@inflexa-ai/harness 0.1.1
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/LICENSE +202 -0
- package/NOTICE +5 -0
- package/README.md +58 -0
- package/dist/agents/conversation-agent.d.ts +105 -0
- package/dist/agents/conversation-agent.js +140 -0
- package/dist/agents/report-builder.d.ts +32 -0
- package/dist/agents/report-builder.js +31 -0
- package/dist/agents/sandbox/__fixtures__/deps.d.ts +23 -0
- package/dist/agents/sandbox/__fixtures__/deps.js +96 -0
- package/dist/agents/sandbox/bulk-transcriptomics-agent.d.ts +8 -0
- package/dist/agents/sandbox/bulk-transcriptomics-agent.js +22 -0
- package/dist/agents/sandbox/cheminformatics-agent.d.ts +9 -0
- package/dist/agents/sandbox/cheminformatics-agent.js +62 -0
- package/dist/agents/sandbox/chromatin-agent.d.ts +8 -0
- package/dist/agents/sandbox/chromatin-agent.js +24 -0
- package/dist/agents/sandbox/data-profiler.d.ts +10 -0
- package/dist/agents/sandbox/data-profiler.js +24 -0
- package/dist/agents/sandbox/dna-methylation-agent.d.ts +8 -0
- package/dist/agents/sandbox/dna-methylation-agent.js +24 -0
- package/dist/agents/sandbox/drug-repurposing-agent.d.ts +8 -0
- package/dist/agents/sandbox/drug-repurposing-agent.js +54 -0
- package/dist/agents/sandbox/enrichment-agent.d.ts +8 -0
- package/dist/agents/sandbox/enrichment-agent.js +24 -0
- package/dist/agents/sandbox/ephemeral-executor.d.ts +9 -0
- package/dist/agents/sandbox/ephemeral-executor.js +29 -0
- package/dist/agents/sandbox/genomic-variant-agent.d.ts +8 -0
- package/dist/agents/sandbox/genomic-variant-agent.js +27 -0
- package/dist/agents/sandbox/immune-profiling-agent.d.ts +8 -0
- package/dist/agents/sandbox/immune-profiling-agent.js +43 -0
- package/dist/agents/sandbox/index.d.ts +31 -0
- package/dist/agents/sandbox/index.js +96 -0
- package/dist/agents/sandbox/metabolomics-agent.d.ts +8 -0
- package/dist/agents/sandbox/metabolomics-agent.js +15 -0
- package/dist/agents/sandbox/microbiome-agent.d.ts +8 -0
- package/dist/agents/sandbox/microbiome-agent.js +15 -0
- package/dist/agents/sandbox/multi-omics-integration-agent.d.ts +8 -0
- package/dist/agents/sandbox/multi-omics-integration-agent.js +33 -0
- package/dist/agents/sandbox/multimodal-sc-agent.d.ts +8 -0
- package/dist/agents/sandbox/multimodal-sc-agent.js +15 -0
- package/dist/agents/sandbox/network-agent.d.ts +8 -0
- package/dist/agents/sandbox/network-agent.js +25 -0
- package/dist/agents/sandbox/pkpd-clinical-response-agent.d.ts +8 -0
- package/dist/agents/sandbox/pkpd-clinical-response-agent.js +59 -0
- package/dist/agents/sandbox/proteomics-agent.d.ts +8 -0
- package/dist/agents/sandbox/proteomics-agent.js +15 -0
- package/dist/agents/sandbox/scientific-executor.d.ts +9 -0
- package/dist/agents/sandbox/scientific-executor.js +56 -0
- package/dist/agents/sandbox/shared.d.ts +100 -0
- package/dist/agents/sandbox/shared.js +195 -0
- package/dist/agents/sandbox/single-cell-agent.d.ts +8 -0
- package/dist/agents/sandbox/single-cell-agent.js +25 -0
- package/dist/agents/sandbox/spatial-omics-agent.d.ts +8 -0
- package/dist/agents/sandbox/spatial-omics-agent.js +15 -0
- package/dist/agents/sandbox/statistical-modeling-agent.d.ts +8 -0
- package/dist/agents/sandbox/statistical-modeling-agent.js +37 -0
- package/dist/agents/sandbox/translational-safety-agent.d.ts +8 -0
- package/dist/agents/sandbox/translational-safety-agent.js +59 -0
- package/dist/agents/sandbox/types.d.ts +34 -0
- package/dist/agents/sandbox/types.js +15 -0
- package/dist/agents/sandbox/validate-skills.d.ts +18 -0
- package/dist/agents/sandbox/validate-skills.js +40 -0
- package/dist/agents/sandbox-catalog.d.ts +33 -0
- package/dist/agents/sandbox-catalog.js +44 -0
- package/dist/agents/system-prompt.d.ts +25 -0
- package/dist/agents/system-prompt.js +23 -0
- package/dist/app/chat-turn.d.ts +35 -0
- package/dist/app/chat-turn.js +64 -0
- package/dist/app/data-profile-policy.d.ts +36 -0
- package/dist/app/data-profile-policy.js +37 -0
- package/dist/app/message-assembly.d.ts +65 -0
- package/dist/app/message-assembly.js +61 -0
- package/dist/app/synthesize-run.d.ts +57 -0
- package/dist/app/synthesize-run.js +103 -0
- package/dist/auth/local-auth-context.d.ts +19 -0
- package/dist/auth/local-auth-context.js +20 -0
- package/dist/auth/local-run-authorizer.d.ts +10 -0
- package/dist/auth/local-run-authorizer.js +23 -0
- package/dist/auth/types.d.ts +166 -0
- package/dist/auth/types.js +61 -0
- package/dist/billing/cached-resolver.d.ts +23 -0
- package/dist/billing/cached-resolver.js +61 -0
- package/dist/billing/noop-resolver.d.ts +6 -0
- package/dist/billing/noop-resolver.js +7 -0
- package/dist/billing/noop-run-charge.d.ts +6 -0
- package/dist/billing/noop-run-charge.js +10 -0
- package/dist/billing/resolver.d.ts +64 -0
- package/dist/billing/resolver.js +24 -0
- package/dist/billing/run-charge.d.ts +24 -0
- package/dist/billing/run-charge.js +9 -0
- package/dist/config/resource-limits.d.ts +76 -0
- package/dist/config/resource-limits.js +116 -0
- package/dist/contracts/analogy-report.d.ts +120 -0
- package/dist/contracts/analogy-report.js +50 -0
- package/dist/contracts/chat-events.d.ts +61 -0
- package/dist/contracts/chat-events.js +13 -0
- package/dist/contracts/chat-parts.d.ts +308 -0
- package/dist/contracts/chat-parts.js +13 -0
