@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
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  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
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  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
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  731. package/dist/workflows/target-assessment/lib/clinical-evidence-attribution.d.ts +45 -0
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  823. package/package.json +101 -0
@@ -0,0 +1,94 @@
1
+ /**
2
+ * Dependency-gated scheduler for `executeAnalysis`.
3
+ *
4
+ * Three pure functions over a plan DAG, unit-testable in isolation:
5
+ *
6
+ * - `validatePlanDag` — cycle + missing-dependency detection, typed errors.
7
+ * - `scheduleReady` — given the completed set, return every step whose
8
+ * dependencies are now satisfied and that has not
9
+ * already been started.
10
+ * - `computeTopologicalLevels` — UI-only depth per step (level 0 = no deps,
11
+ * level N = max(level(deps)) + 1). Persisted
12
+ * on `cortex_step_executions.wave` and emitted
13
+ * on `data-dag-state`; does NOT gate execution.
14
+ *
15
+ * The parent workflow drives the scheduler — it owns the in-flight handle
16
+ * map and reacts to child completions / failures. Keeping the scheduler
17
+ * pure means parent recovery replays the same dispatch sequence given the
18
+ * same persisted child outcomes.
19
+ */
20
+ import type { MachineBudget, ResourceSpec } from "../config/resource-limits.js";
21
+ /**
22
+ * The minimum shape the scheduler needs from a plan step. Larger workflow-state
23
+ * schemas are a superset of this, keeping the scheduler decoupled.
24
+ */
25
+ export interface PlanStep {
26
+ readonly id: string;
27
+ readonly depends_on: readonly string[];
28
+ }
29
+ /** Budget-admission inputs — the snapshotted machine budget from the workflow
30
+ * input plus each step's plan-declared resources. */
31
+ export interface BudgetAdmission {
32
+ readonly budget: MachineBudget;
33
+ readonly resourcesByStepId: Readonly<Record<string, ResourceSpec>>;
34
+ }
35
+ /** Partition of the dependency-satisfied steps under budget admission. */
36
+ export interface ScheduledSteps {
37
+ /** Steps to start now — they fit the remaining budget capacity. */
38
+ readonly admit: readonly string[];
39
+ /** Dependency-satisfied steps held until in-flight steps free capacity. */
40
+ readonly heldForCapacity: readonly string[];
41
+ /** Steps whose declared resources exceed the budget outright — they could
42
+ * never be admitted even against an empty budget. */
43
+ readonly neverFits: readonly string[];
44
+ }
45
+ /** Thrown when the plan DAG contains a dependency cycle. */
46
+ export declare class CycleError extends Error {
47
+ readonly involvedSteps: readonly string[];
48
+ constructor(involvedSteps: readonly string[]);
49
+ }
50
+ /** Thrown when a step references a `depends_on` id that does not exist. */
51
+ export declare class MissingDependencyError extends Error {
52
+ readonly stepId: string;
53
+ readonly missingDependency: string;
54
+ constructor(stepId: string, missingDependency: string);
55
+ }
56
+ /** Thrown when two steps share the same `id`. */
57
+ export declare class DuplicateStepIdError extends Error {
58
+ readonly stepId: string;
59
+ constructor(stepId: string);
60
+ }
61
+ /**
62
+ * Validate a plan DAG. Throws on duplicate ids, missing dependencies, or
63
+ * cycles. Returns the validated step map for convenient downstream use.
64
+ */
65
+ export declare function validatePlanDag<S extends PlanStep>(steps: readonly S[]): Map<string, S>;
66
+ /**
67
+ * Return every step that is now eligible to start: all of its `depends_on`
68
+ * are in `completedSet`, and the step itself is not yet in `startedSet`.
69
+ *
70
+ * Pure function — the parent workflow recomputes this after every child
71
+ * completion (or on parent recovery) and dispatches each returned id via
72
+ * `DBOS.startWorkflow`. Order in the returned array follows the plan's
73
+ * declared order for deterministic dispatch.
