@inflexa-ai/harness 0.1.1

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 (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
  75. package/dist/auth/local-auth-context.js +20 -0
  76. package/dist/auth/local-run-authorizer.d.ts +10 -0
  77. package/dist/auth/local-run-authorizer.js +23 -0
  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
  81. package/dist/billing/cached-resolver.js +61 -0
  82. package/dist/billing/noop-resolver.d.ts +6 -0
  83. package/dist/billing/noop-resolver.js +7 -0
  84. package/dist/billing/noop-run-charge.d.ts +6 -0
  85. package/dist/billing/noop-run-charge.js +10 -0
  86. package/dist/billing/resolver.d.ts +64 -0
  87. package/dist/billing/resolver.js +24 -0
  88. package/dist/billing/run-charge.d.ts +24 -0
  89. package/dist/billing/run-charge.js +9 -0
  90. package/dist/config/resource-limits.d.ts +76 -0
  91. package/dist/config/resource-limits.js +116 -0
  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
  95. package/dist/contracts/chat-events.js +13 -0
  96. package/dist/contracts/chat-parts.d.ts +308 -0
  97. package/dist/contracts/chat-parts.js +13 -0
  98. package/dist/contracts/content-url.d.ts +49 -0
  99. package/dist/contracts/content-url.js +56 -0
  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
  140. package/dist/execution/post-step.js +65 -0
  141. package/dist/execution/reconcile-manifest.d.ts +25 -0
  142. package/dist/execution/reconcile-manifest.js +132 -0
  143. package/dist/execution/report-render.d.ts +39 -0
  144. package/dist/execution/report-render.js +98 -0
  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
  148. package/dist/execution/run-authorizer.js +17 -0
  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
  156. package/dist/execution/step-summary-metrics.js +22 -0
  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
  172. package/dist/lib/fs-helpers.js +119 -0
  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
  188. package/dist/lib/regulatory-corpus/fetch-ich.js +173 -0
  189. package/dist/lib/regulatory-corpus.d.ts +88 -0
  190. package/dist/lib/regulatory-corpus.js +141 -0
  191. package/dist/lib/result.d.ts +87 -0
  192. package/dist/lib/result.js +103 -0
  193. package/dist/lib/storage.d.ts +29 -0
  194. package/dist/lib/storage.js +37 -0
  195. package/dist/lib/streamed-download.d.ts +28 -0
  196. package/dist/lib/streamed-download.js +111 -0
  197. package/dist/lib/trace-context.d.ts +11 -0
  198. package/dist/lib/trace-context.js +49 -0
  199. package/dist/loop/__fixtures__/scripted-provider.d.ts +31 -0
  200. package/dist/loop/__fixtures__/scripted-provider.js +57 -0
  201. package/dist/loop/budget-exceeded.d.ts +22 -0
  202. package/dist/loop/budget-exceeded.js +41 -0
  203. package/dist/loop/metrics.d.ts +25 -0
  204. package/dist/loop/metrics.js +46 -0
  205. package/dist/loop/run-agent.d.ts +28 -0
  206. package/dist/loop/run-agent.js +204 -0
  207. package/dist/loop/run-step.d.ts +29 -0
  208. package/dist/loop/run-step.js +34 -0
  209. package/dist/loop/run-to-terminal.d.ts +46 -0
  210. package/dist/loop/run-to-terminal.js +51 -0
  211. package/dist/loop/types.d.ts +95 -0
  212. package/dist/loop/types.js +10 -0
  213. package/dist/memory/ai-sdk-message-storage.d.ts +20 -0
  214. package/dist/memory/ai-sdk-message-storage.js +114 -0
  215. package/dist/memory/card-builders.d.ts +114 -0
  216. package/dist/memory/card-builders.js +231 -0
  217. package/dist/memory/content-to-cortex.d.ts +42 -0
  218. package/dist/memory/content-to-cortex.js +85 -0
  219. package/dist/memory/count-tokens.d.ts +18 -0
  220. package/dist/memory/count-tokens.js +64 -0
  221. package/dist/memory/derive-thread-title.d.ts +14 -0
  222. package/dist/memory/derive-thread-title.js +26 -0
  223. package/dist/memory/message-backfill.d.ts +2 -0
  224. package/dist/memory/message-backfill.js +38 -0
  225. package/dist/memory/reconstruct-cards.d.ts +23 -0
  226. package/dist/memory/reconstruct-cards.js +64 -0
  227. package/dist/memory/thread-history.d.ts +80 -0
  228. package/dist/memory/thread-history.js +187 -0
  229. package/dist/memory/thread-store.d.ts +66 -0
  230. package/dist/memory/thread-store.js +88 -0
  231. package/dist/memory/working-memory.d.ts +135 -0
  232. package/dist/memory/working-memory.js +185 -0
  233. package/dist/prompts/SOUL.d.ts +17 -0
  234. package/dist/prompts/SOUL.js +173 -0
  235. package/dist/prompts/analogical-reasoner.d.ts +1 -0
  236. package/dist/prompts/analogical-reasoner.js +170 -0
  237. package/dist/prompts/conversation.d.ts +1 -0
  238. package/dist/prompts/conversation.js +697 -0
  239. package/dist/prompts/execute-analysis/step-summary.d.ts +1 -0
  240. package/dist/prompts/execute-analysis/step-summary.js +38 -0
  241. package/dist/prompts/literature-reviewer.d.ts +1 -0
  242. package/dist/prompts/literature-reviewer.js +107 -0
  243. package/dist/prompts/planner.d.ts +2 -0
  244. package/dist/prompts/planner.js +259 -0
  245. package/dist/prompts/report-builder.d.ts +1 -0
  246. package/dist/prompts/report-builder.js +127 -0
  247. package/dist/prompts/sandbox/bulk-transcriptomics-agent.d.ts +1 -0
  248. package/dist/prompts/sandbox/bulk-transcriptomics-agent.js +78 -0
  249. package/dist/prompts/sandbox/cheminformatics-agent.d.ts +1 -0
  250. package/dist/prompts/sandbox/cheminformatics-agent.js +224 -0
  251. package/dist/prompts/sandbox/chromatin-agent.d.ts +1 -0
  252. package/dist/prompts/sandbox/chromatin-agent.js +100 -0
  253. package/dist/prompts/sandbox/data-profiler.d.ts +1 -0
  254. package/dist/prompts/sandbox/data-profiler.js +291 -0
  255. package/dist/prompts/sandbox/dna-methylation-agent.d.ts +1 -0
  256. package/dist/prompts/sandbox/dna-methylation-agent.js +96 -0
  257. package/dist/prompts/sandbox/drug-repurposing-agent.d.ts +1 -0
  258. package/dist/prompts/sandbox/drug-repurposing-agent.js +144 -0
  259. package/dist/prompts/sandbox/enrichment-agent.d.ts +1 -0
  260. package/dist/prompts/sandbox/enrichment-agent.js +89 -0
  261. package/dist/prompts/sandbox/ephemeral-executor.d.ts +1 -0
  262. package/dist/prompts/sandbox/ephemeral-executor.js +66 -0
  263. package/dist/prompts/sandbox/genomic-variant-agent.d.ts +1 -0
  264. package/dist/prompts/sandbox/genomic-variant-agent.js +83 -0
  265. package/dist/prompts/sandbox/immune-profiling-agent.d.ts +1 -0
  266. package/dist/prompts/sandbox/immune-profiling-agent.js +101 -0
  267. package/dist/prompts/sandbox/metabolomics-agent.d.ts +1 -0
  268. package/dist/prompts/sandbox/metabolomics-agent.js +89 -0
  269. package/dist/prompts/sandbox/microbiome-agent.d.ts +1 -0
  270. package/dist/prompts/sandbox/microbiome-agent.js +109 -0
  271. package/dist/prompts/sandbox/multi-omics-integration-agent.d.ts +1 -0
  272. package/dist/prompts/sandbox/multi-omics-integration-agent.js +122 -0
  273. package/dist/prompts/sandbox/multimodal-sc-agent.d.ts +1 -0
  274. package/dist/prompts/sandbox/multimodal-sc-agent.js +90 -0
  275. package/dist/prompts/sandbox/network-agent.d.ts +1 -0
  276. package/dist/prompts/sandbox/network-agent.js +95 -0
  277. package/dist/prompts/sandbox/pkpd-clinical-response-agent.d.ts +1 -0
  278. package/dist/prompts/sandbox/pkpd-clinical-response-agent.js +71 -0
  279. package/dist/prompts/sandbox/proteomics-agent.d.ts +1 -0
  280. package/dist/prompts/sandbox/proteomics-agent.js +93 -0
  281. package/dist/prompts/sandbox/scientific-executor.d.ts +1 -0
  282. package/dist/prompts/sandbox/scientific-executor.js +68 -0
  283. package/dist/prompts/sandbox/single-cell-agent.d.ts +1 -0
  284. package/dist/prompts/sandbox/single-cell-agent.js +129 -0
  285. package/dist/prompts/sandbox/spatial-omics-agent.d.ts +1 -0
  286. package/dist/prompts/sandbox/spatial-omics-agent.js +94 -0
  287. package/dist/prompts/sandbox/statistical-modeling-agent.d.ts +1 -0
  288. package/dist/prompts/sandbox/statistical-modeling-agent.js +112 -0
  289. package/dist/prompts/sandbox/translational-safety-agent.d.ts +1 -0
  290. package/dist/prompts/sandbox/translational-safety-agent.js +105 -0
  291. package/dist/prompts/sandbox-standards.d.ts +18 -0
  292. package/dist/prompts/sandbox-standards.js +358 -0
  293. package/dist/prompts/synthesis-agent.d.ts +1 -0
  294. package/dist/prompts/synthesis-agent.js +289 -0