- package/dist/contracts/content-url.d.ts +49 -0
- package/dist/contracts/content-url.js +56 -0
- package/dist/contracts/index.d.ts +12 -0
- package/dist/contracts/index.js +5 -0
- package/dist/contracts/message.d.ts +36 -0
- package/dist/contracts/message.js +9 -0
- package/dist/contracts/part-registry.d.ts +18 -0
- package/dist/contracts/part-registry.js +28 -0
- package/dist/contracts/schemas/chat-events.d.ts +90 -0
- package/dist/contracts/schemas/chat-events.js +43 -0
- package/dist/contracts/schemas/chat-parts.d.ts +683 -0
- package/dist/contracts/schemas/chat-parts.js +295 -0
- package/dist/contracts/schemas/index.d.ts +2 -0
- package/dist/contracts/schemas/index.js +2 -0
- package/dist/contracts/target-assessment-row.d.ts +85 -0
- package/dist/contracts/target-assessment-row.js +37 -0
- package/dist/contracts/target-dossier.d.ts +16720 -0
- package/dist/contracts/target-dossier.js +1339 -0
- package/dist/data/clinical-benchmarks.json +108 -0
- package/dist/data/protein-family-modality.json +101 -0
- package/dist/data/safety-panel-schema.d.ts +64 -0
- package/dist/data/safety-panel-schema.js +34 -0
- package/dist/data/safety-panel.json +436 -0
- package/dist/execution/artifact-metadata.d.ts +74 -0
- package/dist/execution/artifact-metadata.js +203 -0
- package/dist/execution/artifact-record.d.ts +19 -0
- package/dist/execution/artifact-record.js +7 -0
- package/dist/execution/artifact-registration.d.ts +36 -0
- package/dist/execution/artifact-registration.js +61 -0
- package/dist/execution/artifact-registry.d.ts +82 -0
- package/dist/execution/artifact-registry.js +17 -0
- package/dist/execution/dbos-run-launcher.d.ts +7 -0
- package/dist/execution/dbos-run-launcher.js +38 -0
- package/dist/execution/ephemeral-runner.d.ts +81 -0
- package/dist/execution/ephemeral-runner.js +161 -0
- package/dist/execution/filesystem-artifact-registry.d.ts +57 -0
- package/dist/execution/filesystem-artifact-registry.js +92 -0
- package/dist/execution/noop-artifact-registry.d.ts +11 -0
- package/dist/execution/noop-artifact-registry.js +17 -0
- package/dist/execution/post-step-pipeline.d.ts +70 -0
- package/dist/execution/post-step-pipeline.js +207 -0
- package/dist/execution/post-step.d.ts +20 -0
- package/dist/execution/post-step.js +65 -0
- package/dist/execution/reconcile-manifest.d.ts +25 -0
- package/dist/execution/reconcile-manifest.js +132 -0
- package/dist/execution/report-render.d.ts +39 -0
- package/dist/execution/report-render.js +98 -0
- package/dist/execution/report-runner.d.ts +87 -0
- package/dist/execution/report-runner.js +227 -0
- package/dist/execution/run-authorizer.d.ts +43 -0
- package/dist/execution/run-authorizer.js +17 -0
- package/dist/execution/run-launcher.d.ts +36 -0
- package/dist/execution/run-launcher.js +15 -0
- package/dist/execution/run-synthesis.d.ts +107 -0
- package/dist/execution/run-synthesis.js +329 -0
- package/dist/execution/staged-input.d.ts +41 -0
- package/dist/execution/staged-input.js +15 -0
- package/dist/execution/step-summary-metrics.d.ts +10 -0
- package/dist/execution/step-summary-metrics.js +22 -0
- package/dist/execution/step-summary.d.ts +55 -0
- package/dist/execution/step-summary.js +106 -0
- package/dist/execution/topo-sort.d.ts +33 -0
- package/dist/execution/topo-sort.js +99 -0
- package/dist/index.d.ts +112 -0
- package/dist/index.js +157 -0
- package/dist/input-sanitization.d.ts +22 -0
- package/dist/input-sanitization.js +64 -0
- package/dist/lib/async-utils.d.ts +10 -0
- package/dist/lib/async-utils.js +24 -0
- package/dist/lib/chrome.d.ts +15 -0
- package/dist/lib/chrome.js +95 -0
- package/dist/lib/db-result.d.ts +93 -0
- package/dist/lib/db-result.js +197 -0
- package/dist/lib/fs-helpers.d.ts +74 -0
- package/dist/lib/fs-helpers.js +119 -0
- package/dist/lib/fs-result.d.ts +98 -0
- package/dist/lib/fs-result.js +137 -0
- package/dist/lib/host-concurrency.d.ts +16 -0
- package/dist/lib/host-concurrency.js +60 -0
- package/dist/lib/identifiers.d.ts +8 -0
- package/dist/lib/identifiers.js +10 -0
- package/dist/lib/metrics.d.ts +7 -0
- package/dist/lib/metrics.js +12 -0
- package/dist/lib/mime-detect.d.ts +17 -0
- package/dist/lib/mime-detect.js +29 -0
- package/dist/lib/otel.d.ts +30 -0
- package/dist/lib/otel.js +102 -0
- package/dist/lib/regulatory-corpus/fetch-fda-guidance.d.ts +35 -0
- package/dist/lib/regulatory-corpus/fetch-fda-guidance.js +107 -0
- package/dist/lib/regulatory-corpus/fetch-ich.d.ts +46 -0
- package/dist/lib/regulatory-corpus/fetch-ich.js +173 -0
- package/dist/lib/regulatory-corpus.d.ts +88 -0
- package/dist/lib/regulatory-corpus.js +141 -0
- package/dist/lib/result.d.ts +87 -0
- package/dist/lib/result.js +103 -0
- package/dist/lib/storage.d.ts +29 -0
- package/dist/lib/storage.js +37 -0
- package/dist/lib/streamed-download.d.ts +28 -0
- package/dist/lib/streamed-download.js +111 -0
- package/dist/lib/trace-context.d.ts +11 -0
- package/dist/lib/trace-context.js +49 -0
- package/dist/loop/__fixtures__/scripted-provider.d.ts +31 -0
- package/dist/loop/__fixtures__/scripted-provider.js +57 -0
- package/dist/loop/budget-exceeded.d.ts +22 -0
- package/dist/loop/budget-exceeded.js +41 -0
- package/dist/loop/metrics.d.ts +25 -0
- package/dist/loop/metrics.js +46 -0
- package/dist/loop/run-agent.d.ts +28 -0
- package/dist/loop/run-agent.js +204 -0
