@burdenoff/mcp-libs 2026.720.2 → 2026.731.1

package/dist/modules/labsofscience/index.cjs

@@ -310,9 +310,10 @@ var ARCHIVE_DATASET = `
   }
 `;
 var LIST_PIPELINES = `
-  query LabsofscienceListPipelines {
-    labListPipelines {
-      ${PIPELINE_FIELDS}
+  query LabsofscienceListPipelines($pagination: PaginationInput) {
+    labListPipelines(pagination: $pagination) {
+      items { ${PIPELINE_FIELDS} }
+      ${PAGE_INFO}
     }
   }
 `;
@@ -362,9 +363,14 @@ var GET_INSTRUMENT = `
   }
 `;
 var LIST_INSTRUMENTS = `
-  query LabsofscienceListInstruments($status: LabInstrumentStatus) {
-    labListInstruments(status: $status) {
-      ${INSTRUMENT_FIELDS}
+  query LabsofscienceListInstruments(
+    $status: LabInstrumentStatus
+    $search: String
+    $pagination: PaginationInput
+  ) {
+    labListInstruments(status: $status, search: $search, pagination: $pagination) {
+      items { ${INSTRUMENT_FIELDS} }
+      ${PAGE_INFO}
     }
   }
 `;
@@ -445,6 +451,13 @@ var LIST_NOTEBOOK_ENTRIES = `
     }
   }
 `;
+var GET_NOTEBOOK_ENTRY = `
+  query LabsofscienceGetNotebookEntry($id: ID!) {
+    labNotebookEntry(id: $id) {
+      ${NOTEBOOK_FIELDS}
+    }
+  }
+`;
 var CREATE_NOTEBOOK_ENTRY = `
   mutation LabsofscienceCreateNotebookEntry($input: LabCreateNotebookEntryInput!) {
     labCreateNotebookEntry(input: $input) {
@@ -459,6 +472,13 @@ var SIGN_NOTEBOOK_ENTRY = `
     }
   }
 `;
+var WITNESS_NOTEBOOK_ENTRY = `
+  mutation LabsofscienceWitnessNotebookEntry($id: ID!) {
+    labWitnessNotebookEntry(id: $id) {
+      ${NOTEBOOK_FIELDS}
+    }
+  }
+`;
 var HEALTH = `
   query LabsofscienceHealth {
     labHealth
@@ -643,7 +663,11 @@ function registerProjectTools(server, ctx, track) {
     {
       title: "Archive Research Project",
       description: "Archive a research project. Returns true on success.",
-      inputSchema: { id: zod.z.string().describe("Project ID") }
+      inputSchema: { id: zod.z.string().describe("Project ID") },
+      // BOFF-3611: irreversible via this tool surface — see datasets.ts's
+      // datasets_archive for why this is an explicit per-tool override
+      // rather than a fleet-wide tool-name.ts regex change.
+      annotations: { destructiveHint: true }
     },
     async ({ id }) => {
       try {
@@ -1071,7 +1095,12 @@ function registerProtocolTools(server, ctx, track) {
     {
       title: "Publish Protocol",
       description: "Publish a draft protocol, freezing its version for reproducibility. Returns the published protocol with its steps.",
-      inputSchema: { id: zod.z.string().describe("Protocol ID") }
+      inputSchema: { id: zod.z.string().describe("Protocol ID") },
+      // BOFF-3611: irreversible via this tool surface — publishing freezes
+      // the version; there is no "unpublish" mutation. Explicit override —
+      // see datasets.ts's datasets_archive for why per-tool, not a
+      // fleet-wide tool-name.ts regex change.
+      annotations: { destructiveHint: true }
     },
     async ({ id }) => {
       try {
@@ -1205,7 +1234,12 @@ function registerDatasetTools(server, ctx, track) {
     {
       title: "Archive Dataset",
       description: "Archive a dataset. Returns true on success.",
-      inputSchema: { id: zod.z.string().describe("Dataset ID") }
+      inputSchema: { id: zod.z.string().describe("Dataset ID") },
+      // BOFF-3611: irreversible via this tool surface — the backend has no
+      // "unarchive" mutation. Explicit override because tool-name.ts's
+      // fleet-wide inference only matches "delete"; declaring it here (not
+      // by widening that shared regex) keeps the blast radius to this tool.
