@inflexa-ai/harness 0.2.0 → 0.4.0

package/dist/tasks/data-profile.js

@@ -23,6 +23,7 @@ import { forSubAgent } from "../auth/types.js";
 import { createDataProfilerAgent } from "../agents/sandbox/data-profiler.js";
 import { runToTerminal } from "../loop/run-to-terminal.js";
 import { durableStep } from "../loop/run-step.js";
+import { createNoopLogger } from "../lib/console-logger.js";
 import { unwrapOrThrow } from "../lib/result.js";
 import { defineTool } from "../tools/define-tool.js";
 import { renderWorkspace } from "../prompts/briefing.js";
@@ -128,6 +129,7 @@ export function registerDataProfileWorkflow(deps) {
  * 'failed' on error, and revokes the run authorization on every terminal path.
  */
 export async function runDataProfileBody(input, deps) {
+    const logger = (deps.logger ?? createNoopLogger()).named("data-profile").with({ analysisId: input.analysisId });
     // Ownership defaults to true for inputs persisted before the field existed
     // (a #247 workflow recovered across this deploy): those were always
     // Cortex-owned and must be revoked here.
@@ -138,9 +140,9 @@ export async function runDataProfileBody(input, deps) {
         // embedder populated the tree and handed us this manifest in the workflow
         // input. The body never downloads.
         if (stagedInputs.length === 0) {
-            console.warn(`[data-profile] No input files staged for ${analysisId}`);
+            logger.warn("no input files staged");
             if (!unwrapOrThrow(await completeDataProfile(deps.pool, analysisId)))
-                logTerminalNoop(analysisId, "completion");
+                logTerminalNoop(logger, analysisId, "completion");
             await deps.runAuthorizer.revoke(authorization, "data-profile-completed");
             return;
         }
@@ -190,7 +192,7 @@ export async function runDataProfileBody(input, deps) {
             ``,
             `All file paths in your response must be relative to the analysis root and must EXACTLY match the paths listed above.`,
         ].join("\n");
-        console.log(`[data-profile] execution=${executionId} analysis=${analysisId} starting sandbox`);
+        logger.info("starting sandbox", { executionId });
         const sandbox = await deps.sandboxClient.createSandbox({
             runId: DATA_PROFILE_RUN_LITERAL,
             stepId: DATA_PROFILE_STEP_LITERAL,
@@ -310,13 +312,16 @@ export async function runDataProfileBody(input, deps) {
                 indexed++;
             }
             if (fallbackCount > 0) {
-                console.warn(`[data-profile] ${fallbackCount}/${stagedInputs.length} input file(s) used a deterministic fallback description (analysis=${analysisId}) — profiler omitted them`);
+                logger.warn("input file(s) used a deterministic fallback description — profiler omitted them", {
+                    fallbackCount,
+                    stagedCount: stagedInputs.length,
+                });
             }
-            console.log(`[data-profile] Indexed ${indexed} file(s) for ${analysisId}`);
+            logger.info("indexed file(s)", { indexed });
             // 5. Complete — store the FULL profiler finding plus the input snapshot for
             // staleness detection. The scratch tree is gone; this row is all that survives.
             if (!unwrapOrThrow(await completeDataProfile(deps.pool, analysisId, buildDataProfileResult(profilerData, stagedInputs, new Date().toISOString())))) {
-                logTerminalNoop(analysisId, "completion");
+                logTerminalNoop(logger, analysisId, "completion");
             }
             await deps.runAuthorizer.revoke(authorization, "data-profile-completed");
         }
@@ -325,14 +330,14 @@ export async function runDataProfileBody(input, deps) {
                 await deps.sandboxClient.teardown(sandbox);
             }
             catch (teardownErr) {
-                console.warn(`[data-profile] execution=${executionId} teardown failed (non-fatal):`, teardownErr);
+                logger.warn("teardown failed (non-fatal)", { executionId, ...logger.errorFields(teardownErr) });
             }
         }
     }
     catch (err) {
-        console.error(`[data-profile] Failed for ${analysisId}:`, err);
+        logger.error("profile failed", logger.errorFields(err));
         if (!unwrapOrThrow(await failDataProfile(deps.pool, analysisId, profileFailureReason(err))))