- package/dist/loop/run-step.d.ts +29 -0
- package/dist/loop/run-step.js +34 -0
- package/dist/loop/run-to-terminal.d.ts +46 -0
- package/dist/loop/run-to-terminal.js +51 -0
- package/dist/loop/types.d.ts +95 -0
- package/dist/loop/types.js +10 -0
- package/dist/memory/ai-sdk-message-storage.d.ts +20 -0
- package/dist/memory/ai-sdk-message-storage.js +114 -0
- package/dist/memory/card-builders.d.ts +114 -0
- package/dist/memory/card-builders.js +231 -0
- package/dist/memory/content-to-cortex.d.ts +42 -0
- package/dist/memory/content-to-cortex.js +85 -0
- package/dist/memory/count-tokens.d.ts +18 -0
- package/dist/memory/count-tokens.js +64 -0
- package/dist/memory/derive-thread-title.d.ts +14 -0
- package/dist/memory/derive-thread-title.js +26 -0
- package/dist/memory/message-backfill.d.ts +2 -0
- package/dist/memory/message-backfill.js +38 -0
- package/dist/memory/reconstruct-cards.d.ts +23 -0
- package/dist/memory/reconstruct-cards.js +64 -0
- package/dist/memory/thread-history.d.ts +80 -0
- package/dist/memory/thread-history.js +187 -0
- package/dist/memory/thread-store.d.ts +66 -0
- package/dist/memory/thread-store.js +88 -0
- package/dist/memory/working-memory.d.ts +135 -0
- package/dist/memory/working-memory.js +185 -0
- package/dist/prompts/SOUL.d.ts +17 -0
- package/dist/prompts/SOUL.js +173 -0
- package/dist/prompts/analogical-reasoner.d.ts +1 -0
- package/dist/prompts/analogical-reasoner.js +170 -0
- package/dist/prompts/conversation.d.ts +1 -0
- package/dist/prompts/conversation.js +697 -0
- package/dist/prompts/execute-analysis/step-summary.d.ts +1 -0
- package/dist/prompts/execute-analysis/step-summary.js +38 -0
- package/dist/prompts/literature-reviewer.d.ts +1 -0
- package/dist/prompts/literature-reviewer.js +107 -0
- package/dist/prompts/planner.d.ts +2 -0
- package/dist/prompts/planner.js +259 -0
- package/dist/prompts/report-builder.d.ts +1 -0
- package/dist/prompts/report-builder.js +127 -0
- package/dist/prompts/sandbox/bulk-transcriptomics-agent.d.ts +1 -0
- package/dist/prompts/sandbox/bulk-transcriptomics-agent.js +78 -0
- package/dist/prompts/sandbox/cheminformatics-agent.d.ts +1 -0
- package/dist/prompts/sandbox/cheminformatics-agent.js +224 -0
- package/dist/prompts/sandbox/chromatin-agent.d.ts +1 -0
- package/dist/prompts/sandbox/chromatin-agent.js +100 -0
- package/dist/prompts/sandbox/data-profiler.d.ts +1 -0
- package/dist/prompts/sandbox/data-profiler.js +291 -0
- package/dist/prompts/sandbox/dna-methylation-agent.d.ts +1 -0
- package/dist/prompts/sandbox/dna-methylation-agent.js +96 -0
- package/dist/prompts/sandbox/drug-repurposing-agent.d.ts +1 -0
- package/dist/prompts/sandbox/drug-repurposing-agent.js +144 -0
- package/dist/prompts/sandbox/enrichment-agent.d.ts +1 -0
- package/dist/prompts/sandbox/enrichment-agent.js +89 -0
- package/dist/prompts/sandbox/ephemeral-executor.d.ts +1 -0
- package/dist/prompts/sandbox/ephemeral-executor.js +66 -0
- package/dist/prompts/sandbox/genomic-variant-agent.d.ts +1 -0
- package/dist/prompts/sandbox/genomic-variant-agent.js +83 -0
- package/dist/prompts/sandbox/immune-profiling-agent.d.ts +1 -0
- package/dist/prompts/sandbox/immune-profiling-agent.js +101 -0
- package/dist/prompts/sandbox/metabolomics-agent.d.ts +1 -0
- package/dist/prompts/sandbox/metabolomics-agent.js +89 -0
- package/dist/prompts/sandbox/microbiome-agent.d.ts +1 -0
- package/dist/prompts/sandbox/microbiome-agent.js +109 -0
- package/dist/prompts/sandbox/multi-omics-integration-agent.d.ts +1 -0
- package/dist/prompts/sandbox/multi-omics-integration-agent.js +122 -0
- package/dist/prompts/sandbox/multimodal-sc-agent.d.ts +1 -0
- package/dist/prompts/sandbox/multimodal-sc-agent.js +90 -0
- package/dist/prompts/sandbox/network-agent.d.ts +1 -0
- package/dist/prompts/sandbox/network-agent.js +95 -0
- package/dist/prompts/sandbox/pkpd-clinical-response-agent.d.ts +1 -0
- package/dist/prompts/sandbox/pkpd-clinical-response-agent.js +71 -0
- package/dist/prompts/sandbox/proteomics-agent.d.ts +1 -0
- package/dist/prompts/sandbox/proteomics-agent.js +93 -0
- package/dist/prompts/sandbox/scientific-executor.d.ts +1 -0
- package/dist/prompts/sandbox/scientific-executor.js +68 -0
- package/dist/prompts/sandbox/single-cell-agent.d.ts +1 -0
- package/dist/prompts/sandbox/single-cell-agent.js +129 -0
- package/dist/prompts/sandbox/spatial-omics-agent.d.ts +1 -0
- package/dist/prompts/sandbox/spatial-omics-agent.js +94 -0
- package/dist/prompts/sandbox/statistical-modeling-agent.d.ts +1 -0
- package/dist/prompts/sandbox/statistical-modeling-agent.js +112 -0
- package/dist/prompts/sandbox/translational-safety-agent.d.ts +1 -0
- package/dist/prompts/sandbox/translational-safety-agent.js +105 -0
- package/dist/prompts/sandbox-standards.d.ts +18 -0
- package/dist/prompts/sandbox-standards.js +358 -0
- package/dist/prompts/synthesis-agent.d.ts +1 -0
- package/dist/prompts/synthesis-agent.js +289 -0
- package/dist/prompts/target-assessment/briefs/executive-recommendation.d.ts +1 -0
- package/dist/prompts/target-assessment/briefs/executive-recommendation.js +85 -0
- package/dist/prompts/target-assessment/briefs/index.d.ts +4 -0
- package/dist/prompts/target-assessment/briefs/index.js +4 -0
- package/dist/prompts/target-assessment/briefs/liability-bullets.d.ts +1 -0
