@cyanheads/interpro-mcp-server 0.1.2 → 0.2.0

package/dist/services/interpro/structure-schemas.js

@@ -0,0 +1,74 @@
+/**
+ * @fileoverview PDB identifier grammar and lossless structure match schemas.
+ * @module services/interpro/structure-schemas
+ */
+import { z } from '@cyanheads/mcp-ts-core';
+import { EntrySummarySchema, JsonValueSchema, LocationSchema } from './schemas.js';
+/** Classic four-character PDB IDs; InterPro answers extended `pdb_0000…` IDs with 404. */
+export const PDB_ID_PATTERN = /^[0-9][A-Za-z0-9]{3}$/;
+/** Chain IDs as InterPro lists them: case-sensitive, one to four letters or digits. */
+export const CHAIN_PATTERN = /^[A-Za-z0-9]{1,4}$/;
+/** Caller-supplied PDB ID, matched case-insensitively and sent lowercase. */
+export const PdbIdSchema = z
+    .string()
+    .trim()
+    .max(4)
+    .regex(PDB_ID_PATTERN, 'Expected a four-character PDB ID such as 1tsr.')
+    .describe('Four-character PDB ID such as 1tsr; case-insensitive. Extended pdb_0000… IDs are not supported.');
+/** Caller-supplied chain ID, compared exactly against the structure's protein chains. */
+export const ChainSchema = z
+    .string()
+    .trim()
+    .max(4)
+    .regex(CHAIN_PATTERN, 'Expected a chain ID of one to four letters or digits.')
+    .describe('Case-sensitive PDB chain ID, one to four letters or digits.');
+/** Whether an upstream value is exactly a chain ID, the only form server-written text names it in. */
+export const isChain = (value) => typeof value === 'string' && CHAIN_PATTERN.test(value);
+/** Structure detail metadata: `chains` lists protein chains only; other fields are retained. */
+export const StructureMetadataSchema = z
+    .object({
+    accession: z.string().describe('Lowercase PDB ID.'),
+    source_database: z.string().describe('Structure source database.'),
+    chains: z
+        .array(z.string().describe('Protein chain ID.'))
+        .describe('Protein chain IDs; nucleic-acid chains are not listed.'),
+})
+    .catchall(JsonValueSchema)
+    .describe('Complete upstream structure metadata.');
+/**
+ * One upstream chain record of a structure match. `entry_structure_locations` fragments carry
+ * 1-based chain `start`/`end` beside author `auth_start`/`auth_end`, which may be null; the
+ * UniProt `protein`, its residue maps, and both protein-side location arrays may be null or empty.
+ */
+export const StructureRecordSchema = z
+    .object({
+    accession: z.string().describe('Lowercase PDB ID.'),
+    chain: z.string().describe('Case-sensitive chain ID.'),
+    protein: z
+        .string()
+        .nullable()
+        .describe('Lowercase UniProt accession mapped to the chain; null when unmapped.'),
+    entry_structure_locations: z
+        .array(LocationSchema)
+        .describe('Match locations in chain numbering: start/end are 1-based chain positions; auth_start/auth_end are author residue numbers, possibly null.'),
+    entry_protein_locations: z
+        .array(LocationSchema)
+        .nullable()
+        .optional()
+        .describe('Match locations in UniProt numbering; null or empty without a usable mapping.'),
+    structure_protein_locations: z
+        .array(LocationSchema)
+        .nullable()
+        .optional()
+        .describe('Chain-to-UniProt residue maps: start/end in chain numbering, protein_start/protein_end in UniProt numbering.'),
+})
+    .catchall(JsonValueSchema)
+    .describe('Complete upstream chain record.');
+/** Upstream structure match row: entry metadata plus at most 20 nested chain records. */
+export const StructureMatchSchema = z
+    .object({
+    metadata: EntrySummarySchema.describe('Entry metadata.'),
+    structures: z.array(StructureRecordSchema).describe('Nested chain records.'),
+})
+    .catchall(JsonValueSchema);
+//# sourceMappingURL=structure-schemas.js.map

package/dist/services/interpro/structure-schemas.js.map

@@ -0,0 +1 @@
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package/dist/services/sequence-scan/scan-output.d.ts

