@inflexa-ai/harness 0.1.1

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Files changed (823) hide show
  1. package/LICENSE +202 -0
  2. package/NOTICE +5 -0
  3. package/README.md +58 -0
  4. package/dist/agents/conversation-agent.d.ts +105 -0
  5. package/dist/agents/conversation-agent.js +140 -0
  6. package/dist/agents/report-builder.d.ts +32 -0
  7. package/dist/agents/report-builder.js +31 -0
  8. package/dist/agents/sandbox/__fixtures__/deps.d.ts +23 -0
  9. package/dist/agents/sandbox/__fixtures__/deps.js +96 -0
  10. package/dist/agents/sandbox/bulk-transcriptomics-agent.d.ts +8 -0
  11. package/dist/agents/sandbox/bulk-transcriptomics-agent.js +22 -0
  12. package/dist/agents/sandbox/cheminformatics-agent.d.ts +9 -0
  13. package/dist/agents/sandbox/cheminformatics-agent.js +62 -0
  14. package/dist/agents/sandbox/chromatin-agent.d.ts +8 -0
  15. package/dist/agents/sandbox/chromatin-agent.js +24 -0
  16. package/dist/agents/sandbox/data-profiler.d.ts +10 -0
  17. package/dist/agents/sandbox/data-profiler.js +24 -0
  18. package/dist/agents/sandbox/dna-methylation-agent.d.ts +8 -0
  19. package/dist/agents/sandbox/dna-methylation-agent.js +24 -0
  20. package/dist/agents/sandbox/drug-repurposing-agent.d.ts +8 -0
  21. package/dist/agents/sandbox/drug-repurposing-agent.js +54 -0
  22. package/dist/agents/sandbox/enrichment-agent.d.ts +8 -0
  23. package/dist/agents/sandbox/enrichment-agent.js +24 -0
  24. package/dist/agents/sandbox/ephemeral-executor.d.ts +9 -0
  25. package/dist/agents/sandbox/ephemeral-executor.js +29 -0
  26. package/dist/agents/sandbox/genomic-variant-agent.d.ts +8 -0
  27. package/dist/agents/sandbox/genomic-variant-agent.js +27 -0
  28. package/dist/agents/sandbox/immune-profiling-agent.d.ts +8 -0
  29. package/dist/agents/sandbox/immune-profiling-agent.js +43 -0
  30. package/dist/agents/sandbox/index.d.ts +31 -0
  31. package/dist/agents/sandbox/index.js +96 -0
  32. package/dist/agents/sandbox/metabolomics-agent.d.ts +8 -0
  33. package/dist/agents/sandbox/metabolomics-agent.js +15 -0
  34. package/dist/agents/sandbox/microbiome-agent.d.ts +8 -0
  35. package/dist/agents/sandbox/microbiome-agent.js +15 -0
  36. package/dist/agents/sandbox/multi-omics-integration-agent.d.ts +8 -0
  37. package/dist/agents/sandbox/multi-omics-integration-agent.js +33 -0
  38. package/dist/agents/sandbox/multimodal-sc-agent.d.ts +8 -0
  39. package/dist/agents/sandbox/multimodal-sc-agent.js +15 -0
  40. package/dist/agents/sandbox/network-agent.d.ts +8 -0
  41. package/dist/agents/sandbox/network-agent.js +25 -0
  42. package/dist/agents/sandbox/pkpd-clinical-response-agent.d.ts +8 -0
  43. package/dist/agents/sandbox/pkpd-clinical-response-agent.js +59 -0
  44. package/dist/agents/sandbox/proteomics-agent.d.ts +8 -0
  45. package/dist/agents/sandbox/proteomics-agent.js +15 -0
  46. package/dist/agents/sandbox/scientific-executor.d.ts +9 -0
  47. package/dist/agents/sandbox/scientific-executor.js +56 -0
  48. package/dist/agents/sandbox/shared.d.ts +100 -0
  49. package/dist/agents/sandbox/shared.js +195 -0
  50. package/dist/agents/sandbox/single-cell-agent.d.ts +8 -0
  51. package/dist/agents/sandbox/single-cell-agent.js +25 -0
  52. package/dist/agents/sandbox/spatial-omics-agent.d.ts +8 -0
  53. package/dist/agents/sandbox/spatial-omics-agent.js +15 -0
  54. package/dist/agents/sandbox/statistical-modeling-agent.d.ts +8 -0
  55. package/dist/agents/sandbox/statistical-modeling-agent.js +37 -0
  56. package/dist/agents/sandbox/translational-safety-agent.d.ts +8 -0
  57. package/dist/agents/sandbox/translational-safety-agent.js +59 -0
  58. package/dist/agents/sandbox/types.d.ts +34 -0
  59. package/dist/agents/sandbox/types.js +15 -0
  60. package/dist/agents/sandbox/validate-skills.d.ts +18 -0
  61. package/dist/agents/sandbox/validate-skills.js +40 -0
  62. package/dist/agents/sandbox-catalog.d.ts +33 -0
  63. package/dist/agents/sandbox-catalog.js +44 -0
  64. package/dist/agents/system-prompt.d.ts +25 -0
  65. package/dist/agents/system-prompt.js +23 -0
  66. package/dist/app/chat-turn.d.ts +35 -0
  67. package/dist/app/chat-turn.js +64 -0
  68. package/dist/app/data-profile-policy.d.ts +36 -0
  69. package/dist/app/data-profile-policy.js +37 -0
  70. package/dist/app/message-assembly.d.ts +65 -0
  71. package/dist/app/message-assembly.js +61 -0
  72. package/dist/app/synthesize-run.d.ts +57 -0
  73. package/dist/app/synthesize-run.js +103 -0
  74. package/dist/auth/local-auth-context.d.ts +19 -0
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  76. package/dist/auth/local-run-authorizer.d.ts +10 -0
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  78. package/dist/auth/types.d.ts +166 -0
  79. package/dist/auth/types.js +61 -0
  80. package/dist/billing/cached-resolver.d.ts +23 -0
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  82. package/dist/billing/noop-resolver.d.ts +6 -0
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  88. package/dist/billing/run-charge.d.ts +24 -0
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  90. package/dist/config/resource-limits.d.ts +76 -0
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  92. package/dist/contracts/analogy-report.d.ts +120 -0
  93. package/dist/contracts/analogy-report.js +50 -0
  94. package/dist/contracts/chat-events.d.ts +61 -0
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  100. package/dist/contracts/index.d.ts +12 -0
  101. package/dist/contracts/index.js +5 -0
  102. package/dist/contracts/message.d.ts +36 -0
  103. package/dist/contracts/message.js +9 -0
  104. package/dist/contracts/part-registry.d.ts +18 -0
  105. package/dist/contracts/part-registry.js +28 -0
  106. package/dist/contracts/schemas/chat-events.d.ts +90 -0
  107. package/dist/contracts/schemas/chat-events.js +43 -0
  108. package/dist/contracts/schemas/chat-parts.d.ts +683 -0
  109. package/dist/contracts/schemas/chat-parts.js +295 -0
  110. package/dist/contracts/schemas/index.d.ts +2 -0
  111. package/dist/contracts/schemas/index.js +2 -0
  112. package/dist/contracts/target-assessment-row.d.ts +85 -0
  113. package/dist/contracts/target-assessment-row.js +37 -0
  114. package/dist/contracts/target-dossier.d.ts +16720 -0
  115. package/dist/contracts/target-dossier.js +1339 -0
  116. package/dist/data/clinical-benchmarks.json +108 -0
  117. package/dist/data/protein-family-modality.json +101 -0
  118. package/dist/data/safety-panel-schema.d.ts +64 -0
  119. package/dist/data/safety-panel-schema.js +34 -0
  120. package/dist/data/safety-panel.json +436 -0
  121. package/dist/execution/artifact-metadata.d.ts +74 -0