  295. package/dist/prompts/target-assessment/briefs/executive-recommendation.d.ts +1 -0
  296. package/dist/prompts/target-assessment/briefs/executive-recommendation.js +85 -0
  297. package/dist/prompts/target-assessment/briefs/index.d.ts +4 -0
  298. package/dist/prompts/target-assessment/briefs/index.js +4 -0
  299. package/dist/prompts/target-assessment/briefs/liability-bullets.d.ts +1 -0
  300. package/dist/prompts/target-assessment/briefs/liability-bullets.js +114 -0
  301. package/dist/prompts/target-assessment/briefs/target-organ-liabilities.d.ts +1 -0
  302. package/dist/prompts/target-assessment/briefs/target-organ-liabilities.js +29 -0
  303. package/dist/prompts/target-assessment/briefs/translational-commentary.d.ts +1 -0
  304. package/dist/prompts/target-assessment/briefs/translational-commentary.js +23 -0
  305. package/dist/prompts/target-assessment/drugs-in-class.d.ts +1 -0
  306. package/dist/prompts/target-assessment/drugs-in-class.js +29 -0
  307. package/dist/prompts/target-assessment/modulator-triage.d.ts +1 -0
  308. package/dist/prompts/target-assessment/modulator-triage.js +31 -0
  309. package/dist/prompts/target-assessment/off-target-annotator.d.ts +1 -0
  310. package/dist/prompts/target-assessment/off-target-annotator.js +28 -0
  311. package/dist/prompts/target-assessment/tox-voice/core.d.ts +1 -0
  312. package/dist/prompts/target-assessment/tox-voice/core.js +74 -0
  313. package/dist/prompts/target-assessment/tox-voice/critique.d.ts +7 -0
  314. package/dist/prompts/target-assessment/tox-voice/critique.js +109 -0
  315. package/dist/prompts/target-assessment/tox-voice/exemplars.d.ts +8 -0
  316. package/dist/prompts/target-assessment/tox-voice/exemplars.js +24 -0
  317. package/dist/prompts/target-assessment/tox-voice/index.d.ts +4 -0
  318. package/dist/prompts/target-assessment/tox-voice/index.js +4 -0
  319. package/dist/prompts/target-assessment/tox-voice/vocabulary.d.ts +15 -0
  320. package/dist/prompts/target-assessment/tox-voice/vocabulary.js +72 -0
  321. package/dist/provenance/collector.d.ts +148 -0
  322. package/dist/provenance/collector.js +296 -0
  323. package/dist/provenance/exec-frame.d.ts +36 -0
  324. package/dist/provenance/exec-frame.js +49 -0
  325. package/dist/provenance/types.d.ts +95 -0
  326. package/dist/provenance/types.js +64 -0
  327. package/dist/providers/__fixtures__/session.d.ts +16 -0
  328. package/dist/providers/__fixtures__/session.js +20 -0
  329. package/dist/providers/ai-sdk.d.ts +47 -0
  330. package/dist/providers/ai-sdk.js +142 -0
  331. package/dist/providers/anthropic.d.ts +22 -0
  332. package/dist/providers/anthropic.js +26 -0
  333. package/dist/providers/embedding.d.ts +32 -0
  334. package/dist/providers/embedding.js +42 -0
  335. package/dist/providers/errors.d.ts +80 -0
  336. package/dist/providers/errors.js +137 -0
  337. package/dist/providers/llm-capabilities.d.ts +33 -0
  338. package/dist/providers/llm-capabilities.js +58 -0
  339. package/dist/providers/streaming-chat.d.ts +23 -0
  340. package/dist/providers/streaming-chat.js +61 -0
  341. package/dist/providers/types.d.ts +59 -0
  342. package/dist/providers/types.js +8 -0
  343. package/dist/runtime/assemble.d.ts +68 -0
  344. package/dist/runtime/assemble.js +46 -0
  345. package/dist/runtime/boot.d.ts +73 -0
  346. package/dist/runtime/boot.js +65 -0
  347. package/dist/runtime/connection-budget.d.ts +48 -0
  348. package/dist/runtime/connection-budget.js +57 -0
  349. package/dist/runtime/dbos.d.ts +94 -0
  350. package/dist/runtime/dbos.js +160 -0
  351. package/dist/runtime/lifecycle.d.ts +12 -0
  352. package/dist/runtime/lifecycle.js +19 -0
  353. package/dist/runtime/pools.d.ts +25 -0
  354. package/dist/runtime/pools.js +30 -0
  355. package/dist/runtime/shutdown.d.ts +33 -0
  356. package/dist/runtime/shutdown.js +39 -0
  357. package/dist/sandbox/await-exec.d.ts +143 -0
  358. package/dist/sandbox/await-exec.js +406 -0
  359. package/dist/sandbox/client.d.ts +82 -0
  360. package/dist/sandbox/client.js +23 -0
  361. package/dist/sandbox/create-sandbox.d.ts +105 -0
  362. package/dist/sandbox/create-sandbox.js +132 -0
  363. package/dist/sandbox/deliver-exec-event.d.ts +25 -0
  364. package/dist/sandbox/deliver-exec-event.js +29 -0
  365. package/dist/sandbox/docker-client.d.ts +75 -0
  366. package/dist/sandbox/docker-client.js +315 -0
  367. package/dist/sandbox/estimate-data-profile-resources.d.ts +5 -0
  368. package/dist/sandbox/estimate-data-profile-resources.js +73 -0
  369. package/dist/sandbox/exec-id.d.ts +12 -0
  370. package/dist/sandbox/exec-id.js +20 -0
  371. package/dist/sandbox/execution-id.d.ts +30 -0
  372. package/dist/sandbox/execution-id.js +47 -0
  373. package/dist/sandbox/hmac.d.ts +54 -0
  374. package/dist/sandbox/hmac.js +67 -0
  375. package/dist/sandbox/identity.d.ts +15 -0
  376. package/dist/sandbox/identity.js +22 -0
  377. package/dist/sandbox/ignored-dirs.d.ts +7 -0
  378. package/dist/sandbox/ignored-dirs.js +7 -0
  379. package/dist/sandbox/k8s-client.d.ts +71 -0
  380. package/dist/sandbox/k8s-client.js +488 -0
  381. package/dist/sandbox/liveness.d.ts +60 -0
  382. package/dist/sandbox/liveness.js +82 -0
  383. package/dist/sandbox/mount-plan.d.ts +77 -0
  384. package/dist/sandbox/mount-plan.js +84 -0
  385. package/dist/sandbox/notification-sweep.d.ts +42 -0
  386. package/dist/sandbox/notification-sweep.js +74 -0
  387. package/dist/sandbox/reaper.d.ts +70 -0
  388. package/dist/sandbox/reaper.js +124 -0
  389. package/dist/sandbox/sandbox-error.d.ts +105 -0
  390. package/dist/sandbox/sandbox-error.js +92 -0
  391. package/dist/sandbox/sandbox-step-translate.d.ts +35 -0
  392. package/dist/sandbox/sandbox-step-translate.js +76 -0
  393. package/dist/sandbox/submit-exec.d.ts +33 -0
  394. package/dist/sandbox/submit-exec.js +68 -0
  395. package/dist/sandbox/types.d.ts +277 -0
  396. package/dist/sandbox/types.js +147 -0
  397. package/dist/sandbox/watchdog.d.ts +71 -0
  398. package/dist/sandbox/watchdog.js +150 -0
  399. package/dist/schemas/artifact-manifest.d.ts +34 -0
  400. package/dist/schemas/artifact-manifest.js +36 -0
  401. package/dist/schemas/data-profile-schemas.d.ts +92 -0
  402. package/dist/schemas/data-profile-schemas.js +89 -0
  403. package/dist/schemas/file-metadata.d.ts +51 -0
  404. package/dist/schemas/file-metadata.js +39 -0
  405. package/dist/schemas/plan-schemas.d.ts +110 -0
  406. package/dist/schemas/plan-schemas.js +50 -0
  407. package/dist/schemas/render-step-prompt.d.ts +32 -0
  408. package/dist/schemas/render-step-prompt.js +76 -0
  409. package/dist/schemas/run-synthesis.d.ts +148 -0
  410. package/dist/schemas/run-synthesis.js +87 -0
  411. package/dist/schemas/step-summary.d.ts +18 -0
  412. package/dist/schemas/step-summary.js +20 -0
  413. package/dist/schemas/validate-plan.d.ts +39 -0
  414. package/dist/schemas/validate-plan.js +120 -0
  415. package/dist/schemas/workflow-state.d.ts +314 -0
  416. package/dist/schemas/workflow-state.js +139 -0
  417. package/dist/state/active-sandboxes.d.ts +58 -0
  418. package/dist/state/active-sandboxes.js +100 -0
  419. package/dist/state/analyses-metrics.d.ts +21 -0
  420. package/dist/state/analyses-metrics.js +59 -0
  421. package/dist/state/analyses.d.ts +58 -0
  422. package/dist/state/analyses.js +132 -0
  423. package/dist/state/artifacts.d.ts +53 -0
  424. package/dist/state/artifacts.js +175 -0
  425. package/dist/state/data-profile.d.ts +176 -0
  426. package/dist/state/data-profile.js +284 -0
  427. package/dist/state/db.d.ts +10 -0
  428. package/dist/state/db.js +9 -0
  429. package/dist/state/index.d.ts +29 -0
  430. package/dist/state/index.js +20 -0
  431. package/dist/state/init.d.ts +14 -0
  432. package/dist/state/init.js +406 -0
  433. package/dist/state/plans.d.ts +56 -0
  434. package/dist/state/plans.js +117 -0
  435. package/dist/state/runs.d.ts +69 -0
  436. package/dist/state/runs.js +206 -0
  437. package/dist/state/schema.d.ts +150 -0
  438. package/dist/state/schema.js +100 -0
  439. package/dist/state/step-executions.d.ts +77 -0
  440. package/dist/state/step-executions.js +175 -0
  441. package/dist/state/target-assessments.d.ts +68 -0
  442. package/dist/state/target-assessments.js +222 -0
