@inflexa-ai/harness 0.1.1 → 0.3.0

package/README.md

@@ -37,6 +37,9 @@ import {
     createNoopArtifactRegistry,     // ArtifactRegistry seam
     UnavailablePreviewPublisher,    // PreviewPublisher seam
     createDbosRunLauncher,          // shared RunLauncher
+    createConsoleLogger,            // Logger — writes to console
+    createNoopLogger,               // Logger — discards (the fallback when none is wired)
+    defaultErrorFields,             // the shipped `Logger.errorFields` mapping
     defineTool,
     runAgent,
     makeLocalAuth,
@@ -45,6 +48,51 @@ import {
 
 `assembleCoreRuntime` is the single composition point: it registers the durable workflows and builds the conversation agent over them. The harness declares **five capability seams** an embedder wires — `RunAuthorizer`, `ResolveBilling`, `ArtifactRegistry`, `RunCharge`, `PreviewPublisher` — plus the **shared `RunLauncher`** (one host-neutral realization, `createDbosRunLauncher`). Local, dependency-free realizations of all five ship from the barrel; an embedder constructs them (or its own) and passes them in. The harness only ever sees the interface.
 
+## Logging
+
+The harness names no logging library. It logs through a `Logger` you supply, so the destination, format, and verbosity stay yours:
+
+```ts
+export interface Logger {
+    debug(msg: string, fields?: LogFields): void;
+    info(msg: string, fields?: LogFields): void;
+    warn(msg: string, fields?: LogFields): void;
+    error(msg: string, fields?: LogFields): void;
+    with(fields: LogFields): Logger;        // bind context onto every record (slog's `With`)
+    named(name: string): Logger;            // bind a namespace, rendered as a `[a.b]` message prefix
+    errorFields(err: unknown): LogFields;   // normalize a thrown value; `defaultErrorFields` is the shipped mapping
+}
+```
+
+Pass `createConsoleLogger()` if you have no logging infrastructure. Wire nothing and the harness falls back to `createNoopLogger()` — it never falls back to `console`, because a host whose UI owns stdout (an alternate-screen TUI, say) discards console output, and a diagnostic written to a discarded stream is worse than no diagnostic at all.
+
+`errorFields` is on the interface, not a helper we own, so your realization can defer to your sink's native error handling rather than a shape we imposed.
+
+**Migrating from a version that took a `pino.Logger`** — `bootHarness` and the deps bags now take this interface. pino is object-first where this is message-first, so pass an adapter:
+
+```ts
+import type { LogFields, Logger } from "@inflexa-ai/harness";
+import type pino from "pino";
+
+function pinoAsHarnessLogger(p: pino.Logger, names: readonly string[] = []): Logger {
+    const prefixed = (msg: string): string => (names.length > 0 ? `[${names.join(".")}] ${msg}` : msg);
+    const emit =
+        (level: "debug" | "info" | "warn" | "error") =>
+        (msg: string, fields?: LogFields): void => {
+            p[level](fields ?? {}, prefixed(msg));
+        };
+    return {
+        debug: emit("debug"),
+        info: emit("info"),
+        warn: emit("warn"),
+        error: emit("error"),
+        with: (fields) => pinoAsHarnessLogger(p.child(fields), names),
+        named: (name) => pinoAsHarnessLogger(p, [...names, name]),
+        errorFields: (err) => ({ err }), // let pino's own `err` serializer render it
+    };
+}
+```
+
 ## How it executes
 
 Chat is a plain in-process turn (`prepareChatTurn` → `runAgent` → `appendTurn`); the harness ships no HTTP layer, so the host owns the route. Compute-heavy work runs as **durable workflows** — `executeAnalysis` starts a child workflow per plan step once its dependencies have completed, and each step drives a sandbox agent inside a container. The same `runAgent` primitive runs in both modes; durability and the event sink are injected, so the loop body is identical.

