@hongmaple0820/med-scale-research-os 0.43.0

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 (1104) hide show
  1. package/.scale/mcp-servers.yaml +144 -0
  2. package/.scale/skills.json +830 -0
  3. package/.scale/verification.json +52 -0
  4. package/LICENSE +15 -0
  5. package/README.en.md +156 -0
  6. package/README.md +156 -0
  7. package/dist/adapters/AiderAdapter.d.ts +22 -0
  8. package/dist/adapters/AiderAdapter.js +262 -0
  9. package/dist/adapters/AiderAdapter.js.map +1 -0
  10. package/dist/adapters/AntigravityAdapter.d.ts +4 -0
  11. package/dist/adapters/AntigravityAdapter.js +21 -0
  12. package/dist/adapters/AntigravityAdapter.js.map +1 -0
  13. package/dist/adapters/ClaudeCodeAdapter.d.ts +54 -0
  14. package/dist/adapters/ClaudeCodeAdapter.js +185 -0
  15. package/dist/adapters/ClaudeCodeAdapter.js.map +1 -0
  16. package/dist/adapters/ClineAdapter.d.ts +4 -0
  17. package/dist/adapters/ClineAdapter.js +20 -0
  18. package/dist/adapters/ClineAdapter.js.map +1 -0
  19. package/dist/adapters/CodexAdapter.d.ts +15 -0
  20. package/dist/adapters/CodexAdapter.js +160 -0
  21. package/dist/adapters/CodexAdapter.js.map +1 -0
  22. package/dist/adapters/CursorAdapter.d.ts +14 -0
  23. package/dist/adapters/CursorAdapter.js +171 -0
  24. package/dist/adapters/CursorAdapter.js.map +1 -0
  25. package/dist/adapters/DeepSeekTuiAdapter.d.ts +19 -0
  26. package/dist/adapters/DeepSeekTuiAdapter.js +263 -0
  27. package/dist/adapters/DeepSeekTuiAdapter.js.map +1 -0
  28. package/dist/adapters/DoubaoAdapter.d.ts +14 -0
  29. package/dist/adapters/DoubaoAdapter.js +184 -0
  30. package/dist/adapters/DoubaoAdapter.js.map +1 -0
  31. package/dist/adapters/GeminiAdapter.d.ts +14 -0
  32. package/dist/adapters/GeminiAdapter.js +163 -0
  33. package/dist/adapters/GeminiAdapter.js.map +1 -0
  34. package/dist/adapters/GenericProjectAgentAdapter.d.ts +29 -0
  35. package/dist/adapters/GenericProjectAgentAdapter.js +204 -0
  36. package/dist/adapters/GenericProjectAgentAdapter.js.map +1 -0
  37. package/dist/adapters/HermesAdapter.d.ts +14 -0
  38. package/dist/adapters/HermesAdapter.js +163 -0
  39. package/dist/adapters/HermesAdapter.js.map +1 -0
  40. package/dist/adapters/JCodeAdapter.d.ts +4 -0
  41. package/dist/adapters/JCodeAdapter.js +19 -0
  42. package/dist/adapters/JCodeAdapter.js.map +1 -0
  43. package/dist/adapters/KiloCodeAdapter.d.ts +4 -0
  44. package/dist/adapters/KiloCodeAdapter.js +20 -0
  45. package/dist/adapters/KiloCodeAdapter.js.map +1 -0
  46. package/dist/adapters/KimiAdapter.d.ts +14 -0
  47. package/dist/adapters/KimiAdapter.js +183 -0
  48. package/dist/adapters/KimiAdapter.js.map +1 -0
  49. package/dist/adapters/KiroAdapter.d.ts +14 -0
  50. package/dist/adapters/KiroAdapter.js +180 -0
  51. package/dist/adapters/KiroAdapter.js.map +1 -0
  52. package/dist/adapters/OpenClawAdapter.d.ts +14 -0
  53. package/dist/adapters/OpenClawAdapter.js +163 -0
  54. package/dist/adapters/OpenClawAdapter.js.map +1 -0
  55. package/dist/adapters/OpenCodeAdapter.d.ts +14 -0
  56. package/dist/adapters/OpenCodeAdapter.js +172 -0
  57. package/dist/adapters/OpenCodeAdapter.js.map +1 -0
  58. package/dist/adapters/QCoderAdapter.d.ts +14 -0
  59. package/dist/adapters/QCoderAdapter.js +159 -0
  60. package/dist/adapters/QCoderAdapter.js.map +1 -0
  61. package/dist/adapters/QoderAdapter.d.ts +4 -0
  62. package/dist/adapters/QoderAdapter.js +21 -0
  63. package/dist/adapters/QoderAdapter.js.map +1 -0
  64. package/dist/adapters/TraeAdapter.d.ts +14 -0
  65. package/dist/adapters/TraeAdapter.js +159 -0
  66. package/dist/adapters/TraeAdapter.js.map +1 -0
  67. package/dist/adapters/VSCAdapter.d.ts +14 -0
  68. package/dist/adapters/VSCAdapter.js +159 -0
  69. package/dist/adapters/VSCAdapter.js.map +1 -0
  70. package/dist/adapters/WindsurfAdapter.d.ts +14 -0
  71. package/dist/adapters/WindsurfAdapter.js +185 -0
  72. package/dist/adapters/WindsurfAdapter.js.map +1 -0
  73. package/dist/adapters/WorkBuddyAdapter.d.ts +14 -0
  74. package/dist/adapters/WorkBuddyAdapter.js +159 -0
  75. package/dist/adapters/WorkBuddyAdapter.js.map +1 -0
  76. package/dist/adapters/index.d.ts +32 -0
  77. package/dist/adapters/index.js +87 -0
  78. package/dist/adapters/index.js.map +1 -0
  79. package/dist/agents/AgentChannel.d.ts +43 -0
  80. package/dist/agents/AgentChannel.js +136 -0
  81. package/dist/agents/AgentChannel.js.map +1 -0
  82. package/dist/agents/AgentCoordinator.d.ts +29 -0
  83. package/dist/agents/AgentCoordinator.js +136 -0
  84. package/dist/agents/AgentCoordinator.js.map +1 -0
  85. package/dist/agents/AgentDispatcher.d.ts +24 -0
  86. package/dist/agents/AgentDispatcher.js +112 -0
  87. package/dist/agents/AgentDispatcher.js.map +1 -0
  88. package/dist/agents/AgentManager.d.ts +14 -0
  89. package/dist/agents/AgentManager.js +85 -0
  90. package/dist/agents/AgentManager.js.map +1 -0
