@inflexa-ai/harness 0.45.1 → 0.46.2

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 (790) hide show
  1. package/README.md +6 -3
  2. package/dist/agents/conversation-agent.d.ts +9 -3
  3. package/dist/agents/conversation-agent.js +34 -33
  4. package/dist/agents/report-session-agent.d.ts +15 -15
  5. package/dist/agents/report-session-agent.js +23 -15
  6. package/dist/agents/sandbox/index.d.ts +1 -1
  7. package/dist/agents/sandbox/index.js +1 -1
  8. package/dist/agents/sandbox/shared.d.ts +12 -14
  9. package/dist/agents/sandbox/shared.js +18 -12
  10. package/dist/agents/sandbox/types.d.ts +4 -4
  11. package/dist/agents/sandbox/validate-skills.d.ts +2 -2
  12. package/dist/agents/sandbox/validate-skills.js +3 -1
  13. package/dist/agents/sandbox-catalog.d.ts +2 -2
  14. package/dist/agents/sandbox-catalog.js +3 -3
  15. package/dist/agents/system-prompt.d.ts +2 -2
  16. package/dist/app/chat-turn-workflow.d.ts +114 -0
  17. package/dist/app/chat-turn-workflow.js +306 -0
  18. package/dist/app/chat-turn.d.ts +85 -57
  19. package/dist/app/chat-turn.js +123 -100
  20. package/dist/app/data-profile-orientation.js +10 -8
  21. package/dist/app/data-profile-view.d.ts +4 -4
  22. package/dist/app/data-profile-view.js +9 -8
  23. package/dist/app/in-process-turn.d.ts +42 -0
  24. package/dist/app/in-process-turn.js +139 -0
  25. package/dist/app/message-assembly.d.ts +10 -4
  26. package/dist/app/message-assembly.js +13 -8
  27. package/dist/app/report-session-runtime.d.ts +4 -4
  28. package/dist/app/report-session-runtime.js +36 -21
  29. package/dist/app/spawn-report-session.d.ts +33 -28
  30. package/dist/app/spawn-report-session.js +25 -40
  31. package/dist/app/synthesize-run.d.ts +22 -16
  32. package/dist/app/synthesize-run.js +41 -35
  33. package/dist/app/work.d.ts +96 -0
  34. package/dist/app/work.js +147 -0
  35. package/dist/auth/local-auth-context.d.ts +1 -3
  36. package/dist/auth/local-auth-context.js +1 -3
  37. package/dist/auth/local-run-authorizer.d.ts +1 -1
  38. package/dist/auth/local-run-authorizer.js +5 -3
  39. package/dist/auth/types.d.ts +26 -26
  40. package/dist/billing/cached-resolver.d.ts +4 -4
  41. package/dist/billing/run-charge.d.ts +5 -8
  42. package/dist/billing/run-charge.js +2 -2
  43. package/dist/billing/usage-recorder.d.ts +9 -9
  44. package/dist/citations/aggregate.js +1 -1
  45. package/dist/citations/clients/arxiv.d.ts +2 -2
  46. package/dist/citations/clients/arxiv.js +12 -4
  47. package/dist/citations/clients/common.js +4 -2
  48. package/dist/citations/clients/crossref.d.ts +2 -2
  49. package/dist/citations/clients/crossref.js +37 -37
  50. package/dist/citations/clients/doi-registry.js +15 -16
  51. package/dist/citations/clients/pubmed.d.ts +2 -2
  52. package/dist/citations/clients/pubmed.js +20 -13
  53. package/dist/citations/clients/semantic-scholar.d.ts +2 -2
  54. package/dist/citations/clients/semantic-scholar.js +9 -9
  55. package/dist/citations/compare.js +2 -2
  56. package/dist/citations/match.d.ts +2 -2
  57. package/dist/citations/match.js +12 -7
  58. package/dist/citations/normalize.js +35 -26
  59. package/dist/citations/plan.js +6 -2
  60. package/dist/citations/resolve.d.ts +6 -6
  61. package/dist/citations/resolve.js +34 -25
  62. package/dist/citations/types.d.ts +77 -77
  63. package/dist/config/environment-stores.d.ts +6 -6
  64. package/dist/config/resource-limits.js +1 -3
  65. package/dist/contracts/analogy-report.d.ts +7 -7
  66. package/dist/contracts/analogy-report.js +2 -2
  67. package/dist/contracts/chat-events.d.ts +38 -24
  68. package/dist/contracts/chat-frame.d.ts +15 -5
  69. package/dist/contracts/chat-frame.js +64 -41
  70. package/dist/contracts/chat-parts.d.ts +130 -67
  71. package/dist/contracts/chat-parts.js +1 -0
  72. package/dist/contracts/content-url.js +16 -2
  73. package/dist/contracts/data-profile.d.ts +38 -38
  74. package/dist/contracts/index.d.ts +2 -2
  75. package/dist/contracts/index.js +1 -1
  76. package/dist/contracts/message.d.ts +6 -6
  77. package/dist/contracts/organ-system.d.ts +11 -11
  78. package/dist/contracts/part-registry.d.ts +5 -4
  79. package/dist/contracts/part-registry.js +5 -0
  80. package/dist/contracts/profile-vocabulary.d.ts +11 -10
  81. package/dist/contracts/profile-vocabulary.js +10 -3
  82. package/dist/contracts/report-blocks.d.ts +329 -329
  83. package/dist/contracts/report-reference.d.ts +105 -81
  84. package/dist/contracts/report-reference.js +30 -13
  85. package/dist/contracts/schemas/chat-events.d.ts +30 -16
  86. package/dist/contracts/schemas/chat-events.js +15 -6
  87. package/dist/contracts/schemas/chat-parts.d.ts +175 -102
  88. package/dist/contracts/schemas/chat-parts.js +33 -7
  89. package/dist/contracts/severity.d.ts +1 -1
  90. package/dist/contracts/structure-source.d.ts +3 -3
  91. package/dist/contracts/structure-source.js +6 -2
  92. package/dist/contracts/subagent-activity.d.ts +2 -2
  93. package/dist/contracts/subagent-activity.js +5 -3
  94. package/dist/contracts/usage.d.ts +2 -2
  95. package/dist/data/safety-panel-schema.d.ts +25 -25
  96. package/dist/data/safety-panel-schema.js +13 -4
  97. package/dist/execution/artifact-metadata.d.ts +23 -15
  98. package/dist/execution/artifact-metadata.js +33 -10
  99. package/dist/execution/artifact-record.d.ts +2 -2
  100. package/dist/execution/artifact-registration.d.ts +5 -5
  101. package/dist/execution/artifact-registry.d.ts +8 -8
  102. package/dist/execution/dbos-run-launcher.d.ts +24 -4
  103. package/dist/execution/dbos-run-launcher.js +58 -4
  104. package/dist/execution/dbos-workflow-purger.d.ts +5 -6
  105. package/dist/execution/dbos-workflow-purger.js +8 -7
  106. package/dist/execution/input-signature.d.ts +2 -2
  107. package/dist/execution/post-step-pipeline.d.ts +9 -9
  108. package/dist/execution/post-step-pipeline.js +1 -1
  109. package/dist/execution/post-step.js +2 -2
  110. package/dist/execution/reconcile-manifest.d.ts +4 -4
  111. package/dist/execution/reconcile-manifest.js +3 -2
  112. package/dist/execution/run-authorizer.d.ts +46 -37
  113. package/dist/execution/run-authorizer.js +8 -8
  114. package/dist/execution/run-canceler.d.ts +7 -7
  115. package/dist/execution/run-canceler.js +14 -7
  116. package/dist/execution/run-end-record.d.ts +2 -3
  117. package/dist/execution/run-event-parts.d.ts +0 -8
  118. package/dist/execution/run-event-parts.js +29 -24
  119. package/dist/execution/run-event-stream.d.ts +8 -8
  120. package/dist/execution/run-event-stream.js +3 -4
  121. package/dist/execution/run-launcher.d.ts +4 -4
  122. package/dist/execution/run-synthesis.d.ts +49 -48
  123. package/dist/execution/run-synthesis.js +96 -255
  124. package/dist/execution/staged-input.d.ts +2 -2
  125. package/dist/execution/step-summary.d.ts +6 -6
  126. package/dist/execution/step-summary.js +4 -8
  127. package/dist/execution/topo-sort.js +4 -3
  128. package/dist/execution/workflow-purger.d.ts +2 -2
  129. package/dist/index.d.ts +17 -20
  130. package/dist/index.js +25 -36
  131. package/dist/input-sanitization.js +9 -2
  132. package/dist/input-scan/clustering.d.ts +6 -6
  133. package/dist/input-scan/clustering.js +11 -5
  134. package/dist/input-scan/companions.js +3 -2
  135. package/dist/input-scan/detect-sets.d.ts +2 -2
  136. package/dist/input-scan/detect-sets.js +25 -21
  137. package/dist/input-scan/enrich.d.ts +6 -6
  138. package/dist/input-scan/enrich.js +29 -12
  139. package/dist/input-scan/formats.d.ts +2 -2
  140. package/dist/input-scan/formats.js +8 -2
  141. package/dist/input-scan/markers.d.ts +2 -2
