@inflexa-ai/harness 0.17.0 → 0.18.0

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 (221) hide show
  1. package/dist/agents/report-builder.d.ts +2 -0
  2. package/dist/agents/report-builder.js +2 -0
  3. package/dist/app/spawn-report-session.d.ts +85 -0
  4. package/dist/app/spawn-report-session.js +83 -0
  5. package/dist/contracts/chat-events.d.ts +9 -0
  6. package/dist/contracts/index.d.ts +6 -2
  7. package/dist/contracts/index.js +3 -1
  8. package/dist/contracts/organ-system.d.ts +49 -0
  9. package/dist/contracts/organ-system.js +67 -0
  10. package/dist/contracts/report-blocks.d.ts +564 -0
  11. package/dist/contracts/report-blocks.js +117 -0
  12. package/dist/contracts/report-reference.d.ts +459 -0
  13. package/dist/contracts/report-reference.js +256 -0
  14. package/dist/contracts/schemas/chat-events.d.ts +2 -0
  15. package/dist/contracts/schemas/chat-events.js +2 -0
  16. package/dist/contracts/severity.d.ts +15 -0
  17. package/dist/contracts/severity.js +10 -0
  18. package/dist/contracts/target-dossier.d.ts +8675 -12972
  19. package/dist/contracts/target-dossier.js +534 -591
  20. package/dist/data/safety-panel-schema.d.ts +18 -5
  21. package/dist/data/safety-panel-schema.js +4 -4
  22. package/dist/execution/artifact-metadata.js +1 -0
  23. package/dist/execution/report-runner.js +1 -3
  24. package/dist/execution/run-synthesis.js +2 -0
  25. package/dist/index.d.ts +6 -0
  26. package/dist/index.js +19 -0
  27. package/dist/lib/async-utils.d.ts +16 -4
  28. package/dist/lib/async-utils.js +20 -15
  29. package/dist/lib/host-concurrency.js +1 -0
  30. package/dist/loop/__fixtures__/scripted-provider.js +23 -2
  31. package/dist/loop/run-agent.js +58 -10
  32. package/dist/loop/tool-detail.d.ts +40 -0
  33. package/dist/loop/tool-detail.js +35 -3
  34. package/dist/loop/types.d.ts +13 -0
  35. package/dist/memory/thread-history.d.ts +10 -0
  36. package/dist/memory/thread-history.js +12 -1
  37. package/dist/prompts/target-assessment/briefs/executive-recommendation.d.ts +1 -1
  38. package/dist/prompts/target-assessment/briefs/executive-recommendation.js +5 -5
  39. package/dist/prompts/target-assessment/briefs/liability-bullets.d.ts +1 -1
  40. package/dist/prompts/target-assessment/briefs/liability-bullets.js +1 -1
  41. package/dist/prompts/target-assessment/briefs/target-organ-liabilities.d.ts +1 -1
  42. package/dist/prompts/target-assessment/briefs/target-organ-liabilities.js +11 -3
  43. package/dist/prompts/target-assessment/investigation/adversarial-critique.d.ts +1 -0
  44. package/dist/prompts/target-assessment/investigation/adversarial-critique.js +67 -0
  45. package/dist/prompts/target-assessment/investigation/claim-reverification.d.ts +1 -0
  46. package/dist/prompts/target-assessment/investigation/claim-reverification.js +49 -0
  47. package/dist/prompts/target-assessment/investigation/index.d.ts +3 -0
  48. package/dist/prompts/target-assessment/investigation/index.js +3 -0
  49. package/dist/prompts/target-assessment/investigation/mechanism-proposal.d.ts +1 -0
  50. package/dist/prompts/target-assessment/investigation/mechanism-proposal.js +49 -0
  51. package/dist/prompts/target-assessment/tox-voice/index.d.ts +1 -1
  52. package/dist/prompts/target-assessment/tox-voice/vocabulary.d.ts +8 -5
  53. package/dist/prompts/target-assessment/tox-voice/vocabulary.js +9 -20
  54. package/dist/providers/__fixtures__/session.d.ts +5 -4
  55. package/dist/providers/__fixtures__/session.js +4 -4
  56. package/dist/report-model/block-walk.d.ts +56 -0
  57. package/dist/report-model/block-walk.js +89 -0
