@inflexa-ai/harness 0.1.1 → 0.3.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (330) hide show
  1. package/README.md +48 -0
  2. package/dist/agents/conversation-agent.d.ts +15 -11
  3. package/dist/agents/conversation-agent.js +31 -34
  4. package/dist/agents/report-builder.js +2 -1
  5. package/dist/agents/sandbox/bulk-transcriptomics-agent.js +1 -1
  6. package/dist/agents/sandbox/cheminformatics-agent.js +1 -19
  7. package/dist/agents/sandbox/chromatin-agent.js +1 -10
  8. package/dist/agents/sandbox/dna-methylation-agent.js +1 -10
  9. package/dist/agents/sandbox/drug-repurposing-agent.js +4 -14
  10. package/dist/agents/sandbox/enrichment-agent.js +1 -10
  11. package/dist/agents/sandbox/ephemeral-executor.js +1 -10
  12. package/dist/agents/sandbox/genomic-variant-agent.js +1 -3
  13. package/dist/agents/sandbox/immune-profiling-agent.js +1 -13
  14. package/dist/agents/sandbox/metabolomics-agent.js +1 -1
  15. package/dist/agents/sandbox/microbiome-agent.js +1 -1
  16. package/dist/agents/sandbox/multi-omics-integration-agent.js +1 -12
  17. package/dist/agents/sandbox/multimodal-sc-agent.js +1 -1
  18. package/dist/agents/sandbox/network-agent.js +1 -10
  19. package/dist/agents/sandbox/pkpd-clinical-response-agent.js +2 -8
  20. package/dist/agents/sandbox/proteomics-agent.js +1 -1
  21. package/dist/agents/sandbox/scientific-executor.js +1 -10
  22. package/dist/agents/sandbox/shared.d.ts +20 -6
  23. package/dist/agents/sandbox/shared.js +50 -39
  24. package/dist/agents/sandbox/single-cell-agent.js +1 -1
  25. package/dist/agents/sandbox/spatial-omics-agent.js +1 -1
  26. package/dist/agents/sandbox/statistical-modeling-agent.js +1 -1
  27. package/dist/agents/sandbox/translational-safety-agent.js +3 -9
  28. package/dist/agents/sandbox/types.d.ts +1 -1
  29. package/dist/agents/system-prompt.d.ts +37 -11
  30. package/dist/agents/system-prompt.js +35 -12
  31. package/dist/app/chat-turn.d.ts +3 -0
  32. package/dist/app/chat-turn.js +3 -1
  33. package/dist/app/data-profile-orientation.d.ts +34 -0
  34. package/dist/app/data-profile-orientation.js +117 -0
  35. package/dist/app/synthesize-run.d.ts +3 -0
  36. package/dist/app/synthesize-run.js +3 -1
  37. package/dist/contracts/schemas/chat-parts.d.ts +9 -9
  38. package/dist/execution/artifact-metadata.d.ts +3 -0
  39. package/dist/execution/artifact-metadata.js +10 -3
  40. package/dist/execution/artifact-registration.d.ts +2 -1
  41. package/dist/execution/artifact-registration.js +8 -2
  42. package/dist/execution/ephemeral-runner.d.ts +16 -0
  43. package/dist/execution/ephemeral-runner.js +31 -5
  44. package/dist/execution/post-step-pipeline.d.ts +3 -0
  45. package/dist/execution/post-step-pipeline.js +24 -4
  46. package/dist/execution/reconcile-manifest.d.ts +7 -0
  47. package/dist/execution/reconcile-manifest.js +19 -5
  48. package/dist/execution/report-runner.d.ts +3 -0
  49. package/dist/execution/report-runner.js +4 -4
  50. package/dist/execution/run-synthesis.js +20 -19
  51. package/dist/execution/step-summary.d.ts +3 -0
  52. package/dist/execution/step-summary.js +6 -3
  53. package/dist/index.d.ts +9 -2
  54. package/dist/index.js +24 -5
  55. package/dist/lib/chrome.d.ts +4 -1
  56. package/dist/lib/chrome.js +10 -7
  57. package/dist/lib/console-logger.d.ts +19 -0
  58. package/dist/lib/console-logger.js +62 -0
  59. package/dist/lib/logger.d.ts +88 -0