  91. package/dist/agents/AgentPool.d.ts +59 -0
  92. package/dist/agents/AgentPool.js +192 -0
  93. package/dist/agents/AgentPool.js.map +1 -0
  94. package/dist/agents/AgentRegistry.d.ts +20 -0
  95. package/dist/agents/AgentRegistry.js +36 -0
  96. package/dist/agents/AgentRegistry.js.map +1 -0
  97. package/dist/agents/AgentSourceLoader.d.ts +73 -0
  98. package/dist/agents/AgentSourceLoader.js +103 -0
  99. package/dist/agents/AgentSourceLoader.js.map +1 -0
  100. package/dist/agents/IAgent.d.ts +53 -0
  101. package/dist/agents/IAgent.js +4 -0
  102. package/dist/agents/IAgent.js.map +1 -0
  103. package/dist/agents/LeadershipPresets.d.ts +16 -0
  104. package/dist/agents/LeadershipPresets.js +152 -0
  105. package/dist/agents/LeadershipPresets.js.map +1 -0
  106. package/dist/agents/definitions/debugger.d.ts +2 -0
  107. package/dist/agents/definitions/debugger.js +6 -0
  108. package/dist/agents/definitions/debugger.js.map +1 -0
  109. package/dist/agents/definitions/doc-writer.d.ts +2 -0
  110. package/dist/agents/definitions/doc-writer.js +6 -0
  111. package/dist/agents/definitions/doc-writer.js.map +1 -0
  112. package/dist/agents/definitions/implementer.d.ts +2 -0
  113. package/dist/agents/definitions/implementer.js +6 -0
  114. package/dist/agents/definitions/implementer.js.map +1 -0
  115. package/dist/agents/definitions/planner.d.ts +2 -0
  116. package/dist/agents/definitions/planner.js +6 -0
  117. package/dist/agents/definitions/planner.js.map +1 -0
  118. package/dist/agents/definitions/researcher.d.ts +2 -0
  119. package/dist/agents/definitions/researcher.js +6 -0
  120. package/dist/agents/definitions/researcher.js.map +1 -0
  121. package/dist/agents/definitions/reviewer.d.ts +2 -0
  122. package/dist/agents/definitions/reviewer.js +6 -0
  123. package/dist/agents/definitions/reviewer.js.map +1 -0
  124. package/dist/agents/definitions/security.d.ts +2 -0
  125. package/dist/agents/definitions/security.js +6 -0
  126. package/dist/agents/definitions/security.js.map +1 -0
  127. package/dist/agents/definitions/tester.d.ts +2 -0
  128. package/dist/agents/definitions/tester.js +6 -0
  129. package/dist/agents/definitions/tester.js.map +1 -0
  130. package/dist/agents/index.d.ts +23 -0
  131. package/dist/agents/index.js +44 -0
  132. package/dist/agents/index.js.map +1 -0
  133. package/dist/agents/profiles.d.ts +26 -0
  134. package/dist/agents/profiles.js +197 -0
  135. package/dist/agents/profiles.js.map +1 -0
  136. package/dist/agents/types.d.ts +262 -0
  137. package/dist/agents/types.js +4 -0
  138. package/dist/agents/types.js.map +1 -0
  139. package/dist/api/cli.d.ts +2 -0
  140. package/dist/api/cli.js +6678 -0
  141. package/dist/api/cli.js.map +1 -0
  142. package/dist/api/doctor.d.ts +83 -0
  143. package/dist/api/doctor.js +982 -0
  144. package/dist/api/doctor.js.map +1 -0
  145. package/dist/api/mcp.d.ts +32 -0
  146. package/dist/api/mcp.js +223 -0
  147. package/dist/api/mcp.js.map +1 -0
  148. package/dist/api/medscale.d.ts +2 -0
  149. package/dist/api/medscale.js +20 -0
  150. package/dist/api/medscale.js.map +1 -0
  151. package/dist/api/quickstart.d.ts +86 -0
  152. package/dist/api/quickstart.js +291 -0
  153. package/dist/api/quickstart.js.map +1 -0
  154. package/dist/artifact/fsm.d.ts +41 -0
  155. package/dist/artifact/fsm.js +221 -0
  156. package/dist/artifact/fsm.js.map +1 -0
  157. package/dist/artifact/fsmDefinitions.d.ts +18 -0
  158. package/dist/artifact/fsmDefinitions.js +296 -0
  159. package/dist/artifact/fsmDefinitions.js.map +1 -0
  160. package/dist/artifact/sqliteStore.d.ts +61 -0
  161. package/dist/artifact/sqliteStore.js +381 -0
  162. package/dist/artifact/sqliteStore.js.map +1 -0
  163. package/dist/artifact/store.d.ts +49 -0
  164. package/dist/artifact/store.js +116 -0
  165. package/dist/artifact/store.js.map +1 -0
  166. package/dist/artifact/types.d.ts +535 -0
  167. package/dist/artifact/types.js +74 -0
  168. package/dist/artifact/types.js.map +1 -0
  169. package/dist/bootstrap/DependencyBootstrap.d.ts +112 -0
  170. package/dist/bootstrap/DependencyBootstrap.js +1046 -0
  171. package/dist/bootstrap/DependencyBootstrap.js.map +1 -0
  172. package/dist/bootstrap/DependencyBootstrapRenderer.d.ts +3 -0
  173. package/dist/bootstrap/DependencyBootstrapRenderer.js +138 -0
  174. package/dist/bootstrap/DependencyBootstrapRenderer.js.map +1 -0
  175. package/dist/bridge/PythonBridge.d.ts +80 -0
  176. package/dist/bridge/PythonBridge.js +437 -0
  177. package/dist/bridge/PythonBridge.js.map +1 -0
  178. package/dist/bridge/index.d.ts +2 -0
  179. package/dist/bridge/index.js +7 -0
  180. package/dist/bridge/index.js.map +1 -0
  181. package/dist/bridge/medicalWorkflows.d.ts +29 -0
  182. package/dist/bridge/medicalWorkflows.js +156 -0
  183. package/dist/bridge/medicalWorkflows.js.map +1 -0