74
+ *
75
+ * With `admission`, the dependency-satisfied steps are additionally gated on
76
+ * the machine budget and partitioned instead of returned flat: a step is
77
+ * admitted only while the declared resources of the in-flight steps
78
+ * (`startedSet`) plus every step admitted earlier in the round leave room for
79
+ * it. Admission is greedy in plan order with skip-over — a candidate that does
80
+ * not fit never blocks a later, smaller one. Determinism holds because every
81
+ * input derives from the workflow input and checkpointed completion state.
82
+ */
83
+ export declare function scheduleReady<S extends PlanStep>(steps: readonly S[], completedSet: ReadonlySet<string>, startedSet?: ReadonlySet<string>): string[];
84
+ export declare function scheduleReady<S extends PlanStep>(steps: readonly S[], completedSet: ReadonlySet<string>, startedSet: ReadonlySet<string>, admission: BudgetAdmission): ScheduledSteps;
85
+ /**
86
+ * Compute a depth per step. A step with no dependencies is level 0; a step
87
+ * with deps is `max(level(dep)) + 1`. Used by the UI for column layout in
88
+ * the DAG view and persisted as `cortex_step_executions.wave` for legacy
89
+ * compatibility — it does NOT gate execution.
90
+ *
91
+ * Pre-condition: `validatePlanDag` has been called (no cycles, no missing
92
+ * deps). Behaviour is undefined on an invalid DAG.
93
+ */
94
+ export declare function computeTopologicalLevels<S extends PlanStep>(steps: readonly S[]): Map<string, number>;
@@ -0,0 +1,186 @@
1
+ /**
2
+ * Dependency-gated scheduler for `executeAnalysis`.
3
+ *
4
+ * Three pure functions over a plan DAG, unit-testable in isolation:
5
+ *
6
+ * - `validatePlanDag` — cycle + missing-dependency detection, typed errors.
7
+ * - `scheduleReady` — given the completed set, return every step whose
8
+ * dependencies are now satisfied and that has not
9
+ * already been started.
10
+ * - `computeTopologicalLevels` — UI-only depth per step (level 0 = no deps,
11
+ * level N = max(level(deps)) + 1). Persisted
12
+ * on `cortex_step_executions.wave` and emitted
13
+ * on `data-dag-state`; does NOT gate execution.
14
+ *
15
+ * The parent workflow drives the scheduler — it owns the in-flight handle
16
+ * map and reacts to child completions / failures. Keeping the scheduler
17
+ * pure means parent recovery replays the same dispatch sequence given the
18
+ * same persisted child outcomes.
19
+ */
20
+ // ── Errors ───────────────────────────────────────────────────────────
21
+ /** Thrown when the plan DAG contains a dependency cycle. */
22
+ export class CycleError extends Error {
23
+ involvedSteps;
24
+ constructor(involvedSteps) {
25
+ super(`dependency cycle detected involving steps: ${involvedSteps.join(", ")}`);
26
+ this.involvedSteps = involvedSteps;
27
+ this.name = "CycleError";
28
+ }
29
+ }
30
+ /** Thrown when a step references a `depends_on` id that does not exist. */
31
+ export class MissingDependencyError extends Error {
32
+ stepId;
33
+ missingDependency;
34
+ constructor(stepId, missingDependency) {
35
+ super(`step "${stepId}" depends on "${missingDependency}" which is not in the plan`);
36
+ this.stepId = stepId;
37
+ this.missingDependency = missingDependency;
38
+ this.name = "MissingDependencyError";
39
+ }
40
+ }
41
+ /** Thrown when two steps share the same `id`. */
42
+ export class DuplicateStepIdError extends Error {
43
+ stepId;
44
+ constructor(stepId) {
45
+ super(`plan contains duplicate step id "${stepId}"`);
46
+ this.stepId = stepId;
47
+ this.name = "DuplicateStepIdError";
48
+ }
49
+ }
50
+ // ── Validation ───────────────────────────────────────────────────────
51
+ /**
52
+ * Validate a plan DAG. Throws on duplicate ids, missing dependencies, or
53
+ * cycles. Returns the validated step map for convenient downstream use.
