@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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@@ -0,0 +1,560 @@
1
+ /**
2
+ * Phase-5 synthesis functions for the harness DBOS workflow.
3
+ *
4
+ * Four functions:
5
+ * - `liabilityBullets` (per-section, parallel-safe)
6
+ * - `safetyFlagsTrail` (per-section, parallel-safe)
7
+ * - `translationalCommentary` (per-section, parallel-safe)
8
+ * - `dossierRecommendation` (whole-dossier, sequential after the three above)
9
+ *
10
+ * Each function is a pure async `(input, deps) => Promise<EnvelopeWithDiagnostic>`.
11
+ * Every call is single-shot structured-output through `structuredLlmCall`.
12
+ *
13
+ * The `runSynthesisWithProbe` helper preserves the bounded-retry-on-probe-
14
+ * failure semantics: attempt 1 → probe → critique-driven retry → probe.
15
+ * Each attempt is its own attempt-numbered DBOS step so a resumed
16
+ * post-402 call lands a fresh cache slot.
17
+ */
18
+ import { z } from "zod";
19
+ import { type DossierV4Body } from "@inflexa-ai/harness/contracts/target-dossier.js";
20
+ import type { AgentSession } from "../../../auth/types.js";
21
+ import type { AgentChat } from "../../../providers/types.js";
22
+ import { BUDGET_EXCEEDED_SENTINEL } from "../lib/llm-step.js";
23
+ export declare const LiabilityBulletsOutputSchema: z.ZodObject<{
24
+ bullets: z.ZodArray<z.ZodObject<{
25
+ organ_or_axis: z.ZodString;
26
+ severity: z.ZodEnum<{
27
+ high: "high";
28
+ medium: "medium";
29
+ low: "low";
30
+ }>;
31
+ text: z.ZodString;
32
+ evidence_pointer: z.ZodString;
33
+ rationale: z.ZodString;
34
+ category: z.ZodEnum<{
35
+ other: "other";
36
+ fatal_post_market: "fatal_post_market";
37
+ class_liability: "class_liability";
38
+ off_target_safety: "off_target_safety";
39
+ high_safety_organ_expression: "high_safety_organ_expression";
40
+ broad_expression: "broad_expression";
41
+ }>;
42
+ }, z.core.$strip>>;
43
+ notes: z.ZodString;
44
+ }, z.core.$strip>;
45
+ export type LiabilityBulletsOutput = z.infer<typeof LiabilityBulletsOutputSchema>;
46
+ export declare const SafetyFlagsTrailOutputSchema: z.ZodObject<{
47
+ flags: z.ZodArray<z.ZodObject<{
48
+ organ: z.ZodString;
49
+ trail: z.ZodString;
50
+ mechanism_hypothesis: z.ZodNullable<z.ZodString>;
51
+ }, z.core.$strip>>;
52
+ }, z.core.$strip>;
53
+ export type SafetyFlagsTrailOutput = z.infer<typeof SafetyFlagsTrailOutputSchema>;
54
+ export declare const TranslationalCommentaryOutputSchema: z.ZodObject<{
55
+ rows: z.ZodArray<z.ZodObject<{
56
+ topic: z.ZodEnum<{
57
+ ko_phenotype: "ko_phenotype";
58
+ expression_translation: "expression_translation";
59
+ organ_system_match: "organ_system_match";
60
+ family_context: "family_context";
61
+ }>;
62
+ predicate: z.ZodString;
63
+ commentary: z.ZodString;
64
+ }, z.core.$strip>>;
65
+ }, z.core.$strip>;
66
+ export type TranslationalCommentaryOutput = z.infer<typeof TranslationalCommentaryOutputSchema>;
67
+ export declare const ExternalCitationSchema: z.ZodObject<{
68
+ id: z.ZodString;
69
+ kind: z.ZodEnum<{
70
+ pubmed: "pubmed";
71
+ fda_anda: "fda_anda";
72
+ fda_nda: "fda_nda";
73
+ clinicaltrials: "clinicaltrials";
74
+ regulatory_guidance: "regulatory_guidance";