  122. package/dist/execution/artifact-metadata.js +203 -0
  123. package/dist/execution/artifact-record.d.ts +19 -0
  124. package/dist/execution/artifact-record.js +7 -0
  125. package/dist/execution/artifact-registration.d.ts +36 -0
  126. package/dist/execution/artifact-registration.js +61 -0
  127. package/dist/execution/artifact-registry.d.ts +82 -0
  128. package/dist/execution/artifact-registry.js +17 -0
  129. package/dist/execution/dbos-run-launcher.d.ts +7 -0
  130. package/dist/execution/dbos-run-launcher.js +38 -0
  131. package/dist/execution/ephemeral-runner.d.ts +81 -0
  132. package/dist/execution/ephemeral-runner.js +161 -0
  133. package/dist/execution/filesystem-artifact-registry.d.ts +57 -0
  134. package/dist/execution/filesystem-artifact-registry.js +92 -0
  135. package/dist/execution/noop-artifact-registry.d.ts +11 -0
  136. package/dist/execution/noop-artifact-registry.js +17 -0
  137. package/dist/execution/post-step-pipeline.d.ts +70 -0
  138. package/dist/execution/post-step-pipeline.js +207 -0
  139. package/dist/execution/post-step.d.ts +20 -0
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  141. package/dist/execution/reconcile-manifest.d.ts +25 -0
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  143. package/dist/execution/report-render.d.ts +39 -0
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  145. package/dist/execution/report-runner.d.ts +87 -0
  146. package/dist/execution/report-runner.js +227 -0
  147. package/dist/execution/run-authorizer.d.ts +43 -0
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  149. package/dist/execution/run-launcher.d.ts +36 -0
  150. package/dist/execution/run-launcher.js +15 -0
  151. package/dist/execution/run-synthesis.d.ts +107 -0
  152. package/dist/execution/run-synthesis.js +329 -0
  153. package/dist/execution/staged-input.d.ts +41 -0
  154. package/dist/execution/staged-input.js +15 -0
  155. package/dist/execution/step-summary-metrics.d.ts +10 -0
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  157. package/dist/execution/step-summary.d.ts +55 -0
  158. package/dist/execution/step-summary.js +106 -0
  159. package/dist/execution/topo-sort.d.ts +33 -0
  160. package/dist/execution/topo-sort.js +99 -0
  161. package/dist/index.d.ts +112 -0
  162. package/dist/index.js +157 -0
  163. package/dist/input-sanitization.d.ts +22 -0
  164. package/dist/input-sanitization.js +64 -0
  165. package/dist/lib/async-utils.d.ts +10 -0
  166. package/dist/lib/async-utils.js +24 -0
  167. package/dist/lib/chrome.d.ts +15 -0
  168. package/dist/lib/chrome.js +95 -0
  169. package/dist/lib/db-result.d.ts +93 -0
  170. package/dist/lib/db-result.js +197 -0
  171. package/dist/lib/fs-helpers.d.ts +74 -0
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  173. package/dist/lib/fs-result.d.ts +98 -0
  174. package/dist/lib/fs-result.js +137 -0
  175. package/dist/lib/host-concurrency.d.ts +16 -0
  176. package/dist/lib/host-concurrency.js +60 -0
  177. package/dist/lib/identifiers.d.ts +8 -0
  178. package/dist/lib/identifiers.js +10 -0
  179. package/dist/lib/metrics.d.ts +7 -0
  180. package/dist/lib/metrics.js +12 -0
  181. package/dist/lib/mime-detect.d.ts +17 -0
  182. package/dist/lib/mime-detect.js +29 -0
  183. package/dist/lib/otel.d.ts +30 -0
  184. package/dist/lib/otel.js +102 -0
  185. package/dist/lib/regulatory-corpus/fetch-fda-guidance.d.ts +35 -0
  186. package/dist/lib/regulatory-corpus/fetch-fda-guidance.js +107 -0
  187. package/dist/lib/regulatory-corpus/fetch-ich.d.ts +46 -0
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  189. package/dist/lib/regulatory-corpus.d.ts +88 -0
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  191. package/dist/lib/result.d.ts +87 -0
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  193. package/dist/lib/storage.d.ts +29 -0
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  197. package/dist/lib/trace-context.d.ts +11 -0
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  199. package/dist/loop/__fixtures__/scripted-provider.d.ts +31 -0
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  201. package/dist/loop/budget-exceeded.d.ts +22 -0
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  203. package/dist/loop/metrics.d.ts +25 -0
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  205. package/dist/loop/run-agent.d.ts +28 -0
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  211. package/dist/loop/types.d.ts +95 -0
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  213. package/dist/memory/ai-sdk-message-storage.d.ts +20 -0
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  235. package/dist/prompts/analogical-reasoner.d.ts +1 -0
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  237. package/dist/prompts/conversation.d.ts +1 -0
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  239. package/dist/prompts/execute-analysis/step-summary.d.ts +1 -0
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  249. package/dist/prompts/sandbox/cheminformatics-agent.d.ts +1 -0
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  255. package/dist/prompts/sandbox/dna-methylation-agent.d.ts +1 -0
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  257. package/dist/prompts/sandbox/drug-repurposing-agent.d.ts +1 -0
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  259. package/dist/prompts/sandbox/enrichment-agent.d.ts +1 -0
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  263. package/dist/prompts/sandbox/genomic-variant-agent.d.ts +1 -0
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  265. package/dist/prompts/sandbox/immune-profiling-agent.d.ts +1 -0
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  267. package/dist/prompts/sandbox/metabolomics-agent.d.ts +1 -0
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  277. package/dist/prompts/sandbox/pkpd-clinical-response-agent.d.ts +1 -0
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  695. package/dist/workflows/metrics.d.ts +37 -0
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  697. package/dist/workflows/plan/level.d.ts +12 -0
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  700. package/dist/workflows/register-workflows.js +48 -0
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  704. package/dist/workflows/sandbox-step.js +573 -0
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  730. package/dist/workflows/target-assessment/lib/clinical-consequence-annotator.js +172 -0
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  736. package/dist/workflows/target-assessment/lib/compute-selectivity.js +18 -0
