@inflexa-ai/harness 0.35.8 → 0.36.1
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.
- package/dist/auth/types.d.ts +5 -14
- package/dist/auth/types.js +3 -10
- package/dist/billing/usage-recorder.d.ts +1 -1
- package/dist/contracts/analogy-report.d.ts +1 -1
- package/dist/contracts/analogy-report.js +1 -1
- package/dist/contracts/chat-parts.d.ts +2 -3
- package/dist/contracts/index.d.ts +0 -4
- package/dist/contracts/index.js +0 -2
- package/dist/index.d.ts +0 -7
- package/dist/index.js +0 -21
- package/dist/lib/metrics.d.ts +1 -1
- package/dist/lib/otel-spans.d.ts +0 -2
- package/dist/lib/otel-spans.js +0 -2
- package/dist/loop/genai-spans.d.ts +14 -0
- package/dist/loop/genai-spans.js +35 -0
- package/dist/loop/run-agent.d.ts +1 -1
- package/dist/loop/run-agent.js +37 -4
- package/dist/runtime/assemble.d.ts +0 -3
- package/dist/runtime/assemble.js +0 -3
- package/dist/state/index.d.ts +0 -2
- package/dist/state/index.js +0 -1
- package/dist/state/init.js +1 -60
- package/dist/state/purge-analysis.d.ts +1 -2
- package/dist/state/purge-analysis.js +1 -2
- package/dist/tasks/regulatory-corpus-boot-refresh.js +1 -1
- package/dist/tools/bio/gene-preclinical-profile.d.ts +1 -3
- package/dist/tools/bio/gene-preclinical-profile.js +1 -3
- package/dist/tools/lib/chembl-client.d.ts +1 -4
- package/dist/tools/lib/chembl-client.js +1 -4
- package/dist/tools/lib/clinical-benchmarks-client.d.ts +1 -1
- package/dist/tools/lib/clinical-benchmarks-client.js +1 -1
- package/dist/tools/lib/clinical-trials-client.d.ts +0 -3
- package/dist/tools/lib/clinical-trials-client.js +0 -3
- package/dist/tools/lib/identifier-resolver.d.ts +5 -7
- package/dist/tools/lib/identifier-resolver.js +5 -7
- package/dist/tools/lib/iuphar-client.d.ts +1 -3
- package/dist/tools/lib/iuphar-client.js +1 -3
- package/dist/tools/lib/opentargets-client.d.ts +1 -1
- package/dist/tools/lib/opentargets-client.js +1 -1
- package/dist/tools/lib/protein-family-normalize.d.ts +5 -7
- package/dist/tools/lib/protein-family-normalize.js +5 -7
- package/dist/tools/lib/uniprot-client.d.ts +0 -7
- package/dist/tools/lib/uniprot-client.js +2 -9
- package/package.json +1 -1
- package/dist/contracts/target-assessment-row.d.ts +0 -85
- package/dist/contracts/target-assessment-row.js +0 -37
- package/dist/contracts/target-dossier.d.ts +0 -12423
- package/dist/contracts/target-dossier.js +0 -1282
- package/dist/prompts/target-assessment/briefs/executive-recommendation.d.ts +0 -1
- package/dist/prompts/target-assessment/briefs/executive-recommendation.js +0 -85
- package/dist/prompts/target-assessment/briefs/index.d.ts +0 -4
- package/dist/prompts/target-assessment/briefs/index.js +0 -4
- package/dist/prompts/target-assessment/briefs/liability-bullets.d.ts +0 -1
- package/dist/prompts/target-assessment/briefs/liability-bullets.js +0 -114
- package/dist/prompts/target-assessment/briefs/target-organ-liabilities.d.ts +0 -1
- package/dist/prompts/target-assessment/briefs/target-organ-liabilities.js +0 -37
- package/dist/prompts/target-assessment/briefs/translational-commentary.d.ts +0 -1
- package/dist/prompts/target-assessment/briefs/translational-commentary.js +0 -23
- package/dist/prompts/target-assessment/drugs-in-class.d.ts +0 -1
- package/dist/prompts/target-assessment/drugs-in-class.js +0 -29
- package/dist/prompts/target-assessment/investigation/adversarial-critique.d.ts +0 -1
- package/dist/prompts/target-assessment/investigation/adversarial-critique.js +0 -67