  184. package/dist/bridge/types.d.ts +381 -0
  185. package/dist/bridge/types.js +113 -0
  186. package/dist/bridge/types.js.map +1 -0
  187. package/dist/cache/ScanCache.d.ts +41 -0
  188. package/dist/cache/ScanCache.js +120 -0
  189. package/dist/cache/ScanCache.js.map +1 -0
  190. package/dist/capabilities/BrowserCapability.d.ts +30 -0
  191. package/dist/capabilities/BrowserCapability.js +73 -0
  192. package/dist/capabilities/BrowserCapability.js.map +1 -0
  193. package/dist/capabilities/BrowserQACapability.d.ts +165 -0
  194. package/dist/capabilities/BrowserQACapability.js +438 -0
  195. package/dist/capabilities/BrowserQACapability.js.map +1 -0
  196. package/dist/capabilities/CapabilityRegistry.d.ts +17 -0
  197. package/dist/capabilities/CapabilityRegistry.js +65 -0
  198. package/dist/capabilities/CapabilityRegistry.js.map +1 -0
  199. package/dist/capabilities/ComputerCapability.d.ts +28 -0
  200. package/dist/capabilities/ComputerCapability.js +40 -0
  201. package/dist/capabilities/ComputerCapability.js.map +1 -0
  202. package/dist/capabilities/InstalledSkillsIntegration.d.ts +69 -0
  203. package/dist/capabilities/InstalledSkillsIntegration.js +240 -0
  204. package/dist/capabilities/InstalledSkillsIntegration.js.map +1 -0
  205. package/dist/capabilities/SearchCapability.d.ts +46 -0
  206. package/dist/capabilities/SearchCapability.js +88 -0
  207. package/dist/capabilities/SearchCapability.js.map +1 -0
  208. package/dist/capabilities/index.d.ts +6 -0
  209. package/dist/capabilities/index.js +9 -0
  210. package/dist/capabilities/index.js.map +1 -0
  211. package/dist/capabilities/types.d.ts +92 -0
  212. package/dist/capabilities/types.js +7 -0
  213. package/dist/capabilities/types.js.map +1 -0
  214. package/dist/cli/autofixCommands.d.ts +22 -0
  215. package/dist/cli/autofixCommands.js +32 -0
  216. package/dist/cli/autofixCommands.js.map +1 -0
  217. package/dist/cli/cortexCommands.d.ts +71 -0
  218. package/dist/cli/cortexCommands.js +335 -0
  219. package/dist/cli/cortexCommands.js.map +1 -0
  220. package/dist/cli/costCommands.d.ts +13 -0
  221. package/dist/cli/costCommands.js +48 -0
  222. package/dist/cli/costCommands.js.map +1 -0
  223. package/dist/cli/evolutionCommands.d.ts +112 -0
  224. package/dist/cli/evolutionCommands.js +246 -0
  225. package/dist/cli/evolutionCommands.js.map +1 -0
  226. package/dist/cli/gateStatusCommands.d.ts +1 -0
  227. package/dist/cli/gateStatusCommands.js +52 -0
  228. package/dist/cli/gateStatusCommands.js.map +1 -0
  229. package/dist/cli/liteCommands.d.ts +81 -0
  230. package/dist/cli/liteCommands.js +148 -0
  231. package/dist/cli/liteCommands.js.map +1 -0
  232. package/dist/cli/orchCommands.d.ts +43 -0
  233. package/dist/cli/orchCommands.js +135 -0
  234. package/dist/cli/orchCommands.js.map +1 -0
  235. package/dist/cli/phaseCommands.d.ts +248 -0
  236. package/dist/cli/phaseCommands.js +1878 -0
  237. package/dist/cli/phaseCommands.js.map +1 -0
  238. package/dist/cli/promptCommands.d.ts +1 -0
  239. package/dist/cli/promptCommands.js +57 -0
  240. package/dist/cli/promptCommands.js.map +1 -0
  241. package/dist/cli/qaCommands.d.ts +22 -0
  242. package/dist/cli/qaCommands.js +84 -0
  243. package/dist/cli/qaCommands.js.map +1 -0
  244. package/dist/cli/quickstartCommands.d.ts +17 -0
  245. package/dist/cli/quickstartCommands.js +47 -0
  246. package/dist/cli/quickstartCommands.js.map +1 -0
  247. package/dist/cli/runCommand.d.ts +39 -0
  248. package/dist/cli/runCommand.js +113 -0
  249. package/dist/cli/runCommand.js.map +1 -0
  250. package/dist/cli/scoreCommands.d.ts +1 -0
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  253. package/dist/cli/shieldCommands.d.ts +30 -0
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  256. package/dist/cli/targetCommands.d.ts +552 -0
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  259. package/dist/cli/tuiCommands.d.ts +7 -0
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  262. package/dist/cli/vibeCommands.d.ts +64 -0
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  265. package/dist/codegraph/CodeIntelligence.d.ts +147 -0
  266. package/dist/codegraph/CodeIntelligence.js +681 -0
  267. package/dist/codegraph/CodeIntelligence.js.map +1 -0
  268. package/dist/config/profiles.d.ts +64 -0
  269. package/dist/config/profiles.js +223 -0
  270. package/dist/config/profiles.js.map +1 -0
  271. package/dist/context/AntiPatternRegistry.d.ts +38 -0
  272. package/dist/context/AntiPatternRegistry.js +203 -0
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  274. package/dist/context/CavemanCompressor.d.ts +20 -0
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  277. package/dist/context/ContextBudget.d.ts +128 -0
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  280. package/dist/context/ContextBuilder.d.ts +71 -0
