@inflexa-ai/harness 0.35.7 → 0.36.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (199) 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 +20 -0
  15. package/dist/loop/genai-spans.js +53 -0
  16. package/dist/loop/run-agent.d.ts +1 -1
  17. package/dist/loop/run-agent.js +9 -4
  18. package/dist/providers/ai-sdk.js +8 -0
  19. package/dist/runtime/assemble.d.ts +0 -3
  20. package/dist/runtime/assemble.js +0 -3
  21. package/dist/state/index.d.ts +0 -2
  22. package/dist/state/index.js +0 -1
  23. package/dist/state/init.js +1 -60
  24. package/dist/state/purge-analysis.d.ts +1 -2
  25. package/dist/state/purge-analysis.js +1 -2
  26. package/dist/tasks/regulatory-corpus-boot-refresh.js +1 -1
  27. package/dist/tools/bio/gene-preclinical-profile.d.ts +1 -3
  28. package/dist/tools/bio/gene-preclinical-profile.js +1 -3
  29. package/dist/tools/lib/chembl-client.d.ts +1 -4
  30. package/dist/tools/lib/chembl-client.js +1 -4
  31. package/dist/tools/lib/clinical-benchmarks-client.d.ts +1 -1
  32. package/dist/tools/lib/clinical-benchmarks-client.js +1 -1
  33. package/dist/tools/lib/clinical-trials-client.d.ts +0 -3
  34. package/dist/tools/lib/clinical-trials-client.js +0 -3
  35. package/dist/tools/lib/identifier-resolver.d.ts +5 -7
  36. package/dist/tools/lib/identifier-resolver.js +5 -7
  37. package/dist/tools/lib/iuphar-client.d.ts +1 -3
  38. package/dist/tools/lib/iuphar-client.js +1 -3
  39. package/dist/tools/lib/opentargets-client.d.ts +1 -1
  40. package/dist/tools/lib/opentargets-client.js +1 -1
  41. package/dist/tools/lib/protein-family-normalize.d.ts +5 -7
  42. package/dist/tools/lib/protein-family-normalize.js +5 -7
  43. package/dist/tools/lib/uniprot-client.d.ts +0 -7
  44. package/dist/tools/lib/uniprot-client.js +2 -9
  45. package/package.json +9 -8
  46. package/dist/contracts/target-assessment-row.d.ts +0 -85
  47. package/dist/contracts/target-assessment-row.js +0 -37
  48. package/dist/contracts/target-dossier.d.ts +0 -12423
  49. package/dist/contracts/target-dossier.js +0 -1282
  50. package/dist/prompts/target-assessment/briefs/executive-recommendation.d.ts +0 -1
  51. package/dist/prompts/target-assessment/briefs/executive-recommendation.js +0 -85
  52. package/dist/prompts/target-assessment/briefs/index.d.ts +0 -4
  53. package/dist/prompts/target-assessment/briefs/index.js +0 -4
  54. package/dist/prompts/target-assessment/briefs/liability-bullets.d.ts +0 -1
  55. package/dist/prompts/target-assessment/briefs/liability-bullets.js +0 -114
  56. package/dist/prompts/target-assessment/briefs/target-organ-liabilities.d.ts +0 -1
  57. package/dist/prompts/target-assessment/briefs/target-organ-liabilities.js +0 -37
  58. package/dist/prompts/target-assessment/briefs/translational-commentary.d.ts +0 -1
  59. package/dist/prompts/target-assessment/briefs/translational-commentary.js +0 -23
  60. package/dist/prompts/target-assessment/drugs-in-class.d.ts +0 -1
  61. package/dist/prompts/target-assessment/drugs-in-class.js +0 -29
  62. package/dist/prompts/target-assessment/investigation/adversarial-critique.d.ts +0 -1
  63. package/dist/prompts/target-assessment/investigation/adversarial-critique.js +0 -67
  64. package/dist/prompts/target-assessment/investigation/claim-reverification.d.ts +0 -1
  65. package/dist/prompts/target-assessment/investigation/claim-reverification.js +0 -49
  66. package/dist/prompts/target-assessment/investigation/index.d.ts +0 -3
  67. package/dist/prompts/target-assessment/investigation/index.js +0 -3
  68. package/dist/prompts/target-assessment/investigation/mechanism-proposal.d.ts +0 -1