  142. package/dist/input-scan/markers.js +14 -5
  143. package/dist/input-scan/menu.d.ts +10 -10
  144. package/dist/input-scan/menu.js +0 -0
  145. package/dist/input-scan/quarantine.d.ts +2 -2
  146. package/dist/input-scan/quarantine.js +23 -18
  147. package/dist/input-scan/readout-budget.d.ts +2 -2
  148. package/dist/input-scan/readout-budget.js +1 -1
  149. package/dist/input-scan/readout.d.ts +2 -2
  150. package/dist/input-scan/readout.js +47 -34
  151. package/dist/input-scan/scan.d.ts +2 -2
  152. package/dist/input-scan/scan.js +7 -5
  153. package/dist/input-scan/set-types.d.ts +28 -28
  154. package/dist/input-scan/shapes.d.ts +4 -4
  155. package/dist/input-scan/shapes.js +0 -0
  156. package/dist/input-scan/templates.d.ts +10 -10
  157. package/dist/input-scan/templates.js +30 -22
  158. package/dist/input-scan/tokens.d.ts +6 -4
  159. package/dist/input-scan/tokens.js +100 -38
  160. package/dist/input-scan/types.d.ts +22 -22
  161. package/dist/lib/async-utils.d.ts +3 -7
  162. package/dist/lib/async-utils.js +5 -9
  163. package/dist/lib/cache.js +1 -1
  164. package/dist/lib/chrome.d.ts +46 -6
  165. package/dist/lib/console-logger.js +2 -2
  166. package/dist/lib/db-result.d.ts +22 -6
  167. package/dist/lib/db-result.js +9 -13
  168. package/dist/lib/eyes.d.ts +4 -4
  169. package/dist/lib/eyes.js +1 -1
  170. package/dist/lib/fs-helpers.js +18 -6
  171. package/dist/lib/fs-result.d.ts +1 -0
  172. package/dist/lib/fs-result.js +5 -6
  173. package/dist/lib/hooks.d.ts +32 -7
  174. package/dist/lib/hooks.js +22 -3
  175. package/dist/lib/host-concurrency.js +3 -2
  176. package/dist/lib/logger.d.ts +2 -2
  177. package/dist/lib/logger.js +2 -1
  178. package/dist/lib/metrics.d.ts +1 -1
  179. package/dist/lib/null-proto.d.ts +6 -0
  180. package/dist/lib/null-proto.js +17 -0
  181. package/dist/lib/otel-spans.d.ts +1 -1
  182. package/dist/lib/otel-spans.js +9 -5
  183. package/dist/lib/otel.d.ts +4 -2
  184. package/dist/lib/otel.js +10 -2
  185. package/dist/lib/page-capture.d.ts +8 -8
  186. package/dist/lib/page-capture.js +9 -4
  187. package/dist/lib/parse-json.d.ts +5 -0
  188. package/dist/lib/parse-json.js +12 -0
  189. package/dist/lib/present.d.ts +12 -0
  190. package/dist/lib/present.js +39 -0
  191. package/dist/lib/rate-limit.d.ts +4 -4
  192. package/dist/lib/rate-limit.js +12 -13
  193. package/dist/lib/regulatory-corpus/fetch-fda-guidance.d.ts +4 -4
  194. package/dist/lib/regulatory-corpus/fetch-fda-guidance.js +4 -10
  195. package/dist/lib/regulatory-corpus/fetch-ich.d.ts +4 -4
  196. package/dist/lib/regulatory-corpus/fetch-ich.js +18 -14
  197. package/dist/lib/regulatory-corpus/normalize-whitespace.d.ts +6 -0
  198. package/dist/lib/regulatory-corpus/normalize-whitespace.js +41 -0
  199. package/dist/lib/regulatory-corpus.d.ts +10 -10
  200. package/dist/lib/regulatory-corpus.js +3 -1
  201. package/dist/lib/result.d.ts +10 -11
  202. package/dist/lib/result.js +15 -13
  203. package/dist/lib/storage.d.ts +2 -2
  204. package/dist/lib/test/async-iterable.d.ts +9 -0
  205. package/dist/lib/test/async-iterable.js +28 -0
  206. package/dist/lib/test/request-url.d.ts +5 -0
  207. package/dist/lib/test/request-url.js +7 -0
  208. package/dist/lib/test/result-assert.d.ts +12 -0
  209. package/dist/lib/test/result-assert.js +17 -0
  210. package/dist/lib/test/text-shapes.d.ts +24 -0
  211. package/dist/lib/test/text-shapes.js +63 -0
  212. package/dist/lib/text.d.ts +22 -0
  213. package/dist/lib/text.js +68 -0
  214. package/dist/lib/thrown.d.ts +18 -0
  215. package/dist/lib/thrown.js +30 -0
  216. package/dist/lib/unknown-array.d.ts +6 -0
  217. package/dist/lib/unknown-array.js +8 -0
  218. package/dist/lib/unknown-containers.d.ts +14 -0
  219. package/dist/lib/unknown-containers.js +17 -0
  220. package/dist/lib/unknown-text.d.ts +8 -0
  221. package/dist/lib/unknown-text.js +28 -0
  222. package/dist/lib/zod-issue-shape.d.ts +1 -1
  223. package/dist/lib/zod-issue-shape.js +31 -31
  224. package/dist/lib/zod-issues.d.ts +3 -3
  225. package/dist/lib/zod-issues.js +30 -17
  226. package/dist/literature/sources/arxiv.d.ts +6 -6
  227. package/dist/literature/sources/arxiv.js +92 -35
  228. package/dist/literature/sources/http.d.ts +2 -2
  229. package/dist/literature/sources/http.js +16 -15
  230. package/dist/literature/sources/pubmed.d.ts +16 -16
  231. package/dist/literature/sources/pubmed.js +96 -61
  232. package/dist/literature/sources/semantic-scholar.d.ts +8 -8
  233. package/dist/literature/sources/semantic-scholar.js +22 -13
  234. package/dist/loop/accounting.d.ts +63 -0
  235. package/dist/loop/accounting.js +141 -0
  236. package/dist/loop/call-policy.d.ts +73 -0
  237. package/dist/loop/call-policy.js +109 -0
  238. package/dist/loop/chat-stream.d.ts +62 -0
  239. package/dist/loop/chat-stream.js +237 -0
  240. package/dist/loop/compaction.d.ts +9 -9
  241. package/dist/loop/compaction.js +1 -1
  242. package/dist/loop/metrics.d.ts +12 -15
  243. package/dist/loop/metrics.js +14 -26
  244. package/dist/loop/run-loop.d.ts +233 -0
  245. package/dist/loop/run-loop.js +770 -0
  246. package/dist/loop/sub-agent.d.ts +61 -0
  247. package/dist/loop/sub-agent.js +160 -0
  248. package/dist/loop/tool-adapter.d.ts +98 -0
  249. package/dist/loop/tool-adapter.js +364 -0
  250. package/dist/loop/tool-detail.d.ts +1 -1
  251. package/dist/loop/tool-detail.js +6 -5
  252. package/dist/loop/tool-outcome.d.ts +1 -1
  253. package/dist/loop/tool-output.d.ts +4 -4
  254. package/dist/loop/tool-output.js +2 -2
  255. package/dist/loop/turn-credentials.d.ts +39 -0
  256. package/dist/loop/turn-credentials.js +90 -0
  257. package/dist/loop/types.d.ts +29 -38
  258. package/dist/loop/types.js +2 -7
  259. package/dist/memory/ai-sdk-message-storage.d.ts +5 -5
  260. package/dist/memory/ai-sdk-message-storage.js +13 -11
  261. package/dist/memory/card-builders.d.ts +14 -14
  262. package/dist/memory/card-builders.js +19 -15
  263. package/dist/memory/conversation-display-recorder.d.ts +22 -4
  264. package/dist/memory/conversation-display-recorder.js +43 -24
  265. package/dist/memory/conversation-display-replay.js +3 -2
  266. package/dist/memory/conversation-display-storage.d.ts +15 -7
  267. package/dist/memory/conversation-display-storage.js +141 -36
  268. package/dist/memory/conversation-view.d.ts +4 -4
  269. package/dist/memory/conversation-view.js +5 -4
  270. package/dist/memory/count-tokens.js +10 -8
  271. package/dist/memory/derive-thread-title.d.ts +0 -13
  272. package/dist/memory/derive-thread-title.js +2 -1
  273. package/dist/memory/message-backfill.d.ts +12 -5
  274. package/dist/memory/message-backfill.js +5 -3
  275. package/dist/memory/thread-history.d.ts +36 -21
  276. package/dist/memory/thread-history.js +78 -54
  277. package/dist/memory/thread-store.d.ts +26 -17
  278. package/dist/memory/thread-store.js +15 -9
  279. package/dist/memory/tool-call-integrity.d.ts +2 -2
  280. package/dist/memory/tool-call-integrity.js +4 -3
  281. package/dist/memory/working-memory.d.ts +16 -12
  282. package/dist/memory/working-memory.js +72 -61
  283. package/dist/prompts/briefing.d.ts +12 -12
  284. package/dist/prompts/briefing.js +1 -1
  285. package/dist/prompts/synthesis-agent.d.ts +1 -1
  286. package/dist/prompts/synthesis-agent.js +6 -14
  287. package/dist/provenance/collector.d.ts +6 -6
  288. package/dist/provenance/collector.js +15 -8
  289. package/dist/provenance/exec-frame.d.ts +2 -2
  290. package/dist/provenance/exec-frame.js +6 -1
  291. package/dist/provenance/seam.d.ts +1 -4
  292. package/dist/provenance/types.d.ts +6 -6
