@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
@@ -8,6 +8,7 @@
8
8
  * Approval: data-ask (a tool's pending user-approval prompt),
9
9
  * data-plan-approval (the record of an approved plan)
10
10
  * Compaction: data-compaction (a compaction of the conversation thread)
11
+ * Model retry: data-model-retry (a retry of a model request inside the retry envelope of the provider)
11
12
  * Run lifecycle: run-started, dag-state, run-completed, run-failed, run-synthesis,
12
13
  * synthesis-progress
13
14
  * Per-step live: step-activity, step-file-tree
@@ -16,7 +17,7 @@
16
17
  */
17
18
  import type { ToolCallOutcome } from "./chat-events.js";
18
19
  import type { TokenUsageRollup } from "./usage.js";
19
- export interface PlanStep {
20
+ export type PlanStep = {
20
21
  id: string;
21
22
  name: string;
22
23
  agent: string;
@@ -35,7 +36,7 @@ export interface PlanStep {
35
36
  acceptance_criteria?: string[];
36
37
  constraints?: string[];
37
38
  caveats?: string[];
38
- }
39
+ };
39
40
  export type PresentationContent =
40
41
  /** `dataPath` (optional): an analysis-rooted CSV artifact path the host loads and injects as the
41
42
  * chart's `dataset.source` at render time — the data never rides through the context window. */
@@ -71,13 +72,13 @@ export type PresentationContent =
71
72
  accession: string;
72
73
  version: number;
73
74
  };
74
- export interface PresentationPart {
75
+ export type PresentationPart = {
75
76
  type: "data-presentation";
76
77
  id: string;
77
78
  title?: string;
78
79
  content: PresentationContent;
79
- }
80
- export interface PlanPart {
80
+ };
81
+ export type PlanPart = {
81
82
  type: "data-plan";
82
83
  id: string;
83
84
  planId: string;
@@ -88,40 +89,40 @@ export interface PlanPart {
88
89
  analytical_narrative?: string;
89
90
  omicsType?: string;
90
91
  omicsSubtype?: string;
91
- }
92
- export interface RunCardPart {
92
+ };
93
+ export type RunCardPart = {
93
94
  type: "data-run-card";
94
95
  id: string;
95
96
  runId: string;
96
97
  planId: string;
97
98
  title: string;
98
99
  stepCount: number;
99
- }
100
- export interface PlanApprovalPart {
100
+ };
101
+ export type PlanApprovalPart = {
101
102
  type: "data-plan-approval";
102
103
  planId: string;
103
104
  /** The run that the approval started. */
104
105
  runId: string;
105
106
  /** ISO 8601. The instant of the approval, equal to the time of the `approve-plan` provenance event. */
106
107
  approvedAt: string;
107
- }
108
- export interface FileReferenceEntry {
108
+ };
109
+ export type FileReferenceEntry = {
109
110
  path: string;
110
111
  runId?: string;
111
112
  caption?: string;
112
- }
113
- export interface FileReferencePart {
113
+ };
114
+ export type FileReferencePart = {
114
115
  type: "data-file-reference";
115
116
  id: string;
116
117
  title?: string;
117
118
  files: FileReferenceEntry[];
118
- }
119
+ };
119
120
  /**
120
121
  * A tool's pending request for an explicit user decision. Re-emitted under the
121
122
  * same `id` when the ask reaches a terminal status, so reconciling readers fold
122
123
  * pending → outcome latest-wins.