- package/dist/prompts/target-assessment/investigation/claim-reverification.d.ts +0 -1
- package/dist/prompts/target-assessment/investigation/claim-reverification.js +0 -49
- package/dist/prompts/target-assessment/investigation/index.d.ts +0 -3
- package/dist/prompts/target-assessment/investigation/index.js +0 -3
- package/dist/prompts/target-assessment/investigation/mechanism-proposal.d.ts +0 -1
- package/dist/prompts/target-assessment/investigation/mechanism-proposal.js +0 -49
- package/dist/prompts/target-assessment/modulator-triage.d.ts +0 -1
- package/dist/prompts/target-assessment/modulator-triage.js +0 -31
- package/dist/prompts/target-assessment/off-target-annotator.d.ts +0 -1
- package/dist/prompts/target-assessment/off-target-annotator.js +0 -28
- package/dist/prompts/target-assessment/tox-voice/core.d.ts +0 -1
- package/dist/prompts/target-assessment/tox-voice/core.js +0 -74
- package/dist/prompts/target-assessment/tox-voice/critique.d.ts +0 -7
- package/dist/prompts/target-assessment/tox-voice/critique.js +0 -109
- package/dist/prompts/target-assessment/tox-voice/exemplars.d.ts +0 -8
- package/dist/prompts/target-assessment/tox-voice/exemplars.js +0 -24
- package/dist/prompts/target-assessment/tox-voice/index.d.ts +0 -4
- package/dist/prompts/target-assessment/tox-voice/index.js +0 -4
- package/dist/prompts/target-assessment/tox-voice/vocabulary.d.ts +0 -18
- package/dist/prompts/target-assessment/tox-voice/vocabulary.js +0 -61
- package/dist/state/target-assessments.d.ts +0 -68
- package/dist/state/target-assessments.js +0 -222
- package/dist/workflows/execute-target-assessment.d.ts +0 -118
- package/dist/workflows/execute-target-assessment.js +0 -631
- package/dist/workflows/target-assessment/assemblers/index.d.ts +0 -5
- package/dist/workflows/target-assessment/assemblers/index.js +0 -4
- package/dist/workflows/target-assessment/assemblers/literature.d.ts +0 -281
- package/dist/workflows/target-assessment/assemblers/literature.js +0 -971
- package/dist/workflows/target-assessment/assemblers/orchestrator.d.ts +0 -118
- package/dist/workflows/target-assessment/assemblers/orchestrator.js +0 -945
- package/dist/workflows/target-assessment/assemblers/safety.d.ts +0 -374
- package/dist/workflows/target-assessment/assemblers/safety.js +0 -1068
- package/dist/workflows/target-assessment/assemblers/trials.d.ts +0 -30
- package/dist/workflows/target-assessment/assemblers/trials.js +0 -75
- package/dist/workflows/target-assessment/collectors/index.d.ts +0 -114
- package/dist/workflows/target-assessment/collectors/index.js +0 -538
- package/dist/workflows/target-assessment/coverage.d.ts +0 -97
- package/dist/workflows/target-assessment/coverage.js +0 -86
- package/dist/workflows/target-assessment/decisions/index.d.ts +0 -86
- package/dist/workflows/target-assessment/decisions/index.js +0 -127
- package/dist/workflows/target-assessment/fanout/index.d.ts +0 -32
- package/dist/workflows/target-assessment/fanout/index.js +0 -156
- package/dist/workflows/target-assessment/investigation/index.d.ts +0 -97
- package/dist/workflows/target-assessment/investigation/index.js +0 -419
- package/dist/workflows/target-assessment/lib/approval-precedents.d.ts +0 -73
- package/dist/workflows/target-assessment/lib/approval-precedents.js +0 -185
- package/dist/workflows/target-assessment/lib/citation-validator.d.ts +0 -46
- package/dist/workflows/target-assessment/lib/citation-validator.js +0 -316
- package/dist/workflows/target-assessment/lib/clinical-consequence-annotator.d.ts +0 -65