  58. package/dist/report-model/draft-finish.d.ts +60 -0
  59. package/dist/report-model/draft-finish.js +56 -0
  60. package/dist/report-model/draft-operations.d.ts +125 -0
  61. package/dist/report-model/draft-operations.js +341 -0
  62. package/dist/report-model/draft-read.d.ts +59 -0
  63. package/dist/report-model/draft-read.js +109 -0
  64. package/dist/report-model/draft.d.ts +51 -0
  65. package/dist/report-model/draft.js +32 -0
  66. package/dist/report-model/fixture-resolver.d.ts +8 -0
  67. package/dist/report-model/fixture-resolver.js +252 -0
  68. package/dist/report-model/mint-snapshot.d.ts +30 -0
  69. package/dist/report-model/mint-snapshot.js +40 -0
  70. package/dist/report-model/reference-resolver.d.ts +113 -0
  71. package/dist/report-model/reference-resolver.js +60 -0
  72. package/dist/report-model/structural-validation.d.ts +22 -0
  73. package/dist/report-model/structural-validation.js +68 -0
  74. package/dist/report-model/validate.d.ts +40 -0
  75. package/dist/report-model/validate.js +80 -0
  76. package/dist/report-render/chart.d.ts +33 -0
  77. package/dist/report-render/chart.js +538 -0
  78. package/dist/report-render/page.d.ts +127 -0
  79. package/dist/report-render/page.js +307 -0
  80. package/dist/report-render/references.d.ts +32 -0
  81. package/dist/report-render/references.js +44 -0
  82. package/dist/report-render/render.d.ts +25 -0
  83. package/dist/report-render/render.js +125 -0
  84. package/dist/report-render/script-json.d.ts +13 -0
  85. package/dist/report-render/script-json.js +15 -0
  86. package/dist/report-render/types.d.ts +39 -0
  87. package/dist/report-render/types.js +10 -0
  88. package/dist/report-render/views/chart-view.d.ts +11 -0
  89. package/dist/report-render/views/chart-view.js +23 -0
  90. package/dist/report-render/views/page-view.d.ts +20 -0
  91. package/dist/report-render/views/page-view.js +49 -0
  92. package/dist/report-render/views/prose.d.ts +28 -0
  93. package/dist/report-render/views/prose.js +75 -0
  94. package/dist/report-render/views/references-view.d.ts +20 -0
  95. package/dist/report-render/views/references-view.js +64 -0
  96. package/dist/report-render/views/values.d.ts +42 -0
  97. package/dist/report-render/views/values.js +43 -0
  98. package/dist/runtime/boot.d.ts +3 -3
  99. package/dist/runtime/boot.js +15 -4
  100. package/dist/runtime/dbos.d.ts +4 -4
  101. package/dist/state/artifacts.d.ts +16 -0
  102. package/dist/state/artifacts.js +18 -0
  103. package/dist/state/init.js +31 -0
  104. package/dist/state/purge-analysis.js +1 -0
  105. package/dist/state/report-versions.d.ts +132 -0
  106. package/dist/state/report-versions.js +194 -0
  107. package/dist/tasks/data-profile.js +1 -0
  108. package/dist/tools/bio/chembl.js +1 -0
  109. package/dist/tools/bio/comptox.js +1 -0
  110. package/dist/tools/bio/drug-gene-interactions.js +1 -0
  111. package/dist/tools/bio/gene-disease-evidence.js +1 -0
  112. package/dist/tools/bio/gene-preclinical-profile.js +1 -0
  113. package/dist/tools/bio/keys.d.ts +3 -2
  114. package/dist/tools/bio/keys.js +3 -2
  115. package/dist/tools/bio/lookup-annotation.js +1 -0
  116. package/dist/tools/bio/opentargets.d.ts +3 -3
  117. package/dist/tools/bio/opentargets.js +4 -3
  118. package/dist/tools/bio/pubchem.js +1 -0
  119. package/dist/tools/bio/search-clinical-trials.js +1 -0
  120. package/dist/tools/bio/search-faers.js +1 -0
  121. package/dist/tools/bio/search-geo-datasets.js +1 -0
  122. package/dist/tools/bio/search-interactions.js +1 -0
  123. package/dist/tools/bio/target-safety.d.ts +4 -6
