@oneshot-agent/mcp-server 0.42.0 → 0.43.0

package/dist/index.js

@@ -50,7 +50,7 @@ async function main() {
     const agent = await initAgent();
     const server = new Server({
         name: "oneshot-mcp",
-        version: "0.42.0", // keep in sync with package.json; guarded by version.test.ts
+        version: "0.43.0", // keep in sync with package.json; guarded by version.test.ts
     }, {
         capabilities: {
             tools: {},

package/dist/tools/lookup-manifest.generated.js

@@ -806,6 +806,36 @@ export const LOOKUP_MANIFEST = [
             "height_in": 48
         }
     },
+    {
+        "name": "gene_pathways",
+        "path": "lookup/gene-pathways",
+        "title": "Gene Pathways",
+        "description": "Find the lowest-level pathways a gene’s products take part in, from Reactome. Covers curated human pathways and pathways inferred for other species. Pass the gene’s own organism as taxon_id (human, 9606, by default): a Gene ID belongs to one organism. Inferred pathways are computed from human pathways by orthology rather than curated for this species; in_disease pathways describe disease mechanisms. Returns up to limit pathways in source order, with total counting all pathways the source returned. An unknown gene, a gene with no pathways, or an organism mismatch returns an empty list. Reactome data is CC0 and refreshed in quarterly releases; no diagrams or images are returned.",
+        "inputSchema": {
+            "type": "object",
+            "properties": {
+                "gene_id": {
+                    "type": "string",
+                    "description": "An NCBI Gene ID, for example 7157. Digits only, 1 to 12."
+                },
+                "taxon_id": {
+                    "type": "integer",
+                    "description": "The gene’s own organism as an NCBI Taxonomy ID; 9606 is human, 10090 is mouse. From 1 to 999999999. Defaults to `9606`."
+                },
+                "limit": {
+                    "type": "integer",
+                    "description": "Maximum pathways returned, in source order. From 1 to 100. Defaults to `50`."
+                }
+            },
+            "required": [
+                "gene_id"
+            ]
+        },
+        "example": {
+            "gene_id": "7157",
+            "limit": 1
+        }
+    },
     {
         "name": "gene_resolve",
         "path": "resolve/gene",
@@ -862,6 +892,88 @@ export const LOOKUP_MANIFEST = [
             "symbol": "TP53"
         }
     },
+    {
+        "name": "gene_variants_find",
+        "path": "find/gene-variants",
+        "title": "Gene Variants",
+        "description": "Reports what a public registry, ClinVar, says about variants in a gene, for research; not medical advice. Classifications are submitters' and expert panels' interpretations. Supply exactly one NCBI Gene ID or official human gene symbol, never a person's genome, sequencing data or a VCF file. Aliases do not match: use gene_resolve to resolve aliases first. Optionally filter by ClinVar classification properties and expert panel review; these properties can include combined classifications. By default, single_gene excludes large deletions and duplications spanning multiple genes; include_multi_gene includes them. Returns up to 20 variants in search order and the total ClinVar search count. Empty classifications are null; no match returns total 0 and an empty variants list. Each vcv can be passed to variant_clinical_significance for details, including somatic and oncogenicity classifications. ClinVar refreshes weekly; classifications carry their last evaluated dates. NCBI places no restriction on use of ClinVar.",
+        "inputSchema": {
+            "type": "object",
+            "properties": {
+                "gene_id": {
+                    "type": "string",
+                    "description": "NCBI Gene ID, for example 672; supply exactly one of gene_id or symbol. 1 to 12 characters."
+                },
+                "symbol": {
+                    "type": "string",
+                    "description": "Official human gene symbol, for example BRCA1; use gene_resolve for aliases. 1 to 30 characters."
+                },
+                "classification": {
+                    "type": "string",
+                    "enum": [
+                        "pathogenic",
+                        "likely_pathogenic",
+                        "uncertain",
+                        "likely_benign",
+                        "benign",
+                        "conflicting"
+                    ],
+                    "description": "ClinVar classification property filter; may include combined classifications"
+                },
+                "expert_panel_only": {
+                    "type": "boolean",
+                    "description": "Only variants reviewed by an expert panel. Defaults to `false`."
+                },
+                "include_multi_gene": {
+                    "type": "boolean",
+                    "description": "Include variants spanning multiple genes. Defaults to `false`."
+                },
+                "limit": {
+                    "type": "integer",
+                    "description": "Maximum number of variants returned. From 1 to 20. Defaults to `10`."