- package/dist/workflows/target-assessment/lib/clinical-consequence-annotator.js +0 -174
- package/dist/workflows/target-assessment/lib/clinical-evidence-attribution.d.ts +0 -44
- package/dist/workflows/target-assessment/lib/clinical-evidence-attribution.js +0 -152
- package/dist/workflows/target-assessment/lib/compute-derived.d.ts +0 -20
- package/dist/workflows/target-assessment/lib/compute-derived.js +0 -261
- package/dist/workflows/target-assessment/lib/compute-selectivity.d.ts +0 -15
- package/dist/workflows/target-assessment/lib/compute-selectivity.js +0 -18
- package/dist/workflows/target-assessment/lib/dedup-modulators.d.ts +0 -37
- package/dist/workflows/target-assessment/lib/dedup-modulators.js +0 -157
- package/dist/workflows/target-assessment/lib/evidence-conflict-detector.d.ts +0 -17
- package/dist/workflows/target-assessment/lib/evidence-conflict-detector.js +0 -100
- package/dist/workflows/target-assessment/lib/expression-constants.d.ts +0 -21
- package/dist/workflows/target-assessment/lib/expression-constants.js +0 -21
- package/dist/workflows/target-assessment/lib/family-complex-supplement.d.ts +0 -20
- package/dist/workflows/target-assessment/lib/family-complex-supplement.js +0 -36
- package/dist/workflows/target-assessment/lib/fda-label-safety.d.ts +0 -72
- package/dist/workflows/target-assessment/lib/fda-label-safety.js +0 -166
- package/dist/workflows/target-assessment/lib/heterodimer-filter.d.ts +0 -30
- package/dist/workflows/target-assessment/lib/heterodimer-filter.js +0 -44
- package/dist/workflows/target-assessment/lib/hpo-organ-map.d.ts +0 -34
- package/dist/workflows/target-assessment/lib/hpo-organ-map.js +0 -63
- package/dist/workflows/target-assessment/lib/impc-organ-map.d.ts +0 -19
- package/dist/workflows/target-assessment/lib/impc-organ-map.js +0 -39
- package/dist/workflows/target-assessment/lib/intended-polypharm-filter.d.ts +0 -4
- package/dist/workflows/target-assessment/lib/intended-polypharm-filter.js +0 -24
- package/dist/workflows/target-assessment/lib/llm-step.d.ts +0 -80
- package/dist/workflows/target-assessment/lib/llm-step.js +0 -101
- package/dist/workflows/target-assessment/lib/meddra-organ-map.d.ts +0 -40
- package/dist/workflows/target-assessment/lib/meddra-organ-map.js +0 -138
- package/dist/workflows/target-assessment/lib/recommendation-quality-gates.d.ts +0 -17
- package/dist/workflows/target-assessment/lib/recommendation-quality-gates.js +0 -99
- package/dist/workflows/target-assessment/lib/recommendation-sanitizer.d.ts +0 -2
- package/dist/workflows/target-assessment/lib/recommendation-sanitizer.js +0 -51
- package/dist/workflows/target-assessment/lib/regulatory-actions.d.ts +0 -25
- package/dist/workflows/target-assessment/lib/regulatory-actions.js +0 -176
- package/dist/workflows/target-assessment/lib/safety-corroboration.d.ts +0 -44
- package/dist/workflows/target-assessment/lib/safety-corroboration.js +0 -273
- package/dist/workflows/target-assessment/lib/structured-llm.d.ts +0 -61
- package/dist/workflows/target-assessment/lib/structured-llm.js +0 -102
- package/dist/workflows/target-assessment/lib/target-identity-filter.d.ts +0 -59
- package/dist/workflows/target-assessment/lib/target-identity-filter.js +0 -95
- package/dist/workflows/target-assessment/lib/therapeutic-programs.d.ts +0 -20
- package/dist/workflows/target-assessment/lib/therapeutic-programs.js +0 -68
- package/dist/workflows/target-assessment/metrics.d.ts +0 -16
- package/dist/workflows/target-assessment/metrics.js +0 -30
