qwen-sci 0.2.2__py3-none-any.whl

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Files changed (549) hide show
  1. qwen_sci-0.2.2.dist-info/METADATA +492 -0
  2. qwen_sci-0.2.2.dist-info/RECORD +549 -0
  3. qwen_sci-0.2.2.dist-info/WHEEL +4 -0
  4. qwen_sci-0.2.2.dist-info/entry_points.txt +6 -0
  5. qwen_sci-0.2.2.dist-info/licenses/LICENSE +21 -0
  6. src/1.txt +1 -0
  7. src/__init__.py +1 -0
  8. src/__main__.py +5 -0
  9. src/agents/__init__.py +1 -0
  10. src/agents/experiment_design_agent/__init__.py +268 -0
  11. src/agents/experiment_design_agent/artifacts.py +747 -0
  12. src/agents/experiment_design_agent/cache.py +319 -0
  13. src/agents/experiment_design_agent/completeness.py +130 -0
  14. src/agents/experiment_design_agent/contracts.py +771 -0
  15. src/agents/experiment_design_agent/counterexample_analyzer.py +187 -0
  16. src/agents/experiment_design_agent/design_evidence_paper_screener.py +470 -0
  17. src/agents/experiment_design_agent/discipline_catalog.py +178 -0
  18. src/agents/experiment_design_agent/evidence_cards.py +338 -0
  19. src/agents/experiment_design_agent/evidence_planner.py +452 -0
  20. src/agents/experiment_design_agent/formal_reasoning_planner.py +884 -0
  21. src/agents/experiment_design_agent/fulltext_acquisition.py +863 -0
  22. src/agents/experiment_design_agent/idea_adapter.py +100 -0
  23. src/agents/experiment_design_agent/idea_intake.py +87 -0
  24. src/agents/experiment_design_agent/llm_json.py +328 -0
  25. src/agents/experiment_design_agent/orchestrator.py +1220 -0
  26. src/agents/experiment_design_agent/reasoning_context.py +183 -0
  27. src/agents/experiment_design_agent/reasoning_validation.py +546 -0
  28. src/agents/experiment_design_agent/run.py +481 -0
  29. src/agents/experiment_design_agent/run_logging.py +292 -0
  30. src/agents/experiment_design_agent/scope_gate.py +198 -0
  31. src/agents/experiment_design_agent/study_type_composer.py +1360 -0
  32. src/agents/experiment_design_agent/survey_evidence.py +1381 -0
  33. src/agents/experiment_design_agent/template_router.py +195 -0
  34. src/agents/experiment_design_agent/variable_claim_extractor.py +93 -0
  35. src/agents/idea_agent/__init__.py +1 -0
  36. src/agents/idea_agent/agent/__init__.py +6 -0
  37. src/agents/idea_agent/agent/artifacts.py +308 -0
  38. src/agents/idea_agent/agent/base.py +122 -0
  39. src/agents/idea_agent/agent/ligagent.py +488 -0
  40. src/agents/idea_agent/agent/mcts.py +2060 -0
  41. src/agents/idea_agent/agent/prompts/__init__.py +48 -0
  42. src/agents/idea_agent/agent/prompts/advanced_analysis.py +235 -0
  43. src/agents/idea_agent/agent/prompts/algorithm_alignment.py +55 -0
  44. src/agents/idea_agent/agent/prompts/algorithm_structuring.py +48 -0
  45. src/agents/idea_agent/agent/prompts/component_extraction.py +62 -0
  46. src/agents/idea_agent/agent/prompts/component_novelty_evaluation.py +54 -0
  47. src/agents/idea_agent/agent/prompts/experiment_findings_extraction.py +39 -0
  48. src/agents/idea_agent/agent/prompts/idea_fusion.py +295 -0
  49. src/agents/idea_agent/agent/prompts/idea_introduction.py +30 -0
  50. src/agents/idea_agent/agent/prompts/idea_result_alignment.py +39 -0
  51. src/agents/idea_agent/agent/prompts/input_interpreter.py +52 -0
  52. src/agents/idea_agent/agent/prompts/keynote_ops.py +78 -0
  53. src/agents/idea_agent/agent/prompts/mcts_evaluation.py +235 -0
  54. src/agents/idea_agent/agent/prompts/mcts_generation.py +140 -0
  55. src/agents/idea_agent/agent/prompts/mechanism_commit_query.py +99 -0
  56. src/agents/idea_agent/agent/prompts/memory_selection.py +0 -0
  57. src/agents/idea_agent/agent/prompts/prompt_modes.py +16 -0
  58. src/agents/idea_agent/agent/prompts/rag_query.py +34 -0
  59. src/agents/idea_agent/agent/prompts/re_analysis_replan.py +48 -0
  60. src/agents/idea_agent/agent/prompts/reference_grounding.py +34 -0
  61. src/agents/idea_agent/agent/prompts/root_domain_classification.py +32 -0
  62. src/agents/idea_agent/agent/prompts/scientific_debate.py +88 -0
  63. src/agents/idea_agent/agent/prompts/scientific_materialization.py +45 -0
  64. src/agents/idea_agent/agent/prompts/skill_instantiation.py +193 -0
  65. src/agents/idea_agent/agent/prompts/theory_transfer_query.py +93 -0
  66. src/agents/idea_agent/agent/prompts/topic_background.py +15 -0
  67. src/agents/idea_agent/agent/skills/DEFAULT_SKILL_TEMPLATES.json +263 -0
  68. src/agents/idea_agent/agent/skills/edit_operator_skills/alternative-path-contrast/SKILL.md +40 -0
  69. src/agents/idea_agent/agent/skills/edit_operator_skills/alternative-path-contrast/references/contrast_patterns.md +22 -0
  70. src/agents/idea_agent/agent/skills/edit_operator_skills/feedback-closed-loop/SKILL.md +40 -0
  71. src/agents/idea_agent/agent/skills/edit_operator_skills/feedback-closed-loop/references/mechanism_cards.md +24 -0
  72. src/agents/idea_agent/agent/skills/edit_operator_skills/hierarchical-decomposition/SKILL.md +39 -0
  73. src/agents/idea_agent/agent/skills/edit_operator_skills/hierarchical-decomposition/references/hierarchy_patterns.md +22 -0
  74. src/agents/idea_agent/agent/skills/edit_operator_skills/mechanism-commit-innovation/SKILL.md +39 -0
  75. src/agents/idea_agent/agent/skills/edit_operator_skills/mechanism-commit-innovation/references/mechanism_commit_patterns.md +24 -0
  76. src/agents/idea_agent/agent/skills/edit_operator_skills/multi-scale-coordinator/SKILL.md +39 -0
  77. src/agents/idea_agent/agent/skills/edit_operator_skills/multi-scale-coordinator/references/coordination_patterns.md +22 -0
  78. src/agents/idea_agent/agent/skills/edit_operator_skills/speculative-execution-with-repair/SKILL.md +41 -0
  79. src/agents/idea_agent/agent/skills/edit_operator_skills/speculative-execution-with-repair/references/speculation_patterns.md +22 -0
  80. src/agents/idea_agent/agent/skills/edit_operator_skills/surgical-modularity/SKILL.md +39 -0
  81. src/agents/idea_agent/agent/skills/edit_operator_skills/surgical-modularity/references/modularity_patterns.md +22 -0
  82. src/agents/idea_agent/agent/skills/edit_operator_skills/theory-transfer-injection/SKILL.md +40 -0
  83. src/agents/idea_agent/agent/skills/edit_operator_skills/theory-transfer-injection/references/transfer_patterns.md +24 -0
  84. src/agents/idea_agent/example/idea_result.json +900 -0
  85. src/agents/idea_agent/run.py +276 -0
  86. src/agents/idea_agent/tests/test_advanced_analysis_contract.py +90 -0
  87. src/agents/idea_agent/tests/test_gap_hypothesis_bridge.py +166 -0
  88. src/agents/idea_agent/tests/test_idea_debate.py +480 -0
  89. src/agents/idea_agent/tests/test_idea_result_v5.py +99 -0
  90. src/agents/idea_agent/tests/test_idea_synthesis.py +92 -0
  91. src/agents/idea_agent/tests/test_mature_idea_sources.py +27 -0
  92. src/agents/idea_agent/tests/test_multimodal_idea_integration.py +386 -0
  93. src/agents/idea_agent/tests/test_profile_materialization_and_scoring.py +219 -0