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

@@ -17,13 +17,14 @@
  * `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. `iterateReport` is wired here too — in-process Nunjucks
- * rendering driven by the in-process `report-builder` agent (no sandbox);
- * the 4 custom report tools (`build_report`, `submit_report`,
- * `preview_snapshot`, `mint_preview_url`) plus the version-fs write tools
- * (`write_file`, `edit_file`, `read_file`, `mkdir` from `createVersionFsTools`)
- * are constructed inside the runner so they share closure-captured outcome
- * state + preview-dir paths.
+ * the workflow and it is never recovered. 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
+ * sandbox). The 4 custom tools the builder itself drives (`build_report`, its
+ * own terminal `submit_report`, `preview_snapshot`, `mint_preview_url`) are
+ * constructed inside the runner so they share closure-captured outcome state +
+ * preview-dir paths.
  * The workspace read surface (`read_file`, `grep`, `workspace_search`) is
  * wired here over the `WorkspaceFilesystem` seam.
  */
@@ -38,12 +39,15 @@ import type { ResolveWorkspaceRoot } from "../workspace/paths.js";
 import { type BioToolKeys } from "../tools/bio/keys.js";
 import type { RunAuthorizer } from "../execution/run-authorizer.js";
 import type { RunLauncher } from "../execution/run-launcher.js";
-import { type IterateReportDeps } from "../tools/iterate-report.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";
 /** The shared dependencies the composition root explodes apart. */
 export interface ConversationAgentDeps {
+    /** Operational logging seam; omitted falls back to no-op. */
+    readonly logger?: Logger;
     /** The LLM seam every loop-driving tool runs its sub-agent on. */
     readonly provider: ChatProvider;
     /** Postgres pool — plan persistence, run inspection, workspace index, working memory. */
@@ -80,14 +84,14 @@ export interface ConversationAgentDeps {
      */
     readonly runLauncher: RunLauncher;
     /**
-     * Preview-publishing seam factory for `iterate_report` — injected, not
+     * Preview-publishing seam factory for `submit_report` — injected, not
      * constructed here. The managed root closes its platform deps over this; the
      * OSS root returns the "unavailable" publisher.
      */
-    readonly createPreviewPublisher: IterateReportDeps["createPreviewPublisher"];
+    readonly createPreviewPublisher: SubmitReportDeps["createPreviewPublisher"];
     /** API keys for the external bio/chem data sources. */
     readonly bioKeys: BioToolKeys;
-    /** Root templates dir for in-process report rendering (`iterateReport`). */
+    /** Root templates dir for in-process report rendering (`submit_report`). */
     readonly templatesDir: string;
     /** Skills root; the in-process report-builder gets `report-html` skill tools. */
     readonly skillsDir: string;

