@inflexa-ai/harness 0.12.0 → 0.14.0

package/dist/agents/conversation-agent.d.ts

@@ -11,13 +11,10 @@
  * The system prompt is static composition — SOUL kernel + SOUL conversational
  * + the conversation prompt — with no processor pipeline.
  *
- * `executePlan` is wired here — it launches the DBOS `executeAnalysis` parent
+ * `execute_analysis` is wired here — it launches the DBOS `executeAnalysis` parent
  * workflow under `workflowId = runId` (the bare run UUID) through the
  * `RunLauncher` seam and returns the runId (results are pull-only via
- * `inspectRun` on a later turn). `run_ephemeral`
- * is wired here too — it mints a run authorization, starts the turn-scoped DBOS
- * `ephemeral` workflow, and awaits the result inline; chat disconnect cancels
- * the workflow and it is never recovered. Report authoring is wired here as the
+ * `inspectRun` on a later turn). Report authoring is wired here as the
  * pair `plan_report` (returns the report-brief schema + authoring rules
  * just-in-time as its result) + `submit_report` (validates the composed brief
  * and drives in-process Nunjucks rendering via the `report-builder` agent, no
@@ -42,7 +39,6 @@ import type { EnvironmentStorePaths } from "../config/environment-stores.js";
 import type { RunAuthorizer } from "../execution/run-authorizer.js";
 import type { RunLauncher } from "../execution/run-launcher.js";
 import { type SubmitReportDeps } from "../tools/iterate-report.js";
-import type { EphemeralWorkflowInput, EphemeralResult } from "../execution/ephemeral-runner.js";
 import type { Logger } from "../lib/logger.js";
 /** Canonical agent id — the single source of truth. */
 export declare const CONVERSATION_AGENT_ID: "conversation-agent";
@@ -65,28 +61,26 @@ export interface ConversationAgentDeps extends EnvironmentStorePaths {
     readonly workspaceFs: WorkspaceFilesystem;
     /** Model id — provenance / metric label; the provider owns the wire model. */
     readonly model: string;
+    /** Dedicated lower-cost model/provider for ad hoc specialist routing. */
+    readonly utilityProvider: ChatProvider;
+    readonly utilityModel: string;
     /**
      * Registered `executeAnalysis` workflow callable — produced by
-     * `registerExecuteAnalysis` (wired by `assembleCoreRuntime`). `executePlan`
+     * `registerExecuteAnalysis` (wired by `assembleCoreRuntime`). `execute_analysis`
      * launches it through the `RunLauncher` seam to start the run.
      */
     readonly executeAnalysisWorkflow: (input: ExecuteAnalysisInput) => Promise<ExecuteAnalysisResult>;
-    /**
-     * Registered `ephemeral` workflow — `run_ephemeral` mints a run authorization,
-     * starts it, and awaits the result inline within the chat turn.
-     */
-    readonly ephemeralWorkflow: (input: EphemeralWorkflowInput) => Promise<EphemeralResult>;
     /** Workspace-root resolution seam (see workspace/paths.ts). */
     readonly resolveWorkspaceRoot: ResolveWorkspaceRoot;
     /**
      * Async-edge run-authorization seam — injected, not constructed here.
-     * `execute_plan` and `run_ephemeral` turn the caller's opaque auth into a
+     * `execute_analysis` turns the caller's opaque auth into a
      * durable `RunSession` through it. The managed root injects the platform
      * realization; the OSS root injects the local one.
      */
     readonly runAuthorizer: RunAuthorizer;
     /**
-     * Durable-run launch seam — `execute_plan` and `run_ephemeral` start their
+     * Durable-run launch seam — `execute_analysis` starts its
      * workflows through it so the durability engine stays out of the tools.
      */
     readonly runLauncher: RunLauncher;
@@ -107,7 +101,7 @@ export interface ConversationAgentDeps extends EnvironmentStorePaths {
     /**
      * Host resource policy — per-step ceilings + machine budget. `generate_plan`
      * states the ceilings to the planner and validates against them;
-     * `execute_plan` snapshots the budget into the workflow input. Absent,
+     * `execute_analysis` snapshots the budget into the workflow input. Absent,
      * planning guidance and scheduling keep their legacy behavior.
      */
     readonly resourcePolicy?: ResourcePolicy;