@@ -0,0 +1,94 @@
+/**
+ * @fileoverview Output schema and budget-bounded segments of whole match records shared by the
+ * scan and scan-result tools, with cursors scoped to the sequence MD5 or the job ID.
+ * @module services/sequence-scan/scan-output
+ */
+import { z } from '@cyanheads/mcp-ts-core';
+import type { ScanOutcome } from './sequence-scan-service.js';
+declare const PositionSchema: z.ZodObject<{
+    offset: z.ZodNumber;
+    total: z.ZodNumber;
+}, z.core.$strict>;
+type Position = z.infer<typeof PositionSchema>;
+/** Output fields both tools return. */
+export declare const ScanOutputSchema: z.ZodObject<{
+    source: z.ZodEnum<{
+        interproscan: "interproscan";
+        precalculated: "precalculated";
+    }>;
+    status: z.ZodEnum<{
+        finished: "finished";
+        queued: "queued";
+        running: "running";
+        submitted: "submitted";
+    }>;
+    jobId: z.ZodOptional<z.ZodString>;
+    md5: z.ZodOptional<z.ZodString>;
+    length: z.ZodOptional<z.ZodNumber>;
+    interproVersion: z.ZodOptional<z.ZodString>;
+    interproscanVersion: z.ZodOptional<z.ZodString>;
+    matches: z.ZodOptional<z.ZodArray<z.ZodObject<{
+        signature: z.ZodObject<{
+            accession: z.ZodString;
+            signatureLibraryRelease: z.ZodObject<{
+                library: z.ZodString;
+                version: z.ZodString;
+            }, z.core.$catchall<z.ZodJSONSchema>>;
+            entry: z.ZodOptional<z.ZodNullable<z.ZodObject<{
+                accession: z.ZodString;
+            }, z.core.$catchall<z.ZodJSONSchema>>>>;
+        }, z.core.$catchall<z.ZodJSONSchema>>;
+        'model-ac': z.ZodNullable<z.ZodString>;
+        source: z.ZodString;
+        locations: z.ZodArray<z.ZodObject<{
+            start: z.ZodNumber;
+            end: z.ZodNumber;
+            'location-fragments': z.ZodArray<z.ZodObject<{
+                start: z.ZodNumber;
+                end: z.ZodNumber;
+                'dc-status': z.ZodString;
+            }, z.core.$catchall<z.ZodJSONSchema>>>;
+        }, z.core.$catchall<z.ZodJSONSchema>>>;
+    }, z.core.$catchall<z.ZodJSONSchema>>>>;
+    coverage: z.ZodOptional<z.ZodObject<{
+        totalMatches: z.ZodNumber;
+        offset: z.ZodNumber;
+        returnedMatches: z.ZodNumber;
+        hasMore: z.ZodBoolean;
+        nextCursor: z.ZodOptional<z.ZodString>;
+    }, z.core.$strip>>;
+    sourceUrl: z.ZodString;
+}, z.core.$strip>;
+export type ScanOutput = z.infer<typeof ScanOutputSchema>;
+/** Enrichment fields both tools declare. */
+export declare const ScanEnrichment: {
+    notice: z.ZodOptional<z.ZodString>;
+    totalCount: z.ZodOptional<z.ZodNumber>;
+    truncated: z.ZodOptional<z.ZodBoolean>;
+    shown: z.ZodOptional<z.ZodNumber>;
+};
+/** Decode a continuation for the given target before any upstream request. */
+export declare function decodeScanCursor(cursor: string | undefined, target: {
+    readonly md5: string;
+} | {
+    readonly jobId: string;
+}): Position | undefined;
+interface Enrich {
+    notice(text: string): void;
+    total(count: number): void;
+    truncated(details: {
+        shown: number;
+    }): void;
+}
+/**
+ * Build one segment of a finished result, or the pending output, and the notices that go with
+ * it. `continuation` names the call that reads the next segment, as the agent should make it.
+ */
+export declare function buildScanOutput(enrich: Enrich, state: ScanOutcome, options: {
+    readonly md5?: string;
+    readonly length?: number;
+    readonly start?: Position;
+    readonly continuation: (cursor: string) => string;
+}): ScanOutput;
+export {};
+//# sourceMappingURL=scan-output.d.ts.map