- package/dist/workflows/target-assessment/phase4-assemble.d.ts +0 -3182
- package/dist/workflows/target-assessment/phase4-assemble.js +0 -39
- package/dist/workflows/target-assessment/phase5-persist.d.ts +0 -59
- package/dist/workflows/target-assessment/phase5-persist.js +0 -349
- package/dist/workflows/target-assessment/progress-stream.d.ts +0 -75
- package/dist/workflows/target-assessment/progress-stream.js +0 -110
- package/dist/workflows/target-assessment/progress.d.ts +0 -39
- package/dist/workflows/target-assessment/progress.js +0 -77
- package/dist/workflows/target-assessment/schemas.d.ts +0 -970
- package/dist/workflows/target-assessment/schemas.js +0 -318
- package/dist/workflows/target-assessment/steps/collectors/pathways.d.ts +0 -15
- package/dist/workflows/target-assessment/steps/collectors/pathways.js +0 -58
- package/dist/workflows/target-assessment/steps/fanout/aes-for-one-class-drug-step.d.ts +0 -34
- package/dist/workflows/target-assessment/steps/fanout/aes-for-one-class-drug-step.js +0 -31
- package/dist/workflows/target-assessment/steps/fanout/aes-for-one-trial-step.d.ts +0 -57
- package/dist/workflows/target-assessment/steps/fanout/aes-for-one-trial-step.js +0 -54
- package/dist/workflows/target-assessment/steps/fanout/faers-for-one-modulator-step.d.ts +0 -35
- package/dist/workflows/target-assessment/steps/fanout/faers-for-one-modulator-step.js +0 -32
- package/dist/workflows/target-assessment/steps/fanout/index.d.ts +0 -14
- package/dist/workflows/target-assessment/steps/fanout/index.js +0 -10
- package/dist/workflows/target-assessment/steps/fanout/polypharm-for-one-modulator-step.d.ts +0 -29
- package/dist/workflows/target-assessment/steps/fanout/polypharm-for-one-modulator-step.js +0 -29
- package/dist/workflows/target-assessment/steps/phase2-aggregate.d.ts +0 -657
- package/dist/workflows/target-assessment/steps/phase2-aggregate.js +0 -34
- package/dist/workflows/target-assessment/steps/phase3-aggregate.d.ts +0 -806
- package/dist/workflows/target-assessment/steps/phase3-aggregate.js +0 -16
- package/dist/workflows/target-assessment/steps/synthesis/diagnostics.d.ts +0 -28
- package/dist/workflows/target-assessment/steps/synthesis/diagnostics.js +0 -27
- package/dist/workflows/target-assessment/sub-workflows/index.d.ts +0 -15
- package/dist/workflows/target-assessment/sub-workflows/index.js +0 -11
- package/dist/workflows/target-assessment/sub-workflows/per-class-drug-aes.d.ts +0 -41
- package/dist/workflows/target-assessment/sub-workflows/per-class-drug-aes.js +0 -12
- package/dist/workflows/target-assessment/sub-workflows/per-modulator-faers.d.ts +0 -41
- package/dist/workflows/target-assessment/sub-workflows/per-modulator-faers.js +0 -12
- package/dist/workflows/target-assessment/sub-workflows/per-modulator-polypharm.d.ts +0 -37
- package/dist/workflows/target-assessment/sub-workflows/per-modulator-polypharm.js +0 -12
- package/dist/workflows/target-assessment/sub-workflows/per-trial-aes.d.ts +0 -66
- package/dist/workflows/target-assessment/sub-workflows/per-trial-aes.js +0 -12
- package/dist/workflows/target-assessment/synthesis/index.d.ts +0 -607
- package/dist/workflows/target-assessment/synthesis/index.js +0 -354
- package/dist/workflows/target-assessment/synthesis-probes.d.ts +0 -56
- package/dist/workflows/target-assessment/synthesis-probes.js +0 -320
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/**
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* `executeTargetAssessment` — the parent DBOS workflow.