package/dist/agents/conversation-agent.js

@@ -11,13 +11,10 @@
  * The system prompt is static composition — SOUL kernel + SOUL conversational
  * + the conversation prompt — with no processor pipeline.
  *
- * `executePlan` is wired here — it launches the DBOS `executeAnalysis` parent
+ * `execute_analysis` is wired here — it launches the DBOS `executeAnalysis` parent
  * workflow under `workflowId = runId` (the bare run UUID) through the
  * `RunLauncher` seam and returns the runId (results are pull-only via
- * `inspectRun` on a later turn). `run_ephemeral`
- * is wired here too — it mints a run authorization, starts the turn-scoped DBOS
- * `ephemeral` workflow, and awaits the result inline; chat disconnect cancels
- * the workflow and it is never recovered. Report authoring is wired here as the
+ * `inspectRun` on a later turn). Report authoring is wired here as the
  * pair `plan_report` (returns the report-brief schema + authoring rules
  * just-in-time as its result) + `submit_report` (validates the composed brief
  * and drives in-process Nunjucks rendering via the `report-builder` agent, no
@@ -32,7 +29,7 @@ import { createWorkingMemory } from "../memory/working-memory.js";
 import { conversationPrompt } from "../prompts/conversation.js";
 import { composeSystemPrompt } from "./system-prompt.js";
 // Bio-lookup leaf tools (pure — no dependencies).
-import { searchGeneTool, searchPathwayTool, lookupGoTermTool, searchInteractionsTool, chemblTool, pubchemTool, openTargetsTool, searchGwasCatalogTool, searchPharmgkbTool, searchFaersTool, searchClinicalTrialsTool, searchGeoDatasetsTool, createSearchDgidbTool, searchBgeeExpressionTool, getImpcKoProfileTool, checkSafetyPanelTool, } from "../tools/bio/index.js";
+import { searchGeneTool, lookupAnnotationTool, searchInteractionsTool, chemblTool, pubchemTool, openTargetsTool, searchFaersTool, searchClinicalTrialsTool, searchGeoDatasetsTool, genePreclinicalProfileTool, targetSafetyTool, } from "../tools/bio/index.js";
 import { createNcbiTools, createChemDbTools } from "../tools/bio/keys.js";
 // Dependency-bearing tool factories.
 import { createGeneratePlanTool, createLiteratureReviewerTool, createInspectRunTool, createInspectDataProfileTool, createGenerateAnalogyReportTool, } from "../tools/research/index.js";
@@ -41,8 +38,7 @@ import { showUserTool } from "../tools/display/index.js";
 import { createUpdateWorkingMemoryTool } from "../tools/memory/index.js";
 import { createListAvailablePackagesTool } from "../tools/sandbox/list-available-packages.js";
 import { createListAvailableRefsTool } from "../tools/sandbox/list-available-refs.js";
-import { createExecutePlanTool } from "../tools/execute-plan.js";
-import { createRunEphemeralTool } from "../tools/run-ephemeral.js";
+import { createExecuteAnalysisTool } from "../tools/execute-analysis.js";
 import { planReportTool, createReportSubmitTool } from "../tools/iterate-report.js";
 /** Canonical agent id — the single source of truth. */
 export const CONVERSATION_AGENT_ID = "conversation-agent";
@@ -50,15 +46,16 @@ export const CONVERSATION_AGENT_ID = "conversation-agent";
 const CONVERSATION_MAX_ITERATIONS = 50;
 /** Build the conversation `AgentDefinition` with every tool fully dep-bound. */
 export function createConversationAgent(deps) {
-    const { provider, pool, embedding, workspaceFs, model, executeAnalysisWorkflow, ephemeralWorkflow, resolveWorkspaceRoot, runAuthorizer, runLauncher, createPreviewPublisher, bioKeys, templatesDir, skillsDir, chrome, resourcePolicy, hostTools, refStorePath, packagesFile, } = deps;
+    const { provider, pool, embedding, workspaceFs, model, utilityProvider, utilityModel, executeAnalysisWorkflow, resolveWorkspaceRoot, runAuthorizer, runLauncher, createPreviewPublisher, bioKeys, templatesDir, skillsDir, chrome, resourcePolicy, hostTools, refStorePath, packagesFile, } = deps;
     const workingMemory = createWorkingMemory(pool);
     const ncbi = createNcbiTools(bioKeys);
-    const chemDb = createChemDbTools(bioKeys);
+    const chemDb = createChemDbTools(bioKeys, { ...(deps.logger ? { logger: deps.logger } : {}) });
     const tools = [
-        // Bio-lookup.
+        // Identifier resolution — the ENSG most other bio tools key off.
         searchGeneTool,
-        searchPathwayTool,
-        lookupGoTermTool,
+        // Functional annotation (GO / KEGG / Reactome behind one vocabulary) and
+        // STRING networks + gene-set enrichment.
+        lookupAnnotationTool,
         searchInteractionsTool,
         // Literature (search / details / fulltext behind one action).
         ncbi.pubmed,
@@ -66,20 +63,19 @@ export function createConversationAgent(deps) {
         chemblTool,
         // PubChem (compound / crossrefs / assays behind one action).
         pubchemTool,
-        // Translational medicine.
+        // Target assessment: the integrated scored view, then the underlying records.
         openTargetsTool,
-        // Genetic evidence — SNP-trait associations for target validation / MR support.
-        searchGwasCatalogTool,
-        searchPharmgkbTool,
+        // Genetic evidence — GWAS Catalog + DisGeNET + ClinVar behind one `sources`.
+        chemDb.geneDiseaseEvidence,
+        // Drug↔gene interactions — DGIdb + DrugBank + PharmGKB behind one `sources`.
+        chemDb.drugGeneInteractions,
         searchFaersTool,
         searchClinicalTrialsTool,
         searchGeoDatasetsTool,
-        createSearchDgidbTool({ ...(deps.logger ? { logger: deps.logger } : {}) }),
-        // Preclinical.
-        searchBgeeExpressionTool,
-        getImpcKoProfileTool,
-        // Off-target liability.
-        checkSafetyPanelTool,
+        // Preclinical — baseline expression + mouse knockout in one call.
+        genePreclinicalProfileTool,
+        // Target-level safety — the curated panel + Open Targets liabilities.
+        targetSafetyTool,
         // EPA CompTox (toxcast / hazard / chemical / exposure behind one dataset).
         chemDb.comptox,
         // What reference data this install actually holds. The conversation agent is
@@ -90,24 +86,29 @@ export function createConversationAgent(deps) {
         createListAvailableRefsTool({ ...(refStorePath ? { refStorePath } : {}) }),
         // What is importable inside a sandbox. Reads the same manifest a sandbox agent
         // reads, host-side — so "is scanpy available?" is a manifest lookup here rather
-        // than a whole ephemeral container spun up to run one import.
+        // than launching analysis computation to run one import.
         createListAvailablePackagesTool({ ...(packagesFile ? { packagesFile } : {}) }),
         // Execution.
         createInspectRunTool(pool),
         // The dataset's own record. No file backs it — the DB row is the only copy.
         createInspectDataProfileTool(pool),
-        createGeneratePlanTool({ provider, pool, model, resourcePolicy, ...(refStorePath ? { refStorePath } : {}), ...(packagesFile ? { packagesFile } : {}) }),
-        createExecutePlanTool({
+        createGeneratePlanTool({
+            conversation: { provider, model },
             pool,
-            executeAnalysisWorkflow,
-            runAuthorizer,
-            runLauncher,
             resourcePolicy,
+            ...(refStorePath ? { refStorePath } : {}),
+            ...(packagesFile ? { packagesFile } : {}),
+            ...(deps.logger ? { logger: deps.logger } : {}),
         }),
-        createRunEphemeralTool({
-            workflow: ephemeralWorkflow,
+        createExecuteAnalysisTool({
+            pool,
+            executeAnalysisWorkflow,
             runAuthorizer,
             runLauncher,
+            resourcePolicy,
+            utilityProvider,
+            utilityModel,
+            ...(deps.logger ? { logger: deps.logger } : {}),
         }),
         // Report authoring: the always-on `plan_report` trigger delivers the
         // heavy brief schema + rules just-in-time as its result; `submit_report`