  94. src/agents/idea_agent/tests/test_profile_native_skill_rendering.py +122 -0
  95. src/agents/idea_agent/tests/test_result_persistence.py +183 -0
  96. src/agents/idea_agent/tests/test_scientific_intervention_profiles.py +241 -0
  97. src/agents/idea_agent/tests/test_scientific_rubric_and_prompts.py +559 -0
  98. src/agents/idea_agent/tests/test_strict_json_object_responses.py +48 -0
  99. src/agents/idea_agent/utils/core/__init__.py +1 -0
  100. src/agents/idea_agent/utils/core/ablation_inputs.py +60 -0
  101. src/agents/idea_agent/utils/core/chat_errors.py +95 -0
  102. src/agents/idea_agent/utils/core/chat_router.py +130 -0
  103. src/agents/idea_agent/utils/core/chat_transport.py +188 -0
  104. src/agents/idea_agent/utils/core/config_loader.py +166 -0
  105. src/agents/idea_agent/utils/core/json_utils.py +28 -0
  106. src/agents/idea_agent/utils/core/logger.py +287 -0
  107. src/agents/idea_agent/utils/core/progress.py +58 -0
  108. src/agents/idea_agent/utils/core/response_parsing.py +57 -0
  109. src/agents/idea_agent/utils/core/run_inputs.py +198 -0
  110. src/agents/idea_agent/utils/mcts/__init__.py +1 -0
  111. src/agents/idea_agent/utils/mcts/component_novelty.py +342 -0
  112. src/agents/idea_agent/utils/mcts/defect_registry.py +302 -0
  113. src/agents/idea_agent/utils/mcts/idea_routes.py +61 -0
  114. src/agents/idea_agent/utils/mcts/idea_taste_presets.py +312 -0
  115. src/agents/idea_agent/utils/mcts/mcts_helpers.py +738 -0
  116. src/agents/idea_agent/utils/mcts/mcts_runtime.py +3000 -0
  117. src/agents/idea_agent/utils/mcts/scientific_intervention_ontology.py +1561 -0
  118. src/agents/idea_agent/utils/mcts/scientific_rubric.py +211 -0
  119. src/agents/idea_agent/utils/mcts/skill_parsing.py +92 -0
  120. src/agents/idea_agent/utils/papers/__init__.py +1 -0
  121. src/agents/idea_agent/utils/papers/paper_graph_vector_store.py +499 -0
  122. src/agents/idea_agent/utils/papers/paper_repository.py +372 -0
  123. src/agents/idea_agent/utils/prompting/__init__.py +1 -0
  124. src/agents/idea_agent/utils/prompting/prompt_views.py +637 -0
  125. src/agents/idea_agent/utils/workflow/__init__.py +1 -0
  126. src/agents/idea_agent/utils/workflow/advanced_analysis_contract.py +244 -0
  127. src/agents/idea_agent/utils/workflow/gap_hypothesis_bridge.py +461 -0
  128. src/agents/idea_agent/utils/workflow/idea_contract.py +426 -0
  129. src/agents/idea_agent/utils/workflow/idea_debate.py +1238 -0
  130. src/agents/idea_agent/utils/workflow/idea_diversity.py +163 -0
  131. src/agents/idea_agent/utils/workflow/idea_fusion.py +889 -0
  132. src/agents/idea_agent/utils/workflow/idea_helpers.py +478 -0
  133. src/agents/idea_agent/utils/workflow/idea_portfolio.py +422 -0
  134. src/agents/idea_agent/utils/workflow/idea_synthesis.py +482 -0
  135. src/agents/idea_agent/utils/workflow/ligagent_flow.py +581 -0
  136. src/agents/idea_agent/utils/workflow/ligagent_handlers.py +1836 -0
  137. src/agents/idea_agent/utils/workflow/ligagent_helpers.py +1331 -0
  138. src/agents/idea_agent/utils/workflow/ligagent_utils.py +322 -0
  139. src/agents/idea_agent/utils/workflow/mature_idea_sources.py +648 -0
  140. src/agents/idea_agent/utils/workflow/multimodal_data_anchoring.py +578 -0
  141. src/agents/idea_agent/utils/workflow/result_persistence.py +774 -0
  142. src/agents/idea_agent/utils/workflow/stage_contract.py +76 -0
  143. src/agents/idea_agent/utils/workflow/workflow_runtime.py +288 -0
  144. src/agents/research_plan_author/__init__.py +50 -0
  145. src/agents/research_plan_author/artifacts.py +270 -0
  146. src/agents/research_plan_author/authoring_blueprint.py +1246 -0
  147. src/agents/research_plan_author/bibtex_renderer.py +252 -0
  148. src/agents/research_plan_author/contract_repair.py +131 -0
  149. src/agents/research_plan_author/contracts.py +745 -0
  150. src/agents/research_plan_author/cross_section_editor.py +232 -0
  151. src/agents/research_plan_author/document_quality.py +987 -0
  152. src/agents/research_plan_author/idea_evolution.py +223 -0
  153. src/agents/research_plan_author/input_loader.py +76 -0
  154. src/agents/research_plan_author/latex_compiler.py +260 -0
  155. src/agents/research_plan_author/latex_safety.py +159 -0
  156. src/agents/research_plan_author/llm_json.py +74 -0
  157. src/agents/research_plan_author/markdown_renderer.py +275 -0
  158. src/agents/research_plan_author/pdf_validator.py +149 -0
  159. src/agents/research_plan_author/render.py +166 -0
  160. src/agents/research_plan_author/render_artifacts.py +187 -0
  161. src/agents/research_plan_author/run.py +765 -0
  162. src/agents/research_plan_author/run_logging.py +209 -0
  163. src/agents/research_plan_author/section_cache.py +184 -0
  164. src/agents/research_plan_author/section_composer.py +1764 -0
  165. src/agents/research_plan_author/section_router.py +209 -0
  166. src/agents/research_plan_author/semantic_validator.py +254 -0
  167. src/agents/research_plan_author/source_bundle.py +46 -0
  168. src/agents/research_plan_author/source_registry.py +208 -0
  169. src/agents/research_plan_author/survey_source_loader.py +137 -0
  170. src/agents/research_plan_author/template_adapter.py +173 -0
  171. src/agents/research_plan_author/template_profile.py +204 -0
  172. src/agents/research_plan_author/tex_renderer.py +496 -0
  173. src/agents/research_plan_author/theory_presentation.py +134 -0
  174. src/agents/research_plan_author/theory_spine.py +703 -0
  175. src/agents/survey_agent/Dockerfile +54 -0
  176. src/agents/survey_agent/README.md +350 -0
  177. src/agents/survey_agent/config/deep_survey.yaml +217 -0
  178. src/agents/survey_agent/config/deep_survey_batch.yaml +176 -0
  179. src/agents/survey_agent/config/deep_survey_fast.yaml +183 -0
  180. src/agents/survey_agent/config/evaluate_baseline.yaml +197 -0
  181. src/agents/survey_agent/config/outcomeRAG.yaml +159 -0
  182. src/agents/survey_agent/env_report.md +348 -0
  183. src/agents/survey_agent/modules/__init__.py +0 -0
  184. src/agents/survey_agent/modules/code_collector.py +2194 -0
  185. src/agents/survey_agent/modules/code_report_generator.py +1282 -0
  186. src/agents/survey_agent/modules/data_manager.py +1713 -0
  187. src/agents/survey_agent/modules/database.py +167 -0
  188. src/agents/survey_agent/modules/fulltext_download_cache.py +462 -0
  189. src/agents/survey_agent/modules/fulltext_http.py +134 -0
  190. src/agents/survey_agent/modules/fulltext_resolution.py +749 -0
  191. src/agents/survey_agent/modules/judge.py +434 -0
  192. src/agents/survey_agent/modules/outcome_RAG.py +236 -0
  193. src/agents/survey_agent/modules/paper_graph_retriever.py +1075 -0
  194. src/agents/survey_agent/modules/pe.py +1729 -0
  195. src/agents/survey_agent/modules/pseudo_creator.py +782 -0
  196. src/agents/survey_agent/modules/pseudo_reviser.py +537 -0
  197. src/agents/survey_agent/modules/refine_agent.py +1952 -0
