@inflexa-ai/harness 0.35.8 → 0.36.1

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Files changed (198) hide show
  1. package/dist/auth/types.d.ts +5 -14
  2. package/dist/auth/types.js +3 -10
  3. package/dist/billing/usage-recorder.d.ts +1 -1
  4. package/dist/contracts/analogy-report.d.ts +1 -1
  5. package/dist/contracts/analogy-report.js +1 -1
  6. package/dist/contracts/chat-parts.d.ts +2 -3
  7. package/dist/contracts/index.d.ts +0 -4
  8. package/dist/contracts/index.js +0 -2
  9. package/dist/index.d.ts +0 -7
  10. package/dist/index.js +0 -21
  11. package/dist/lib/metrics.d.ts +1 -1
  12. package/dist/lib/otel-spans.d.ts +0 -2
  13. package/dist/lib/otel-spans.js +0 -2
  14. package/dist/loop/genai-spans.d.ts +14 -0
  15. package/dist/loop/genai-spans.js +35 -0
  16. package/dist/loop/run-agent.d.ts +1 -1
  17. package/dist/loop/run-agent.js +37 -4
  18. package/dist/runtime/assemble.d.ts +0 -3
  19. package/dist/runtime/assemble.js +0 -3
  20. package/dist/state/index.d.ts +0 -2
  21. package/dist/state/index.js +0 -1
  22. package/dist/state/init.js +1 -60
  23. package/dist/state/purge-analysis.d.ts +1 -2
  24. package/dist/state/purge-analysis.js +1 -2
  25. package/dist/tasks/regulatory-corpus-boot-refresh.js +1 -1
  26. package/dist/tools/bio/gene-preclinical-profile.d.ts +1 -3
  27. package/dist/tools/bio/gene-preclinical-profile.js +1 -3
  28. package/dist/tools/lib/chembl-client.d.ts +1 -4
  29. package/dist/tools/lib/chembl-client.js +1 -4
  30. package/dist/tools/lib/clinical-benchmarks-client.d.ts +1 -1
  31. package/dist/tools/lib/clinical-benchmarks-client.js +1 -1
  32. package/dist/tools/lib/clinical-trials-client.d.ts +0 -3
  33. package/dist/tools/lib/clinical-trials-client.js +0 -3
  34. package/dist/tools/lib/identifier-resolver.d.ts +5 -7
  35. package/dist/tools/lib/identifier-resolver.js +5 -7
  36. package/dist/tools/lib/iuphar-client.d.ts +1 -3
  37. package/dist/tools/lib/iuphar-client.js +1 -3
  38. package/dist/tools/lib/opentargets-client.d.ts +1 -1
  39. package/dist/tools/lib/opentargets-client.js +1 -1
  40. package/dist/tools/lib/protein-family-normalize.d.ts +5 -7
  41. package/dist/tools/lib/protein-family-normalize.js +5 -7
  42. package/dist/tools/lib/uniprot-client.d.ts +0 -7
  43. package/dist/tools/lib/uniprot-client.js +2 -9
  44. package/package.json +1 -1
  45. package/dist/contracts/target-assessment-row.d.ts +0 -85
  46. package/dist/contracts/target-assessment-row.js +0 -37
  47. package/dist/contracts/target-dossier.d.ts +0 -12423
  48. package/dist/contracts/target-dossier.js +0 -1282
  49. package/dist/prompts/target-assessment/briefs/executive-recommendation.d.ts +0 -1
  50. package/dist/prompts/target-assessment/briefs/executive-recommendation.js +0 -85
  51. package/dist/prompts/target-assessment/briefs/index.d.ts +0 -4
  52. package/dist/prompts/target-assessment/briefs/index.js +0 -4
  53. package/dist/prompts/target-assessment/briefs/liability-bullets.d.ts +0 -1
  54. package/dist/prompts/target-assessment/briefs/liability-bullets.js +0 -114
  55. package/dist/prompts/target-assessment/briefs/target-organ-liabilities.d.ts +0 -1
  56. package/dist/prompts/target-assessment/briefs/target-organ-liabilities.js +0 -37
  57. package/dist/prompts/target-assessment/briefs/translational-commentary.d.ts +0 -1
  58. package/dist/prompts/target-assessment/briefs/translational-commentary.js +0 -23
  59. package/dist/prompts/target-assessment/drugs-in-class.d.ts +0 -1
  60. package/dist/prompts/target-assessment/drugs-in-class.js +0 -29
  61. package/dist/prompts/target-assessment/investigation/adversarial-critique.d.ts +0 -1
  62. package/dist/prompts/target-assessment/investigation/adversarial-critique.js +0 -67
  63. package/dist/prompts/target-assessment/investigation/claim-reverification.d.ts +0 -1
  64. package/dist/prompts/target-assessment/investigation/claim-reverification.js +0 -49
  65. package/dist/prompts/target-assessment/investigation/index.d.ts +0 -3
  66. package/dist/prompts/target-assessment/investigation/index.js +0 -3