package/dist/agents/conversation-agent.js

@@ -17,13 +17,14 @@
  * `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. `iterateReport` is wired here too — in-process Nunjucks
- * rendering driven by the in-process `report-builder` agent (no sandbox);
- * the 4 custom report tools (`build_report`, `submit_report`,
- * `preview_snapshot`, `mint_preview_url`) plus the version-fs write tools
- * (`write_file`, `edit_file`, `read_file`, `mkdir` from `createVersionFsTools`)
- * are constructed inside the runner so they share closure-captured outcome
- * state + preview-dir paths.
+ * the workflow and it is never recovered. 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
+ * sandbox). The 4 custom tools the builder itself drives (`build_report`, its
+ * own terminal `submit_report`, `preview_snapshot`, `mint_preview_url`) are
+ * constructed inside the runner so they share closure-captured outcome state +
+ * preview-dir paths.
  * The workspace read surface (`read_file`, `grep`, `workspace_search`) is
  * wired here over the `WorkspaceFilesystem` seam.
  */
@@ -31,16 +32,16 @@ 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, searchCompoundsTool, getBioactivityTool, searchTargetsTool, getMechanismTool, getDrugInfoTool, searchPubchemCompoundTool, getPubchemCrossRefsTool, getPubchemAssaysTool, searchOpenTargetsTool, getTargetSafetyTool, searchPharmgkbTool, searchFaersTool, searchClinicalTrialsTool, searchGeoDatasetsTool, searchDgidbTool, searchBgeeExpressionTool, getImpcKoProfileTool, checkSafetyPanelTool, } from "../tools/bio/index.js";
+import { searchGeneTool, searchPathwayTool, lookupGoTermTool, searchInteractionsTool, chemblTool, pubchemTool, openTargetsTool, searchPharmgkbTool, searchFaersTool, searchClinicalTrialsTool, searchGeoDatasetsTool, createSearchDgidbTool, searchBgeeExpressionTool, getImpcKoProfileTool, checkSafetyPanelTool, } from "../tools/bio/index.js";
 import { createNcbiTools, createChemDbTools } from "../tools/bio/keys.js";
 // Dependency-bearing tool factories.
-import { createGeneratePlanTool, createLiteratureReviewerTool, createInspectRunTool, createGenerateAnalogyReportTool } from "../tools/research/index.js";
+import { createGeneratePlanTool, createLiteratureReviewerTool, createInspectRunTool, createInspectDataProfileTool, createGenerateAnalogyReportTool, } from "../tools/research/index.js";
 import { createFileStatTool, createGrepTool, createListFilesTool, createReadFileTool, createShowPlanTool, createWorkspaceSearchTool, showFileTool, } from "../tools/workspace/index.js";
 import { showUserTool } from "../tools/display/index.js";
 import { createUpdateWorkingMemoryTool } from "../tools/memory/index.js";
 import { createExecutePlanTool } from "../tools/execute-plan.js";
 import { createRunEphemeralTool } from "../tools/run-ephemeral.js";
-import { createIterateReportTool } from "../tools/iterate-report.js";
+import { planReportTool, createReportSubmitTool } from "../tools/iterate-report.js";
 /** Canonical agent id — the single source of truth. */
 export const CONVERSATION_AGENT_ID = "conversation-agent";
 /** Runaway guard — heavy tool-driving turns need generous headroom. */
@@ -57,39 +58,30 @@ export function createConversationAgent(deps) {
         searchPathwayTool,
         lookupGoTermTool,
         searchInteractionsTool,
-        ncbi.searchPubMed,
-        ncbi.getArticleDetails,
-        ncbi.getArticleFullText,
-        // ChEMBL.
-        searchCompoundsTool,
-        getBioactivityTool,
-        searchTargetsTool,
-        getMechanismTool,
-        getDrugInfoTool,
-        // PubChem.
-        searchPubchemCompoundTool,
-        getPubchemCrossRefsTool,
-        getPubchemAssaysTool,
+        // Literature (search / details / fulltext behind one action).
+        ncbi.pubmed,
+        // ChEMBL (compounds / drug / mechanism / bioactivity / targets behind one action).
+        chemblTool,
+        // PubChem (compound / crossrefs / assays behind one action).
+        pubchemTool,
         // Translational medicine.
-        searchOpenTargetsTool,
-        getTargetSafetyTool,
+        openTargetsTool,
         searchPharmgkbTool,
         searchFaersTool,
         searchClinicalTrialsTool,
         searchGeoDatasetsTool,
-        searchDgidbTool,
+        createSearchDgidbTool({ ...(deps.logger ? { logger: deps.logger } : {}) }),
         // Preclinical.
         searchBgeeExpressionTool,
         getImpcKoProfileTool,
         // Off-target liability.
         checkSafetyPanelTool,
-        // EPA CompTox.
-        chemDb.searchToxcast,
-        chemDb.searchCtxHazard,
-        chemDb.searchCtxChemical,
-        chemDb.searchCtxExposure,
+        // EPA CompTox (toxcast / hazard / chemical / exposure behind one dataset).
+        chemDb.comptox,
         // 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 }),
         createExecutePlanTool({
             pool,
@@ -103,7 +95,12 @@ export function createConversationAgent(deps) {
             runAuthorizer,
             runLauncher,
         }),
-        createIterateReportTool({
+        // Report authoring: the always-on `plan_report` trigger delivers the
+        // heavy brief schema + rules just-in-time as its result; `submit_report`
+        // takes the composed brief as `unknown` and validates it in-execute, so
+        // the ~12k schema never rides the always-on tool surface.
+        planReportTool,
+        createReportSubmitTool({
             provider,
             pool,
             resolveWorkspaceRoot,
@@ -128,11 +125,11 @@ export function createConversationAgent(deps) {
         createFileStatTool(workspaceFs),
         createGrepTool(workspaceFs),
         // Working memory.
-        createUpdateWorkingMemoryTool(workingMemory),
+        createUpdateWorkingMemoryTool(workingMemory, pool),
     ];
     return {
         id: CONVERSATION_AGENT_ID,
-        systemPrompt: composeSystemPrompt(conversationPrompt),
+        systemPrompt: composeSystemPrompt(conversationPrompt, { identity: true, conversational: true }),
         model,
         tools,
         maxIterations: CONVERSATION_MAX_ITERATIONS,