  69. package/dist/prompts/target-assessment/investigation/mechanism-proposal.js +0 -49
  70. package/dist/prompts/target-assessment/modulator-triage.d.ts +0 -1
  71. package/dist/prompts/target-assessment/modulator-triage.js +0 -31
  72. package/dist/prompts/target-assessment/off-target-annotator.d.ts +0 -1
  73. package/dist/prompts/target-assessment/off-target-annotator.js +0 -28
  74. package/dist/prompts/target-assessment/tox-voice/core.d.ts +0 -1
  75. package/dist/prompts/target-assessment/tox-voice/core.js +0 -74
  76. package/dist/prompts/target-assessment/tox-voice/critique.d.ts +0 -7
  77. package/dist/prompts/target-assessment/tox-voice/critique.js +0 -109
  78. package/dist/prompts/target-assessment/tox-voice/exemplars.d.ts +0 -8
  79. package/dist/prompts/target-assessment/tox-voice/exemplars.js +0 -24
  80. package/dist/prompts/target-assessment/tox-voice/index.d.ts +0 -4
  81. package/dist/prompts/target-assessment/tox-voice/index.js +0 -4
  82. package/dist/prompts/target-assessment/tox-voice/vocabulary.d.ts +0 -18
  83. package/dist/prompts/target-assessment/tox-voice/vocabulary.js +0 -61
  84. package/dist/state/target-assessments.d.ts +0 -68
  85. package/dist/state/target-assessments.js +0 -222
  86. package/dist/workflows/execute-target-assessment.d.ts +0 -118
  87. package/dist/workflows/execute-target-assessment.js +0 -631
  88. package/dist/workflows/target-assessment/assemblers/index.d.ts +0 -5
  89. package/dist/workflows/target-assessment/assemblers/index.js +0 -4
  90. package/dist/workflows/target-assessment/assemblers/literature.d.ts +0 -281
  91. package/dist/workflows/target-assessment/assemblers/literature.js +0 -971
  92. package/dist/workflows/target-assessment/assemblers/orchestrator.d.ts +0 -118
  93. package/dist/workflows/target-assessment/assemblers/orchestrator.js +0 -945
  94. package/dist/workflows/target-assessment/assemblers/safety.d.ts +0 -374
  95. package/dist/workflows/target-assessment/assemblers/safety.js +0 -1068
  96. package/dist/workflows/target-assessment/assemblers/trials.d.ts +0 -30
  97. package/dist/workflows/target-assessment/assemblers/trials.js +0 -75
  98. package/dist/workflows/target-assessment/collectors/index.d.ts +0 -114
  99. package/dist/workflows/target-assessment/collectors/index.js +0 -538
  100. package/dist/workflows/target-assessment/coverage.d.ts +0 -97
  101. package/dist/workflows/target-assessment/coverage.js +0 -86
  102. package/dist/workflows/target-assessment/decisions/index.d.ts +0 -86
  103. package/dist/workflows/target-assessment/decisions/index.js +0 -127
  104. package/dist/workflows/target-assessment/fanout/index.d.ts +0 -32
  105. package/dist/workflows/target-assessment/fanout/index.js +0 -156
  106. package/dist/workflows/target-assessment/investigation/index.d.ts +0 -97
  107. package/dist/workflows/target-assessment/investigation/index.js +0 -419
  108. package/dist/workflows/target-assessment/lib/approval-precedents.d.ts +0 -73
  109. package/dist/workflows/target-assessment/lib/approval-precedents.js +0 -185
  110. package/dist/workflows/target-assessment/lib/citation-validator.d.ts +0 -46
  111. package/dist/workflows/target-assessment/lib/citation-validator.js +0 -316
  112. package/dist/workflows/target-assessment/lib/clinical-consequence-annotator.d.ts +0 -65
  113. package/dist/workflows/target-assessment/lib/clinical-consequence-annotator.js +0 -174
  114. package/dist/workflows/target-assessment/lib/clinical-evidence-attribution.d.ts +0 -44