  124. package/dist/tools/bio/target-safety.js +7 -6
  125. package/dist/tools/define-tool.d.ts +19 -12
  126. package/dist/tools/define-tool.js +4 -2
  127. package/dist/tools/display/show-user.js +1 -0
  128. package/dist/tools/iterate-report.js +2 -0
  129. package/dist/tools/lib/chembl-client.d.ts +2 -0
  130. package/dist/tools/lib/chembl-client.js +1 -0
  131. package/dist/tools/lib/monarch-client.d.ts +42 -0
  132. package/dist/tools/lib/monarch-client.js +100 -0
  133. package/dist/tools/report/build-report.js +1 -0
  134. package/dist/tools/report/mint-preview-url.js +1 -0
  135. package/dist/tools/report/preview-snapshot.js +1 -0
  136. package/dist/tools/report/submit-report.js +1 -0
  137. package/dist/tools/report/version-fs.js +4 -0
  138. package/dist/tools/report-authoring/authoring-tools.d.ts +134 -0
  139. package/dist/tools/report-authoring/authoring-tools.js +352 -0
  140. package/dist/tools/research/context7-docs.js +2 -0
  141. package/dist/tools/research/generate-analogy-report.js +1 -0
  142. package/dist/tools/research/generate-plan.js +3 -0
  143. package/dist/tools/research/inspect-data-profile.js +4 -0
  144. package/dist/tools/research/literature-reviewer.js +1 -0
  145. package/dist/tools/research/search-arxiv.js +1 -0
  146. package/dist/tools/research/search-github-repos.js +1 -0
  147. package/dist/tools/research/search-semantic-scholar.js +1 -0
  148. package/dist/tools/sandbox/list-available-packages.js +23 -0
  149. package/dist/tools/sandbox/list-available-refs.js +36 -0
  150. package/dist/tools/sandbox/report-blocker.js +1 -0
  151. package/dist/tools/sandbox/skills.js +2 -0
  152. package/dist/tools/workspace/file-stat.js +1 -0
  153. package/dist/tools/workspace/show-file.js +2 -0
  154. package/dist/tools/workspace/show-plan.js +1 -0
  155. package/dist/workflows/execute-analysis.d.ts +5 -1
  156. package/dist/workflows/execute-analysis.js +5 -5
  157. package/dist/workflows/execute-target-assessment.d.ts +13 -2
  158. package/dist/workflows/execute-target-assessment.js +78 -16
  159. package/dist/workflows/target-assessment/assemblers/index.d.ts +1 -1
  160. package/dist/workflows/target-assessment/assemblers/index.js +1 -1
  161. package/dist/workflows/target-assessment/assemblers/literature.d.ts +9 -27
  162. package/dist/workflows/target-assessment/assemblers/literature.js +32 -48
  163. package/dist/workflows/target-assessment/assemblers/orchestrator.d.ts +17 -9
  164. package/dist/workflows/target-assessment/assemblers/orchestrator.js +195 -85
  165. package/dist/workflows/target-assessment/assemblers/safety.d.ts +70 -48
  166. package/dist/workflows/target-assessment/assemblers/safety.js +125 -42
  167. package/dist/workflows/target-assessment/collectors/index.d.ts +5 -2
  168. package/dist/workflows/target-assessment/collectors/index.js +48 -5
  169. package/dist/workflows/target-assessment/coverage.d.ts +43 -27
  170. package/dist/workflows/target-assessment/coverage.js +33 -29
  171. package/dist/workflows/target-assessment/fanout/index.js +1 -0
  172. package/dist/workflows/target-assessment/investigation/index.d.ts +97 -0
  173. package/dist/workflows/target-assessment/investigation/index.js +419 -0
  174. package/dist/workflows/target-assessment/lib/approval-precedents.d.ts +26 -5
  175. package/dist/workflows/target-assessment/lib/approval-precedents.js +95 -29
  176. package/dist/workflows/target-assessment/lib/citation-validator.js +1 -1
  177. package/dist/workflows/target-assessment/lib/clinical-consequence-annotator.d.ts +2 -2