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  748. package/dist/workflows/target-assessment/lib/intended-polypharm-filter.js +24 -0
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  764. package/dist/workflows/target-assessment/lib/therapeutic-programs.js +68 -0
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  772. package/dist/workflows/target-assessment/progress.js +76 -0
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  794. package/dist/workflows/target-assessment/steps/phase3-aggregate.js +22 -0
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  800. package/dist/workflows/target-assessment/sub-workflows/per-class-drug-aes.js +12 -0
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  813. package/dist/workspace/mount-strategy.d.ts +50 -0
  814. package/dist/workspace/mount-strategy.js +67 -0
  815. package/dist/workspace/paths.d.ts +185 -0
  816. package/dist/workspace/paths.js +219 -0
  817. package/dist/workspace/provenance-collector.d.ts +34 -0
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  820. package/dist/workspace/search-config.js +43 -0
  821. package/dist/workspace/workspace-paths.d.ts +26 -0
  822. package/dist/workspace/workspace-paths.js +31 -0
  823. package/package.json +101 -0
package/dist/workflows/target-assessment/steps/phase3-aggregate.d.ts ADDED
@@ -0,0 +1,936 @@
1
+ /**
2
+ * Phase 3 aggregator — schema definitions retained for downstream
3
+ * type-checking. The DBOS workflow assembles the Phase-3 bundle inline.
4
+ */
5
+ import { z } from "zod";
6
+ export declare const Phase3AggregateInputSchema: z.ZodObject<{
7
+ "per-modulator-faers": z.ZodObject<{
8
+ results: z.ZodArray<z.ZodDiscriminatedUnion<[z.ZodObject<{
9
+ coverage: z.ZodLiteral<"available">;
10
+ data: z.ZodObject<{
11
+ moleculeChemblId: z.ZodString;
12
+ preferredName: z.ZodString;
13
+ totalReports: z.ZodNullable<z.ZodNumber>;
14
+ topReactions: z.ZodArray<z.ZodObject<{
15
+ reaction: z.ZodString;
16
+ count: z.ZodNumber;
17
+ }, z.core.$strip>>;
18
+ seriousness: z.ZodNullable<z.ZodObject<{
19
+ totalReports: z.ZodNumber;
20
+ fatalCount: z.ZodNumber;
21
+ hospitalizationCount: z.ZodNumber;
22
+ lifeThreateningCount: z.ZodNumber;
23
+ disablingCount: z.ZodNumber;
24
+ congenitalAnomalyCount: z.ZodDefault<z.ZodNumber>;
25
+ otherSeriousCount: z.ZodDefault<z.ZodNumber>;
26
+ }, z.core.$strip>>;
27
+ }, z.core.$strip>;
28
+ }, z.core.$strip>, z.ZodObject<{
29
+ coverage: z.ZodLiteral<"queried_no_data">;
30
+ error: z.ZodOptional<z.ZodObject<{
31
+ message: z.ZodString;
32
+ name: z.ZodOptional<z.ZodString>;
33
+ stack: z.ZodOptional<z.ZodString>;
34
+ }, z.core.$strip>>;
35
+ }, z.core.$strip>, z.ZodObject<{
36
+ coverage: z.ZodLiteral<"not_loaded">;
37
+ reason: z.ZodOptional<z.ZodString>;
38
+ }, z.core.$strip>], "coverage">>;
39
+ }, z.core.$strip>;
40
+ "per-trial-aes": z.ZodObject<{
41
+ results: z.ZodArray<z.ZodDiscriminatedUnion<[z.ZodObject<{
42
+ coverage: z.ZodLiteral<"available">;
43
+ data: z.ZodObject<{
44
+ nctId: z.ZodString;
45
+ title: z.ZodString;
46
+ whyStopped: z.ZodNullable<z.ZodString>;
47
+ outcomes: z.ZodDefault<z.ZodArray<z.ZodObject<{
48
+ type: z.ZodEnum<{
49
+ other: "other";
50
+ primary: "primary";
51
+ secondary: "secondary";
52
+ }>;
53
+ measure: z.ZodString;
54
+ description: z.ZodNullable<z.ZodString>;
55
+ timeFrame: z.ZodNullable<z.ZodString>;
56
+ effect: z.ZodDiscriminatedUnion<[z.ZodObject<{
57
+ kind: z.ZodLiteral<"quantitative">;
58
+ value: z.ZodNumber;
59
+ units: z.ZodString;
60
+ ci_low: z.ZodOptional<z.ZodNumber>;
61
+ ci_high: z.ZodOptional<z.ZodNumber>;
62
+ }, z.core.$strip>, z.ZodObject<{
63
+ kind: z.ZodLiteral<"not_extracted">;
64
+ reason: z.ZodEnum<{
65
+ ctgov_no_numeric_result: "ctgov_no_numeric_result";
66
+ ctgov_no_result_groups: "ctgov_no_result_groups";
67
+ }>;
68
+ }, z.core.$strip>], "kind">;
69
+ }, z.core.$strip>>>;
70
+ groups: z.ZodArray<z.ZodObject<{
71
+ groupId: z.ZodString;
72
+ title: z.ZodString;
73
+ description: z.ZodNullable<z.ZodString>;
74
+ }, z.core.$strip>>;
75
+ events: z.ZodArray<z.ZodObject<{
76
+ serious: z.ZodBoolean;
77
+ term: z.ZodString;
78
+ organSystem: z.ZodNullable<z.ZodString>;
79
+ counts: z.ZodArray<z.ZodObject<{
80
+ groupId: z.ZodString;
81
+ numAffected: z.ZodNullable<z.ZodNumber>;
82
+ numAtRisk: z.ZodNullable<z.ZodNumber>;
83
+ }, z.core.$strip>>;
84
+ }, z.core.$strip>>;
85
+ }, z.core.$strip>;
86
+ }, z.core.$strip>, z.ZodObject<{
87
+ coverage: z.ZodLiteral<"queried_no_data">;
88
+ error: z.ZodOptional<z.ZodObject<{
89
+ message: z.ZodString;
90
+ name: z.ZodOptional<z.ZodString>;
91
+ stack: z.ZodOptional<z.ZodString>;
92
+ }, z.core.$strip>>;
93
+ }, z.core.$strip>, z.ZodObject<{
94
+ coverage: z.ZodLiteral<"not_loaded">;
95
+ reason: z.ZodOptional<z.ZodString>;
96
+ }, z.core.$strip>], "coverage">>;
97
+ }, z.core.$strip>;
98
+ "per-modulator-polypharm": z.ZodObject<{
99
+ results: z.ZodArray<z.ZodDiscriminatedUnion<[z.ZodObject<{
100
+ coverage: z.ZodLiteral<"available">;
101
+ data: z.ZodObject<{
102
+ moleculeChemblId: z.ZodString;
103
+ preferredName: z.ZodString;
104
+ primaryPchembl: z.ZodNullable<z.ZodNumber>;
105
+ hits: z.ZodArray<z.ZodObject<{
106
+ targetChemblId: z.ZodString;
107
+ targetName: z.ZodNullable<z.ZodString>;
108
+ pchemblValue: z.ZodNullable<z.ZodNumber>;
109
+ standardType: z.ZodNullable<z.ZodString>;
110
+ standardValue: z.ZodNullable<z.ZodNumber>;
111
+ standardUnits: z.ZodNullable<z.ZodString>;
112
+ }, z.core.$strip>>;
113
+ }, z.core.$strip>;
114
+ }, z.core.$strip>, z.ZodObject<{
115
+ coverage: z.ZodLiteral<"queried_no_data">;
116
+ error: z.ZodOptional<z.ZodObject<{
117
+ message: z.ZodString;
118
+ name: z.ZodOptional<z.ZodString>;
119
+ stack: z.ZodOptional<z.ZodString>;
120
+ }, z.core.$strip>>;
121
+ }, z.core.$strip>, z.ZodObject<{
122
+ coverage: z.ZodLiteral<"not_loaded">;
123
+ reason: z.ZodOptional<z.ZodString>;
124
+ }, z.core.$strip>], "coverage">>;
125
+ }, z.core.$strip>;
126
+ "per-class-drug-aes": z.ZodObject<{
127
+ results: z.ZodArray<z.ZodDiscriminatedUnion<[z.ZodObject<{
128
+ coverage: z.ZodLiteral<"available">;
129
+ data: z.ZodObject<{
130
+ moleculeChemblId: z.ZodString;
131
+ preferredName: z.ZodString;
132
+ totalReports: z.ZodNullable<z.ZodNumber>;
133
+ topReactions: z.ZodArray<z.ZodObject<{
134
+ reaction: z.ZodString;
135
+ count: z.ZodNumber;
136
+ }, z.core.$strip>>;
137
+ seriousness: z.ZodNullable<z.ZodObject<{
138
+ totalReports: z.ZodNumber;
139
+ fatalCount: z.ZodNumber;
140
+ hospitalizationCount: z.ZodNumber;
141
+ lifeThreateningCount: z.ZodNumber;
142
+ disablingCount: z.ZodNumber;
143
+ congenitalAnomalyCount: z.ZodDefault<z.ZodNumber>;
144