package/dist/agents/sandbox/cheminformatics-agent.js

@@ -37,7 +37,7 @@ export const meta = {
         "perturbation-signatures",
     ],
     skills: ["cheminformatics", "shared/omics-general"],
-    tools: [...BASE_SANDBOX_TOOLS, "pubmed", "searchGene", "searchPathway", "lookupGoTerm", "searchInteractions", "chembl", "searchDgidb", "pubchem"],
+    tools: [...BASE_SANDBOX_TOOLS, "pubmed", "searchGene", "lookupAnnotation", "searchInteractions", "chembl", "drugGeneInteractions", "pubchem"],
 };
 export function createCheminformaticsAgent(deps) {
     return createSandboxAgent(deps, meta, cheminformaticsAgentPrompt);

package/dist/agents/sandbox/chromatin-agent.js

@@ -8,7 +8,7 @@ export const meta = {
     capabilities: ["peak calling", "differential binding", "differential accessibility", "motif analysis", "footprinting", "signal visualization"],
     suitableFor: ["atac-seq", "chip-seq", "cut-and-tag", "cut-and-run", "scatac-seq"],
     skills: ["chromatin-regulation", "shared/omics-general"],
-    tools: [...BASE_SANDBOX_TOOLS, "pubmed", "searchGene", "searchPathway", "lookupGoTerm", "searchInteractions"],
+    tools: [...BASE_SANDBOX_TOOLS, "pubmed", "searchGene", "lookupAnnotation", "searchInteractions"],
 };
 export function createChromatinAgent(deps) {
     return createSandboxAgent(deps, meta, chromatinAgentPrompt);

