@cyanheads/ensembl-mcp-server 0.1.1

package/dist/services/ensembl/ensembl-service.js

@@ -0,0 +1,366 @@
+/**
+ * @fileoverview Ensembl REST API service — HTTP client, rate-limit-aware retry,
+ * error normalization, and typed methods per endpoint family.
+ * @module services/ensembl/ensembl-service
+ */
+import { notFound, serviceUnavailable, validationError } from '@cyanheads/mcp-ts-core/errors';
+import { requestContextService, withRetry } from '@cyanheads/mcp-ts-core/utils';
+import { getServerConfig } from '../../config/server-config.js';
+// --- Normalizers ---
+function normalizeGene(raw) {
+    const desc = raw.description?.split('[')[0]?.trim();
+    return {
+        id: raw.id,
+        ...(raw.species && { species: raw.species }),
+        ...(raw.display_name && { displayName: raw.display_name }),
+        ...(desc ? { description: desc } : {}),
+        ...(raw.biotype && { biotype: raw.biotype }),
+        ...(raw.seq_region_name && { chromosome: raw.seq_region_name }),
+        ...(typeof raw.start === 'number' && { start: raw.start }),
+        ...(typeof raw.end === 'number' && { end: raw.end }),
+        ...(typeof raw.strand === 'number' && { strand: raw.strand }),
+        ...(raw.assembly_name && { assemblyName: raw.assembly_name }),
+        ...(raw.Transcript && {
+            transcripts: raw.Transcript.map((t) => ({
+                id: t.id,
+                ...(t.display_name && { displayName: t.display_name }),
+                ...(t.biotype && { biotype: t.biotype }),
+                isCanonical: t.is_canonical === 1,
+                ...(typeof t.start === 'number' && { start: t.start }),
+                ...(typeof t.end === 'number' && { end: t.end }),
+                ...(typeof t.strand === 'number' && { strand: t.strand }),
+                ...(typeof t.length === 'number' && { lengthInBp: t.length }),
+            })),
+        }),
+    };
+}
+function normalizeTranscript(raw) {
+    return {
+        id: raw.id,
+        ...(raw.Parent && { parentGeneId: raw.Parent }),
+        ...(raw.display_name && { displayName: raw.display_name }),
+        ...(raw.biotype && { biotype: raw.biotype }),
+        isCanonical: raw.is_canonical === 1,
+        ...(raw.species && { species: raw.species }),
+        ...(raw.seq_region_name && { chromosome: raw.seq_region_name }),
+        ...(typeof raw.start === 'number' && { start: raw.start }),
+        ...(typeof raw.end === 'number' && { end: raw.end }),
+        ...(typeof raw.strand === 'number' && { strand: raw.strand }),
+        ...(raw.assembly_name && { assemblyName: raw.assembly_name }),
+        ...(typeof raw.length === 'number' && { lengthInBp: raw.length }),
+    };
+}
+function normalizeSequence(raw, type) {
+    return {
+        id: raw.id,
+        type,
+        seq: raw.seq,
+        lengthInBp: raw.seq.length,
+        ...(raw.desc && { description: raw.desc }),
+    };
+}
+function normalizeOverlapFeature(raw) {
+    return {
+        ...(raw.id && { id: raw.id }),
+        ...(raw.external_name && { name: raw.external_name }),
+        featureType: raw.feature_type ?? 'unknown',
+        ...(raw.biotype && { biotype: raw.biotype }),
+        chromosome: raw.seq_region_name ?? '',
+        start: raw.start ?? 0,
+        end: raw.end ?? 0,
+        ...(typeof raw.strand === 'number' && { strand: raw.strand }),
+        ...(raw.description && { description: raw.description }),
+        ...(raw.consequence_type && { consequenceType: raw.consequence_type }),
+        ...(raw.clinical_significance?.length && {
+            clinicalSignificance: raw.clinical_significance,
+        }),
+    };
+}
+function normalizeVep(raw) {
+    return {
+        ...(raw.input && { input: raw.input }),
+        ...(raw.seq_region_name && { chromosome: raw.seq_region_name }),
+        ...(typeof raw.start === 'number' && { start: raw.start }),
+        ...(typeof raw.end === 'number' && { end: raw.end }),
+        ...(raw.assembly_name && { assemblyName: raw.assembly_name }),
+        ...(raw.most_severe_consequence && {