- package/dist/prompts/target-assessment/briefs/liability-bullets.js +114 -0
- package/dist/prompts/target-assessment/briefs/target-organ-liabilities.d.ts +1 -0
- package/dist/prompts/target-assessment/briefs/target-organ-liabilities.js +29 -0
- package/dist/prompts/target-assessment/briefs/translational-commentary.d.ts +1 -0
- package/dist/prompts/target-assessment/briefs/translational-commentary.js +23 -0
- package/dist/prompts/target-assessment/drugs-in-class.d.ts +1 -0
- package/dist/prompts/target-assessment/drugs-in-class.js +29 -0
- package/dist/prompts/target-assessment/modulator-triage.d.ts +1 -0
- package/dist/prompts/target-assessment/modulator-triage.js +31 -0
- package/dist/prompts/target-assessment/off-target-annotator.d.ts +1 -0
- package/dist/prompts/target-assessment/off-target-annotator.js +28 -0
- package/dist/prompts/target-assessment/tox-voice/core.d.ts +1 -0
- package/dist/prompts/target-assessment/tox-voice/core.js +74 -0
- package/dist/prompts/target-assessment/tox-voice/critique.d.ts +7 -0
- package/dist/prompts/target-assessment/tox-voice/critique.js +109 -0
- package/dist/prompts/target-assessment/tox-voice/exemplars.d.ts +8 -0
- package/dist/prompts/target-assessment/tox-voice/exemplars.js +24 -0
- package/dist/prompts/target-assessment/tox-voice/index.d.ts +4 -0
- package/dist/prompts/target-assessment/tox-voice/index.js +4 -0
- package/dist/prompts/target-assessment/tox-voice/vocabulary.d.ts +15 -0
- package/dist/prompts/target-assessment/tox-voice/vocabulary.js +72 -0
- package/dist/provenance/collector.d.ts +148 -0
- package/dist/provenance/collector.js +296 -0
- package/dist/provenance/exec-frame.d.ts +36 -0
- package/dist/provenance/exec-frame.js +49 -0
- package/dist/provenance/types.d.ts +95 -0
- package/dist/provenance/types.js +64 -0
- package/dist/providers/__fixtures__/session.d.ts +16 -0
- package/dist/providers/__fixtures__/session.js +20 -0
- package/dist/providers/ai-sdk.d.ts +47 -0
- package/dist/providers/ai-sdk.js +142 -0
- package/dist/providers/anthropic.d.ts +22 -0
- package/dist/providers/anthropic.js +26 -0
- package/dist/providers/embedding.d.ts +32 -0
- package/dist/providers/embedding.js +42 -0
- package/dist/providers/errors.d.ts +80 -0
- package/dist/providers/errors.js +137 -0
- package/dist/providers/llm-capabilities.d.ts +33 -0
- package/dist/providers/llm-capabilities.js +58 -0
- package/dist/providers/streaming-chat.d.ts +23 -0
- package/dist/providers/streaming-chat.js +61 -0
- package/dist/providers/types.d.ts +59 -0
- package/dist/providers/types.js +8 -0
- package/dist/runtime/assemble.d.ts +68 -0
- package/dist/runtime/assemble.js +46 -0
- package/dist/runtime/boot.d.ts +73 -0
- package/dist/runtime/boot.js +65 -0
- package/dist/runtime/connection-budget.d.ts +48 -0
- package/dist/runtime/connection-budget.js +57 -0
- package/dist/runtime/dbos.d.ts +94 -0
- package/dist/runtime/dbos.js +160 -0
- package/dist/runtime/lifecycle.d.ts +12 -0
- package/dist/runtime/lifecycle.js +19 -0
- package/dist/runtime/pools.d.ts +25 -0
- package/dist/runtime/pools.js +30 -0
- package/dist/runtime/shutdown.d.ts +33 -0
- package/dist/runtime/shutdown.js +39 -0
- package/dist/sandbox/await-exec.d.ts +143 -0
- package/dist/sandbox/await-exec.js +406 -0
- package/dist/sandbox/client.d.ts +82 -0
- package/dist/sandbox/client.js +23 -0
- package/dist/sandbox/create-sandbox.d.ts +105 -0
- package/dist/sandbox/create-sandbox.js +132 -0
- package/dist/sandbox/deliver-exec-event.d.ts +25 -0
- package/dist/sandbox/deliver-exec-event.js +29 -0
- package/dist/sandbox/docker-client.d.ts +75 -0
- package/dist/sandbox/docker-client.js +315 -0
- package/dist/sandbox/estimate-data-profile-resources.d.ts +5 -0
- package/dist/sandbox/estimate-data-profile-resources.js +73 -0
- package/dist/sandbox/exec-id.d.ts +12 -0
- package/dist/sandbox/exec-id.js +20 -0
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- package/dist/workflows/target-assessment/lib/dedup-modulators.js +157 -0
- package/dist/workflows/target-assessment/lib/evidence-conflict-detector.d.ts +17 -0
- package/dist/workflows/target-assessment/lib/evidence-conflict-detector.js +100 -0
- package/dist/workflows/target-assessment/lib/expression-constants.d.ts +21 -0
- package/dist/workflows/target-assessment/lib/expression-constants.js +21 -0
- package/dist/workflows/target-assessment/lib/family-complex-supplement.d.ts +21 -0
- package/dist/workflows/target-assessment/lib/family-complex-supplement.js +37 -0
- package/dist/workflows/target-assessment/lib/heterodimer-filter.d.ts +39 -0
- package/dist/workflows/target-assessment/lib/heterodimer-filter.js +54 -0
- package/dist/workflows/target-assessment/lib/intended-polypharm-filter.d.ts +4 -0
- package/dist/workflows/target-assessment/lib/intended-polypharm-filter.js +24 -0
- package/dist/workflows/target-assessment/lib/llm-step.d.ts +77 -0
- package/dist/workflows/target-assessment/lib/llm-step.js +99 -0
- package/dist/workflows/target-assessment/lib/meddra-organ-map.d.ts +30 -0
- package/dist/workflows/target-assessment/lib/meddra-organ-map.js +126 -0
- package/dist/workflows/target-assessment/lib/recommendation-quality-gates.d.ts +17 -0
- package/dist/workflows/target-assessment/lib/recommendation-quality-gates.js +99 -0
- package/dist/workflows/target-assessment/lib/recommendation-sanitizer.d.ts +2 -0