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  286. package/dist/context/ProjectAnatomy.d.ts +18 -0
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  289. package/dist/context/SessionStartSequence.d.ts +54 -0
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  292. package/dist/core/ExternalCommand.d.ts +9 -0
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  295. package/dist/core/GbrainRuntime.d.ts +25 -0
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  298. package/dist/core/container.d.ts +14 -0
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  307. package/dist/cortex/GovernanceMetrics.d.ts +66 -0
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  310. package/dist/cortex/InstinctExtractor.d.ts +61 -0
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  319. package/dist/cortex/SessionInjector.d.ts +44 -0
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  322. package/dist/cortex/adapters/ClaudeAdapter.d.ts +17 -0
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  325. package/dist/cortex/adapters/CodexAdapter.d.ts +10 -0
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  328. package/dist/cortex/adapters/CursorAdapter.d.ts +10 -0
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  337. package/dist/dashboard/MedicalWorkflowData.d.ts +155 -0
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  343. package/dist/dashboard/index.d.ts +4 -0
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  346. package/dist/dashboard/server.d.ts +52 -0
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  349. package/dist/env/EnvironmentDoctor.d.ts +66 -0
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  1059. package/target-research-platform/src/analysis/stage3_deep_research/competitive_landscape.py +479 -0
  1060. package/target-research-platform/src/analysis/stage3_deep_research/pipeline.py +763 -0
  1061. package/target-research-platform/src/analysis/stage3_deep_research/target_function.py +290 -0
  1062. package/target-research-platform/src/analysis/stage4_business/__init__.py +12 -0
  1063. package/target-research-platform/src/analysis/stage4_business/business_plan.py +816 -0
  1064. package/target-research-platform/src/analysis/stage4_business/milestone_planner.py +844 -0
  1065. package/target-research-platform/src/analysis/stage4_business/pipeline.py +284 -0
  1066. package/target-research-platform/src/api_clients/__init__.py +29 -0
  1067. package/target-research-platform/src/api_clients/aminer_client.py +163 -0
  1068. package/target-research-platform/src/api_clients/base_client.py +186 -0
  1069. package/target-research-platform/src/api_clients/clinicaltrials_client.py +411 -0
  1070. package/target-research-platform/src/api_clients/geo_client.py +1420 -0
  1071. package/target-research-platform/src/api_clients/gtex_client.py +209 -0
  1072. package/target-research-platform/src/api_clients/hpa_client.py +170 -0
  1073. package/target-research-platform/src/api_clients/immune_data_manager.py +247 -0
  1074. package/target-research-platform/src/api_clients/openalex_client.py +86 -0
  1075. package/target-research-platform/src/api_clients/opentargets_client.py +558 -0
  1076. package/target-research-platform/src/api_clients/pubmed_client.py +361 -0
  1077. package/target-research-platform/src/api_clients/tcga_client.py +712 -0
  1078. package/target-research-platform/src/api_clients/timer_client.py +169 -0
  1079. package/target-research-platform/src/dashboard/app.py +2283 -0
  1080. package/target-research-platform/src/dashboard/deliverables.py +710 -0
  1081. package/target-research-platform/src/dashboard/static/artifactPreview.js +96 -0
  1082. package/target-research-platform/src/dashboard/static/index.html +1292 -0
  1083. package/target-research-platform/src/dashboard/status_tracker.py +237 -0
  1084. package/target-research-platform/src/output/__init__.py +42 -0
  1085. package/target-research-platform/src/output/agent_llm_provider.py +171 -0
  1086. package/target-research-platform/src/output/chart_generator.py +550 -0
  1087. package/target-research-platform/src/output/data_exporter.py +215 -0
  1088. package/target-research-platform/src/output/delivery_packager.py +791 -0
  1089. package/target-research-platform/src/output/evidence_package.py +230 -0
  1090. package/target-research-platform/src/output/journal_templates.py +193 -0
  1091. package/target-research-platform/src/output/literature_enricher.py +395 -0
  1092. package/target-research-platform/src/output/literature_reviewer.py +420 -0
  1093. package/target-research-platform/src/output/manuscript_fact_checker.py +279 -0
  1094. package/target-research-platform/src/output/manuscript_generator.py +1189 -0
  1095. package/target-research-platform/src/output/manuscript_quality.py +401 -0
  1096. package/target-research-platform/src/output/medical_skills_bridge.py +140 -0