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*
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* Progress `emitProgress("assembling")`
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* Phase 4 `phase4Assemble` — aggregation + cached annotator
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* Phase 4a `ta-approval-precedents` — one openFDA lookup, two projections
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* - schema violation: markFailed → "schema-violation"
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* - other throw: markFailed → "unexpected-throw"
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* - 402 self-cancel: markAssessmentSuspended → "suspended_insufficient_funds"
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* - operator cancel: markFailed → "operator-cancelled"
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*
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* directly. No `:runId` suffix.
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import type { Pool } from "pg";
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import { z } from "zod";
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import type { RunSession } from "../auth/types.js";
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import type { RunAuthorizer } from "../execution/run-authorizer.js";
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import type { Logger } from "../lib/logger.js";
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import type { UsageRecorder } from "../billing/usage-recorder.js";
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import type { AgentChat } from "../providers/types.js";
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import { TargetAssessmentInputSchema } from "./target-assessment/schemas.js";
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import { type ClaimInvestigationConfig } from "./target-assessment/investigation/index.js";
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import { type ProgressPhase } from "./target-assessment/progress.js";
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export declare const ExecuteTargetAssessmentInputSchema: z.ZodObject<{
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assessmentId: z.ZodString;
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goal: z.ZodOptional<z.ZodNullable<z.ZodString>>;
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organizationId: z.ZodString;
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requestedBy: z.ZodString;
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type SerializedInput = z.infer<typeof ExecuteTargetAssessmentInputSchema>;
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};
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export interface ExecuteTargetAssessmentResult {
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}
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export interface ExecuteTargetAssessmentDeps {
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readonly pool: Pool;
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readonly runAuthorizer: RunAuthorizer;
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/** NCBI E-utilities key for the ClinVar / PubMed Phase-1 collectors. */
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readonly ncbiApiKey?: string;
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/**
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* Chat provider — billing resolution is closure-wrapped via the TA
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* resolver in `harness/billing/target-assessment-resolver.ts` (see §12
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readonly chatProvider: AgentChat;
|
|
92
|
-
/** Billing-gateway model for decision agents — typically `env.TARGET_ASSESSMENT_DECISION_MODEL`. */
|
|
93
|
-
readonly decisionModel: string;
|
|
94
|
-
/** Billing-gateway model for synthesis agents — typically `env.TARGET_ASSESSMENT_SYNTHESIS_MODEL`. */
|
|
95
|
-
readonly synthesisModel: string;
|
|
96
|
-
/** LLM usage-accounting seam for the assessment's agent loops; omitted falls back to the no-op recorder. */
|
|
97
|
-
readonly usageRecorder?: UsageRecorder;
|
|
98
|
-
/**
|
|
99
|
-
* Bounds the claim-investigation phase runs under. Omitted falls back to
|
|
100
|
-
* `DEFAULT_CLAIM_INVESTIGATION_CONFIG` — the values are cost and termination
|
|
101
|
-
* bounds, not domain constants, so an embedder wanting a deeper pass sets
|
|
102
|
-
* its own and the dossier reports what was in force.
|
|
103
|
-
*/
|
|
104
|
-
readonly claimInvestigation?: Partial<ClaimInvestigationConfig>;
|
|
105
|
-
}
|
|
106
|
-
/**
|
|
107
|
-
* Register the executeTargetAssessment workflow with DBOS. Caller is
|
|
108
|
-
* responsible for setting `workflowID = assessmentId` via
|
|
109
|
-
* `DBOS.startWorkflow(_, { workflowID })`.
|
|
110
|
-
*/
|
|
111
|
-
export declare function registerExecuteTargetAssessment(deps: ExecuteTargetAssessmentDeps): (input: ExecuteTargetAssessmentInput) => Promise<ExecuteTargetAssessmentResult>;
|
|
112
|
-
/**
|
|
113
|
-
* Body extracted so tests can drive it without registering a workflow
|
|
114
|
-
* (the DBOS calls inside still rely on a workflow context being present).
|
|
115
|
-
*/
|
|
116
|
-
export declare function runExecuteTargetAssessmentBody(input: ExecuteTargetAssessmentInput, deps: ExecuteTargetAssessmentDeps): Promise<ExecuteTargetAssessmentResult>;
|
|
117
|
-
export { TargetAssessmentInputSchema };
|
|
118
|
-
export type { ProgressPhase };
|