package/dist/agents/sandbox/dna-methylation-agent.js

@@ -8,7 +8,7 @@ export const meta = {
     capabilities: ["methylation array analysis", "bisulfite-seq analysis", "DMP detection", "DMR detection", "methylation clocks", "cell type deconvolution"],
     suitableFor: ["methylation-array", "wgbs", "rrbs", "epic", "450k"],
     skills: ["dna-methylation", "shared/omics-general"],
-    tools: [...BASE_SANDBOX_TOOLS, "pubmed", "searchGene", "searchPathway", "lookupGoTerm", "searchInteractions"],
+    tools: [...BASE_SANDBOX_TOOLS, "pubmed", "searchGene", "lookupAnnotation", "searchInteractions"],
 };
 export function createDnaMethylationAgent(deps) {
     return createSandboxAgent(deps, meta, dnaMethylationAgentPrompt);

package/dist/agents/sandbox/drug-repurposing-agent.js

@@ -19,23 +19,18 @@ export const meta = {
     skills: ["drug-repurposing", "cheminformatics", "shared/omics-general"],
     tools: [
         ...BASE_SANDBOX_TOOLS,
-        "checkSafetyPanel",
+        "targetSafety",
         "pubmed",
         "searchGene",
-        "searchPathway",
-        "lookupGoTerm",
+        "lookupAnnotation",
         "searchInteractions",
         "chembl",
         "opentargets",
         "searchClinicalTrials",
         "searchFaers",
-        "searchGwasCatalog",
-        "searchClinvar",
-        "searchDisgenet",
-        "searchDrugbank",
-        "searchDgidb",
-        "searchBgeeExpression",
-        "getImpcKoProfile",
+        "geneDiseaseEvidence",
+        "drugGeneInteractions",
+        "genePreclinicalProfile",
         "comptox",
     ],
 };

package/dist/agents/sandbox/enrichment-agent.js

@@ -8,7 +8,7 @@ export const meta = {
     capabilities: ["pathway enrichment", "gene set enrichment", "GO analysis", "functional annotation"],
     suitableFor: ["gene-lists", "ranked-lists", "score-matrices", "general-omics"],
     skills: ["enrichment", "shared/omics-general"],
-    tools: [...BASE_SANDBOX_TOOLS, "pubmed", "searchGene", "searchPathway", "lookupGoTerm", "searchInteractions"],
+    tools: [...BASE_SANDBOX_TOOLS, "pubmed", "searchGene", "lookupAnnotation", "searchInteractions"],
 };
 export function createEnrichmentAgent(deps) {
     return createSandboxAgent(deps, meta, enrichmentAgentPrompt);

package/dist/agents/sandbox/genomic-variant-agent.js

@@ -8,17 +8,7 @@ export const meta = {
     capabilities: ["variant calling", "variant annotation", "GWAS", "CNV detection", "structural variant detection", "variant filtering"],
     suitableFor: ["wgs", "wes", "gwas", "cnv-sv", "targeted-panels"],
     skills: ["genomic-variants", "shared/omics-general"],
-    tools: [
-        ...BASE_SANDBOX_TOOLS,
-        "pubmed",
-        "searchGene",
-        "searchPathway",
-        "lookupGoTerm",
-        "searchInteractions",
-        "searchClinvar",
-        "searchDgidb",
-        "searchGwasCatalog",
-    ],
+    tools: [...BASE_SANDBOX_TOOLS, "pubmed", "searchGene", "lookupAnnotation", "searchInteractions", "geneDiseaseEvidence", "drugGeneInteractions"],
 };
 export function createGenomicVariantAgent(deps) {
     return createSandboxAgent(deps, meta, genomicVariantAgentPrompt);

package/dist/agents/sandbox/immune-profiling-agent.js

@@ -24,7 +24,7 @@ export const meta = {
         "immune-cell-composition",
     ],
     skills: ["immune-profiling", "shared/omics-general"],
-    tools: [...BASE_SANDBOX_TOOLS, "pubmed", "searchGene", "searchPathway", "lookupGoTerm", "searchInteractions", "searchGeoDatasets", "opentargets"],
+    tools: [...BASE_SANDBOX_TOOLS, "pubmed", "searchGene", "lookupAnnotation", "searchInteractions", "searchGeoDatasets", "opentargets"],
 };
 export function createImmuneProfilingAgent(deps) {
     return createSandboxAgent(deps, meta, immuneProfilingAgentPrompt);