  115. package/dist/workflows/target-assessment/lib/clinical-evidence-attribution.js +0 -152
  116. package/dist/workflows/target-assessment/lib/compute-derived.d.ts +0 -20
  117. package/dist/workflows/target-assessment/lib/compute-derived.js +0 -261
  118. package/dist/workflows/target-assessment/lib/compute-selectivity.d.ts +0 -15
  119. package/dist/workflows/target-assessment/lib/compute-selectivity.js +0 -18
  120. package/dist/workflows/target-assessment/lib/dedup-modulators.d.ts +0 -37
  121. package/dist/workflows/target-assessment/lib/dedup-modulators.js +0 -157
  122. package/dist/workflows/target-assessment/lib/evidence-conflict-detector.d.ts +0 -17
  123. package/dist/workflows/target-assessment/lib/evidence-conflict-detector.js +0 -100
  124. package/dist/workflows/target-assessment/lib/expression-constants.d.ts +0 -21
  125. package/dist/workflows/target-assessment/lib/expression-constants.js +0 -21
  126. package/dist/workflows/target-assessment/lib/family-complex-supplement.d.ts +0 -20
  127. package/dist/workflows/target-assessment/lib/family-complex-supplement.js +0 -36
  128. package/dist/workflows/target-assessment/lib/fda-label-safety.d.ts +0 -72
  129. package/dist/workflows/target-assessment/lib/fda-label-safety.js +0 -166
  130. package/dist/workflows/target-assessment/lib/heterodimer-filter.d.ts +0 -30
  131. package/dist/workflows/target-assessment/lib/heterodimer-filter.js +0 -44
  132. package/dist/workflows/target-assessment/lib/hpo-organ-map.d.ts +0 -34
  133. package/dist/workflows/target-assessment/lib/hpo-organ-map.js +0 -63
  134. package/dist/workflows/target-assessment/lib/impc-organ-map.d.ts +0 -19
  135. package/dist/workflows/target-assessment/lib/impc-organ-map.js +0 -39
  136. package/dist/workflows/target-assessment/lib/intended-polypharm-filter.d.ts +0 -4
  137. package/dist/workflows/target-assessment/lib/intended-polypharm-filter.js +0 -24
  138. package/dist/workflows/target-assessment/lib/llm-step.d.ts +0 -80
  139. package/dist/workflows/target-assessment/lib/llm-step.js +0 -101
  140. package/dist/workflows/target-assessment/lib/meddra-organ-map.d.ts +0 -40
  141. package/dist/workflows/target-assessment/lib/meddra-organ-map.js +0 -138
  142. package/dist/workflows/target-assessment/lib/recommendation-quality-gates.d.ts +0 -17
  143. package/dist/workflows/target-assessment/lib/recommendation-quality-gates.js +0 -99
  144. package/dist/workflows/target-assessment/lib/recommendation-sanitizer.d.ts +0 -2
  145. package/dist/workflows/target-assessment/lib/recommendation-sanitizer.js +0 -51
  146. package/dist/workflows/target-assessment/lib/regulatory-actions.d.ts +0 -25
  147. package/dist/workflows/target-assessment/lib/regulatory-actions.js +0 -176
  148. package/dist/workflows/target-assessment/lib/safety-corroboration.d.ts +0 -44
  149. package/dist/workflows/target-assessment/lib/safety-corroboration.js +0 -273
  150. package/dist/workflows/target-assessment/lib/structured-llm.d.ts +0 -61
  151. package/dist/workflows/target-assessment/lib/structured-llm.js +0 -102
  152. package/dist/workflows/target-assessment/lib/target-identity-filter.d.ts +0 -59
  153. package/dist/workflows/target-assessment/lib/target-identity-filter.js +0 -95
  154. package/dist/workflows/target-assessment/lib/therapeutic-programs.d.ts +0 -20
  155. package/dist/workflows/target-assessment/lib/therapeutic-programs.js +0 -68
  156. package/dist/workflows/target-assessment/metrics.d.ts +0 -16
  157. package/dist/workflows/target-assessment/metrics.js +0 -30
  158. package/dist/workflows/target-assessment/phase4-assemble.d.ts +0 -3182