+ otherSeriousCount: z.ZodDefault<z.ZodNumber>;
145
+ }, z.core.$strip>>;
146
+ }, z.core.$strip>;
147
+ }, z.core.$strip>, z.ZodObject<{
148
+ coverage: z.ZodLiteral<"queried_no_data">;
149
+ error: z.ZodOptional<z.ZodObject<{
150
+ message: z.ZodString;
151
+ name: z.ZodOptional<z.ZodString>;
152
+ stack: z.ZodOptional<z.ZodString>;
153
+ }, z.core.$strip>>;
154
+ }, z.core.$strip>, z.ZodObject<{
155
+ coverage: z.ZodLiteral<"not_loaded">;
156
+ reason: z.ZodOptional<z.ZodString>;
157
+ }, z.core.$strip>], "coverage">>;
158
+ }, z.core.$strip>;
159
+ }, z.core.$strip>;
160
+ export declare const Phase3BundleSchema: z.ZodObject<{
161
+ phase2: z.ZodObject<{
162
+ phase1: z.ZodObject<{
163
+ resolved: z.ZodObject<{
164
+ assessmentId: z.ZodString;
165
+ goal: z.ZodNullable<z.ZodString>;
166
+ canonicalId: z.ZodString;
167
+ canonicalOntology: z.ZodEnum<{
168
+ ensembl: "ensembl";
169
+ hgnc: "hgnc";
170
+ }>;
171
+ geneSymbol: z.ZodString;
172
+ approvedName: z.ZodString;
173
+ ids: z.ZodObject<{
174
+ hgnc: z.ZodNullable<z.ZodString>;
175
+ ensembl: z.ZodNullable<z.ZodString>;
176
+ uniprot: z.ZodNullable<z.ZodString>;
177
+ chembl: z.ZodNullable<z.ZodString>;
178
+ entrez: z.ZodNullable<z.ZodString>;
179
+ }, z.core.$strip>;
180
+ synonyms: z.ZodArray<z.ZodString>;
181
+ proteinSynonyms: z.ZodArray<z.ZodString>;
182
+ proteinFamily: z.ZodNullable<z.ZodString>;
183
+ resolutionCoverage: z.ZodObject<{
184
+ hgnc: z.ZodBoolean;
185
+ uniprot: z.ZodBoolean;
186
+ ensembl: z.ZodBoolean;
187
+ chembl: z.ZodBoolean;
188
+ }, z.core.$strip>;
189
+ }, z.core.$strip>;
190
+ collectors: z.ZodObject<{
191
+ opentargets: z.ZodDiscriminatedUnion<[z.ZodObject<{
192
+ coverage: z.ZodLiteral<"available">;
193
+ data: z.ZodObject<{
194
+ ensemblId: z.ZodString;
195
+ approvedSymbol: z.ZodString;
196
+ approvedName: z.ZodString;
197
+ tractability: z.ZodNullable<z.ZodObject<{
198
+ smallMolecule: z.ZodNullable<z.ZodBoolean>;
199
+ antibody: z.ZodNullable<z.ZodBoolean>;
200
+ otherModalities: z.ZodNullable<z.ZodBoolean>;
201
+ }, z.core.$strip>>;
202
+ associations: z.ZodArray<z.ZodObject<{
203
+ diseaseId: z.ZodString;
204
+ diseaseName: z.ZodString;
205
+ score: z.ZodNumber;
206
+ geneticAssociationScore: z.ZodNullable<z.ZodNumber>;
207
+ knownDrugScore: z.ZodNullable<z.ZodNumber>;
208
+ literatureScore: z.ZodNullable<z.ZodNumber>;
209
+ animalModelScore: z.ZodDefault<z.ZodNullable<z.ZodNumber>>;
210
+ somaticMutationScore: z.ZodDefault<z.ZodNullable<z.ZodNumber>>;
211
+ literaturePmids: z.ZodDefault<z.ZodArray<z.ZodString>>;
212
+ }, z.core.$strip>>;
213
+ safetyLiabilities: z.ZodArray<z.ZodObject<{
214
+ event: z.ZodString;
215
+ biosamples: z.ZodArray<z.ZodString>;
216
+ effects: z.ZodNullable<z.ZodString>;
217
+ source: z.ZodString;
218
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219
+ baselineExpression: z.ZodArray<z.ZodObject<{
220
+ tissueId: z.ZodString;
221
+ tissueLabel: z.ZodString;
222
+ organSystem: z.ZodNullable<z.ZodString>;
223
+ rna: z.ZodNullable<z.ZodObject<{
224
+ value: z.ZodNumber;
225
+ unit: z.ZodString;
226
+ }, z.core.$strip>>;
227
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229
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230
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231
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232
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233
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236
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237
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239
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241
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242
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243
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+ coverage: z.ZodLiteral<"available">;
245
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246
+ targetChemblId: z.ZodNullable<z.ZodString>;
247
+ modulators: z.ZodArray<z.ZodObject<{
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+ moleculeChemblId: z.ZodString;
249
+ parentChemblId: z.ZodNullable<z.ZodString>;
250
+ preferredName: z.ZodNullable<z.ZodString>;
251
+ maxPhase: z.ZodNullable<z.ZodNumber>;
252
+ moleculeType: z.ZodNullable<z.ZodString>;
253
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254
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255
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256
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257
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+ active: z.ZodArray<z.ZodObject<{
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278
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282
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283
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286
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287
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288
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289
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290
+ whyStopped: z.ZodNullable<z.ZodString>;
291
+ briefSummary: z.ZodNullable<z.ZodString>;
292
+ detailedDescription: z.ZodNullable<z.ZodString>;
293
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294
+ collection_query: z.ZodOptional<z.ZodString>;
295
+ collection_channel: z.ZodOptional<z.ZodEnum<{
296
+ class_modulator: "class_modulator";
297
+ target_symbol: "target_symbol";
298
+ therapeutic_program: "therapeutic_program";
299
+ biomarker_context: "biomarker_context";
300
+ failed_intervention: "failed_intervention";
301
+ }>>;
302
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303
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304
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305
+ title: z.ZodString;
306
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307
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308
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309
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310
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311
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312
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313
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315
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316
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317
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318
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319
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320
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321
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322