  293. package/dist/providers/ai-sdk.d.ts +113 -62
  294. package/dist/providers/ai-sdk.js +283 -518
  295. package/dist/providers/embedding.d.ts +2 -2
  296. package/dist/providers/embedding.js +1 -1
  297. package/dist/providers/errors.d.ts +22 -2
  298. package/dist/providers/errors.js +98 -50
  299. package/dist/providers/prompt-cache.d.ts +8 -8
  300. package/dist/providers/prompt-cache.js +13 -11
  301. package/dist/providers/reasoning.d.ts +2 -2
  302. package/dist/providers/reasoning.js +2 -2
  303. package/dist/providers/request-headers.js +12 -3
  304. package/dist/providers/types.d.ts +55 -94
  305. package/dist/reference-data/catalog.d.ts +2 -15
  306. package/dist/reference-data/catalog.js +25 -8
  307. package/dist/reference-data/receipt.d.ts +2 -2
  308. package/dist/report-model/assert-rules.js +1 -1
  309. package/dist/report-model/authoring-grammar.d.ts +211 -233
  310. package/dist/report-model/block-walk.d.ts +10 -10
  311. package/dist/report-model/block-walk.js +2 -0
  312. package/dist/report-model/draft-finish.d.ts +8 -8
  313. package/dist/report-model/draft-finish.js +1 -1
  314. package/dist/report-model/draft-hash.js +8 -7
  315. package/dist/report-model/draft-operations.d.ts +22 -10
  316. package/dist/report-model/draft-operations.js +48 -30
  317. package/dist/report-model/draft-read.d.ts +19 -7
  318. package/dist/report-model/draft-read.js +16 -6
  319. package/dist/report-model/draft.d.ts +844 -2
  320. package/dist/report-model/draft.js +3 -1
  321. package/dist/report-model/fixture-resolver.js +39 -16
  322. package/dist/report-model/pin-snapshot.d.ts +2 -2
  323. package/dist/report-model/pin-snapshot.js +15 -15
  324. package/dist/report-model/production-resolver.d.ts +18 -18
  325. package/dist/report-model/production-resolver.js +50 -42
  326. package/dist/report-model/reference-resolver.d.ts +26 -10
  327. package/dist/report-model/reference-resolver.js +68 -5
  328. package/dist/report-model/reference-stamp.js +30 -38
  329. package/dist/report-model/structural-validation.js +12 -4
  330. package/dist/report-model/validate.d.ts +7 -7
  331. package/dist/report-model/validate.js +6 -6
  332. package/dist/report-render/assets.d.ts +2 -2
  333. package/dist/report-render/assets.js +27 -3
  334. package/dist/report-render/chart-export.d.ts +10 -2
  335. package/dist/report-render/chart-export.js +37 -11
  336. package/dist/report-render/chart-presets.d.ts +8 -8
  337. package/dist/report-render/chart-presets.js +3 -3
  338. package/dist/report-render/chart-renderers.d.ts +23 -16
  339. package/dist/report-render/chart-renderers.js +74 -53
  340. package/dist/report-render/chart-toolbox.d.ts +2 -2
  341. package/dist/report-render/chart-toolbox.js +7 -6
  342. package/dist/report-render/chart.d.ts +15 -16
  343. package/dist/report-render/chart.js +369 -252
  344. package/dist/report-render/design.d.ts +36 -297
  345. package/dist/report-render/design.js +0 -12
  346. package/dist/report-render/figures/common.d.ts +12 -12
  347. package/dist/report-render/figures/common.js +42 -31
  348. package/dist/report-render/figures/dendrogram.d.ts +3 -3
  349. package/dist/report-render/figures/dendrogram.js +10 -10
  350. package/dist/report-render/figures/dense.js +15 -8
  351. package/dist/report-render/figures/dotplot.js +46 -33
  352. package/dist/report-render/figures/embedding.js +52 -43
  353. package/dist/report-render/figures/equal-units.d.ts +10 -10
  354. package/dist/report-render/figures/equal-units.js +27 -27
  355. package/dist/report-render/figures/forest.js +9 -7
  356. package/dist/report-render/figures/gsea.js +21 -11
  357. package/dist/report-render/figures/heatmap.js +13 -9
  358. package/dist/report-render/figures/index.d.ts +10 -10
  359. package/dist/report-render/figures/index.js +4 -2
  360. package/dist/report-render/figures/km.js +10 -9
  361. package/dist/report-render/figures/label-room.d.ts +12 -12
  362. package/dist/report-render/figures/label-room.js +7 -2
  363. package/dist/report-render/figures/locuszoom.d.ts +2 -2
  364. package/dist/report-render/figures/locuszoom.js +59 -31
  365. package/dist/report-render/figures/lollipop.js +3 -2
  366. package/dist/report-render/figures/ma.js +8 -4
  367. package/dist/report-render/figures/manhattan.d.ts +1 -2
  368. package/dist/report-render/figures/manhattan.js +52 -34
  369. package/dist/report-render/figures/oncoprint.js +4 -5
  370. package/dist/report-render/figures/pca.js +25 -11
  371. package/dist/report-render/figures/qq.js +20 -9
  372. package/dist/report-render/figures/roc.js +1 -1
  373. package/dist/report-render/figures/sankey.d.ts +2 -2
  374. package/dist/report-render/figures/sankey.js +11 -10
  375. package/dist/report-render/figures/upset.d.ts +6 -6
  376. package/dist/report-render/figures/upset.js +7 -4
  377. package/dist/report-render/figures/volcano.js +12 -10
  378. package/dist/report-render/hybrid-svg.d.ts +4 -4
  379. package/dist/report-render/hybrid-svg.js +7 -5
  380. package/dist/report-render/number-format.d.ts +4 -4
  381. package/dist/report-render/number-format.js +62 -27
  382. package/dist/report-render/page.js +2 -1
  383. package/dist/report-render/provenance-data.d.ts +2 -2
  384. package/dist/report-render/references.d.ts +4 -4
  385. package/dist/report-render/render.d.ts +2 -2
  386. package/dist/report-render/render.js +10 -11
  387. package/dist/report-render/script-json.js +1 -1
  388. package/dist/report-render/table-data.d.ts +6 -6
  389. package/dist/report-render/test/options.d.ts +49 -0
  390. package/dist/report-render/test/options.js +143 -0
  391. package/dist/report-render/test/page-function.d.ts +19 -0
  392. package/dist/report-render/test/page-function.js +33 -0
  393. package/dist/report-render/types.d.ts +10 -10
  394. package/dist/report-render/value-bridge.d.ts +4 -4
  395. package/dist/report-render/value-bridge.js +27 -14
  396. package/dist/report-render/views/chart-view.d.ts +2 -2
  397. package/dist/report-render/views/chart-view.js +2 -2
  398. package/dist/report-render/views/lineage.d.ts +6 -6
  399. package/dist/report-render/views/lineage.js +2 -0
  400. package/dist/report-render/views/page-view.d.ts +2 -2
  401. package/dist/report-render/views/page-view.js +1 -0
  402. package/dist/report-render/views/prose.js +25 -8
  403. package/dist/report-render/views/references-view.js +12 -1
  404. package/dist/report-render/views/values.js +1 -1
  405. package/dist/runtime/assemble.d.ts +53 -26
  406. package/dist/runtime/assemble.js +103 -56
  407. package/dist/runtime/boot.d.ts +8 -7
  408. package/dist/runtime/boot.js +1 -1
  409. package/dist/runtime/connection-budget.d.ts +6 -6
  410. package/dist/runtime/connection-budget.js +1 -1
  411. package/dist/runtime/dbos.d.ts +29 -19
  412. package/dist/runtime/dbos.js +35 -20
  413. package/dist/runtime/result-serialization.js +18 -5
  414. package/dist/runtime/shutdown.d.ts +2 -2
  415. package/dist/sandbox/client.d.ts +7 -3
  416. package/dist/sandbox/cpu-files.d.ts +2 -2
  417. package/dist/sandbox/cpu-files.js +21 -4
  418. package/dist/sandbox/create-sandbox.d.ts +7 -8
  419. package/dist/sandbox/create-sandbox.js +6 -12
  420. package/dist/sandbox/docker-client.d.ts +48 -3
  421. package/dist/sandbox/docker-client.js +10 -6
  422. package/dist/sandbox/estimate-data-profile-resources.js +2 -7
  423. package/dist/sandbox/exec-outcome.d.ts +2 -2
  424. package/dist/sandbox/exec-outcome.js +1 -1
  425. package/dist/sandbox/exec.d.ts +10 -6
  426. package/dist/sandbox/exec.js +27 -12
  427. package/dist/sandbox/execution-id.js +14 -6