  60. package/dist/lib/logger.js +37 -0
  61. package/dist/lib/otel.d.ts +2 -1
  62. package/dist/lib/otel.js +8 -3
  63. package/dist/loop/__fixtures__/scripted-provider.d.ts +2 -2
  64. package/dist/loop/__fixtures__/scripted-provider.js +2 -1
  65. package/dist/loop/metrics.d.ts +33 -1
  66. package/dist/loop/metrics.js +56 -2
  67. package/dist/loop/run-agent.d.ts +13 -1
  68. package/dist/loop/run-agent.js +19 -4
  69. package/dist/memory/card-builders.d.ts +8 -1
  70. package/dist/memory/card-builders.js +20 -3
  71. package/dist/memory/reconstruct-cards.js +4 -3
  72. package/dist/memory/thread-history.d.ts +27 -2
  73. package/dist/memory/thread-history.js +45 -5
  74. package/dist/memory/working-memory.d.ts +93 -10
  75. package/dist/memory/working-memory.js +220 -84
  76. package/dist/prompts/SOUL.d.ts +22 -9
  77. package/dist/prompts/SOUL.js +56 -37
  78. package/dist/prompts/analogical-reasoner.d.ts +1 -1
  79. package/dist/prompts/analogical-reasoner.js +2 -2
  80. package/dist/prompts/briefing.d.ts +100 -0
  81. package/dist/prompts/briefing.js +166 -0
  82. package/dist/prompts/conversation.d.ts +1 -1
  83. package/dist/prompts/conversation.js +94 -440
  84. package/dist/prompts/literature-reviewer.d.ts +1 -1
  85. package/dist/prompts/literature-reviewer.js +10 -10
  86. package/dist/prompts/planner.js +28 -59
  87. package/dist/prompts/report-builder.d.ts +1 -1
  88. package/dist/prompts/report-builder.js +71 -24
  89. package/dist/prompts/sandbox/bulk-transcriptomics-agent.d.ts +1 -1
  90. package/dist/prompts/sandbox/bulk-transcriptomics-agent.js +2 -7
  91. package/dist/prompts/sandbox/cheminformatics-agent.d.ts +1 -1
  92. package/dist/prompts/sandbox/cheminformatics-agent.js +11 -15
  93. package/dist/prompts/sandbox/chromatin-agent.d.ts +1 -1
  94. package/dist/prompts/sandbox/chromatin-agent.js +3 -7
  95. package/dist/prompts/sandbox/data-profiler.d.ts +1 -1
  96. package/dist/prompts/sandbox/data-profiler.js +13 -8
  97. package/dist/prompts/sandbox/dna-methylation-agent.d.ts +1 -1
  98. package/dist/prompts/sandbox/dna-methylation-agent.js +2 -7
  99. package/dist/prompts/sandbox/drug-repurposing-agent.d.ts +1 -1
  100. package/dist/prompts/sandbox/drug-repurposing-agent.js +15 -16
  101. package/dist/prompts/sandbox/enrichment-agent.d.ts +1 -1
  102. package/dist/prompts/sandbox/enrichment-agent.js +2 -9
  103. package/dist/prompts/sandbox/genomic-variant-agent.d.ts +1 -1
  104. package/dist/prompts/sandbox/genomic-variant-agent.js +2 -6
  105. package/dist/prompts/sandbox/immune-profiling-agent.d.ts +1 -1
  106. package/dist/prompts/sandbox/immune-profiling-agent.js +3 -8
  107. package/dist/prompts/sandbox/metabolomics-agent.d.ts +1 -1
  108. package/dist/prompts/sandbox/metabolomics-agent.js +1 -7
  109. package/dist/prompts/sandbox/microbiome-agent.d.ts +1 -1
  110. package/dist/prompts/sandbox/microbiome-agent.js +2 -7
  111. package/dist/prompts/sandbox/multi-omics-integration-agent.d.ts +1 -1
  112. package/dist/prompts/sandbox/multi-omics-integration-agent.js +2 -8
  113. package/dist/prompts/sandbox/multimodal-sc-agent.d.ts +1 -1
  114. package/dist/prompts/sandbox/multimodal-sc-agent.js +2 -7
  115. package/dist/prompts/sandbox/network-agent.d.ts +1 -1
  116. package/dist/prompts/sandbox/network-agent.js +2 -7
  117. package/dist/prompts/sandbox/proteomics-agent.d.ts +1 -1