package/dist/agents/report-builder.js

@@ -17,13 +17,14 @@
  * `AgentDefinition`.
  */
 import { reportBuilderPrompt } from "../prompts/report-builder.js";
+import { composeSystemPrompt } from "./system-prompt.js";
 export const REPORT_BUILDER_AGENT_ID = "report-builder";
 /** Runaway guard — Jinja recovery may take several build/edit cycles. */
 const REPORT_BUILDER_MAX_ITERATIONS = 75;
 export function createReportBuilderAgent(deps) {
     return {
         id: REPORT_BUILDER_AGENT_ID,
-        systemPrompt: reportBuilderPrompt,
+        systemPrompt: composeSystemPrompt(reportBuilderPrompt),
         model: deps.model,
         tools: deps.tools,
         maxIterations: REPORT_BUILDER_MAX_ITERATIONS,

package/dist/agents/sandbox/bulk-transcriptomics-agent.js

@@ -15,7 +15,7 @@ export const meta = {
     ],
     suitableFor: ["bulk-rna-seq", "microarray"],
     skills: ["bulk-transcriptomics", "shared/omics-general"],
-    tools: [...BASE_SANDBOX_TOOLS, "searchPubMed", "getArticleDetails", "getArticleFullText", "searchGeoDatasets"],
+    tools: [...BASE_SANDBOX_TOOLS, "pubmed", "searchGeoDatasets"],
 };
 export function createBulkTranscriptomicsAgent(deps) {
     return createSandboxAgent(deps, meta, bulkTranscriptomicsAgentPrompt);

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

@@ -37,25 +37,7 @@ export const meta = {
         "perturbation-signatures",
     ],
     skills: ["cheminformatics", "shared/omics-general"],
-    tools: [
-        ...BASE_SANDBOX_TOOLS,
-        "searchPubMed",
-        "getArticleDetails",
-        "getArticleFullText",
-        "searchGene",
-        "searchPathway",
-        "lookupGoTerm",
-        "searchInteractions",
-        "searchCompounds",
-        "getBioactivity",
-        "searchTargets",
-        "getMechanism",
-        "getDrugInfo",
-        "searchDgidb",
-        "searchPubchemCompound",
-        "getPubchemCrossRefs",
-        "getPubchemAssays",
-    ],
+    tools: [...BASE_SANDBOX_TOOLS, "pubmed", "searchGene", "searchPathway", "lookupGoTerm", "searchInteractions", "chembl", "searchDgidb", "pubchem"],
 };
 export function createCheminformaticsAgent(deps) {
     return createSandboxAgent(deps, meta, cheminformaticsAgentPrompt);

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

@@ -8,16 +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,
-        "searchPubMed",
-        "getArticleDetails",
-        "getArticleFullText",
-        "searchGene",
-        "searchPathway",
-        "lookupGoTerm",
-        "searchInteractions",
-    ],
+    tools: [...BASE_SANDBOX_TOOLS, "pubmed", "searchGene", "searchPathway", "lookupGoTerm", "searchInteractions"],
 };
 export function createChromatinAgent(deps) {
     return createSandboxAgent(deps, meta, chromatinAgentPrompt);

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

@@ -8,16 +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,
-        "searchPubMed",
-        "getArticleDetails",
-        "getArticleFullText",
-        "searchGene",
-        "searchPathway",
-        "lookupGoTerm",
-        "searchInteractions",
-    ],
+    tools: [...BASE_SANDBOX_TOOLS, "pubmed", "searchGene", "searchPathway", "lookupGoTerm", "searchInteractions"],
 };
 export function createDnaMethylationAgent(deps) {
     return createSandboxAgent(deps, meta, dnaMethylationAgentPrompt);