  428. package/dist/sandbox/farm.d.ts +2 -2
  429. package/dist/sandbox/farm.js +22 -27
  430. package/dist/sandbox/identity.d.ts +7 -0
  431. package/dist/sandbox/identity.js +14 -3
  432. package/dist/sandbox/image-packages.js +15 -27
  433. package/dist/sandbox/k8s-client.d.ts +35 -8
  434. package/dist/sandbox/k8s-client.js +6 -5
  435. package/dist/sandbox/labels.js +1 -0
  436. package/dist/sandbox/liveness.js +3 -1
  437. package/dist/sandbox/mount-plan.d.ts +10 -10
  438. package/dist/sandbox/mount-plan.js +13 -14
  439. package/dist/sandbox/notification-sweep.d.ts +4 -4
  440. package/dist/sandbox/notification-sweep.js +4 -7
  441. package/dist/sandbox/package-identity.d.ts +6 -13
  442. package/dist/sandbox/package-identity.js +46 -28
  443. package/dist/sandbox/reaper.d.ts +10 -10
  444. package/dist/sandbox/reaper.js +4 -6
  445. package/dist/sandbox/sandbox-error.d.ts +2 -9
  446. package/dist/sandbox/sandbox-error.js +21 -8
  447. package/dist/sandbox/sandbox-step-translate.d.ts +8 -5
  448. package/dist/sandbox/sandbox-step-translate.js +22 -8
  449. package/dist/sandbox/step-sandbox.d.ts +47 -0
  450. package/dist/sandbox/step-sandbox.js +53 -0
  451. package/dist/sandbox/types.d.ts +18 -19
  452. package/dist/sandbox/types.js +1 -1
  453. package/dist/schemas/artifact-manifest.d.ts +4 -4
  454. package/dist/schemas/data-profile-schemas.d.ts +343 -298
  455. package/dist/schemas/file-metadata.js +2 -4
  456. package/dist/schemas/plan-schemas.d.ts +31 -31
  457. package/dist/schemas/run-synthesis.d.ts +95 -26
  458. package/dist/schemas/run-synthesis.js +3 -1
  459. package/dist/schemas/validate-plan.d.ts +4 -4
  460. package/dist/schemas/validate-plan.js +17 -5
  461. package/dist/schemas/workflow-state.d.ts +19 -19
  462. package/dist/schemas/workflow-state.js +2 -2
  463. package/dist/state/active-turns.d.ts +36 -0
  464. package/dist/state/active-turns.js +67 -0
  465. package/dist/state/analyses-metrics.d.ts +8 -8
  466. package/dist/state/analyses-metrics.js +4 -4
  467. package/dist/state/analyses.d.ts +0 -14
  468. package/dist/state/analyses.js +0 -32
  469. package/dist/state/artifacts.d.ts +32 -19
  470. package/dist/state/artifacts.js +28 -5
  471. package/dist/state/data-profile.d.ts +2 -2
  472. package/dist/state/db.d.ts +12 -2
  473. package/dist/state/db.js +5 -0
  474. package/dist/state/edit-intents.d.ts +4 -0
  475. package/dist/state/edit-intents.js +71 -0
  476. package/dist/state/index.d.ts +4 -4
  477. package/dist/state/index.js +2 -2
  478. package/dist/state/init.d.ts +2 -1
  479. package/dist/state/init.js +5 -2
  480. package/dist/state/migrations/20260927120000_baseline.js +3 -1
  481. package/dist/state/migrations/20261026120000_add_the_edit_intents.d.ts +7 -0
  482. package/dist/state/migrations/20261026120000_add_the_edit_intents.js +21 -0
  483. package/dist/state/migrations/20261027120000_record_the_applied_memory_edits.d.ts +7 -0
  484. package/dist/state/migrations/20261027120000_record_the_applied_memory_edits.js +16 -0
  485. package/dist/state/migrations/20261027120100_store_the_authoring_results.d.ts +8 -0
  486. package/dist/state/migrations/20261027120100_store_the_authoring_results.js +20 -0
  487. package/dist/state/migrations/20261027120200_key_the_groups_of_a_turn.d.ts +7 -0
  488. package/dist/state/migrations/20261027120200_key_the_groups_of_a_turn.js +12 -0
  489. package/dist/state/migrations/20261027120300_mark_the_active_turn_of_a_thread.d.ts +7 -0
  490. package/dist/state/migrations/20261027120300_mark_the_active_turn_of_a_thread.js +11 -0
  491. package/dist/state/migrations/20261028120000_record_the_paused_work.d.ts +7 -0
  492. package/dist/state/migrations/20261028120000_record_the_paused_work.js +25 -0
  493. package/dist/state/migrations/20261028120100_end_the_suspended_runs.d.ts +8 -0
  494. package/dist/state/migrations/20261028120100_end_the_suspended_runs.js +13 -0
  495. package/dist/state/migrations/20261029120000_reference_the_run_mandate.d.ts +7 -0
  496. package/dist/state/migrations/20261029120000_reference_the_run_mandate.js +23 -0
  497. package/dist/state/migrations/20261029120100_record_the_run_session_of_a_pause.d.ts +7 -0
  498. package/dist/state/migrations/20261029120100_record_the_run_session_of_a_pause.js +11 -0
  499. package/dist/state/migrations/index.js +18 -0
  500. package/dist/state/paused-work.d.ts +52 -0
  501. package/dist/state/paused-work.js +105 -0
  502. package/dist/state/plans.d.ts +27 -8
  503. package/dist/state/plans.js +14 -11
  504. package/dist/state/purge-analysis.d.ts +6 -6
  505. package/dist/state/purge-analysis.js +10 -2
  506. package/dist/state/report-session-state.d.ts +43 -18
  507. package/dist/state/report-session-state.js +43 -4
  508. package/dist/state/report-versions.d.ts +16 -11
  509. package/dist/state/report-versions.js +5 -3
  510. package/dist/state/runs.d.ts +30 -19
  511. package/dist/state/runs.js +43 -51
  512. package/dist/state/schema.d.ts +18 -21
  513. package/dist/state/schema.js +4 -5
  514. package/dist/state/snapshot-parse.d.ts +2 -2
  515. package/dist/state/snapshot-parse.js +14 -8
  516. package/dist/state/step-executions.d.ts +20 -8
  517. package/dist/state/step-executions.js +6 -4
  518. package/dist/state/tool-outputs.d.ts +2 -2
  519. package/dist/state/tool-outputs.js +2 -1
  520. package/dist/state/vector-store.d.ts +16 -16
  521. package/dist/state/vector-store.js +11 -7
  522. package/dist/tasks/data-profile-absorb.d.ts +3 -3
  523. package/dist/tasks/data-profile-absorb.js +21 -16
  524. package/dist/tasks/data-profile-activity.d.ts +5 -5
  525. package/dist/tasks/data-profile-activity.js +5 -5
  526. package/dist/tasks/data-profile-index.d.ts +4 -4
  527. package/dist/tasks/data-profile-index.js +32 -17
  528. package/dist/tasks/data-profile-resolve.d.ts +8 -8
  529. package/dist/tasks/data-profile-resolve.js +88 -62
  530. package/dist/tasks/data-profile.d.ts +40 -31
  531. package/dist/tasks/data-profile.js +138 -95
  532. package/dist/tasks/extract-values.d.ts +26 -79
  533. package/dist/tasks/extract-values.js +48 -108
  534. package/dist/tasks/refresh-regulatory-corpus.d.ts +4 -20
  535. package/dist/tasks/refresh-regulatory-corpus.js +12 -8
  536. package/dist/tasks/regulatory-corpus-boot-refresh.d.ts +2 -2
  537. package/dist/tasks/regulatory-corpus-boot-refresh.js +12 -10
  538. package/dist/testing.d.ts +62 -0
  539. package/dist/testing.js +101 -0
  540. package/dist/tools/ad-hoc-router.d.ts +9 -9
  541. package/dist/tools/ad-hoc-router.js +65 -52
  542. package/dist/tools/analysis-invocation.d.ts +7 -0
  543. package/dist/tools/analysis-invocation.js +29 -5
  544. package/dist/tools/approval/contract.d.ts +8 -52
  545. package/dist/tools/approval/contract.js +7 -36
  546. package/dist/tools/approval/gateway.d.ts +27 -28
  547. package/dist/tools/approval/gateway.js +33 -130
  548. package/dist/tools/approval/queries.d.ts +6 -11
  549. package/dist/tools/approval/queries.js +43 -29
  550. package/dist/tools/approval/uuidv7.js +2 -2
  551. package/dist/tools/bio/chembl.d.ts +3 -3
  552. package/dist/tools/bio/chembl.js +10 -0
  553. package/dist/tools/bio/comptox.d.ts +25 -8
  554. package/dist/tools/bio/comptox.js +4 -2
  555. package/dist/tools/bio/drug-gene-interactions.d.ts +27 -17
  556. package/dist/tools/bio/drug-gene-interactions.js +11 -8
  557. package/dist/tools/bio/gene-disease-evidence.d.ts +61 -15
  558. package/dist/tools/bio/gene-disease-evidence.js +10 -6
  559. package/dist/tools/bio/gene-preclinical-profile.d.ts +11 -11
  560. package/dist/tools/bio/keys.d.ts +2 -2