+                }
+            },
+            "required": []
+        },
+        "example": {
+            "gene_id": "7157",
+            "classification": "pathogenic",
+            "expert_panel_only": true,
+            "limit": 1
+        }
+    },
+    {
+        "name": "business_health_inspections",
+        "path": "lookup/business-health-inspections",
+        "title": "Health Inspections",
+        "description": "Given a New York City establishment id (CAMIS) or part of a trade name, return the matching food service establishments with their health inspections from the New York City Department of Health and Mental Hygiene: name, address, borough, ZIP code, cuisine and location, then for each inspection its date, type, score, letter grade with its date, the action taken and the violations cited, each with its code, description and whether it is critical. Give at least one of `establishment_id` and `name`; the id takes precedence when both are given. `name` matches anywhere in the trade name, ignoring case; `zipcode` narrows either search. Inspections are newest first, at most `limit` per establishment. The call reads the 200 newest violation rows that match, so a name shared by many establishments may leave out older inspections: add `zipcode` or use the id; when those rows all fall on one date the call fails as invalid input for the same reason. An establishment not yet inspected has an empty `inspections` list. Dates are YYYY-MM-DD and a value the source does not give is null. No match is a completed result with an empty `establishments` list.",
+        "inputSchema": {
+            "type": "object",
+            "properties": {
+                "establishment_id": {
+                    "type": "string",
+                    "description": "The city's establishment id (CAMIS), for example 40732665; takes precedence over name. establishment_id must be digits."
+                },
+                "name": {
+                    "type": "string",
+                    "description": "Part of the trade name, matched anywhere in it and ignoring case, for example Katz's Delicatessen. 2 to 100 characters."
+                },
+                "zipcode": {
+                    "type": "string",
+                    "description": "Five-digit ZIP code of the establishment. zipcode must be five digits."
+                },
+                "limit": {
+                    "type": "integer",
+                    "description": "Most inspections to return per establishment. From 1 to 20. Defaults to `5`."
+                }
+            },
+            "required": []
+        },
+        "example": {
+            "establishment_id": "40732665",
+            "limit": 3
+        }
+    },
     {
         "name": "person_health_provider",
         "path": "lookup/person-health-provider",
@@ -1238,6 +1350,29 @@ export const LOOKUP_MANIFEST = [
             "rsid": "rs80357906"
         }
     },
+    {
+        "name": "variant_resolve",
+        "path": "resolve/variant",
+        "title": "Variant Resolve",
+        "description": "Says which variant a public registry, ClinVar, records under one identifier, for research; not medical advice. Supply exactly one HGVS expression on a reference sequence accession (genomic, coding, non-coding or protein) or one dbSNP rsID, never a person's genome, sequencing data or a VCF file. The expression is matched as one quoted variant name; expressions containing double quotes or square brackets are refused, so use the rsID for repeat notation. An rsID can match several alleles at one position: returns up to five variations carrying that rsID. A short protein change can match several variants too; ambiguous is then true. No match returns an empty variants list. Identity only: no germline, somatic or oncogenicity classification, conditions or submissions; pass vcv to variant_clinical_significance for those. ClinVar refreshes weekly, and accession versions change when records change. NCBI places no restriction on use of ClinVar.",
+        "inputSchema": {
+            "type": "object",
+            "properties": {
+                "hgvs": {
+                    "type": "string",
+                    "description": "HGVS expression starting with a reference sequence accession, for example NM_007294.4:c.5266dup or NM_007294.4(BRCA1):c.5266dup; supply only hgvs or rsid. 5 to 200 characters."
+                },
+                "rsid": {
+                    "type": "string",
+                    "description": "dbSNP identifier, for example rs80357906; supply only rsid or hgvs"
+                }
+            },
+            "required": []
+        },
+        "example": {
+            "hgvs": "NM_007294.4:c.5266dup"
+        }
+    },
     {
         "name": "company_vat_registration",
         "path": "lookup/company-vat-registration",

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@oneshot-agent/mcp-server",
-  "version": "0.42.0",
-  "description": "MCP server for OneShot - 150 tools for AI agents",
+  "version": "0.43.0",
+  "description": "MCP server for OneShot - 154 tools for AI agents",
   "type": "module",
   "main": "dist/index.js",
   "types": "dist/index.d.ts",