75
+ }>;
76
+ retrieved_via: z.ZodString;
77
+ fetched_at: z.ZodOptional<z.ZodString>;
78
+ excerpt: z.ZodString;
79
+ }, z.core.$strip>;
80
+ export type ExternalCitation = z.infer<typeof ExternalCitationSchema>;
81
+ export declare const DossierRecommendationOutputSchema: z.ZodObject<{
82
+ disposition: z.ZodEnum<{
83
+ pursue: "pursue";
84
+ conditional: "conditional";
85
+ de_prioritize: "de_prioritize";
86
+ insufficient_evidence: "insufficient_evidence";
87
+ }>;
88
+ confidence: z.ZodEnum<{
89
+ high: "high";
90
+ medium: "medium";
91
+ low: "low";
92
+ }>;
93
+ rationale: z.ZodString;
94
+ key_strengths: z.ZodArray<z.ZodString>;
95
+ key_risks: z.ZodArray<z.ZodString>;
96
+ modality_choice: z.ZodObject<{
97
+ modality: z.ZodString;
98
+ rationale: z.ZodString;
99
+ }, z.core.$strip>;
100
+ coverage_qualifier: z.ZodObject<{
101
+ sections_consulted: z.ZodArray<z.ZodString>;
102
+ sections_unavailable: z.ZodArray<z.ZodString>;
103
+ note: z.ZodString;
104
+ }, z.core.$strip>;
105
+ external_citations: z.ZodDefault<z.ZodArray<z.ZodObject<{
106
+ id: z.ZodString;
107
+ kind: z.ZodEnum<{
108
+ pubmed: "pubmed";
109
+ fda_anda: "fda_anda";
110
+ fda_nda: "fda_nda";
111
+ clinicaltrials: "clinicaltrials";
112
+ regulatory_guidance: "regulatory_guidance";
113
+ }>;
114
+ retrieved_via: z.ZodString;
115
+ fetched_at: z.ZodOptional<z.ZodString>;
116
+ excerpt: z.ZodString;
117
+ }, z.core.$strip>>>;
118
+ }, z.core.$strip>;
119
+ export type DossierRecommendationOutput = z.infer<typeof DossierRecommendationOutputSchema>;
120
+ export declare const LiabilityBulletsStepOutputSchema: z.ZodDiscriminatedUnion<[z.ZodObject<{
121
+ coverage: z.ZodLiteral<"available">;
122
+ data: z.ZodObject<{
123
+ bullets: z.ZodArray<z.ZodObject<{
124
+ organ_or_axis: z.ZodString;
125
+ severity: z.ZodEnum<{
126
+ high: "high";
127
+ medium: "medium";
128
+ low: "low";
129
+ }>;
130
+ text: z.ZodString;
131
+ evidence_pointer: z.ZodString;
132
+ rationale: z.ZodString;
133
+ category: z.ZodEnum<{
134
+ other: "other";
135
+ fatal_post_market: "fatal_post_market";
136
+ class_liability: "class_liability";
137
+ off_target_safety: "off_target_safety";
138
+ high_safety_organ_expression: "high_safety_organ_expression";
139
+ broad_expression: "broad_expression";
140
+ }>;
141
+ }, z.core.$strip>>;
142
+ notes: z.ZodString;
143
+ }, z.core.$strip>;
144
+ diagnostic: z.ZodObject<{
145
+ step_id: z.ZodEnum<{
146
+ "liability-bullets": "liability-bullets";
147
+ "safety-flags-trail": "safety-flags-trail";
148
+ "translational-commentary": "translational-commentary";
149
+ "dossier-recommendation": "dossier-recommendation";
150
+ }>;
151
+ model_id: z.ZodString;
152
+ attempt_count: z.ZodNumber;
153
+ retry_critique: z.ZodNullable<z.ZodString>;
154
+ output_chars: z.ZodNumber;
155
+ probe_verdict: z.ZodEnum<{
156
+ skipped: "skipped";
157
+ pass: "pass";
158
+ "fail-length": "fail-length";
159
+ "fail-section-references": "fail-section-references";
160
+ "fail-key-strengths-risks": "fail-key-strengths-risks";
161
+ "fail-source-references": "fail-source-references";
162
+ "fail-numeric-claim": "fail-numeric-claim";
163
+ "fail-voice": "fail-voice";
164
+ relaxed: "relaxed";
165