  67. package/dist/prompts/target-assessment/investigation/mechanism-proposal.d.ts +0 -1
  68. package/dist/prompts/target-assessment/investigation/mechanism-proposal.js +0 -49
  69. package/dist/prompts/target-assessment/modulator-triage.d.ts +0 -1
  70. package/dist/prompts/target-assessment/modulator-triage.js +0 -31
  71. package/dist/prompts/target-assessment/off-target-annotator.d.ts +0 -1
  72. package/dist/prompts/target-assessment/off-target-annotator.js +0 -28
  73. package/dist/prompts/target-assessment/tox-voice/core.d.ts +0 -1
  74. package/dist/prompts/target-assessment/tox-voice/core.js +0 -74
  75. package/dist/prompts/target-assessment/tox-voice/critique.d.ts +0 -7
  76. package/dist/prompts/target-assessment/tox-voice/critique.js +0 -109
  77. package/dist/prompts/target-assessment/tox-voice/exemplars.d.ts +0 -8
  78. package/dist/prompts/target-assessment/tox-voice/exemplars.js +0 -24
  79. package/dist/prompts/target-assessment/tox-voice/index.d.ts +0 -4
  80. package/dist/prompts/target-assessment/tox-voice/index.js +0 -4
  81. package/dist/prompts/target-assessment/tox-voice/vocabulary.d.ts +0 -18
  82. package/dist/prompts/target-assessment/tox-voice/vocabulary.js +0 -61
  83. package/dist/state/target-assessments.d.ts +0 -68
  84. package/dist/state/target-assessments.js +0 -222
  85. package/dist/workflows/execute-target-assessment.d.ts +0 -118
  86. package/dist/workflows/execute-target-assessment.js +0 -631
  87. package/dist/workflows/target-assessment/assemblers/index.d.ts +0 -5
  88. package/dist/workflows/target-assessment/assemblers/index.js +0 -4
  89. package/dist/workflows/target-assessment/assemblers/literature.d.ts +0 -281
  90. package/dist/workflows/target-assessment/assemblers/literature.js +0 -971
  91. package/dist/workflows/target-assessment/assemblers/orchestrator.d.ts +0 -118
  92. package/dist/workflows/target-assessment/assemblers/orchestrator.js +0 -945
  93. package/dist/workflows/target-assessment/assemblers/safety.d.ts +0 -374
  94. package/dist/workflows/target-assessment/assemblers/safety.js +0 -1068
  95. package/dist/workflows/target-assessment/assemblers/trials.d.ts +0 -30
  96. package/dist/workflows/target-assessment/assemblers/trials.js +0 -75
  97. package/dist/workflows/target-assessment/collectors/index.d.ts +0 -114
  98. package/dist/workflows/target-assessment/collectors/index.js +0 -538
  99. package/dist/workflows/target-assessment/coverage.d.ts +0 -97
  100. package/dist/workflows/target-assessment/coverage.js +0 -86
  101. package/dist/workflows/target-assessment/decisions/index.d.ts +0 -86
  102. package/dist/workflows/target-assessment/decisions/index.js +0 -127
  103. package/dist/workflows/target-assessment/fanout/index.d.ts +0 -32
  104. package/dist/workflows/target-assessment/fanout/index.js +0 -156
  105. package/dist/workflows/target-assessment/investigation/index.d.ts +0 -97
  106. package/dist/workflows/target-assessment/investigation/index.js +0 -419
  107. package/dist/workflows/target-assessment/lib/approval-precedents.d.ts +0 -73
  108. package/dist/workflows/target-assessment/lib/approval-precedents.js +0 -185
  109. package/dist/workflows/target-assessment/lib/citation-validator.d.ts +0 -46
  110. package/dist/workflows/target-assessment/lib/citation-validator.js +0 -316
  111. package/dist/workflows/target-assessment/lib/clinical-consequence-annotator.d.ts +0 -65
  112. package/dist/workflows/target-assessment/lib/clinical-consequence-annotator.js +0 -174
  113. package/dist/workflows/target-assessment/lib/clinical-evidence-attribution.d.ts +0 -44
  114. package/dist/workflows/target-assessment/lib/clinical-evidence-attribution.js +0 -152
  115. package/dist/workflows/target-assessment/lib/compute-derived.d.ts +0 -20
  116. package/dist/workflows/target-assessment/lib/compute-derived.js +0 -261
  117. package/dist/workflows/target-assessment/lib/compute-selectivity.d.ts +0 -15
  118. package/dist/workflows/target-assessment/lib/compute-selectivity.js +0 -18
  119. package/dist/workflows/target-assessment/lib/dedup-modulators.d.ts +0 -37
  120. package/dist/workflows/target-assessment/lib/dedup-modulators.js +0 -157