54
+ */
55
+ export function validatePlanDag(steps) {
56
+ const stepById = new Map();
57
+ for (const step of steps) {
58
+ if (stepById.has(step.id)) {
59
+ throw new DuplicateStepIdError(step.id);
60
+ }
61
+ stepById.set(step.id, step);
62
+ }
63
+ for (const step of steps) {
64
+ for (const dep of step.depends_on) {
65
+ if (!stepById.has(dep)) {
66
+ throw new MissingDependencyError(step.id, dep);
67
+ }
68
+ }
69
+ }
70
+ detectCycle(steps);
71
+ return stepById;
72
+ }
73
+ /**
74
+ * Iterative DFS cycle detection — Kahn-style would also work, but DFS lets
75
+ * us surface the participating step ids directly when a cycle is found.
76
+ */
77
+ function detectCycle(steps) {
78
+ const VISITING = 1;
79
+ const DONE = 2;
80
+ const state = new Map();
81
+ const stepById = new Map(steps.map((s) => [s.id, s]));
82
+ for (const start of steps) {
83
+ if (state.get(start.id) === DONE)
84
+ continue;
85
+ // Iterative DFS — preserves the in-progress chain so we can report it.
86
+ const stack = [{ id: start.id, iter: stepById.get(start.id).depends_on[Symbol.iterator]() }];
87
+ state.set(start.id, VISITING);
88
+ while (stack.length > 0) {
89
+ const frame = stack[stack.length - 1];
90
+ const next = frame.iter.next();
91
+ if (next.done) {
92
+ state.set(frame.id, DONE);
93
+ stack.pop();
94
+ continue;
95
+ }
96
+ const childId = next.value;
97
+ const childState = state.get(childId);
98
+ if (childState === VISITING) {
99
+ const cycle = stack.map((f) => f.id);
100
+ cycle.push(childId);
101
+ throw new CycleError(cycle);
102
+ }
103
+ if (childState === DONE)
104
+ continue;
105
+ state.set(childId, VISITING);
106
+ stack.push({
107
+ id: childId,
108
+ iter: stepById.get(childId).depends_on[Symbol.iterator](),
109
+ });
110
+ }
111
+ }
112
+ }
113
+ export function scheduleReady(steps, completedSet, startedSet = new Set(), admission) {
114
+ const ready = [];
115
+ for (const step of steps) {
116
+ if (startedSet.has(step.id) || completedSet.has(step.id))
117
+ continue;
118
+ if (step.depends_on.every((d) => completedSet.has(d))) {
119
+ ready.push(step.id);
120
+ }
121
+ }
122
+ if (!admission)
123
+ return ready;
124
+ const { budget, resourcesByStepId } = admission;
125
+ // A step with no declared resources weighs nothing — it is never throttled,
126
+ // matching the unbudgeted legacy behavior for that step.
127
+ const weightOf = (id) => resourcesByStepId[id] ?? { cpu: 0, memoryGb: 0 };
128
+ let usedCpu = 0;
129
+ let usedMemoryGb = 0;
130
+ for (const id of startedSet) {
131
+ const w = weightOf(id);
132
+ usedCpu += w.cpu;
133
+ usedMemoryGb += w.memoryGb;
134
+ }
135
+ const admit = [];
136
+ const heldForCapacity = [];
137
+ const neverFits = [];
138
+ for (const id of ready) {
139
+ const w = weightOf(id);
140
+ if (w.cpu > budget.cpu || w.memoryGb > budget.memoryGb) {
141
+ neverFits.push(id);
142
+ }
143
+ else if (usedCpu + w.cpu <= budget.cpu && usedMemoryGb + w.memoryGb <= budget.memoryGb) {
144
+ admit.push(id);
145
+ usedCpu += w.cpu;
146
+ usedMemoryGb += w.memoryGb;
147
+ }
148
+ else {
149
+ heldForCapacity.push(id);
150
+ }
151
+ }
152
+ return { admit, heldForCapacity, neverFits };
153
+ }
154
+ // ── Topological levels (UI layout) ───────────────────────────────────
155
+ /**
156
+ * Compute a depth per step. A step with no dependencies is level 0; a step
157
+ * with deps is `max(level(dep)) + 1`. Used by the UI for column layout in
158
+ * the DAG view and persisted as `cortex_step_executions.wave` for legacy
159
+ * compatibility — it does NOT gate execution.
