        const rows = res.value.PropertyTable?.Properties ?? [];
-        return ok({ results: rows });
-    },
-});

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

@@ -1,17 +0,0 @@
-/**
- * searchPubMed — search PubMed via NCBI E-utilities.
- */
-export declare function createSearchPubMedTool(deps: {
-    ncbiApiKey?: string;
-}): import("../define-tool.js").Tool<{
-    query: string;
-    maxResults: number;
-    sort: "date" | "relevance";
-    dateRange?: {
-        from: string;
-        to: string;
-    } | undefined;
-}, {
-    totalFound: number;
-    results: import("../lib/ncbi-utils.js").PubMedSummary[];
-}>;