-            logTerminalNoop(analysisId, "failure");
+            logTerminalNoop(logger, analysisId, "failure");
         await deps.runAuthorizer.revoke(authorization, "data-profile-failed");
     }
 }
@@ -342,8 +347,8 @@ export async function runDataProfileBody(input, deps) {
  * there is no `running` row to stamp. Not an error — the ledger correctly moved
  * on; the workflow still revokes its own authorization on the same terminal path.
  */
-function logTerminalNoop(analysisId, write) {
-    console.warn(`[data-profile] ${write} write skipped for ${analysisId}: ledger row not running (cleared or expired concurrently)`);
+function logTerminalNoop(logger, analysisId, write) {
+    logger.warn("terminal write skipped: ledger row not running (cleared or expired concurrently)", { analysisId, write });
 }
 /**
  * Resolve the `RunSession` the workflow runs under. Whether the authorization
@@ -409,6 +414,7 @@ async function startDataProfileWorkflow(deps, params) {
  * Returns what happened, so the caller can surface it (e.g. in the seed response).
  */
 export async function triggerDataProfile(deps, params) {
+    const logger = (deps.logger ?? createNoopLogger()).named("data-profile").with({ analysisId: params.analysisId });
     const { analysisId } = params;
     try {
         // ADVISORY pre-check, not the enforcement — the claim CAS carries the same seed
@@ -420,7 +426,7 @@ export async function triggerDataProfile(deps, params) {
         // a NULL-seed row (`loadDataProfileStatus` would hide the seed of a cleared row).
         const seeded = unwrapOrThrow(await loadSeedInputFileIds(deps.pool, analysisId));
         if (seeded === null || seeded.length === 0) {
-            console.error(`[data-profile] Trigger rejected for ${analysisId}: no seeded input set (missing analysis row or caller skipped seeding)`);
+            logger.error("trigger rejected: no seeded input set (missing analysis row or caller skipped seeding)");
             return "failed";
         }
         // The trigger validates the ledger seed above; it must also validate the manifest
@@ -429,7 +435,7 @@ export async function triggerDataProfile(deps, params) {
         // NULL result while the seed still names files, an incoherence a staleness policy
         // then loops on re-triggering. Refuse the divergence before any claim.
         if (params.stagedInputs.length === 0) {
-            console.error(`[data-profile] Trigger rejected for ${analysisId}: empty manifest dispatched against a seed naming ${seeded.length} file(s)`);
+            logger.error("trigger rejected: empty manifest dispatched against a non-empty seed", { seededCount: seeded.length });
             return "failed";
         }
         const started = unwrapOrThrow(await tryStartDataProfile(deps.pool, analysisId));
@@ -448,7 +454,7 @@ export async function triggerDataProfile(deps, params) {
         return "failed";
     }
     catch (err) {
-        console.error(`[data-profile] Trigger error for ${analysisId}:`, err);
+        logger.error("trigger error", logger.errorFields(err));
         return "failed";
     }
 }
@@ -462,17 +468,18 @@ export async function triggerDataProfile(deps, params) {
  * there is no further channel to report it on.
  */
 async function compensateStartFailure(deps, analysisId, phase, err) {
-    console.error(`[data-profile] ${phase} error for ${analysisId}:`, err);
+    const logger = (deps.logger ?? createNoopLogger()).named("data-profile").with({ analysisId });
+    logger.error("start failed", { phase, ...logger.errorFields(err) });
     const failed = await failDataProfile(deps.pool, analysisId, profileFailureReason(err));
     if (failed.isErr()) {
-        console.error(`[data-profile] Failed to mark ${analysisId} failed after a start error:`, failed.error);
+        logger.error("failed to mark failed after a start error", { phase, err: failed.error });
     }
     else if (!failed.value) {
         // The row this compensation was written to fail is no longer `running` — a
         // concurrent clear/expire already moved it on, so the running-CAS refused the
         // stamp. Nothing wedged at `running`, which is the outcome compensation exists
         // to guarantee; just record the no-op.
-        logTerminalNoop(analysisId, "compensation");
+        logTerminalNoop(logger, analysisId, "compensation");
     }
 }
 /**