160
+ *
161
+ * Pre-condition: `validatePlanDag` has been called (no cycles, no missing
162
+ * deps). Behaviour is undefined on an invalid DAG.
163
+ */
164
+ export function computeTopologicalLevels(steps) {
165
+ const stepById = new Map(steps.map((s) => [s.id, s]));
166
+ const levels = new Map();
167
+ function levelOf(id) {
168
+ const cached = levels.get(id);
169
+ if (cached !== undefined)
170
+ return cached;
171
+ const step = stepById.get(id);
172
+ if (step === undefined) {
173
+ throw new MissingDependencyError("(internal)", id);
174
+ }
175
+ let level = 0;
176
+ for (const dep of step.depends_on) {
177
+ level = Math.max(level, levelOf(dep) + 1);
178
+ }
179
+ levels.set(id, level);
180
+ return level;
181
+ }
182
+ for (const step of steps) {
183
+ levelOf(step.id);
184
+ }
185
+ return levels;
186
+ }
@@ -0,0 +1,271 @@
1
+ /**
2
+ * `executeAnalysis` — the parent DBOS workflow.
3
+ *
4
+ * Shape (every external interaction is a `DBOS.runStep` so a crashed parent
5
+ * replays from the cache instead of repeating side effects):
6
+ *
7
+ * 1. `validateAndInit`
8
+ * - validate the plan DAG (cycle / missing-dep / dup-id)
9
+ * - create the run dir
10
+ * - open the running charge
11
+ * - emit `data-run-started`
12
+ * Inputs are NOT materialized here: the workspace tree's `data/` inputs must
13
+ * already be populated by the embedder before the run is triggered — the
14
+ * workflow neither downloads nor stages input data.
15
+ * The run authorization is minted at the async edge (`executePlan` / TA
16
+ * trigger / `runDataProfile`) and rides in `input.runSession` — the
17
+ * workflow body never mints, never reads the JWT back from `cortex_runs`.
18
+ * 2. Scheduler loop
19
+ * - maintain `completedSet` + `inFlightHandles`
20
+ * - dispatch every `scheduleReady(plan, completedSet, startedSet)` via
21
+ * `DBOS.startWorkflow` with deterministic child id
22
+ * `"${parent.workflowID}-${N}"` (N is the step's stable index)
23
+ * - each child input is `forStep(input.runSession, stepId)` for the
24
+ * session field
25
+ * - emit `data-dag-state` (reconciling by id) on every dispatch +
26
+ * completion
27
+ * - await child results via `getResult` (these are themselves cached
28
+ * in DBOS, so parent recovery does NOT re-run completed children)
29
+ * 3. Fail-fast cascade
30
+ * - on the first non-resumable child failure (or on external parent
31
+ * cancel): stop scheduling, then
32
+ * `Promise.allSettled(handles.map(h => DBOS.cancelWorkflow(h.workflowID)))`
33
+ * - each cancelled child tears down its sandbox in its own terminal path
34
+ * 4. Pause cascade (402)
35
+ * - on a child cancelling itself with `budget_exceeded`: cancel siblings
36
+ * then self-cancel the parent to `CANCELLED` (NOT `ERROR` — ERROR
37
+ * isn't resumable; NOTES #3)
38
+ * - the analysis flips to `suspended_insufficient_funds` in
39
+ * `collectAndComplete`. The paused parent lands in `CANCELLED`, a
40
+ * durably reschedulable state; re-driving it after a top-up is a
41
+ * future enhancement, not yet wired here.