  118. package/dist/prompts/sandbox/proteomics-agent.js +2 -9
  119. package/dist/prompts/sandbox/single-cell-agent.d.ts +1 -1
  120. package/dist/prompts/sandbox/single-cell-agent.js +2 -9
  121. package/dist/prompts/sandbox/spatial-omics-agent.d.ts +1 -1
  122. package/dist/prompts/sandbox/spatial-omics-agent.js +3 -6
  123. package/dist/prompts/sandbox/statistical-modeling-agent.d.ts +1 -1
  124. package/dist/prompts/sandbox/statistical-modeling-agent.js +2 -7
  125. package/dist/prompts/sandbox/translational-safety-agent.d.ts +1 -1
  126. package/dist/prompts/sandbox/translational-safety-agent.js +13 -14
  127. package/dist/prompts/sandbox-standards.d.ts +22 -14
  128. package/dist/prompts/sandbox-standards.js +91 -71
  129. package/dist/prompts/synthesis-agent.d.ts +1 -1
  130. package/dist/prompts/synthesis-agent.js +33 -131
  131. package/dist/provenance/collector.js +1 -1
  132. package/dist/providers/ai-sdk.js +31 -4
  133. package/dist/providers/prompt-cache.d.ts +74 -0
  134. package/dist/providers/prompt-cache.js +77 -0
  135. package/dist/providers/types.d.ts +33 -0
  136. package/dist/reference-data/catalog.d.ts +131 -0
  137. package/dist/reference-data/catalog.js +348 -0
  138. package/dist/reference-data/receipt.d.ts +41 -0
  139. package/dist/reference-data/receipt.js +40 -0
  140. package/dist/runtime/boot.d.ts +2 -2
  141. package/dist/runtime/boot.js +1 -1
  142. package/dist/runtime/connection-budget.d.ts +2 -2
  143. package/dist/runtime/connection-budget.js +5 -3
  144. package/dist/runtime/dbos.d.ts +7 -7
  145. package/dist/runtime/dbos.js +14 -11
  146. package/dist/runtime/shutdown.d.ts +2 -2
  147. package/dist/runtime/shutdown.js +4 -3
  148. package/dist/sandbox/create-sandbox.d.ts +2 -2
  149. package/dist/sandbox/docker-client.d.ts +2 -2
  150. package/dist/sandbox/docker-client.js +4 -1
  151. package/dist/sandbox/k8s-client.d.ts +3 -0
  152. package/dist/sandbox/k8s-client.js +5 -4
  153. package/dist/sandbox/notification-sweep.d.ts +3 -3
  154. package/dist/sandbox/notification-sweep.js +4 -2
  155. package/dist/sandbox/reaper.d.ts +3 -3
  156. package/dist/sandbox/reaper.js +7 -4
  157. package/dist/sandbox/watchdog.d.ts +3 -3
  158. package/dist/sandbox/watchdog.js +8 -2
  159. package/dist/schemas/data-profile-schemas.js +5 -3
  160. package/dist/schemas/plan-schemas.d.ts +21 -21
  161. package/dist/schemas/plan-schemas.js +9 -3
  162. package/dist/schemas/run-synthesis.d.ts +8 -4
  163. package/dist/schemas/run-synthesis.js +92 -56
  164. package/dist/schemas/validate-plan.js +1 -1
  165. package/dist/schemas/workflow-state.d.ts +7 -1
  166. package/dist/schemas/workflow-state.js +33 -19
  167. package/dist/state/artifacts.d.ts +13 -0
  168. package/dist/state/artifacts.js +27 -0
  169. package/dist/state/data-profile.d.ts +64 -5
  170. package/dist/state/index.d.ts +3 -3
  171. package/dist/state/index.js +1 -1
  172. package/dist/state/init.d.ts +2 -1
  173. package/dist/state/init.js +5 -6
  174. package/dist/tasks/data-profile.d.ts +25 -2
  175. package/dist/tasks/data-profile.js +95 -39
  176. package/dist/tools/bio/chembl.d.ts +38 -0
  177. package/dist/tools/bio/chembl.js +138 -0
  178. package/dist/tools/bio/comptox.d.ts +50 -0
  179. package/dist/tools/bio/comptox.js +149 -0
  180. package/dist/tools/bio/get-impc-ko-profile.js +9 -6
  181. package/dist/tools/bio/index.d.ts +5 -17
  182. package/dist/tools/bio/index.js +5 -17