package/dist/services/sequence-scan/scan-output.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"scan-output.d.ts","sourceRoot":"","sources":["../../../src/services/sequence-scan/scan-output.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AACH,OAAO,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAS3C,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,4BAA4B,CAAC;AAI9D,QAAA,MAAM,cAAc;;;kBAET,CAAC;AACZ,KAAK,QAAQ,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,cAAc,CAAC,CAAC;AAE/C,uCAAuC;AACvC,eAAO,MAAM,gBAAgB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;iBAiD3B,CAAC;AACH,MAAM,MAAM,UAAU,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,gBAAgB,CAAC,CAAC;AAE1D,4CAA4C;AAC5C,eAAO,MAAM,cAAc;IACzB,MAAM;IACN,UAAU;IACV,SAAS;IACT,KAAK;CACN,CAAC;AAOF,8EAA8E;AAC9E,wBAAgB,gBAAgB,CAC9B,MAAM,EAAE,MAAM,GAAG,SAAS,EAC1B,MAAM,EAAE;IAAE,QAAQ,CAAC,GAAG,EAAE,MAAM,CAAA;CAAE,GAAG;IAAE,QAAQ,CAAC,KAAK,EAAE,MAAM,CAAA;CAAE,GAC5D,QAAQ,GAAG,SAAS,CAItB;AAsBD,UAAU,MAAM;IACd,MAAM,CAAC,IAAI,EAAE,MAAM,GAAG,IAAI,CAAC;IAC3B,KAAK,CAAC,KAAK,EAAE,MAAM,GAAG,IAAI,CAAC;IAC3B,SAAS,CAAC,OAAO,EAAE;QAAE,KAAK,EAAE,MAAM,CAAA;KAAE,GAAG,IAAI,CAAC;CAC7C;AAED;;;GAGG;AACH,wBAAgB,eAAe,CAC7B,MAAM,EAAE,MAAM,EACd,KAAK,EAAE,WAAW,EAClB,OAAO,EAAE;IACP,QAAQ,CAAC,GAAG,CAAC,EAAE,MAAM,CAAC;IACtB,QAAQ,CAAC,MAAM,CAAC,EAAE,MAAM,CAAC;IACzB,QAAQ,CAAC,KAAK,CAAC,EAAE,QAAQ,CAAC;IAC1B,QAAQ,CAAC,YAAY,EAAE,CAAC,MAAM,EAAE,MAAM,KAAK,MAAM,CAAC;CACnD,GACA,UAAU,CAwFZ"}