42
+ * 5. `synthesizeFindings` (single sequential block, no sandbox)
43
+ * 6. `collectAndComplete` (terminal — runs on ALL paths)
44
+ * - determine final status from completed/cancelled/failed counts
45
+ * - update `cortex_runs.status` + `error`
46
+ * - close running charge with matching reason
47
+ * - revoke run authorization via the injected `runAuthorizer` seam
48
+ * - emit terminal stream part
49
+ * - WRITES NOTHING to the conversation thread (results are pull-only
50
+ * via `inspectRun`)
51
+ */
52
+ import type { Pool } from "pg";
53
+ import type { MachineBudget, ResourceSpec } from "../config/resource-limits.js";
54
+ import type { RunSession } from "../auth/types.js";
55
+ import type { RunAuthorizer } from "../execution/run-authorizer.js";
56
+ import type { ChatProvider, EmbeddingProvider } from "../providers/types.js";
57
+ import type { BioToolKeys } from "../tools/bio/keys.js";
58
+ import type { RunCharge } from "../billing/run-charge.js";
59
+ import { type ResolveWorkspaceRoot } from "../workspace/paths.js";
60
+ import { type PlanStep } from "./execute-analysis-scheduler.js";
61
+ import { type SandboxStepInput, type SandboxStepResult } from "./sandbox-step.js";
62
+ /** Registered child sandbox-step callable the parent's child-dispatch closes over. */
63
+ type SandboxStepCallable = (input: SandboxStepInput) => Promise<SandboxStepResult>;
64
+ /** Quick-display finding on the run-completed card. Mirrors the wire schema's RunCompletedFinding. */
65
+ export interface RunFinding {
66
+ readonly title: string;
67
+ readonly confidence: "high" | "medium" | "low";
68
+ }
69
+ export interface ExecuteAnalysisInput {
70
+ readonly analysisId: string;
71
+ /** Plan id — the dedup key for the partial-unique index on cortex_runs. */
72
+ readonly planId: string;
73
+ /** Human-readable plan summary for the run-started card (title or narrative). */
74
+ readonly planSummary: string;
75
+ /** Plan steps with `id` and `depends_on`. Validated before any side effect. */
76
+ readonly steps: readonly PlanStep[];
77
+ /** Optional thread id for cortex_runs.thread_id (UI breadcrumb only). */
78
+ readonly threadId?: string | null;
79
+ /** Per-step prompt body the child workflow forwards to its agent. */
80
+ readonly promptByStepId: Readonly<Record<string, string>>;
81
+ /** Per-step agent id (sandbox catalog entry). */
82
+ readonly agentByStepId: Readonly<Record<string, string>>;
83
+ /** Per-step planner-estimated sandbox resource request. */
84
+ readonly resourcesByStepId: Readonly<Record<string, ResourceSpec>>;
85
+ /**
86
+ * Per-step execution timeout in seconds, from the plan's `step.timeout`.
87
+ * Only present for steps that declared one; the child falls back to
88
+ * `DEFAULT_STEP_TIMEOUT_SECONDS` when a step is absent here.
89
+ */
90
+ readonly timeoutByStepId?: Readonly<Record<string, number>>;
91
+ /**
92
+ * Machine resource budget snapshotted by `executePlan` at the async edge.
93
+ * The scheduler admits dependency-satisfied steps only while the declared
94
+ * resources of concurrently running steps fit within it. Absent (no policy
95
+ * configured, or a workflow persisted before this field existed), every
96
+ * dependency-satisfied step starts immediately — the legacy fan-out.
97
+ */
98
+ readonly budget?: MachineBudget;
99
+ /**
100
+ * Durable `RunSession` minted at the async edge by `executePlan`.
101
+ * Carries the run-authorization credential, identity, scope, and `runFrame.runId`.
102
+ * DBOS replay reconstructs it from the serialized workflow input on
103
+ * resume — no DB read, no in-process cache.
104
+ */
105
+ readonly runSession: RunSession;
106
+ /**
107
+ * True when Cortex owns the run-authorization lifecycle and therefore must
108
+ * revoke it on the terminal path. The ownership decision is made by the
109
+ * `RunAuthorizer` seam at the async edge (`executePlan`).
110
+ *
111
+ * Optional because a workflow persisted before this field existed (recovered
112
+ * across the deploy that added it) deserializes without it; the body defaults
113
+ * absent → true, matching the prior Cortex-owned behavior.
114
+ */
115
+ readonly ownsMandate?: boolean;
116
+ }
117
+ /**
118
+ * Outcome of the trigger. `running` is what the dedup-collision recovery
119
+ * path returns — the caller joined an in-flight run, no new workflow was
120
+ * started. Every other variant is a terminal status the parent reached.