package/dist/tools/bio/search-dgidb.d.ts

@@ -8,6 +8,7 @@
  *   - searchType="gene": input HUGO symbols, returns drugs interacting with each.
  *   - searchType="drug": input drug names/concept IDs, returns genes each acts on.
  */
+import type { Logger } from "../../lib/logger.js";
 interface Interaction {
     geneName: string;
     drugName: string;
@@ -26,7 +27,16 @@ interface Interaction {
         value: string;
     }[];
 }
-export declare const searchDgidbTool: import("../define-tool.js").Tool<{
+/**
+ * A factory rather than a bare const (unlike its bio-leaf siblings) because it
+ * logs: DGIdb answers GraphQL partial errors alongside usable data, and an
+ * operator debugging odd interaction results needs to see them. `ToolContext`
+ * carries no deps by design, so a tool that logs is dep-bearing — the same
+ * reason `createSearchClinvarTool` takes its key that way.
+ */
+export declare function createSearchDgidbTool(deps?: {
+    readonly logger?: Logger;
+}): import("../define-tool.js").Tool<{
     query: string | string[];
     searchType: "drug" | "gene";
     minSources: number;

package/dist/tools/bio/search-dgidb.js

@@ -11,6 +11,7 @@
 import { ok } from "neverthrow";
 import { z } from "zod";
 import { defineTool } from "../define-tool.js";
+import { createNoopLogger } from "../../lib/console-logger.js";
 import { apiFetchValidated, describeApiError } from "../lib/api-utils.js";
 const DGIDB_GRAPHQL_URL = "https://dgidb.org/api/graphql";
 const GENE_INTERACTIONS_QUERY = `query($genes: [String!]!) {
@@ -115,85 +116,98 @@ function applyFilters(interactions, filters) {
     }
     return out;
 }
-export const searchDgidbTool = defineTool({
-    id: "search_dgidb",
-    description: "Query the Drug-Gene Interaction Database (DGIdb) for drug-gene interactions. " +
-        "DGIdb aggregates 30+ sources (ChEMBL, DrugBank, TTD, PharmGKB, GuideToPharmacology, CIViC, etc.) " +
-        "and returns source counts as a confidence signal. " +
-        "searchType='gene' returns drugs interacting with input HUGO gene symbols (most common: 'what drugs hit my gene set?'). " +
-        "searchType='drug' returns the genes each input drug is known to act on. " +
-        "Free, no API key required. Sorted by source count desc.",
-    inputSchema: z.object({
-        query: z
-            .union([z.string(), z.array(z.string()).max(50)])
-            .describe("Single identifier or list of up to 50. For searchType='gene': HUGO symbols. For searchType='drug': drug names or DGIdb concept IDs."),
-        searchType: z.enum(["gene", "drug"]).default("gene"),
-        interactionTypes: z.array(z.string()).optional().describe("Case-insensitive substring filter on interaction type. e.g. ['inhibitor', 'antagonist']"),
-        sources: z.array(z.string()).optional().describe("Restrict to interactions from these source DBs (case-insensitive substring)."),
-        minSources: z.number().int().min(1).default(1).describe("Drop interactions supported by fewer than this many sources."),
-        limit: z.number().int().min(1).max(200).default(50).describe("Max interactions per input gene/drug after filtering."),
-    }),
-    execute: async ({ query, searchType = "gene", interactionTypes, sources, minSources = 1, limit = 50 }) => {
-        const inputs = typeof query === "string" ? [query] : query;
-        if (inputs.length === 0 || inputs.every((s) => !s.trim())) {
-            throw new Error("query must contain at least one identifier");
-        }
-        const isGene = searchType === "gene";
-        const variableName = isGene ? "genes" : "drugs";
-        const queryString = isGene ? GENE_INTERACTIONS_QUERY : DRUG_INTERACTIONS_QUERY;