  443. package/dist/state/vector-store.d.ts +53 -0
  444. package/dist/state/vector-store.js +89 -0
  445. package/dist/tasks/data-profile.d.ts +171 -0
  446. package/dist/tasks/data-profile.js +461 -0
  447. package/dist/tasks/refresh-regulatory-corpus.d.ts +59 -0
  448. package/dist/tasks/refresh-regulatory-corpus.js +146 -0
  449. package/dist/tasks/regulatory-corpus-boot-refresh.d.ts +55 -0
  450. package/dist/tasks/regulatory-corpus-boot-refresh.js +149 -0
  451. package/dist/tools/__fixtures__/tool-context.d.ts +13 -0
  452. package/dist/tools/__fixtures__/tool-context.js +18 -0
  453. package/dist/tools/bio/check-safety-panel.d.ts +35 -0
  454. package/dist/tools/bio/check-safety-panel.js +76 -0
  455. package/dist/tools/bio/find-approval-precedent.d.ts +32 -0
  456. package/dist/tools/bio/find-approval-precedent.js +72 -0
  457. package/dist/tools/bio/get-article-details.d.ts +11 -0
  458. package/dist/tools/bio/get-article-details.js +20 -0
  459. package/dist/tools/bio/get-article-full-text.d.ts +19 -0
  460. package/dist/tools/bio/get-article-full-text.js +32 -0
  461. package/dist/tools/bio/get-bioactivity.d.ts +11 -0
  462. package/dist/tools/bio/get-bioactivity.js +23 -0
  463. package/dist/tools/bio/get-drug-info.d.ts +9 -0
  464. package/dist/tools/bio/get-drug-info.js +22 -0
  465. package/dist/tools/bio/get-impc-ko-profile.d.ts +9 -0
  466. package/dist/tools/bio/get-impc-ko-profile.js +20 -0
  467. package/dist/tools/bio/get-mechanism.d.ts +8 -0
  468. package/dist/tools/bio/get-mechanism.js +18 -0
  469. package/dist/tools/bio/get-pubchem-assays.d.ts +22 -0
  470. package/dist/tools/bio/get-pubchem-assays.js +107 -0
  471. package/dist/tools/bio/get-pubchem-cross-refs.d.ts +15 -0
  472. package/dist/tools/bio/get-pubchem-cross-refs.js +68 -0
  473. package/dist/tools/bio/get-target-safety.d.ts +18 -0
  474. package/dist/tools/bio/get-target-safety.js +26 -0
  475. package/dist/tools/bio/index.d.ts +41 -0
  476. package/dist/tools/bio/index.js +48 -0
  477. package/dist/tools/bio/keys.d.ts +31 -0
  478. package/dist/tools/bio/keys.js +30 -0
  479. package/dist/tools/bio/lookup-go-term.d.ts +31 -0
  480. package/dist/tools/bio/lookup-go-term.js +116 -0
  481. package/dist/tools/bio/search-bgee-expression.d.ts +10 -0
  482. package/dist/tools/bio/search-bgee-expression.js +24 -0
  483. package/dist/tools/bio/search-clinical-trials.d.ts +12 -0
  484. package/dist/tools/bio/search-clinical-trials.js +21 -0
  485. package/dist/tools/bio/search-clinvar.d.ts +13 -0
  486. package/dist/tools/bio/search-clinvar.js +28 -0
  487. package/dist/tools/bio/search-compounds.d.ts +22 -0
  488. package/dist/tools/bio/search-compounds.js +160 -0
  489. package/dist/tools/bio/search-ctx-chemical.d.ts +50 -0
  490. package/dist/tools/bio/search-ctx-chemical.js +130 -0
  491. package/dist/tools/bio/search-ctx-exposure.d.ts +55 -0
  492. package/dist/tools/bio/search-ctx-exposure.js +176 -0
  493. package/dist/tools/bio/search-ctx-hazard.d.ts +111 -0
  494. package/dist/tools/bio/search-ctx-hazard.js +178 -0
  495. package/dist/tools/bio/search-dgidb.d.ts +43 -0
  496. package/dist/tools/bio/search-dgidb.js +199 -0
  497. package/dist/tools/bio/search-disgenet.d.ts +30 -0
  498. package/dist/tools/bio/search-disgenet.js +84 -0
  499. package/dist/tools/bio/search-drugbank.d.ts +38 -0
  500. package/dist/tools/bio/search-drugbank.js +109 -0
  501. package/dist/tools/bio/search-faers.d.ts +11 -0
  502. package/dist/tools/bio/search-faers.js +23 -0
  503. package/dist/tools/bio/search-gene.d.ts +11 -0
  504. package/dist/tools/bio/search-gene.js +19 -0
  505. package/dist/tools/bio/search-geo-datasets.d.ts +20 -0
  506. package/dist/tools/bio/search-geo-datasets.js +86 -0
  507. package/dist/tools/bio/search-gwas-catalog.d.ts +33 -0
  508. package/dist/tools/bio/search-gwas-catalog.js +172 -0
  509. package/dist/tools/bio/search-interactions.d.ts +17 -0
  510. package/dist/tools/bio/search-interactions.js +31 -0
  511. package/dist/tools/bio/search-opentargets.d.ts +11 -0
  512. package/dist/tools/bio/search-opentargets.js +25 -0
  513. package/dist/tools/bio/search-pathway.d.ts +12 -0
  514. package/dist/tools/bio/search-pathway.js +32 -0
  515. package/dist/tools/bio/search-pharmgkb.d.ts +17 -0
  516. package/dist/tools/bio/search-pharmgkb.js +46 -0
  517. package/dist/tools/bio/search-pubchem-compound.d.ts +26 -0
  518. package/dist/tools/bio/search-pubchem-compound.js +110 -0
  519. package/dist/tools/bio/search-pubmed.d.ts +17 -0
  520. package/dist/tools/bio/search-pubmed.js +31 -0
  521. package/dist/tools/bio/search-targets.d.ts +9 -0
  522. package/dist/tools/bio/search-targets.js +20 -0
  523. package/dist/tools/bio/search-toxcast.d.ts +36 -0
  524. package/dist/tools/bio/search-toxcast.js +141 -0
  525. package/dist/tools/define-tool.d.ts +80 -0
  526. package/dist/tools/define-tool.js +48 -0
  527. package/dist/tools/display/index.d.ts +4 -0
  528. package/dist/tools/display/index.js +4 -0
  529. package/dist/tools/display/show-user.d.ts +33 -0
  530. package/dist/tools/display/show-user.js +67 -0
  531. package/dist/tools/execute-plan.d.ts +64 -0
  532. package/dist/tools/execute-plan.js +208 -0
  533. package/dist/tools/iterate-report.d.ts +172 -0
  534. package/dist/tools/iterate-report.js +521 -0
  535. package/dist/tools/lib/api-utils.d.ts +80 -0
  536. package/dist/tools/lib/api-utils.js +128 -0
  537. package/dist/tools/lib/bgee-client.d.ts +36 -0
  538. package/dist/tools/lib/bgee-client.js +150 -0
  539. package/dist/tools/lib/cbioportal-client.d.ts +34 -0
  540. package/dist/tools/lib/cbioportal-client.js +159 -0
  541. package/dist/tools/lib/chembl-client.d.ts +123 -0
  542. package/dist/tools/lib/chembl-client.js +458 -0
  543. package/dist/tools/lib/chembl-config.d.ts +5 -0
  544. package/dist/tools/lib/chembl-config.js +3 -0
  545. package/dist/tools/lib/clinical-benchmarks-client.d.ts +33 -0
  546. package/dist/tools/lib/clinical-benchmarks-client.js +54 -0
  547. package/dist/tools/lib/clinical-trials-client.d.ts +216 -0
  548. package/dist/tools/lib/clinical-trials-client.js +339 -0
  549. package/dist/tools/lib/clinicaltrials-config.d.ts +4 -0
  550. package/dist/tools/lib/clinicaltrials-config.js +2 -0
  551. package/dist/tools/lib/clinvar-client.d.ts +25 -0
  552. package/dist/tools/lib/clinvar-client.js +126 -0
  553. package/dist/tools/lib/disgenet-config.d.ts +2 -0
  554. package/dist/tools/lib/disgenet-config.js +11 -0
  555. package/dist/tools/lib/drugbank-config.d.ts +2 -0
  556. package/dist/tools/lib/drugbank-config.js +12 -0
  557. package/dist/tools/lib/ema-client.d.ts +45 -0
  558. package/dist/tools/lib/ema-client.js +127 -0
  559. package/dist/tools/lib/ema-config.d.ts +7 -0
  560. package/dist/tools/lib/ema-config.js +7 -0
  561. package/dist/tools/lib/ensembl-client.d.ts +27 -0
  562. package/dist/tools/lib/ensembl-client.js +82 -0
  563. package/dist/tools/lib/gwas-catalog-config.d.ts +4 -0
  564. package/dist/tools/lib/gwas-catalog-config.js +2 -0
  565. package/dist/tools/lib/identifier-resolver.d.ts +85 -0
  566. package/dist/tools/lib/identifier-resolver.js +333 -0
  567. package/dist/tools/lib/impc-client.d.ts +44 -0
  568. package/dist/tools/lib/impc-client.js +239 -0
  569. package/dist/tools/lib/iuphar-client.d.ts +75 -0
  570. package/dist/tools/lib/iuphar-client.js +230 -0
  571. package/dist/tools/lib/iuphar-config.d.ts +5 -0
  572. package/dist/tools/lib/iuphar-config.js +3 -0
  573. package/dist/tools/lib/ncbi-utils.d.ts +58 -0
  574. package/dist/tools/lib/ncbi-utils.js +286 -0
  575. package/dist/tools/lib/openfda-client.d.ts +53 -0
  576. package/dist/tools/lib/openfda-client.js +192 -0
  577. package/dist/tools/lib/openfda-config.d.ts +2 -0
  578. package/dist/tools/lib/openfda-config.js +2 -0
  579. package/dist/tools/lib/opentargets-client.d.ts +64 -0
  580. package/dist/tools/lib/opentargets-client.js +290 -0
  581. package/dist/tools/lib/opentargets-config.d.ts +5 -0
  582. package/dist/tools/lib/opentargets-config.js +5 -0
  583. package/dist/tools/lib/path-validation.d.ts +14 -0
  584. package/dist/tools/lib/path-validation.js +26 -0
  585. package/dist/tools/lib/pathway-client.d.ts +27 -0