  198. src/agents/survey_agent/modules/survey_generator.py +5691 -0
  199. src/agents/survey_agent/modules/survey_visualizer.py +1817 -0
  200. src/agents/survey_agent/modules/visual_prompts.py +327 -0
  201. src/agents/survey_agent/modules/work_analyzer.py +2750 -0
  202. src/agents/survey_agent/modules/work_collector.py +5649 -0
  203. src/agents/survey_agent/scripts/baseline_evaluation.py +411 -0
  204. src/agents/survey_agent/scripts/run_deep_survey.py +224 -0
  205. src/agents/survey_agent/scripts/run_deep_survey_adapter.py +407 -0
  206. src/agents/survey_agent/scripts/run_deep_survey_adapter_with_input.py +409 -0
  207. src/agents/survey_agent/scripts/run_deep_survey_batch.py +228 -0
  208. src/agents/survey_agent/scripts/run_deep_survey_batch_arg.py +243 -0
  209. src/agents/survey_agent/scripts/run_deep_survey_batch_settings.py +218 -0
  210. src/agents/survey_agent/scripts/run_keynotes_gen.py +128 -0
  211. src/agents/survey_agent/scripts/run_work_clusters.py +140 -0
  212. src/agents/survey_agent/utils/__init__.py +0 -0
  213. src/agents/survey_agent/utils/ablation_utils.py +317 -0
  214. src/agents/survey_agent/utils/api_call.py +2518 -0
  215. src/agents/survey_agent/utils/chat_utils.py +82 -0
  216. src/agents/survey_agent/utils/config_utils.py +70 -0
  217. src/agents/survey_agent/utils/convert_to_md.py +29 -0
  218. src/agents/survey_agent/utils/err_info.py +24 -0
  219. src/agents/survey_agent/utils/file_utils.py +176 -0
  220. src/agents/survey_agent/utils/gpu_utils.py +145 -0
  221. src/agents/survey_agent/utils/graph_visualizer.py +279 -0
  222. src/agents/survey_agent/utils/html_utils.py +181 -0
  223. src/agents/survey_agent/utils/latex_generator_intra_cluster.py +529 -0
  224. src/agents/survey_agent/utils/latex_generator_relation_table.py +193 -0
  225. src/agents/survey_agent/utils/mineru_section_packer.py +334 -0
  226. src/agents/survey_agent/utils/mineru_utils.py +396 -0
  227. src/agents/survey_agent/utils/paper.py +144 -0
  228. src/agents/survey_agent/utils/read_yaml.py +15 -0
  229. src/agents/survey_agent/utils/repo_utils.py +167 -0
  230. src/agents/survey_agent/utils/rich_logger.py +77 -0
  231. src/agents/survey_agent/utils/step2v2.py +874 -0
  232. src/agents/survey_agent/utils/step2v2_extractor.py +856 -0
  233. src/agents/survey_agent/utils/topic_survey_storage.py +309 -0
  234. src/agents/survey_agent/utils/utils.py +118 -0
  235. src/agents/survey_agent/utils/work.py +2 -0
  236. src/cli.py +1611 -0
  237. src/config/__init__.py +213 -0
  238. src/config/default.yaml +1122 -0
  239. src/harness/LICENSE +21 -0
  240. src/harness/VENDORED.md +14 -0
  241. src/harness/src/__init__.py +0 -0
  242. src/harness/src/openharness/__init__.py +0 -0
  243. src/harness/src/openharness/__main__.py +6 -0
  244. src/harness/src/openharness/api/__init__.py +21 -0
  245. src/harness/src/openharness/api/client.py +281 -0
  246. src/harness/src/openharness/api/codex_client.py +407 -0
  247. src/harness/src/openharness/api/copilot_auth.py +240 -0
  248. src/harness/src/openharness/api/copilot_client.py +134 -0
  249. src/harness/src/openharness/api/errors.py +19 -0
  250. src/harness/src/openharness/api/openai_client.py +577 -0
  251. src/harness/src/openharness/api/provider.py +186 -0
  252. src/harness/src/openharness/api/registry.py +437 -0
  253. src/harness/src/openharness/api/usage.py +17 -0
  254. src/harness/src/openharness/auth/__init__.py +29 -0
  255. src/harness/src/openharness/auth/external.py +610 -0
  256. src/harness/src/openharness/auth/flows.py +189 -0
  257. src/harness/src/openharness/auth/manager.py +482 -0
  258. src/harness/src/openharness/auth/storage.py +269 -0
  259. src/harness/src/openharness/autopilot/__init__.py +23 -0
  260. src/harness/src/openharness/autopilot/service.py +2239 -0
  261. src/harness/src/openharness/autopilot/types.py +91 -0
  262. src/harness/src/openharness/bridge/__init__.py +20 -0
  263. src/harness/src/openharness/bridge/manager.py +106 -0
  264. src/harness/src/openharness/bridge/session_runner.py +46 -0
  265. src/harness/src/openharness/bridge/types.py +37 -0
  266. src/harness/src/openharness/bridge/work_secret.py +41 -0
  267. src/harness/src/openharness/channels/UPSTREAM +6 -0
  268. src/harness/src/openharness/channels/__init__.py +22 -0
  269. src/harness/src/openharness/channels/adapter.py +131 -0
  270. src/harness/src/openharness/channels/bus/__init__.py +6 -0
  271. src/harness/src/openharness/channels/bus/events.py +38 -0
  272. src/harness/src/openharness/channels/bus/queue.py +44 -0
  273. src/harness/src/openharness/channels/impl/__init__.py +6 -0
  274. src/harness/src/openharness/channels/impl/base.py +141 -0
  275. src/harness/src/openharness/channels/impl/dingtalk.py +445 -0
  276. src/harness/src/openharness/channels/impl/discord.py +311 -0
  277. src/harness/src/openharness/channels/impl/email.py +410 -0
  278. src/harness/src/openharness/channels/impl/feishu.py +1342 -0
  279. src/harness/src/openharness/channels/impl/manager.py +257 -0
  280. src/harness/src/openharness/channels/impl/matrix.py +700 -0
  281. src/harness/src/openharness/channels/impl/mochat.py +897 -0
  282. src/harness/src/openharness/channels/impl/qq.py +141 -0
  283. src/harness/src/openharness/channels/impl/slack.py +284 -0
  284. src/harness/src/openharness/channels/impl/telegram.py +525 -0
  285. src/harness/src/openharness/channels/impl/whatsapp.py +159 -0
  286. src/harness/src/openharness/cli.py +2551 -0
  287. src/harness/src/openharness/commands/__init__.py +21 -0
  288. src/harness/src/openharness/commands/registry.py +2783 -0
  289. src/harness/src/openharness/config/__init__.py +34 -0
  290. src/harness/src/openharness/config/paths.py +160 -0
  291. src/harness/src/openharness/config/schema.py +119 -0
  292. src/harness/src/openharness/config/settings.py +1104 -0
  293. src/harness/src/openharness/coordinator/__init__.py +12 -0
  294. src/harness/src/openharness/coordinator/agent_definitions.py +975 -0
  295. src/harness/src/openharness/coordinator/coordinator_mode.py +520 -0
  296. src/harness/src/openharness/engine/__init__.py +80 -0
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  538. src/pipeline/subhypothesis_decomposition.py +392 -0
  539. src/pipeline/subhypothesis_evidence.py +856 -0
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  541. src/pipeline/survey_gap_adjudication.py +647 -0
  542. src/pipeline/survey_gap_candidates.py +840 -0
  543. src/pipeline/survey_gap_ledger.py +683 -0
  544. src/pipeline/survey_gap_triage.py +401 -0
  545. src/pipeline/survey_handoff_persistence.py +481 -0
  546. src/pipeline/survey_handoff_projection.py +457 -0
  547. src/pipeline/survey_idea_handoff.py +1112 -0
  548. src/pipeline/survey_idea_loader.py +289 -0
  549. src/research_run_ids.py +11 -0
@@ -0,0 +1,771 @@
1
+ """Versioned JSON contracts for ExperimentDesign Agent's design-only phase."""
