@inflexa-ai/harness 0.1.1

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Files changed (823) hide show
  1. package/LICENSE +202 -0
  2. package/NOTICE +5 -0
  3. package/README.md +58 -0
  4. package/dist/agents/conversation-agent.d.ts +105 -0
  5. package/dist/agents/conversation-agent.js +140 -0
  6. package/dist/agents/report-builder.d.ts +32 -0
  7. package/dist/agents/report-builder.js +31 -0
  8. package/dist/agents/sandbox/__fixtures__/deps.d.ts +23 -0
  9. package/dist/agents/sandbox/__fixtures__/deps.js +96 -0
  10. package/dist/agents/sandbox/bulk-transcriptomics-agent.d.ts +8 -0
  11. package/dist/agents/sandbox/bulk-transcriptomics-agent.js +22 -0
  12. package/dist/agents/sandbox/cheminformatics-agent.d.ts +9 -0
  13. package/dist/agents/sandbox/cheminformatics-agent.js +62 -0
  14. package/dist/agents/sandbox/chromatin-agent.d.ts +8 -0
  15. package/dist/agents/sandbox/chromatin-agent.js +24 -0
  16. package/dist/agents/sandbox/data-profiler.d.ts +10 -0
  17. package/dist/agents/sandbox/data-profiler.js +24 -0
  18. package/dist/agents/sandbox/dna-methylation-agent.d.ts +8 -0
  19. package/dist/agents/sandbox/dna-methylation-agent.js +24 -0
  20. package/dist/agents/sandbox/drug-repurposing-agent.d.ts +8 -0
  21. package/dist/agents/sandbox/drug-repurposing-agent.js +54 -0
  22. package/dist/agents/sandbox/enrichment-agent.d.ts +8 -0
  23. package/dist/agents/sandbox/enrichment-agent.js +24 -0
  24. package/dist/agents/sandbox/ephemeral-executor.d.ts +9 -0
  25. package/dist/agents/sandbox/ephemeral-executor.js +29 -0
  26. package/dist/agents/sandbox/genomic-variant-agent.d.ts +8 -0
  27. package/dist/agents/sandbox/genomic-variant-agent.js +27 -0
  28. package/dist/agents/sandbox/immune-profiling-agent.d.ts +8 -0
  29. package/dist/agents/sandbox/immune-profiling-agent.js +43 -0
  30. package/dist/agents/sandbox/index.d.ts +31 -0
  31. package/dist/agents/sandbox/index.js +96 -0
  32. package/dist/agents/sandbox/metabolomics-agent.d.ts +8 -0
  33. package/dist/agents/sandbox/metabolomics-agent.js +15 -0
  34. package/dist/agents/sandbox/microbiome-agent.d.ts +8 -0
  35. package/dist/agents/sandbox/microbiome-agent.js +15 -0
  36. package/dist/agents/sandbox/multi-omics-integration-agent.d.ts +8 -0
  37. package/dist/agents/sandbox/multi-omics-integration-agent.js +33 -0
  38. package/dist/agents/sandbox/multimodal-sc-agent.d.ts +8 -0
  39. package/dist/agents/sandbox/multimodal-sc-agent.js +15 -0
  40. package/dist/agents/sandbox/network-agent.d.ts +8 -0
  41. package/dist/agents/sandbox/network-agent.js +25 -0
  42. package/dist/agents/sandbox/pkpd-clinical-response-agent.d.ts +8 -0
  43. package/dist/agents/sandbox/pkpd-clinical-response-agent.js +59 -0
  44. package/dist/agents/sandbox/proteomics-agent.d.ts +8 -0
  45. package/dist/agents/sandbox/proteomics-agent.js +15 -0
  46. package/dist/agents/sandbox/scientific-executor.d.ts +9 -0
  47. package/dist/agents/sandbox/scientific-executor.js +56 -0
  48. package/dist/agents/sandbox/shared.d.ts +100 -0
  49. package/dist/agents/sandbox/shared.js +195 -0
  50. package/dist/agents/sandbox/single-cell-agent.d.ts +8 -0
  51. package/dist/agents/sandbox/single-cell-agent.js +25 -0
  52. package/dist/agents/sandbox/spatial-omics-agent.d.ts +8 -0
  53. package/dist/agents/sandbox/spatial-omics-agent.js +15 -0
  54. package/dist/agents/sandbox/statistical-modeling-agent.d.ts +8 -0
  55. package/dist/agents/sandbox/statistical-modeling-agent.js +37 -0
  56. package/dist/agents/sandbox/translational-safety-agent.d.ts +8 -0
  57. package/dist/agents/sandbox/translational-safety-agent.js +59 -0
  58. package/dist/agents/sandbox/types.d.ts +34 -0
  59. package/dist/agents/sandbox/types.js +15 -0
  60. package/dist/agents/sandbox/validate-skills.d.ts +18 -0
  61. package/dist/agents/sandbox/validate-skills.js +40 -0
  62. package/dist/agents/sandbox-catalog.d.ts +33 -0
  63. package/dist/agents/sandbox-catalog.js +44 -0
  64. package/dist/agents/system-prompt.d.ts +25 -0
  65. package/dist/agents/system-prompt.js +23 -0
  66. package/dist/app/chat-turn.d.ts +35 -0
  67. package/dist/app/chat-turn.js +64 -0
  68. package/dist/app/data-profile-policy.d.ts +36 -0
  69. package/dist/app/data-profile-policy.js +37 -0
  70. package/dist/app/message-assembly.d.ts +65 -0
  71. package/dist/app/message-assembly.js +61 -0
  72. package/dist/app/synthesize-run.d.ts +57 -0
  73. package/dist/app/synthesize-run.js +103 -0
  74. package/dist/auth/local-auth-context.d.ts +19 -0
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  76. package/dist/auth/local-run-authorizer.d.ts +10 -0
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  78. package/dist/auth/types.d.ts +166 -0
  79. package/dist/auth/types.js +61 -0
  80. package/dist/billing/cached-resolver.d.ts +23 -0
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  82. package/dist/billing/noop-resolver.d.ts +6 -0
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  88. package/dist/billing/run-charge.d.ts +24 -0