  178. package/dist/workflows/target-assessment/lib/clinical-evidence-attribution.d.ts +2 -3
  179. package/dist/workflows/target-assessment/lib/clinical-evidence-attribution.js +0 -4
  180. package/dist/workflows/target-assessment/lib/compute-derived.d.ts +6 -5
  181. package/dist/workflows/target-assessment/lib/compute-derived.js +14 -5
  182. package/dist/workflows/target-assessment/lib/family-complex-supplement.d.ts +5 -6
  183. package/dist/workflows/target-assessment/lib/family-complex-supplement.js +2 -3
  184. package/dist/workflows/target-assessment/lib/fda-label-safety.d.ts +72 -0
  185. package/dist/workflows/target-assessment/lib/fda-label-safety.js +166 -0
  186. package/dist/workflows/target-assessment/lib/heterodimer-filter.d.ts +0 -9
  187. package/dist/workflows/target-assessment/lib/heterodimer-filter.js +0 -10
  188. package/dist/workflows/target-assessment/lib/hpo-organ-map.d.ts +34 -0
  189. package/dist/workflows/target-assessment/lib/hpo-organ-map.js +63 -0
  190. package/dist/workflows/target-assessment/lib/impc-organ-map.d.ts +19 -0
  191. package/dist/workflows/target-assessment/lib/impc-organ-map.js +39 -0
  192. package/dist/workflows/target-assessment/lib/meddra-organ-map.d.ts +24 -14
  193. package/dist/workflows/target-assessment/lib/meddra-organ-map.js +59 -47
  194. package/dist/workflows/target-assessment/lib/recommendation-sanitizer.js +1 -1
  195. package/dist/workflows/target-assessment/lib/regulatory-actions.d.ts +2 -3
  196. package/dist/workflows/target-assessment/lib/regulatory-actions.js +33 -4
  197. package/dist/workflows/target-assessment/lib/safety-corroboration.d.ts +44 -0
  198. package/dist/workflows/target-assessment/lib/safety-corroboration.js +273 -0
  199. package/dist/workflows/target-assessment/lib/target-identity-filter.d.ts +5 -7
  200. package/dist/workflows/target-assessment/lib/target-identity-filter.js +5 -7
  201. package/dist/workflows/target-assessment/metrics.d.ts +1 -6
  202. package/dist/workflows/target-assessment/metrics.js +1 -13
  203. package/dist/workflows/target-assessment/phase4-assemble.d.ts +2147 -807
  204. package/dist/workflows/target-assessment/phase4-assemble.js +19 -19
  205. package/dist/workflows/target-assessment/phase5-persist.d.ts +20 -21
  206. package/dist/workflows/target-assessment/phase5-persist.js +56 -173
  207. package/dist/workflows/target-assessment/schemas.d.ts +46 -1
  208. package/dist/workflows/target-assessment/schemas.js +19 -0
  209. package/dist/workflows/target-assessment/steps/fanout/polypharm-for-one-modulator-step.d.ts +1 -0
  210. package/dist/workflows/target-assessment/steps/fanout/polypharm-for-one-modulator-step.js +2 -0
  211. package/dist/workflows/target-assessment/steps/phase2-aggregate.d.ts +26 -62
  212. package/dist/workflows/target-assessment/steps/phase2-aggregate.js +0 -4
  213. package/dist/workflows/target-assessment/steps/phase3-aggregate.d.ts +27 -154
  214. package/dist/workflows/target-assessment/steps/phase3-aggregate.js +0 -6
  215. package/dist/workflows/target-assessment/steps/synthesis/diagnostics.d.ts +0 -6
  216. package/dist/workflows/target-assessment/steps/synthesis/diagnostics.js +0 -18
  217. package/dist/workflows/target-assessment/sub-workflows/per-modulator-polypharm.d.ts +1 -0
  218. package/dist/workflows/target-assessment/synthesis/index.d.ts +52 -5
  219. package/dist/workflows/target-assessment/synthesis/index.js +4 -1
  220. package/dist/workflows/target-assessment/synthesis-probes.d.ts +3 -3
  221. package/package.json +4 -1

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