2
+
3
+ from __future__ import annotations
4
+
5
+ from copy import deepcopy
6
+ from typing import Any, Mapping
7
+
8
+ from jsonschema import Draft202012Validator
9
+
10
+ from .reasoning_context import (
11
+ REASONING_CONTEXT_SCHEMA,
12
+ REASONING_CONTEXT_SCHEMA_VERSION,
13
+ build_reasoning_context_from_idea_result,
14
+ )
15
+
16
+ from .discipline_catalog import (
17
+ DESIGN_ONLY,
18
+ DIGITAL_EXECUTION_ELIGIBLE,
19
+ normalize_discipline_ids,
20
+ resolve_design_scope,
21
+ resolve_execution_policy,
22
+ )
23
+
24
+
25
+ RESEARCH_BRIEF_SCHEMA_VERSION = "research_brief_v1"
26
+ EVIDENCE_BUNDLE_SCHEMA_VERSION = "evidence_bundle_v1"
27
+ OUTCOME_BRANCH_SCHEMA_VERSION = "outcome_branch_v1"
28
+ EXPERIMENT_DESIGN_SCHEMA_VERSION = "experiment_design_v1"
29
+
30
+ _NONEMPTY_STRING = {"type": "string", "minLength": 1}
31
+ _STRING_LIST = {"type": "array", "items": _NONEMPTY_STRING}
32
+ _STATUS_VALUE = {
33
+ "type": "string",
34
+ "enum": [
35
+ "evidence_backed",
36
+ "user_declared",
37
+ "design_assumption",
38
+ "needs_human_input",
39
+ "not_applicable",
40
+ ],
41
+ }
42
+
43
+ RESEARCH_BRIEF_SCHEMA: dict[str, Any] = {
44
+ "$schema": "https://json-schema.org/draft/2020-12/schema",
45
+ "title": "ResearchBrief v1",
46
+ "type": "object",
47
+ "additionalProperties": False,
48
+ "required": [
49
+ "schema_version",
50
+ "brief_id",
51
+ "topic",
52
+ "discipline_ids",
53
+ "selected_direction",
54
+ "research_object",
55
+ "evidence_status",
56
+ "known_unknowns",
57
+ "source",
58
+ "reasoning_context",
59
+ ],
60
+ "properties": {
61
+ "schema_version": {"const": RESEARCH_BRIEF_SCHEMA_VERSION},
62
+ "brief_id": _NONEMPTY_STRING,
63
+ "topic": _NONEMPTY_STRING,
64
+ "discipline_ids": {"type": "array", "minItems": 1, "uniqueItems": True, "items": _NONEMPTY_STRING},
65
+ "selected_direction": {
66
+ "type": "object",
67
+ "additionalProperties": False,
68
+ "required": ["id", "title", "central_hypothesis", "mechanism_or_relation"],
69
+ "properties": {
70
+ "id": _NONEMPTY_STRING,
71
+ "title": _NONEMPTY_STRING,
72
+ "central_hypothesis": _NONEMPTY_STRING,
73
+ "mechanism_or_relation": {"type": "string"},
74
+ },
75
+ },
76
+ "research_object": {"type": "object", "minProperties": 1},
77
+ "intervention_or_transformation": {"type": "string"},
78
+ "discriminating_observations": _STRING_LIST,
79
+ "boundary_conditions": _STRING_LIST,
80
+ "alternative_explanations": _STRING_LIST,
81
+ "known_unknowns": _STRING_LIST,
82
+ "evidence_status": {"const": "PROPOSED"},
83
+ "source": {
84
+ "type": "object",
85
+ "additionalProperties": False,
86
+ "required": ["idea_result_schema", "direction_id"],
87
+ "properties": {
88
+ "idea_result_schema": {"const": "idea_result_v5"},
89
+ "direction_id": _NONEMPTY_STRING,
90
+ "survey_binding": {"type": "object"},
91
+ "upstream_source_paths": {"type": "object"},
92
+ "missing_audit_sources": _STRING_LIST,
93
+ },
94
+ },
95
+ "reasoning_context": deepcopy(REASONING_CONTEXT_SCHEMA),
96
+ },
97
+ }
98
+
99
+ EVIDENCE_BUNDLE_SCHEMA: dict[str, Any] = {
100
+ "$schema": "https://json-schema.org/draft/2020-12/schema",
101
+ "title": "EvidenceBundle v1",
102
+ "type": "object",
103
+ "additionalProperties": False,
104
+ "required": ["schema_version", "brief_id", "evidence_cards", "coverage"],
105
+ "properties": {
106
+ "schema_version": {"const": EVIDENCE_BUNDLE_SCHEMA_VERSION},
107
+ "brief_id": _NONEMPTY_STRING,
108
+ "evidence_cards": {
109
+ "type": "array",
110
+ "items": {
111
+ "type": "object",
112
+ "additionalProperties": False,
113
+ "required": [
114
+ "card_id",
115
+ "claim_slot",
116
+ "statement",
117
+ "design_implication",
118
+ "source_id",
119
+ "source_location",
120
+ "evidence_level",
121
+ "evidence_excerpt",
122
+ "limitations",
123
+ "does_not_establish",
124
+ ],
125
+ "properties": {
126
+ "card_id": _NONEMPTY_STRING,
127
+ "claim_slot": _NONEMPTY_STRING,
128
+ "statement": _NONEMPTY_STRING,
129
+ "design_implication": _NONEMPTY_STRING,
130
+ "source_id": _NONEMPTY_STRING,
131
+ "source_location": _NONEMPTY_STRING,
132
+ "evidence_level": {"enum": ["fulltext", "abstract", "metadata", "user_supplied"]},
133
+ "evidence_excerpt": _NONEMPTY_STRING,
134
+ "limitations": _STRING_LIST,
135
+ "does_not_establish": _STRING_LIST,
136
+ },
137
+ },
138
+ },
139
+ "paper_registry": {
140
+ "type": "array",
141
+ "items": {
142
+ "type": "object",
143
+ "additionalProperties": False,
144
+ "required": [
145
+ "canonical_paper_id",
146
+ "title",
147
+ "provider_ids",
148
+ "providers",
149
+ "query_task_ids",
150
+ "content_availability",
151
+ "fulltext_source_location",
152
+ ],
153
+ "properties": {
154
+ "canonical_paper_id": _NONEMPTY_STRING,
155
+ "title": _NONEMPTY_STRING,
156
+ "doi": {"type": "string"},
157
+ "authors": _STRING_LIST,
158
+ "year": {"type": "string"},
159
+ "venue": {"type": "string"},
160
+ "url": {"type": "string"},
161
+ "citation_rendering_status": {
162
+ "enum": ["RENDERABLE", "NOT_RENDERABLE_NEEDS_HUMAN_METADATA"]
163
+ },
164
+ "citation_missing_fields": _STRING_LIST,
165
+ "provider_ids": {"type": "object", "minProperties": 1},
166
+ "providers": _STRING_LIST,
167
+ "query_task_ids": _STRING_LIST,
168
+ "content_availability": {"enum": ["fulltext", "abstract", "metadata", "user_supplied", "unavailable"]},
169
+ "fulltext_source_location": {"type": "string"},
170
+ "keynote_status": {"enum": ["TRACEABLE_CARDS_AVAILABLE", "NO_CARDS_EXTRACTED", "NO_ELIGIBLE_TEXT"]},
171
+ },
172
+ },
173
+ },
174
+ "keynotes": {
175
+ "type": "array",
176
+ "items": {
177
+ "type": "object",
178
+ "additionalProperties": False,
179
+ "required": ["canonical_paper_id", "status", "evidence_card_ids", "covered_slots", "source_locations"],
180
+ "properties": {
181
+ "canonical_paper_id": _NONEMPTY_STRING,
182
+ "status": {"enum": ["TRACEABLE_CARDS_AVAILABLE", "NO_CARDS_EXTRACTED", "NO_ELIGIBLE_TEXT"]},
183
+ "evidence_card_ids": _STRING_LIST,
184
+ "covered_slots": _STRING_LIST,
185
+ "source_locations": _STRING_LIST,