  121. package/dist/workflows/target-assessment/lib/evidence-conflict-detector.d.ts +0 -17
  122. package/dist/workflows/target-assessment/lib/evidence-conflict-detector.js +0 -100
  123. package/dist/workflows/target-assessment/lib/expression-constants.d.ts +0 -21
  124. package/dist/workflows/target-assessment/lib/expression-constants.js +0 -21
  125. package/dist/workflows/target-assessment/lib/family-complex-supplement.d.ts +0 -20
  126. package/dist/workflows/target-assessment/lib/family-complex-supplement.js +0 -36
  127. package/dist/workflows/target-assessment/lib/fda-label-safety.d.ts +0 -72
  128. package/dist/workflows/target-assessment/lib/fda-label-safety.js +0 -166
  129. package/dist/workflows/target-assessment/lib/heterodimer-filter.d.ts +0 -30
  130. package/dist/workflows/target-assessment/lib/heterodimer-filter.js +0 -44
  131. package/dist/workflows/target-assessment/lib/hpo-organ-map.d.ts +0 -34
  132. package/dist/workflows/target-assessment/lib/hpo-organ-map.js +0 -63
  133. package/dist/workflows/target-assessment/lib/impc-organ-map.d.ts +0 -19
  134. package/dist/workflows/target-assessment/lib/impc-organ-map.js +0 -39
  135. package/dist/workflows/target-assessment/lib/intended-polypharm-filter.d.ts +0 -4
  136. package/dist/workflows/target-assessment/lib/intended-polypharm-filter.js +0 -24
  137. package/dist/workflows/target-assessment/lib/llm-step.d.ts +0 -80
  138. package/dist/workflows/target-assessment/lib/llm-step.js +0 -101
  139. package/dist/workflows/target-assessment/lib/meddra-organ-map.d.ts +0 -40
  140. package/dist/workflows/target-assessment/lib/meddra-organ-map.js +0 -138
  141. package/dist/workflows/target-assessment/lib/recommendation-quality-gates.d.ts +0 -17
  142. package/dist/workflows/target-assessment/lib/recommendation-quality-gates.js +0 -99
  143. package/dist/workflows/target-assessment/lib/recommendation-sanitizer.d.ts +0 -2
  144. package/dist/workflows/target-assessment/lib/recommendation-sanitizer.js +0 -51
  145. package/dist/workflows/target-assessment/lib/regulatory-actions.d.ts +0 -25
  146. package/dist/workflows/target-assessment/lib/regulatory-actions.js +0 -176
  147. package/dist/workflows/target-assessment/lib/safety-corroboration.d.ts +0 -44
  148. package/dist/workflows/target-assessment/lib/safety-corroboration.js +0 -273
  149. package/dist/workflows/target-assessment/lib/structured-llm.d.ts +0 -61
  150. package/dist/workflows/target-assessment/lib/structured-llm.js +0 -102
  151. package/dist/workflows/target-assessment/lib/target-identity-filter.d.ts +0 -59
  152. package/dist/workflows/target-assessment/lib/target-identity-filter.js +0 -95
  153. package/dist/workflows/target-assessment/lib/therapeutic-programs.d.ts +0 -20
  154. package/dist/workflows/target-assessment/lib/therapeutic-programs.js +0 -68
  155. package/dist/workflows/target-assessment/metrics.d.ts +0 -16
  156. package/dist/workflows/target-assessment/metrics.js +0 -30
  157. package/dist/workflows/target-assessment/phase4-assemble.d.ts +0 -3182
  158. package/dist/workflows/target-assessment/phase4-assemble.js +0 -39
  159. package/dist/workflows/target-assessment/phase5-persist.d.ts +0 -59
  160. package/dist/workflows/target-assessment/phase5-persist.js +0 -349
  161. package/dist/workflows/target-assessment/progress-stream.d.ts +0 -75
  162. package/dist/workflows/target-assessment/progress-stream.js +0 -110
  163. package/dist/workflows/target-assessment/progress.d.ts +0 -39
  164. package/dist/workflows/target-assessment/progress.js +0 -77
  165. package/dist/workflows/target-assessment/schemas.d.ts +0 -970
  166. package/dist/workflows/target-assessment/schemas.js +0 -318
  167. package/dist/workflows/target-assessment/steps/collectors/pathways.d.ts +0 -15
  168. package/dist/workflows/target-assessment/steps/collectors/pathways.js +0 -58
  169. package/dist/workflows/target-assessment/steps/fanout/aes-for-one-class-drug-step.d.ts +0 -34
  170. package/dist/workflows/target-assessment/steps/fanout/aes-for-one-class-drug-step.js +0 -31