  586. package/dist/tools/lib/pathway-client.js +149 -0
  587. package/dist/tools/lib/pharmgkb-config.d.ts +4 -0
  588. package/dist/tools/lib/pharmgkb-config.js +2 -0
  589. package/dist/tools/lib/preview-lock.d.ts +20 -0
  590. package/dist/tools/lib/preview-lock.js +35 -0
  591. package/dist/tools/lib/protein-family-modality.d.ts +16 -0
  592. package/dist/tools/lib/protein-family-modality.js +42 -0
  593. package/dist/tools/lib/protein-family-normalize.d.ts +12 -0
  594. package/dist/tools/lib/protein-family-normalize.js +46 -0
  595. package/dist/tools/lib/pubchem-client.d.ts +40 -0
  596. package/dist/tools/lib/pubchem-client.js +128 -0
  597. package/dist/tools/lib/pubchem-config.d.ts +5 -0
  598. package/dist/tools/lib/pubchem-config.js +3 -0
  599. package/dist/tools/lib/pubmed-client.d.ts +28 -0
  600. package/dist/tools/lib/pubmed-client.js +91 -0
  601. package/dist/tools/lib/report-preflight.d.ts +39 -0
  602. package/dist/tools/lib/report-preflight.js +283 -0
  603. package/dist/tools/lib/string-client.d.ts +33 -0
  604. package/dist/tools/lib/string-client.js +93 -0
  605. package/dist/tools/lib/toxcast-config.d.ts +2 -0
  606. package/dist/tools/lib/toxcast-config.js +11 -0
  607. package/dist/tools/lib/uniprot-client.d.ts +28 -0
  608. package/dist/tools/lib/uniprot-client.js +103 -0
  609. package/dist/tools/lib/uniprot-config.d.ts +5 -0
  610. package/dist/tools/lib/uniprot-config.js +3 -0
  611. package/dist/tools/memory/index.d.ts +4 -0
  612. package/dist/tools/memory/index.js +4 -0
  613. package/dist/tools/memory/update-working-memory.d.ts +25 -0
  614. package/dist/tools/memory/update-working-memory.js +112 -0
  615. package/dist/tools/registry.d.ts +15 -0
  616. package/dist/tools/registry.js +26 -0
  617. package/dist/tools/report/build-report.d.ts +13 -0
  618. package/dist/tools/report/build-report.js +26 -0
  619. package/dist/tools/report/index.d.ts +14 -0
  620. package/dist/tools/report/index.js +14 -0
  621. package/dist/tools/report/mint-preview-url.d.ts +26 -0
  622. package/dist/tools/report/mint-preview-url.js +44 -0
  623. package/dist/tools/report/preview-publisher.d.ts +37 -0
  624. package/dist/tools/report/preview-publisher.js +25 -0
  625. package/dist/tools/report/preview-snapshot.d.ts +26 -0
  626. package/dist/tools/report/preview-snapshot.js +121 -0
  627. package/dist/tools/report/submit-report.d.ts +25 -0
  628. package/dist/tools/report/submit-report.js +126 -0
  629. package/dist/tools/report/version-fs.d.ts +15 -0
  630. package/dist/tools/report/version-fs.js +154 -0
  631. package/dist/tools/research/context7-docs.d.ts +31 -0
  632. package/dist/tools/research/context7-docs.js +61 -0
  633. package/dist/tools/research/generate-analogy-report.d.ts +60 -0
  634. package/dist/tools/research/generate-analogy-report.js +288 -0
  635. package/dist/tools/research/generate-plan.d.ts +39 -0
  636. package/dist/tools/research/generate-plan.js +393 -0
  637. package/dist/tools/research/index.d.ts +15 -0
  638. package/dist/tools/research/index.js +15 -0
  639. package/dist/tools/research/inspect-run.d.ts +54 -0
  640. package/dist/tools/research/inspect-run.js +85 -0
  641. package/dist/tools/research/literature-reviewer.d.ts +29 -0
  642. package/dist/tools/research/literature-reviewer.js +84 -0
  643. package/dist/tools/research/search-arxiv.d.ts +32 -0
  644. package/dist/tools/research/search-arxiv.js +123 -0
  645. package/dist/tools/research/search-github-repos.d.ts +32 -0
  646. package/dist/tools/research/search-github-repos.js +86 -0
  647. package/dist/tools/research/search-semantic-scholar.d.ts +33 -0
  648. package/dist/tools/research/search-semantic-scholar.js +93 -0
  649. package/dist/tools/run-ephemeral.d.ts +33 -0
  650. package/dist/tools/run-ephemeral.js +65 -0
  651. package/dist/tools/sandbox/index.d.ts +7 -0
  652. package/dist/tools/sandbox/index.js +7 -0
  653. package/dist/tools/sandbox/list-available-packages.d.ts +7 -0
  654. package/dist/tools/sandbox/list-available-packages.js +27 -0
  655. package/dist/tools/sandbox/list-available-refs.d.ts +7 -0
  656. package/dist/tools/sandbox/list-available-refs.js +147 -0
  657. package/dist/tools/sandbox/report-blocker.d.ts +23 -0
  658. package/dist/tools/sandbox/report-blocker.js +39 -0
  659. package/dist/tools/sandbox/skills.d.ts +72 -0
  660. package/dist/tools/sandbox/skills.js +144 -0
  661. package/dist/tools/workspace/edit-file.d.ts +46 -0
  662. package/dist/tools/workspace/edit-file.js +100 -0
  663. package/dist/tools/workspace/execute-command.d.ts +80 -0
  664. package/dist/tools/workspace/execute-command.js +95 -0
  665. package/dist/tools/workspace/file-stat.d.ts +24 -0
  666. package/dist/tools/workspace/file-stat.js +37 -0
  667. package/dist/tools/workspace/grep.d.ts +57 -0
  668. package/dist/tools/workspace/grep.js +154 -0
  669. package/dist/tools/workspace/index.d.ts +26 -0
  670. package/dist/tools/workspace/index.js +27 -0
  671. package/dist/tools/workspace/list-files.d.ts +24 -0
  672. package/dist/tools/workspace/list-files.js +38 -0
  673. package/dist/tools/workspace/mutator.d.ts +83 -0
  674. package/dist/tools/workspace/mutator.js +81 -0
  675. package/dist/tools/workspace/read-file.d.ts +39 -0
  676. package/dist/tools/workspace/read-file.js +93 -0
  677. package/dist/tools/workspace/result-bounds.d.ts +42 -0
  678. package/dist/tools/workspace/result-bounds.js +50 -0
  679. package/dist/tools/workspace/run-exec.d.ts +32 -0
  680. package/dist/tools/workspace/run-exec.js +34 -0
  681. package/dist/tools/workspace/show-file.d.ts +37 -0
  682. package/dist/tools/workspace/show-file.js +54 -0
  683. package/dist/tools/workspace/show-plan.d.ts +23 -0
  684. package/dist/tools/workspace/show-plan.js +44 -0
  685. package/dist/tools/workspace/workspace-search.d.ts +25 -0
  686. package/dist/tools/workspace/workspace-search.js +78 -0
  687. package/dist/tools/workspace/write-file.d.ts +16 -0
  688. package/dist/tools/workspace/write-file.js +33 -0
  689. package/dist/workflows/execute-analysis-scheduler.d.ts +94 -0
  690. package/dist/workflows/execute-analysis-scheduler.js +186 -0
  691. package/dist/workflows/execute-analysis.d.ts +271 -0
  692. package/dist/workflows/execute-analysis.js +746 -0
  693. package/dist/workflows/execute-target-assessment.d.ts +101 -0
  694. package/dist/workflows/execute-target-assessment.js +528 -0
  695. package/dist/workflows/metrics.d.ts +37 -0
  696. package/dist/workflows/metrics.js +55 -0
  697. package/dist/workflows/plan/level.d.ts +12 -0
  698. package/dist/workflows/plan/level.js +12 -0
  699. package/dist/workflows/register-workflows.d.ts +51 -0
  700. package/dist/workflows/register-workflows.js +48 -0
  701. package/dist/workflows/resume-execute-analysis.d.ts +70 -0
  702. package/dist/workflows/resume-execute-analysis.js +80 -0
  703. package/dist/workflows/sandbox-step.d.ts +243 -0
  704. package/dist/workflows/sandbox-step.js +573 -0
  705. package/dist/workflows/target-assessment/assemblers/index.d.ts +5 -0
  706. package/dist/workflows/target-assessment/assemblers/index.js +4 -0
  707. package/dist/workflows/target-assessment/assemblers/literature.d.ts +299 -0
  708. package/dist/workflows/target-assessment/assemblers/literature.js +987 -0
  709. package/dist/workflows/target-assessment/assemblers/orchestrator.d.ts +109 -0
  710. package/dist/workflows/target-assessment/assemblers/orchestrator.js +835 -0
  711. package/dist/workflows/target-assessment/assemblers/safety.d.ts +352 -0
  712. package/dist/workflows/target-assessment/assemblers/safety.js +985 -0
  713. package/dist/workflows/target-assessment/assemblers/trials.d.ts +30 -0
  714. package/dist/workflows/target-assessment/assemblers/trials.js +75 -0
  715. package/dist/workflows/target-assessment/collectors/index.d.ts +105 -0
  716. package/dist/workflows/target-assessment/collectors/index.js +468 -0
  717. package/dist/workflows/target-assessment/correction-loop.d.ts +45 -0
  718. package/dist/workflows/target-assessment/correction-loop.js +62 -0
  719. package/dist/workflows/target-assessment/coverage.d.ts +81 -0
  720. package/dist/workflows/target-assessment/coverage.js +82 -0
  721. package/dist/workflows/target-assessment/decisions/index.d.ts +86 -0
