@inflexa-ai/harness 0.41.0 → 0.41.2

package/dist/workflows/execute-analysis.js

@@ -82,7 +82,7 @@ import { unwrapOrThrow } from "../lib/result.js";
 import { countArtifactsForRun, insertStepExecution, loadDataProfileStatus, queryActiveRun, queryStepArtifactPaths, queryStepsByRun, seedStepExecutions, setRunSynthesisOutcome, suspendAnalysis as suspendAnalysisQuery, sweepPendingStepExecutions, updateRunStatus, updateStepExecution, } from "../state/index.js";
 import { addChatUsage, hasReportedUsage } from "../loop/metrics.js";
 import { SYNTHESIS_AGENT_ID, loadStepSummariesFromDisk } from "../execution/run-synthesis.js";
-import { MAX_UPSTREAM_ARTIFACTS, composeStepBriefing } from "../prompts/briefing.js";
+import { MAX_UPSTREAM_ARTIFACTS, composeStepBriefing, emptyStepMemory } from "../prompts/briefing.js";
 import { SYNTHESIS_STEP_ID, runDir, runStepDir, stepSubdir, stepWritePrefix, toSandboxPath } from "../workspace/paths.js";
 import { isChatDataPart } from "../sandbox/sandbox-step-translate.js";
 import { synthesizeRun } from "../app/synthesize-run.js";
@@ -220,17 +220,30 @@ export function buildChildInput(args) {
  * rendered any earlier (at plan submission, say) cannot mention them, and the
  * agent is left to rediscover its own upstream.
  *
- * Everything read here is durable state written by an already-settled child
- * (`output/summary.md`, `cortex_artifacts`) or by the profiler
- * (`cortex_analysis_state`) — never live in-flight state, which would not
- * reproduce.
- *
  * REPLAY: the caller wraps this in a `DBOS.runStep`, so the composed string is
  * checkpointed and a replay returns it verbatim — the DB and disk are not read
  * again and cannot drift the seed under a recovered run. Never call it
  * unwrapped from the workflow body.
  */
 export async function composeStepSeed(args) {
+    return composeStepBriefing(await gatherStepPackage(args));
+}
+/**
+ * Do every read of one step's package and give the data its seed is rendered
+ * from. All reads live here, so `composeStepBriefing` stays a pure renderer.
+ *
+ * Everything read is durable state: written by an already-settled child
+ * (`output/summary.md`, `cortex_artifacts`), by the profiler
+ * (`cortex_analysis_state`), or by the conversation agent
+ * (`cortex_working_memory`). The working memory is the one read that can
+ * change while the run is live — it is read per dispatch, not once per run,
+ * so an edit during a run reaches each later step, and two steps of one run
+ * can carry different copies.
+ *
+ * A read failure throws (house rules): a swallowed error would be frozen into
+ * the checkpointed seed and served to every replay of this step.
+ */
+export async function gatherStepPackage(args) {
     const { input, stepId, runId, deps } = args;
     const step = input.planStepById[stepId];
     if (!step) {
@@ -246,9 +259,19 @@ export async function composeStepSeed(args) {
         analysisId,
         workingDir: toSandboxPath(workspaceRoot, analysisId, stepWritePrefix({ workspaceRoot, runId, stepId })),
     };
-    // A DB failure here throws (house rules): a swallowed error would be frozen
-    // into the checkpointed seed and served to every replay of this step.
     const profile = unwrapOrThrow(await loadDataProfileStatus(deps.pool, analysisId));
+    // A failed memory read leaves the section out: the step runs without the copy of the memory, not without a seed.
+    const memoryRead = await deps.workingMemory.load(analysisId);
+    if (memoryRead.isErr()) {
+        const log = (deps.logger ?? createNoopLogger()).named("executeAnalysis.seed");
+        log.warn("the working-memory read failed, thus the seed has no memory section", {
+            analysisId,
+            stepId,
+            error: describeDbError(memoryRead.error),
+            ...log.errorFields(memoryRead.error.cause),
+        });
+    }
+    const memory = memoryRead.isOk() ? memoryRead.value : emptyStepMemory();
     const upstream = await collectUpstreamHandoffs({
         analysisId,
         runId,
@@ -257,12 +280,13 @@ export async function composeStepSeed(args) {
         agentByStepId: input.agentByStepId,
         pool: deps.pool,
     });
-    return composeStepBriefing({
+    return {
         step,
         workspace,
         profile: profile?.result ?? null,
         upstream,
-    });
+        memory: { goal: memory.goal, constraints: memory.constraints },
+    };
 }
 /**
  * Gather what each completed dependency produced. Dependency order is the

package/package.json

@@ -1,6 +1,6 @@
 {
     "name": "@inflexa-ai/harness",
-    "version": "0.41.0",
+    "version": "0.41.2",
     "description": "Host-agnostic bioinformatics agent harness — hand-rolled agent loop, DBOS-durable workflows, sandboxed compute.",
     "license": "Apache-2.0",
     "type": "module",
@@ -77,6 +77,7 @@
         "hono": "^4.12.34",
         "hyparquet": "^1.28.1",
         "js-tiktoken": "^1.0.21",
+        "kysely": "^0.29.6",
         "mime": "^4.1.0",
         "nanoid": "^5.1.16",
         "neverthrow": "^8.2.0",