  1097. package/target-research-platform/src/output/report_generator.py +542 -0
  1098. package/target-research-platform/src/output/usage_envelope.py +193 -0
  1099. package/target-research-platform/src/utils/__init__.py +1 -0
  1100. package/target-research-platform/src/utils/config.py +125 -0
  1101. package/target-research-platform/src/utils/logger.py +71 -0
  1102. package/target-research-platform/src/validators/__init__.py +13 -0
  1103. package/target-research-platform/src/validators/cross_validator.py +394 -0
  1104. package/target-research-platform/src/validators/data_provenance.py +298 -0
package/target-research-platform/src/output/report_generator.py ADDED
@@ -0,0 +1,542 @@
1
+ """
2
+ 报告生成器
3
+ 生成 HTML / PDF / DOCX 研究报告
4
+ """
5
+ import json
6
+ from pathlib import Path
7
+ from typing import Optional
8
+ from datetime import datetime
9
+
10
+ from jinja2 import Environment, FileSystemLoader, BaseLoader
11
+
12
+
13
+ # HTML 报告模板（内联，不依赖外部文件）
14
+ HTML_TEMPLATE = r"""<!DOCTYPE html>
15
+ <html lang="zh-CN">
16
+ <head>
17
+ <meta charset="UTF-8">
18
+ <meta name="viewport" content="width=device-width, initial-scale=1.0">
19
+ <title>{{ title }}</title>
20
+ <style>
21
+ * { margin: 0; padding: 0; box-sizing: border-box; }
22
+ body { font-family: -apple-system, 'Segoe UI', Roboto, 'SimHei', sans-serif; background: #f5f7fa; color: #2c3e50; line-height: 1.6; }
23
+ .container { max-width: 1200px; margin: 0 auto; padding: 20px; }
24
+ .header { background: linear-gradient(135deg, #1a5276, #2980b9); color: white; padding: 40px; border-radius: 12px; margin-bottom: 24px; }
25
+ .header h1 { font-size: 28px; margin-bottom: 8px; }
26
+ .header .meta { opacity: 0.85; font-size: 14px; }
27
+ .grid { display: grid; grid-template-columns: 1fr 1fr; gap: 20px; margin-bottom: 20px; }
28
+ .card { background: white; border-radius: 10px; padding: 24px; box-shadow: 0 2px 8px rgba(0,0,0,0.06); }
29
+ .card.full { grid-column: 1 / -1; }
30
+ .card h2 { font-size: 18px; color: #1a5276; margin-bottom: 16px; padding-bottom: 8px; border-bottom: 2px solid #eee; }
31
+ .card h3 { font-size: 15px; color: #555; margin: 12px 0 8px; }
32
+ table { width: 100%; border-collapse: collapse; font-size: 14px; }
33
+ th { background: #f8f9fa; text-align: left; padding: 10px 12px; font-weight: 600; color: #555; }
34
+ td { padding: 8px 12px; border-bottom: 1px solid #eee; }
35
+ tr.sig td { background: #fff8e1; }
36
+ .badge { padding: 2px 8px; border-radius: 4px; font-size: 12px; font-weight: 600; }
37
+ .badge.tchem { background: #e8f5e9; color: #2e7d32; }
38
+ .badge.tbio { background: #fff3e0; color: #e65100; }
39
+ .badge.tclin { background: #e3f2fd; color: #1565c0; }
40
+ .bar-container { display: flex; align-items: center; gap: 8px; }
41
+ .bar { height: 20px; background: linear-gradient(90deg, #2980b9, #3498db); border-radius: 4px; min-width: 4px; }
42
+ .kpi { display: flex; gap: 16px; flex-wrap: wrap; }
43
+ .kpi-item { flex: 1; min-width: 120px; text-align: center; padding: 16px; background: #f8f9fa; border-radius: 8px; }
44
+ .kpi-value { font-size: 28px; font-weight: 700; color: #1a5276; }
45
+ .kpi-label { font-size: 12px; color: #888; margin-top: 4px; }
46
+ .summary-box { background: #e8f5e9; border-left: 4px solid #4CAF50; padding: 16px; border-radius: 0 8px 8px 0; margin-top: 12px; }
47
+ .warning-box { background: #fff3e0; border-left: 4px solid #FF9800; padding: 16px; border-radius: 0 8px 8px 0; margin-top: 12px; }
48
+ .footer { text-align: center; color: #aaa; font-size: 12px; margin-top: 32px; padding: 16px; }
49
+ .stage-tag { display: inline-block; background: #2980b9; color: white; padding: 2px 10px; border-radius: 12px; font-size: 12px; margin-bottom: 8px; }
50
+ .stage-tag.s1 { background: #27ae60; }
51
+ .stage-tag.s2 { background: #8e44ad; }
52
+ .stage-tag.s3 { background: #e67e22; }
53
+ .stage-tag.s4 { background: #c0392b; }
54
+ .chart-img { max-width: 100%; height: auto; border-radius: 8px; margin: 12px 0; }
55
+ .evidence-list { list-style: none; padding: 0; }
56
+ .evidence-list li { padding: 8px 0; border-bottom: 1px solid #f0f0f0; }
57
+ .evidence-list li::before { content: ""; display: inline-block; width: 8px; height: 8px; background: #2980b9; border-radius: 50%; margin-right: 8px; }
58
+ @media (max-width: 768px) { .grid { grid-template-columns: 1fr; } }
59
+ @media print { body { background: white; } .container { max-width: 100%; } }
60
+ </style>
61
+ </head>
62
+ <body>
63
+ <div class="container">
64
+
65
+ <div class="header">
66
+ <h1>{{ title }}</h1>
67
+ <div class="meta">
68
+ 生成时间: {{ generated_at }} &nbsp;|&nbsp;
69
+ 数据来源: {{ data_sources }} &nbsp;|&nbsp;
70
+ Pipeline: drug-target-research-platform v1.0
71
+ </div>
72
+ </div>
73
+
74
+ {% if kpis %}
75
+ <div class="card full">
76
+ <div class="kpi">
77
+ {% for kpi in kpis %}
78
+ <div class="kpi-item">