  183. package/dist/tools/bio/keys.d.ts +14 -9
  184. package/dist/tools/bio/keys.js +16 -16
  185. package/dist/tools/bio/opentargets.d.ts +38 -0
  186. package/dist/tools/bio/opentargets.js +89 -0
  187. package/dist/tools/bio/pubchem.d.ts +29 -0
  188. package/dist/tools/bio/pubchem.js +92 -0
  189. package/dist/tools/bio/pubmed.d.ts +51 -0
  190. package/dist/tools/bio/pubmed.js +100 -0
  191. package/dist/tools/bio/search-bgee-expression.js +12 -6
  192. package/dist/tools/bio/search-clinical-trials.js +16 -5
  193. package/dist/tools/bio/search-dgidb.d.ts +11 -1
  194. package/dist/tools/bio/search-dgidb.js +92 -78
  195. package/dist/tools/bio/search-faers.js +8 -4
  196. package/dist/tools/bio/search-geo-datasets.js +20 -6
  197. package/dist/tools/bio/search-gwas-catalog.d.ts +1 -1
  198. package/dist/tools/bio/search-pharmgkb.js +10 -4
  199. package/dist/tools/display/index.d.ts +1 -0
  200. package/dist/tools/display/index.js +1 -0
  201. package/dist/tools/display/normalize-echart-spec.d.ts +61 -0
  202. package/dist/tools/display/normalize-echart-spec.js +211 -0
  203. package/dist/tools/display/show-user.d.ts +6 -1
  204. package/dist/tools/display/show-user.js +25 -12
  205. package/dist/tools/execute-plan.js +5 -2
  206. package/dist/tools/iterate-report.d.ts +171 -118
  207. package/dist/tools/iterate-report.js +336 -96
  208. package/dist/tools/lib/chembl-client.d.ts +12 -0
  209. package/dist/tools/lib/chembl-client.js +127 -0
  210. package/dist/tools/lib/ctx-ops.d.ts +224 -0
  211. package/dist/tools/lib/ctx-ops.js +450 -0
  212. package/dist/tools/lib/iuphar-client.js +10 -1
  213. package/dist/tools/lib/openfda-client.js +11 -3
  214. package/dist/tools/lib/pathway-client.js +10 -4
  215. package/dist/tools/lib/pubchem-ops.d.ts +74 -0
  216. package/dist/tools/lib/pubchem-ops.js +224 -0
  217. package/dist/tools/memory/update-working-memory.d.ts +45 -7
  218. package/dist/tools/memory/update-working-memory.js +111 -41
  219. package/dist/tools/report/index.d.ts +3 -2
  220. package/dist/tools/report/index.js +3 -2
  221. package/dist/tools/research/generate-analogy-report.js +25 -12
  222. package/dist/tools/research/generate-plan.d.ts +12 -5
  223. package/dist/tools/research/generate-plan.js +168 -37
  224. package/dist/tools/research/index.d.ts +1 -0
  225. package/dist/tools/research/index.js +1 -0
  226. package/dist/tools/research/inspect-data-profile.d.ts +85 -0
  227. package/dist/tools/research/inspect-data-profile.js +161 -0
  228. package/dist/tools/research/literature-reviewer.d.ts +3 -0
  229. package/dist/tools/research/literature-reviewer.js +5 -6
  230. package/dist/tools/sandbox/list-available-packages.d.ts +79 -5
  231. package/dist/tools/sandbox/list-available-packages.js +152 -10
  232. package/dist/tools/sandbox/list-available-refs.d.ts +141 -5
  233. package/dist/tools/sandbox/list-available-refs.js +647 -134
  234. package/dist/tools/sandbox/report-blocker.d.ts +39 -9
  235. package/dist/tools/sandbox/report-blocker.js +43 -20
  236. package/dist/tools/workspace/execute-command.d.ts +3 -0
  237. package/dist/tools/workspace/execute-command.js +3 -1
  238. package/dist/tools/workspace/read-file.js +4 -5
  239. package/dist/tools/workspace/run-exec.d.ts +4 -4
  240. package/dist/tools/workspace/run-exec.js +4 -4
  241. package/dist/tools/workspace/show-file.js +10 -6