186
+ },
187
+ },
188
+ },
189
+ "field_evidence_ledger": {
190
+ "type": "array",
191
+ "items": {
192
+ "type": "object",
193
+ "additionalProperties": False,
194
+ "required": ["field_path", "status", "card_ids", "source_ids", "required_evidence_levels", "reason"],
195
+ "properties": {
196
+ "field_path": _NONEMPTY_STRING,
197
+ "status": _STATUS_VALUE,
198
+ "card_ids": _STRING_LIST,
199
+ "source_ids": _STRING_LIST,
200
+ "required_evidence_levels": _STRING_LIST,
201
+ "reason": _NONEMPTY_STRING,
202
+ },
203
+ },
204
+ },
205
+ "retrieval_audit": {"type": "object"},
206
+ "coverage": {
207
+ "type": "object",
208
+ "additionalProperties": False,
209
+ "required": ["required_slots", "covered_slots", "uncovered_slots"],
210
+ "properties": {
211
+ "required_slots": _STRING_LIST,
212
+ "covered_slots": _STRING_LIST,
213
+ "uncovered_slots": _STRING_LIST,
214
+ },
215
+ },
216
+ },
217
+ }
218
+
219
+ OUTCOME_BRANCH_SCHEMA: dict[str, Any] = {
220
+ "$schema": "https://json-schema.org/draft/2020-12/schema",
221
+ "title": "OutcomeBranch v1",
222
+ "type": "object",
223
+ "additionalProperties": False,
224
+ "required": [
225
+ "schema_version",
226
+ "branch_id",
227
+ "trigger",
228
+ "interpretation",
229
+ "conclusion_scope",
230
+ "improvement_actions",
231
+ "evidence_status",
232
+ ],
233
+ "properties": {
234
+ "schema_version": {"const": OUTCOME_BRANCH_SCHEMA_VERSION},
235
+ "branch_id": {"enum": ["supports_mechanism", "partial_or_heterogeneous", "null_or_contradictory", "uninformative_or_invalid"]},
236
+ "trigger": _NONEMPTY_STRING,
237
+ "interpretation": _NONEMPTY_STRING,
238
+ "conclusion_scope": _NONEMPTY_STRING,
239
+ "improvement_actions": {"type": "array", "minItems": 1, "items": _NONEMPTY_STRING},
240
+ "evidence_status": {"const": "EXPECTED_NOT_OBSERVED"},
241
+ },
242
+ }
243
+
244
+ EXPERIMENT_DESIGN_SCHEMA: dict[str, Any] = {
245
+ "$schema": "https://json-schema.org/draft/2020-12/schema",
246
+ "title": "ExperimentDesign v1",
247
+ "type": "object",
248
+ "additionalProperties": False,
249
+ "required": [
250
+ "schema_version",
251
+ "design_id",
252
+ "evidence_status",
253
+ "execution_policy",
254
+ "research_brief",
255
+ "evidence_bundle",
256
+ "research_design",
257
+ "hypothesis_mapping",
258
+ "variables_and_operationalization",
259
+ "sampling_and_eligibility",
260
+ "measurement_and_calibration",
261
+ "comparison_and_robustness",
262
+ "analysis_plan",
263
+ "data_governance_and_reproducibility",
264
+ "field_statuses",
265
+ "outcome_branches",
266
+ "risk_and_human_review",
267
+ "open_design_questions",
268
+ "observed_results",
269
+ "validation_report",
270
+ ],
271
+ "properties": {
272
+ "schema_version": {"const": EXPERIMENT_DESIGN_SCHEMA_VERSION},
273
+ "design_id": _NONEMPTY_STRING,
274
+ "evidence_status": {"const": "DESIGNED_NOT_EXECUTED"},
275
+ "execution_policy": {
276
+ "type": "object",
277
+ "additionalProperties": False,
278
+ "required": ["mode", "allow_digital_execution", "reason"],
279
+ "properties": {
280
+ "mode": {"enum": [DESIGN_ONLY, DIGITAL_EXECUTION_ELIGIBLE]},
281
+ "allow_digital_execution": {"type": "boolean"},
282
+ "reason": _NONEMPTY_STRING,
283
+ },
284
+ },
285
+ "research_brief": deepcopy(RESEARCH_BRIEF_SCHEMA),
286
+ "evidence_bundle": deepcopy(EVIDENCE_BUNDLE_SCHEMA),
287
+ "variable_claim_model": {"type": "object"},
288
+ "formal_reasoning_plan": {"type": "object"},
289
+ "counterexample_analysis": {"type": "object"},
290
+ "reasoning_validation_report": {"type": "object"},
291
+ "research_design": {
292
+ "type": "object",
293
+ "additionalProperties": False,
294
+ "required": ["design_type", "experimental_unit", "time_structure"],
295
+ "properties": {
296
+ "design_type": _NONEMPTY_STRING,
297
+ "experimental_unit": _NONEMPTY_STRING,
298
+ "time_structure": _NONEMPTY_STRING,
299
+ },
300
+ },
301
+ "hypothesis_mapping": {
302
+ "type": "array",
303
+ "minItems": 1,
304
+ "items": {
305
+ "type": "object",
306
+ "additionalProperties": False,
307
+ "required": ["hypothesis_id", "claim", "observables", "decision_rule"],
308
+ "properties": {
309
+ "hypothesis_id": _NONEMPTY_STRING,
310
+ "claim": _NONEMPTY_STRING,
311
+ "observables": _STRING_LIST,
312
+ "decision_rule": _NONEMPTY_STRING,
313
+ },
314
+ },
315
+ },
316
+ "variables_and_operationalization": {
317
+ "type": "object",
318
+ "additionalProperties": False,
319
+ "required": ["independent_variables", "dependent_variables", "control_variables", "confounders", "operational_definitions"],
320
+ "properties": {
321
+ "independent_variables": {"type": "array"},
322
+ "dependent_variables": {"type": "array"},
323
+ "control_variables": {"type": "array"},
324
+ "confounders": {"type": "array"},
325
+ "operational_definitions": {"type": "array"},
326
+ },
327
+ },
328
+ "sampling_and_eligibility": {
329
+ "type": "object",
330
+ "additionalProperties": False,
331
+ "required": ["source", "eligibility_criteria", "sample_size_or_power_basis"],
332
+ "properties": {
333
+ "source": {"type": "object"},
334
+ "eligibility_criteria": {"type": "object"},
335
+ "sample_size_or_power_basis": {"type": "object"},
336
+ },
337
+ },
338
+ "measurement_and_calibration": {
339
+ "type": "object",
340
+ "additionalProperties": False,
341
+ "required": ["instruments", "measurement_plan", "calibration", "quality_control"],
342
+ "properties": {
343
+ "instruments": {"type": "array"},
344
+ "measurement_plan": {"type": "object"},
345
+ "calibration": {"type": "object"},
346
+ "quality_control": {"type": "object"},
347
+ },
348
+ },
349
+ "comparison_and_robustness": {
350
+ "type": "object",
351
+ "additionalProperties": False,
352
+ "required": ["groups", "controls", "baselines", "comparisons", "ablation_sensitivity_robustness"],
353
+ "properties": {
354
+ "groups": {"type": "array"},
355
+ "controls": {"type": "array"},
356
+ "baselines": {"type": "array"},
357
+ "comparisons": {"type": "array"},
358
+ "ablation_sensitivity_robustness": {"type": "array"},
359
+ },