- package/dist/workflows/target-assessment/lib/recommendation-sanitizer.js +51 -0
- package/dist/workflows/target-assessment/lib/regulatory-actions.d.ts +26 -0
- package/dist/workflows/target-assessment/lib/regulatory-actions.js +147 -0
- package/dist/workflows/target-assessment/lib/structured-llm.d.ts +58 -0
- package/dist/workflows/target-assessment/lib/structured-llm.js +101 -0
- package/dist/workflows/target-assessment/lib/target-identity-filter.d.ts +60 -0
- package/dist/workflows/target-assessment/lib/target-identity-filter.js +86 -0
- package/dist/workflows/target-assessment/lib/therapeutic-programs.d.ts +20 -0
- package/dist/workflows/target-assessment/lib/therapeutic-programs.js +68 -0
- package/dist/workflows/target-assessment/metrics.d.ts +21 -0
- package/dist/workflows/target-assessment/metrics.js +42 -0
- package/dist/workflows/target-assessment/phase4-assemble.d.ts +1841 -0
- package/dist/workflows/target-assessment/phase4-assemble.js +39 -0
- package/dist/workflows/target-assessment/phase5-persist.d.ts +57 -0
- package/dist/workflows/target-assessment/phase5-persist.js +461 -0
- package/dist/workflows/target-assessment/progress.d.ts +38 -0
- package/dist/workflows/target-assessment/progress.js +76 -0
- package/dist/workflows/target-assessment/schemas.d.ts +931 -0
- package/dist/workflows/target-assessment/schemas.js +293 -0
- package/dist/workflows/target-assessment/steps/collectors/pathways.d.ts +15 -0
- package/dist/workflows/target-assessment/steps/collectors/pathways.js +58 -0
- package/dist/workflows/target-assessment/steps/fanout/aes-for-one-class-drug-step.d.ts +34 -0
- package/dist/workflows/target-assessment/steps/fanout/aes-for-one-class-drug-step.js +31 -0
- package/dist/workflows/target-assessment/steps/fanout/aes-for-one-trial-step.d.ts +57 -0
- package/dist/workflows/target-assessment/steps/fanout/aes-for-one-trial-step.js +54 -0
- package/dist/workflows/target-assessment/steps/fanout/faers-for-one-modulator-step.d.ts +35 -0
- package/dist/workflows/target-assessment/steps/fanout/faers-for-one-modulator-step.js +32 -0
- package/dist/workflows/target-assessment/steps/fanout/index.d.ts +14 -0
- package/dist/workflows/target-assessment/steps/fanout/index.js +10 -0
- package/dist/workflows/target-assessment/steps/fanout/polypharm-for-one-modulator-step.d.ts +28 -0
- package/dist/workflows/target-assessment/steps/fanout/polypharm-for-one-modulator-step.js +27 -0
- package/dist/workflows/target-assessment/steps/phase0-resolve.d.ts +71 -0
- package/dist/workflows/target-assessment/steps/phase0-resolve.js +21 -0
- package/dist/workflows/target-assessment/steps/phase1-aggregate.d.ts +1018 -0
- package/dist/workflows/target-assessment/steps/phase1-aggregate.js +25 -0
- package/dist/workflows/target-assessment/steps/phase2-aggregate.d.ts +696 -0
- package/dist/workflows/target-assessment/steps/phase2-aggregate.js +38 -0
- package/dist/workflows/target-assessment/steps/phase3-aggregate.d.ts +936 -0
- package/dist/workflows/target-assessment/steps/phase3-aggregate.js +22 -0
- package/dist/workflows/target-assessment/steps/synthesis/diagnostics.d.ts +34 -0
- package/dist/workflows/target-assessment/steps/synthesis/diagnostics.js +45 -0
- package/dist/workflows/target-assessment/sub-workflows/index.d.ts +15 -0
- package/dist/workflows/target-assessment/sub-workflows/index.js +11 -0
- package/dist/workflows/target-assessment/sub-workflows/per-class-drug-aes.d.ts +41 -0
- package/dist/workflows/target-assessment/sub-workflows/per-class-drug-aes.js +12 -0
- package/dist/workflows/target-assessment/sub-workflows/per-modulator-faers.d.ts +41 -0
- package/dist/workflows/target-assessment/sub-workflows/per-modulator-faers.js +12 -0
- package/dist/workflows/target-assessment/sub-workflows/per-modulator-polypharm.d.ts +36 -0
- package/dist/workflows/target-assessment/sub-workflows/per-modulator-polypharm.js +12 -0
- package/dist/workflows/target-assessment/sub-workflows/per-trial-aes.d.ts +66 -0
- package/dist/workflows/target-assessment/sub-workflows/per-trial-aes.js +12 -0
- package/dist/workflows/target-assessment/synthesis/index.d.ts +560 -0
- package/dist/workflows/target-assessment/synthesis/index.js +351 -0
- package/dist/workflows/target-assessment/synthesis-probes.d.ts +56 -0
- package/dist/workflows/target-assessment/synthesis-probes.js +320 -0
- package/dist/workspace/filesystem.d.ts +117 -0
- package/dist/workspace/filesystem.js +304 -0
- package/dist/workspace/mount-strategy.d.ts +50 -0
- package/dist/workspace/mount-strategy.js +67 -0
- package/dist/workspace/paths.d.ts +185 -0
- package/dist/workspace/paths.js +219 -0
- package/dist/workspace/provenance-collector.d.ts +34 -0
- package/dist/workspace/provenance-collector.js +16 -0
- package/dist/workspace/search-config.d.ts +23 -0
- package/dist/workspace/search-config.js +43 -0
- package/dist/workspace/workspace-paths.d.ts +26 -0
- package/dist/workspace/workspace-paths.js +31 -0
- package/package.json +101 -0
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/**
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* Planning schemas — used by the generatePlan tool and executeAnalysis
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* workflow to produce and validate analysis plans.