-        const res = await apiFetchValidated(DGIDB_GRAPHQL_URL, DgidbResponseSchema, {
-            method: "POST",
-            headers: { "Content-Type": "application/json" },
-            body: JSON.stringify({
-                query: queryString,
-                variables: { [variableName]: inputs },
-            }),
-        });
-        if (res.isErr())
-            throw new Error(describeApiError(res.error));
-        const body = res.value;
-        if (!body || !body.data)
-            throw new Error("DGIdb returned no data");
-        if (body.errors?.length) {
-            console.warn("dgidb.partial_errors", { errors: body.errors.slice(0, 3) });
-        }
-        const nodes = (isGene ? body.data.genes?.nodes : body.data.drugs?.nodes) ?? [];
-        const nodeMap = new Map();
-        for (const node of nodes) {
-            nodeMap.set(node.name.toLowerCase(), node);
-            if (!isGene && node.conceptId) {
-                nodeMap.set(node.conceptId.toLowerCase(), node);
-            }
-        }
-        const results = inputs.map((input) => {
-            const node = nodeMap.get(input.toLowerCase());
-            if (!node) {
-                return { input, found: false, interactions: [] };
+/**
+ * A factory rather than a bare const (unlike its bio-leaf siblings) because it
+ * logs: DGIdb answers GraphQL partial errors alongside usable data, and an
+ * operator debugging odd interaction results needs to see them. `ToolContext`
+ * carries no deps by design, so a tool that logs is dep-bearing — the same
+ * reason `createSearchClinvarTool` takes its key that way.
+ */
+export function createSearchDgidbTool(deps = {}) {
+    const logger = (deps.logger ?? createNoopLogger()).named("search_dgidb");
+    return defineTool({
+        id: "search_dgidb",
+        description: "Query the Drug-Gene Interaction Database (DGIdb) for drug-gene interactions. " +
+            "DGIdb aggregates 30+ sources (ChEMBL, DrugBank, TTD, PharmGKB, GuideToPharmacology, CIViC, etc.) " +
+            "and returns source counts as a confidence signal. " +
+            "searchType='gene' returns drugs interacting with input HUGO gene symbols (most common: 'what drugs hit my gene set?'). " +
+            "searchType='drug' returns the genes each input drug is known to act on. " +
+            "Free, no API key required. Sorted by source count desc.",
+        inputSchema: z.object({
+            query: z
+                .union([z.string(), z.array(z.string()).max(50)])
+                .describe("Single identifier or list of up to 50. For searchType='gene': HUGO symbols. For searchType='drug': drug names or DGIdb concept IDs."),
+            searchType: z.enum(["gene", "drug"]).default("gene"),
+            interactionTypes: z
+                .array(z.string())
+                .optional()
+                .describe("Case-insensitive substring filter on interaction type. e.g. ['inhibitor', 'antagonist']"),
+            sources: z.array(z.string()).optional().describe("Restrict to interactions from these source DBs (case-insensitive substring)."),
+            minSources: z.number().int().min(1).default(1).describe("Drop interactions supported by fewer than this many sources."),
+            limit: z.number().int().min(1).max(200).default(50).describe("Max interactions per input gene/drug after filtering."),
+        }),
+        execute: async ({ query, searchType = "gene", interactionTypes, sources, minSources = 1, limit = 50 }) => {
+            const inputs = typeof query === "string" ? [query] : query;
+            if (inputs.length === 0 || inputs.every((s) => !s.trim())) {