+ }>;
166
+ final_coverage: z.ZodEnum<{
167
+ available: "available";
168
+ queried_no_data: "queried_no_data";
169
+ }>;
170
+ error_kind: z.ZodOptional<z.ZodNullable<z.ZodEnum<{
171
+ "synthesis-too-shallow": "synthesis-too-shallow";
172
+ "synthesis-unavailable": "synthesis-unavailable";
173
+ "voice-violation": "voice-violation";
174
+ }>>>;
175
+ error_message: z.ZodOptional<z.ZodNullable<z.ZodString>>;
176
+ }, z.core.$strip>;
177
+ }, z.core.$strip>, z.ZodObject<{
178
+ coverage: z.ZodLiteral<"queried_no_data">;
179
+ error: z.ZodOptional<z.ZodObject<{
180
+ message: z.ZodString;
181
+ name: z.ZodOptional<z.ZodString>;
182
+ stack: z.ZodOptional<z.ZodString>;
183
+ kind: z.ZodOptional<z.ZodEnum<{
184
+ "synthesis-too-shallow": "synthesis-too-shallow";
185
+ "synthesis-unavailable": "synthesis-unavailable";
186
+ "voice-violation": "voice-violation";
187
+ }>>;
188
+ }, z.core.$strip>>;
189
+ diagnostic: z.ZodObject<{
190
+ step_id: z.ZodEnum<{
191
+ "liability-bullets": "liability-bullets";
192
+ "safety-flags-trail": "safety-flags-trail";
193
+ "translational-commentary": "translational-commentary";
194
+ "dossier-recommendation": "dossier-recommendation";
195
+ }>;
196
+ model_id: z.ZodString;
197
+ attempt_count: z.ZodNumber;
198
+ retry_critique: z.ZodNullable<z.ZodString>;
199
+ output_chars: z.ZodNumber;
200
+ probe_verdict: z.ZodEnum<{
201
+ skipped: "skipped";
202
+ pass: "pass";
203
+ "fail-length": "fail-length";
204
+ "fail-section-references": "fail-section-references";
205
+ "fail-key-strengths-risks": "fail-key-strengths-risks";
206
+ "fail-source-references": "fail-source-references";
207
+ "fail-numeric-claim": "fail-numeric-claim";
208
+ "fail-voice": "fail-voice";
209
+ relaxed: "relaxed";
210
+ }>;
211
+ final_coverage: z.ZodEnum<{
212
+ available: "available";
213
+ queried_no_data: "queried_no_data";
214
+ }>;
215
+ error_kind: z.ZodOptional<z.ZodNullable<z.ZodEnum<{
216
+ "synthesis-too-shallow": "synthesis-too-shallow";
217
+ "synthesis-unavailable": "synthesis-unavailable";
218
+ "voice-violation": "voice-violation";
219
+ }>>>;
220
+ error_message: z.ZodOptional<z.ZodNullable<z.ZodString>>;
221
+ }, z.core.$strip>;
222
+ }, z.core.$strip>], "coverage">;
223
+ export type LiabilityBulletsStepOutput = z.infer<typeof LiabilityBulletsStepOutputSchema>;
224
+ export declare const SafetyFlagsTrailStepOutputSchema: z.ZodDiscriminatedUnion<[z.ZodObject<{
225
+ coverage: z.ZodLiteral<"available">;
226
+ data: z.ZodObject<{
227
+ flags: z.ZodArray<z.ZodObject<{
228
+ organ: z.ZodString;
229
+ trail: z.ZodString;
230
+ mechanism_hypothesis: z.ZodNullable<z.ZodString>;
231
+ }, z.core.$strip>>;
232
+ }, z.core.$strip>;
233
+ diagnostic: z.ZodObject<{
234
+ step_id: z.ZodEnum<{
235
+ "liability-bullets": "liability-bullets";
236
+ "safety-flags-trail": "safety-flags-trail";
237
+ "translational-commentary": "translational-commentary";
238
+ "dossier-recommendation": "dossier-recommendation";
239
+ }>;
240
+ model_id: z.ZodString;
241
+ attempt_count: z.ZodNumber;
242
+ retry_critique: z.ZodNullable<z.ZodString>;
243
+ output_chars: z.ZodNumber;
244
+ probe_verdict: z.ZodEnum<{
245
+ skipped: "skipped";
246
+ pass: "pass";
247