+            mostSevereConsequence: raw.most_severe_consequence,
+        }),
+        transcriptConsequences: (raw.transcript_consequences ?? []).map((tc) => ({
+            ...(tc.transcript_id && { transcriptId: tc.transcript_id }),
+            ...(tc.gene_id && { geneId: tc.gene_id }),
+            ...(tc.gene_symbol && { geneSymbol: tc.gene_symbol }),
+            consequenceTerms: tc.consequence_terms ?? [],
+            ...(tc.impact && { impact: tc.impact }),
+            ...(tc.biotype && { biotype: tc.biotype }),
+            ...(tc.hgvsc && { hgvsc: tc.hgvsc }),
+            ...(tc.hgvsp && { hgvsp: tc.hgvsp }),
+            ...(tc.amino_acids && { aminoAcids: tc.amino_acids }),
+            ...(tc.sift && { sift: tc.sift }),
+            ...(tc.polyphen && { polyphen: tc.polyphen }),
+        })),
+        colocatedVariants: (raw.colocated_variants ?? []).map((cv) => ({
+            ...(cv.id && { id: cv.id }),
+            ...(cv.allele_string && { alleleString: cv.allele_string }),
+            ...(cv.clinical_significance?.length && {
+                clinicalSignificance: cv.clinical_significance,
+            }),
+            ...(cv.pubmed?.length && { pubmed: cv.pubmed }),
+        })),
+    };
+}
+function normalizeHomology(raw, sourceId) {
+    const dataEntry = raw.data?.find((d) => d.id === sourceId) ?? raw.data?.[0];
+    if (!dataEntry?.homologies)
+        return [];
+    return dataEntry.homologies.map((h) => ({
+        targetId: h.target?.id ?? h.id,
+        ...(h.target?.species
+            ? { targetSpecies: h.target.species }
+            : h.species
+                ? { targetSpecies: h.species }
+                : {}),
+        ...(h.type && { type: h.type }),
+        ...(typeof (h.target?.perc_id ?? h.perc_id) === 'number' && {
+            percId: h.target?.perc_id ?? h.perc_id,
+        }),
+        ...(typeof (h.target?.perc_pos ?? h.perc_pos) === 'number' && {
+            percPos: h.target?.perc_pos ?? h.perc_pos,
+        }),
+        ...(h.taxonomy_level && { taxonomyLevel: h.taxonomy_level }),
+    }));
+}
+function normalizeXref(raw) {
+    return {
+        ...(raw.dbname && { dbname: raw.dbname }),
+        ...(raw.db_display_name && { dbDisplayName: raw.db_display_name }),
+        ...(raw.primary_id && { primaryId: raw.primary_id }),
+        ...(raw.display_id && { displayId: raw.display_id }),
+        ...(raw.description && { description: raw.description }),
+    };
+}
+function normalizeSpecies(raw) {
+    return (raw.species ?? []).map((s) => ({
+        name: s.name ?? '',
+        ...(s.display_name && { displayName: s.display_name }),
+        ...(s.common_name && { commonName: s.common_name }),
+        ...(s.taxon_id && { taxonId: s.taxon_id }),
+        ...(s.assembly && { assembly: s.assembly }),
+        ...(s.division && { division: s.division }),
+    }));
+}
+// --- Service ---
+export class EnsemblService {
+    baseUrl;
+    constructor(_config, _storage) {
+        this.baseUrl = getServerConfig().baseUrl;
+    }
+    // --- Core fetch ---
+    async fetchJson(path, ctx, options) {
+        const url = `${this.baseUrl}${path}`;
+        const method = options?.method ?? 'GET';
+        const fetchOptions = {
+            method,
+            headers: {
+                Accept: 'application/json',
+                'Content-Type': 'application/json',
+            },
+            signal: options?.signal ?? ctx.signal,
+        };
+        if (options?.body !== undefined) {
+            fetchOptions.body = JSON.stringify(options.body);
+        }
+        ctx.log.debug('Ensembl request', { url, method });
+        const response = await fetch(url, fetchOptions);
+        if (response.status === 429) {
+            const retryAfter = response.headers.get('Retry-After');
+            throw serviceUnavailable(`Ensembl rate limit exceeded.${retryAfter ? ` Retry after ${retryAfter}s.` : ''}`, { retryAfter: retryAfter ? Number(retryAfter) : undefined });
+        }
+        const text = await response.text();
+        // Detect HTML error pages