+                throw new Error("query must contain at least one identifier");
             }
-            const inputSide = isGene
-                ? { geneName: node.name }
-                : {
-                    drugName: node.name,
-                    drugConceptId: node.conceptId ?? undefined,
-                };
-            const mapped = (node.interactions ?? []).map((raw) => mapInteraction(raw, searchType, inputSide));
-            const filtered = applyFilters(mapped, {
-                interactionTypes,
-                sources,
-                minSources,
+            const isGene = searchType === "gene";
+            const variableName = isGene ? "genes" : "drugs";
+            const queryString = isGene ? GENE_INTERACTIONS_QUERY : DRUG_INTERACTIONS_QUERY;
+            const res = await apiFetchValidated(DGIDB_GRAPHQL_URL, DgidbResponseSchema, {
+                method: "POST",
+                headers: { "Content-Type": "application/json" },
+                body: JSON.stringify({
+                    query: queryString,
+                    variables: { [variableName]: inputs },
+                }),
             });
-            const sorted = filtered.sort((a, b) => {
-                if (b.sourceCount !== a.sourceCount) {
-                    return b.sourceCount - a.sourceCount;
+            if (res.isErr())
+                throw new Error(describeApiError(res.error));
+            const body = res.value;
+            if (!body || !body.data)
+                throw new Error("DGIdb returned no data");
+            if (body.errors?.length) {
+                logger.warn("dgidb partial errors alongside data", { errors: body.errors.slice(0, 3) });
+            }
+            const nodes = (isGene ? body.data.genes?.nodes : body.data.drugs?.nodes) ?? [];
+            const nodeMap = new Map();
+            for (const node of nodes) {
+                nodeMap.set(node.name.toLowerCase(), node);
+                if (!isGene && node.conceptId) {
+                    nodeMap.set(node.conceptId.toLowerCase(), node);
                 }
-                return (b.interactionScore ?? 0) - (a.interactionScore ?? 0);
+            }
+            const results = inputs.map((input) => {
+                const node = nodeMap.get(input.toLowerCase());
+                if (!node) {
+                    return { input, found: false, interactions: [] };
+                }
+                const inputSide = isGene
+                    ? { geneName: node.name }
+                    : {
+                        drugName: node.name,
+                        drugConceptId: node.conceptId ?? undefined,
+                    };
+                const mapped = (node.interactions ?? []).map((raw) => mapInteraction(raw, searchType, inputSide));
+                const filtered = applyFilters(mapped, {
+                    interactionTypes,
+                    sources,
+                    minSources,
+                });
+                const sorted = filtered.sort((a, b) => {
+                    if (b.sourceCount !== a.sourceCount) {
+                        return b.sourceCount - a.sourceCount;
+                    }
+                    return (b.interactionScore ?? 0) - (a.interactionScore ?? 0);
+                });
+                return {
+                    input,
+                    found: true,
+                    interactions: sorted.slice(0, limit),
+                };
             });
-            return {
-                input,
-                found: true,
-                interactions: sorted.slice(0, limit),
-            };
-        });
-        return ok({ results });
-    },
-});
+            return ok({ results });
+        },
+    });
+}