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  90. package/dist/config/resource-limits.d.ts +76 -0
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  92. package/dist/contracts/analogy-report.d.ts +120 -0
  93. package/dist/contracts/analogy-report.js +50 -0
  94. package/dist/contracts/chat-events.d.ts +61 -0
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  100. package/dist/contracts/index.d.ts +12 -0
  101. package/dist/contracts/index.js +5 -0
  102. package/dist/contracts/message.d.ts +36 -0
  103. package/dist/contracts/message.js +9 -0
  104. package/dist/contracts/part-registry.d.ts +18 -0
  105. package/dist/contracts/part-registry.js +28 -0
  106. package/dist/contracts/schemas/chat-events.d.ts +90 -0
  107. package/dist/contracts/schemas/chat-events.js +43 -0
  108. package/dist/contracts/schemas/chat-parts.d.ts +683 -0
  109. package/dist/contracts/schemas/chat-parts.js +295 -0
  110. package/dist/contracts/schemas/index.d.ts +2 -0
  111. package/dist/contracts/schemas/index.js +2 -0
  112. package/dist/contracts/target-assessment-row.d.ts +85 -0
  113. package/dist/contracts/target-assessment-row.js +37 -0
  114. package/dist/contracts/target-dossier.d.ts +16720 -0
  115. package/dist/contracts/target-dossier.js +1339 -0
  116. package/dist/data/clinical-benchmarks.json +108 -0
  117. package/dist/data/protein-family-modality.json +101 -0
  118. package/dist/data/safety-panel-schema.d.ts +64 -0
  119. package/dist/data/safety-panel-schema.js +34 -0
  120. package/dist/data/safety-panel.json +436 -0
  121. package/dist/execution/artifact-metadata.d.ts +74 -0
  122. package/dist/execution/artifact-metadata.js +203 -0
  123. package/dist/execution/artifact-record.d.ts +19 -0
  124. package/dist/execution/artifact-record.js +7 -0
  125. package/dist/execution/artifact-registration.d.ts +36 -0
  126. package/dist/execution/artifact-registration.js +61 -0
  127. package/dist/execution/artifact-registry.d.ts +82 -0
  128. package/dist/execution/artifact-registry.js +17 -0
  129. package/dist/execution/dbos-run-launcher.d.ts +7 -0
  130. package/dist/execution/dbos-run-launcher.js +38 -0
  131. package/dist/execution/ephemeral-runner.d.ts +81 -0
  132. package/dist/execution/ephemeral-runner.js +161 -0
  133. package/dist/execution/filesystem-artifact-registry.d.ts +57 -0
  134. package/dist/execution/filesystem-artifact-registry.js +92 -0
  135. package/dist/execution/noop-artifact-registry.d.ts +11 -0
  136. package/dist/execution/noop-artifact-registry.js +17 -0
  137. package/dist/execution/post-step-pipeline.d.ts +70 -0
  138. package/dist/execution/post-step-pipeline.js +207 -0
  139. package/dist/execution/post-step.d.ts +20 -0
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  141. package/dist/execution/reconcile-manifest.d.ts +25 -0
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  143. package/dist/execution/report-render.d.ts +39 -0
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  145. package/dist/execution/report-runner.d.ts +87 -0
  146. package/dist/execution/report-runner.js +227 -0
  147. package/dist/execution/run-authorizer.d.ts +43 -0
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  149. package/dist/execution/run-launcher.d.ts +36 -0
  150. package/dist/execution/run-launcher.js +15 -0
  151. package/dist/execution/run-synthesis.d.ts +107 -0
  152. package/dist/execution/run-synthesis.js +329 -0
  153. package/dist/execution/staged-input.d.ts +41 -0
  154. package/dist/execution/staged-input.js +15 -0
  155. package/dist/execution/step-summary-metrics.d.ts +10 -0
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  157. package/dist/execution/step-summary.d.ts +55 -0
  158. package/dist/execution/step-summary.js +106 -0
  159. package/dist/execution/topo-sort.d.ts +33 -0
  160. package/dist/execution/topo-sort.js +99 -0
  161. package/dist/index.d.ts +112 -0
  162. package/dist/index.js +157 -0
  163. package/dist/input-sanitization.d.ts +22 -0
  164. package/dist/input-sanitization.js +64 -0
  165. package/dist/lib/async-utils.d.ts +10 -0
  166. package/dist/lib/async-utils.js +24 -0
  167. package/dist/lib/chrome.d.ts +15 -0
  168. package/dist/lib/chrome.js +95 -0
  169. package/dist/lib/db-result.d.ts +93 -0
  170. package/dist/lib/db-result.js +197 -0
  171. package/dist/lib/fs-helpers.d.ts +74 -0
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  173. package/dist/lib/fs-result.d.ts +98 -0
  174. package/dist/lib/fs-result.js +137 -0
  175. package/dist/lib/host-concurrency.d.ts +16 -0
  176. package/dist/lib/host-concurrency.js +60 -0
  177. package/dist/lib/identifiers.d.ts +8 -0
  178. package/dist/lib/identifiers.js +10 -0
  179. package/dist/lib/metrics.d.ts +7 -0
  180. package/dist/lib/metrics.js +12 -0
  181. package/dist/lib/mime-detect.d.ts +17 -0
  182. package/dist/lib/mime-detect.js +29 -0
  183. package/dist/lib/otel.d.ts +30 -0
  184. package/dist/lib/otel.js +102 -0
  185. package/dist/lib/regulatory-corpus/fetch-fda-guidance.d.ts +35 -0