  171. package/dist/workflows/target-assessment/steps/fanout/aes-for-one-trial-step.d.ts +0 -57
  172. package/dist/workflows/target-assessment/steps/fanout/aes-for-one-trial-step.js +0 -54
  173. package/dist/workflows/target-assessment/steps/fanout/faers-for-one-modulator-step.d.ts +0 -35
  174. package/dist/workflows/target-assessment/steps/fanout/faers-for-one-modulator-step.js +0 -32
  175. package/dist/workflows/target-assessment/steps/fanout/index.d.ts +0 -14
  176. package/dist/workflows/target-assessment/steps/fanout/index.js +0 -10
  177. package/dist/workflows/target-assessment/steps/fanout/polypharm-for-one-modulator-step.d.ts +0 -29
  178. package/dist/workflows/target-assessment/steps/fanout/polypharm-for-one-modulator-step.js +0 -29
  179. package/dist/workflows/target-assessment/steps/phase2-aggregate.d.ts +0 -657
  180. package/dist/workflows/target-assessment/steps/phase2-aggregate.js +0 -34
  181. package/dist/workflows/target-assessment/steps/phase3-aggregate.d.ts +0 -806
  182. package/dist/workflows/target-assessment/steps/phase3-aggregate.js +0 -16
  183. package/dist/workflows/target-assessment/steps/synthesis/diagnostics.d.ts +0 -28
  184. package/dist/workflows/target-assessment/steps/synthesis/diagnostics.js +0 -27
  185. package/dist/workflows/target-assessment/sub-workflows/index.d.ts +0 -15
  186. package/dist/workflows/target-assessment/sub-workflows/index.js +0 -11
  187. package/dist/workflows/target-assessment/sub-workflows/per-class-drug-aes.d.ts +0 -41
  188. package/dist/workflows/target-assessment/sub-workflows/per-class-drug-aes.js +0 -12
  189. package/dist/workflows/target-assessment/sub-workflows/per-modulator-faers.d.ts +0 -41
  190. package/dist/workflows/target-assessment/sub-workflows/per-modulator-faers.js +0 -12
  191. package/dist/workflows/target-assessment/sub-workflows/per-modulator-polypharm.d.ts +0 -37
  192. package/dist/workflows/target-assessment/sub-workflows/per-modulator-polypharm.js +0 -12
  193. package/dist/workflows/target-assessment/sub-workflows/per-trial-aes.d.ts +0 -66
  194. package/dist/workflows/target-assessment/sub-workflows/per-trial-aes.js +0 -12
  195. package/dist/workflows/target-assessment/synthesis/index.d.ts +0 -607
  196. package/dist/workflows/target-assessment/synthesis/index.js +0 -354
  197. package/dist/workflows/target-assessment/synthesis-probes.d.ts +0 -56
  198. package/dist/workflows/target-assessment/synthesis-probes.js +0 -320
@@ -1,118 +0,0 @@
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- /**
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- * `executeTargetAssessment` — the parent DBOS workflow.
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- *
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- * Shape (every external interaction is a `DBOS.runStep` so a crashed
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- * workflow replays from the cache instead of repeating side effects):
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- *
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- * Phase 0 `phase0Resolve` — only step allowed to throw
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- * (terminates → `target-unresolved`)
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- * Phase 1 15 collectors in parallel — coverage-envelope failures
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- * Progress `emitProgress("deciding")`
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- * Phase 2 2 decisions in parallel — LLM calls, attempt-numbered
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- * Progress `emitProgress("fanning_out")`
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- * Phase 3 4 fan-out blocks in parallel — per-item HTTP, withHost semaphore
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- * Progress `emitProgress("assembling")`
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- * Phase 4 `phase4Assemble` — aggregation + cached annotator
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- * Phase 4a `ta-approval-precedents` — one openFDA lookup, two projections