121
+ */
122
+ export type ExecuteAnalysisFinalStatus = "running" | "completed" | "partial" | "failed" | "canceled";
123
+ export interface ExecuteAnalysisResult {
124
+ readonly runId: string;
125
+ readonly workflowId: string;
126
+ readonly status: ExecuteAnalysisFinalStatus;
127
+ readonly completedSteps: readonly string[];
128
+ readonly failedSteps: readonly string[];
129
+ readonly canceledSteps: readonly string[];
130
+ }
131
+ /**
132
+ * A run-lifecycle provenance observation handed to an optional host observer.
133
+ * Harness-owned plain union — the harness stays tsprov-free and bus-free; the
134
+ * host maps these execution facts onto its own ledger vocabulary.
135
+ *
136
+ * Every `atMs` is epoch milliseconds read via `await DBOS.now()`, a checkpointed
137
+ * step: a body re-executed by DBOS recovery reads the recorded value, so a
138
+ * re-emitted event carries the identical timestamp and merges on the host's
139
+ * ledger without a value conflict. Never source these from a wall clock
140
+ * (`Date.now()`) — that would diverge across replays and defeat the merge.
141
+ *
142
+ * `run_completed.durationMs` is the terminal `atMs` minus the `run_started`
143
+ * `atMs` (both `DBOS.now()` reads) — the true workflow-observed run span.
144
+ *
145
+ * `step_completed` fires once at EVERY scheduler-loop settlement — the only site
146
+ * that observes every executed step (registration sees only artifact-producing
147
+ * steps, and a child cannot observe its own parent-driven cancel). Steps that
148
+ * were never dispatched (dependents of a failed sibling) emit nothing by design;
149
+ * the run's terminal status carries that outcome. `status` maps the settlement
150
+ * outcome: `complete` → `"completed"`, `canceled` → `"canceled"`,
151
+ * `failed`/`blocked`/child-error → `"failed"`.
152
+ *
153
+ * `run_completed` fires at BOTH terminal boundaries (success and failure); the
154
+ * `status` field distinguishes them.
155
+ */
156
+ export type RunProvenanceEvent = {
157
+ type: "run_started";
158
+ analysisId: string;
159
+ runId: string;
160
+ planSummary: string;
161
+ stepCount: number;
162
+ atMs: number;
163
+ } | {
164
+ type: "step_completed";
165
+ analysisId: string;
166
+ runId: string;
167
+ stepId: string;
168
+ /** Settlement outcome mapped to a terminal step status. */
169
+ status: "completed" | "failed" | "canceled";
170
+ /** The child's durable execution duration; absent when the child settled by throwing. */
171
+ durationMs?: number;
172
+ atMs: number;
173
+ } | {
174
+ type: "run_completed";
175
+ analysisId: string;
176
+ runId: string;
177
+ /**
178
+ * The body's terminal status. Both boundary sites resolve it through `deriveFinalStatus`,
179
+ * which records a budget pause as `"canceled"` — so `"suspended_insufficient_funds"` (a
180
+ * `RunStatus` member) is never emitted here and is deliberately absent from this narrower
181
+ * `ExecuteAnalysisFinalStatus`-minus-`"running"` set.
182
+ */
183
+ status: Exclude<ExecuteAnalysisFinalStatus, "running">;
184
+ atMs: number;
185
+ /** `atMs − run_started.atMs`: the workflow-observed run span in ms. */
186
+ durationMs: number;
187
+ };
188
+ /**
189
+ * Construction-time deps for the parent workflow. The order-of-operations is
190
+ * the body's own: it brackets the run, dispatches children, and synthesizes
191
+ * directly via `DBOS.*` + the harness's helpers. Only the genuinely host-specific seams
192
+ * stay injected — the run-charge bracket, run-authorization revoke, and the
193
+ * registered sandbox-step callable — plus the construction inputs (provider,
194
+ * embedder, model, keys, roots) the in-body synthesis needs.