123
124
  */
124
- export interface AskPart {
125
+ export type AskPart = {
125
126
  type: "data-ask";
126
127
  /** The ask's ledger uuidv7 id — what a surface passes back to `answer`. */
127
128
  id: string;
@@ -134,19 +135,19 @@ export interface AskPart {
134
135
  status: "pending" | "resolved" | "rejected" | "aborted" | "expired";
135
136
  /** The kind of the ledger reply. Only a `resolved` or `rejected` part carries it, and never the rejection feedback. */
136
137
  reply?: "once" | "always" | "reject";
137
- }
138
- export interface RunStartedPart {
138
+ };
139
+ export type RunStartedPart = {
139
140
  type: "data-run-started";
140
141
  runId: string;
141
142
  planSummary: string;
142
143
  stepCount: number;
143
- }
144
+ };
144
145
  /** `"pending"` = waiting on dependencies; `"queued"` = dependencies satisfied,
145
146
  * held until in-flight steps free machine-budget capacity; `"skipped"` =
146
147
  * unreachable — an upstream dependency failed or blocked, so the step can
147
148
  * never be dispatched. */
148
149
  export type StepStatus = "pending" | "queued" | "running" | "completed" | "failed" | "skipped";
149
- export interface DagStepState {
150
+ export type DagStepState = {
150
151
  id: string;
151
152
  name: string;
152
153
  agent: string;
@@ -166,16 +167,16 @@ export interface DagStepState {
166
167
  summary?: string;
167
168
  /** Error message (set on failure). */
168
169
  error?: string;
169
- }
170
+ };
170
171
  /** One step of the stored plan graph: the fields of {@link DagStepState} that the plan alone fixes. */
171
172
  export type PlanGraphStep = Pick<DagStepState, "id" | "name" | "agent" | "dependsOn" | "level">;
172
- export interface DagStatePart {
173
+ export type DagStatePart = {
173
174
  type: "data-dag-state";
174
175
  /** Stable ID for reconciliation — same across all updates for a run. */
175
176
  id: string;
176
177
  runId: string;
177
178
  steps: DagStepState[];
178
- }
179
+ };
179
180
  export type StepPhase = "sandbox-init" | "executing" | "generating-metadata" | "generating-summary" | "indexing"
180
181
  /** Step bytes are uploading to the artifact store inline (per-step sync). */
181
182
  | "persisting" | "complete" | "failed"
@@ -183,7 +184,7 @@ export type StepPhase = "sandbox-init" | "executing" | "generating-metadata" | "
183
184
  | "retrying"
184
185
  /** Non-fatal warning emitted during step execution (e.g., maxSteps hit). */
185
186
  | "warning";
186
- export interface StepActivityPart {
187
+ export type StepActivityPart = {
187
188
  type: "data-step-activity";
188
189
  /** Stable ID for reconciliation — unique per step within a run. */
189
190
  id: string;
@@ -195,12 +196,12 @@ export interface StepActivityPart {
195
196
  activity: string;
196
197
  /** ISO 8601 time of the emission. Absent on a part that an older harness wrote. */
197
198
  at?: string;
198
- }
199
+ };
199
200
  /**
200
201
  * One activity emission of a step or a data profile, kept in the run stream with no reconciliation. The fold
201
202
  * delivers each entry in write order.