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*/
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import { z } from "zod";
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import type { AnalysisPlan } from "./workflow-state.js";
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/** Step schema for planner output — omits fields populated at execution time
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* and the hardcoded sandbox turn budget. */
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export declare const PlanStepSchema: z.ZodObject<{
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name: z.ZodString;
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id: z.ZodString;
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context: z.ZodOptional<z.ZodString>;
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description: z.ZodOptional<z.ZodString>;
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resources: z.ZodNonOptional<z.ZodOptional<z.ZodObject<{
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cpu: z.ZodNumber;
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memoryGb: z.ZodNumber;
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gpu: z.ZodOptional<z.ZodObject<{
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count: z.ZodNumber;
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}, z.core.$strip>>;
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}, z.core.$strip>>>;
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constraints: z.ZodOptional<z.ZodArray<z.ZodString>>;
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track: z.ZodString;
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step_type: z.ZodString;
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question: z.ZodString;
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acceptance_criteria: z.ZodArray<z.ZodString>;
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caveats: z.ZodOptional<z.ZodArray<z.ZodString>>;
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depends_on: z.ZodArray<z.ZodString>;
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agent: z.ZodEnum<{
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[x: string]: string;
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}>;
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}, z.core.$strip>;
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export type PlanStep = z.infer<typeof PlanStepSchema>;
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/** Plan schema for planner output — uses PlanStepSchema for steps and requires
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* a concise title (optional on the persistence schema for historical plans). */
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export declare const PlannerPlanSchema: z.ZodObject<{
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analytical_narrative: z.ZodString;
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created_at: z.ZodString;
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omicsType: z.ZodOptional<z.ZodString>;
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omicsSubtype: z.ZodOptional<z.ZodString>;
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title: z.ZodString;
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steps: z.ZodArray<z.ZodObject<{
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name: z.ZodString;
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id: z.ZodString;
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context: z.ZodOptional<z.ZodString>;
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description: z.ZodOptional<z.ZodString>;
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resources: z.ZodNonOptional<z.ZodOptional<z.ZodObject<{
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cpu: z.ZodNumber;
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memoryGb: z.ZodNumber;
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gpu: z.ZodOptional<z.ZodObject<{
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count: z.ZodNumber;
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}, z.core.$strip>>;
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}, z.core.$strip>>>;
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constraints: z.ZodOptional<z.ZodArray<z.ZodString>>;
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track: z.ZodString;
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step_type: z.ZodString;
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question: z.ZodString;
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acceptance_criteria: z.ZodArray<z.ZodString>;
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caveats: z.ZodOptional<z.ZodArray<z.ZodString>>;
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depends_on: z.ZodArray<z.ZodString>;
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agent: z.ZodEnum<{
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[x: string]: string;
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}>;
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}, z.core.$strip>>;
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}, z.core.$strip>;
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export type PlannerPlan = z.infer<typeof PlannerPlanSchema>;
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/** Hydrate slim planner output into a full AnalysisPlan with execution-time defaults. */
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export declare function hydratePlanSteps(plannerPlan: PlannerPlan): AnalysisPlan;
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/** Schema for the planning agent's structured output. */
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export declare const PlanningAgentOutputSchema: z.ZodObject<{
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event: z.ZodEnum<{
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error: "error";
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plan_complete: "plan_complete";
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clarification_needed: "clarification_needed";
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}>;
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planId: z.ZodOptional<z.ZodString>;
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plan: z.ZodOptional<z.ZodObject<{
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analytical_narrative: z.ZodString;
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created_at: z.ZodString;
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omicsType: z.ZodOptional<z.ZodString>;
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omicsSubtype: z.ZodOptional<z.ZodString>;
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title: z.ZodString;
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steps: z.ZodArray<z.ZodObject<{
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name: z.ZodString;
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id: z.ZodString;
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context: z.ZodOptional<z.ZodString>;
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description: z.ZodOptional<z.ZodString>;
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resources: z.ZodNonOptional<z.ZodOptional<z.ZodObject<{
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cpu: z.ZodNumber;
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memoryGb: z.ZodNumber;
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gpu: z.ZodOptional<z.ZodObject<{
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count: z.ZodNumber;
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}, z.core.$strip>>;
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}, z.core.$strip>>>;
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constraints: z.ZodOptional<z.ZodArray<z.ZodString>>;
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track: z.ZodString;
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step_type: z.ZodString;
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question: z.ZodString;
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acceptance_criteria: z.ZodArray<z.ZodString>;
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caveats: z.ZodOptional<z.ZodArray<z.ZodString>>;
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depends_on: z.ZodArray<z.ZodString>;
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agent: z.ZodEnum<{
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[x: string]: string;
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}>;
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}, z.core.$strip>>;
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}, z.core.$strip>>;
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question: z.ZodOptional<z.ZodString>;
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questionContext: z.ZodOptional<z.ZodString>;
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error: z.ZodOptional<z.ZodString>;
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}, z.core.$strip>;
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export type PlanningAgentOutput = z.infer<typeof PlanningAgentOutputSchema>;
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/**
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* Planning schemas — used by the generatePlan tool and executeAnalysis
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* workflow to produce and validate analysis plans.