package/dist/tools/iterate-report.d.ts

@@ -47,6 +47,7 @@ import { type ResolveWorkspaceRoot } from "../workspace/paths.js";
 import { type StagedAsset } from "./lib/report-preflight.js";
 import type { PreviewPublisher } from "./report/preview-publisher.js";
 import type { ChromeConfig } from "../lib/chrome.js";
+import type { Logger } from "../lib/logger.js";
 /**
  * The report brief the conversation agent composes: title/audience + sources +
  * the section union. This is the ~12k-char schema that `plan_report` hands back
@@ -183,6 +184,8 @@ export declare const submitReportInputSchema: z.ZodObject<{
  */
 export declare const planReportTool: Tool;
 export interface SubmitReportDeps {
+    /** Operational logging seam; omitted falls back to no-op. */
+    readonly logger?: Logger;
     readonly provider: ChatProvider;
     readonly pool: Pool;
     /** Embedder-supplied workspace-root resolution seam (see workspace/paths.ts). */

package/dist/tools/iterate-report.js

@@ -49,6 +49,7 @@ import { defineTool } from "./define-tool.js";
 import { previewDir } from "../workspace/paths.js";
 import { runReportIteration } from "../execution/report-runner.js";
 import { formatBytes, stageReportAssets } from "./lib/report-preflight.js";
+import { createNoopLogger } from "../lib/console-logger.js";
 const REPORT_TOOL_ACCESS_TTL_SECONDS = 3600;
 const PREVIEW_META_FILE = "preview-meta.json";
 async function readPreviewMeta(metaPath) {
@@ -577,7 +578,8 @@ export function createReportSubmitTool(deps) {
                     });
                 }
                 catch (err) {
-                    console.warn(`[submit-report] failed to persist preview meta: ${err instanceof Error ? err.message : err}`);
+                    const logger = (deps.logger ?? createNoopLogger()).named("submit-report");
+                    logger.warn("failed to persist preview meta", logger.errorFields(err));
                 }
             }
             const previewTitle = brief?.title ?? existingMeta?.title ?? "Report";

package/dist/tools/research/literature-reviewer.d.ts

@@ -17,7 +17,10 @@
 import { type ChatProvider } from "../../providers/types.js";
 import { type Tool } from "../define-tool.js";
 import { type BioToolKeys } from "../bio/keys.js";
+import type { Logger } from "../../lib/logger.js";
 export interface LiteratureReviewerDeps {
+    /** Operational logging seam; omitted falls back to no-op. */
+    readonly logger?: Logger;
     /** The LLM seam the child loop runs on. */
     readonly provider: ChatProvider;
     /** Model id — provenance / metric label; the provider owns the wire model. */

package/dist/tools/research/literature-reviewer.js

@@ -26,7 +26,7 @@ import { createNcbiTools } from "../bio/keys.js";
 import { getImpcKoProfileTool } from "../bio/get-impc-ko-profile.js";
 import { lookupGoTermTool } from "../bio/lookup-go-term.js";
 import { searchBgeeExpressionTool } from "../bio/search-bgee-expression.js";
-import { searchDgidbTool } from "../bio/search-dgidb.js";
+import { createSearchDgidbTool } from "../bio/search-dgidb.js";
 import { searchGeneTool } from "../bio/search-gene.js";
 import { searchInteractionsTool } from "../bio/search-interactions.js";
 import { searchPathwayTool } from "../bio/search-pathway.js";
@@ -43,7 +43,7 @@ export function createLiteratureReviewerTool(deps) {
         lookupGoTermTool,
         searchInteractionsTool,
         ncbi.pubmed,
-        searchDgidbTool,
+        createSearchDgidbTool({ ...(deps.logger ? { logger: deps.logger } : {}) }),
         searchBgeeExpressionTool,
         getImpcKoProfileTool,
     ];

package/dist/tools/workspace/execute-command.d.ts

@@ -22,7 +22,10 @@
 import type { SandboxClient } from "../../sandbox/client.js";
 import type { SandboxRef } from "../../sandbox/types.js";
 import type { ProvenanceCollector } from "../../provenance/collector.js";
+import type { Logger } from "../../lib/logger.js";
 export interface ExecuteCommandDeps {
+    /** Operational logging seam; omitted falls back to no-op. */
+    readonly logger?: Logger;
     readonly sandboxClient: SandboxClient;
     /** Live sandbox handle for the step. Created once per step at composition root. */
     readonly sandbox: SandboxRef;

