@inflexa-ai/harness 0.44.0 → 0.45.1

package/dist/workflows/sandbox-step.js

@@ -38,7 +38,7 @@ import { durableStep } from "../loop/run-step.js";
 import { maskExcept } from "../loop/tool-mask.js";
 import { READ_TOOL_OUTPUT_TOOL_ID } from "../loop/tool-output.js";
 import { lastExecOutcome } from "../sandbox/exec-outcome.js";
-import { activityForTool, applyTreeDelta, isChatDataPart, sandboxTreeDelta, stepPartId } from "../sandbox/sandbox-step-translate.js";
+import { activityEmission, activityForTool, applyTreeDelta, isChatDataPart, sandboxTreeDelta, stepPartId } from "../sandbox/sandbox-step-translate.js";
 import { createDetailResolver } from "../tools/detail-resolver.js";
 import { forSubAgent } from "../auth/types.js";
 import { walkStepArtifacts } from "../execution/post-step.js";
@@ -266,17 +266,19 @@ export async function runSandboxStepBody(input, deps) {
             logger.warn("emitToParentStream failed (non-fatal)", logger.errorFields(err));
         }
     };
-    // Schema-conformant step-activity emitter — stable id per (runId, stepId)
-    // so the run-stream fold collapses every phase transition latest-wins.
-    const activityId = stepPartId("step-activity", input.runId, input.stepId);
-    const emitActivity = (phase, activity) => safeEmit({
-        type: "data-step-activity",
-        id: activityId,
-        runId: input.runId,
-        stepId: input.stepId,
-        phase,
-        activity,
-    });
+    // Schema-conformant step-activity emitter. `data-step-activity` has a stable id per (runId, stepId),
+    // so the run-stream fold collapses every phase transition latest-wins. Each emission also leaves one
+    // `data-activity-entry` that the fold keeps, thus a late subscriber gets each line with its time. The
+    // two parts share one checkpointed clock read. `activitySeq` advances before the clock read and the
+    // writes, and each write fails alone through `safeEmit`.
+    let activitySeq = 0;
+    const emitActivity = async (phase, activity) => {
+        const seq = activitySeq++;
+        const at = new Date(await DBOS.now()).toISOString();
+        const parts = activityEmission(input, seq, phase, activity, at);
+        await safeEmit(parts.activity);
+        await safeEmit(parts.entry);
+    };
     // Single exit for the two terminal failure paths (agent loop, lineage
     // attestation). Tears the sandbox down, logs the internal detail for
     // operators, then persists + emits only a generic phrase and re-raises a

package/package.json

@@ -1,6 +1,6 @@
 {
     "name": "@inflexa-ai/harness",
-    "version": "0.44.0",
+    "version": "0.45.1",
     "description": "Host-agnostic bioinformatics agent harness — hand-rolled agent loop, DBOS-durable workflows, sandboxed compute.",
     "license": "Apache-2.0",
     "type": "module",
@@ -61,6 +61,7 @@
         "@fontsource/ibm-plex-mono": "5.1.1",
         "@inflexa-ai/tsprov": "0.6.0",
         "@kubernetes/client-node": "^1.4.0",
+        "@mozilla/readability": "^0.6.0",
         "@opentelemetry/api": "^1.9.1",
         "@opentelemetry/core": "^2.9.0",
         "@opentelemetry/exporter-metrics-otlp-http": "^0.219.0",
@@ -72,6 +73,7 @@
         "@opentelemetry/semantic-conventions": "^1.43.0",
         "@types/dockerode": "^3.3.47",
         "@types/pg": "^8.20.0",
+        "@types/turndown": "^5.0.6",
         "ag-grid-community": "36.1.0",
         "ai": "^7.0.113",
         "cheerio": "^1.2.0",
@@ -82,6 +84,7 @@
         "hyparquet": "^1.28.1",
         "js-tiktoken": "^1.0.21",
         "kysely": "^0.29.6",
+        "linkedom": "^0.18.14",
         "mime": "^4.1.0",
         "nanoid": "^5.1.16",
         "neverthrow": "^8.2.0",
@@ -90,6 +93,7 @@
         "pdf-parse": "^2.4.5",
         "pg": "^8.22.0",
         "puppeteer-core": "^23.11.1",
+        "turndown": "^7.2.4",
         "zod": "^4.4.3"
     },
     "overrides": {