+ "fail-length": "fail-length";
248
+ "fail-section-references": "fail-section-references";
249
+ "fail-key-strengths-risks": "fail-key-strengths-risks";
250
+ "fail-source-references": "fail-source-references";
251
+ "fail-numeric-claim": "fail-numeric-claim";
252
+ "fail-voice": "fail-voice";
253
+ relaxed: "relaxed";
254
+ }>;
255
+ final_coverage: z.ZodEnum<{
256
+ available: "available";
257
+ queried_no_data: "queried_no_data";
258
+ }>;
259
+ error_kind: z.ZodOptional<z.ZodNullable<z.ZodEnum<{
260
+ "synthesis-too-shallow": "synthesis-too-shallow";
261
+ "synthesis-unavailable": "synthesis-unavailable";
262
+ "voice-violation": "voice-violation";
263
+ }>>>;
264
+ error_message: z.ZodOptional<z.ZodNullable<z.ZodString>>;
265
+ }, z.core.$strip>;
266
+ }, z.core.$strip>, z.ZodObject<{
267
+ coverage: z.ZodLiteral<"queried_no_data">;
268
+ error: z.ZodOptional<z.ZodObject<{
269
+ message: z.ZodString;
270
+ name: z.ZodOptional<z.ZodString>;
271
+ stack: z.ZodOptional<z.ZodString>;
272
+ kind: z.ZodOptional<z.ZodEnum<{
273
+ "synthesis-too-shallow": "synthesis-too-shallow";
274
+ "synthesis-unavailable": "synthesis-unavailable";
275
+ "voice-violation": "voice-violation";
276
+ }>>;
277
+ }, z.core.$strip>>;
278
+ diagnostic: z.ZodObject<{
279
+ step_id: z.ZodEnum<{
280
+ "liability-bullets": "liability-bullets";
281
+ "safety-flags-trail": "safety-flags-trail";
282
+ "translational-commentary": "translational-commentary";
283
+ "dossier-recommendation": "dossier-recommendation";
284
+ }>;
285
+ model_id: z.ZodString;
286
+ attempt_count: z.ZodNumber;
287
+ retry_critique: z.ZodNullable<z.ZodString>;
288
+ output_chars: z.ZodNumber;
289
+ probe_verdict: z.ZodEnum<{
290
+ skipped: "skipped";
291
+ pass: "pass";
292
+ "fail-length": "fail-length";
293
+ "fail-section-references": "fail-section-references";
294
+ "fail-key-strengths-risks": "fail-key-strengths-risks";
295
+ "fail-source-references": "fail-source-references";
296
+ "fail-numeric-claim": "fail-numeric-claim";
297
+ "fail-voice": "fail-voice";
298
+ relaxed: "relaxed";
299
+ }>;
300
+ final_coverage: z.ZodEnum<{
301
+ available: "available";
302
+ queried_no_data: "queried_no_data";
303
+ }>;
304
+ error_kind: z.ZodOptional<z.ZodNullable<z.ZodEnum<{
305
+ "synthesis-too-shallow": "synthesis-too-shallow";
306
+ "synthesis-unavailable": "synthesis-unavailable";
307
+ "voice-violation": "voice-violation";
308
+ }>>>;
309
+ error_message: z.ZodOptional<z.ZodNullable<z.ZodString>>;
310
+ }, z.core.$strip>;
311
+ }, z.core.$strip>], "coverage">;
312
+ export type SafetyFlagsTrailStepOutput = z.infer<typeof SafetyFlagsTrailStepOutputSchema>;
313
+ export declare const TranslationalCommentaryStepOutputSchema: z.ZodDiscriminatedUnion<[z.ZodObject<{
314
+ coverage: z.ZodLiteral<"available">;
315
+ data: z.ZodObject<{
316
+ rows: z.ZodArray<z.ZodObject<{
317
+ topic: z.ZodEnum<{
318
+ ko_phenotype: "ko_phenotype";
319
+ expression_translation: "expression_translation";
320
+ organ_system_match: "organ_system_match";
321
+ family_context: "family_context";
322
+ }>;
323
+ predicate: z.ZodString;
324
+ commentary: z.ZodString;
325
+ }, z.core.$strip>>;
326
+ }, z.core.$strip>;
327
+ diagnostic: z.ZodObject<{