  722. package/dist/workflows/target-assessment/decisions/index.js +127 -0
  723. package/dist/workflows/target-assessment/fanout/index.d.ts +31 -0
  724. package/dist/workflows/target-assessment/fanout/index.js +155 -0
  725. package/dist/workflows/target-assessment/lib/approval-precedents.d.ts +52 -0
  726. package/dist/workflows/target-assessment/lib/approval-precedents.js +119 -0
  727. package/dist/workflows/target-assessment/lib/citation-validator.d.ts +46 -0
  728. package/dist/workflows/target-assessment/lib/citation-validator.js +316 -0
  729. package/dist/workflows/target-assessment/lib/clinical-consequence-annotator.d.ts +62 -0
  730. package/dist/workflows/target-assessment/lib/clinical-consequence-annotator.js +172 -0
  731. package/dist/workflows/target-assessment/lib/clinical-evidence-attribution.d.ts +45 -0
  732. package/dist/workflows/target-assessment/lib/clinical-evidence-attribution.js +156 -0
  733. package/dist/workflows/target-assessment/lib/compute-derived.d.ts +19 -0
  734. package/dist/workflows/target-assessment/lib/compute-derived.js +252 -0
  735. package/dist/workflows/target-assessment/lib/compute-selectivity.d.ts +15 -0
  736. package/dist/workflows/target-assessment/lib/compute-selectivity.js +18 -0
  737. package/dist/workflows/target-assessment/lib/dedup-modulators.d.ts +37 -0
  738. package/dist/workflows/target-assessment/lib/dedup-modulators.js +157 -0
  739. package/dist/workflows/target-assessment/lib/evidence-conflict-detector.d.ts +17 -0
  740. package/dist/workflows/target-assessment/lib/evidence-conflict-detector.js +100 -0
  741. package/dist/workflows/target-assessment/lib/expression-constants.d.ts +21 -0
  742. package/dist/workflows/target-assessment/lib/expression-constants.js +21 -0
  743. package/dist/workflows/target-assessment/lib/family-complex-supplement.d.ts +21 -0
  744. package/dist/workflows/target-assessment/lib/family-complex-supplement.js +37 -0
  745. package/dist/workflows/target-assessment/lib/heterodimer-filter.d.ts +39 -0
  746. package/dist/workflows/target-assessment/lib/heterodimer-filter.js +54 -0
  747. package/dist/workflows/target-assessment/lib/intended-polypharm-filter.d.ts +4 -0
  748. package/dist/workflows/target-assessment/lib/intended-polypharm-filter.js +24 -0
  749. package/dist/workflows/target-assessment/lib/llm-step.d.ts +77 -0
  750. package/dist/workflows/target-assessment/lib/llm-step.js +99 -0
  751. package/dist/workflows/target-assessment/lib/meddra-organ-map.d.ts +30 -0
  752. package/dist/workflows/target-assessment/lib/meddra-organ-map.js +126 -0
  753. package/dist/workflows/target-assessment/lib/recommendation-quality-gates.d.ts +17 -0
  754. package/dist/workflows/target-assessment/lib/recommendation-quality-gates.js +99 -0
  755. package/dist/workflows/target-assessment/lib/recommendation-sanitizer.d.ts +2 -0
  756. package/dist/workflows/target-assessment/lib/recommendation-sanitizer.js +51 -0
  757. package/dist/workflows/target-assessment/lib/regulatory-actions.d.ts +26 -0
  758. package/dist/workflows/target-assessment/lib/regulatory-actions.js +147 -0
  759. package/dist/workflows/target-assessment/lib/structured-llm.d.ts +58 -0
  760. package/dist/workflows/target-assessment/lib/structured-llm.js +101 -0
  761. package/dist/workflows/target-assessment/lib/target-identity-filter.d.ts +60 -0
  762. package/dist/workflows/target-assessment/lib/target-identity-filter.js +86 -0
  763. package/dist/workflows/target-assessment/lib/therapeutic-programs.d.ts +20 -0
  764. package/dist/workflows/target-assessment/lib/therapeutic-programs.js +68 -0
  765. package/dist/workflows/target-assessment/metrics.d.ts +21 -0
  766. package/dist/workflows/target-assessment/metrics.js +42 -0
  767. package/dist/workflows/target-assessment/phase4-assemble.d.ts +1841 -0
  768. package/dist/workflows/target-assessment/phase4-assemble.js +39 -0
  769. package/dist/workflows/target-assessment/phase5-persist.d.ts +57 -0
  770. package/dist/workflows/target-assessment/phase5-persist.js +461 -0
  771. package/dist/workflows/target-assessment/progress.d.ts +38 -0
  772. package/dist/workflows/target-assessment/progress.js +76 -0
  773. package/dist/workflows/target-assessment/schemas.d.ts +931 -0
  774. package/dist/workflows/target-assessment/schemas.js +293 -0
  775. package/dist/workflows/target-assessment/steps/collectors/pathways.d.ts +15 -0
  776. package/dist/workflows/target-assessment/steps/collectors/pathways.js +58 -0
  777. package/dist/workflows/target-assessment/steps/fanout/aes-for-one-class-drug-step.d.ts +34 -0
  778. package/dist/workflows/target-assessment/steps/fanout/aes-for-one-class-drug-step.js +31 -0
  779. package/dist/workflows/target-assessment/steps/fanout/aes-for-one-trial-step.d.ts +57 -0
  780. package/dist/workflows/target-assessment/steps/fanout/aes-for-one-trial-step.js +54 -0
  781. package/dist/workflows/target-assessment/steps/fanout/faers-for-one-modulator-step.d.ts +35 -0
  782. package/dist/workflows/target-assessment/steps/fanout/faers-for-one-modulator-step.js +32 -0
  783. package/dist/workflows/target-assessment/steps/fanout/index.d.ts +14 -0
  784. package/dist/workflows/target-assessment/steps/fanout/index.js +10 -0
  785. package/dist/workflows/target-assessment/steps/fanout/polypharm-for-one-modulator-step.d.ts +28 -0
  786. package/dist/workflows/target-assessment/steps/fanout/polypharm-for-one-modulator-step.js +27 -0
  787. package/dist/workflows/target-assessment/steps/phase0-resolve.d.ts +71 -0
  788. package/dist/workflows/target-assessment/steps/phase0-resolve.js +21 -0
  789. package/dist/workflows/target-assessment/steps/phase1-aggregate.d.ts +1018 -0
  790. package/dist/workflows/target-assessment/steps/phase1-aggregate.js +25 -0
  791. package/dist/workflows/target-assessment/steps/phase2-aggregate.d.ts +696 -0
  792. package/dist/workflows/target-assessment/steps/phase2-aggregate.js +38 -0
  793. package/dist/workflows/target-assessment/steps/phase3-aggregate.d.ts +936 -0
  794. package/dist/workflows/target-assessment/steps/phase3-aggregate.js +22 -0
  795. package/dist/workflows/target-assessment/steps/synthesis/diagnostics.d.ts +34 -0
  796. package/dist/workflows/target-assessment/steps/synthesis/diagnostics.js +45 -0
  797. package/dist/workflows/target-assessment/sub-workflows/index.d.ts +15 -0
  798. package/dist/workflows/target-assessment/sub-workflows/index.js +11 -0
  799. package/dist/workflows/target-assessment/sub-workflows/per-class-drug-aes.d.ts +41 -0
  800. package/dist/workflows/target-assessment/sub-workflows/per-class-drug-aes.js +12 -0
  801. package/dist/workflows/target-assessment/sub-workflows/per-modulator-faers.d.ts +41 -0
  802. package/dist/workflows/target-assessment/sub-workflows/per-modulator-faers.js +12 -0
  803. package/dist/workflows/target-assessment/sub-workflows/per-modulator-polypharm.d.ts +36 -0
  804. package/dist/workflows/target-assessment/sub-workflows/per-modulator-polypharm.js +12 -0
  805. package/dist/workflows/target-assessment/sub-workflows/per-trial-aes.d.ts +66 -0
  806. package/dist/workflows/target-assessment/sub-workflows/per-trial-aes.js +12 -0
  807. package/dist/workflows/target-assessment/synthesis/index.d.ts +560 -0
  808. package/dist/workflows/target-assessment/synthesis/index.js +351 -0
  809. package/dist/workflows/target-assessment/synthesis-probes.d.ts +56 -0
  810. package/dist/workflows/target-assessment/synthesis-probes.js +320 -0
  811. package/dist/workspace/filesystem.d.ts +117 -0
  812. package/dist/workspace/filesystem.js +304 -0
  813. package/dist/workspace/mount-strategy.d.ts +50 -0
  814. package/dist/workspace/mount-strategy.js +67 -0
  815. package/dist/workspace/paths.d.ts +185 -0
  816. package/dist/workspace/paths.js +219 -0
  817. package/dist/workspace/provenance-collector.d.ts +34 -0
  818. package/dist/workspace/provenance-collector.js +16 -0
  819. package/dist/workspace/search-config.d.ts +23 -0
  820. package/dist/workspace/search-config.js +43 -0
  821. package/dist/workspace/workspace-paths.d.ts +26 -0
  822. package/dist/workspace/workspace-paths.js +31 -0
  823. package/package.json +101 -0
@@ -0,0 +1,458 @@
1
+ /**
2
+ * Pure async client functions for the ChEMBL REST API.