79
+ <div class="kpi-value">{{ kpi.value }}</div>
80
+ <div class="kpi-label">{{ kpi.label }}</div>
81
+ </div>
82
+ {% endfor %}
83
+ </div>
84
+ </div>
85
+ {% endif %}
86
+
87
+ {% for section in sections %}
88
+ <div class="card {{ 'full' if section.get('full', false) else '' }}">
89
+ {% if section.get('stage') %}
90
+ <span class="stage-tag s{{ section.stage }}">Stage {{ section.stage }}</span>
91
+ {% endif %}
92
+ <h2>{{ section.title }}</h2>
93
+
94
+ {% if section.get('chart') %}
95
+ <img class="chart-img" src="{{ section.chart }}" alt="{{ section.title }}">
96
+ {% endif %}
97
+
98
+ {% if section.get('table') %}
99
+ <table>
100
+ <tr>
101
+ {% for col in section.table.columns %}
102
+ <th>{{ col }}</th>
103
+ {% endfor %}
104
+ </tr>
105
+ {% for row in section.table.rows %}
106
+ <tr class="{{ 'sig' if row.get('significant') else '' }}">
107
+ {% for col in section.table.columns %}
108
+ <td>{{ row.get(col, '') }}</td>
109
+ {% endfor %}
110
+ </tr>
111
+ {% endfor %}
112
+ </table>
113
+ {% endif %}
114
+
115
+ {% if section.get('summary') %}
116
+ <div class="summary-box">{{ section.summary }}</div>
117
+ {% endif %}
118
+
119
+ {% if section.get('warning') %}
120
+ <div class="warning-box">{{ section.warning }}</div>
121
+ {% endif %}
122
+
123
+ {% if section.get('content') %}
124
+ {{ section.content }}
125
+ {% endif %}
126
+ </div>
127
+ {% endfor %}
128
+
129
+ {% if recommendations %}
130
+ <div class="card full">
131
+ <h2>综合评估与建议</h2>
132
+ <div class="grid" style="grid-template-columns:1fr 1fr">
133
+ <div>
134
+ <h3>优势</h3>
135
+ <ul class="evidence-list">
136
+ {% for item in recommendations.strengths %}
137
+ <li>{{ item }}</li>
138
+ {% endfor %}
139
+ </ul>
140
+ </div>
141
+ <div>
142
+ <h3>风险</h3>
143
+ <ul class="evidence-list">
144
+ {% for item in recommendations.risks %}
145
+ <li>{{ item }}</li>
146
+ {% endfor %}
147
+ </ul>
148
+ </div>
149
+ </div>
150
+ {% if recommendations.get('conclusion') %}
151
+ <div class="summary-box" style="margin-top:16px">
152
+ <strong>结论:</strong> {{ recommendations.conclusion }}
153
+ </div>
154
+ {% endif %}
155
+ </div>
156
+ {% endif %}
157
+
158
+ {% if provenance %}
159
+ <div class="card full">
160
+ <h2>数据溯源</h2>
161
+ <table>
162
+ <tr><th>数据源</th><th>版本/日期</th><th>访问方式</th><th>用途</th></tr>
163
+ {% for p in provenance %}
164
+ <tr>
165
+ <td>{{ p.source }}</td>
166
+ <td>{{ p.version }}</td>
167
+ <td>{{ p.access }}</td>
168
+ <td>{{ p.purpose }}</td>
169
+ </tr>
170
+ {% endfor %}
171
+ </table>
172
+ </div>
173
+ {% endif %}
174
+
175
+ <div class="footer">
176
+ 药物靶点智能研究平台 — 自动生成报告 &nbsp;|&nbsp;
177
+ 数据来源: GTEx, TCGA/GDC, GEO, OpenTargets, PubMed, ClinicalTrials.gov
178
+ </div>
179
+ </div>
180
+ </body>
181
+ </html>"""
182
+
183
+
184
+ class ReportGenerator:
185
+ """生成 HTML/PDF/DOCX 研究报告"""
186
+
187
+ def __init__(self, output_dir: str):
188
+ self.output_dir = Path(output_dir)
189
+ self.output_dir.mkdir(parents=True, exist_ok=True)
190
+ self.env = Environment(loader=BaseLoader())
191
+ self.env.globals["now"] = datetime.now().strftime("%Y-%m-%d %H:%M")
192
+
193
+ def _build_stage1_context(self, stage_data: dict, gene_symbol: str) -> list[dict]:
194
+ """从 Stage1 数据构建报告上下文"""
195
+ sections = []
196
+
197
+ # 组织表达
198
+ tissues = stage_data.get("tissue_expression", {}).get("gtex", {}).get("tissues", {})
199
+ if tissues:
200
+ sorted_t = sorted(tissues.items(), key=lambda x: x[1], reverse=True)[:10]
201
+ sections.append({
202
+ "stage": 1,
203
+ "title": "正常组织表达 (GTEx)",
204
+ "table": {
205
+ "columns": ["rank", "tissue", "tpm"],
206
+ "rows": [
207
+ {"rank": i + 1, "tissue": name, "tpm": f"{val:.1f}"}
208
+ for i, (name, val) in enumerate(sorted_t)
209
+ ]
210
+ }
211
+ })
212
+
213
+ # 生存分析
214
+ survival = stage_data.get("survival", {})
215
+ if survival:
216
+ rows = []
217
+ for ct, data in survival.items():
218
+ if isinstance(data, dict):
219
+ rows.append({
220
+ "cancer_type": ct,
221
+ "median_high": data.get("median_high", ""),
222
+ "median_low": data.get("median_low", ""),
223
+ "hr": data.get("hr", ""),
224
+ "p_value": data.get("p_value", ""),
225
+ "significant": data.get("p_value", 1) < 0.05,
226
+ })
227
+ if rows:
228
+ sections.append({
229
+ "stage": 1,
230
+ "title": "生存预后分析",
231
+ "table": {
232
+ "columns": ["cancer_type", "median_high", "median_low", "hr", "p_value"],
233
+ "rows": rows,
234
+ }
235
+ })
236
+
237
+ # 免疫相关性
238
+ immune = stage_data.get("immune", {})
239
+ for cancer_type, corr_data in immune.items():
240
+ if isinstance(corr_data, dict) and "correlations" in corr_data:
241
+ rows = []
242
+ for cell, info in corr_data["correlations"].items():
243
+ pval = info.get("p_value", 1)
244
+ rows.append({
245
+ "immune_cell": cell.replace("_", " "),
246
+ "correlation": f"{info.get('correlation', 0):+.3f}",
247
+ "p_value": f"{pval:.2e}",
248