package/dist/services/sequence-scan/scan-output.js

@@ -0,0 +1,174 @@
+/**
+ * @fileoverview Output schema and budget-bounded segments of whole match records shared by the
+ * scan and scan-result tools, with cursors scoped to the sequence MD5 or the job ID.
+ * @module services/sequence-scan/scan-output
+ */
+import { z } from '@cyanheads/mcp-ts-core';
+import { validationError } from '@cyanheads/mcp-ts-core/errors';
+import { BUDGET_LABEL, fitWithinBudget } from '../interpro/budget.js';
+import { compareText, decodePositionCursor, encodePositionCursor, } from '../interpro/cursors.js';
+import { ScanMatchSchema } from './scan-schemas.js';
+const PRECALCULATED_OPERATION = 'interpro_scan_sequence.precalculated';
+const JOB_OPERATION = 'interpro_get_scan_result.job';
+const PositionSchema = z
+    .object({ offset: z.number().int().positive(), total: z.number().int().positive() })
+    .strict();
+/** Output fields both tools return. */
+export const ScanOutputSchema = z.object({
+    source: z
+        .enum(['precalculated', 'interproscan'])
+        .describe('Which path produced the result: precalculated matches from the InterPro Matches API, or an InterProScan 6 job run through the EBI Job Dispatcher.'),
+    status: z
+        .enum(['finished', 'queued', 'running', 'submitted'])
+        .describe('finished: matches are present. queued or running: the job is pending; read it later with interpro_get_scan_result. submitted: accepted in this call and not yet polled.'),
+    jobId: z
+        .string()
+        .optional()
+        .describe('InterProScan job ID on the interproscan path; results stay retrievable for seven days.'),
+    md5: z
+        .string()
+        .optional()
+        .describe('Uppercase hex MD5 of the uppercased residues, the UniParc sequence digest.'),
+    length: z.number().int().optional().describe('Sequence length in residues.'),
+    interproVersion: z
+        .string()
+        .optional()
+        .describe('InterPro release of a finished InterProScan job.'),
+    interproscanVersion: z.string().optional().describe('InterProScan version of a finished job.'),
+    matches: z
+        .array(ScanMatchSchema)
+        .optional()
+        .describe('Whole match records in this segment when finished, sorted by earliest location start then signature accession; coordinates are 1-based and inclusive. Each record keeps its own source and signatureLibraryRelease.'),
+    coverage: z
+        .object({
+        totalMatches: z.number().int().describe('Match records in the complete result.'),
+        offset: z.number().int().describe('Match records that precede this segment.'),
+        returnedMatches: z.number().int().describe('Match records in this segment.'),
+        hasMore: z.boolean().describe('Whether another segment remains.'),
+        nextCursor: z
+            .string()
+            .optional()
+            .describe('Opaque cursor for the next segment; pass it unchanged to the tool the notice names.'),
+    })
+        .optional()
+        .describe('Where this segment sits in the complete match list; present when finished.'),
+    sourceUrl: z.string().describe('Upstream endpoint that supplied this result.'),
+});
+/** Enrichment fields both tools declare. */
+export const ScanEnrichment = {
+    notice: z.string().optional().describe('Job, continuation, or empty-result guidance.'),
+    totalCount: z.number().optional().describe('Match records in the complete result.'),
+    truncated: z.boolean().optional().describe('More segments remain.'),
+    shown: z.number().int().optional().describe('Match records in this segment.'),
+};
+const cursorTarget = (state, md5) => state.source === 'precalculated'
+    ? { operation: PRECALCULATED_OPERATION, scope: { md5 } }
+    : { operation: JOB_OPERATION, scope: { jobId: state.jobId } };
+/** Decode a continuation for the given target before any upstream request. */
+export function decodeScanCursor(cursor, target) {
+    return 'md5' in target
+        ? decodePositionCursor(cursor, PRECALCULATED_OPERATION, { md5: target.md5 }, PositionSchema)
+        : decodePositionCursor(cursor, JOB_OPERATION, { jobId: target.jobId }, PositionSchema);
+}
+function minStart(match) {
+    let start = Number.POSITIVE_INFINITY;
+    for (const location of match.locations)
+        start = Math.min(start, location.start);
+    return start;
+}
+/** Deterministic order, so a cursor offset names the same record on every read. */
+function sortMatches(matches) {