202
203
  */
203
- export interface ActivityEntryPart {
204
+ export type ActivityEntryPart = {
204
205
  type: "data-activity-entry";
205
206
  /** Unique per emission within a stream. */
206
207
  id: string;
@@ -211,13 +212,13 @@ export interface ActivityEntryPart {
211
212
  activity: string;
212
213
  /** ISO 8601 time of the emission. */
213
214
  at: string;
214
- }
215
- export interface FileTreeEntry {
215
+ };
216
+ export type FileTreeEntry = {
216
217
  path: string;
217
218
  size?: number;
218
219
  type: "file" | "directory";
219
- }
220
- export interface StepFileTreePart {
220
+ };
221
+ export type StepFileTreePart = {
221
222
  type: "data-step-file-tree";
222
223
  /** Stable ID for reconciliation — unique per step within a run. */
223
224
  id: string;
@@ -225,16 +226,16 @@ export interface StepFileTreePart {
225
226
  stepId: string;
226
227
  /** Current file tree snapshot. May be empty if sandbox hasn't written to disk yet. */
227
228
  files: FileTreeEntry[];
228
- }
229
- export interface StepOutputFile {
229
+ };
230
+ export type StepOutputFile = {
230
231
  path: string;
231
232
  size: number;
232
233
  /** File category for grouping/icons. */
233
234
  fileType: "script" | "output" | "figure" | "log" | "notebook" | "summary";
234
235
  /** LLM-generated description of the file contents. */
235
236
  description: string;
236
- }
237
- export interface StepOutputPart {
237
+ };
238
+ export type StepOutputPart = {
238
239
  type: "data-step-output";
239
240
  id: string;
240
241
  runId: string;
@@ -247,9 +248,9 @@ export interface StepOutputPart {
247
248
  finishReason?: string;
248
249
  /** True when the agent exhausted its maxSteps turn budget. */
249
250
  hitMaxSteps?: boolean;
250
- }
251
+ };
251
252
  /** Step summary — free-form markdown body, rendered verbatim by the UI. */
252
- export interface StepSummaryPart {
253
+ export type StepSummaryPart = {
253
254
  type: "data-step-summary";
254
255
  id: string;
255
256
  runId: string;
@@ -257,7 +258,7 @@ export interface StepSummaryPart {
257
258
  agentId: string;
258
259
  /** Free-form markdown body. Render with a markdown renderer. */
259
260
  markdown: string;
260
- }
261
+ };
261
262
  /**
262
263
  * What one analysis-run step's agent loop reported spending, emitted when that
263
264
  * loop completes.
@@ -270,7 +271,7 @@ export interface StepSummaryPart {
270
271
  * Scoped to analysis runs. Workflows without step parts (ephemeral runs, data
271
272
  * profiling) reach the ledger through the recorder seam and carry no usage part.
272
273
  */
273
- export interface StepUsagePart {
274
+ export type StepUsagePart = {
274
275
  type: "data-step-usage";
275
276
  /** Stable ID for reconciliation — unique per step within a run. */
276
277
  id: string;
@@ -286,13 +287,13 @@ export interface StepUsagePart {
286
287
  modelId: string;
287
288
  /** Summed token usage across this step loop's LLM calls. */
288
289
  usage: TokenUsageRollup;
289
- }
290
+ };
290
291
  /**
291
292
  * Emitted when a step agent declares it cannot fulfil its step via
292
293
  * `report_blocker` (see the harness-sandbox-agents spec). A blocked step has no deliverables; the
293
294
  * reason surfaces in the run side panel.
294
295
  */
295
- export interface StepBlockedPart {
296
+ export type StepBlockedPart = {
296
297
  type: "data-step-blocked";
297
298
  id: string;
298
299
  runId: string;
@@ -300,12 +301,12 @@ export interface StepBlockedPart {
300
301
  agentId: string;
301
302
  /** Agent-declared reason the step could not be fulfilled. */
302
303
  reason: string;
303
- }
304
- export interface RunCompletedFinding {
304
+ };
305
+ export type RunCompletedFinding = {
305
306
  title: string;
306
307
  confidence: "high" | "medium" | "low";
307
- }
308
- export interface RunCompletedPart {
308
+ };
309
+ export type RunCompletedPart = {
309
310
  type: "data-run-completed";
310
311
  runId: string;
311
312
  status: "completed" | "partial";
@@ -324,14 +325,14 @@ export interface RunCompletedPart {
324
325
  * Absent when no step reported any, never an all-zero figure.