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- * Phase 4b `assembleSafetyCorroboration` — pure fold, no step of its own
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- * Phase 4c `investigateClaims` — propose / critique / re-verify / converge
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- * Progress `emitProgress("synthesizing")`
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- * Phase 5a 3 per-section syntheses in parallel
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- * Phase 5b `dossierRecommendation` sequential
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- * Phase 5c `phase5Persist` (pure)
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- * Terminal outermost try/finally:
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- * - normal: setDossier → status="completed"
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- * - phase0 throw: markFailed → "target-unresolved"
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- * - schema violation: markFailed → "schema-violation"
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- * - other throw: markFailed → "unexpected-throw"
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- * - 402 self-cancel: markAssessmentSuspended → "suspended_insufficient_funds"
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- * - operator cancel: markFailed → "operator-cancelled"
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- * - soft-deleted row: no-op
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- *
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- * Workflow ID convention: `workflowID === assessmentId`. TA is one-shot
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- * (re-runs create new rows), so the workflowID equals the assessmentId
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- * directly. No `:runId` suffix.
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- */
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- import type { Pool } from "pg";
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- import { z } from "zod";
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- import type { RunSession } from "../auth/types.js";
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- import type { RunAuthorizer } from "../execution/run-authorizer.js";
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- import type { Logger } from "../lib/logger.js";
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- import type { UsageRecorder } from "../billing/usage-recorder.js";
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- import type { AgentChat } from "../providers/types.js";
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- import { TargetAssessmentInputSchema } from "./target-assessment/schemas.js";
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- import { type ClaimInvestigationConfig } from "./target-assessment/investigation/index.js";
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- import { type ProgressPhase } from "./target-assessment/progress.js";
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- export declare const ExecuteTargetAssessmentInputSchema: z.ZodObject<{
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- assessmentId: z.ZodString;
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- target: z.ZodString;
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- goal: z.ZodOptional<z.ZodNullable<z.ZodString>>;
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- organizationId: z.ZodString;
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- requestedBy: z.ZodString;
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- billingContextId: z.ZodString;
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- }, z.core.$strip>;
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- type SerializedInput = z.infer<typeof ExecuteTargetAssessmentInputSchema>;
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- /**
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- * Workflow input includes the `runSession` minted at the trigger route.