+      annotations: { destructiveHint: true }
     },
     async ({ id }) => {
       try {
@@ -1228,12 +1262,18 @@ function registerPipelineTools(server, ctx, track) {
     track(mcpToolName(ctx.productName, "pipelines_list")),
     {
       title: "List Analysis Pipelines",
-      description: "List all analysis pipelines in the bound workspace.",
-      inputSchema: {}
+      description: "List analysis pipelines in the bound workspace, with pagination. Returns a connection ({ items, pageInfo }).",
+      inputSchema: {
+        limit: zod.z.number().int().optional().describe("Page size (default 50)"),
+        offset: zod.z.number().int().optional().describe("Pagination offset (default 0)"),
+        cursor: zod.z.string().optional().describe("Opaque pagination cursor")
+      }
     },
-    async () => {
+    async ({ limit, offset, cursor }) => {
       try {
-        const data = await ctx.gql.workspace.request(LIST_PIPELINES, {});
+        const data = await ctx.gql.workspace.request(LIST_PIPELINES, {
+          pagination: { limit: limit ?? 50, offset: offset ?? 0, cursor }
+        });
         return jsonResult(data.labListPipelines);
       } catch (error) {
         ctx.logger.error("labsofscience pipelines_list failed", { error: String(error) });
@@ -1383,14 +1423,22 @@ function registerInstrumentTools(server, ctx, track) {
     track(mcpToolName(ctx.productName, "instruments_list")),
     {
       title: "List Instruments",
-      description: "List lab instruments, optionally filtered by availability status.",
+      description: "List lab instruments, optionally filtered by availability status and/or a name/model search term, with pagination. Returns a connection ({ items, pageInfo }).",
       inputSchema: {
-        status: InstrumentStatusEnum.optional().describe("Filter by instrument status")
+        status: InstrumentStatusEnum.optional().describe("Filter by instrument status"),
+        search: zod.z.string().optional().describe("Search by name or model"),
+        limit: zod.z.number().int().optional().describe("Page size (default 50)"),
+        offset: zod.z.number().int().optional().describe("Pagination offset (default 0)"),
+        cursor: zod.z.string().optional().describe("Opaque pagination cursor")
       }
     },
-    async ({ status }) => {
+    async ({ status, search, limit, offset, cursor }) => {
       try {
-        const data = await ctx.gql.workspace.request(LIST_INSTRUMENTS, { status });
+        const data = await ctx.gql.workspace.request(LIST_INSTRUMENTS, {
+          status,
+          search,
+          pagination: { limit: limit ?? 50, offset: offset ?? 0, cursor }
+        });
         return jsonResult(data.labListInstruments);
       } catch (error) {
         ctx.logger.error("labsofscience instruments_list failed", { error: String(error) });
@@ -1617,7 +1665,11 @@ function registerInventoryTools(server, ctx, track) {
     {
       title: "Archive Inventory Item",
       description: "Archive an inventory item. Returns true on success.",
-      inputSchema: { id: zod.z.string().describe("Inventory item ID") }
+      inputSchema: { id: zod.z.string().describe("Inventory item ID") },
+      // BOFF-3611: irreversible via this tool surface — see datasets.ts's
+      // datasets_archive for why this is an explicit per-tool override
+      // rather than a fleet-wide tool-name.ts regex change.
+      annotations: { destructiveHint: true }
     },
     async ({ id }) => {
       try {
@@ -1667,6 +1719,26 @@ function registerNotebookTools(server, ctx, track) {
       }
     }
   );
+  server.registerTool(
+    track(mcpToolName(ctx.productName, "notebook_get")),
+    {
+      title: "Get Notebook Entry",
+      description: "Fetch a single ELN entry by ID.",
+      inputSchema: { id: zod.z.string().describe("Notebook entry ID") }
+    },
+    async ({ id }) => {
+      try {
+        const data = await ctx.gql.workspace.request(GET_NOTEBOOK_ENTRY, { id });
+        if (!data.labNotebookEntry) return errorResult(`Notebook entry ${id} not found`);
+        return jsonResult(data.labNotebookEntry);
+      } catch (error) {
+        ctx.logger.error("labsofscience notebook_get failed", { error: String(error) });
+        return errorResult(
+          `Failed to get notebook entry: ${error instanceof Error ? error.message : String(error)}`
+        );
+      }
+    }
+  );
   server.registerTool(
     track(mcpToolName(ctx.productName, "notebook_create")),
     {
@@ -1705,7 +1777,11 @@ function registerNotebookTools(server, ctx, track) {
     {
       title: "Sign Notebook Entry",
       description: "Sign an ELN entry for record integrity (locks editable content). Returns the signed entry.",
-      inputSchema: { id: zod.z.string().describe("Notebook entry ID") }
+      inputSchema: { id: zod.z.string().describe("Notebook entry ID") },
+      // BOFF-3611: irreversible — there is no "unsign" mutation. Explicit
+      // override — see datasets.ts's datasets_archive for why per-tool,
+      // not a fleet-wide tool-name.ts regex change.