  159. package/dist/workflows/target-assessment/phase4-assemble.js +0 -39
  160. package/dist/workflows/target-assessment/phase5-persist.d.ts +0 -59
  161. package/dist/workflows/target-assessment/phase5-persist.js +0 -349
  162. package/dist/workflows/target-assessment/progress-stream.d.ts +0 -75
  163. package/dist/workflows/target-assessment/progress-stream.js +0 -110
  164. package/dist/workflows/target-assessment/progress.d.ts +0 -39
  165. package/dist/workflows/target-assessment/progress.js +0 -77
  166. package/dist/workflows/target-assessment/schemas.d.ts +0 -970
  167. package/dist/workflows/target-assessment/schemas.js +0 -318
  168. package/dist/workflows/target-assessment/steps/collectors/pathways.d.ts +0 -15
  169. package/dist/workflows/target-assessment/steps/collectors/pathways.js +0 -58
  170. package/dist/workflows/target-assessment/steps/fanout/aes-for-one-class-drug-step.d.ts +0 -34
  171. package/dist/workflows/target-assessment/steps/fanout/aes-for-one-class-drug-step.js +0 -31
  172. package/dist/workflows/target-assessment/steps/fanout/aes-for-one-trial-step.d.ts +0 -57
  173. package/dist/workflows/target-assessment/steps/fanout/aes-for-one-trial-step.js +0 -54
  174. package/dist/workflows/target-assessment/steps/fanout/faers-for-one-modulator-step.d.ts +0 -35
  175. package/dist/workflows/target-assessment/steps/fanout/faers-for-one-modulator-step.js +0 -32
  176. package/dist/workflows/target-assessment/steps/fanout/index.d.ts +0 -14
  177. package/dist/workflows/target-assessment/steps/fanout/index.js +0 -10
  178. package/dist/workflows/target-assessment/steps/fanout/polypharm-for-one-modulator-step.d.ts +0 -29
  179. package/dist/workflows/target-assessment/steps/fanout/polypharm-for-one-modulator-step.js +0 -29
  180. package/dist/workflows/target-assessment/steps/phase2-aggregate.d.ts +0 -657
  181. package/dist/workflows/target-assessment/steps/phase2-aggregate.js +0 -34
  182. package/dist/workflows/target-assessment/steps/phase3-aggregate.d.ts +0 -806
  183. package/dist/workflows/target-assessment/steps/phase3-aggregate.js +0 -16
  184. package/dist/workflows/target-assessment/steps/synthesis/diagnostics.d.ts +0 -28
  185. package/dist/workflows/target-assessment/steps/synthesis/diagnostics.js +0 -27
  186. package/dist/workflows/target-assessment/sub-workflows/index.d.ts +0 -15
  187. package/dist/workflows/target-assessment/sub-workflows/index.js +0 -11
  188. package/dist/workflows/target-assessment/sub-workflows/per-class-drug-aes.d.ts +0 -41
  189. package/dist/workflows/target-assessment/sub-workflows/per-class-drug-aes.js +0 -12
  190. package/dist/workflows/target-assessment/sub-workflows/per-modulator-faers.d.ts +0 -41
  191. package/dist/workflows/target-assessment/sub-workflows/per-modulator-faers.js +0 -12
  192. package/dist/workflows/target-assessment/sub-workflows/per-modulator-polypharm.d.ts +0 -37
  193. package/dist/workflows/target-assessment/sub-workflows/per-modulator-polypharm.js +0 -12
  194. package/dist/workflows/target-assessment/sub-workflows/per-trial-aes.d.ts +0 -66
  195. package/dist/workflows/target-assessment/sub-workflows/per-trial-aes.js +0 -12
  196. package/dist/workflows/target-assessment/synthesis/index.d.ts +0 -607
  197. package/dist/workflows/target-assessment/synthesis/index.js +0 -354
  198. package/dist/workflows/target-assessment/synthesis-probes.d.ts +0 -56
  199. package/dist/workflows/target-assessment/synthesis-probes.js +0 -320

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