  242. package/dist/tools/workspace/show-plan.js +12 -6
  243. package/dist/tools/workspace/workspace-search.d.ts +1 -1
  244. package/dist/tools/workspace/workspace-search.js +11 -5
  245. package/dist/workflows/execute-analysis.d.ts +46 -4
  246. package/dist/workflows/execute-analysis.js +118 -13
  247. package/dist/workflows/execute-target-assessment.d.ts +3 -0
  248. package/dist/workflows/execute-target-assessment.js +19 -15
  249. package/dist/workflows/sandbox-step.d.ts +9 -0
  250. package/dist/workflows/sandbox-step.js +39 -17
  251. package/dist/workflows/target-assessment/lib/citation-validator.js +2 -2
  252. package/dist/workflows/target-assessment/lib/clinical-consequence-annotator.js +2 -1
  253. package/dist/workflows/target-assessment/lib/llm-step.d.ts +3 -0
  254. package/dist/workflows/target-assessment/lib/llm-step.js +3 -1
  255. package/dist/workflows/target-assessment/lib/structured-llm.d.ts +3 -0
  256. package/dist/workflows/target-assessment/lib/structured-llm.js +1 -0
  257. package/dist/workflows/target-assessment/phase5-persist.d.ts +3 -0
  258. package/dist/workflows/target-assessment/phase5-persist.js +8 -3
  259. package/dist/workflows/target-assessment/progress.d.ts +2 -1
  260. package/dist/workflows/target-assessment/progress.js +4 -3
  261. package/dist/workspace/filesystem.js +163 -74
  262. package/dist/workspace/paths.d.ts +2 -2
  263. package/dist/workspace/paths.js +2 -2
  264. package/package.json +95 -96
  265. package/dist/execution/filesystem-artifact-registry.d.ts +0 -57
  266. package/dist/execution/filesystem-artifact-registry.js +0 -92
  267. package/dist/lib/identifiers.d.ts +0 -8
  268. package/dist/lib/identifiers.js +0 -10
  269. package/dist/lib/mime-detect.d.ts +0 -17
  270. package/dist/lib/mime-detect.js +0 -29
  271. package/dist/lib/streamed-download.d.ts +0 -28
  272. package/dist/lib/streamed-download.js +0 -111
  273. package/dist/lib/trace-context.d.ts +0 -11
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  275. package/dist/providers/llm-capabilities.d.ts +0 -33
  276. package/dist/providers/llm-capabilities.js +0 -58
  277. package/dist/schemas/render-step-prompt.d.ts +0 -32
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  279. package/dist/tools/bio/find-approval-precedent.d.ts +0 -32
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  281. package/dist/tools/bio/get-article-details.d.ts +0 -11
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  283. package/dist/tools/bio/get-article-full-text.d.ts +0 -19
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  285. package/dist/tools/bio/get-bioactivity.d.ts +0 -11
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  287. package/dist/tools/bio/get-drug-info.d.ts +0 -9
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  289. package/dist/tools/bio/get-mechanism.d.ts +0 -8
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  291. package/dist/tools/bio/get-pubchem-assays.d.ts +0 -22
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  293. package/dist/tools/bio/get-pubchem-cross-refs.d.ts +0 -15
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  295. package/dist/tools/bio/get-target-safety.d.ts +0 -18
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  297. package/dist/tools/bio/search-compounds.d.ts +0 -22
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  299. package/dist/tools/bio/search-ctx-chemical.d.ts +0 -50