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- * The schema is for the serialised wire shape (input persisted by DBOS);
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- * the `runSession` is added at the type level so the workflow body can
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- * read the run-authorization credential directly.
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- */
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- export type ExecuteTargetAssessmentInput = SerializedInput & {
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- readonly runSession: RunSession;
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- /**
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- * True when Cortex owns the run-authorization lifecycle and therefore must
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- * revoke it on the terminal path. Optional because a workflow persisted
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- * before this field existed (recovered across the deploy that added it)
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- * deserializes without it; the body defaults absent → true, matching the
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- * prior Cortex-owned behavior.
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- */
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- readonly ownsMandate?: boolean;
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- };
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- export interface ExecuteTargetAssessmentResult {
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- readonly assessmentId: string;
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- readonly status: "completed" | "failed" | "suspended_insufficient_funds" | "deleted";
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- readonly bytes: number;
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- }
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- export interface ExecuteTargetAssessmentDeps {
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- /** Operational logging seam; omitted falls back to no-op. */
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- readonly logger?: Logger;
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- readonly pool: Pool;
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- /** Run-authorization seam — the terminal path revokes through `revoke`. */
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- readonly runAuthorizer: RunAuthorizer;
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- /** NCBI E-utilities key for the ClinVar / PubMed Phase-1 collectors. */
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- readonly ncbiApiKey?: string;
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- /**
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- * Chat provider — billing resolution is closure-wrapped via the TA
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- * resolver in `harness/billing/target-assessment-resolver.ts` (see §12
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- * registration). The session's `scope.kind === "target-assessment"`
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- * carries the `billingContextId` the resolver keys on.
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- */
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- readonly chatProvider: AgentChat;
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- /** Billing-gateway model for decision agents — typically `env.TARGET_ASSESSMENT_DECISION_MODEL`. */
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- readonly decisionModel: string;
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- /** Billing-gateway model for synthesis agents — typically `env.TARGET_ASSESSMENT_SYNTHESIS_MODEL`. */
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- readonly synthesisModel: string;
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- /** LLM usage-accounting seam for the assessment's agent loops; omitted falls back to the no-op recorder. */
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- readonly usageRecorder?: UsageRecorder;
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- /**
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- * Bounds the claim-investigation phase runs under. Omitted falls back to
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- * `DEFAULT_CLAIM_INVESTIGATION_CONFIG` — the values are cost and termination
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- * bounds, not domain constants, so an embedder wanting a deeper pass sets
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- * its own and the dossier reports what was in force.
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- */
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- readonly claimInvestigation?: Partial<ClaimInvestigationConfig>;
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- }
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- /**
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- * Register the executeTargetAssessment workflow with DBOS. Caller is
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- * responsible for setting `workflowID = assessmentId` via
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- * `DBOS.startWorkflow(_, { workflowID })`.
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- */
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- export declare function registerExecuteTargetAssessment(deps: ExecuteTargetAssessmentDeps): (input: ExecuteTargetAssessmentInput) => Promise<ExecuteTargetAssessmentResult>;
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- /**
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- * Body extracted so tests can drive it without registering a workflow
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- * (the DBOS calls inside still rely on a workflow context being present).
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- */
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- export declare function runExecuteTargetAssessmentBody(input: ExecuteTargetAssessmentInput, deps: ExecuteTargetAssessmentDeps): Promise<ExecuteTargetAssessmentResult>;
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- export { TargetAssessmentInputSchema };
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- export type { ProgressPhase };