package/dist/agents/sandbox/index.js

@@ -18,7 +18,6 @@ import { createDataProfilerAgent, meta as dataProfilerMeta } from "./data-profil
 import { createDnaMethylationAgent, meta as dnaMethylationMeta } from "./dna-methylation-agent.js";
 import { createDrugRepurposingAgent, meta as drugRepurposingMeta } from "./drug-repurposing-agent.js";
 import { createEnrichmentAgent, meta as enrichmentMeta } from "./enrichment-agent.js";
-import { createEphemeralExecutorAgent, meta as ephemeralExecutorMeta } from "./ephemeral-executor.js";
 import { createGenomicVariantAgent, meta as genomicVariantMeta } from "./genomic-variant-agent.js";
 import { createImmuneProfilingAgent, meta as immuneProfilingMeta } from "./immune-profiling-agent.js";
 import { createMetabolomicsAgent, meta as metabolomicsMeta } from "./metabolomics-agent.js";
@@ -62,7 +61,6 @@ export const SANDBOX_AGENT_META = {
     [immuneProfilingMeta.id]: immuneProfilingMeta,
     [drugRepurposingMeta.id]: drugRepurposingMeta,
     [scientificExecutorMeta.id]: scientificExecutorMeta,
-    [ephemeralExecutorMeta.id]: ephemeralExecutorMeta,
 };
 /**
  * Build every sandbox `AgentDefinition` from the shared deps. The returned
@@ -91,6 +89,5 @@ export function createSandboxAgents(deps) {
         [immuneProfilingMeta.id]: createImmuneProfilingAgent(deps),
         [drugRepurposingMeta.id]: createDrugRepurposingAgent(deps),
         [scientificExecutorMeta.id]: createScientificExecutorAgent(deps),
-        [ephemeralExecutorMeta.id]: createEphemeralExecutorAgent(deps),
     };
 }

package/dist/agents/sandbox/multi-omics-integration-agent.js

@@ -15,7 +15,7 @@ export const meta = {
     ],
     suitableFor: ["multi-omics", "cross-modality-integration"],
     skills: ["multi-omics-integration", "shared/omics-general"],
-    tools: [...BASE_SANDBOX_TOOLS, "pubmed", "searchGene", "searchPathway", "lookupGoTerm", "searchInteractions", "searchBgeeExpression", "getImpcKoProfile"],
+    tools: [...BASE_SANDBOX_TOOLS, "pubmed", "searchGene", "lookupAnnotation", "searchInteractions", "genePreclinicalProfile"],
 };
 export function createMultiOmicsIntegrationAgent(deps) {
     return createSandboxAgent(deps, meta, multiOmicsIntegrationAgentPrompt);

package/dist/agents/sandbox/network-agent.js

@@ -8,7 +8,7 @@ export const meta = {
     capabilities: ["network analysis", "co-expression networks", "regulatory analysis", "module detection", "TF activity inference"],
     suitableFor: ["expression-matrices", "correlation-matrices", "general-omics"],
     skills: ["network-regulatory", "shared/omics-general"],
-    tools: [...BASE_SANDBOX_TOOLS, "pubmed", "searchGene", "searchPathway", "lookupGoTerm", "searchInteractions"],
+    tools: [...BASE_SANDBOX_TOOLS, "pubmed", "searchGene", "lookupAnnotation", "searchInteractions"],
     defaultMaxSteps: 35,
 };
 export function createNetworkAgent(deps) {

package/dist/agents/sandbox/pkpd-clinical-response-agent.js

@@ -36,16 +36,13 @@ export const meta = {
         ...BASE_SANDBOX_TOOLS,
         "pubmed",
         "searchGene",
-        "searchPathway",
-        "lookupGoTerm",
+        "lookupAnnotation",
         "searchInteractions",
         "searchClinicalTrials",
         "searchFaers",
-        "searchPharmgkb",
+        "drugGeneInteractions",
         "chembl",
-        "searchDgidb",
-        "searchBgeeExpression",
-        "getImpcKoProfile",
+        "genePreclinicalProfile",
     ],
 };
 export function createPkpdClinicalResponseAgent(deps) {

package/dist/agents/sandbox/scientific-executor.js

@@ -39,7 +39,7 @@ export const meta = {
         "drug-repurposing",
         "shared/omics-general",
     ],
-    tools: [...BASE_SANDBOX_TOOLS, "pubmed", "searchGene", "searchPathway", "lookupGoTerm", "searchInteractions"],
+    tools: [...BASE_SANDBOX_TOOLS, "pubmed", "searchGene", "lookupAnnotation", "searchInteractions"],
     plannable: false,
 };
 export function createScientificExecutorAgent(deps) {

package/dist/agents/sandbox/shared.d.ts

@@ -78,7 +78,7 @@ export interface SandboxAgentDeps extends EnvironmentStorePaths {
      * Per-run blocker cell (see the harness-sandbox-agents spec). When present, the agent gets a
      * `report_blocker` tool that records `{ kind: "blocker", reason }` into it;
      * the sandbox-step body reads `holder.outcome` after the loop. Omit for
-     * agents that have no terminal status to declare (ephemeral, data profiler).
+     * agents that have no terminal status to declare (such as the data profiler).
      */
     readonly blockerHolder?: BlockerHolder;
 }
@@ -89,7 +89,7 @@ export interface SandboxAgentPromptOptions {
     /**
      * Enforced read-only: omit `write_file` + `edit_file` from the workspace
      * surface. `execute_command` and all read tools stay. Pair with a sandbox
-     * provisioned with no read-write mount (ephemeral) so no writable location
+     * provisioned with no read-write mount so no writable location
      * exists outside container-local `/tmp`. Defaults to false.
      */
     readonly readOnly?: boolean;