+ "significant": pval < 0.05,
249
+ })
250
+ if rows:
251
+ sections.append({
252
+ "stage": 1,
253
+ "title": f"免疫微环境相关性 ({cancer_type})",
254
+ "table": {
255
+ "columns": ["immune_cell", "correlation", "p_value"],
256
+ "rows": rows,
257
+ }
258
+ })
259
+
260
+ return sections
261
+
262
+ def _build_stage2_context(self, stage_data: dict) -> list[dict]:
263
+ """从 Stage2 数据构建报告上下文"""
264
+ sections = []
265
+
266
+ # 候选靶点排名
267
+ targets = stage_data.get("top_targets", [])
268
+ if targets:
269
+ rows = []
270
+ for i, t in enumerate(targets):
271
+ rows.append({
272
+ "rank": i + 1,
273
+ "gene": t.get("gene", ""),
274
+ "composite_score": f"{t.get('composite_score', 0):.3f}",
275
+ "de_score": f"{t.get('de_score', 0):.3f}",
276
+ "druggability_score": f"{t.get('druggability_score', 0):.3f}",
277
+ "druggability_class": t.get("druggability_class", ""),
278
+ })
279
+ sections.append({
280
+ "stage": 2,
281
+ "title": "候选靶点综合排名",
282
+ "full": True,
283
+ "table": {
284
+ "columns": ["rank", "gene", "composite_score", "de_score", "druggability_score", "druggability_class"],
285
+ "rows": rows,
286
+ }
287
+ })
288
+
289
+ return sections
290
+
291
+ def _build_stage3_context(self, stage_data: dict) -> list[dict]:
292
+ """从 Stage3 数据构建报告上下文"""
293
+ sections = []
294
+ developability = stage_data.get("developability", {})
295
+
296
+ if developability:
297
+ sections.append({
298
+ "stage": 3,
299
+ "title": "可开发性评估",
300
+ "content": f"""
301
+ <div class="kpi">
302
+ <div class="kpi-item">
303
+ <div class="kpi-value">{developability.get('score', 'N/A')}</div>
304
+ <div class="kpi-label">可开发性评分</div>
305
+ </div>
306
+ <div class="kpi-item">
307
+ <div class="kpi-value">{developability.get('level', 'N/A')}</div>
308
+ <div class="kpi-label">等级</div>
309
+ </div>
310
+ </div>
311
+ <p style="margin-top:12px">{developability.get('interpretation', '')}</p>
312
+ """
313
+ })
314
+
315
+ recommendations = stage_data.get("recommendations", [])
316
+ if recommendations:
317
+ sections.append({
318
+ "stage": 3,
319
+ "title": "策略建议",
320
+ "content": "<ul>" + "".join(f"<li>{r}</li>" for r in recommendations) + "</ul>"
321
+ })
322
+
323
+ return sections
324
+
325
+ def _build_stage4_context(self, stage_data: dict) -> list[dict]:
326
+ """从 Stage4 数据构建报告上下文"""
327
+ sections = []
328
+ milestones = stage_data.get("milestones", {})
329
+
330
+ if milestones:
331
+ sections.append({
332
+ "stage": 4,
333
+ "title": "开发里程碑",
334
+ "content": f"""
335
+ <div class="kpi">
336
+ <div class="kpi-item">
337
+ <div class="kpi-value">{milestones.get('total_duration', 'N/A')}</div>
338
+ <div class="kpi-label">总时长</div>
339
+ </div>
340
+ <div class="kpi-item">
341
+ <div class="kpi-value">{milestones.get('total_cost', 'N/A')}</div>
342
+ <div class="kpi-label">总成本</div>
343
+ </div>
344
+ <div class="kpi-item">
345
+ <div class="kpi-value">{milestones.get('success_rate', 'N/A')}</div>
346
+ <div class="kpi-label">综合成功率</div>
347
+ </div>
348
+ </div>
349
+ """
350
+ })
351
+
352
+ return sections
353
+
354
+ def generate_html(
355
+ self,
356
+ pipeline_results: dict,
357
+ gene_symbol: str,
358
+ disease: str,
359
+ title: str = None,
360
+ provenance: list[dict] = None,
361
+ chart_files: dict[str, str] = None,
362
+ ) -> str:
363
+ """从 pipeline 结果生成 HTML 报告"""
364
+ sections = []
365
+
366
+ stages = pipeline_results.get("stages", pipeline_results)
367
+
368
+ # Stage1
369
+ s1 = stages.get("stage1", stages.get("tissue_expression", {}))
370
+ if s1:
371
+ sections.extend(self._build_stage1_context(s1.get("summary", s1), gene_symbol))
372
+
373
+ # Stage2
374
+ s2 = stages.get("stage2", {})
375
+ if s2:
376
+ sections.extend(self._build_stage2_context(s2.get("summary", s2)))
377
+
378
+ # Stage3
379
+ s3 = stages.get("stage3", {})
380
+ if s3:
381
+ sections.extend(self._build_stage3_context(s3.get("summary", s3)))
382
+
383
+ # Stage4
384
+ s4 = stages.get("stage4", {})
385
+ if s4:
386
+ sections.extend(self._build_stage4_context(s4.get("summary", s4)))
387
+
388
+ # KPI 概览
389
+ kpis = []
390
+ if gene_symbol:
391
+ kpis.append({"value": gene_symbol, "label": "靶点"})
392
+ if disease:
393
+ kpis.append({"value": disease, "label": "疾病"})
394
+
395
+ # 默认溯源
396
+ if provenance is None:
397
+ provenance = [
398
+ {"source": "GTEx", "version": "v8", "access": "REST API", "purpose": "正常组织表达"},
399
+ {"source": "TCGA/GDC", "version": "2024", "access": "GDC API", "purpose": "肿瘤表达与生存"},
400
+ {"source": "GEO", "version": "2024", "access": "NCBI E-utilities", "purpose": "差异表达"},
401
+ {"source": "OpenTargets", "version": "2024.02", "access": "GraphQL API", "purpose": "靶点-疾病关联"},
402
+ ]
403
+
404
+ template = self.env.from_string(HTML_TEMPLATE)
405
+ html = template.render(
406
+ title=title or f"{gene_symbol} — {disease} 靶点研究报告",
407
+ generated_at=datetime.now().strftime("%Y-%m-%d %H:%M"),