3
+ *
4
+ * Used directly by target-assessment workflow steps and by tool wrappers.
5
+ */
6
+ import { z } from "zod";
7
+ import { apiFetchValidated, describeApiError } from "./api-utils.js";
8
+ import { CHEMBL_BASE, CHEMBL_HEADERS as HEADERS } from "./chembl-config.js";
9
+ const TargetComponentSynonymSchema = z.object({
10
+ syn_type: z.string().optional(),
11
+ component_synonym: z.string().optional(),
12
+ });
13
+ const TargetComponentSchema = z.object({
14
+ accession: z.string().optional(),
15
+ target_component_synonyms: z.array(TargetComponentSynonymSchema).optional(),
16
+ });
17
+ const RawTargetSchema = z.object({
18
+ target_chembl_id: z.string().optional(),
19
+ pref_name: z.string().optional(),
20
+ target_type: z.string().optional(),
21
+ organism: z.string().optional(),
22
+ target_components: z.array(TargetComponentSchema).optional(),
23
+ });
24
+ /** A raw activity row from the ChEMBL `activity` endpoint. */
25
+ const RawChemblActivitySchema = z.object({
26
+ activity_id: z.number().optional(),
27
+ molecule_chembl_id: z.string().optional(),
28
+ target_chembl_id: z.string().optional(),
29
+ standard_type: z.string().optional(),
30
+ standard_value: z.union([z.string(), z.number()]).nullable().optional(),
31
+ standard_units: z.string().optional(),
32
+ assay_chembl_id: z.string().optional(),
33
+ assay_type: z.string().optional(),
34
+ pchembl_value: z.union([z.string(), z.number()]).nullable().optional(),
35
+ });
36
+ /** A raw mechanism row from the ChEMBL `mechanism` endpoint. */
37
+ const RawChemblMechanismSchema = z.object({
38
+ mechanism_of_action: z.string().optional(),
39
+ action_type: z.string().optional(),
40
+ target_chembl_id: z.string().optional(),
41
+ molecule_chembl_id: z.string().optional(),
42
+ });
43
+ /** A drug-indication record nested inside a ChEMBL molecule/drug record. */
44
+ const DrugIndicationRecordSchema = z.object({
45
+ mesh_heading: z.string().optional(),
46
+ efo_term: z.string().optional(),
47
+ });
48
+ /** A raw molecule/drug record from the ChEMBL `molecule` / `drug` endpoints. */
49
+ const RawChemblMoleculeSchema = z.object({
50
+ molecule_chembl_id: z.string().optional(),
51
+ pref_name: z.string().optional(),
52
+ max_phase: z.number().nullable().optional(),
53
+ molecule_type: z.string().optional(),
54
+ first_approval: z.number().nullable().optional(),
55
+ drug_indications: z.array(DrugIndicationRecordSchema).optional(),
56
+ molecule_hierarchy: z.object({ parent_chembl_id: z.string().optional() }).optional(),
57
+ });
58
+ // Response envelopes returned by the ChEMBL list/record endpoints, validated at
59
+ // the fetch boundary. Every wrapper field is optional because the API omits it
60
+ // when there is no data (a 404 is handled separately as an expected empty).
61
+ const TargetSearchResponseSchema = z.object({ targets: z.array(RawTargetSchema).optional() });
62
+ const ActivitiesResponseSchema = z.object({ activities: z.array(RawChemblActivitySchema).optional() });
63
+ const MechanismsResponseSchema = z.object({ mechanisms: z.array(RawChemblMechanismSchema).optional() });
64
+ const DrugSearchResponseSchema = z.object({ drugs: z.array(RawChemblMoleculeSchema).optional() });
65
+ const MoleculeSearchResponseSchema = z.object({ molecules: z.array(RawChemblMoleculeSchema).optional() });
66
+ const TargetNameResponseSchema = z.object({ pref_name: z.string().optional() });
67
+ const MoleculeStructuresResponseSchema = z.object({
68
+ molecule_structures: z.object({ standard_inchi_key: z.string().nullable().optional() }).optional(),
69
+ });
70
+ const TargetComponentsResponseSchema = z.object({
71
+ target_components: z.array(z.object({ accession: z.string().optional(), component_type: z.string().optional() })).optional(),
72
+ });
73
+ function extractGeneNames(components) {
74
+ if (!components?.length)
75
+ return [];
76
+ const genes = new Set();
77
+ for (const comp of components) {
78
+ for (const syn of comp.target_component_synonyms ?? []) {
79
+ if (syn.syn_type === "GENE_SYMBOL" && syn.component_synonym) {
80
+ genes.add(syn.component_synonym);
81
+ }
82
+ }
83
+ }
84
+ if (genes.size === 0) {
85
+ for (const comp of components) {
86
+ if (comp.accession)
87
+ genes.add(comp.accession);
88
+ }
89
+ }
90
+ return [...genes];
91
+ }
92
+ function mapTarget(raw) {
93
+ return {
94
+ targetChemblId: raw.target_chembl_id ?? "",
95
+ preferredName: raw.pref_name ?? null,
96
+ targetType: raw.target_type ?? null,
97
+ organism: raw.organism ?? null,
98
+ geneNames: extractGeneNames(raw.target_components),
99
+ };
100
+ }
101
+ function parseNumeric(val) {
102
+ if (val == null)
103
+ return null;
104
+ const n = typeof val === "number" ? val : parseFloat(val);
105
+ return Number.isNaN(n) ? null : n;
106
+ }
107
+ export async function searchTargets(query, limit = 25) {
108
+ const url = `${CHEMBL_BASE}/target/search.json?q=${encodeURIComponent(query)}&limit=${limit}`;
109
+ const res = await apiFetchValidated(url, TargetSearchResponseSchema, { headers: HEADERS });
110
+ if (res.isErr()) {
111
+ if (res.error.type === "http_status" && res.error.status === 404)
112
+ return [];
113
+ throw new Error(describeApiError(res.error));
114
+ }
115
+ return (res.value.targets ?? []).map(mapTarget);
116
+ }
117
+ export async function getBioactivity(chemblId, type, options = {}) {
118
+ const limit = options.limit ?? 500;
119
+ const idParam = type === "compound" ? `molecule_chembl_id=${encodeURIComponent(chemblId)}` : `target_chembl_id=${encodeURIComponent(chemblId)}`;
120
+ let url = `${CHEMBL_BASE}/activity.json?${idParam}&limit=${limit}`;
121
+ if (options.activityType) {
122
+ url += `&standard_type=${encodeURIComponent(options.activityType)}`;
123
+ }
124
+ const res = await apiFetchValidated(url, ActivitiesResponseSchema, { headers: HEADERS });
125
+ if (res.isErr()) {
126
+ if (res.error.type === "http_status" && res.error.status === 404)
127
+ return [];
128
+ throw new Error(describeApiError(res.error));
129
+ }
130
+ return (res.value.activities ?? []).map((raw) => ({
131
+ activityId: raw.activity_id != null ? raw.activity_id : null,
132
+ compoundChemblId: raw.molecule_chembl_id ?? "",
133
+ targetChemblId: raw.target_chembl_id ?? null,
134
+ standardType: raw.standard_type ?? null,
135
+ standardValue: parseNumeric(raw.standard_value),
136
+ standardUnits: raw.standard_units ?? null,
137
+ assayChemblId: raw.assay_chembl_id ?? null,
138
+ assayType: raw.assay_type ?? null,
139
+ pchemblValue: parseNumeric(raw.pchembl_value),
140
+ }));
141
+ }
142
+ async function fetchTargetName(targetChemblId) {
143
+ const res = await apiFetchValidated(`${CHEMBL_BASE}/target/${targetChemblId}.json`, TargetNameResponseSchema, { headers: HEADERS });
144
+ if (res.isErr() || !res.value.pref_name)
145
+ return null;
146
+ return res.value.pref_name;
147
+ }
148
+ export async function getMechanism(chemblId) {
149
+ const url = `${CHEMBL_BASE}/mechanism.json?molecule_chembl_id=${encodeURIComponent(chemblId)}`;
150
+ const res = await apiFetchValidated(url, MechanismsResponseSchema, { headers: HEADERS });
151
+ if (res.isErr()) {
152
+ if (res.error.type === "http_status" && res.error.status === 404)
153
+ return [];
154
+ throw new Error(describeApiError(res.error));
155
+ }
156
+ const rawMechanisms = res.value.mechanisms ?? [];
157
+ const targetIds = new Set();
158
+ for (const mech of rawMechanisms) {
159
+ if (mech.target_chembl_id)
160
+ targetIds.add(mech.target_chembl_id);
161
+ }
162
+ const targetNames = new Map();
163
+ const targetIdArray = [...targetIds];
164
+ const concurrency = 5;
165
+ for (let i = 0; i < targetIdArray.length; i += concurrency) {
166
+ const batch = targetIdArray.slice(i, i + concurrency);
167
+ const names = await Promise.all(batch.map(fetchTargetName));
168
+ for (const [idx, id] of batch.entries()) {
169
+ const name = names[idx];
170
+ if (name)
171
+ targetNames.set(id, name);
172
+ }
173
+ }
174
+ return rawMechanisms.map((raw) => ({