  186. package/dist/lib/regulatory-corpus/fetch-fda-guidance.js +107 -0
  187. package/dist/lib/regulatory-corpus/fetch-ich.d.ts +46 -0
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  189. package/dist/lib/regulatory-corpus.d.ts +88 -0
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  191. package/dist/lib/result.d.ts +87 -0
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  193. package/dist/lib/storage.d.ts +29 -0
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  197. package/dist/lib/trace-context.d.ts +11 -0
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  199. package/dist/loop/__fixtures__/scripted-provider.d.ts +31 -0
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  201. package/dist/loop/budget-exceeded.d.ts +22 -0
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  203. package/dist/loop/metrics.d.ts +25 -0
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  205. package/dist/loop/run-agent.d.ts +28 -0
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  211. package/dist/loop/types.d.ts +95 -0
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  213. package/dist/memory/ai-sdk-message-storage.d.ts +20 -0
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  235. package/dist/prompts/analogical-reasoner.d.ts +1 -0
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  237. package/dist/prompts/conversation.d.ts +1 -0
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  239. package/dist/prompts/execute-analysis/step-summary.d.ts +1 -0
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  249. package/dist/prompts/sandbox/cheminformatics-agent.d.ts +1 -0
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  255. package/dist/prompts/sandbox/dna-methylation-agent.d.ts +1 -0
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  257. package/dist/prompts/sandbox/drug-repurposing-agent.d.ts +1 -0
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  259. package/dist/prompts/sandbox/enrichment-agent.d.ts +1 -0
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  263. package/dist/prompts/sandbox/genomic-variant-agent.d.ts +1 -0
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  265. package/dist/prompts/sandbox/immune-profiling-agent.d.ts +1 -0
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  267. package/dist/prompts/sandbox/metabolomics-agent.d.ts +1 -0
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  277. package/dist/prompts/sandbox/pkpd-clinical-response-agent.d.ts +1 -0
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  685. package/dist/tools/workspace/workspace-search.d.ts +25 -0
  686. package/dist/tools/workspace/workspace-search.js +78 -0
  687. package/dist/tools/workspace/write-file.d.ts +16 -0
  688. package/dist/tools/workspace/write-file.js +33 -0
  689. package/dist/workflows/execute-analysis-scheduler.d.ts +94 -0
  690. package/dist/workflows/execute-analysis-scheduler.js +186 -0
  691. package/dist/workflows/execute-analysis.d.ts +271 -0
  692. package/dist/workflows/execute-analysis.js +746 -0
  693. package/dist/workflows/execute-target-assessment.d.ts +101 -0
  694. package/dist/workflows/execute-target-assessment.js +528 -0
  695. package/dist/workflows/metrics.d.ts +37 -0
  696. package/dist/workflows/metrics.js +55 -0
  697. package/dist/workflows/plan/level.d.ts +12 -0
  698. package/dist/workflows/plan/level.js +12 -0
  699. package/dist/workflows/register-workflows.d.ts +51 -0
  700. package/dist/workflows/register-workflows.js +48 -0
  701. package/dist/workflows/resume-execute-analysis.d.ts +70 -0
  702. package/dist/workflows/resume-execute-analysis.js +80 -0
  703. package/dist/workflows/sandbox-step.d.ts +243 -0
  704. package/dist/workflows/sandbox-step.js +573 -0
  705. package/dist/workflows/target-assessment/assemblers/index.d.ts +5 -0
  706. package/dist/workflows/target-assessment/assemblers/index.js +4 -0
  707. package/dist/workflows/target-assessment/assemblers/literature.d.ts +299 -0
  708. package/dist/workflows/target-assessment/assemblers/literature.js +987 -0
  709. package/dist/workflows/target-assessment/assemblers/orchestrator.d.ts +109 -0
  710. package/dist/workflows/target-assessment/assemblers/orchestrator.js +835 -0
  711. package/dist/workflows/target-assessment/assemblers/safety.d.ts +352 -0
  712. package/dist/workflows/target-assessment/assemblers/safety.js +985 -0
  713. package/dist/workflows/target-assessment/assemblers/trials.d.ts +30 -0
  714. package/dist/workflows/target-assessment/assemblers/trials.js +75 -0
  715. package/dist/workflows/target-assessment/collectors/index.d.ts +105 -0
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  717. package/dist/workflows/target-assessment/correction-loop.d.ts +45 -0
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  719. package/dist/workflows/target-assessment/coverage.d.ts +81 -0
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  721. package/dist/workflows/target-assessment/decisions/index.d.ts +86 -0