  561. package/dist/tools/bio/keys.js +3 -3
  562. package/dist/tools/bio/lookup-annotation.d.ts +5 -5
  563. package/dist/tools/bio/lookup-annotation.js +3 -0
  564. package/dist/tools/bio/opentargets.d.ts +1 -1
  565. package/dist/tools/bio/opentargets.js +6 -0
  566. package/dist/tools/bio/pubchem.d.ts +2 -2
  567. package/dist/tools/bio/pubchem.js +6 -0
  568. package/dist/tools/bio/pubmed.d.ts +26 -16
  569. package/dist/tools/bio/pubmed.js +9 -3
  570. package/dist/tools/bio/search-clinical-trials.d.ts +4 -4
  571. package/dist/tools/bio/search-clinical-trials.js +5 -1
  572. package/dist/tools/bio/search-faers.d.ts +2 -2
  573. package/dist/tools/bio/search-faers.js +1 -1
  574. package/dist/tools/bio/search-gene.d.ts +2 -2
  575. package/dist/tools/bio/search-gene.js +1 -0
  576. package/dist/tools/bio/search-geo-datasets.d.ts +4 -4
  577. package/dist/tools/bio/search-geo-datasets.js +5 -5
  578. package/dist/tools/bio/search-interactions.d.ts +1 -1
  579. package/dist/tools/bio/search-patents.d.ts +28 -22
  580. package/dist/tools/bio/search-patents.js +20 -17
  581. package/dist/tools/bio/search-protein.d.ts +2 -2
  582. package/dist/tools/bio/search-protein.js +1 -1
  583. package/dist/tools/bio/search-regulatory-approvals.d.ts +64 -18
  584. package/dist/tools/bio/search-regulatory-approvals.js +21 -16
  585. package/dist/tools/bio/target-safety.d.ts +8 -8
  586. package/dist/tools/bio/target-safety.js +11 -6
  587. package/dist/tools/capability-data.d.ts +9 -5
  588. package/dist/tools/capability-data.js +2 -1
  589. package/dist/tools/define-tool.d.ts +55 -46
  590. package/dist/tools/define-tool.js +39 -27
  591. package/dist/tools/display/normalize-echart-spec.d.ts +2 -2
  592. package/dist/tools/display/normalize-echart-spec.js +51 -27
  593. package/dist/tools/display/show-user.d.ts +2 -2
  594. package/dist/tools/display/show-user.js +1 -1
  595. package/dist/tools/execute-analysis.d.ts +19 -10
  596. package/dist/tools/execute-analysis.js +83 -62
  597. package/dist/tools/knowledge/check.d.ts +166 -44
  598. package/dist/tools/knowledge/check.js +5 -3
  599. package/dist/tools/knowledge/client.d.ts +31 -62
  600. package/dist/tools/knowledge/client.js +44 -27
  601. package/dist/tools/knowledge/environment.d.ts +6 -6
  602. package/dist/tools/knowledge/environment.js +18 -7
  603. package/dist/tools/knowledge/index.d.ts +2 -2
  604. package/dist/tools/knowledge/index.js +9 -9
  605. package/dist/tools/knowledge/local-slots.d.ts +4 -4
  606. package/dist/tools/knowledge/local-slots.js +11 -4
  607. package/dist/tools/knowledge/pin.d.ts +2 -2
  608. package/dist/tools/knowledge/recommend.d.ts +20 -45
  609. package/dist/tools/knowledge/recommend.js +27 -19
  610. package/dist/tools/knowledge/situation.d.ts +40 -40
  611. package/dist/tools/knowledge/situation.js +2 -9
  612. package/dist/tools/knowledge/skeleton.d.ts +4 -4
  613. package/dist/tools/knowledge/skeleton.js +10 -11
  614. package/dist/tools/knowledge/template.d.ts +20 -18
  615. package/dist/tools/knowledge/template.js +38 -32
  616. package/dist/tools/lib/alphafold-client.js +2 -1
  617. package/dist/tools/lib/amass-client.d.ts +28 -28
  618. package/dist/tools/lib/amass-client.js +20 -10
  619. package/dist/tools/lib/api-utils.d.ts +13 -3
  620. package/dist/tools/lib/api-utils.js +17 -3
  621. package/dist/tools/lib/bgee-client.d.ts +6 -6
  622. package/dist/tools/lib/bgee-client.js +16 -10
  623. package/dist/tools/lib/cbioportal-client.d.ts +4 -4
  624. package/dist/tools/lib/cbioportal-client.js +9 -8
  625. package/dist/tools/lib/chembl-client.d.ts +14 -14
  626. package/dist/tools/lib/chembl-client.js +11 -4
  627. package/dist/tools/lib/clinical-benchmarks-client.d.ts +4 -4
  628. package/dist/tools/lib/clinical-benchmarks-client.js +4 -7
  629. package/dist/tools/lib/clinical-trials-client.d.ts +18 -18
  630. package/dist/tools/lib/clinical-trials-client.js +10 -10
  631. package/dist/tools/lib/clinvar-client.d.ts +2 -2
  632. package/dist/tools/lib/clinvar-client.js +6 -6
  633. package/dist/tools/lib/ctx-ops.d.ts +23 -23
  634. package/dist/tools/lib/ctx-ops.js +13 -10
  635. package/dist/tools/lib/dgidb-client.d.ts +6 -6
  636. package/dist/tools/lib/dgidb-client.js +10 -12
  637. package/dist/tools/lib/disgenet-client.d.ts +4 -4
  638. package/dist/tools/lib/ema-client.d.ts +2 -2
  639. package/dist/tools/lib/ensembl-client.d.ts +4 -4
  640. package/dist/tools/lib/ensembl-client.js +5 -4
  641. package/dist/tools/lib/gwas-catalog-client.d.ts +4 -4
  642. package/dist/tools/lib/gwas-catalog-client.js +17 -17
  643. package/dist/tools/lib/html-text.d.ts +6 -0
  644. package/dist/tools/lib/html-text.js +9 -0
  645. package/dist/tools/lib/identifier-resolver.d.ts +4 -4
  646. package/dist/tools/lib/identifier-resolver.js +7 -3
  647. package/dist/tools/lib/impc-client.d.ts +8 -8
  648. package/dist/tools/lib/impc-client.js +46 -35
  649. package/dist/tools/lib/iuphar-client.d.ts +2 -2
  650. package/dist/tools/lib/iuphar-client.js +7 -16
  651. package/dist/tools/lib/monarch-client.d.ts +4 -4
  652. package/dist/tools/lib/openfda-client.d.ts +22 -22
  653. package/dist/tools/lib/openfda-client.js +23 -22
  654. package/dist/tools/lib/opentargets-client.d.ts +12 -12
  655. package/dist/tools/lib/pathway-client.d.ts +4 -4
  656. package/dist/tools/lib/pathway-client.js +15 -19
  657. package/dist/tools/lib/pharmgkb-client.d.ts +2 -2
  658. package/dist/tools/lib/pharmgkb-client.js +1 -1
  659. package/dist/tools/lib/protein-family-modality.d.ts +2 -2
  660. package/dist/tools/lib/protein-family-modality.js +0 -2
  661. package/dist/tools/lib/protein-family-normalize.js +7 -0
  662. package/dist/tools/lib/pubchem-client.d.ts +2 -2
  663. package/dist/tools/lib/pubchem-client.js +1 -0
  664. package/dist/tools/lib/pubchem-ops.d.ts +4 -4
  665. package/dist/tools/lib/pubchem-ops.js +8 -0
  666. package/dist/tools/lib/pubmed-client.d.ts +9 -9
  667. package/dist/tools/lib/pubmed-client.js +1 -1
  668. package/dist/tools/lib/string-client.d.ts +6 -6
  669. package/dist/tools/lib/uniprot-client.d.ts +8 -8
  670. package/dist/tools/lib/uniprot-client.js +5 -1
  671. package/dist/tools/memory/update-working-memory.d.ts +16 -13
  672. package/dist/tools/memory/update-working-memory.js +21 -3
  673. package/dist/tools/read-tool-output.js +8 -2
  674. package/dist/tools/registry.d.ts +2 -2
  675. package/dist/tools/report-authoring/authoring-tools.d.ts +54 -23
  676. package/dist/tools/report-authoring/authoring-tools.js +128 -62
  677. package/dist/tools/report-session/derive-table.d.ts +19 -59
  678. package/dist/tools/report-session/derive-table.js +120 -122
  679. package/dist/tools/report-session/examine-page.d.ts +6 -6
  680. package/dist/tools/report-session/examine-page.js +14 -12
  681. package/dist/tools/report-session/list-artifacts.d.ts +6 -6
  682. package/dist/tools/report-session/list-artifacts.js +5 -5
  683. package/dist/tools/report-session/page-faults.d.ts +6 -6
  684. package/dist/tools/report-session/page-faults.js +3 -1
  685. package/dist/tools/report-session/preview-report.d.ts +4 -3
  686. package/dist/tools/report-session/preview-report.js +26 -7
  687. package/dist/tools/report-session/record-version.d.ts +9 -4
  688. package/dist/tools/report-session/record-version.js +16 -9
  689. package/dist/tools/report-session/session-page-publisher.d.ts +6 -6
  690. package/dist/tools/research/generate-analogy-report.d.ts +14 -7
  691. package/dist/tools/research/generate-analogy-report.js +80 -76
  692. package/dist/tools/research/generate-plan.d.ts +16 -16