360
+ },
361
+ "analysis_plan": {
362
+ "type": "object",
363
+ "additionalProperties": False,
364
+ "required": ["randomization", "blinding", "repetitions", "batch_effects", "missing_data", "statistical_analysis"],
365
+ "properties": {
366
+ "randomization": {"type": "object"},
367
+ "blinding": {"type": "object"},
368
+ "repetitions": {"type": "object"},
369
+ "batch_effects": {"type": "object"},
370
+ "missing_data": {"type": "object"},
371
+ "statistical_analysis": {"type": "object"},
372
+ },
373
+ },
374
+ "data_governance_and_reproducibility": {
375
+ "type": "object",
376
+ "additionalProperties": False,
377
+ "required": ["data_management", "reproducibility"],
378
+ "properties": {
379
+ "data_management": {"type": "object"},
380
+ "reproducibility": {"type": "object"},
381
+ },
382
+ },
383
+ "outcome_branches": {"type": "array", "minItems": 4, "items": deepcopy(OUTCOME_BRANCH_SCHEMA)},
384
+ "risk_and_human_review": {
385
+ "type": "object",
386
+ "additionalProperties": False,
387
+ "required": ["risk_level", "human_review_required", "review_triggers", "execution_prohibited"],
388
+ "properties": {
389
+ "risk_level": {"enum": ["low", "medium", "high", "critical"]},
390
+ "human_review_required": {"type": "boolean"},
391
+ "review_triggers": _STRING_LIST,
392
+ "approval_dependencies": _STRING_LIST,
393
+ "restricted_content": _STRING_LIST,
394
+ "execution_prohibited": {"type": "boolean"},
395
+ },
396
+ },
397
+ "template_composition": {
398
+ "type": "object",
399
+ "additionalProperties": False,
400
+ "required": ["template_id", "secondary_template", "submode", "prompt_variant", "llm_used"],
401
+ "properties": {
402
+ "template_id": _NONEMPTY_STRING,
403
+ "secondary_template": {"type": "string"},
404
+ "submode": {"type": "string"},
405
+ "prompt_variant": _NONEMPTY_STRING,
406
+ "llm_used": {"type": "boolean"},
407
+ },
408
+ },
409
+ "template_details": {"type": "object"},
410
+ "field_statuses": {
411
+ "type": "object",
412
+ "additionalProperties": _NONEMPTY_STRING,
413
+ },
414
+ "open_design_questions": {"type": "array"},
415
+ "observed_results": {"type": "array", "maxItems": 0},
416
+ "validation_report": {
417
+ "type": "object",
418
+ "additionalProperties": False,
419
+ "required": ["status", "errors", "warnings"],
420
+ "properties": {
421
+ "status": {"enum": ["READY_FOR_HUMAN_REVIEW", "DRAFT_REQUIRES_INPUT", "BLOCKED_BY_SCOPE", "BLOCKED_BY_RISK_REVIEW"]},
422
+ "errors": _STRING_LIST,
423
+ "warnings": _STRING_LIST,
424
+ },
425
+ },
426
+ },
427
+ }
428
+
429
+
430
+ def _schema_errors(payload: Any, schema: Mapping[str, Any], *, prefix: str = "$") -> list[str]:
431
+ errors: list[str] = []
432
+ for error in sorted(Draft202012Validator(schema).iter_errors(payload), key=lambda item: list(item.absolute_path)):
433
+ path = "/".join(str(part) for part in error.absolute_path)
434
+ errors.append(f"{prefix}/{path}: {error.message}" if path else f"{prefix}: {error.message}")
435
+ return errors
436
+
437
+
438
+ def _scope_errors(discipline_ids: object) -> list[str]:
439
+ scope = resolve_design_scope(discipline_ids)
440
+ if scope["status"] == "IN_SCOPE":
441
+ return []
442
+ errors: list[str] = []
443
+ errors.extend(f"excluded_discipline:{identifier}" for identifier in scope["excluded_discipline_ids"])
444
+ errors.extend(f"unresolved_discipline:{identifier}" for identifier in scope["unresolved_disciplines"])
445
+ if not errors:
446
+ errors.append("discipline_scope_requires_clarification")
447
+ return errors
448
+
449
+
450
+ def validate_research_brief(payload: Any) -> list[str]:
451
+ errors = _schema_errors(payload, RESEARCH_BRIEF_SCHEMA)
452
+ if isinstance(payload, Mapping):
453
+ errors.extend(_scope_errors(payload.get("discipline_ids")))
454
+ return errors
455
+
456
+
457
+ def validate_evidence_bundle(payload: Any) -> list[str]:
458
+ errors = _schema_errors(payload, EVIDENCE_BUNDLE_SCHEMA)
459
+ if not isinstance(payload, Mapping):
460
+ return errors
461
+ registry = payload.get("paper_registry")
462
+ paper_ids = {
463
+ str(record.get("canonical_paper_id") or "").strip()
464
+ for record in registry
465
+ if isinstance(record, Mapping)
466
+ } if isinstance(registry, list) else set()
467
+ if isinstance(registry, list) and len(paper_ids) != len(registry):
468
+ errors.append("paper_registry_contains_missing_or_duplicate_canonical_paper_id")
469
+ if isinstance(registry, list):
470
+ for record in registry:
471
+ if not isinstance(record, Mapping):
472
+ continue
473
+ rendering_status = str(record.get("citation_rendering_status") or "").strip()
474
+ if not rendering_status:
475
+ continue
476
+ missing_fields = {
477
+ str(field).strip()
478
+ for field in record.get("citation_missing_fields") or []
479
+ if str(field).strip()
480
+ }
481
+ expected_missing_fields = {
482
+ field
483
+ for field, value in (
484
+ ("authors", record.get("authors")),
485
+ ("year", record.get("year")),
486
+ ("venue", record.get("venue")),
487
+ )
488
+ if not value
489
+ }
490
+ if rendering_status == "RENDERABLE" and missing_fields:
491
+ errors.append("renderable_citation_lists_missing_metadata")
492
+ elif rendering_status == "RENDERABLE" and expected_missing_fields:
493
+ errors.append("renderable_citation_is_missing_required_metadata")
494
+ elif rendering_status == "NOT_RENDERABLE_NEEDS_HUMAN_METADATA":
495
+ if not missing_fields:
496
+ errors.append("non_renderable_citation_omits_missing_metadata")
497
+ elif missing_fields != expected_missing_fields:
498
+ errors.append("non_renderable_citation_missing_metadata_mismatch")
499
+ cards = payload.get("evidence_cards")
500
+ card_ids: set[str] = set()
501
+ card_by_id: dict[str, Mapping[str, Any]] = {}
502
+ if isinstance(cards, list):
503
+ if cards and not isinstance(registry, list):
504
+ errors.append("evidence_cards_require_paper_registry")
505
+ for card in cards:
506
+ if not isinstance(card, Mapping):
507
+ continue
508
+ card_id = str(card.get("card_id") or "").strip()
509
