@inflexa-ai/harness 0.13.0 → 0.14.0

package/dist/agents/conversation-agent.js

@@ -29,7 +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";
@@ -49,12 +49,13 @@ export function createConversationAgent(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,
@@ -62,20 +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
@@ -92,7 +92,14 @@ export function createConversationAgent(deps) {
         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 } : {}) }),
+        createGeneratePlanTool({
+            conversation: { provider, model },
+            pool,
+            resourcePolicy,
+            ...(refStorePath ? { refStorePath } : {}),
+            ...(packagesFile ? { packagesFile } : {}),
+            ...(deps.logger ? { logger: deps.logger } : {}),
+        }),
         createExecuteAnalysisTool({
             pool,
             executeAnalysisWorkflow,

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/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.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();

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;

package/dist/app/run-activity.js

@@ -0,0 +1,51 @@
+/**
+ * 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.
+ */
+/** Maximum detailed run rows paid into every conversation turn. */
+export const RUN_ACTIVITY_DETAIL_LIMIT = 20;
+function compactAge(startedAt, nowMs) {
+    const startedMs = Date.parse(startedAt);
+    if (!Number.isFinite(startedMs))
+        return "unknown age";
+    const elapsedSeconds = Math.max(0, Math.floor((nowMs - startedMs) / 1_000));
+    if (elapsedSeconds < 60)
+        return `${elapsedSeconds}s ago`;
+    const elapsedMinutes = Math.floor(elapsedSeconds / 60);
+    if (elapsedMinutes < 60)
+        return `${elapsedMinutes}m ago`;
+    const elapsedHours = Math.floor(elapsedMinutes / 60);
+    if (elapsedHours < 24)
+        return `${elapsedHours}h ago`;
+    return `${Math.floor(elapsedHours / 24)}d ago`;
+}
+function renderRows(label, rows, nowMs) {
+    if (rows.length === 0)
+        return [];
+    return [
+        `${label}:`,
+        ...rows.map((run) => `- runId: ${run.runId} | planId: ${run.planId ?? "none"} | startedAt: ${run.startedAt} | started: ${compactAge(run.startedAt, nowMs)}`),
+    ];
+}
+/** Render the bounded run-activity snapshot injected into a conversation tail. */
+export function renderRunActivity(activity, nowMs = Date.now()) {
+    const lines = ["[Run Activity]"];
+    if (activity.total === 0) {
+        lines.push("No runs are currently running or suspended.");
+        return lines.join("\n");
+    }
+    const running = activity.runs.filter((run) => run.status === "running");
+    const suspended = activity.runs.filter((run) => run.status === "suspended_insufficient_funds");
+    lines.push(...renderRows("Running", running, nowMs), ...renderRows("Suspended", suspended, nowMs));
+    const omitted = activity.total - activity.runs.length;
+    if (omitted > 0) {
+        lines.push(`Showing ${activity.runs.length} of ${activity.total} non-terminal runs; ${omitted} omitted. Use inspect_run to page the full list.`);
+    }
+    return lines.join("\n");
+}
+/** Render an honest degraded state when the activity projection cannot be read. */
+export function renderRunActivityUnavailable() {
+    return "[Run Activity]\nRun status is temporarily unavailable. Do not infer that no active runs exist.";
+}