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  723. package/dist/workflows/target-assessment/fanout/index.d.ts +31 -0
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  725. package/dist/workflows/target-assessment/lib/approval-precedents.d.ts +52 -0
  726. package/dist/workflows/target-assessment/lib/approval-precedents.js +119 -0
  727. package/dist/workflows/target-assessment/lib/citation-validator.d.ts +46 -0
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  729. package/dist/workflows/target-assessment/lib/clinical-consequence-annotator.d.ts +62 -0
  730. package/dist/workflows/target-assessment/lib/clinical-consequence-annotator.js +172 -0
  731. package/dist/workflows/target-assessment/lib/clinical-evidence-attribution.d.ts +45 -0
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  733. package/dist/workflows/target-assessment/lib/compute-derived.d.ts +19 -0
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  739. package/dist/workflows/target-assessment/lib/evidence-conflict-detector.d.ts +17 -0
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  749. package/dist/workflows/target-assessment/lib/llm-step.d.ts +77 -0
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  755. package/dist/workflows/target-assessment/lib/recommendation-sanitizer.d.ts +2 -0
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  823. package/package.json +101 -0
@@ -0,0 +1,160 @@
1
+ /**
2
+ * DBOS Transact bootstrap.
3
+ *
4
+ * This is the only module that imports `@dbos-inc/dbos-sdk` directly. The
5
+ * agent loop and routes depend on the `RunStep` shape (`harness/loop/types.ts`),
6
+ * so DBOS stays swappable and the chat path never reaches into the workflow
7
+ * runtime. `harness/loop/run-step.ts` wraps `DBOS.runStep` for the durable
8
+ * variant; nothing else here.
9
+ *
10
+ * Launch is dormant — this change registers no workflows. The durability seam
11
+ * exists; the engine is running; nothing is durable yet.
12
+ *
13
+ * See `openspec/changes/harness-dbos-runtime`.
14
+ */
15
+ import { DBOS } from "@dbos-inc/dbos-sdk";
16
+ import { DBOS_SYSTEM_POOL_SIZE } from "./pools.js";
17
+ const state = {
18
+ launched: false,
19
+ recoveryStarted: false,
20
+ };
21
+ /**
22
+ * Build the Postgres URL DBOS uses for its system database. Reuses the
23
+ * existing `DB_PG_*` env vars; sslmode is propagated as a query string so
24
+ * DBOS's underlying `pg.Pool` honours it.
25
+ *
26
+ * The sslmode must mirror the app pool's mapping in `lib/storage.ts`:
27
+ * `require` means "encrypt, don't verify the chain" there, but
28
+ * `pg-connection-string` parses bare `require` as an alias for `verify-full`
29
+ * (full chain verification). Against RDS — whose CA isn't in Node's default
30
+ * trust store — that fails with SELF_SIGNED_CERT_IN_CHAIN. Emit `no-verify`
31
+ * so DBOS's pool gets `rejectUnauthorized: false`, matching the app pool.
32
+ */
33
+ function dbosSslMode(mode) {
34
+ if (mode === "disable")
35
+ return "disable";
36
+ if (mode === "verify-ca" || mode === "verify-full")
37
+ return "verify-full";
38
+ return "no-verify";
39
+ }
40
+ function systemDatabaseUrl(config) {
41
+ const user = encodeURIComponent(config.dbUser);
42
+ const password = encodeURIComponent(config.dbPassword);
43
+ const host = config.dbHost;
44
+ const port = config.dbPort;
45
+ const database = encodeURIComponent(config.dbName);
46
+ return `postgresql://${user}:${password}@${host}:${port}/${database}?sslmode=${dbosSslMode(config.dbSslMode)}`;
47
+ }
48
+ /**
49
+ * Launch DBOS. Idempotent — a second call is a no-op so tests that drive
50
+ * the harness twice (or accidentally double-import) don't re-launch.
51
+ *
52
+ * Order is load-bearing: `setConfig` must precede `launch`, and `launch`
53
+ * must resolve before the HTTP listener accepts traffic (otherwise the
54
+ * readiness probe could 200 against a runtime that can't own workflows).
55
+ */
56
+ export async function launchDbos({ config, logger }) {
57
+ if (state.launched)
58
+ return;
59
+ const executorID = config.executorId;
60
+ const adminPort = parseInt(config.adminPort, 10);
61
+ DBOS.setConfig({
62
+ name: config.appName,
63
+ systemDatabaseUrl: systemDatabaseUrl(config),
64
+ systemDatabasePoolSize: DBOS_SYSTEM_POOL_SIZE,
65
+ executorID,
66
+ applicationVersion: config.applicationVersion,
67
+ adminPort,
68
+ logLevel: config.logLevel,
69
+ });
70
+ const start = performance.now();
71
+ await DBOS.launch();
72
+ state.launched = true;
73
+ state.recoveryStarted = true;
74
+ logger.info({
75
+ executorID,
76
+ applicationVersion: config.applicationVersion,
77
+ adminPort,
78
+ durationMs: Math.round(performance.now() - start),
79
+ }, "[dbos] launched");
80
+ }
81
+ /**
82
+ * Shut DBOS down. In-flight workflows are marked recoverable so another
83
+ * replica (or this pod on restart) can adopt them. Never throws — the
84
+ * outer shutdown sequence must close the pg.Pool and flush exporters even
85
+ * if DBOS shutdown fails.