+        if (/^\s*<(!DOCTYPE\s+html|html[\s>])/i.test(text)) {
+            throw serviceUnavailable('Ensembl API returned HTML instead of JSON — service may be degraded.');
+        }
+        let parsed;
+        try {
+            parsed = JSON.parse(text);
+        }
+        catch {
+            throw serviceUnavailable(`Ensembl API returned unparseable response.`, {
+                status: response.status,
+            });
+        }
+        // Ensembl error envelope: { error: "..." }
+        if (typeof parsed === 'object' &&
+            parsed !== null &&
+            'error' in parsed &&
+            typeof parsed.error === 'string') {
+            const msg = parsed.error;
+            // Classify based on message content
+            if (/not found|not exist|does not exist|no stable id/i.test(msg)) {
+                throw notFound(msg);
+            }
+            if (/invalid|unrecognized|malformed|bad request/i.test(msg)) {
+                throw validationError(msg);
+            }
+            // Generic API error — treat as not found for ID-based lookups
+            throw notFound(msg);
+        }
+        if (!response.ok) {
+            throw serviceUnavailable(`Ensembl API returned HTTP ${response.status}.`, {
+                status: response.status,
+            });
+        }
+        return parsed;
+    }
+    // --- withRetry wrapper ---
+    fetchWithRetry(path, ctx, options) {
+        const operation = `EnsemblService.fetch:${path.split('?')[0]}`;
+        const reqCtx = requestContextService.createRequestContext({
+            operation,
+            parentContext: { requestId: ctx.requestId },
+        });
+        return withRetry(() => this.fetchJson(path, ctx, options), {
+            operation,
+            context: reqCtx,
+            baseDelayMs: 1000,
+            signal: ctx.signal,
+        });
+    }
+    // --- Gene lookup ---
+    async lookupGene(symbol, species, expandTranscripts, ctx) {
+        const expand = expandTranscripts ? '?expand=1' : '';
+        const path = `/lookup/symbol/${encodeURIComponent(species)}/${encodeURIComponent(symbol)}${expand}`;
+        const raw = await this.fetchWithRetry(path, ctx);
+        return normalizeGene(raw);
+    }
+    async lookupGeneById(id, expandTranscripts, ctx) {
+        const expand = expandTranscripts ? '?expand=1' : '';
+        const path = `/lookup/id/${encodeURIComponent(id)}${expand}`;
+        const raw = await this.fetchWithRetry(path, ctx);
+        return normalizeGene(raw);
+    }
+    async lookupGenesBatch(ids, expandTranscripts, ctx) {
+        const body = { ids };
+        if (expandTranscripts)
+            body.expand = 1;
+        const raw = await this.fetchWithRetry('/lookup/id', ctx, {
+            method: 'POST',
+            body,
+        });
+        const result = new Map();
+        for (const [k, v] of Object.entries(raw)) {
+            if (v)
+                result.set(k, normalizeGene(v));
+        }
+        return result;
+    }
+    async lookupSymbolsBatch(symbols, species, expandTranscripts, ctx) {
+        const body = { symbols };
+        if (expandTranscripts)
+            body.expand = 1;
+        const raw = await this.fetchWithRetry(`/lookup/symbol/${encodeURIComponent(species)}`, ctx, { method: 'POST', body });
+        const result = new Map();
+        for (const [k, v] of Object.entries(raw)) {
+            if (v)
+                result.set(k, normalizeGene(v));
+        }
+        return result;
+    }
+    // --- Transcript lookup ---
+    async lookupTranscript(id, ctx) {
+        const path = `/lookup/id/${encodeURIComponent(id)}`;
+        const raw = await this.fetchWithRetry(path, ctx);
+        return normalizeTranscript(raw);
+    }
+    // --- Sequence ---
+    async getSequenceById(id, type, ctx) {
+        const path = `/sequence/id/${encodeURIComponent(id)}?type=${encodeURIComponent(type)}`;
+        const raw = await this.fetchWithRetry(path, ctx);
+        return normalizeSequence(raw, type);
+    }
+    async getSequenceByRegion(species, region, expand5prime, expand3prime, ctx) {