+    return matches
+        .map((match) => ({ match, start: minStart(match), json: JSON.stringify(match) }))
+        .sort((a, b) => a.start - b.start ||
+        compareText(a.match.signature.accession, b.match.signature.accession) ||
+        compareText(a.match.source, b.match.source) ||
+        compareText(a.json, b.json))
+        .map(({ match }) => match);
+}
+/**
+ * Build one segment of a finished result, or the pending output, and the notices that go with
+ * it. `continuation` names the call that reads the next segment, as the agent should make it.
+ */
+export function buildScanOutput(enrich, state, options) {
+    const base = {
+        source: state.source,
+        ...(state.source === 'interproscan' ? { jobId: state.jobId } : {}),
+    };
+    if (state.source === 'interproscan' && state.status !== 'FINISHED') {
+        const status = state.status === 'submitted' ? 'submitted' : state.status === 'QUEUED' ? 'queued' : 'running';
+        enrich.notice(`InterProScan job ${state.jobId} is ${status}; de novo scans commonly take about ten minutes. Call interpro_get_scan_result ${JSON.stringify({ jobId: state.jobId })} to wait for it. Results stay retrievable for seven days.`);
+        return {
+            ...base,
+            status,
+            ...(options.md5 ? { md5: options.md5 } : {}),
+            ...(options.length ? { length: options.length } : {}),
+            sourceUrl: state.sourceUrl,
+        };
+    }
+    const finished = state.source === 'precalculated'
+        ? { matches: state.matches, md5: options.md5, length: options.length }
+        : {
+            matches: state.result.matches,
+            md5: state.result.md5,
+            length: state.result.length,
+            interproVersion: state.result.interproVersion,
+            interproscanVersion: state.result.interproscanVersion,
+        };
+    const all = sortMatches(finished.matches);
+    const total = all.length;
+    const offset = options.start?.offset ?? 0;
+    if (options.start && (options.start.total !== total || offset >= total))
+        throw validationError('Cursor no longer matches this result; restart without cursor.', {
+            reason: 'invalid_cursor',
+            retryable: false,
+        });
+    const { operation, scope } = cursorTarget(state, finished.md5);
+    const remaining = total - offset;
+    const segment = (count) => {
+        const end = offset + count;
+        return {
+            ...base,
+            status: 'finished',
+            ...(finished.md5 ? { md5: finished.md5 } : {}),
+            ...(finished.length ? { length: finished.length } : {}),
+            ...('interproVersion' in finished
+                ? {
+                    interproVersion: finished.interproVersion,
+                    interproscanVersion: finished.interproscanVersion,
+                }
+                : {}),
+            matches: all.slice(offset, end),
+            coverage: {
+                totalMatches: total,
+                offset,
+                returnedMatches: count,
+                hasMore: end < total,
+                ...(end < total
+                    ? { nextCursor: encodePositionCursor(operation, scope, { offset: end, total }) }
+                    : {}),
+            },
+            sourceUrl: state.sourceUrl,
+        };
+    };
+    const { count, output, oversized } = remaining
+        ? fitWithinBudget(remaining, segment)
+        : { count: 0, output: segment(0), oversized: false };
+    const notices = [];
+    if (oversized)
+        notices.push(`Match ${all[offset]?.signature.accession} cannot be split, so this segment holds it alone and exceeds the ${BUDGET_LABEL}.`);
+    const next = output.coverage?.nextCursor;
+    if (next) {
+        notices.push(`This segment holds matches ${offset + 1}–${offset + count} of ${total} and stopped at the ${BUDGET_LABEL}. Continue with ${options.continuation(next)} before concluding a region has no match.`);
+        enrich.truncated({ shown: count });
+    }
+    else if (!total)
+        notices.push(state.source === 'precalculated'
+            ? 'The InterPro Matches API holds a precalculated result for this sequence with no signature matches.'
+            : 'InterProScan finished and reported no signature matches for this sequence.');
+    enrich.total(total);
+    if (notices.length)
+        enrich.notice(notices.join(' '));
+    return output;
+}
+//# sourceMappingURL=scan-output.js.map