175
+ mechanismOfAction: raw.mechanism_of_action ?? null,
176
+ actionType: raw.action_type ?? null,
177
+ targetChemblId: raw.target_chembl_id ?? null,
178
+ targetName: targetNames.get(raw.target_chembl_id ?? "") ?? null,
179
+ moleculeChemblId: raw.molecule_chembl_id ?? "",
180
+ }));
181
+ }
182
+ function extractIndication(indications) {
183
+ if (!indications?.length)
184
+ return null;
185
+ const terms = new Set();
186
+ for (const ind of indications) {
187
+ if (ind.mesh_heading)
188
+ terms.add(ind.mesh_heading);
189
+ else if (ind.efo_term)
190
+ terms.add(ind.efo_term);
191
+ }
192
+ return terms.size > 0 ? [...terms].join("; ") : null;
193
+ }
194
+ export async function getDrugInfo(query, limit = 25) {
195
+ const drugUrl = `${CHEMBL_BASE}/drug/search.json?q=${encodeURIComponent(query)}&limit=${limit}`;
196
+ const drugRes = await apiFetchValidated(drugUrl, DrugSearchResponseSchema, { headers: HEADERS });
197
+ if (drugRes.isOk() && drugRes.value.drugs?.length) {
198
+ return drugRes.value.drugs.map((raw) => ({
199
+ moleculeChemblId: raw.molecule_chembl_id ?? "",
200
+ preferredName: raw.pref_name ?? null,
201
+ maxPhase: raw.max_phase != null ? Number(raw.max_phase) : null,
202
+ moleculeType: raw.molecule_type ?? null,
203
+ firstApproval: raw.first_approval ?? null,
204
+ indication: extractIndication(raw.drug_indications),
205
+ }));
206
+ }
207
+ if (drugRes.isErr() && !(drugRes.error.type === "http_status" && drugRes.error.status === 404)) {
208
+ throw new Error(describeApiError(drugRes.error));
209
+ }
210
+ const molUrl = `${CHEMBL_BASE}/molecule/search.json?q=${encodeURIComponent(query)}&limit=${limit}`;
211
+ const molRes = await apiFetchValidated(molUrl, MoleculeSearchResponseSchema, { headers: HEADERS });
212
+ if (molRes.isErr()) {
213
+ if (molRes.error.type === "http_status" && molRes.error.status === 404)
214
+ return [];
215
+ throw new Error(describeApiError(molRes.error));
216
+ }
217
+ const approved = (molRes.value.molecules ?? []).filter((mol) => mol.max_phase != null && mol.max_phase >= 4);
218
+ return approved.map((raw) => ({
219
+ moleculeChemblId: raw.molecule_chembl_id ?? "",
220
+ preferredName: raw.pref_name ?? null,
221
+ maxPhase: raw.max_phase != null ? Number(raw.max_phase) : null,
222
+ moleculeType: raw.molecule_type ?? null,
223
+ firstApproval: raw.first_approval ?? null,
224
+ indication: null,
225
+ }));
226
+ }
227
+ /**
228
+ * Fetch all clinical-stage modulators (max_phase ≥ 2 by default) for a target.
229
+ * Used for §2.6.6 (class precedent) and as the input to §2.6.4 (off-target panel).
230
+ */
231
+ export async function getTargetModulators(targetChemblId, options = {}) {
232
+ const minPhase = options.minPhase ?? 2;
233
+ const limit = options.limit ?? 200;
234
+ const mechUrl = `${CHEMBL_BASE}/mechanism.json?target_chembl_id=${encodeURIComponent(targetChemblId)}` + `&limit=${limit}`;
235
+ const mechRes = await apiFetchValidated(mechUrl, MechanismsResponseSchema, { headers: HEADERS });
236
+ if (mechRes.isErr()) {
237
+ if (mechRes.error.type === "http_status" && mechRes.error.status === 404)
238
+ return [];
239
+ throw new Error(describeApiError(mechRes.error));
240
+ }
241
+ const moleculeIds = new Set();
242
+ for (const mech of mechRes.value.mechanisms ?? []) {
243
+ if (mech.molecule_chembl_id)
244
+ moleculeIds.add(mech.molecule_chembl_id);
245
+ }
246
+ if (moleculeIds.size === 0)
247
+ return [];
248
+ const modulators = [];
249
+ const ids = [...moleculeIds];
250
+ const concurrency = 5;
251
+ for (let i = 0; i < ids.length; i += concurrency) {
252
+ const batch = ids.slice(i, i + concurrency);
253
+ const results = await Promise.all(batch.map(async (id) => {
254
+ const res = await apiFetchValidated(`${CHEMBL_BASE}/molecule/${id}.json`, RawChemblMoleculeSchema, {
255
+ headers: HEADERS,
256
+ });
257
+ if (res.isErr())
258
+ return null;
259
+ const m = res.value;
260
+ const phase = m.max_phase != null ? Number(m.max_phase) : null;
261
+ if (phase == null || phase < minPhase)
262
+ return null;
263
+ return {
264
+ moleculeChemblId: m.molecule_chembl_id ?? id,
265
+ parentChemblId: m.molecule_hierarchy?.parent_chembl_id ?? null,
266
+ preferredName: m.pref_name ?? null,
267
+ maxPhase: phase,
268
+ moleculeType: m.molecule_type ?? null,
269
+ firstApproval: m.first_approval ?? null,
270
+ };
271
+ }));
272
+ for (const r of results)
273
+ if (r)
274
+ modulators.push(r);
275
+ }
276
+ return modulators;
277
+ }
278
+ /**
279
+ * Fetch off-target binding hits for a modulator: every target the molecule
280
+ * has been measured against (excluding the primary target), with potency.
281
+ * Used for §2.6.4 / §2.8 off-target panel.
282
+ */
283
+ export async function getModulatorPolypharmacology(moleculeChemblId, options = {}) {
284
+ const minPchembl = options.minPchembl ?? 5;
285
+ const limit = options.limit ?? 200;
286
+ const url = `${CHEMBL_BASE}/activity.json?molecule_chembl_id=${encodeURIComponent(moleculeChemblId)}` + `&limit=${limit}&pchembl_value__gte=${minPchembl}`;
287
+ const res = await apiFetchValidated(url, ActivitiesResponseSchema, { headers: HEADERS });
288
+ if (res.isErr()) {
289
+ if (res.error.type === "http_status" && res.error.status === 404)
290
+ return [];
291
+ throw new Error(describeApiError(res.error));
292
+ }
293
+ const byTarget = new Map();
294
+ for (const raw of res.value.activities ?? []) {
295
+ const tid = raw.target_chembl_id;
296
+ if (!tid)
297
+ continue;
298
+ if (options.excludeTargetChemblId && tid === options.excludeTargetChemblId)
299
+ continue;
300
+ const pchembl = parseNumeric(raw.pchembl_value);
301
+ const existing = byTarget.get(tid);
302
+ if (!existing || (pchembl != null && (existing.pchemblValue == null || pchembl > existing.pchemblValue))) {
303
+ byTarget.set(tid, {
304
+ moleculeChemblId,
305
+ targetChemblId: tid,
306
+ targetName: null,
307
+ standardType: raw.standard_type ?? null,
308
+ standardValue: parseNumeric(raw.standard_value),
309
+ standardUnits: raw.standard_units ?? null,
310
+ pchemblValue: pchembl,
311
+ });
312
+ }
313
+ }
314
+ const hits = [...byTarget.values()];
315
+ const tids = hits.map((h) => h.targetChemblId);
316
+ const concurrency = 5;
317
+ for (let i = 0; i < tids.length; i += concurrency) {
318
+ const batch = tids.slice(i, i + concurrency);
319
+ const names = await Promise.all(batch.map(fetchTargetName));
320
+ for (const [idx, id] of batch.entries()) {
321
+ const hit = hits.find((h) => h.targetChemblId === id);
322
+ if (hit)
323
+ hit.targetName = names[idx];
324
+ }
325
+ }
326
+ return hits.sort((a, b) => (b.pchemblValue ?? 0) - (a.pchemblValue ?? 0));
327
+ }
328
+ /**
329
+ * Fetch the median pChEMBL value for a modulator measured against its primary
330
+ * on-target. Filters to activities with non-null pchembl_value against the
331
+ * specified target ChEMBL ID. Returns null when no activities are found.
332
+ *
333
+ * Used by the polypharm fanout step so the assembler's computeSelectivity
334
+ * can produce real fold values instead of selectivity_unknown.
335
+ */
336
+ export async function getModulatorOnTargetPchembl(modulatorChemblId, targetChemblId) {
337
+ const url = `${CHEMBL_BASE}/activity.json?molecule_chembl_id=${encodeURIComponent(modulatorChemblId)}` +
338
+ `&target_chembl_id=${encodeURIComponent(targetChemblId)}` +
339
+ `&pchembl_value__isnull=false&limit=10`;
340
+ const res = await apiFetchValidated(url, ActivitiesResponseSchema, { headers: HEADERS });
341
+ if (res.isErr())
342
+ return null;
343
+ const values = (res.value.activities ?? []).map((a) => parseNumeric(a.pchembl_value)).filter((v) => v !== null);
344
+ if (values.length === 0)
345
+ return null;
346
+ values.sort((a, b) => a - b);
347
+ const mid = Math.floor(values.length / 2);
348
+ return values.length % 2 === 1 ? values[mid] : (values[mid - 1] + values[mid]) / 2;
349
+ }
350
+ /**
351
+ * Secondary path: fetch clinical-stage small molecules via the activity table.