+        let path = `/sequence/region/${encodeURIComponent(species)}/${encodeURIComponent(region)}`;
+        const params = [];
+        if (expand5prime > 0)
+            params.push(`expand_5prime=${expand5prime}`);
+        if (expand3prime > 0)
+            params.push(`expand_3prime=${expand3prime}`);
+        if (params.length > 0)
+            path += `?${params.join('&')}`;
+        const raw = await this.fetchWithRetry(path, ctx);
+        return normalizeSequence(raw, 'genomic');
+    }
+    // --- Overlap/region ---
+    async queryRegion(species, region, features, biotype, ctx) {
+        const featureParams = features.map((f) => `feature=${encodeURIComponent(f)}`).join('&');
+        let path = `/overlap/region/${encodeURIComponent(species)}/${encodeURIComponent(region)}?${featureParams}`;
+        if (biotype)
+            path += `&biotype=${encodeURIComponent(biotype)}`;
+        const raw = await this.fetchWithRetry(path, ctx);
+        if (!Array.isArray(raw))
+            return [];
+        return raw.map(normalizeOverlapFeature);
+    }
+    // --- VEP ---
+    async predictVariantHgvs(notation, species, ctx) {
+        const path = `/vep/${encodeURIComponent(species)}/hgvs/${encodeURIComponent(notation)}`;
+        const raw = await this.fetchWithRetry(path, ctx);
+        if (!Array.isArray(raw))
+            return [];
+        return raw.map(normalizeVep);
+    }
+    async predictVariantRegion(chr, start, end, strand, allele, species, ctx) {
+        const regionAllele = `${encodeURIComponent(`${chr}:${start}:${end}:${strand}`)}/${encodeURIComponent(allele)}`;
+        const path = `/vep/${encodeURIComponent(species)}/region/${regionAllele}`;
+        const raw = await this.fetchWithRetry(path, ctx);
+        if (!Array.isArray(raw))
+            return [];
+        return raw.map(normalizeVep);
+    }
+    // --- Homology ---
+    async getHomologyBySymbol(symbol, species, type, targetSpecies, ctx) {
+        let path = `/homology/symbol/${encodeURIComponent(species)}/${encodeURIComponent(symbol)}?type=${encodeURIComponent(type)}`;
+        if (targetSpecies)
+            path += `&target_species=${encodeURIComponent(targetSpecies)}`;
+        const raw = await this.fetchWithRetry(path, ctx);
+        return normalizeHomology(raw, symbol);
+    }
+    async getHomologyById(id, species, type, targetSpecies, ctx) {
+        let path = `/homology/id/${encodeURIComponent(species)}/${encodeURIComponent(id)}?type=${encodeURIComponent(type)}`;
+        if (targetSpecies)
+            path += `&target_species=${encodeURIComponent(targetSpecies)}`;
+        const raw = await this.fetchWithRetry(path, ctx);
+        return normalizeHomology(raw, id);
+    }
+    // --- Xrefs ---
+    async getXrefsById(id, dbname, ctx) {
+        let path = `/xrefs/id/${encodeURIComponent(id)}`;
+        if (dbname)
+            path += `?external_db=${encodeURIComponent(dbname)}`;
+        const raw = await this.fetchWithRetry(path, ctx);
+        if (!Array.isArray(raw))
+            return [];
+        return raw.map(normalizeXref);
+    }
+    // --- Species ---
+    async listSpecies(division, ctx) {
+        let path = '/info/species';
+        if (division)
+            path += `?division=${encodeURIComponent(division)}`;
+        const raw = await this.fetchWithRetry(path, ctx);
+        return normalizeSpecies(raw);
+    }
+}
+// --- Init/accessor pattern ---
+let _service;
+export function initEnsemblService(config, storage) {
+    _service = new EnsemblService(config, storage);
+}
+export function getEnsemblService() {
+    if (!_service) {
+        throw new Error('EnsemblService not initialized — call initEnsemblService() in setup()');
+    }
+    return _service;
+}
+//# sourceMappingURL=ensembl-service.js.map

package/dist/services/ensembl/ensembl-service.js.map

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package/dist/services/ensembl/types.d.ts

@@ -0,0 +1,289 @@
+/**
+ * @fileoverview Ensembl REST API response types confirmed against live API payloads.