328
+ step_id: z.ZodEnum<{
329
+ "liability-bullets": "liability-bullets";
330
+ "safety-flags-trail": "safety-flags-trail";
331
+ "translational-commentary": "translational-commentary";
332
+ "dossier-recommendation": "dossier-recommendation";
333
+ }>;
334
+ model_id: z.ZodString;
335
+ attempt_count: z.ZodNumber;
336
+ retry_critique: z.ZodNullable<z.ZodString>;
337
+ output_chars: z.ZodNumber;
338
+ probe_verdict: z.ZodEnum<{
339
+ skipped: "skipped";
340
+ pass: "pass";
341
+ "fail-length": "fail-length";
342
+ "fail-section-references": "fail-section-references";
343
+ "fail-key-strengths-risks": "fail-key-strengths-risks";
344
+ "fail-source-references": "fail-source-references";
345
+ "fail-numeric-claim": "fail-numeric-claim";
346
+ "fail-voice": "fail-voice";
347
+ relaxed: "relaxed";
348
+ }>;
349
+ final_coverage: z.ZodEnum<{
350
+ available: "available";
351
+ queried_no_data: "queried_no_data";
352
+ }>;
353
+ error_kind: z.ZodOptional<z.ZodNullable<z.ZodEnum<{
354
+ "synthesis-too-shallow": "synthesis-too-shallow";
355
+ "synthesis-unavailable": "synthesis-unavailable";
356
+ "voice-violation": "voice-violation";
357
+ }>>>;
358
+ error_message: z.ZodOptional<z.ZodNullable<z.ZodString>>;
359
+ }, z.core.$strip>;
360
+ }, z.core.$strip>, z.ZodObject<{
361
+ coverage: z.ZodLiteral<"queried_no_data">;
362
+ error: z.ZodOptional<z.ZodObject<{
363
+ message: z.ZodString;
364
+ name: z.ZodOptional<z.ZodString>;
365
+ stack: z.ZodOptional<z.ZodString>;
366
+ kind: z.ZodOptional<z.ZodEnum<{
367
+ "synthesis-too-shallow": "synthesis-too-shallow";
368
+ "synthesis-unavailable": "synthesis-unavailable";
369
+ "voice-violation": "voice-violation";
370
+ }>>;
371
+ }, z.core.$strip>>;
372
+ diagnostic: z.ZodObject<{
373
+ step_id: z.ZodEnum<{
374
+ "liability-bullets": "liability-bullets";
375
+ "safety-flags-trail": "safety-flags-trail";
376
+ "translational-commentary": "translational-commentary";
377
+ "dossier-recommendation": "dossier-recommendation";
378
+ }>;
379
+ model_id: z.ZodString;
380
+ attempt_count: z.ZodNumber;
381
+ retry_critique: z.ZodNullable<z.ZodString>;
382
+ output_chars: z.ZodNumber;
383
+ probe_verdict: z.ZodEnum<{
384
+ skipped: "skipped";
385
+ pass: "pass";
386
+ "fail-length": "fail-length";
387
+ "fail-section-references": "fail-section-references";
388
+ "fail-key-strengths-risks": "fail-key-strengths-risks";
389
+ "fail-source-references": "fail-source-references";
390
+ "fail-numeric-claim": "fail-numeric-claim";
391
+ "fail-voice": "fail-voice";
392
+ relaxed: "relaxed";
393
+ }>;
394
+ final_coverage: z.ZodEnum<{
395
+ available: "available";
396
+ queried_no_data: "queried_no_data";
397
+ }>;
398
+ error_kind: z.ZodOptional<z.ZodNullable<z.ZodEnum<{
399
+ "synthesis-too-shallow": "synthesis-too-shallow";
400
+ "synthesis-unavailable": "synthesis-unavailable";
401
+ "voice-violation": "voice-violation";
402
+ }>>>;
403
+ error_message: z.ZodOptional<z.ZodNullable<z.ZodString>>;
404
+ }, z.core.$strip>;
405
+ }, z.core.$strip>], "coverage">;
406
+ export type TranslationalCommentaryStepOutput = z.infer<typeof TranslationalCommentaryStepOutputSchema>;
407