86
+ *
87
+ * Must run after HTTP has drained (so no inbound request is orphaned) and
88
+ * before the application pool closes (DBOS needs the system DB).
89
+ */
90
+ export async function shutdownDbos({ logger }) {
91
+ if (!state.launched)
92
+ return;
93
+ const start = performance.now();
94
+ try {
95
+ await DBOS.shutdown();
96
+ logger.info({ durationMs: Math.round(performance.now() - start) }, "[dbos] shutdown");
97
+ }
98
+ catch (err) {
99
+ logger.error({
100
+ err: err instanceof Error ? err.message : String(err),
101
+ durationMs: Math.round(performance.now() - start),
102
+ }, "[dbos] shutdown failed");
103
+ }
104
+ finally {
105
+ state.launched = false;
106
+ state.recoveryStarted = false;
107
+ }
108
+ }
109
+ /**
110
+ * Cancel any `ephemeral:`-prefixed PENDING workflow this executor owns —
111
+ * called BEFORE `launchDbos`, whose recovery would otherwise re-dispatch them.
112
+ *
113
+ * Ephemeral runs are turn-scoped: a run whose pod died mid-flight has no live
114
+ * awaiter and must never re-execute. DBOS has no "zero recovery" knob, and
115
+ * `launch()` starts recovery itself, so there is no post-launch window to
116
+ * cancel from — the only race-free point is a direct system-DB UPDATE before
117
+ * launch. A CANCELLED row is excluded from the recovery query (which selects
118
+ * `status='PENDING'`). The `dbos.workflow_status` coupling is the price of
119
+ * pre-launch timing, and this is the sole module that owns DBOS. The system
120
+ * DB is the same database as the app pool, so the pool reaches it directly.
121
+ */
122
+ export async function sweepEphemeralWorkflows({ pool, logger, executorId, }) {
123
+ const executorID = executorId;
124
+ try {
125
+ const { rowCount } = await pool.query({
126
+ text: `UPDATE dbos.workflow_status
127
+ SET status = 'CANCELLED', updated_at = $1
128
+ WHERE status = 'PENDING'
129
+ AND executor_id = $2
130
+ AND workflow_uuid LIKE 'ephemeral:%'`,
131
+ values: [Date.now(), executorID],
132
+ });
133
+ if (rowCount && rowCount > 0) {
134
+ logger.info({ executorID, swept: rowCount }, "[dbos] swept orphaned ephemeral workflows");
135
+ }
136
+ }
137
+ catch (err) {
138
+ // First-ever boot: DBOS has not created its schema yet — nothing to sweep.
139
+ if (err && typeof err === "object" && "code" in err && err.code === "42P01") {
140
+ return;
141
+ }
142
+ logger.error({ executorID, err: err instanceof Error ? err.message : String(err) }, "[dbos] ephemeral sweep failed");
143
+ }
144
+ }
145
+ /** Snapshot of DBOS lifecycle state — read by the readiness probe. */
146
+ export function dbosState() {
147
+ return { ...state };
148
+ }
149
+ /** Test hook: force-reset state without calling DBOS. Test-only. */
150
+ export function __resetDbosStateForTest() {
151
+ state.launched = false;
152
+ state.recoveryStarted = false;
153
+ }
154
+ /** Test hook: mark launched without calling DBOS. Test-only. */
155
+ export function __setDbosStateForTest(next) {
156
+ if (next.launched !== undefined)
157
+ state.launched = next.launched;
158
+ if (next.recoveryStarted !== undefined)
159
+ state.recoveryStarted = next.recoveryStarted;
160
+ }
@@ -0,0 +1,12 @@
1
+ /**
2
+ * Process-wide lifecycle flags shared between the readiness probe and the
3
+ * shutdown sequence.
4
+ *
5
+ * `draining` flips true the moment SIGTERM/SIGINT is received, so the
6
+ * readiness probe drops the pod out of LB rotation before the HTTP
7
+ * server starts refusing requests.
8
+ */
9
+ export declare function isDraining(): boolean;
10
+ export declare function markDraining(): void;
11
+ /** Test hook — reset the flag between tests. */
12
+ export declare function __resetLifecycleForTest(): void;
@@ -0,0 +1,19 @@
1
+ /**
2
+ * Process-wide lifecycle flags shared between the readiness probe and the
3
+ * shutdown sequence.
4
+ *
5
+ * `draining` flips true the moment SIGTERM/SIGINT is received, so the
6
+ * readiness probe drops the pod out of LB rotation before the HTTP
7
+ * server starts refusing requests.
8
+ */
9
+ let draining = false;
10
+ export function isDraining() {
11
+ return draining;
12
+ }
13
+ export function markDraining() {
14
+ draining = true;
15
+ }
16
+ /** Test hook — reset the flag between tests. */
17
+ export function __resetLifecycleForTest() {
18
+ draining = false;
19
+ }
@@ -0,0 +1,25 @@
1
+ /**
2
+ * Per-pod Postgres pool sizing — the single source of truth.