+ * @module services/ensembl/types
+ */
+export type RawGeneRecord = {
+    id: string;
+    display_name?: string;
+    description?: string;
+    biotype?: string;
+    species?: string;
+    seq_region_name?: string;
+    start?: number;
+    end?: number;
+    strand?: number;
+    assembly_name?: string;
+    Transcript?: RawTranscriptSummary[];
+    is_canonical?: number;
+    version?: number;
+    object_type?: string;
+    logic_name?: string;
+    db_type?: string;
+    source?: string;
+};
+export type RawTranscriptSummary = {
+    id: string;
+    display_name?: string;
+    biotype?: string;
+    is_canonical?: number;
+    start?: number;
+    end?: number;
+    strand?: number;
+    length?: number;
+    Parent?: string;
+    object_type?: string;
+};
+export type RawTranscriptRecord = {
+    id: string;
+    display_name?: string;
+    biotype?: string;
+    is_canonical?: number;
+    start?: number;
+    end?: number;
+    strand?: number;
+    length?: number;
+    Parent?: string;
+    species?: string;
+    seq_region_name?: string;
+    assembly_name?: string;
+    Exon?: Array<{
+        id: string;
+        start: number;
+        end: number;
+        strand: number;
+    }>;
+    object_type?: string;
+    db_type?: string;
+    source?: string;
+    version?: number;
+};
+export type RawSequenceRecord = {
+    id: string;
+    seq: string;
+    molecule?: string;
+    desc?: string;
+    version?: number;
+    query?: string;
+};
+export type RawOverlapFeature = {
+    id?: string;
+    external_name?: string;
+    biotype?: string;
+    feature_type?: string;
+    seq_region_name?: string;
+    start?: number;
+    end?: number;
+    strand?: number;
+    assembly_name?: string;
+    description?: string;
+    consequence_type?: string;
+    clinical_significance?: string[];
+    alleles?: string[];
+    source?: string;
+};
+export type RawVepTranscriptConsequence = {
+    transcript_id?: string;
+    gene_id?: string;
+    gene_symbol?: string;
+    consequence_terms?: string[];
+    impact?: string;
+    biotype?: string;
+    strand?: number;
+    amino_acids?: string;
+    codons?: string;
+    hgvsc?: string;
+    hgvsp?: string;
+    protein_id?: string;
+    sift?: {
+        prediction: string;
+        score: number;
+    };
+    polyphen?: {
+        prediction: string;
+        score: number;
+    };
+};
+export type RawColocatedVariant = {
+    id?: string;
+    allele_string?: string;
+    clinical_significance?: string[];
+    frequencies?: Record<string, unknown>;
+    pubmed?: number[];
+    somatic?: number;
+};
+export type RawVepRecord = {
+    input?: string;
+    allele_string?: string;
+    start?: number;
+    end?: number;
+    strand?: number;
+    seq_region_name?: string;
+    assembly_name?: string;
+    most_severe_consequence?: string;
+    transcript_consequences?: RawVepTranscriptConsequence[];
+    colocated_variants?: RawColocatedVariant[];
+};
+export type RawHomologyEntry = {
+    id: string;
+    species?: string;
+    type?: string;
+    perc_id?: number;
+    perc_pos?: number;
+    taxonomy_level?: string;
+    target?: {
+        id?: string;
+        species?: string;
+        perc_id?: number;
+        perc_pos?: number;
+    };
+};
+export type RawHomologyResponse = {
+    data?: Array<{
+        id: string;
+        homologies?: RawHomologyEntry[];