+ export declare const DossierRecommendationStepOutputSchema: z.ZodDiscriminatedUnion<[z.ZodObject<{
408
+ coverage: z.ZodLiteral<"available">;
409
+ data: z.ZodObject<{
410
+ disposition: z.ZodEnum<{
411
+ pursue: "pursue";
412
+ conditional: "conditional";
413
+ de_prioritize: "de_prioritize";
414
+ insufficient_evidence: "insufficient_evidence";
415
+ }>;
416
+ confidence: z.ZodEnum<{
417
+ high: "high";
418
+ medium: "medium";
419
+ low: "low";
420
+ }>;
421
+ rationale: z.ZodString;
422
+ key_strengths: z.ZodArray<z.ZodString>;
423
+ key_risks: z.ZodArray<z.ZodString>;
424
+ modality_choice: z.ZodObject<{
425
+ modality: z.ZodString;
426
+ rationale: z.ZodString;
427
+ }, z.core.$strip>;
428
+ coverage_qualifier: z.ZodObject<{
429
+ sections_consulted: z.ZodArray<z.ZodString>;
430
+ sections_unavailable: z.ZodArray<z.ZodString>;
431
+ note: z.ZodString;
432
+ }, z.core.$strip>;
433
+ external_citations: z.ZodDefault<z.ZodArray<z.ZodObject<{
434
+ id: z.ZodString;
435
+ kind: z.ZodEnum<{
436
+ pubmed: "pubmed";
437
+ fda_anda: "fda_anda";
438
+ fda_nda: "fda_nda";
439
+ clinicaltrials: "clinicaltrials";
440
+ regulatory_guidance: "regulatory_guidance";
441
+ }>;
442
+ retrieved_via: z.ZodString;
443
+ fetched_at: z.ZodOptional<z.ZodString>;
444
+ excerpt: z.ZodString;
445
+ }, z.core.$strip>>>;
446
+ }, z.core.$strip>;
447
+ diagnostic: z.ZodObject<{
448
+ step_id: z.ZodEnum<{
449
+ "liability-bullets": "liability-bullets";
450
+ "safety-flags-trail": "safety-flags-trail";
451
+ "translational-commentary": "translational-commentary";
452
+ "dossier-recommendation": "dossier-recommendation";
453
+ }>;
454
+ model_id: z.ZodString;
455
+ attempt_count: z.ZodNumber;
456
+ retry_critique: z.ZodNullable<z.ZodString>;
457
+ output_chars: z.ZodNumber;
458
+ probe_verdict: z.ZodEnum<{
459
+ skipped: "skipped";
460
+ pass: "pass";
461
+ "fail-length": "fail-length";
462
+ "fail-section-references": "fail-section-references";
463
+ "fail-key-strengths-risks": "fail-key-strengths-risks";
464
+ "fail-source-references": "fail-source-references";
465
+ "fail-numeric-claim": "fail-numeric-claim";
466
+ "fail-voice": "fail-voice";
467
+ relaxed: "relaxed";
468
+ }>;
469
+ final_coverage: z.ZodEnum<{
470
+ available: "available";
471
+ queried_no_data: "queried_no_data";
472
+ }>;
473
+ error_kind: z.ZodOptional<z.ZodNullable<z.ZodEnum<{
474
+ "synthesis-too-shallow": "synthesis-too-shallow";
475
+ "synthesis-unavailable": "synthesis-unavailable";
476
+ "voice-violation": "voice-violation";
477
+ }>>>;
478
+ error_message: z.ZodOptional<z.ZodNullable<z.ZodString>>;
479
+ }, z.core.$strip>;
480
+ }, z.core.$strip>, z.ZodObject<{
481
+ coverage: z.ZodLiteral<"queried_no_data">;
482
+ error: z.ZodOptional<z.ZodObject<{
483
+ message: z.ZodString;
484
+ name: z.ZodOptional<z.ZodString>;
485
+ stack: z.ZodOptional<z.ZodString>;
486
+ kind: z.ZodOptional<z.ZodEnum<{
487
+ "synthesis-too-shallow": "synthesis-too-shallow";
488
+ "synthesis-unavailable": "synthesis-unavailable";
489
+ "voice-violation": "voice-violation";
490
+ }>>;
491
+ }, z.core.$strip>>;
492
+ diagnostic: z.ZodObject<{
493
+ step_id: z.ZodEnum<{
494
+ "liability-bullets": "liability-bullets";
495
+ "safety-flags-trail": "safety-flags-trail";
496