  693. package/dist/tools/research/generate-plan.js +410 -374
  694. package/dist/tools/research/guarded-address.js +3 -2
  695. package/dist/tools/research/inspect-data-profile.d.ts +27 -20
  696. package/dist/tools/research/inspect-data-profile.js +26 -25
  697. package/dist/tools/research/inspect-run.d.ts +54 -27
  698. package/dist/tools/research/inspect-run.js +50 -40
  699. package/dist/tools/research/literature-reviewer.d.ts +8 -7
  700. package/dist/tools/research/literature-reviewer.js +29 -28
  701. package/dist/tools/research/search-arxiv.d.ts +1 -1
  702. package/dist/tools/research/search-arxiv.js +1 -1
  703. package/dist/tools/research/search-github-repos.d.ts +10 -7
  704. package/dist/tools/research/search-github-repos.js +25 -22
  705. package/dist/tools/research/search-semantic-scholar.js +1 -1
  706. package/dist/tools/research/searxng-engine.d.ts +2 -2
  707. package/dist/tools/research/searxng-engine.js +6 -4
  708. package/dist/tools/research/web-fetch.d.ts +24 -21
  709. package/dist/tools/research/web-fetch.js +65 -74
  710. package/dist/tools/research/web-search.d.ts +26 -17
  711. package/dist/tools/research/web-search.js +26 -21
  712. package/dist/tools/sandbox/link-packages.d.ts +11 -7
  713. package/dist/tools/sandbox/link-packages.js +11 -8
  714. package/dist/tools/sandbox/list-available-packages.d.ts +17 -8
  715. package/dist/tools/sandbox/list-available-packages.js +31 -25
  716. package/dist/tools/sandbox/list-available-refs.d.ts +17 -14
  717. package/dist/tools/sandbox/list-available-refs.js +61 -36
  718. package/dist/tools/sandbox/report-blocker.d.ts +30 -37
  719. package/dist/tools/sandbox/report-blocker.js +23 -73
  720. package/dist/tools/sandbox/skills.d.ts +16 -12
  721. package/dist/tools/sandbox/skills.js +16 -12
  722. package/dist/tools/sandbox/submit-file-metadata.d.ts +12 -9
  723. package/dist/tools/sandbox/submit-file-metadata.js +18 -21
  724. package/dist/tools/start-report-session.d.ts +13 -5
  725. package/dist/tools/start-report-session.js +35 -8
  726. package/dist/tools/terminal-text.d.ts +5 -2
  727. package/dist/tools/terminal-text.js +35 -3
  728. package/dist/tools/workspace/decision-record.d.ts +4 -4
  729. package/dist/tools/workspace/decision-record.js +23 -13
  730. package/dist/tools/workspace/edit-file.d.ts +59 -20
  731. package/dist/tools/workspace/edit-file.js +81 -16
  732. package/dist/tools/workspace/execute-command.d.ts +15 -13
  733. package/dist/tools/workspace/execute-command.js +11 -9
  734. package/dist/tools/workspace/file-stat.d.ts +6 -3
  735. package/dist/tools/workspace/grep.d.ts +10 -7
  736. package/dist/tools/workspace/grep.js +9 -3
  737. package/dist/tools/workspace/list-files.d.ts +6 -3
  738. package/dist/tools/workspace/mutator.d.ts +28 -15
  739. package/dist/tools/workspace/mutator.js +107 -53
  740. package/dist/tools/workspace/read-file.d.ts +8 -5
  741. package/dist/tools/workspace/result-bounds.d.ts +5 -5
  742. package/dist/tools/workspace/result-bounds.js +4 -2
  743. package/dist/tools/workspace/run-exec.d.ts +2 -2
  744. package/dist/tools/workspace/run-exec.js +3 -3
  745. package/dist/tools/workspace/scan-inputs.d.ts +8 -5
  746. package/dist/tools/workspace/scan-inputs.js +17 -5
  747. package/dist/tools/workspace/show-file.d.ts +1 -1
  748. package/dist/tools/workspace/show-file.js +2 -1
  749. package/dist/tools/workspace/show-plan.d.ts +8 -5
  750. package/dist/tools/workspace/show-plan.js +9 -8
  751. package/dist/tools/workspace/workspace-search.d.ts +41 -13
  752. package/dist/tools/workspace/workspace-search.js +27 -14
  753. package/dist/tools/workspace/write-file.d.ts +9 -7
  754. package/dist/workflows/execute-analysis-scheduler.d.ts +9 -9
  755. package/dist/workflows/execute-analysis-scheduler.js +6 -3
  756. package/dist/workflows/execute-analysis.d.ts +46 -62
  757. package/dist/workflows/execute-analysis.js +137 -219
  758. package/dist/workflows/pause.d.ts +71 -0
  759. package/dist/workflows/pause.js +173 -0
  760. package/dist/workflows/sandbox-step.d.ts +38 -61
  761. package/dist/workflows/sandbox-step.js +99 -106
  762. package/dist/workflows/test/sql-writes.d.ts +21 -0
  763. package/dist/workflows/test/sql-writes.js +36 -0
  764. package/dist/workspace/filesystem.d.ts +6 -6
  765. package/dist/workspace/filesystem.js +10 -8
  766. package/dist/workspace/paths.d.ts +1 -1
  767. package/dist/workspace/paths.js +15 -4
  768. package/dist/workspace/search-config.d.ts +2 -2
  769. package/dist/workspace/search-config.js +1 -1
  770. package/package.json +21 -22
  771. package/dist/loop/call-guard.d.ts +0 -50
  772. package/dist/loop/call-guard.js +0 -90
  773. package/dist/loop/continue-agent.d.ts +0 -40
  774. package/dist/loop/continue-agent.js +0 -38
  775. package/dist/loop/genai-spans.d.ts +0 -47
  776. package/dist/loop/genai-spans.js +0 -134
  777. package/dist/loop/run-agent.d.ts +0 -245
  778. package/dist/loop/run-agent.js +0 -1124
  779. package/dist/loop/run-step.d.ts +0 -29
  780. package/dist/loop/run-step.js +0 -34
  781. package/dist/loop/run-to-terminal.d.ts +0 -66
  782. package/dist/loop/run-to-terminal.js +0 -93
  783. package/dist/loop/tool-mask.d.ts +0 -23
  784. package/dist/loop/tool-mask.js +0 -46
  785. package/dist/providers/streaming-chat.d.ts +0 -32
  786. package/dist/providers/streaming-chat.js +0 -91
  787. package/dist/tasks/derive-table-exec.d.ts +0 -54
  788. package/dist/tasks/derive-table-exec.js +0 -86
  789. package/dist/workflows/suspension.d.ts +0 -32
  790. package/dist/workflows/suspension.js +0 -38
@@ -7,8 +7,23 @@
7
7
  * They live apart from the reader, thus a test drives them directly instead of
8
8
  * through a subscription.
9
9
  */
10
+ import { setTimeout as sleep } from "node:timers/promises";
10
11
  import { reconcileKey } from "../contracts/chat-frame.js";
11
12
  import { PART_REGISTRY } from "../contracts/part-registry.js";
13
+ import { parseUnknownRecord } from "../lib/unknown-containers.js";
14
+ /**
15
+ * The registry is keyed by the discriminant alone, so this validates `type` and
16
+ * trusts the producer for the payload. The part schemas in `contracts/schemas/`
17
+ * are for a consumer at the edge of the package, which parses what it receives.
18
+ * Both ends of this stream are typed against the same union inside this package,
19
+ * so the discriminant is the boundary that can drift (a producer that emits
20
+ * something else entirely), and a part that fails its schema still reaches the
21
+ * consumer for its own check.
22
+ */
23
+ function isChatPartRecord(record) {
24
+ const { type } = record;
25
+ return typeof type === "string" && Object.hasOwn(PART_REGISTRY, type);
26
+ }
12
27
  /**
13
28
  * Narrow one raw stream value to a chat data part, or `null` when it is not one.
14
29
  *
@@ -18,24 +33,12 @@ import { PART_REGISTRY } from "../contracts/part-registry.js";
18
33
  * contract is the `ChatPart` union, so anything the registry does not
19
34
  * classify is not deliverable — which also covers a part written by a producer
20
35
  * newer than the reader.
21
- *
22
- * The registry is keyed by the discriminant alone, so this validates `type` and
23
- * trusts the producer for the payload. The part schemas in `contracts/schemas/`
24
- * are for a consumer at the edge of the package, which parses what it receives.
25
- * Both ends of this stream are typed against the same union inside this package,
26
- * so the discriminant is the boundary that can drift (a producer that emits
27
- * something else entirely), and a part that fails its schema still reaches the
28
- * consumer for its own check.