325
326
  */
326
327
  usage?: TokenUsageRollup;
327
- }
328
- export interface FindingReference {
328
+ };
329
+ export type FindingReference = {
329
330
  pmid: string;
330
331
  citation: string;
331
332
  relevance: string;
332
333
  concordance: "supports" | "contradicts" | "extends" | "contextualizes";
333
- }
334
- export interface SynthesizedFinding {
334
+ };
335
+ export type SynthesizedFinding = {
335
336
  stepId: string;
336
337
  title: string;
337
338
  description: string;
@@ -339,16 +340,16 @@ export interface SynthesizedFinding {
339
340
  noveltyStatus: "novel" | "confirmed" | "partially_confirmed" | "contradicted" | "expected";
340
341
  literatureInterpretation: string;
341
342
  references: FindingReference[];
342
- }
343
- export interface BiologicalTheme {
343
+ };
344
+ export type BiologicalTheme = {
344
345
  name: string;
345
346
  findings: {
346
347
  stepId: string;
347
348
  title: string;
348
349
  }[];
349
350
  narrative: string;
350
- }
351
- export interface RunSynthesisPart {
351
+ };
352
+ export type RunSynthesisPart = {
352
353
  type: "data-run-synthesis";
353
354
  id: string;
354
355
  runId: string;
@@ -362,7 +363,7 @@ export interface RunSynthesisPart {
362
363
  citation: string;
363
364
  description: string;
364
365
  }[];
365
- }
366
+ };
366
367
  export type SynthesisPhase = "starting" | "researching" | "drafting" | "validating" | "refining" | "indexing" | "persisting" | "complete"
367
368
  /**
368
369
  * Synthesizer chose to skip (e.g., technical-only run, summaries with no
@@ -370,7 +371,7 @@ export type SynthesisPhase = "starting" | "researching" | "drafting" | "validati
370
371
  * intentional outcome, not a breakage.
371
372
  */
372
373
  | "skipped" | "failed";
373
- export interface SynthesisProgressPart {
374
+ export type SynthesisProgressPart = {
374
375
  type: "data-synthesis-progress";
375
376
  /** Stable ID for reconciliation — `synthesis-progress-{runId}`. */
376
377
  id: string;
@@ -386,8 +387,8 @@ export interface SynthesisProgressPart {
386
387
  reason?: string;
387
388
  /** Error message — set when phase === "failed". */
388
389
  error?: string;
389
- }
390
- export interface RunFailedPart {
390
+ };
391
+ export type RunFailedPart = {
391
392
  type: "data-run-failed";
392
393
  runId: string;
393
394
  /** Scrubbed error message (no internal details). */
@@ -397,7 +398,7 @@ export interface RunFailedPart {
397
398
  * `canceled` when an external cancel ended the run. Absent for a failure.
398
399
  */
399
400
  reason?: string;
400
- }
401
+ };
401
402
  /**
402
403
  * The record that a turn started a child session. It rides the chat stream
403
404
  * live, and it persists into the turn at the position of the spawn.
@@ -407,7 +408,7 @@ export interface RunFailedPart {
407
408
  * archived state. When the thread of the part is archived or absent, a
408
409
  * consumer renders nothing for it.
409
410
  */
410
- export interface ChildSessionStartedPart {
411
+ export type ChildSessionStartedPart = {
411
412
  type: "data-child-session-started";
412
413
  /** The id of the child thread that the spawn made. */
413
414
  threadId: string;
@@ -418,7 +419,7 @@ export interface ChildSessionStartedPart {
418
419
  * Known values today: `"report"`.
419
420
  */
420
421
  threadType: string;
421
- }
422
+ };
422
423
  /**
423
424
  * The record that a report-session preview rendered the page. It rides the
424
425
  * chat stream live, and it persists into the turn at the position of the
@@ -429,7 +430,7 @@ export interface ChildSessionStartedPart {
429
430
  * the part carries no path, no format, and no URL. A consumer that wants the
430
431
  * page reads those surfaces.