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*/
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import { z } from "zod";
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import { AnalysisStepSchema, AnalysisPlanSchema } from "./workflow-state.js";
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import { PLANNABLE_AGENT_IDS as plannableAgentIds } from "../agents/sandbox-catalog.js";
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import { DEFAULT_SANDBOX_MAX_STEPS } from "../config/resource-limits.js";
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// ── Slim planner schemas (no execution-time fields) ──────────────────
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/** Step schema for planner output — omits fields populated at execution time
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* and the hardcoded sandbox turn budget. */
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export const PlanStepSchema = AnalysisStepSchema.omit({
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status: true,
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timeout: true,
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summary: true,
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artifactIds: true,
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error: true,
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maxSteps: true,
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})
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.required({ agent: true, resources: true })
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.extend({
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agent: z.enum(plannableAgentIds).describe("Sandbox agent ID from the available agents list"),
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});
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/** Plan schema for planner output — uses PlanStepSchema for steps and requires
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* a concise title (optional on the persistence schema for historical plans). */
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export const PlannerPlanSchema = AnalysisPlanSchema.extend({
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title: z.string().min(1).max(80).describe("Concise human-readable plan name (3–8 words)"),
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steps: z.array(PlanStepSchema),
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});
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/** Hydrate slim planner output into a full AnalysisPlan with execution-time defaults. */
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export function hydratePlanSteps(plannerPlan) {
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return {
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...plannerPlan,
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steps: plannerPlan.steps.map((s) => ({
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...s,
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status: "pending",
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maxSteps: DEFAULT_SANDBOX_MAX_STEPS,
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})),
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};
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}
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// ── Planning agent structured output ─────────────────────────────────
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/** Schema for the planning agent's structured output. */
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export const PlanningAgentOutputSchema = z.object({
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event: z.enum(["plan_complete", "clarification_needed", "error"]),
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planId: z.string().optional(),
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plan: PlannerPlanSchema.optional(),
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question: z.string().optional(),
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questionContext: z.string().optional(),
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error: z.string().optional(),
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});
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/**
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* Render an AnalysisStep into the user-content prompt the sandbox agent
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* receives as its initial message.
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*
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* The planner writes the bulk of a step's instructions into structured
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* fields (`constraints`, `acceptance_criteria`, `context`, `caveats`,
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* `description`) alongside the one-line `question`. The execution path
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* forwards a single `prompt` string to the sandbox agent, so every
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* instruction-bearing field must be folded into that string here — otherwise
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* the agent runs against the bare question and improvises the rest.
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*
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* `STEP_PROMPT_INSTRUCTION_FIELDS` / `STEP_PROMPT_NON_INSTRUCTION_FIELDS`
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* partition every AnalysisStep field so the field-coverage guard test can
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* fail when a new field is added to the schema without a deliberate decision
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* about whether the agent needs to see it.
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*/
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import type { AnalysisStep } from "./workflow-state.js";
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/** Fields whose content is agent-facing and MUST appear in the rendered prompt. */
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export declare const STEP_PROMPT_INSTRUCTION_FIELDS: readonly ["name", "question", "description", "context", "constraints", "acceptance_criteria", "caveats"];
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/**
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* Fields deliberately excluded from the prompt: identity/DAG structure
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* threaded separately through the workflow input, execution knobs, and
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* result fields populated after the step runs.
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*/
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export declare const STEP_PROMPT_NON_INSTRUCTION_FIELDS: readonly ["id", "track", "step_type", "depends_on", "status", "resources", "agent", "timeout", "maxSteps", "summary", "artifactIds", "error"];
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/**
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* Compose the agent's initial prompt from a plan step. Only the `question`
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* is guaranteed present; the remaining instruction fields are appended as
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* dedicated sections when populated. Empty strings and empty arrays are
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* skipped so a sparse step renders cleanly.
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*/
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export declare function renderStepPrompt(step: AnalysisStep): string;
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/**
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* Render an AnalysisStep into the user-content prompt the sandbox agent
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* receives as its initial message.
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*
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* The planner writes the bulk of a step's instructions into structured
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* fields (`constraints`, `acceptance_criteria`, `context`, `caveats`,
|
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* `description`) alongside the one-line `question`. The execution path
|
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8
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* forwards a single `prompt` string to the sandbox agent, so every
|
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9
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+
* instruction-bearing field must be folded into that string here — otherwise
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* the agent runs against the bare question and improvises the rest.
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*
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* `STEP_PROMPT_INSTRUCTION_FIELDS` / `STEP_PROMPT_NON_INSTRUCTION_FIELDS`
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* partition every AnalysisStep field so the field-coverage guard test can
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14
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+
* fail when a new field is added to the schema without a deliberate decision
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* about whether the agent needs to see it.
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*/
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/** Fields whose content is agent-facing and MUST appear in the rendered prompt. */
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export const STEP_PROMPT_INSTRUCTION_FIELDS = [
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"name",
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"question",
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"description",
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"context",
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"constraints",
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"acceptance_criteria",
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"caveats",
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+
];
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/**
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* Fields deliberately excluded from the prompt: identity/DAG structure
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* threaded separately through the workflow input, execution knobs, and
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* result fields populated after the step runs.