29
36
  */
30
37
  export function parseRunEventPart(value) {
31
- if (typeof value !== "object" || value === null)
32
- return null;
33
- const type = value.type;
34
- if (typeof type !== "string")
38
+ const record = parseUnknownRecord(value);
39
+ if (record === undefined || !isChatPartRecord(record))
35
40
  return null;
36
- if (!Object.hasOwn(PART_REGISTRY, type))
37
- return null;
38
- return value;
41
+ return record;
39
42
  }
40
43
  /**
41
44
  * Collapse a batch of parts so each reconciling id appears once, carrying its
@@ -78,10 +81,12 @@ export function foldRunEventParts(parts) {
78
81
  export async function pipeFoldedRunEvents(entries, emit, flushMs) {
79
82
  const latestByKey = new Map();
80
83
  const pendingKeys = new Set();
81
- let flushTimer = null;
84
+ // The gate of the one armed flush wait: present while a window is open, so a
85
+ // second entry in the window reuses it instead of arming a second flush.
86
+ let flushGate;
82
87
  let flushChain = Promise.resolve();
83
88
  const flushPending = async () => {
84
- flushTimer = null;
89
+ flushGate = undefined;
85
90
  const keys = [...pendingKeys];
86
91
  pendingKeys.clear();
87
92
  for (const key of keys) {
@@ -91,14 +96,15 @@ export async function pipeFoldedRunEvents(entries, emit, flushMs) {
91
96
  }
92
97
  };
93
98
  const scheduleFlush = () => {
94
- if (flushTimer !== null)
99
+ if (flushGate !== undefined)
95
100
  return;
96
- flushTimer = setTimeout(() => {
101
+ flushGate = new AbortController();
102
+ sleep(flushMs, undefined, { signal: flushGate.signal }).then(() => {
97
103
  // A timed flush has no caller to report to. A lasting emit failure
98
104
  // still reaches the caller, through the next direct emit or the
99
105
  // final flush.
100
106
  flushChain = flushChain.then(flushPending).catch(() => undefined);
101
- }, flushMs);
107
+ }, () => undefined);
102
108
  };
103
109
  try {
104
110
  for await (const entry of entries) {
@@ -114,10 +120,9 @@ export async function pipeFoldedRunEvents(entries, emit, flushMs) {
114
120
  }
115
121
  }
116
122
  finally {
117
- if (flushTimer !== null) {
118
- clearTimeout(flushTimer);
119
- flushTimer = null;
120
- }
123
+ // The abort ends the armed wait, whose rejection the second arm swallows,
124
+ // so the teardown does not wait out the window.
125
+ flushGate?.abort();
121
126
  await flushChain;
122
127
  if (pendingKeys.size > 0)
123
128
  await flushPending();
@@ -37,17 +37,17 @@ import { type DbError } from "../lib/db-result.js";
37
37
  import type { Logger } from "../lib/logger.js";
38
38
  import type { RunStatus } from "../state/schema.js";
39
39
  /** The part of a run row that the terminal part is made from. */
40
- export interface RunEventRunRead {
40
+ export type RunEventRunRead = {
41
41
  readonly status: RunStatus;
42
42
  readonly error: string | null;
43
- }
43
+ };
44
44
  /**
45
45
  * Construction-time dependencies. The pool is the application pool the run
46
46
  * ledger lives in; the logger is where every contained failure is reported, and
47
47
  * defaults to silence so an embedder that wired none sees nothing rather than
48
48
  * having console forced on it.
49
49
  */
50
- export interface RunEventStreamDeps {
50
+ export type RunEventStreamDeps = {
51
51
  readonly pool: Pool;
52
52
  readonly logger?: Logger;
53
53
  /** Reads the status and the error of the run row, `null` when no row exists. Defaults to `queryRun` on `pool`. */
@@ -59,7 +59,7 @@ export interface RunEventStreamDeps {
59
59
  readonly readWorkflowStatus?: (runId: string) => Promise<string | null>;
60
60
  /** The wait between two reads of the run row. Defaults to a timer. */
61
61
  readonly sleep?: (ms: number) => Promise<void>;
62
- }
62
+ };
63
63
  /**
64
64
  * Receives one part. May be async — the subscription awaits it, so a handler is
65
65
  * never invoked concurrently with itself and back-pressure is the caller's to
@@ -67,20 +67,20 @@ export interface RunEventStreamDeps {
67
67
  */
68
68
  export type RunEventPartHandler = (part: ChatPart) => void | Promise<void>;
69
69
  /** Call-time parameters of one subscription. */
70
- export interface RunEventSubscribeOptions {
70
+ export type RunEventSubscribeOptions = {
71
71
  /** The run to observe. Also the parent workflow's id. */
72
72
  readonly runId: string;
73
73
  /** Where each delivered part goes. */
74
74
  readonly onPart: RunEventPartHandler;
75
75
  /** Aborting stops delivery and settles the returned promise. */
76
76
  readonly signal: AbortSignal;
77
- }
77
+ };
78
78
  /**
79
79
  * The run-event read seam. One method, because a run-scoped subscription is the
80
80
  * whole capability: a general-purpose stream reader would leak the engine's model
81
81
  * back into the surface this exists to quarantine.
82
82
  */
83
- export interface RunEventStream {
83
+ export type RunEventStream = {
84
84
  /**
85
85
  * Deliver every part the run produces — parent and children alike — to
86
86
  * `onPart`, resolving when the run is terminal, every stream opened has
@@ -103,7 +103,7 @@ export interface RunEventStream {
103
103
  * `runId`/`stepId` and the reconciling fold is per id.
104
104
  */
105
105
  subscribe(options: RunEventSubscribeOptions): Promise<void>;
106
- }
106
+ };
107
107
  /**
108
108
  * Build the DBOS-backed realization of {@link RunEventStream}.
109
109
  *
@@ -43,10 +43,6 @@ function partOfRow(runId, row) {
43
43
  switch (row.status) {
44
44
  case "canceled":
45
45
  return canceledPart(runId);
46
- case "suspended_insufficient_funds":
47
- return row.error === null
48
- ? { type: "data-run-failed", runId, error: "Run suspended" }
49
- : { type: "data-run-failed", runId, error: row.error, reason: row.error };
50
46
  case "failed":
51
47
  return { type: "data-run-failed", runId, error: row.error ?? "Run failed" };
52
48
  case "completed":
@@ -138,6 +134,7 @@ export function createRunEventStream(deps) {
138
134
  while (pending.length > 0 && !signal.aborted) {
139
135
  const batch = pending.splice(0, pending.length);
140
136
  for (const part of foldRunEventParts(batch)) {
137
+ // oxlint-disable-next-line no-unnecessary-condition -- tsgolint cannot see the event wiring that aborts the signal; the re-check after each part is live (cancel stops delivery).
141
138
  if (signal.aborted)
142
139
  return;
143
140
  try {
@@ -228,6 +225,7 @@ export function createRunEventStream(deps) {
228
225
  if (signal.aborted)
229
226
  return;
230
227
  await discoverChildren();
228
+ // oxlint-disable-next-line no-unnecessary-condition -- tsgolint cannot see the event-wired abort or the parentRead .finally that sets parentDrained; both checks are live (discovery stops on cancel or a drained parent).
231
229
  if (signal.aborted || parentDrained)
232
230
  return;
233
231
  await Promise.race([sleep(CHILD_DISCOVERY_INTERVAL_MS), aborted, parentRead]);
@@ -289,6 +287,7 @@ export function createRunEventStream(deps) {
289
287
  await discovery;
290
288
  await parentRead;
291
289
  await Promise.all(childReads);
290
+ // oxlint-disable-next-line no-unnecessary-condition -- tsgolint cannot see the readWorkflowStream closure that sets sawTerminal or the event-wired abort; the fallback that mints the missing terminal part is live.
292
291
  if (!sawTerminal && !signal.aborted) {
293
292
  const terminal = await missingTerminalPart();
294
293
  if (terminal !== null)
@@ -10,11 +10,11 @@
10
10
  * reference, typed `(input) => Promise<result>`; the launcher only owns the
11
11
  * start/await/cancel mechanics around it.
12
12
  */
13
- export interface LaunchOptions {
13
+ export type LaunchOptions = {
14
14
  /** Caller-chosen durable workflow id (e.g. the runId). */
15
15
  readonly workflowId: string;
16
- }
17
- export interface RunLauncher {
16
+ };
17
+ export type RunLauncher = {
18
18
  /** Fire-and-forget: resolves once the run is durably started. */
19
19
  launch<I>(workflow: (input: I) => Promise<unknown>, opts: LaunchOptions, input: I): Promise<void>;
20
- }
20
+ };
@@ -1,18 +1,16 @@
1
1
  /**
2
- * Run synthesizer — a single-shot agent loop driven through `runAgent`:
2
+ * Run synthesizer — a single-shot agent loop driven through `runWithSalvage`:
3
3
  *
4
- * - `validate_synthesis` — non-terminal: dry-run schema + semantic validation
5
- * of a candidate in any shape. Never records.
6
- * - `submit_synthesis` — terminal: schema + semantic validation, captures
7
- * the outcome. Re-callable; a later valid submission
8
- * supersedes an earlier outcome (last-valid-wins).