431
432
  */
432
- export interface ReportRenderedPart {
433
+ export type ReportRenderedPart = {
433
434
  type: "data-report-rendered";
434
435
  /** Unique per emission. */
435
436
  id: string;
@@ -437,9 +438,9 @@ export interface ReportRenderedPart {
437
438
  renderedAt: string;
438
439
  /** The title of the rendered document. */
439
440
  title?: string;
440
- }
441
+ };
441
442
  /** One compaction of the thread: `running`, then `done` or `failed` under the same id. A reload shows it as a divider. */
442
- export interface CompactionPart {
443
+ export type CompactionPart = {
443
444
  type: "data-compaction";
444
445
  id: string;
445
446
  status: "running" | "done" | "failed";
@@ -450,9 +451,9 @@ export interface CompactionPart {
450
451
  durationMs?: number;
451
452
  /** Before the user message of a turn, or before a later request. */
452
453
  trigger?: "turn-start" | "mid-turn";
453
- }
454
+ };
454
455
  /** One tool call of a sub-agent. It holds no input, no output, and no text of the sub-agent. */
455
- export interface SubAgentActivityEntry {
456
+ export type SubAgentActivityEntry = {
456
457
  agentId: string;
457
458
  callPath: string[];
458
459
  tool: string;
@@ -464,12 +465,12 @@ export interface SubAgentActivityEntry {
464
465
  endedAt?: string;
465
466
  /** Absent while the call is in flight. A stored entry always has it. */
466
467
  outcome?: ToolCallOutcome;
467
- }
468
+ };
468
469
  /**
469
470
  * The tool calls of the sub-agents below one root tool call. Re-emitted under the same `id` after each change,
470
471
  * so reconciling readers keep the latest list.
471
472
  */
472
- export interface SubAgentActivityPart {
473
+ export type SubAgentActivityPart = {
473
474
  type: "data-subagent-activity";
474
475
  id: string;
475
476
  /** The id of the root tool call. */
@@ -477,5 +478,67 @@ export interface SubAgentActivityPart {
477
478
  entries: SubAgentActivityEntry[];
478
479
  /** The count of calls past the cap of the entries. */
479
480
  dropped: number;
480
- }
481
- export type ChatPart = PresentationPart | PlanPart | RunCardPart | PlanApprovalPart | FileReferencePart | AskPart | RunStartedPart | DagStatePart | StepActivityPart | ActivityEntryPart | SubAgentActivityPart | StepFileTreePart | StepOutputPart | StepSummaryPart | StepUsagePart | StepBlockedPart | RunSynthesisPart | SynthesisProgressPart | RunCompletedPart | RunFailedPart | ChildSessionStartedPart | ReportRenderedPart | CompactionPart;
481
+ };
482
+ /**
483
+ * Why durable work waits: a provider outage that outlived its retries, a refusal of the host with its reason, or a
484
+ * credential that the endpoint refused or that the host did not give.
485
+ */
486
+ export type PauseCause = {
487
+ readonly kind: "outage";
488
+ } | {
489
+ readonly kind: "credential";
490
+ } | {
491
+ readonly kind: "host";
492
+ readonly reason: string;
493
+ };
494
+ /**
495
+ * One retry of a model request inside the retry envelope of the provider, before the wait of that retry. Re-emitted
496
+ * under the same `id` for each retry of the request. A later frame of the same agent ends it: the request then gave
497
+ * a reply, or it failed after the last retry.
498
+ */
499
+ export type ModelRetryPart = {
500
+ type: "data-model-retry";
501
+ /** The id of the model request. */
502
+ id: string;
503
+ /** The number of this retry, from 1. */
504
+ attempt: number;
505
+ /** The count of retries that the envelope makes before it gives up. */
506
+ maxRetries: number;
507
+ /** ISO 8601. The time of the next attempt. */
508
+ retryAt: string;
509
+ /** The HTTP status of the failed attempt. Absent for a failure with no status, for example a lost connection. */
510
+ status?: number;
511
+ };
512
+ /** The kind of a durable work, and of the work that a pause belongs to. A sub-agent belongs to its turn, and a sandbox step to its run. */
513
+ export type WorkKind = "turn" | "run" | "profile";
514
+ /**
515
+ * The state of one waiting workflow of paused work. Re-emitted under the same `id` when the wait ends, with the
516
+ * state `running`, so reconciling readers keep the latest state of each workflow.