352
+ *
353
+ * ChEMBL's mechanism table can lag behind for newer programmes (e.g.,
354
+ * orforglipron for GLP1R). Querying the activity table with
355
+ * `max_phase__gte` catches these molecules earlier. The activity table
356
+ * carries `molecule_chembl_id` but not `max_phase` or `molecule_type` —
357
+ * those require a follow-up molecule lookup. We batch unique molecule IDs
358
+ * and fetch molecule records in slices of 5.
359
+ *
360
+ * Returns one `ChemblModulator` per unique molecule that passes the
361
+ * min-phase and molecule-type filters.
362
+ */
363
+ export async function getModulatorsViaActivity(args) {
364
+ const { target_chembl_id, max_phase_min = 2, molecule_type, limit = 50 } = args;
365
+ let url = `${CHEMBL_BASE}/activity.json?target_chembl_id=${encodeURIComponent(target_chembl_id)}` + `&max_phase__gte=${max_phase_min}&limit=${limit}`;
366
+ if (molecule_type) {
367
+ url += `&molecule_type=${encodeURIComponent(molecule_type)}`;
368
+ }
369
+ const res = await apiFetchValidated(url, ActivitiesResponseSchema, { headers: HEADERS });
370
+ if (res.isErr()) {
371
+ if (res.error.type === "http_status" && res.error.status === 404)
372
+ return [];
373
+ throw new Error(describeApiError(res.error));
374
+ }
375
+ // Collect unique molecule IDs from activity rows.
376
+ const moleculeIds = new Set();
377
+ for (const row of res.value.activities ?? []) {
378
+ if (row.molecule_chembl_id)
379
+ moleculeIds.add(row.molecule_chembl_id);
380
+ }
381
+ if (moleculeIds.size === 0)
382
+ return [];
383
+ const modulators = [];
384
+ const ids = [...moleculeIds];
385
+ const concurrency = 5;
386
+ for (let i = 0; i < ids.length; i += concurrency) {
387
+ const batch = ids.slice(i, i + concurrency);
388
+ const results = await Promise.all(batch.map(async (id) => {
389
+ const molRes = await apiFetchValidated(`${CHEMBL_BASE}/molecule/${id}.json`, RawChemblMoleculeSchema, {
390
+ headers: HEADERS,
391
+ });
392
+ if (molRes.isErr())
393
+ return null;
394
+ const m = molRes.value;
395
+ const phase = m.max_phase != null ? Number(m.max_phase) : null;
396
+ if (phase == null || phase < max_phase_min)
397
+ return null;
398
+ const molType = m.molecule_type ?? null;
399
+ if (molecule_type && molType !== molecule_type)
400
+ return null;
401
+ return {
402
+ moleculeChemblId: m.molecule_chembl_id ?? id,
403
+ parentChemblId: m.molecule_hierarchy?.parent_chembl_id ?? null,
404
+ preferredName: m.pref_name ?? null,
405
+ maxPhase: phase,
406
+ moleculeType: molType,
407
+ firstApproval: m.first_approval ?? null,
408
+ };
409
+ }));
410
+ for (const r of results)
411
+ if (r)
412
+ modulators.push(r);
413
+ }
414
+ return modulators;
415
+ }
416
+ /**
417
+ * Fetch the canonical InChI key for a ChEMBL molecule. Returns null when
418
+ * ChEMBL has no recorded structure (typical for peptide/protein entries
419
+ * with `molecule_type: "Unknown"`).
420
+ */
421
+ export async function getMoleculeInChIKey(moleculeChemblId) {
422
+ const res = await apiFetchValidated(`${CHEMBL_BASE}/molecule/${moleculeChemblId}.json`, MoleculeStructuresResponseSchema, { headers: HEADERS });
423
+ if (res.isErr())
424
+ return null;
425
+ return res.value.molecule_structures?.standard_inchi_key ?? null;
426
+ }
427
+ /**
428
+ * Resolve a drug's mechanism-of-action targets to UniProt accessions.
429
+ * Returns deduplicated accessions across all mechanism rows.
430
+ * Empty array on no mechanism, missing target, or non-protein target.
431
+ *
432
+ * Used by target-identity-filter to detect off-target trials (e.g., a
433
+ * trial of a CALCRL drug being surfaced under a CALCR assessment).
434
+ */
435
+ export async function getDrugPrimaryTargetUniprots(moleculeChemblId) {
436
+ const mechRes = await apiFetchValidated(`${CHEMBL_BASE}/mechanism.json?molecule_chembl_id=${encodeURIComponent(moleculeChemblId)}&limit=20`, MechanismsResponseSchema, { headers: HEADERS });
437
+ if (mechRes.isErr())
438
+ return [];
439
+ const targetIds = new Set();
440
+ for (const m of mechRes.value.mechanisms ?? []) {
441
+ if (m.target_chembl_id)
442
+ targetIds.add(m.target_chembl_id);
443
+ }
444
+ if (targetIds.size === 0)
445
+ return [];
446
+ const accessions = new Set();
447
+ for (const targetId of targetIds) {
448
+ const tRes = await apiFetchValidated(`${CHEMBL_BASE}/target/${targetId}.json`, TargetComponentsResponseSchema, { headers: HEADERS });
449
+ if (tRes.isErr())
450
+ continue;
451
+ for (const c of tRes.value.target_components ?? []) {
452
+ if (c.accession && (c.component_type ?? "").toUpperCase() === "PROTEIN") {
453
+ accessions.add(c.accession);
454
+ }
455
+ }
456
+ }
457
+ return [...accessions];
458
+ }
@@ -0,0 +1,5 @@
1
+ /** Shared constants for ChEMBL REST API tools. */
2
+ export declare const CHEMBL_BASE = "https://www.ebi.ac.uk/chembl/api/data";
3
+ export declare const CHEMBL_HEADERS: {
4
+ readonly Accept: "application/json";
5
+ };
@@ -0,0 +1,3 @@
1
+ /** Shared constants for ChEMBL REST API tools. */
2
+ export const CHEMBL_BASE = "https://www.ebi.ac.uk/chembl/api/data";
3
+ export const CHEMBL_HEADERS = { Accept: "application/json" };
@@ -0,0 +1,33 @@
1
+ export interface PhaseTransitions {
2
+ phase1_to_phase2: number;
3
+ phase2_to_phase3: number;
4
+ phase3_to_nda: number;
5
+ nda_to_approval: number;
6
+ phase1_to_approval: number;
7
+ }
8
+ export interface BenchmarkResult {
9
+ therapeutic_area: string;
10
+ source: "available" | "fallback";
11
+ data_version: string;
12
+ data_window: string;
13
+ attribution: string;
14
+ transitions: PhaseTransitions;
15
+ }
16
+ /**
17
+ * Infer therapeutic area from a list of indication labels using the
18
+ * dataset's pattern map. First match wins.
19
+ */
20
+ export declare function inferTherapeuticArea(indicationLabels: string[]): string | null;
21
+ /**
22
+ * Get phase-transition benchmarks for a therapeutic area. Falls back to
23
+ * the all-areas baseline when the requested area is unknown — the
24
+ * `source` field discloses whether the fallback was used.
25
+ */
26
+ export declare function getBenchmarks(therapeuticArea: string | null): BenchmarkResult;
27
+ /** Return the dataset's metadata for transparency in the dossier. */
28
+ export declare function getDatasetAttribution(): {
29
+ data_version: string;
30
+ data_window: string;
31
+ source: string;
32
+ url: string;
33
+ };
@@ -0,0 +1,54 @@
1
+ import benchmarksData from "../../data/clinical-benchmarks.json" with { type: "json" };
2
+ const dataset = benchmarksData;
3
+ if (!dataset.phase_transitions || !dataset.phase_transitions.all) {
4
+ throw new Error("clinical-benchmarks.json is missing phase_transitions.all baseline");
5
+ }
6
+ function loadDataset() {
7
+ return dataset;
8
+ }
9
+ /**
10
+ * Infer therapeutic area from a list of indication labels using the
11
+ * dataset's pattern map. First match wins.
12
+ */
13
+ export function inferTherapeuticArea(indicationLabels) {
14
+ const dataset = loadDataset();
15
+ for (const label of indicationLabels) {
16
+ const lower = label.toLowerCase();
17
+ for (const entry of dataset.indication_to_therapeutic_area) {
18
+ for (const pattern of entry.patterns) {
19
+ if (lower.includes(pattern.toLowerCase())) {
20
+ return entry.therapeutic_area;
21
+ }
22
+ }
23
+ }
24
+ }
25
+ return null;
26
+ }
27
+ /**
28
+ * Get phase-transition benchmarks for a therapeutic area. Falls back to
29
+ * the all-areas baseline when the requested area is unknown — the
30
+ * `source` field discloses whether the fallback was used.
31
+ */
32
+ export function getBenchmarks(therapeuticArea) {
33
+ const dataset = loadDataset();
34
+ const useFallback = !therapeuticArea || !dataset.phase_transitions[therapeuticArea];
35
+ const ta = useFallback ? "all" : therapeuticArea;
36
+ return {
37
+ therapeutic_area: ta,
38
+ source: useFallback ? "fallback" : "available",
39
+ data_version: dataset.data_version,
40
+ data_window: dataset.data_window,
41
+ attribution: dataset.source,
42
+ transitions: dataset.phase_transitions[ta],
43
+ };
44
+ }
45
+ /** Return the dataset's metadata for transparency in the dossier. */
46
+ export function getDatasetAttribution() {
47
+ const ds = loadDataset();
48
+ return {
49
+ data_version: ds.data_version,
50
+ data_window: ds.data_window,
51
+ source: ds.source,
52
+ url: ds.url,
53
+ };
54
+ }