3
+ *
4
+ * Cortex runs two pools per pod against the same cluster (see the postgres-storage-backend spec): the
5
+ * application pool (`lib/storage.ts::createPool()`) and the DBOS system-DB
6
+ * pool (`runtime/dbos.ts`). Both numbers live here so the value DBOS is
7
+ * configured with and the value the boot-time guard reasons about can never
8
+ * drift apart.
9
+ *
10
+ * Fleet-level capacity (how many replicas the cluster can hold) is NOT a
11
+ * per-pod concern and is deliberately absent here — it belongs to the
12
+ * database (`max_connections` sizing) or a connection pooler. See
13
+ * `runtime/connection-budget.ts`.
14
+ */
15
+ /** DBOS system-DB pool size; passed verbatim to `DBOS.setConfig`. */
16
+ export declare const DBOS_SYSTEM_POOL_SIZE = 10;
17
+ /** Application pool size when `DB_POOL_MAX` is unset. */
18
+ export declare const DEFAULT_APP_POOL_SIZE = 12;
19
+ /**
20
+ * Connections reserved outside the two pools: psql admin sessions, a brief
21
+ * overlap during DBOS recovery, replication / monitoring users.
22
+ */
23
+ export declare const SAFETY_MARGIN = 5;
24
+ /** Resolve the app pool size from the optional `DB_POOL_MAX` override. */
25
+ export declare function resolveAppPoolSize(dbPoolMax: string | undefined): number;
@@ -0,0 +1,30 @@
1
+ /**
2
+ * Per-pod Postgres pool sizing — the single source of truth.
3
+ *
4
+ * Cortex runs two pools per pod against the same cluster (see the postgres-storage-backend spec): the
5
+ * application pool (`lib/storage.ts::createPool()`) and the DBOS system-DB
6
+ * pool (`runtime/dbos.ts`). Both numbers live here so the value DBOS is
7
+ * configured with and the value the boot-time guard reasons about can never
8
+ * drift apart.
9
+ *
10
+ * Fleet-level capacity (how many replicas the cluster can hold) is NOT a
11
+ * per-pod concern and is deliberately absent here — it belongs to the
12
+ * database (`max_connections` sizing) or a connection pooler. See
13
+ * `runtime/connection-budget.ts`.
14
+ */
15
+ /** DBOS system-DB pool size; passed verbatim to `DBOS.setConfig`. */
16
+ export const DBOS_SYSTEM_POOL_SIZE = 10;
17
+ /** Application pool size when `DB_POOL_MAX` is unset. */
18
+ export const DEFAULT_APP_POOL_SIZE = 12;
19
+ /**
20
+ * Connections reserved outside the two pools: psql admin sessions, a brief
21
+ * overlap during DBOS recovery, replication / monitoring users.
22
+ */
23
+ export const SAFETY_MARGIN = 5;
24
+ /** Resolve the app pool size from the optional `DB_POOL_MAX` override. */
25
+ export function resolveAppPoolSize(dbPoolMax) {
26
+ if (dbPoolMax === undefined || dbPoolMax === "")
27
+ return DEFAULT_APP_POOL_SIZE;
28
+ const n = Number.parseInt(dbPoolMax, 10);
29
+ return Number.isFinite(n) && n >= 1 ? n : DEFAULT_APP_POOL_SIZE;
30
+ }
@@ -0,0 +1,33 @@
1
+ /**
2
+ * Graceful-shutdown sequence.
3
+ *
4
+ * The order is load-bearing for durability:
5
+ *
6
+ * 1. Flip readiness to NOT_READY (so the LB stops sending new traffic).
7
+ * 2. Drain in-flight HTTP (close the listener, await pending requests).
8
+ * 3. `DBOS.shutdown()` — marks in-flight workflows recoverable.
9
+ * Must run AFTER HTTP drains (so no inbound request is orphaned)
10
+ * and BEFORE the application pool closes (DBOS needs the system DB,
11
+ * though it owns its own pool, the app close happens after).
12
+ * 4. Close the application `pg.Pool`.
13
+ * 5. Flush log + OTel exporters.
14
+ * 6. `process.exit(0)`.
15
+ *
16
+ * Each side effect is injected so the sequence can be tested in isolation
17
+ * (no real server, no real DBOS). Errors at any step are logged and
18
+ * swallowed — once shutdown has started, exiting takes precedence over
19
+ * any single step's failure.
20
+ */
21
+ import type pino from "pino";
22
+ export interface ShutdownDeps {
23
+ signal: string;
24
+ logger: pino.Logger;
25
+ markDraining: () => void;
26
+ closeHttpServer: () => Promise<void>;
27
+ shutdownDbos: () => Promise<void>;
28
+ closePool: () => Promise<void>;
29
+ flushLogger: () => Promise<void>;
30
+ shutdownOtel: () => Promise<void>;
31
+ exit: (code: number) => void;
32
+ }
33
+ export declare function runShutdownSequence(deps: ShutdownDeps): Promise<void>;
@@ -0,0 +1,39 @@
1
+ /**
2
+ * Graceful-shutdown sequence.