+ "translational-commentary": "translational-commentary";
497
+ "dossier-recommendation": "dossier-recommendation";
498
+ }>;
499
+ model_id: z.ZodString;
500
+ attempt_count: z.ZodNumber;
501
+ retry_critique: z.ZodNullable<z.ZodString>;
502
+ output_chars: z.ZodNumber;
503
+ probe_verdict: z.ZodEnum<{
504
+ skipped: "skipped";
505
+ pass: "pass";
506
+ "fail-length": "fail-length";
507
+ "fail-section-references": "fail-section-references";
508
+ "fail-key-strengths-risks": "fail-key-strengths-risks";
509
+ "fail-source-references": "fail-source-references";
510
+ "fail-numeric-claim": "fail-numeric-claim";
511
+ "fail-voice": "fail-voice";
512
+ relaxed: "relaxed";
513
+ }>;
514
+ final_coverage: z.ZodEnum<{
515
+ available: "available";
516
+ queried_no_data: "queried_no_data";
517
+ }>;
518
+ error_kind: z.ZodOptional<z.ZodNullable<z.ZodEnum<{
519
+ "synthesis-too-shallow": "synthesis-too-shallow";
520
+ "synthesis-unavailable": "synthesis-unavailable";
521
+ "voice-violation": "voice-violation";
522
+ }>>>;
523
+ error_message: z.ZodOptional<z.ZodNullable<z.ZodString>>;
524
+ }, z.core.$strip>;
525
+ }, z.core.$strip>], "coverage">;
526
+ export type DossierRecommendationStepOutput = z.infer<typeof DossierRecommendationStepOutputSchema>;
527
+ export interface SynthesisAgentDeps {
528
+ readonly chatProvider: AgentChat;
529
+ readonly session: AgentSession;
530
+ readonly model: string;
531
+ /** Attempt counter — bumped on resume so a 402-cancelled call lands a fresh DBOS step slot. */
532
+ readonly attempt: number;
533
+ /** Pre-fetched FDA approval-precedent markdown block, appended to every synthesis prompt. */
534
+ readonly approvalPrecedents: string;
535
+ }
536
+ export type SynthesisStepResult<TStepOutput> = TStepOutput | {
537
+ readonly kind: "budget-exceeded";
538
+ readonly sentinel: typeof BUDGET_EXCEEDED_SENTINEL;
539
+ };
540
+ declare function isBudgetExceeded<T>(v: SynthesisStepResult<T>): v is {
541
+ kind: "budget-exceeded";
542
+ sentinel: typeof BUDGET_EXCEEDED_SENTINEL;
543
+ };
544
+ interface Phase4Output {
545
+ readonly assessmentId: string;
546
+ readonly dossier: DossierV4Body;
547
+ }
548
+ export declare function liabilityBullets(phase4: Phase4Output, deps: SynthesisAgentDeps): Promise<SynthesisStepResult<LiabilityBulletsStepOutput>>;
549
+ export declare function safetyFlagsTrail(phase4: Phase4Output, deps: SynthesisAgentDeps): Promise<SynthesisStepResult<SafetyFlagsTrailStepOutput>>;
550
+ export declare function translationalCommentary(phase4: Phase4Output, deps: SynthesisAgentDeps): Promise<SynthesisStepResult<TranslationalCommentaryStepOutput>>;
551
+ export interface DossierRecommendationInput {
552
+ readonly phase4: Phase4Output;
553
+ readonly perSection: {
554
+ readonly liabilityBullets: LiabilityBulletsStepOutput;
555
+ readonly safetyFlagsTrail: SafetyFlagsTrailStepOutput;
556
+ readonly translationalCommentary: TranslationalCommentaryStepOutput;
557
+ };
558
+ }
559
+ export declare function dossierRecommendation(input: DossierRecommendationInput, deps: SynthesisAgentDeps): Promise<SynthesisStepResult<DossierRecommendationStepOutput>>;
560
+ export { isBudgetExceeded as isSynthesisBudgetExceeded };