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

@@ -20,20 +20,13 @@ export const meta = {
     tools: [
         ...BASE_SANDBOX_TOOLS,
         "checkSafetyPanel",
-        "searchPubMed",
-        "getArticleDetails",
-        "getArticleFullText",
+        "pubmed",
         "searchGene",
         "searchPathway",
         "lookupGoTerm",
         "searchInteractions",
-        "searchCompounds",
-        "getBioactivity",
-        "searchTargets",
-        "getMechanism",
-        "getDrugInfo",
-        "searchOpenTargets",
-        "getTargetSafety",
+        "chembl",
+        "opentargets",
         "searchClinicalTrials",
         "searchFaers",
         "searchGwasCatalog",
@@ -43,10 +36,7 @@ export const meta = {
         "searchDgidb",
         "searchBgeeExpression",
         "getImpcKoProfile",
-        "searchToxcast",
-        "searchCtxHazard",
-        "searchCtxChemical",
-        "searchCtxExposure",
+        "comptox",
     ],
 };
 export function createDrugRepurposingAgent(deps) {

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

@@ -8,16 +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,
-        "searchPubMed",
-        "getArticleDetails",
-        "getArticleFullText",
-        "searchGene",
-        "searchPathway",
-        "lookupGoTerm",
-        "searchInteractions",
-    ],
+    tools: [...BASE_SANDBOX_TOOLS, "pubmed", "searchGene", "searchPathway", "lookupGoTerm", "searchInteractions"],
 };
 export function createEnrichmentAgent(deps) {
     return createSandboxAgent(deps, meta, enrichmentAgentPrompt);

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

@@ -9,16 +9,7 @@ export const meta = {
     capabilities: ["data inspection", "quick statistics", "data transformation", "table preview"],
     suitableFor: ["bulk-rna-seq", "single-cell", "proteomics", "metabolomics", "genomics", "transcriptomics", "general-omics"],
     skills: ["shared/omics-general"],
-    tools: [
-        ...BASE_SANDBOX_TOOLS,
-        "searchPubMed",
-        "getArticleDetails",
-        "getArticleFullText",
-        "searchGene",
-        "searchPathway",
-        "lookupGoTerm",
-        "searchInteractions",
-    ],
+    tools: [...BASE_SANDBOX_TOOLS, "pubmed", "searchGene", "searchPathway", "lookupGoTerm", "searchInteractions"],
     plannable: false,
 };
 export function createEphemeralExecutorAgent(deps) {

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

@@ -10,9 +10,7 @@ export const meta = {
     skills: ["genomic-variants", "shared/omics-general"],
     tools: [
         ...BASE_SANDBOX_TOOLS,
-        "searchPubMed",
-        "getArticleDetails",
-        "getArticleFullText",
+        "pubmed",
         "searchGene",
         "searchPathway",
         "lookupGoTerm",

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

@@ -24,19 +24,7 @@ export const meta = {
         "immune-cell-composition",
     ],
     skills: ["immune-profiling", "shared/omics-general"],
-    tools: [
-        ...BASE_SANDBOX_TOOLS,
-        "searchPubMed",
-        "getArticleDetails",
-        "getArticleFullText",
-        "searchGene",
-        "searchPathway",
-        "lookupGoTerm",
-        "searchInteractions",
-        "searchGeoDatasets",
-        "searchOpenTargets",
-        "getTargetSafety",
-    ],
+    tools: [...BASE_SANDBOX_TOOLS, "pubmed", "searchGene", "searchPathway", "lookupGoTerm", "searchInteractions", "searchGeoDatasets", "opentargets"],
 };
 export function createImmuneProfilingAgent(deps) {
     return createSandboxAgent(deps, meta, immuneProfilingAgentPrompt);

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

@@ -8,7 +8,7 @@ export const meta = {
     capabilities: ["peak detection", "feature alignment", "metabolite annotation", "normalization", "statistical analysis", "pathway mapping"],
     suitableFor: ["untargeted-metabolomics", "targeted-metabolomics", "lipidomics"],
     skills: ["metabolomics", "shared/omics-general"],
-    tools: [...BASE_SANDBOX_TOOLS, "searchPubMed", "getArticleDetails", "getArticleFullText"],
+    tools: [...BASE_SANDBOX_TOOLS, "pubmed"],
 };
 export function createMetabolomicsAgent(deps) {
     return createSandboxAgent(deps, meta, metabolomicsAgentPrompt);