3
+ *
4
+ * The order is load-bearing for durability:
5
+ *
6
+ * 1. Flip readiness to NOT_READY (so the LB stops sending new traffic).
7
+ * 2. Drain in-flight HTTP (close the listener, await pending requests).
8
+ * 3. `DBOS.shutdown()` — marks in-flight workflows recoverable.
9
+ * Must run AFTER HTTP drains (so no inbound request is orphaned)
10
+ * and BEFORE the application pool closes (DBOS needs the system DB,
11
+ * though it owns its own pool, the app close happens after).
12
+ * 4. Close the application `pg.Pool`.
13
+ * 5. Flush log + OTel exporters.
14
+ * 6. `process.exit(0)`.
15
+ *
16
+ * Each side effect is injected so the sequence can be tested in isolation
17
+ * (no real server, no real DBOS). Errors at any step are logged and
18
+ * swallowed — once shutdown has started, exiting takes precedence over
19
+ * any single step's failure.
20
+ */
21
+ async function safely(logger, step, fn) {
22
+ try {
23
+ await fn();
24
+ }
25
+ catch (err) {
26
+ logger.error({ err: err instanceof Error ? err.message : String(err), step }, `[shutdown] ${step} failed`);
27
+ }
28
+ }
29
+ export async function runShutdownSequence(deps) {
30
+ const { logger, signal } = deps;
31
+ logger.info({ signal }, "[shutdown] requested");
32
+ deps.markDraining();
33
+ await safely(logger, "http-drain", deps.closeHttpServer);
34
+ await safely(logger, "dbos-shutdown", deps.shutdownDbos);
35
+ await safely(logger, "pool-close", deps.closePool);
36
+ await safely(logger, "otel-flush", deps.shutdownOtel);
37
+ await safely(logger, "logger-flush", deps.flushLogger);
38
+ deps.exit(0);
39
+ }
@@ -0,0 +1,143 @@
1
+ /**
2
+ * `awaitExec` — awaits a submitted exec's terminal result, forwarding progress
3
+ * events, under one of two transports selected by `options.transport`:
4
+ *
5
+ * - `poll` (default): {@link awaitExecPoll} loops durable pull steps against
6
+ * `GET /exec/{execId}?since={cursor}`. The sandbox initiates nothing; the
7
+ * host asks. Inherently restart-proof — a recovered workflow just resumes
8
+ * polling from its current identity — so the recovery wedge (#41) does not
9
+ * apply. A machine that dies mid-exec fast-fails in-loop: sustained
10
+ * `unavailable` polls escalate to a backend-inspect probe (`liveness.ts`)
11
+ * and an observably dead machine returns the synthetic-failure result
12
+ * instead of waiting out the deadline.
13
+ * - `callback`: {@link awaitExecCallback} is the recv loop below, with the
14
+ * pull as its recovery backstop.
15
+ *
16
+ * Both run in the workflow body (NOT a step) — `DBOS.recv`, `DBOS.writeStream`,
17
+ * and `DBOS.sleepms` are body-only — and both verify every result against the
18
+ * per-sandbox HMAC, treating a bad/stale signature as a hard cancel.
19
+ *
20
+ * ## Callback mode: the recv loop
21
+ *
22
+ * On each received envelope:
23
+ *
24
+ * 1. If it carries `signature: null` and the payload is a
25
+ * `synthetic-failure` done-marker, accept it — the watchdog is an
26
+ * in-process trusted sender. Any other null-signature message
27
+ * hard-cancels.
28
+ * 2. Otherwise HMAC-verify against the per-sandbox `callbackSecret`.
29
+ * A bad or stale signature throws `HardCancelError`, which DBOS
30
+ * treats as a fatal workflow error (no retry).
31
+ * 3. If the verified payload is a done-marker, return its `result`.
32
+ * 4. Otherwise forward the payload via `emit` and continue.
33
+ *
34
+ * `deadline` is an absolute unix-ms timestamp — the durable backstop
35
+ * (typically `step.timeout`). `T` is liveness-agnostic recv pacing: we
36
+ * use `min(5s, remaining)` so the loop returns often enough to honour
37
+ * the deadline.
38
+ *
39
+ * ## Recv is not the only way home
40
+ *
41
+ * The completion callback is a *push* to an address baked into the container at
42
+ * creation. A host that dies mid-exec comes back with a different ingress port,
43
+ * so the push can never land — the sandbox retries into a void while the
44
+ * recovered recv waits for a message that will never arrive. That is the
45
+ * recovery wedge (#41), and it is silent: a `running` row that never advances.
46
+ *
47
+ * So whenever the topic falls quiet, this loop stops waiting and *asks*:
48
+ * `GET /exec/{execId}` on the sandbox itself returns the terminal result,
49
+ * signed fresh at request time. The bytes are the ones the callback would have
50
+ * carried, so the provenance frame survives the recovery path intact and one
51
+ * verification path serves both. Push remains the fast path; pull is what makes
52
+ * the protocol durable rather than merely optimistic.
53
+ *
54
+ * The pull is a DBOS step, not a bare `fetch`: a body-level call whose result
55
+ * varied between replays would desynchronise the recorded function-ID sequence.