195
+ */
196
+ export interface ExecuteAnalysisDeps {
197
+ readonly pool: Pool;
198
+ /** Chat provider for the in-body literature-grounded synthesis. */
199
+ readonly provider: ChatProvider;
200
+ /** Write-side embedder for indexing the run synthesis. */
201
+ readonly embedding: EmbeddingProvider;
202
+ /** Registered child sandbox-step callable the body dispatches per step. */
203
+ readonly sandboxStepCallable: SandboxStepCallable;
204
+ /** Workspace-root resolution seam — run dir creation + synthesis disk reads. */
205
+ readonly resolveWorkspaceRoot: ResolveWorkspaceRoot;
206
+ /** Model id for the synthesizer agent loop. */
207
+ readonly synthesisModel: string;
208
+ /** API keys for the bio/chem tools the embedded literature reviewer uses. */
209
+ readonly bioKeys: BioToolKeys;
210
+ /** Run-level billing-bracket seam (managed: external bracket; OSS: no-op). */
211
+ readonly runCharge: RunCharge;
212
+ /**
213
+ * When false, skip run-level synthesis entirely (findings stay empty).
214
+ * Config, not a seam. Defaults to true.
215
+ */
216
+ readonly synthesisEnabled?: boolean;
217
+ /** Run-authorization seam — the terminal path revokes through `revoke`. */
218
+ readonly runAuthorizer: RunAuthorizer;
219
+ /**
220
+ * Optional, fire-and-forget provenance observation of the run lifecycle.
221
+ * Deliberately invoked directly in the workflow body (NOT wrapped in
222
+ * `DBOS.runStep`) so that body re-execution on DBOS recovery re-fires it —
223
+ * a cached step would suppress the recovery re-emission, defeating the
224
+ * point. Idempotency is the consumer's job, achieved via the deterministic
225
+ * identifiers the events carry, not via step caching. Every call site is
226
+ * guarded so a throwing observer never fails the run.
227
+ */
228
+ readonly emitProvenance?: (event: RunProvenanceEvent) => void;
229
+ }
230
+ /**
231
+ * Project the sandbox-step input handed to each child. The parent owns the
232
+ * level computation; the rest comes from `ExecuteAnalysisInput`. The body
233
+ * fills in `runSession` via `forStep` after this returns. Exported for the
234
+ * projection/timeout-propagation tests.
235
+ */
236
+ export declare function buildChildInput(args: {
237
+ input: ExecuteAnalysisInput;
238
+ stepId: string;
239
+ level: number;
240
+ runId: string;
241
+ workflowId: string;
242
+ }): Omit<SandboxStepInput, "runSession">;
243
+ /**
244
+ * Run-level literature-grounded synthesis (no sandbox). Returns the
245
+ * quick-display findings for the run-completed card; empty when synthesis is
246
+ * skipped or produced no synthesizable content. A genuine failure re-throws
247
+ * inside the caller's `DBOS.runStep`, failing the run (D10). Exported so
248
+ * integration tests can drive the wired synthesis without a full parent body.
249
+ */
250
+ export declare function synthesizeFindings(args: {
251
+ analysisId: string;
252
+ runId: string;
253
+ completedSteps: readonly string[];
254
+ session: RunSession;
255
+ deps: ExecuteAnalysisDeps;
256
+ }): Promise<{
257
+ findings: readonly RunFinding[];
258
+ }>;
259
+ /**
260
+ * Register the executeAnalysis parent workflow with DBOS. Caller is
261
+ * responsible for setting `workflowID = runId` via
262
+ * `DBOS.startWorkflow(_, { workflowID })` — the body assumes that contract
263
+ * and uses `DBOS.workflowID` as the source of truth.
264
+ */
265
+ export declare function registerExecuteAnalysis(deps: ExecuteAnalysisDeps): (input: ExecuteAnalysisInput) => Promise<ExecuteAnalysisResult>;
266
+ /**
267
+ * Body extracted so tests can drive it without registering a workflow
268
+ * (the DBOS calls inside still rely on a workflow context being present).
269
+ */
270
+ export declare function runExecuteAnalysisBody(input: ExecuteAnalysisInput, deps: ExecuteAnalysisDeps): Promise<ExecuteAnalysisResult>;
271
+ export {};