package/dist/agents/sandbox/shared.js

@@ -26,7 +26,7 @@ import { createInspectRunTool } from "../../tools/research/inspect-run.js";
 // Data-profile retrieval (dependency-bearing) — always-on, see `createSandboxAgent`.
 import { createInspectDataProfileTool } from "../../tools/research/inspect-data-profile.js";
 // Bio leaf tools.
-import { checkSafetyPanelTool, chemblTool, getImpcKoProfileTool, lookupGoTermTool, openTargetsTool, pubchemTool, searchBgeeExpressionTool, searchClinicalTrialsTool, createSearchDgidbTool, searchFaersTool, searchGeneTool, searchGeoDatasetsTool, searchGwasCatalogTool, searchInteractionsTool, searchPathwayTool, searchPharmgkbTool, } from "../../tools/bio/index.js";
+import { chemblTool, genePreclinicalProfileTool, lookupAnnotationTool, openTargetsTool, pubchemTool, searchClinicalTrialsTool, searchFaersTool, searchGeneTool, searchGeoDatasetsTool, searchInteractionsTool, targetSafetyTool, } from "../../tools/bio/index.js";
 import { createNcbiTools, createChemDbTools } from "../../tools/bio/keys.js";
 // Workspace read surface.
 import { createFileStatTool, createGrepTool, createListFilesTool, createReadFileTool, createWorkspaceSearchTool } from "../../tools/workspace/index.js";
@@ -52,7 +52,7 @@ export const BASE_SANDBOX_TOOLS = ["listAvailablePackages", "listAvailableRefs",
  */
 function resolveSandboxTools(deps, tools) {
     const ncbi = createNcbiTools(deps.bioKeys);
-    const chemDb = createChemDbTools(deps.bioKeys);
+    const chemDb = createChemDbTools(deps.bioKeys, { ...(deps.logger ? { logger: deps.logger } : {}) });
     const registry = {
         listAvailablePackages: createListAvailablePackagesTool({ ...(deps.packagesFile ? { packagesFile: deps.packagesFile } : {}) }),
         listAvailableRefs: createListAvailableRefsTool({ ...(deps.refStorePath ? { refStorePath: deps.refStorePath } : {}) }),
@@ -61,24 +61,18 @@ function resolveSandboxTools(deps, tools) {
         inspectRun: createInspectRunTool(deps.pool),
         pubmed: ncbi.pubmed,
         searchGene: searchGeneTool,
-        searchPathway: searchPathwayTool,
-        lookupGoTerm: lookupGoTermTool,
+        lookupAnnotation: lookupAnnotationTool,
         searchInteractions: searchInteractionsTool,
         chembl: chemblTool,
         pubchem: pubchemTool,
         opentargets: openTargetsTool,
-        searchPharmgkb: searchPharmgkbTool,
+        geneDiseaseEvidence: chemDb.geneDiseaseEvidence,
+        drugGeneInteractions: chemDb.drugGeneInteractions,
+        genePreclinicalProfile: genePreclinicalProfileTool,
         searchFaers: searchFaersTool,
         searchClinicalTrials: searchClinicalTrialsTool,
         searchGeoDatasets: searchGeoDatasetsTool,
-        searchClinvar: ncbi.searchClinvar,
-        searchDgidb: createSearchDgidbTool({ ...(deps.logger ? { logger: deps.logger } : {}) }),
-        searchGwasCatalog: searchGwasCatalogTool,
-        searchDisgenet: chemDb.searchDisgenet,
-        searchDrugbank: chemDb.searchDrugbank,
-        searchBgeeExpression: searchBgeeExpressionTool,
-        getImpcKoProfile: getImpcKoProfileTool,
-        checkSafetyPanel: checkSafetyPanelTool,
+        targetSafety: targetSafetyTool,
         comptox: chemDb.comptox,
     };
     const seen = new Set();
@@ -111,7 +105,7 @@ function buildWorkspaceTools(deps, readOnly) {
     // writes are confined here. `allowedWritePrefix` is its host path; the
     // in-sandbox path (the `execute_command` default cwd, see the harness-workspace-tools spec) is the same
     // location under the `/{analysisId}` mount — derived from the host path so
-    // it is correct for non-step agents (data profiler, ephemeral) too.
+    // it is correct for non-step agents such as the data profiler too.
     const hostWorkingDir = step.allowedWritePrefix;
     const sandboxWorkingDir = toSandboxPath(step.workspaceRoot, step.analysisId, hostWorkingDir);
     const mutateTools = readOnly