+ source_id = str(card.get("source_id") or "").strip()
510
+ if card_id in card_ids:
511
+ errors.append(f"duplicate_evidence_card_id:{card_id}")
512
+ if card_id:
513
+ card_ids.add(card_id)
514
+ card_by_id[card_id] = card
515
+ if isinstance(registry, list) and source_id not in paper_ids:
516
+ errors.append(f"evidence_card_unknown_source_id:{source_id}")
517
+ ledger = payload.get("field_evidence_ledger")
518
+ if isinstance(ledger, list):
519
+ seen_fields: set[str] = set()
520
+ for record in ledger:
521
+ if not isinstance(record, Mapping):
522
+ continue
523
+ field_path = str(record.get("field_path") or "").strip()
524
+ if field_path in seen_fields:
525
+ errors.append(f"duplicate_field_evidence_ledger_path:{field_path}")
526
+ if field_path:
527
+ seen_fields.add(field_path)
528
+ referenced_cards = [
529
+ str(card_id).strip()
530
+ for card_id in record.get("card_ids") or []
531
+ if str(card_id).strip()
532
+ ]
533
+ for card_id in referenced_cards:
534
+ if card_id not in card_ids:
535
+ errors.append(f"field_evidence_ledger_unknown_card_id:{field_path}:{card_id}")
536
+ if record.get("status") == "evidence_backed":
537
+ required_levels = set(record.get("required_evidence_levels") or [])
538
+ qualifying = [
539
+ card_by_id[card_id]
540
+ for card_id in referenced_cards
541
+ if card_id in card_by_id
542
+ and card_by_id[card_id].get("evidence_level") in required_levels
543
+ ]
544
+ if not qualifying:
545
+ errors.append(f"evidence_backed_field_without_qualifying_card:{field_path}")
546
+ return errors
547
+
548
+
549
+ def validate_outcome_branch(payload: Any) -> list[str]:
550
+ return _schema_errors(payload, OUTCOME_BRANCH_SCHEMA)
551
+
552
+
553
+ def validate_experiment_design(payload: Any) -> list[str]:
554
+ errors = _schema_errors(payload, EXPERIMENT_DESIGN_SCHEMA)
555
+ if not isinstance(payload, Mapping):
556
+ return errors
557
+ research_brief = payload.get("research_brief")
558
+ evidence_bundle = payload.get("evidence_bundle")
559
+ if isinstance(research_brief, Mapping):
560
+ errors.extend(f"research_brief:{error}" for error in validate_research_brief(research_brief))
561
+ if isinstance(evidence_bundle, Mapping):
562
+ errors.extend(f"evidence_bundle:{error}" for error in validate_evidence_bundle(evidence_bundle))
563
+ if isinstance(research_brief, Mapping) and isinstance(evidence_bundle, Mapping):
564
+ if evidence_bundle.get("brief_id") != research_brief.get("brief_id"):
565
+ errors.append("evidence_bundle_brief_id_mismatch")
566
+ reasoning_context = _mapping(research_brief.get("reasoning_context")) if isinstance(research_brief, Mapping) else {}
567
+ if reasoning_context:
568
+ errors.extend(
569
+ f"research_brief.reasoning_context:{error}"
570
+ for error in _schema_errors(reasoning_context, REASONING_CONTEXT_SCHEMA)
571
+ )
572
+ from .reasoning_validation import validate_reasoning_artifacts
573
+
574
+ errors.extend(
575
+ validate_reasoning_artifacts(
576
+ variable_claim_model=payload.get("variable_claim_model") if isinstance(payload.get("variable_claim_model"), Mapping) else None,
577
+ formal_reasoning_plan=payload.get("formal_reasoning_plan") if isinstance(payload.get("formal_reasoning_plan"), Mapping) else None,
578
+ counterexample_analysis=payload.get("counterexample_analysis") if isinstance(payload.get("counterexample_analysis"), Mapping) else None,
579
+ design=payload,
580
+ template_composition=payload.get("template_composition") if isinstance(payload.get("template_composition"), Mapping) else None,
581
+ )
582
+ )
583
+ field_statuses = payload.get("field_statuses")
584
+ status_sections = {
585
+ "research_design",
586
+ "hypothesis_mapping",
587
+ "variables_and_operationalization",
588
+ "sampling_and_eligibility",
589
+ "measurement_and_calibration",
590
+ "comparison_and_robustness",
591
+ "analysis_plan",
592
+ "data_governance_and_reproducibility",
593
+ "template_details",
594
+ }
595
+ def nested_status_paths(value: object, path: str) -> list[str]:
596
+ found: list[str] = []
597
+ if isinstance(value, Mapping):
598
+ for key, child in value.items():
599
+ child_path = f"{path}.{key}" if path else str(key)
600
+ if key == "status":
601
+ found.append(child_path)
602
+ else:
603
+ found.extend(nested_status_paths(child, child_path))
604
+ elif isinstance(value, list):
605
+ for index, child in enumerate(value):
606
+ found.extend(nested_status_paths(child, f"{path}[{index}]"))
607
+ return found
608
+ for section in status_sections:
609
+ for path in nested_status_paths(payload.get(section), section):
610
+ errors.append(f"{path}:status_must_use_top_level_field_statuses")
611
+ if isinstance(field_statuses, Mapping) and isinstance(evidence_bundle, Mapping):
612
+ qualifying_fields = {
613
+ str(record.get("field_path") or "").strip()
614
+ for record in evidence_bundle.get("field_evidence_ledger") or []
615
+ if isinstance(record, Mapping) and record.get("status") == "evidence_backed"
616
+ }
617
+ for field_path, status in field_statuses.items():
618
+ if status == "evidence_backed" and str(field_path) not in qualifying_fields:
619
+ errors.append(f"field_status_evidence_not_qualified:{field_path}")
620
+ branches = payload.get("outcome_branches")
621
+ if isinstance(branches, list):
622
+ errors.extend(
623
+ f"outcome_branches[{index}]:{error}"
624
+ for index, branch in enumerate(branches)
625
+ for error in validate_outcome_branch(branch)
626
+ )
627
+ expected_ids = {
628
+ "supports_mechanism",
629
+ "partial_or_heterogeneous",
630
+ "null_or_contradictory",
631
+ "uninformative_or_invalid",
632
+ }
633
+ actual_ids = [branch.get("branch_id") for branch in branches if isinstance(branch, Mapping)]
634
+ if set(actual_ids) != expected_ids or len(actual_ids) != len(expected_ids):
635
+ errors.append("outcome_branches_must_cover_each_required_branch_once")
636
+ policy = payload.get("execution_policy")
637
+ if isinstance(research_brief, Mapping) and isinstance(policy, Mapping):
638
+ expected = resolve_execution_policy(