package/dist/tools/workspace/execute-command.js

@@ -26,6 +26,7 @@ import { defineTool } from "../define-tool.js";
 import { feedExecFrame } from "../../provenance/exec-frame.js";
 import { boundExecResult } from "./result-bounds.js";
 import { runSandboxExec } from "./run-exec.js";
+import { createNoopLogger } from "../../lib/console-logger.js";
 const ExecuteCommandInputSchema = z.object({
     command: z
         .array(z.string().min(1))
@@ -86,7 +87,8 @@ export function createExecuteCommandTool(deps) {
                     });
                 }
                 catch (err) {
-                    console.warn(`[execute_command] provenance frame handling failed (non-fatal) for ${execId}: ${err instanceof Error ? err.message : err}`);
+                    const logger = (deps.logger ?? createNoopLogger()).named("execute_command");
+                    logger.warn("provenance frame handling failed (non-fatal)", { execId, ...logger.errorFields(err) });
                 }
             }
             return ok({ status: "ok", ...boundExecResult(result) });

package/dist/workflows/execute-analysis.d.ts

@@ -57,6 +57,7 @@ import type { Pool } from "pg";
 import type { MachineBudget, ResourceSpec } from "../config/resource-limits.js";
 import type { RunSession } from "../auth/types.js";
 import type { RunAuthorizer } from "../execution/run-authorizer.js";
+import type { Logger } from "../lib/logger.js";
 import type { AnalysisStep } from "../schemas/workflow-state.js";
 import type { ChatProvider, EmbeddingProvider } from "../providers/types.js";
 import type { BioToolKeys } from "../tools/bio/keys.js";
@@ -206,6 +207,8 @@ export type RunProvenanceEvent = {
  * embedder, model, keys, roots) the in-body synthesis needs.
  */
 export interface ExecuteAnalysisDeps {
+    /** Operational logging seam; omitted falls back to no-op. */
+    readonly logger?: Logger;
     readonly pool: Pool;
     /** Chat provider for the in-body literature-grounded synthesis. */
     readonly provider: ChatProvider;