package/dist/agents/sandbox/translational-safety-agent.js

@@ -33,19 +33,16 @@ export const meta = {
     skills: ["translational-safety", "cheminformatics", "shared/omics-general"],
     tools: [
         ...BASE_SANDBOX_TOOLS,
-        "checkSafetyPanel",
+        "targetSafety",
         "pubmed",
         "searchGene",
-        "searchPathway",
-        "lookupGoTerm",
+        "lookupAnnotation",
         "searchInteractions",
         "opentargets",
         "searchFaers",
-        "searchPharmgkb",
-        "searchDgidb",
+        "drugGeneInteractions",
         "comptox",
-        "searchBgeeExpression",
-        "getImpcKoProfile",
+        "genePreclinicalProfile",
     ],
 };
 export function createTranslationalSafetyAgent(deps) {

package/dist/agents/sandbox/types.d.ts

@@ -6,13 +6,13 @@
  * each name to a concrete `Tool` (pure leaf or fully dep-bound factory
  * output) — unknown names throw at composition time, not at first LLM call.
  *
- * `searchDisgenet` and `searchDrugbank` require keys (`DISGENET_API_KEY`,
- * `DRUGBANK_API_KEY`); without the key the underlying header builder
- * throws on first call, which the harness surfaces as a tool `is_error`
- * envelope. `searchGwasCatalog` is fully public.
+ * `geneDiseaseEvidence`, `drugGeneInteractions` and `comptox` each span several
+ * corpora, some of which need a key (`DISGENET_API_KEY`, `DRUGBANK_API_KEY`,
+ * `EPA_CCTE_API_KEY`). A missing key degrades that ONE corpus to `unavailable`
+ * in the tool's `perSource` report; the rest of the call still answers.
  */
 /** Closed allowlist of tools any sandbox agent may declare. */
-export type SandboxToolName = "listAvailablePackages" | "listAvailableRefs" | "resolveLibraryId" | "queryDocs" | "inspectRun" | "pubmed" | "searchGene" | "searchPathway" | "lookupGoTerm" | "searchInteractions" | "chembl" | "pubchem" | "opentargets" | "searchPharmgkb" | "searchFaers" | "searchClinicalTrials" | "searchGeoDatasets" | "searchClinvar" | "searchDgidb" | "searchGwasCatalog" | "searchDisgenet" | "searchDrugbank" | "searchBgeeExpression" | "getImpcKoProfile" | "checkSafetyPanel" | "comptox";
+export type SandboxToolName = "listAvailablePackages" | "listAvailableRefs" | "resolveLibraryId" | "queryDocs" | "inspectRun" | "pubmed" | "searchGene" | "lookupAnnotation" | "searchInteractions" | "chembl" | "pubchem" | "opentargets" | "geneDiseaseEvidence" | "drugGeneInteractions" | "genePreclinicalProfile" | "searchFaers" | "searchClinicalTrials" | "searchGeoDatasets" | "targetSafety" | "comptox";
 /** Planner-facing metadata + tool allowlist for one sandbox agent. */
 export interface AgentMeta {
     /** Stable agent id — also the key in the catalog and the `AgentDefinition.id`. */

package/dist/agents/sandbox/types.js

@@ -6,10 +6,10 @@
  * each name to a concrete `Tool` (pure leaf or fully dep-bound factory
  * output) — unknown names throw at composition time, not at first LLM call.
  *
- * `searchDisgenet` and `searchDrugbank` require keys (`DISGENET_API_KEY`,
- * `DRUGBANK_API_KEY`); without the key the underlying header builder
- * throws on first call, which the harness surfaces as a tool `is_error`
- * envelope. `searchGwasCatalog` is fully public.
+ * `geneDiseaseEvidence`, `drugGeneInteractions` and `comptox` each span several
+ * corpora, some of which need a key (`DISGENET_API_KEY`, `DRUGBANK_API_KEY`,
+ * `EPA_CCTE_API_KEY`). A missing key degrades that ONE corpus to `unavailable`
+ * in the tool's `perSource` report; the rest of the call still answers.
  */
 /** Default runaway-guard for sandbox agents. */
 export const SANDBOX_AGENT_DEFAULT_MAX_ITERATIONS = 50;