408
+ data_sources="GTEx, TCGA/GDC, GEO, OpenTargets",
409
+ kpis=kpis,
410
+ sections=sections,
411
+ provenance=provenance,
412
+ )
413
+
414
+ path = self.output_dir / f"report_{gene_symbol}.html"
415
+ path.write_text(html, encoding="utf-8")
416
+ return str(path)
417
+
418
+ def generate_pdf(self, html_path: str, filename: str = None) -> str:
419
+ """HTML → PDF (WeasyPrint)"""
420
+ try:
421
+ from weasyprint import HTML
422
+ except ImportError:
423
+ raise RuntimeError("weasyprint not installed: pip install weasyprint")
424
+
425
+ html_file = Path(html_path)
426
+ if not filename:
427
+ filename = html_file.stem + ".pdf"
428
+ pdf_path = self.output_dir / filename
429
+
430
+ HTML(filename=str(html_file)).write_pdf(str(pdf_path))
431
+ return str(pdf_path)
432
+
433
+ def generate_docx(
434
+ self,
435
+ pipeline_results: dict,
436
+ gene_symbol: str,
437
+ disease: str,
438
+ title: str = None,
439
+ ) -> str:
440
+ """生成 DOCX 报告"""
441
+ try:
442
+ from docx import Document
443
+ from docx.shared import Inches, Pt, RGBColor
444
+ from docx.enum.text import WD_ALIGN_PARAGRAPH
445
+ except ImportError:
446
+ raise RuntimeError("python-docx not installed: pip install python-docx")
447
+
448
+ doc = Document()
449
+
450
+ # 标题
451
+ doc_title = doc.add_heading(title or f"{gene_symbol} — {disease} 靶点研究报告", level=0)
452
+ doc_title.alignment = WD_ALIGN_PARAGRAPH.CENTER
453
+
454
+ # 元信息
455
+ meta = doc.add_paragraph()
456
+ meta.alignment = WD_ALIGN_PARAGRAPH.CENTER
457
+ meta_run = meta.add_run(
458
+ f"生成时间: {datetime.now().strftime('%Y-%m-%d %H:%M')}\n"
459
+ f"数据来源: GTEx, TCGA/GDC, GEO, OpenTargets\n"
460
+ f"Pipeline: drug-target-research-platform v1.0"
461
+ )
462
+ meta_run.font.size = Pt(9)
463
+ meta_run.font.color.rgb = RGBColor(0x88, 0x88, 0x88)
464
+
465
+ doc.add_paragraph() # spacer
466
+
467
+ stages = pipeline_results.get("stages", pipeline_results)
468
+
469
+ # Stage 1
470
+ doc.add_heading("Stage 1: 表达与预后分析", level=1)
471
+ s1 = stages.get("stage1", {}).get("summary", {})
472
+ tissues = s1.get("tissue_expression", {}).get("gtex", {}).get("tissues", {})
473
+ if tissues:
474
+ doc.add_heading("正常组织表达 (GTEx)", level=2)
475
+ sorted_t = sorted(tissues.items(), key=lambda x: x[1], reverse=True)[:10]
476
+ table = doc.add_table(rows=1, cols=3, style="Light Grid Accent 1")
477
+ table.rows[0].cells[0].text = "排名"
478
+ table.rows[0].cells[1].text = "组织"
479
+ table.rows[0].cells[2].text = "TPM"
480
+ for i, (name, val) in enumerate(sorted_t):
481
+ row = table.add_row()
482
+ row.cells[0].text = str(i + 1)
483
+ row.cells[1].text = name
484
+ row.cells[2].text = f"{val:.1f}"
485
+
486
+ # Stage 2
487
+ doc.add_heading("Stage 2: 靶点筛选与排名", level=1)
488
+ s2 = stages.get("stage2", {}).get("summary", {})
489
+ targets = s2.get("top_targets", [])
490
+ if targets:
491
+ table = doc.add_table(rows=1, cols=5, style="Light Grid Accent 1")
492
+ headers = ["排名", "靶点", "综合评分", "DE评分", "成药性"]
493
+ for i, h in enumerate(headers):
494
+ table.rows[0].cells[i].text = h
495
+ for i, t in enumerate(targets):
496
+ row = table.add_row()
497
+ row.cells[0].text = str(i + 1)
498
+ row.cells[1].text = t.get("gene", "")
499
+ row.cells[2].text = f"{t.get('composite_score', 0):.3f}"
500
+ row.cells[3].text = f"{t.get('de_score', 0):.3f}"
501
+ row.cells[4].text = f"{t.get('druggability_score', 0):.3f}"
502
+
503
+ # Stage 3
504
+ doc.add_heading("Stage 3: 深度研究", level=1)
505
+ s3 = stages.get("stage3", {}).get("summary", {})
506
+ dev = s3.get("developability", {})
507
+ if dev:
508
+ doc.add_paragraph(f"可开发性评分: {dev.get('score', 'N/A')} ({dev.get('level', 'N/A')})")
509
+ doc.add_paragraph(dev.get("interpretation", ""))
510
+
511
+ # Stage 4
512
+ doc.add_heading("Stage 4: 商业计划", level=1)
513
+ s4 = stages.get("stage4", {}).get("summary", {})
514
+ milestones = s4.get("milestones", {})
515
+ if milestones:
516
+ doc.add_paragraph(
517
+ f"总时长: {milestones.get('total_duration', 'N/A')}\n"
518
+ f"总成本: {milestones.get('total_cost', 'N/A')}\n"
519
+ f"综合成功率: {milestones.get('success_rate', 'N/A')}"
520
+ )
521
+
522
+ # 溯源
523
+ doc.add_heading("数据溯源", level=1)
524
+ provenance = [
525
+ ("GTEx", "v8", "REST API", "正常组织表达"),
526
+ ("TCGA/GDC", "2024", "GDC API", "肿瘤表达与生存"),
527
+ ("GEO", "2024", "NCBI E-utilities", "差异表达"),
528
+ ("OpenTargets", "2024.02", "GraphQL API", "靶点-疾病关联"),
529
+ ]
530
+ table = doc.add_table(rows=1, cols=4, style="Light Grid Accent 1")
531
+ for i, h in enumerate(["数据源", "版本", "访问方式", "用途"]):
532
+ table.rows[0].cells[i].text = h
533
+ for source, version, access, purpose in provenance:
534
+ row = table.add_row()
535
+ row.cells[0].text = source
536
+ row.cells[1].text = version
537
+ row.cells[2].text = access
538
+ row.cells[3].text = purpose
539
+
540
+ path = self.output_dir / f"report_{gene_symbol}.docx"
541
+ doc.save(str(path))
542
+ return str(path)