package/dist/workflows/execute-analysis.js

@@ -57,6 +57,7 @@ import { DBOS } from "@dbos-inc/dbos-sdk";
 import { mkdir } from "node:fs/promises";
 import { join } from "node:path";
 import { forStep } from "../auth/types.js";
+import { createNoopLogger } from "../lib/console-logger.js";
 import { unwrapOrThrow } from "../lib/result.js";
 import { RunDedupCollisionError, countArtifactsForRun, loadDataProfileStatus, queryActiveRun, queryStepArtifactPaths, seedStepExecutions, suspendAnalysis as suspendAnalysisQuery, sweepPendingStepExecutions, updateRunStatus, } from "../state/index.js";
 import { isBudgetExceeded } from "../loop/budget-exceeded.js";
@@ -81,13 +82,14 @@ function emitStreamPart(part) {
  * host's own ledger, not here.
  */
 function emitProvenanceGuarded(deps, event) {
+    const logger = (deps.logger ?? createNoopLogger()).named("executeAnalysis");
     if (!deps.emitProvenance)
         return;
     try {
         deps.emitProvenance(event);
     }
     catch (err) {
-        console.error(`[executeAnalysis] emitProvenance threw for run ${event.runId} (event=${event.type}):`, err);
+        logger.error("emitProvenance threw", { runId: event.runId, event: event.type, ...logger.errorFields(err) });
     }
 }
 /**
@@ -261,6 +263,7 @@ export function registerExecuteAnalysis(deps) {
  * (the DBOS calls inside still rely on a workflow context being present).
  */
 export async function runExecuteAnalysisBody(input, deps) {
+    const logger = (deps.logger ?? createNoopLogger()).named("executeAnalysis").with({ analysisId: input.analysisId });
     // (0) Validate up-front — no side effects yet, so a malformed plan does
     // NOT leak a runId, run authorization, or running charge.
     validatePlanDag(input.steps);
@@ -344,7 +347,7 @@ export async function runExecuteAnalysisBody(input, deps) {
         }
         catch (err) {
             synthesisError = err;
-            console.error(`[executeAnalysis] synthesizeFindings failed for run ${runId} — failing the run:`, err instanceof Error ? err.message : err);
+            logger.error("synthesizeFindings failed — failing the run", { runId, ...logger.errorFields(err) });
         }
     }
     // (6) collectAndComplete — terminal block. Runs on EVERY path. When synthesis
@@ -693,6 +696,7 @@ async function cancelInFlight(inFlight, cause, canceledByParent) {
 }
 async function collectAndComplete(args) {
     const { input, runId, workflowId, startedAtMs, completed, failed, canceled, budgetExceeded, failureReason, forceFailed, deps } = args;
+    const logger = (deps.logger ?? createNoopLogger()).named("executeAnalysis").with({ runId, analysisId: input.analysisId });
     const status = forceFailed
         ? "failed"
         : deriveFinalStatus({
@@ -735,7 +739,7 @@ async function collectAndComplete(args) {
         }, { name: "persist-final-status" });
     }
     catch (err) {
-        console.error(`[executeAnalysis] persist-final-status failed for run ${runId} (status=${status}):`, err);
+        logger.error("persist-final-status failed", { status, ...logger.errorFields(err) });
     }
     // Sweep never-started steps to `skipped` — but ONLY on genuinely-terminal
     // paths. The gate is the BRANCH, not the written run status: the resumable
@@ -749,7 +753,7 @@ async function collectAndComplete(args) {
             }, { name: "sweep-pending-steps" });
         }
         catch (err) {
-            console.error(`[executeAnalysis] sweep-pending-steps failed for run ${runId}:`, err);
+            logger.error("sweep-pending-steps failed", logger.errorFields(err));
         }
     }
     // A forced failure (synthesis threw) is terminal, not a resumable budget
@@ -761,7 +765,7 @@ async function collectAndComplete(args) {
             }, { name: "suspend-analysis" });
         }
         catch (err) {
-            console.error(`[executeAnalysis] suspend-analysis failed for run ${runId}:`, err);
+            logger.error("suspend-analysis failed", logger.errorFields(err));
         }
     }
     try {
@@ -773,7 +777,7 @@ async function collectAndComplete(args) {
         }), { name: "close-running-charge" });
     }
     catch (err) {
-        console.error(`[executeAnalysis] closeRunningCharge failed for run ${runId} (reason=${chargeReason}):`, err);
+        logger.error("closeRunningCharge failed", { chargeReason, ...logger.errorFields(err) });
     }
     // Revoke the run authorization for the terminal run state. Ownership
     // defaults to true for inputs persisted before the field existed (a
@@ -786,7 +790,7 @@ async function collectAndComplete(args) {
         await DBOS.runStep(() => deps.runAuthorizer.revoke(authorization, revokeReason), { name: "revoke-run-auth" });
     }
     catch (err) {
-        console.error(`[executeAnalysis] revokeRunAuthorization failed for run ${runId} (reason=${revokeReason}):`, err);
+        logger.error("revokeRunAuthorization failed", { revokeReason, ...logger.errorFields(err) });
     }
     // The `run_completed` provenance was already emitted above (before the status write, to
     // beat the CLI's poll-and-shutdown). These branches only fan out the UI stream part, whose

package/dist/workflows/execute-target-assessment.d.ts

@@ -34,6 +34,7 @@ import type { Pool } from "pg";
 import { z } from "zod";
 import type { RunSession } from "../auth/types.js";
 import type { RunAuthorizer } from "../execution/run-authorizer.js";
+import type { Logger } from "../lib/logger.js";
 import type { AgentChat } from "../providers/types.js";
 import { TargetAssessmentInputSchema } from "./target-assessment/schemas.js";
 import { type ProgressPhase } from "./target-assessment/progress.js";
@@ -69,6 +70,8 @@ export interface ExecuteTargetAssessmentResult {
     readonly bytes: number;
 }
 export interface ExecuteTargetAssessmentDeps {
+    /** Operational logging seam; omitted falls back to no-op. */
+    readonly logger?: Logger;
     readonly pool: Pool;
     /** Run-authorization seam — the terminal path revokes through `revoke`. */
     readonly runAuthorizer: RunAuthorizer;