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

@@ -8,7 +8,7 @@ export const meta = {
     capabilities: ["diversity analysis", "differential abundance", "taxonomic profiling", "functional profiling", "compositional analysis"],
     suitableFor: ["16s-amplicon", "its-amplicon", "shotgun-metagenomics", "functional-profiling"],
     skills: ["microbiome", "shared/omics-general"],
-    tools: [...BASE_SANDBOX_TOOLS, "searchPubMed", "getArticleDetails", "getArticleFullText"],
+    tools: [...BASE_SANDBOX_TOOLS, "pubmed"],
 };
 export function createMicrobiomeAgent(deps) {
     return createSandboxAgent(deps, meta, microbiomeAgentPrompt);

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

@@ -15,18 +15,7 @@ export const meta = {
     ],
     suitableFor: ["multi-omics", "cross-modality-integration"],
     skills: ["multi-omics-integration", "shared/omics-general"],
-    tools: [
-        ...BASE_SANDBOX_TOOLS,
-        "searchPubMed",
-        "getArticleDetails",
-        "getArticleFullText",
-        "searchGene",
-        "searchPathway",
-        "lookupGoTerm",
-        "searchInteractions",
-        "searchBgeeExpression",
-        "getImpcKoProfile",
-    ],
+    tools: [...BASE_SANDBOX_TOOLS, "pubmed", "searchGene", "searchPathway", "lookupGoTerm", "searchInteractions", "searchBgeeExpression", "getImpcKoProfile"],
 };
 export function createMultiOmicsIntegrationAgent(deps) {
     return createSandboxAgent(deps, meta, multiOmicsIntegrationAgentPrompt);

package/dist/agents/sandbox/multimodal-sc-agent.js

@@ -8,7 +8,7 @@ export const meta = {
     capabilities: ["multimodal integration", "joint embedding", "cross-modality analysis", "protein quantification", "chromatin accessibility"],
     suitableFor: ["cite-seq", "multiome", "tea-seq", "dogma-seq"],
     skills: ["multimodal-single-cell", "shared/omics-general"],
-    tools: [...BASE_SANDBOX_TOOLS, "searchPubMed", "getArticleDetails", "getArticleFullText"],
+    tools: [...BASE_SANDBOX_TOOLS, "pubmed"],
 };
 export function createMultimodalScAgent(deps) {
     return createSandboxAgent(deps, meta, multimodalScAgentPrompt);

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

@@ -8,16 +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,
-        "searchPubMed",
-        "getArticleDetails",
-        "getArticleFullText",
-        "searchGene",
-        "searchPathway",
-        "lookupGoTerm",
-        "searchInteractions",
-    ],
+    tools: [...BASE_SANDBOX_TOOLS, "pubmed", "searchGene", "searchPathway", "lookupGoTerm", "searchInteractions"],
     defaultMaxSteps: 35,
 };
 export function createNetworkAgent(deps) {

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

@@ -34,9 +34,7 @@ export const meta = {
     skills: ["pkpd-clinical-response", "statistical-modeling", "shared/omics-general"],
     tools: [
         ...BASE_SANDBOX_TOOLS,
-        "searchPubMed",
-        "getArticleDetails",
-        "getArticleFullText",
+        "pubmed",
         "searchGene",
         "searchPathway",
         "lookupGoTerm",
@@ -44,11 +42,7 @@ export const meta = {
         "searchClinicalTrials",
         "searchFaers",
         "searchPharmgkb",
-        "searchCompounds",
-        "getBioactivity",
-        "searchTargets",
-        "getMechanism",
-        "getDrugInfo",
+        "chembl",
         "searchDgidb",
         "searchBgeeExpression",
         "getImpcKoProfile",

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

@@ -8,7 +8,7 @@ export const meta = {
     capabilities: ["protein quantification", "differential abundance", "imputation", "normalization", "PTM analysis", "phosphoproteomics"],
     suitableFor: ["dda-proteomics", "dia-proteomics", "tmt-proteomics", "olink", "somascan"],
     skills: ["proteomics", "shared/omics-general"],
-    tools: [...BASE_SANDBOX_TOOLS, "searchPubMed", "getArticleDetails", "getArticleFullText"],
+    tools: [...BASE_SANDBOX_TOOLS, "pubmed"],
 };
 export function createProteomicsAgent(deps) {
     return createSandboxAgent(deps, meta, proteomicsAgentPrompt);