639
+ research_brief.get("discipline_ids"),
640
+ allow_digital_execution=bool(policy.get("allow_digital_execution")),
641
+ )
642
+ if policy.get("mode") != expected["mode"]:
643
+ errors.append("execution_policy_mode_does_not_match_discipline_scope")
644
+ return errors
645
+
646
+
647
+ def assert_valid(payload: Any, validator) -> dict[str, Any]:
648
+ errors = validator(payload)
649
+ if errors:
650
+ raise ValueError("; ".join(errors))
651
+ return dict(payload)
652
+
653
+
654
+ def _text(value: Any) -> str:
655
+ return str(value or "").strip()
656
+
657
+
658
+ def _mapping(value: object) -> dict[str, Any]:
659
+ return dict(value) if isinstance(value, Mapping) else {}
660
+
661
+
662
+ def _texts(value: Any) -> list[str]:
663
+ values = value if isinstance(value, (list, tuple, set)) else [value]
664
+ result: list[str] = []
665
+ for item in values:
666
+ text = _text(item)
667
+ if text and text not in result:
668
+ result.append(text)
669
+ return result
670
+
671
+
672
+ def _idea_source_layers(
673
+ direction: Mapping[str, Any],
674
+ idea_result: Mapping[str, Any],
675
+ audit_sources: Mapping[str, Any] | None,
676
+ ) -> list[tuple[str, Mapping[str, Any]]]:
677
+ """Expose source precedence without ever combining multiple directions."""
678
+
679
+ layers: list[tuple[str, Mapping[str, Any]]] = []
680
+
681
+ def add_nested(prefix: str, value: object) -> None:
682
+ record = value if isinstance(value, Mapping) else {}
683
+ for nested_key in ("hypothesis", "experiment_handoff"):
684
+ nested = record.get(nested_key)
685
+ if isinstance(nested, Mapping):
686
+ layers.append((f"{prefix}.{nested_key}", nested))
687
+ layers.append((prefix, record))
688
+
689
+ add_nested("selected_direction", direction)
690
+ add_nested("legacy_best_entry", idea_result.get("legacy_best_entry"))
691
+ audit = audit_sources if isinstance(audit_sources, Mapping) else {}
692
+ add_nested("selected_primary_idea", audit.get("selected_primary_idea"))
693
+ add_nested("idea_candidate", audit.get("idea_candidate"))
694
+ return layers
695
+
696
+
697
+ def _first_idea_value(
698
+ layers: list[tuple[str, Mapping[str, Any]]],
699
+ keys: tuple[str, ...],
700
+ ) -> Any:
701
+ for _, layer in layers:
702
+ for key in keys:
703
+ value = layer.get(key)
704
+ if value not in (None, "", [], {}):
705
+ return deepcopy(value)
706
+ return ""
707
+
708
+
709
+ def build_research_brief_from_idea_result(
710
+ idea_result: Mapping[str, Any],
711
+ *,
712
+ discipline_ids: object,
713
+ brief_id: str,
714
+ selected_direction: str = "",
715
+ audit_sources: Mapping[str, Any] | None = None,
716
+ ) -> dict[str, Any]:
717
+ """Create a v1 ResearchBrief from one explicitly selected Idea Agent direction."""
718
+
719
+ if idea_result.get("schema_version") != "idea_result_v5":
720
+ raise ValueError("ResearchBrief v1 requires an idea_result_v5 input.")
721
+ directions = [item for item in idea_result.get("directions") or [] if isinstance(item, Mapping)]
722
+ requested = _text(selected_direction) or _text(idea_result.get("primary_direction"))
723
+ matching = [
724
+ direction
725
+ for direction in directions
726
+ if _text(direction.get("direction_mode")) == requested
727
+ or _text(direction.get("id")) == requested
728
+ or _text(direction.get("title")) == requested
729
+ ]
730
+ if len(matching) != 1:
731
+ raise ValueError("ResearchBrief v1 requires one unambiguous selected Idea Agent direction.")
732
+ direction = matching[0]
733
+ hypothesis = direction.get("hypothesis") if isinstance(direction.get("hypothesis"), Mapping) else {}
734
+ handoff = direction.get("experiment_handoff") if isinstance(direction.get("experiment_handoff"), Mapping) else {}
735
+ direction_id = _text(direction.get("direction_mode")) or _text(direction.get("id")) or _text(direction.get("title"))
736
+ idea_layers = _idea_source_layers(direction, idea_result, audit_sources)
737
+ research_object = _first_idea_value(idea_layers, ("scientific_object", "research_object")) or {}
738
+ if not isinstance(research_object, Mapping):
739
+ research_object = {"description": _text(research_object)} if _text(research_object) else {}
740
+ title = _text(direction.get("title")) or _text(_first_idea_value(idea_layers, ("title",))) or _text(idea_result.get("title"))
741
+ payload = {
742
+ "schema_version": RESEARCH_BRIEF_SCHEMA_VERSION,
743
+ "brief_id": _text(brief_id),
744
+ "topic": _text(idea_result.get("topic")) or _text(idea_result.get("title")) or title,
745
+ "discipline_ids": list(normalize_discipline_ids(discipline_ids)),
746
+ "selected_direction": {
747
+ "id": direction_id,
748
+ "title": title,
749
+ "central_hypothesis": _text(_first_idea_value(idea_layers, ("central_hypothesis", "claim_to_test"))),
750
+ "mechanism_or_relation": _text(_first_idea_value(idea_layers, ("mechanism_or_relation", "mechanism_to_discriminate"))),
751
+ },
752
+ "research_object": dict(research_object),
753
+ "intervention_or_transformation": _text(_first_idea_value(idea_layers, ("intervention_or_transformation",))),
754
+ "discriminating_observations": _texts(_first_idea_value(idea_layers, ("required_observations", "discriminating_observations", "discriminating_observation"))),
755
+ "boundary_conditions": _texts(_first_idea_value(idea_layers, ("boundary_conditions", "boundary_or_failure_condition"))),
756
+ "alternative_explanations": _texts(_first_idea_value(idea_layers, ("alternative_explanations",))),
757
+ "known_unknowns": _texts(_first_idea_value(idea_layers, ("known_unknowns",))),
758
+ "evidence_status": "PROPOSED",
759
+ "source": {
760
+ "idea_result_schema": "idea_result_v5",
761
+ "direction_id": direction_id,
762
+ "survey_binding": dict(idea_result.get("survey_binding") or {}),
763
+ },
764
+ "reasoning_context": build_reasoning_context_from_idea_result(
765
+ idea_result,
766
+ selected_direction=selected_direction,
767
+ audit_sources=audit_sources,
768
+ ),
769
+ }
770
+ assert_valid(payload, validate_research_brief)
771
+ return payload