56
+ */
57
+ import { type ExecEmit, type ExecResult, type SandboxLiveness, type SandboxRef, type SandboxTransport } from "./types.js";
58
+ export declare class HardCancelError extends Error {
59
+ readonly execId: string;
60
+ readonly reason: "bad-signature" | "stale-timestamp" | "missing" | "synthetic-without-marker";
61
+ constructor(execId: string, reason: "bad-signature" | "stale-timestamp" | "missing" | "synthetic-without-marker", detail?: string);
62
+ }
63
+ export declare class ExecTimeoutError extends Error {
64
+ readonly execId: string;
65
+ constructor(execId: string);
66
+ }
67
+ /**
68
+ * Dependency seams of the await loops — every member is an injectable effect
69
+ * (clock, recv, fetch, durable step, durable sleep, warn sink) plus the
70
+ * transport selector. Tuning values (freshness window, pull threshold, poll
71
+ * cadence) are module constants, not options.
72
+ */
73
+ export interface AwaitExecOptions {
74
+ /**
75
+ * Clock source for the deadline check and HMAC freshness. Defaults to the
76
+ * checkpointed `DBOS.now()` so the loop's recv count is replay-stable (a raw
77
+ * `Date.now()` here drifts the recorded `DBOS.recv` function-ID sequence on
78
+ * recovery — see the harness-durable-runtime spec).
79
+ */
80
+ now?: () => number | Promise<number>;
81
+ /** Replaces `DBOS.recv` (callback mode). */
82
+ recv?: <T>(topic: string, timeoutSec: number) => Promise<T | null>;
83
+ /** Defaults to `globalThis.fetch`. */
84
+ fetch?: typeof fetch;
85
+ /** Defaults to `DBOS.runStep`. */
86
+ runStep?: <T>(fn: () => Promise<T>, config: {
87
+ name: string;
88
+ }) => Promise<T>;
89
+ /**
90
+ * Result transport. `poll` (default) runs the durable poll loop; `callback`
91
+ * runs the `DBOS.recv` loop with the pull as its recovery backstop. The
92
+ * composition root passes the same value it hands the container.
93
+ */
94
+ transport?: SandboxTransport;
95
+ /** Replaces the durable inter-poll sleep. Defaults to `DBOS.sleepms`. */
96
+ sleep?: (ms: number) => Promise<void>;
97
+ /**
98
+ * Sink for advisory warnings (poll-mode progress-event loss). Defaults to
99
+ * `DBOS.logger.warn`. Advisory only: the terminal result — not the event
100
+ * stream — is the authoritative outcome.
101
+ */
102
+ warn?: (message: string) => void;
103
+ /**
104
+ * Backend inspect for the poll loop's liveness escalation (`liveness.ts`).
105
+ * Wired by `createSandboxClient` from its backend ops; when absent the
106
+ * loop skips escalation and stays purely deadline-bounded. Throws on
107
+ * transient backend API errors — the escalation treats a throw as an
108
+ * inconclusive probe, never a failed exec.
109
+ */
110
+ isAlive?: (ref: SandboxRef) => Promise<SandboxLiveness>;
111
+ }
112
+ /**
113
+ * Await a submitted exec's terminal result. Dispatches on transport — `poll`
114
+ * (default) or `callback`. Both verify every result against the per-sandbox
115
+ * HMAC and are bounded by `deadlineMs`.
116
+ */
117
+ export declare function awaitExec(ref: SandboxRef, execId: string, emit: ExecEmit, deadlineMs: number, options?: AwaitExecOptions): Promise<ExecResult>;
118
+ /**
119
+ * Body of the recv loop (callback transport). Hoisted so it's testable without
120
+ * spinning up DBOS — `recv` is injectable and `now` is overridable.
121
+ */
122
+ export declare function awaitExecCallback(ref: SandboxRef, execId: string, emit: ExecEmit, deadlineMs: number, options?: AwaitExecOptions): Promise<ExecResult>;
123
+ /**
124
+ * Body of the poll loop (poll transport). No `DBOS.recv`, no per-exec topic, no
125
+ * callback handler: a sequence of durable pull steps named
126
+ * `sandbox.poll-exec-result.${execId}.${n}`, each fetching the signed
127
+ * `{ status, events, cursor, result? }`, verifying it exactly as a pushed
128
+ * completion is verified, forwarding new events via `emit`, advancing the
129
+ * cursor, and returning `result` once terminal. `sleep`, `now`, `fetch`,
130
+ * `runStep`, and `isAlive` are injectable so the loop is testable without DBOS.
131
+ *
132
+ * Liveness: when the `isAlive` seam is wired (the client always wires it),
133
+ * consecutive `unavailable` polls past the module threshold escalate to a
134
+ * durable probe step `sandbox.probe-liveness.${execId}.${k}`; a dead verdict
135
+ * returns the synthetic-failure result in-loop — the poll-mode analogue of the
136
+ * watchdog's synthetic-complete, minus the topic and the race gate, since the
137
+ * verdict is produced and consumed by the same workflow in sequence.
138
+ *
139
+ * The `cursor`, `pollAttempt`, and `probeAttempt` counters are pure functions
140
+ * of the cached step sequence, so a replay issues the same polls and probes in
141
+ * the same order and the DBOS function-ID sequence stays stable.
142
+ */
143
+ export declare function awaitExecPoll(ref: SandboxRef, execId: string, emit: ExecEmit, deadlineMs: number, options?: AwaitExecOptions): Promise<ExecResult>;