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323
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324
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325
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326
+ collection_query: z.ZodOptional<z.ZodString>;
327
+ collection_channel: z.ZodOptional<z.ZodEnum<{
328
+ class_modulator: "class_modulator";
329
+ target_symbol: "target_symbol";
330
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331
+ biomarker_context: "biomarker_context";
332
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333
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334
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335
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336
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338
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340
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341
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346
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347
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348
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349
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350
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351
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352
+ topReactions: z.ZodArray<z.ZodObject<{
353
+ reaction: z.ZodString;
354
+ count: z.ZodNumber;
355
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356
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357
+ totalReports: z.ZodNumber;
358
+ fatalCount: z.ZodNumber;
359
+ hospitalizationCount: z.ZodNumber;
360
+ lifeThreateningCount: z.ZodNumber;
361
+ disablingCount: z.ZodNumber;
362
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363
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364
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365
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366
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370
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371
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373
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376
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377
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378
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379
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380
+ source: z.ZodEnum<{
381
+ gtex: "gtex";
382
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383
+ hpa_rna_tissue: "hpa_rna_tissue";
384
+ }>;
385
+ unit: z.ZodEnum<{
386
+ tpm: "tpm";
387
+ ntpm: "ntpm";
388
+ consensus_normalized: "consensus_normalized";
389
+ }>;
390
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391
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392
+ tissueLabel: z.ZodString;
393
+ organSystem: z.ZodNullable<z.ZodString>;
394
+ value: z.ZodNullable<z.ZodNumber>;
395
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396
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397
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398
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402
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403
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405
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407
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408
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409
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410
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411
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412
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413
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414
+ bySpecies: z.ZodArray<z.ZodObject<{
415
+ species: z.ZodString;
416
+ taxonId: z.ZodNumber;
417
+ ensemblId: z.ZodString;
418
+ source: z.ZodString;
419
+ unit: z.ZodString;
420
+ normalization_notes: z.ZodString;
421
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422
+ tissue: z.ZodString;
423
+ rank: z.ZodEnum<{
424
+ high: "high";
425
+ medium: "medium";
426
+ low: "low";
427
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428
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429
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430
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431
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432
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433
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434
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435
+ coverage: z.ZodLiteral<"queried_no_data">;
436
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438
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439
+ stack: z.ZodOptional<z.ZodString>;
440
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441
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443
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444
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445
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446
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447
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448
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449
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450
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451
+ title: z.ZodString;
452
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453
+ reviewStatus: z.ZodString;
454
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455
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456
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457
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458
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459
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460
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461
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463
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464
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466
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468
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469
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470
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471
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472
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473
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474
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475
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476
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477
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478
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479