517
+ */
518
+ export type PausePart = {
519
+ type: "data-pause";
520
+ /** The id of the workflow that waits. */
521
+ id: string;
522
+ /** The id of the work: the turn, the run, or the profile workflow. A resume names it. */
523
+ workId: string;
524
+ workKind: WorkKind;
525
+ /** `retrying`: the system sends the request again at `retryAt`. `paused`: only a resume ends the wait. */
526
+ state: "retrying" | "paused" | "running";
527
+ /** Absent for the state `running`. */
528
+ cause?: PauseCause;
529
+ /** The count of timer retries before this wait. Absent for the state `running`. */
530
+ attempt?: number;
531
+ /** ISO 8601. Present for the state `retrying` only. */
532
+ retryAt?: string;
533
+ };
534
+ /** The parts whose contracts this version of the package declares — the arms the part registry knows. */
535
+ export type KnownChatPart = PresentationPart | PlanPart | RunCardPart | PlanApprovalPart | FileReferencePart | AskPart | RunStartedPart | DagStatePart | StepActivityPart | ActivityEntryPart | SubAgentActivityPart | StepFileTreePart | StepOutputPart | StepSummaryPart | StepUsagePart | StepBlockedPart | RunSynthesisPart | SynthesisProgressPart | RunCompletedPart | RunFailedPart | ChildSessionStartedPart | ReportRenderedPart | CompactionPart | PausePart | ModelRetryPart;
536
+ /**
537
+ * A part of a known contract, or a part whose type this build does not know. An emitter newer than this
538
+ * build can lead the registry, and such a part already rides through the check boundary and the live view
539
+ * as the record the emitter sent — so the union admits that record shape, with no change to the stored
540
+ * payload or to a known part.
541
+ */
542
+ export type ChatPart = KnownChatPart | ({
543
+ type: `data-${string}`;
544
+ } & Record<string, unknown>);
@@ -8,6 +8,7 @@
8
8
  * Approval: data-ask (a tool's pending user-approval prompt),
9
9
  * data-plan-approval (the record of an approved plan)
10
10
  * Compaction: data-compaction (a compaction of the conversation thread)
11
+ * Model retry: data-model-retry (a retry of a model request inside the retry envelope of the provider)
11
12
  * Run lifecycle: run-started, dag-state, run-completed, run-failed, run-synthesis,
12
13
  * synthesis-progress
13
14
  * Per-step live: step-activity, step-file-tree
@@ -50,8 +50,22 @@ export function reportSessionResourceId(analysisId, threadId) {
50
50
  * @param token - Short-lived content token minted by the storage backend (required)
51
51
  */
52
52
  export function buildReportSessionUrl(contentBaseUrl, analysisId, threadId, pagePath, token) {
53
- const base = contentBaseUrl.replace(/\/+$/, "");
54
- const path = pagePath.replace(/^\/+/, "");
53
+ const base = stripTrailingSlashes(contentBaseUrl);
54
+ const path = stripLeadingSlashes(pagePath);
55
55
  const res = reportSessionResourceId(analysisId, threadId);
56
56
  return `${base}/${res}/${path}?t=${encodeURIComponent(token)}`;
57
57
  }
58
+ /** The text without its trailing slashes. */
59
+ function stripTrailingSlashes(value) {
60
+ let end = value.length;
61
+ while (end > 0 && value.charAt(end - 1) === "/")
62
+ end--;
63
+ return value.slice(0, end);
64
+ }
65
+ /** The text without its leading slashes. */
66
+ function stripLeadingSlashes(value) {
67
+ let start = 0;
68
+ while (start < value.length && value.charAt(start) === "/")
69
+ start++;
70
+ return value.slice(start);
71
+ }