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  301. package/dist/tools/bio/search-ctx-exposure.d.ts +0 -55
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  305. package/dist/tools/bio/search-opentargets.d.ts +0 -11
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  307. package/dist/tools/bio/search-pubchem-compound.d.ts +0 -26
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  309. package/dist/tools/bio/search-pubmed.d.ts +0 -17
  310. package/dist/tools/bio/search-pubmed.js +0 -31
  311. package/dist/tools/bio/search-targets.d.ts +0 -9
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  313. package/dist/tools/bio/search-toxcast.d.ts +0 -36
  314. package/dist/tools/bio/search-toxcast.js +0 -141
  315. package/dist/workflows/register-workflows.d.ts +0 -51
  316. package/dist/workflows/register-workflows.js +0 -48
  317. package/dist/workflows/resume-execute-analysis.d.ts +0 -70
  318. package/dist/workflows/resume-execute-analysis.js +0 -80
  319. package/dist/workflows/target-assessment/correction-loop.d.ts +0 -45
  320. package/dist/workflows/target-assessment/correction-loop.js +0 -62
  321. package/dist/workflows/target-assessment/steps/phase0-resolve.d.ts +0 -71
  322. package/dist/workflows/target-assessment/steps/phase0-resolve.js +0 -21
  323. package/dist/workflows/target-assessment/steps/phase1-aggregate.d.ts +0 -1018
  324. package/dist/workflows/target-assessment/steps/phase1-aggregate.js +0 -25
  325. package/dist/workspace/mount-strategy.d.ts +0 -50
  326. package/dist/workspace/mount-strategy.js +0 -67
  327. package/dist/workspace/provenance-collector.d.ts +0 -34
  328. package/dist/workspace/provenance-collector.js +0 -16
  329. package/dist/workspace/workspace-paths.d.ts +0 -26
  330. package/dist/workspace/workspace-paths.js +0 -31
@@ -1,21 +0,0 @@
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- /**
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- * Phase 0 — target resolution.
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- *
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- * The single step in the workflow allowed to throw. A hard resolution
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- * failure aborts the assessment with `error.kind: "target-unresolved"`.
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- *
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- * The DBOS workflow body re-implements Phase 0 inline; this module is kept
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- * for its schemas (input/output) so dependent modules continue to compile.
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- */
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- import { TargetAssessmentInputSchema, ResolvedTargetSchema } from "../schemas.js";
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- import { resolveTarget } from "../../../tools/lib/identifier-resolver.js";
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- export const phase0InputSchema = TargetAssessmentInputSchema;
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- export const phase0OutputSchema = ResolvedTargetSchema;
14
- export async function phase0Execute(inputData) {
15
- const resolved = await resolveTarget(inputData.target);
16
- return {
17
- assessmentId: inputData.assessmentId,
18
- goal: inputData.goal ?? null,
19
- ...resolved,
20
- };
21
- }