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

@@ -39,16 +39,7 @@ export const meta = {
         "drug-repurposing",
         "shared/omics-general",
     ],
-    tools: [
-        ...BASE_SANDBOX_TOOLS,
-        "searchPubMed",
-        "getArticleDetails",
-        "getArticleFullText",
-        "searchGene",
-        "searchPathway",
-        "lookupGoTerm",
-        "searchInteractions",
-    ],
+    tools: [...BASE_SANDBOX_TOOLS, "pubmed", "searchGene", "searchPathway", "lookupGoTerm", "searchInteractions"],
     plannable: false,
 };
 export function createScientificExecutorAgent(deps) {

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

@@ -8,8 +8,8 @@
  * the workspace mutate trio (`execute_command`, `write_file`, `edit_file`)
  * bound to the shared `SandboxClient` and the step's `allowedWritePrefix`,
  * the workspace read tools (`read_file`, `grep`) over the shared
- * `WorkspaceFilesystem`, and the bio/literature/context7/run-inspection
- * tools its `meta.tools` allowlist names.
+ * `WorkspaceFilesystem`, `inspect_data_profile` over the shared `Pool`, and the
+ * bio/literature/context7/run-inspection tools its `meta.tools` allowlist names.
  *
  * Tool resolution is a single registry lookup — every name in `meta.tools`
  * must map to a concrete `Tool`; unknown names throw at composition time
@@ -25,6 +25,7 @@ import type { ProvenanceCollector as LineageCollector } from "../../provenance/c
 import { type BioToolKeys } from "../../tools/bio/keys.js";
 import { type BlockerHolder } from "../../tools/sandbox/report-blocker.js";
 import type { AgentMeta, SandboxToolName } from "./types.js";
+import type { Logger } from "../../lib/logger.js";
 /**
  * Tools every sandbox agent receives — sandbox-environment introspection,
  * library docs, and run inspection. Spread into each agent's
@@ -50,6 +51,8 @@ export interface SandboxStepCoords {
 }
 /** The shared dependency graph every sandbox agent draws from. */
 export interface SandboxAgentDeps {
+    /** Operational logging seam; omitted falls back to no-op. */
+    readonly logger?: Logger;
     readonly provider: ChatProvider;
     readonly pool: Pool;
     readonly sandboxClient: SandboxClient;
@@ -92,9 +95,20 @@ export interface SandboxAgentPromptOptions {
 }
 /**
  * Build one sandbox `AgentDefinition`. The system prompt is composed once
- * (SOUL kernel + agent body + sandbox standards) — no processors, no
- * conversational layer (sandbox agents are not user-facing). Tools are
- * resolved against the closed allowlist; the workspace surface is always
- * wired regardless of meta.
+ * (SOUL execution core + agent body + sandbox standards) — no processors, and
+ * neither human-facing SOUL layer: a sandbox agent is headless, so the identity
+ * and conversational layers are dead weight in its context while every hard
+ * guardrail it does need rides in the execution core. Tools are resolved
+ * against the closed allowlist; the workspace surface is always wired
+ * regardless of meta.
+ *
+ * The composed `systemPrompt` is a **pure function of the agent type** — nothing
+ * from `deps.step` reaches it, so two steps of one run, and two runs of one
+ * analysis, send a byte-identical ~20k-char prefix that the provider's prompt
+ * cache can actually reuse. Keep it that way: a single interpolated id or path
+ * makes every step's prefix unique again, and each step pays a full cache write
+ * and reads nothing back. Per-step values belong in the step's briefing (its
+ * first user message — see `prompts/briefing.ts`), which names the working
+ * directory, the analysis root, the dataset, and what each dependency produced.
  */
 export declare function createSandboxAgent(deps: SandboxAgentDeps, meta: AgentMeta, body: string, opts?: SandboxAgentPromptOptions): AgentDefinition;