package/dist/services/sequence-scan/scan-output.js.map

@@ -0,0 +1 @@
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package/dist/services/sequence-scan/scan-schemas.d.ts

@@ -0,0 +1,112 @@
+/**
+ * @fileoverview Wire and output schemas for InterProScan match records, Matches API lookups, and
+ * Job Dispatcher iprscan6 jobs. Match records pass through verbatim, unknown fields included.
+ * @module services/sequence-scan/scan-schemas
+ */
+import { z } from '@cyanheads/mcp-ts-core';
+/**
+ * Job Dispatcher iprscan6 job identifier, e.g. `iprscan6-R20261028-131532-0930-13189043-p1m`:
+ * submission channel letter and date, time, two numeric fields, then a short host suffix. The
+ * channel letter and suffix are kept open beyond the observed `R` and `p1m`.
+ */
+export declare const JOB_ID_PATTERN: RegExp;
+/** Longest job identifier the pattern admits, so the input bound and the grammar agree. */
+export declare const MAX_JOB_ID_CHARS = 64;
+/** Job Dispatcher `status` vocabulary; NOT_FOUND arrives as HTTP 200 for unknown and expired IDs. */
+export declare const JobStatusSchema: z.ZodEnum<{
+    ERROR: "ERROR";
+    FAILURE: "FAILURE";
+    FINISHED: "FINISHED";
+    NOT_FOUND: "NOT_FOUND";
+    QUEUED: "QUEUED";
+    RUNNING: "RUNNING";
+}>;
+export type JobStatus = z.infer<typeof JobStatusSchema>;
+/** One InterProScan match record, the shape the Matches API and iprscan6 JSON share. */
+export declare const ScanMatchSchema: z.ZodObject<{
+    signature: z.ZodObject<{
+        accession: z.ZodString;
+        signatureLibraryRelease: z.ZodObject<{
+            library: z.ZodString;
+            version: z.ZodString;
+        }, z.core.$catchall<z.ZodJSONSchema>>;
+        entry: z.ZodOptional<z.ZodNullable<z.ZodObject<{
+            accession: z.ZodString;
+        }, z.core.$catchall<z.ZodJSONSchema>>>>;
+    }, z.core.$catchall<z.ZodJSONSchema>>;
+    'model-ac': z.ZodNullable<z.ZodString>;
+    source: z.ZodString;
+    locations: z.ZodArray<z.ZodObject<{
+        start: z.ZodNumber;
+        end: z.ZodNumber;
+        'location-fragments': z.ZodArray<z.ZodObject<{
+            start: z.ZodNumber;
+            end: z.ZodNumber;
+            'dc-status': z.ZodString;
+        }, z.core.$catchall<z.ZodJSONSchema>>>;
+    }, z.core.$catchall<z.ZodJSONSchema>>>;
+}, z.core.$catchall<z.ZodJSONSchema>>;
+export type ScanMatch = z.infer<typeof ScanMatchSchema>;
+/** `POST /interpro/matches/api/matches` response for one MD5. */
+export declare const MatchesLookupSchema: z.ZodObject<{
+    results: z.ZodArray<z.ZodObject<{
+        md5: z.ZodString;
+        found: z.ZodBoolean;