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480
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481
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482
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483
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484
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485
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486
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487
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488
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489
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490
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493
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494
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495
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496
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497
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498
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499
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500
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501
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502
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503
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504
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505
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506
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507
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508
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509
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510
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511
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512
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513
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514
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515
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516
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517
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518
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519
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520
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521
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522
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523
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525
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526
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527
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528
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530
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531
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532
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533
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534
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535
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536
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537
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538
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539
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540
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541
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542
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543
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544
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545
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546
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547
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549
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550
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551
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552
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554
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555
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556
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557
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558
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559
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560
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561
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562
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563
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564
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565
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566
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567
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568
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569
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570
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571
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572
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573
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574
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575
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577
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578
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579
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580
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582
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583
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584
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585
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586
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588
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589
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590
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591
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592
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593
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594
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595
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596
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597
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598
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600
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601
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602
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603
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605
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606
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607
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608
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609
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610
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611
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612
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613
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614
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615
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616
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617
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618
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619
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620
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621
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622
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623
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624
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625
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626
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627
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629
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630
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631
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632
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633
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634
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635
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636
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637
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638
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639
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640
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641
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642
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643
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644
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645
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646
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647
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648
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649
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650
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651
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652
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653
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654
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655
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656
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657
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658
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659
+ doc_id: z.ZodOptional<z.ZodString>;
660
+ doc_url: z.ZodOptional<z.ZodString>;
661
+ }, z.core.$strip>>;
662
+ }, z.core.$strip>>;
663
+ confidence: z.ZodEnum<{
664
+ high: "high";
665
+ medium: "medium";
666
+ low: "low";
667
+ }>;
668
+ }, z.core.$strip>>;
669
+ }, z.core.$strip>;
670
+ }, z.core.$strip>, z.ZodObject<{
671
+ coverage: z.ZodLiteral<"queried_no_data">;
672
+ error: z.ZodOptional<z.ZodObject<{
673
+ message: z.ZodString;
674
+ name: z.ZodOptional<z.ZodString>;
675
+ stack: z.ZodOptional<z.ZodString>;
676
+ }, z.core.$strip>>;
677
+ }, z.core.$strip>, z.ZodObject<{
678
+ coverage: z.ZodLiteral<"not_loaded">;
679
+ reason: z.ZodOptional<z.ZodString>;
680
+ }, z.core.$strip>], "coverage">>;
681
+ }, z.core.$strip>;
682
+ }, z.core.$strip>;
683
+ decisions: z.ZodObject<{
684
+ modulatorTriage: z.ZodDiscriminatedUnion<[z.ZodObject<{
685
+ coverage: z.ZodLiteral<"available">;
686
+ data: z.ZodObject<{
687
+ shortlist: z.ZodArray<z.ZodObject<{
688
+ moleculeChemblId: z.ZodString;
689
+ preferredName: z.ZodString;
690
+ maxPhase: z.ZodNullable<z.ZodNumber>;
691
+ firstApproval: z.ZodNullable<z.ZodNumber>;
692
+ rationale: z.ZodString;
693
+ }, z.core.$strip>>;
694
+ notes: z.ZodString;
695
+ dropped_synonyms: z.ZodDefault<z.ZodArray<z.ZodObject<{
696
+ chemblId: z.ZodString;
697
+ reason: z.ZodEnum<{
698
+ same_active_substance: "same_active_substance";
699
+ ambiguous_name_synonym: "ambiguous_name_synonym";
700
+ }>;
701
+ keptId: z.ZodNullable<z.ZodString>;
702
+ }, z.core.$strip>>>;
703
+ }, z.core.$strip>;
704
+ }, z.core.$strip>, z.ZodObject<{
705
+ coverage: z.ZodLiteral<"queried_no_data">;
706
+ error: z.ZodOptional<z.ZodObject<{
707
+ message: z.ZodString;
708
+ name: z.ZodOptional<z.ZodString>;
709
+ stack: z.ZodOptional<z.ZodString>;
710
+ }, z.core.$strip>>;
711
+ }, z.core.$strip>, z.ZodObject<{
712
+ coverage: z.ZodLiteral<"not_loaded">;
713
+ reason: z.ZodOptional<z.ZodString>;
714
+ }, z.core.$strip>], "coverage">;
715
+ failedTrialClassifier: z.ZodDiscriminatedUnion<[z.ZodObject<{
716
+ coverage: z.ZodLiteral<"available">;
717
+ data: z.ZodObject<{
718
+ classifications: z.ZodDefault<z.ZodArray<z.ZodUnknown>>;
719
+ }, z.core.$strip>;
720
+ }, z.core.$strip>, z.ZodObject<{
721
+ coverage: z.ZodLiteral<"queried_no_data">;
722
+ error: z.ZodOptional<z.ZodObject<{
723
+ message: z.ZodString;
724
+ name: z.ZodOptional<z.ZodString>;
725
+ stack: z.ZodOptional<z.ZodString>;
726
+ }, z.core.$strip>>;
727
+ }, z.core.$strip>, z.ZodObject<{
728
+ coverage: z.ZodLiteral<"not_loaded">;
729
+ reason: z.ZodOptional<z.ZodString>;
730
+ }, z.core.$strip>], "coverage">;
731
+ offTargetCurator: z.ZodDiscriminatedUnion<[z.ZodObject<{
732
+ coverage: z.ZodLiteral<"available">;
733
+ data: z.ZodObject<{
734
+ panel: z.ZodDefault<z.ZodArray<z.ZodUnknown>>;
735
+ total: z.ZodDefault<z.ZodNumber>;
736
+ truncated: z.ZodDefault<z.ZodBoolean>;
737
+ notes: z.ZodDefault<z.ZodString>;
738
+ }, z.core.$strip>;
739
+ }, z.core.$strip>, z.ZodObject<{
740
+ coverage: z.ZodLiteral<"queried_no_data">;
741
+ error: z.ZodOptional<z.ZodObject<{
742
+ message: z.ZodString;
743
+ name: z.ZodOptional<z.ZodString>;
744
+ stack: z.ZodOptional<z.ZodString>;
745
+ }, z.core.$strip>>;
746
+ }, z.core.$strip>, z.ZodObject<{
747
+ coverage: z.ZodLiteral<"not_loaded">;
748
+ reason: z.ZodOptional<z.ZodString>;
749
+ }, z.core.$strip>], "coverage">;
750
+ drugsInClass: z.ZodDiscriminatedUnion<[z.ZodObject<{
751
+ coverage: z.ZodLiteral<"available">;
752
+ data: z.ZodObject<{
753
+ drugs: z.ZodArray<z.ZodObject<{
754
+ moleculeChemblId: z.ZodString;
755
+ preferredName: z.ZodString;
756
+ maxPhase: z.ZodNullable<z.ZodNumber>;
757