package/dist/contracts/target-dossier.d.ts

@@ -1789,8 +1789,8 @@ export declare const ExpressionHeatmapCellSchema: z.ZodObject<{
         medium: "medium";
         low: "low";
         absent: "absent";
-        not_loaded: "not_loaded";
         no_data: "no_data";
+        not_loaded: "not_loaded";
     }>;
 }, z.core.$strip>;
 export declare const ExpressionHeatmapSchema: z.ZodObject<{
@@ -1808,8 +1808,8 @@ export declare const ExpressionHeatmapSchema: z.ZodObject<{
             medium: "medium";
             low: "low";
             absent: "absent";
-            not_loaded: "not_loaded";
             no_data: "no_data";
+            not_loaded: "not_loaded";
         }>;
     }, z.core.$strip>>;
     per_species_coverage: z.ZodRecord<z.ZodString, z.ZodEnum<{
@@ -1915,8 +1915,8 @@ export declare const PreclinicalProfileSchema: z.ZodObject<{
                     medium: "medium";
                     low: "low";
                     absent: "absent";
-                    not_loaded: "not_loaded";
                     no_data: "no_data";
+                    not_loaded: "not_loaded";
                 }>;
             }, z.core.$strip>>;
             per_species_coverage: z.ZodRecord<z.ZodString, z.ZodEnum<{
@@ -4233,8 +4233,8 @@ export declare const DossierSchema: z.ZodObject<{
                             medium: "medium";
                             low: "low";
                             absent: "absent";
-                            not_loaded: "not_loaded";
                             no_data: "no_data";
+                            not_loaded: "not_loaded";
                         }>;
                     }, z.core.$strip>>;
                     per_species_coverage: z.ZodRecord<z.ZodString, z.ZodEnum<{
@@ -5486,8 +5486,8 @@ export declare const ReferenceBiologyV4Shape: z.ZodObject<{
                         medium: "medium";
                         low: "low";
                         absent: "absent";
-                        not_loaded: "not_loaded";
                         no_data: "no_data";
+                        not_loaded: "not_loaded";
                     }>;
                 }, z.core.$strip>>;
                 per_species_coverage: z.ZodRecord<z.ZodString, z.ZodEnum<{
@@ -6918,8 +6918,8 @@ export declare const DossierV4Schema: z.ZodObject<{
                             medium: "medium";
                             low: "low";
                             absent: "absent";
-                            not_loaded: "not_loaded";
                             no_data: "no_data";
+                            not_loaded: "not_loaded";
                         }>;
                     }, z.core.$strip>>;
                     per_species_coverage: z.ZodRecord<z.ZodString, z.ZodEnum<{
@@ -9135,8 +9135,8 @@ export declare const DossierV4BodySchema: z.ZodObject<{
                             medium: "medium";
                             low: "low";
                             absent: "absent";
-                            not_loaded: "not_loaded";
                             no_data: "no_data";
+                            not_loaded: "not_loaded";
                         }>;
                     }, z.core.$strip>>;
                     per_species_coverage: z.ZodRecord<z.ZodString, z.ZodEnum<{
@@ -12210,8 +12210,8 @@ export declare const DossierV5Schema: z.ZodObject<{
                             medium: "medium";
                             low: "low";
                             absent: "absent";
-                            not_loaded: "not_loaded";
                             no_data: "no_data";
+                            not_loaded: "not_loaded";
                         }>;
                     }, z.core.$strip>>;
                     per_species_coverage: z.ZodRecord<z.ZodString, z.ZodEnum<{
@@ -14932,8 +14932,8 @@ export declare const DossierV5BodySchema: z.ZodObject<{
                             medium: "medium";
                             low: "low";
                             absent: "absent";
-                            not_loaded: "not_loaded";
                             no_data: "no_data";
+                            not_loaded: "not_loaded";
                         }>;
                     }, z.core.$strip>>;
                     per_species_coverage: z.ZodRecord<z.ZodString, z.ZodEnum<{
@@ -16561,8 +16561,8 @@ export declare const DossierSchemaV3Legacy: z.ZodObject<{
                             medium: "medium";
                             low: "low";
                             absent: "absent";
-                            not_loaded: "not_loaded";
                             no_data: "no_data";
+                            not_loaded: "not_loaded";
                         }>;
                     }, z.core.$strip>>;
                     per_species_coverage: z.ZodRecord<z.ZodString, z.ZodEnum<{

package/dist/execution/report-runner.js

@@ -147,8 +147,8 @@ export async function runReportIteration(deps, opts) {
                 signal: opts.signal,
                 emit: opts.emit,
                 runStep: passthroughStep,
-            }, {
                 resolved: () => outcome !== undefined,
+            }, {
                 tools: [buildReportTool, submitReportTool],
                 nudge: "You stopped without calling submit_report, so this report version " +
                     "was not recorded. Build the report if needed, then call " +