+        matches: z.ZodArray<z.ZodObject<{
+            signature: z.ZodObject<{
+                accession: z.ZodString;
+                signatureLibraryRelease: z.ZodObject<{
+                    library: z.ZodString;
+                    version: z.ZodString;
+                }, z.core.$catchall<z.ZodJSONSchema>>;
+                entry: z.ZodOptional<z.ZodNullable<z.ZodObject<{
+                    accession: z.ZodString;
+                }, z.core.$catchall<z.ZodJSONSchema>>>>;
+            }, z.core.$catchall<z.ZodJSONSchema>>;
+            'model-ac': z.ZodNullable<z.ZodString>;
+            source: z.ZodString;
+            locations: z.ZodArray<z.ZodObject<{
+                start: z.ZodNumber;
+                end: z.ZodNumber;
+                'location-fragments': z.ZodArray<z.ZodObject<{
+                    start: z.ZodNumber;
+                    end: z.ZodNumber;
+                    'dc-status': z.ZodString;
+                }, z.core.$catchall<z.ZodJSONSchema>>>;
+            }, z.core.$catchall<z.ZodJSONSchema>>>;
+        }, z.core.$catchall<z.ZodJSONSchema>>>;
+    }, z.core.$strip>>;
+}, z.core.$strip>;
+/** `result/{jobId}/json` body for a single-sequence iprscan6 job. */
+export declare const ScanResultSchema: z.ZodObject<{
+    'interproscan-version': z.ZodString;
+    'interpro-version': z.ZodString;
+    results: z.ZodArray<z.ZodObject<{
+        md5: z.ZodString;
+        sequence: z.ZodString;
+        matches: z.ZodArray<z.ZodObject<{
+            signature: z.ZodObject<{
+                accession: z.ZodString;
+                signatureLibraryRelease: z.ZodObject<{
+                    library: z.ZodString;
+                    version: z.ZodString;
+                }, z.core.$catchall<z.ZodJSONSchema>>;
+                entry: z.ZodOptional<z.ZodNullable<z.ZodObject<{
+                    accession: z.ZodString;
+                }, z.core.$catchall<z.ZodJSONSchema>>>>;
+            }, z.core.$catchall<z.ZodJSONSchema>>;
+            'model-ac': z.ZodNullable<z.ZodString>;
+            source: z.ZodString;
+            locations: z.ZodArray<z.ZodObject<{
+                start: z.ZodNumber;
+                end: z.ZodNumber;
+                'location-fragments': z.ZodArray<z.ZodObject<{
+                    start: z.ZodNumber;
+                    end: z.ZodNumber;
+                    'dc-status': z.ZodString;
+                }, z.core.$catchall<z.ZodJSONSchema>>>;
+            }, z.core.$catchall<z.ZodJSONSchema>>>;
+        }, z.core.$catchall<z.ZodJSONSchema>>>;
+    }, z.core.$catchall<z.ZodJSONSchema>>>;
+}, z.core.$strip>;
+//# sourceMappingURL=scan-schemas.d.ts.map