9
- * - `report_blocker` — terminal: the run produced nothing synthesizable.
10
- * Only records when no outcome exists yet, so a
11
- * blocker can never clobber a real synthesis.
12
- * - `literature_reviewer` — research sub-agent exposed as a tool. The tool
13
- * re-uses `createLiteratureReviewerTool`; the
14
- * sub-agent loop's brief is the only context handed
15
- * across the boundary (forSubAgent semantics).
4
+ * - `submit_synthesis` — checks one synthesis against the schema and the
5
+ * semantic checks, and gives back the issues. It
6
+ * does not end the run. The last accepted
7
+ * submission is the synthesis.
8
+ * - `report_blocker` — the run produced nothing synthesizable. An
9
+ * accepted synthesis wins over a blocker.
10
+ * - `literature_reviewer` — research sub-agent exposed as a tool. The
11
+ * runtime registers it one time and gives it here;
12
+ * the sub-agent loop's brief is the only context
13
+ * handed across the boundary (forSubAgent semantics).
16
14
  *
17
15
  * Two deliverables on a happy path: `synthesis.json` written to the run dir
18
16
  * and a `data-run-synthesis` chat data part emitted via the `emit` callback
@@ -23,17 +21,16 @@
23
21
  * resolves with `{ kind: "failed" }`, the wrapper emits a synthesis-progress
24
22
  * `failed` part. We do not throw here for routine submitter rejections.
25
23
  */
26
- import { type RunSynthesis } from "../schemas/run-synthesis.js";
24
+ import { type RunSynthesis, type SynthesisDraft } from "../schemas/run-synthesis.js";
27
25
  import type { RunSynthesisPart } from "../contracts/chat-parts.js";
28
26
  import type { StepSummary } from "../schemas/step-summary.js";
27
+ import { type LoopOptions, type LoopStep } from "../loop/run-loop.js";
29
28
  import type { ToolOutputStore } from "../loop/tool-output.js";
30
29
  import type { ChatDataPart, EmitFn } from "../loop/types.js";
31
30
  import type { ChatProvider } from "../providers/types.js";
32
31
  import type { UsageRecorder } from "../billing/usage-recorder.js";
33
32
  import type { RunSession } from "../auth/types.js";
34
33
  import { type Tool } from "../tools/define-tool.js";
35
- import type { BioToolKeys } from "../tools/bio/keys.js";
36
- import type { CitationResolver } from "../citations/types.js";
37
34
  /**
38
35
  * The synthesizer's agent identity — the `source.agentId` on its loop events
39
36
  * and the `agent_id` of the run-phase `synthesis` row `executeAnalysis` writes
@@ -41,38 +38,41 @@ import type { CitationResolver } from "../citations/types.js";
41
38
  * events can never disagree about who did the work.
42
39
  */
43
40
  export declare const SYNTHESIS_AGENT_ID = "run-synthesizer";
44
- type SynthesizerOutcome = {
45
- kind: "submitted";
46
- synthesis: RunSynthesis;
41
+ export type ValidationIssue = {
42
+ readonly path: string;
43
+ readonly code: "schema" | "semantic";
44
+ readonly message: string;
45
+ readonly hint?: string;
46
+ };
47
+ export type SubmitSynthesisOutput = {
48
+ accepted: true;
47
49
  } | {
48
- kind: "blocker";
49
- reason: string;
50
+ accepted: false;
51
+ issues: ValidationIssue[];
50
52
  };
51
- interface OutcomeHolder {
52
- outcome: SynthesizerOutcome | null;
53
- }
53
+ /** The last accepted synthesis of a run, from the inputs of the calls of `submit_synthesis` that it accepted. */
54
+ export declare function acceptedSynthesisOf(steps: readonly LoopStep[]): SynthesisDraft | undefined;
54
55
  /**
55
56
  * Test-only — expose the inner-tool factory so unit tests can assert on
56
- * validation + outcome capture without driving the whole agent loop.
57
+ * the checks without driving the whole agent loop.
57
58
  */
58
59
  export declare function __buildInnerToolsForTest(args: {
59
60
  knownStepIds: ReadonlySet<string>;
60
- runId: string;
61
61
  }): {
62
- validate: Tool;
63
- submit: Tool;
64
- blocker: Tool;
65
- holder: OutcomeHolder;
62
+ submit: Tool<{
63
+ synthesis: SynthesisDraft;
64
+ }, SubmitSynthesisOutput>;
65
+ blocker: Tool<{
66
+ reason: string;
67
+ }>;
66
68
  };
67
- export interface GenerateRunSynthesisInput {
69
+ export type GenerateRunSynthesisInput = {
68
70
  readonly provider: ChatProvider;
69
71
  readonly session: RunSession;
70
72
  readonly model: string;
71
- /** API keys for the bio/chem tools the embedded literature reviewer uses. */
72
- readonly bioKeys: BioToolKeys;
73
- /** Shared resolver used by the embedded literature reviewer. */
74
- readonly citationResolver: CitationResolver;
75
- /** LLM usage-accounting seam for the synthesizer + reviewer loops; omitted falls back to the no-op recorder. */
73
+ /** The `literature_reviewer` tool of the synthesizer (`createLiteratureReviewerTool`). */
74
+ readonly literatureReviewer: Tool;
75
+ /** LLM usage-accounting seam for the synthesizer loop; omitted falls back to the no-op recorder. */
76
76
  readonly usageRecorder?: UsageRecorder;
77
77
  /** The store of the synthesizer and reviewer loops and of their read tools. */
78
78
  readonly toolOutputStore?: ToolOutputStore;
@@ -80,13 +80,15 @@ export interface GenerateRunSynthesisInput {
80
80
  readonly summaries: readonly StepSummary[];
81
81
  /** Plan analytical narrative for context. */
82
82
  readonly planNarrative: string;
83
- /** Run id — submitted synthesis must match. */
83
+ /** Run id — the host stamps it on the accepted synthesis. */
84
84
  readonly runId: string;
85
85
  /** Optional cancellation. */
86
86
  readonly signal?: AbortSignal;
87
87
  /** Optional UI event sink (chat data parts forwarded to the parent stream). */
88
88
  readonly emit?: EmitFn;
89
- }
89
+ /** The pause of the run. The body of the run gives it, thus a failed request waits in place. */
90
+ readonly pause?: LoopOptions["pause"];
91
+ };
90
92
  export type GenerateRunSynthesisResult = {
91
93
  kind: "synthesis";
92
94
  synthesis: RunSynthesis;
@@ -95,36 +97,36 @@ export type GenerateRunSynthesisResult = {
95
97
  reason: string;
96
98
  };
97
99
  /**
98
- * Drive the synthesizer agent loop to a terminal outcome — either a
99
- * validated synthesis (`submit_synthesis`) or a blocker (`report_blocker`).
100
- * Throws when neither terminal is reached (loop cap or external abort).
100
+ * Drive the synthesizer agent loop to an outcome — the last accepted
101
+ * synthesis (`submit_synthesis`), else a blocker (`report_blocker`).
102
+ * Throws when the run and its salvage end with neither (loop cap or external abort).
101
103
  */
102
104
  export declare function generateRunSynthesis(input: GenerateRunSynthesisInput): Promise<GenerateRunSynthesisResult>;
103
- export interface LoadStepSummariesInput {
105
+ export type LoadStepSummariesInput = {
104
106
  /** Absolute host root of the analysis's workspace tree. */
105
107
  readonly workspaceRoot: string;
106
108
  readonly runId: string;
107
109
  readonly completedSteps: readonly string[];
108
110
  readonly agentByStepId?: Readonly<Record<string, string>>;
109
- }
111
+ };
110
112
  /**
111
113
  * Read each completed step's `output/summary.md`. Steps with missing or empty
112
114
  * summaries are silently dropped — the caller decides what to do when the
113
115
  * resulting array is empty.
114
116
  */
115
117
  export declare function loadStepSummariesFromDisk(args: LoadStepSummariesInput): Promise<StepSummary[]>;
116
- export interface PersistSynthesisInput {
118
+ export type PersistSynthesisInput = {
117
119
  /** Absolute host root of the analysis's workspace tree. */
118
120
  readonly workspaceRoot: string;
119
121
  readonly runId: string;
120
122
  readonly synthesis: RunSynthesis;
121
- }
123
+ };
122
124
  export declare function persistSynthesis(args: PersistSynthesisInput): Promise<string>;
123
- export interface ReadSynthesisInput {
125
+ export type ReadSynthesisInput = {
124
126
  /** Absolute host root of the analysis's workspace tree. */
125
127
  readonly workspaceRoot: string;
126
128
  readonly runId: string;
127
- }
129
+ };
128
130
  /**
129
131
  * Read the text of a synthesis record under the cap, or give `undefined` when the bytes do not come back.
130
132
  *
@@ -147,4 +149,3 @@ export declare function formatSynthesisEmbeddingText(synthesis: RunSynthesis): s
147
149
  * `RunSynthesisPart` interface — keep them in lockstep.
148
150
  */
149
151
  export declare function buildRunSynthesisPart(runId: string, synthesis: RunSynthesis): ChatDataPart;
150
- export {};