+ firstApproval: z.ZodNullable<z.ZodNumber>;
758
+ moleculeType: z.ZodNullable<z.ZodString>;
759
+ sources: z.ZodArray<z.ZodEnum<{
760
+ chembl: "chembl";
761
+ dgidb: "dgidb";
762
+ drugbank: "drugbank";
763
+ }>>;
764
+ }, z.core.$strip>>;
765
+ total: z.ZodNumber;
766
+ truncated: z.ZodBoolean;
767
+ }, z.core.$strip>;
768
+ }, z.core.$strip>, z.ZodObject<{
769
+ coverage: z.ZodLiteral<"queried_no_data">;
770
+ error: z.ZodOptional<z.ZodObject<{
771
+ message: z.ZodString;
772
+ name: z.ZodOptional<z.ZodString>;
773
+ stack: z.ZodOptional<z.ZodString>;
774
+ }, z.core.$strip>>;
775
+ }, z.core.$strip>, z.ZodObject<{
776
+ coverage: z.ZodLiteral<"not_loaded">;
777
+ reason: z.ZodOptional<z.ZodString>;
778
+ }, z.core.$strip>], "coverage">;
779
+ }, z.core.$strip>;
780
+ }, z.core.$strip>;
781
+ fanout: z.ZodObject<{
782
+ perModulatorFaers: z.ZodObject<{
783
+ results: z.ZodArray<z.ZodDiscriminatedUnion<[z.ZodObject<{
784
+ coverage: z.ZodLiteral<"available">;
785
+ data: z.ZodObject<{
786
+ moleculeChemblId: z.ZodString;
787
+ preferredName: z.ZodString;
788
+ totalReports: z.ZodNullable<z.ZodNumber>;
789
+ topReactions: z.ZodArray<z.ZodObject<{
790
+ reaction: z.ZodString;
791
+ count: z.ZodNumber;
792
+ }, z.core.$strip>>;
793
+ seriousness: z.ZodNullable<z.ZodObject<{
794
+ totalReports: z.ZodNumber;
795
+ fatalCount: z.ZodNumber;
796
+ hospitalizationCount: z.ZodNumber;
797
+ lifeThreateningCount: z.ZodNumber;
798
+ disablingCount: z.ZodNumber;
799
+ congenitalAnomalyCount: z.ZodDefault<z.ZodNumber>;
800
+ otherSeriousCount: z.ZodDefault<z.ZodNumber>;
801
+ }, z.core.$strip>>;
802
+ }, z.core.$strip>;
803
+ }, z.core.$strip>, z.ZodObject<{
804
+ coverage: z.ZodLiteral<"queried_no_data">;
805
+ error: z.ZodOptional<z.ZodObject<{
806
+ message: z.ZodString;
807
+ name: z.ZodOptional<z.ZodString>;
808
+ stack: z.ZodOptional<z.ZodString>;
809
+ }, z.core.$strip>>;
810
+ }, z.core.$strip>, z.ZodObject<{
811
+ coverage: z.ZodLiteral<"not_loaded">;
812
+ reason: z.ZodOptional<z.ZodString>;
813
+ }, z.core.$strip>], "coverage">>;
814
+ }, z.core.$strip>;
815
+ perTrialAes: z.ZodObject<{
816
+ results: z.ZodArray<z.ZodDiscriminatedUnion<[z.ZodObject<{
817
+ coverage: z.ZodLiteral<"available">;
818
+ data: z.ZodObject<{
819
+ nctId: z.ZodString;
820
+ title: z.ZodString;
821
+ whyStopped: z.ZodNullable<z.ZodString>;
822
+ outcomes: z.ZodDefault<z.ZodArray<z.ZodObject<{
823
+ type: z.ZodEnum<{
824
+ other: "other";
825
+ primary: "primary";
826
+ secondary: "secondary";
827
+ }>;
828
+ measure: z.ZodString;
829
+ description: z.ZodNullable<z.ZodString>;
830
+ timeFrame: z.ZodNullable<z.ZodString>;
831
+ effect: z.ZodDiscriminatedUnion<[z.ZodObject<{
832
+ kind: z.ZodLiteral<"quantitative">;
833
+ value: z.ZodNumber;
834
+ units: z.ZodString;
835
+ ci_low: z.ZodOptional<z.ZodNumber>;
836
+ ci_high: z.ZodOptional<z.ZodNumber>;
837
+ }, z.core.$strip>, z.ZodObject<{
838
+ kind: z.ZodLiteral<"not_extracted">;
839
+ reason: z.ZodEnum<{
840
+ ctgov_no_numeric_result: "ctgov_no_numeric_result";
841
+ ctgov_no_result_groups: "ctgov_no_result_groups";
842
+ }>;
843
+ }, z.core.$strip>], "kind">;
844
+ }, z.core.$strip>>>;
845
+ groups: z.ZodArray<z.ZodObject<{
846
+ groupId: z.ZodString;
847
+ title: z.ZodString;
848
+ description: z.ZodNullable<z.ZodString>;
849
+ }, z.core.$strip>>;
850
+ events: z.ZodArray<z.ZodObject<{
851
+ serious: z.ZodBoolean;
852
+ term: z.ZodString;
853
+ organSystem: z.ZodNullable<z.ZodString>;
854
+ counts: z.ZodArray<z.ZodObject<{
855
+ groupId: z.ZodString;
856
+ numAffected: z.ZodNullable<z.ZodNumber>;
857
+ numAtRisk: z.ZodNullable<z.ZodNumber>;
858
+ }, z.core.$strip>>;
859
+ }, z.core.$strip>>;
860
+ }, z.core.$strip>;
861
+ }, z.core.$strip>, z.ZodObject<{
862
+ coverage: z.ZodLiteral<"queried_no_data">;
863
+ error: z.ZodOptional<z.ZodObject<{
864
+ message: z.ZodString;
865
+ name: z.ZodOptional<z.ZodString>;
866
+ stack: z.ZodOptional<z.ZodString>;
867
+ }, z.core.$strip>>;
868
+ }, z.core.$strip>, z.ZodObject<{
869
+ coverage: z.ZodLiteral<"not_loaded">;
870
+ reason: z.ZodOptional<z.ZodString>;
871
+ }, z.core.$strip>], "coverage">>;
872
+ }, z.core.$strip>;
873
+ perModulatorPolypharm: z.ZodObject<{
874
+ results: z.ZodArray<z.ZodDiscriminatedUnion<[z.ZodObject<{
875
+ coverage: z.ZodLiteral<"available">;
876
+ data: z.ZodObject<{
877
+ moleculeChemblId: z.ZodString;
878
+ preferredName: z.ZodString;
879
+ primaryPchembl: z.ZodNullable<z.ZodNumber>;
880
+ hits: z.ZodArray<z.ZodObject<{
881
+ targetChemblId: z.ZodString;
882
+ targetName: z.ZodNullable<z.ZodString>;
883
+ pchemblValue: z.ZodNullable<z.ZodNumber>;
884
+ standardType: z.ZodNullable<z.ZodString>;
885
+ standardValue: z.ZodNullable<z.ZodNumber>;
886
+ standardUnits: z.ZodNullable<z.ZodString>;
887
+ }, z.core.$strip>>;
888
+ }, z.core.$strip>;
889
+ }, z.core.$strip>, z.ZodObject<{
890
+ coverage: z.ZodLiteral<"queried_no_data">;
891
+ error: z.ZodOptional<z.ZodObject<{
892
+ message: z.ZodString;
893
+ name: z.ZodOptional<z.ZodString>;
894
+ stack: z.ZodOptional<z.ZodString>;
895
+ }, z.core.$strip>>;
896
+ }, z.core.$strip>, z.ZodObject<{
897
+ coverage: z.ZodLiteral<"not_loaded">;
898
+ reason: z.ZodOptional<z.ZodString>;
899
+ }, z.core.$strip>], "coverage">>;
900
+ }, z.core.$strip>;
901
+ perClassDrugAes: z.ZodObject<{
902
+ results: z.ZodArray<z.ZodDiscriminatedUnion<[z.ZodObject<{
903
+ coverage: z.ZodLiteral<"available">;
904
+ data: z.ZodObject<{
905
+ moleculeChemblId: z.ZodString;
906
+ preferredName: z.ZodString;
907
+ totalReports: z.ZodNullable<z.ZodNumber>;
908
+ topReactions: z.ZodArray<z.ZodObject<{
909
+ reaction: z.ZodString;
910
+ count: z.ZodNumber;
911
+ }, z.core.$strip>>;
912
+ seriousness: z.ZodNullable<z.ZodObject<{
913
+ totalReports: z.ZodNumber;
914
+ fatalCount: z.ZodNumber;
915
+ hospitalizationCount: z.ZodNumber;
916
+ lifeThreateningCount: z.ZodNumber;
917
+ disablingCount: z.ZodNumber;
918
+ congenitalAnomalyCount: z.ZodDefault<z.ZodNumber>;
919
+ otherSeriousCount: z.ZodDefault<z.ZodNumber>;
920
+ }, z.core.$strip>>;
921
+ }, z.core.$strip>;
922
+ }, z.core.$strip>, z.ZodObject<{
923
+ coverage: z.ZodLiteral<"queried_no_data">;
924
+ error: z.ZodOptional<z.ZodObject<{
925
+ message: z.ZodString;
926
+ name: z.ZodOptional<z.ZodString>;
927
+ stack: z.ZodOptional<z.ZodString>;
928
+ }, z.core.$strip>>;
929
+ }, z.core.$strip>, z.ZodObject<{
930
+ coverage: z.ZodLiteral<"not_loaded">;
931
+ reason: z.ZodOptional<z.ZodString>;
932
+ }, z.core.$strip>], "coverage">>;
933
+ }, z.core.$strip>;
934
+ }, z.core.$strip>;
935
+ }, z.core.$strip>;
936
+ export type Phase3Bundle = z.infer<typeof Phase3BundleSchema>;