package/dist/services/sequence-scan/scan-schemas.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"scan-schemas.d.ts","sourceRoot":"","sources":["../../../src/services/sequence-scan/scan-schemas.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AACH,OAAO,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAG3C;;;;GAIG;AACH,eAAO,MAAM,cAAc,QAA6D,CAAC;AACzF,2FAA2F;AAC3F,eAAO,MAAM,gBAAgB,KAAK,CAAC;AAEnC,qGAAqG;AACrG,eAAO,MAAM,eAAe;;;;;;;EAO1B,CAAC;AACH,MAAM,MAAM,SAAS,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,eAAe,CAAC,CAAC;AA2BxD,wFAAwF;AACxF,eAAO,MAAM,eAAe;;;;;;;;;;;;;;;;;;;;;;qCAkC2B,CAAC;AACxD,MAAM,MAAM,SAAS,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,eAAe,CAAC,CAAC;AAIxD,iEAAiE;AACjE,eAAO,MAAM,mBAAmB;;;;;;;;;;;;;;;;;;;;;;;;;;;;iBAI9B,CAAC;AAEH,qEAAqE;AACrE,eAAO,MAAM,gBAAgB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;iBAU3B,CAAC"}

package/dist/services/sequence-scan/scan-schemas.js

@@ -0,0 +1,97 @@
+/**
+ * @fileoverview Wire and output schemas for InterProScan match records, Matches API lookups, and
+ * Job Dispatcher iprscan6 jobs. Match records pass through verbatim, unknown fields included.
+ * @module services/sequence-scan/scan-schemas
+ */
+import { z } from '@cyanheads/mcp-ts-core';
+import { JsonValueSchema } from '../interpro/schemas.js';
+/**
+ * Job Dispatcher iprscan6 job identifier, e.g. `iprscan6-R20261028-131532-0930-13189043-p1m`:
+ * submission channel letter and date, time, two numeric fields, then a short host suffix. The
+ * channel letter and suffix are kept open beyond the observed `R` and `p1m`.
+ */
+export const JOB_ID_PATTERN = /^iprscan6-[A-Z]\d{8}-\d{6}-\d{4}-\d{1,12}-[a-z0-9]{1,8}$/;
+/** Longest job identifier the pattern admits, so the input bound and the grammar agree. */
+export const MAX_JOB_ID_CHARS = 64;
+/** Job Dispatcher `status` vocabulary; NOT_FOUND arrives as HTTP 200 for unknown and expired IDs. */
+export const JobStatusSchema = z.enum([
+    'QUEUED',
+    'RUNNING',
+    'FINISHED',
+    'ERROR',
+    'FAILURE',
+    'NOT_FOUND',
+]);
+const ScanFragmentSchema = z
+    .object({
+    start: z.number().int().positive().describe('Inclusive 1-based start residue.'),
+    end: z.number().int().positive().describe('Inclusive 1-based end residue.'),
+    'dc-status': z
+        .string()
+        .describe('Discontinuity status, such as CONTINUOUS, N_TERMINAL_DISC, or C_TERMINAL_DISC.'),
+})
+    .catchall(JsonValueSchema)
+    .describe('One continuous piece of a possibly discontinuous match location.');
+const ScanLocationSchema = z
+    .object({
+    start: z.number().int().positive().describe('Inclusive 1-based start residue.'),
+    end: z.number().int().positive().describe('Inclusive 1-based end residue.'),
+    'location-fragments': z
+        .array(ScanFragmentSchema)
+        .min(1)
+        .describe('Nonempty fragments of this location.'),
+})
+    .catchall(JsonValueSchema)
+    .describe('One match location with every upstream field, such as scores, e-values, HMM bounds, envelope, sites, and alignments.');
+/** One InterProScan match record, the shape the Matches API and iprscan6 JSON share. */
+export const ScanMatchSchema = z
+    .object({
+    signature: z
+        .object({
+        accession: z.string().describe('Member-database signature accession, such as PF13499.'),
+        signatureLibraryRelease: z
+            .object({
+            library: z
+                .string()
+                .describe('Member database name exactly as the source spells it, such as Pfam.'),
+            version: z.string().describe('Member database release that produced this match.'),
+        })
+            .catchall(JsonValueSchema)
+            .describe('Library and release of this signature.'),
+        entry: z
+            .object({
+            accession: z.string().describe('Integrated InterPro entry accession.'),
+        })
+            .catchall(JsonValueSchema)
+            .nullable()
+            .optional()
+            .describe('InterPro entry the signature is integrated into; null when unintegrated.'),
+    })
+        .catchall(JsonValueSchema)
+        .describe('Matched signature, including name, description, and type when supplied.'),
+    'model-ac': z.string().nullable().describe('Model accession within the signature.'),
+    source: z
+        .string()
+        .describe('Method that produced the match, such as Pfam or InterPro-N, exactly as the source spells it.'),
+    locations: z.array(ScanLocationSchema).describe('Match locations on the sequence.'),
+})
+    .catchall(JsonValueSchema)
+    .describe('One InterProScan match record, verbatim.');
+const Md5Schema = z.string().regex(/^[0-9a-fA-F]{32}$/);
+/** `POST /interpro/matches/api/matches` response for one MD5. */
+export const MatchesLookupSchema = z.object({
+    results: z
+        .array(z.object({ md5: Md5Schema, found: z.boolean(), matches: z.array(ScanMatchSchema) }))
+        .length(1),
+});
+/** `result/{jobId}/json` body for a single-sequence iprscan6 job. */
+export const ScanResultSchema = z.object({
+    'interproscan-version': z.string(),
+    'interpro-version': z.string(),
+    results: z
+        .array(z
+        .object({ md5: Md5Schema, sequence: z.string(), matches: z.array(ScanMatchSchema) })
+        .catchall(JsonValueSchema))
+        .length(1),
+});
+//# sourceMappingURL=scan-schemas.js.map

package/dist/services/sequence-scan/scan-schemas.js.map

@@ -0,0 +1 @@
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