+    }>;
+};
+export type RawXrefEntry = {
+    dbname?: string;
+    db_display_name?: string;
+    primary_id?: string;
+    display_id?: string;
+    description?: string;
+    info_type?: string;
+    synonyms?: string[];
+    version?: string;
+};
+export type RawSpeciesInfo = {
+    name?: string;
+    display_name?: string;
+    common_name?: string;
+    taxon_id?: string;
+    assembly?: string;
+    division?: string;
+    groups?: string[];
+    aliases?: string[];
+    accession?: string;
+    strain?: string;
+};
+export type RawSpeciesResponse = {
+    species?: RawSpeciesInfo[];
+};
+export type EnsemblErrorEnvelope = {
+    error: string;
+};
+export type GeneRecord = {
+    id: string;
+    species?: string;
+    displayName?: string;
+    description?: string;
+    biotype?: string;
+    chromosome?: string;
+    start?: number;
+    end?: number;
+    strand?: number;
+    assemblyName?: string;
+    transcripts?: TranscriptSummary[];
+};
+export type TranscriptSummary = {
+    id: string;
+    displayName?: string;
+    biotype?: string;
+    isCanonical: boolean;
+    start?: number;
+    end?: number;
+    strand?: number;
+    lengthInBp?: number;
+};
+export type TranscriptRecord = {
+    id: string;
+    parentGeneId?: string;
+    displayName?: string;
+    biotype?: string;
+    isCanonical: boolean;
+    species?: string;
+    chromosome?: string;
+    start?: number;
+    end?: number;
+    strand?: number;
+    assemblyName?: string;
+    lengthInBp?: number;
+};
+export type SequenceRecord = {
+    id: string;
+    type: string;
+    seq: string;
+    lengthInBp: number;
+    description?: string;
+};
+export type OverlapFeature = {
+    id?: string;
+    name?: string;
+    featureType: string;
+    biotype?: string;
+    chromosome: string;
+    start: number;
+    end: number;
+    strand?: number;
+    description?: string;
+    consequenceType?: string;
+    clinicalSignificance?: string[];
+};
+export type VepConsequence = {
+    transcriptId?: string;
+    geneId?: string;
+    geneSymbol?: string;
+    consequenceTerms: string[];
+    impact?: string;
+    biotype?: string;
+    hgvsc?: string;
+    hgvsp?: string;
+    aminoAcids?: string;
+    sift?: {
+        prediction: string;
+        score: number;
+    };
+    polyphen?: {
+        prediction: string;
+        score: number;
+    };
+};
+export type ColocatedVariant = {
+    id?: string;
+    alleleString?: string;
+    clinicalSignificance?: string[];
+    pubmed?: number[];
+};
+export type VepRecord = {
+    input?: string;
+    chromosome?: string;
+    start?: number;
+    end?: number;
+    assemblyName?: string;
+    mostSevereConsequence?: string;
+    transcriptConsequences: VepConsequence[];
+    colocatedVariants: ColocatedVariant[];
+};
+export type HomologyEntry = {
+    targetId: string;
+    targetSpecies?: string;
+    type?: string;
+    percId?: number;
+    percPos?: number;
+    taxonomyLevel?: string;
+};
+export type XrefEntry = {
+    dbname?: string;
+    dbDisplayName?: string;
+    primaryId?: string;
+    displayId?: string;
+    description?: string;
+};
+export type SpeciesInfo = {
+    name: string;
+    displayName?: string;
+    commonName?: string;
+    taxonId?: string;
+    assembly?: string;
+    division?: string;
+};
+//# sourceMappingURL=types.d.ts.map