package/dist/app/chat-turn.js

@@ -17,8 +17,9 @@ import { deriveThreadTitle } from "../memory/derive-thread-title.js";
 import { createThreadHistory } from "../memory/thread-history.js";
 import { createThreadStore } from "../memory/thread-store.js";
 import { createWorkingMemory } from "../memory/working-memory.js";
-import { loadAnalysisStatus } from "../state/index.js";
+import { loadAnalysisStatus, queryNonTerminalRunsByAnalysis } from "../state/index.js";
 import { assembleMessages } from "./message-assembly.js";
+import { renderRunActivity, renderRunActivityUnavailable, RUN_ACTIVITY_DETAIL_LIMIT } from "./run-activity.js";
 import { createNoopLogger } from "../lib/console-logger.js";
 /**
  * Prepare one chat turn: resolve thread ownership, seed the title, load
@@ -53,12 +54,14 @@ export async function prepareChatTurn(deps, params) {
         logger.warn("title-seed failed (non-fatal)", logger.errorFields(err));
     }
     const analysisState = await loadAnalysisStatus(pool, analysisId).unwrapOr(null);
+    const runActivityContext = await queryNonTerminalRunsByAnalysis(pool, analysisId, RUN_ACTIVITY_DETAIL_LIMIT).match((activity) => renderRunActivity(activity), () => renderRunActivityUnavailable());
     const history = createThreadHistory(pool);
     const { messages, userMessage } = await assembleMessages({
         threadId,
         analysisId,
         userInput,
         analysisContext: analysisState?.context ?? null,
+        runActivityContext,
         history,
         workingMemory: createWorkingMemory(pool),
     });

package/dist/app/message-assembly.d.ts

@@ -5,12 +5,13 @@
  *
  *   [ ...loadRecent(threadId, budget)            ← stable, cacheable prefix
  *     {user: cortex_analysis_state.context},     ← tail
+ *     {user: runActivityContext},                 ← tail
  *     {user: render(workingMemory)},             ← tail
  *     {user: normalizeUnicode(redactSecrets(input))} ]  ← tail
  *
  * `system + tools + history` is the cacheable prefix — it only extends
- * turn-to-turn. Working memory and analysis context go in the **tail** as
- * `user` messages: working memory changes every turn, so a system-message
+ * turn-to-turn. Run activity, working memory, and analysis context go in the
+ * **tail** as `user` messages: they change every turn, so a system-message
  * placement would bust the Anthropic cache prefix.
  *
  * Sanitization (`redactSecrets`, `normalizeUnicode`) is applied **once**, to
@@ -41,6 +42,8 @@ export interface AssembleMessagesArgs {
     readonly userInput: string;
     /** `cortex_analysis_state.context`, already read by the route. `null` when absent. */
     readonly analysisContext: string | null;
+    /** Fresh, non-persisted analysis-wide run activity rendered by chat-turn preparation. */
+    readonly runActivityContext: string;
     /** The conversation message store — supplies the history window. */
     readonly history: ThreadHistory;
     /** The working-memory store — rendered into the tail. */

package/dist/app/message-assembly.js

@@ -5,12 +5,13 @@
  *
  *   [ ...loadRecent(threadId, budget)            ← stable, cacheable prefix
  *     {user: cortex_analysis_state.context},     ← tail
+ *     {user: runActivityContext},                 ← tail
  *     {user: render(workingMemory)},             ← tail
  *     {user: normalizeUnicode(redactSecrets(input))} ]  ← tail
  *
  * `system + tools + history` is the cacheable prefix — it only extends
- * turn-to-turn. Working memory and analysis context go in the **tail** as
- * `user` messages: working memory changes every turn, so a system-message
+ * turn-to-turn. Run activity, working memory, and analysis context go in the
+ * **tail** as `user` messages: they change every turn, so a system-message
  * placement would bust the Anthropic cache prefix.
  *
  * Sanitization (`redactSecrets`, `normalizeUnicode`) is applied **once**, to
@@ -50,6 +51,10 @@ export async function assembleMessages(args) {
             content: `[Analysis Context]\n${args.analysisContext}`,
         });
     }
+    tail.push({
+        role: "user",
+        content: args.runActivityContext,
+    });
     // Working memory — agent-authored, trusted. Always injected (its rendered
     // form names the sections even when empty).
     tail.push({

package/dist/app/run-activity.d.ts

@@ -0,0 +1,13 @@
+/**
+ * Ephemeral conversation-tail projection of non-terminal analysis runs.
+ *
+ * This is derived operational state, not memory: callers render it afresh for
+ * each turn and never persist it to the thread.
+ */
+import type { RunPage } from "../state/runs.js";
+/** Maximum detailed run rows paid into every conversation turn. */
+export declare const RUN_ACTIVITY_DETAIL_LIMIT = 20;
+/** Render the bounded run-activity snapshot injected into a conversation tail. */
+export declare function renderRunActivity(activity: RunPage, nowMs?: number): string;
+/** Render an honest degraded state when the activity projection cannot be read. */
+export declare function renderRunActivityUnavailable(): string;