+      annotations: { destructiveHint: true }
     },
     async ({ id }) => {
       try {
@@ -1719,6 +1795,29 @@ function registerNotebookTools(server, ctx, track) {
       }
     }
   );
+  server.registerTool(
+    track(mcpToolName(ctx.productName, "notebook_witness")),
+    {
+      title: "Witness Notebook Entry",
+      description: "Witness a SIGNED ELN entry as a second party for record integrity. Returns the witnessed entry.",
+      inputSchema: { id: zod.z.string().describe("Notebook entry ID") },
+      // BOFF-3611: irreversible — there is no "unwitness" mutation. Explicit
+      // override — see datasets.ts's datasets_archive for why per-tool,
+      // not a fleet-wide tool-name.ts regex change.
+      annotations: { destructiveHint: true }
+    },
+    async ({ id }) => {
+      try {
+        const data = await ctx.gql.workspace.request(WITNESS_NOTEBOOK_ENTRY, { id });
+        return jsonResult(data.labWitnessNotebookEntry);
+      } catch (error) {
+        ctx.logger.error("labsofscience notebook_witness failed", { error: String(error) });
+        return errorResult(
+          `Failed to witness notebook entry: ${error instanceof Error ? error.message : String(error)}`
+        );
+      }
+    }
+  );
 }
 
 // src/modules/labsofscience/tools/health.ts
@@ -1793,9 +1892,9 @@ Science & discovery platform \u2014 a research LIMS / ELN.
 
 ## Tool groups
 projects, experiments, runs, protocols, datasets, pipelines, instruments, inventory, notebook, health.
-List queries return { items, pageInfo } connections and accept a PaginationInput { limit, offset, cursor };
-instruments_list and pipelines_list return plain arrays. All run against the WORKSPACE gateway
-(workspace-scoped) except the public health probe.
+Every list query \u2014 including instruments_list and pipelines_list \u2014 returns { items, pageInfo }
+connections and accepts a PaginationInput { limit, offset, cursor }. All run against the WORKSPACE
+gateway (workspace-scoped) except the public health probe.
 `;
       return {
         contents: [{ uri: schemaUri, text: schema, mimeType: "text/plain" }]
@@ -1845,7 +1944,7 @@ instruments_list and pipelines_list return plain arrays. All run against the WOR
     instrumentsUri,
     {
       title: "Labsofscience Instrument Catalog",
-      description: "All lab instruments in the bound workspace.",
+      description: "The first 50 lab instruments in the bound workspace.",
       mimeType: "application/json"
     },
     async () => {
@@ -1853,7 +1952,7 @@ instruments_list and pipelines_list return plain arrays. All run against the WOR
       try {
         const data = await ctx.gql.workspace.request(
           LIST_INSTRUMENTS,
-          {}
+          { pagination: { limit: 50, offset: 0 } }
         );
         return {
           contents: [
@@ -1884,7 +1983,7 @@ instruments_list and pipelines_list return plain arrays. All run against the WOR
     pipelinesUri,
     {
       title: "Labsofscience Analysis Pipelines",
-      description: "All analysis pipelines in the bound workspace.",
+      description: "The first 50 analysis pipelines in the bound workspace.",
       mimeType: "application/json"
     },
     async () => {
@@ -1892,7 +1991,7 @@ instruments_list and pipelines_list return plain arrays. All run against the WOR
       try {
         const data = await ctx.gql.workspace.request(
           LIST_PIPELINES,
-          {}
+          { pagination: { limit: 50, offset: 0 } }
         );
         return {
           contents: [