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*/
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export const STEP_PROMPT_NON_INSTRUCTION_FIELDS = [
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"id",
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+
"track",
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"step_type",
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"depends_on",
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"status",
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+
"resources",
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+
"agent",
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"timeout",
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+
"maxSteps",
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"summary",
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"artifactIds",
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+
"error",
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+
];
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+
function section(heading, body) {
|
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|
+
return `## ${heading}\n${body}`;
|
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|
+
}
|
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|
+
function bullets(items) {
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+
return items.map((i) => `- ${i}`).join("\n");
|
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+
}
|
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|
+
/**
|
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+
* Compose the agent's initial prompt from a plan step. Only the `question`
|
|
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+
* is guaranteed present; the remaining instruction fields are appended as
|
|
55
|
+
* dedicated sections when populated. Empty strings and empty arrays are
|
|
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|
+
* skipped so a sparse step renders cleanly.
|
|
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|
+
*/
|
|
58
|
+
export function renderStepPrompt(step) {
|
|
59
|
+
const parts = [`# ${step.name}`, section("Task", step.question)];
|
|
60
|
+
if (step.description?.trim()) {
|
|
61
|
+
parts.push(section("What this step produces", step.description.trim()));
|
|
62
|
+
}
|
|
63
|
+
if (step.context?.trim()) {
|
|
64
|
+
parts.push(section("Context", step.context.trim()));
|
|
65
|
+
}
|
|
66
|
+
if (step.constraints && step.constraints.length > 0) {
|
|
67
|
+
parts.push(section("Constraints (these are requirements, not suggestions — follow them exactly)", bullets(step.constraints)));
|
|
68
|
+
}
|
|
69
|
+
if (step.acceptance_criteria && step.acceptance_criteria.length > 0) {
|
|
70
|
+
parts.push(section("Acceptance criteria (the result must satisfy all of these)", bullets(step.acceptance_criteria)));
|
|
71
|
+
}
|
|
72
|
+
if (step.caveats && step.caveats.length > 0) {
|
|
73
|
+
parts.push(section("Caveats", bullets(step.caveats)));
|
|
74
|
+
}
|
|
75
|
+
return parts.join("\n\n");
|
|
76
|
+
}
|
|
@@ -0,0 +1,148 @@
|
|
|
1
|
+
/**
|
|
2
|
+
* Run synthesis schema — cross-step findings grounded in literature.
|
|
3
|
+
*
|
|
4
|
+
* Produced by the synthesis step after all sandbox steps complete.
|
|
5
|
+
* Combines computational findings from step summaries with literature
|
|
6
|
+
* evidence from the literature-reviewer agent.
|
|
7
|
+
*/
|
|
8
|
+
import { z } from "zod";
|
|
9
|
+
export declare const LiteratureReferenceSchema: z.ZodObject<{
|
|
10
|
+
pmid: z.ZodString;
|
|
11
|
+
citation: z.ZodString;
|
|
12
|
+
relevance: z.ZodString;
|
|
13
|
+
concordance: z.ZodEnum<{
|
|
14
|
+
supports: "supports";
|
|
15
|
+
contradicts: "contradicts";
|
|
16
|
+
extends: "extends";
|
|
17
|
+
contextualizes: "contextualizes";
|
|
18
|
+
}>;
|
|
19
|
+
}, z.core.$strip>;
|
|
20
|
+
export declare const SynthesizedFindingSchema: z.ZodObject<{
|
|
21
|
+
stepId: z.ZodString;
|
|
22
|
+
title: z.ZodString;
|
|
23
|
+
description: z.ZodString;
|
|
24
|
+
confidence: z.ZodEnum<{
|
|
25
|
+
high: "high";
|
|
26
|
+
medium: "medium";
|
|
27
|
+
low: "low";
|
|
28
|
+
}>;
|
|
29
|
+
noveltyStatus: z.ZodEnum<{
|
|
30
|
+
expected: "expected";
|
|
31
|
+
novel: "novel";
|
|
32
|
+
confirmed: "confirmed";
|
|
33
|
+
partially_confirmed: "partially_confirmed";
|
|
34
|
+
contradicted: "contradicted";
|
|
35
|
+
}>;
|
|
36
|
+
literatureInterpretation: z.ZodString;
|
|
37
|
+
references: z.ZodArray<z.ZodObject<{
|
|
38
|
+
pmid: z.ZodString;
|
|
39
|
+
citation: z.ZodString;
|
|
40
|
+
relevance: z.ZodString;
|
|
41
|
+
concordance: z.ZodEnum<{
|
|
42
|
+
supports: "supports";
|
|
43
|
+
contradicts: "contradicts";
|
|
44
|
+
extends: "extends";
|
|
45
|
+
contextualizes: "contextualizes";
|
|
46
|
+
}>;
|
|
47
|
+
}, z.core.$strip>>;
|
|
48
|
+
translationalRelevance: z.ZodOptional<z.ZodObject<{
|
|
49
|
+
stage: z.ZodEnum<{
|
|
50
|
+
discovery: "discovery";
|
|
51
|
+
"preclinical-validation": "preclinical-validation";
|
|
52
|
+
"biomarker-candidate": "biomarker-candidate";
|
|
53
|
+
"clinical-evidence": "clinical-evidence";
|
|
54
|
+
}>;
|
|
55
|
+
actionType: z.ZodOptional<z.ZodEnum<{
|
|
56
|
+
none: "none";
|
|
57
|
+
"therapeutic-target": "therapeutic-target";
|
|
58
|
+
"predictive-biomarker": "predictive-biomarker";
|
|
59
|
+
"prognostic-biomarker": "prognostic-biomarker";
|
|
60
|
+
"pharmacodynamic-biomarker": "pharmacodynamic-biomarker";
|
|
61
|
+
"safety-signal": "safety-signal";
|
|
62
|
+
"resistance-mechanism": "resistance-mechanism";
|
|
63
|
+
"patient-stratification": "patient-stratification";
|
|
64
|
+
"mechanism-of-action": "mechanism-of-action";
|
|
65
|
+
}>>;
|
|
66
|
+
rationale: z.ZodString;
|
|
67
|
+
}, z.core.$strip>>;
|
|
68
|
+
}, z.core.$strip>;
|
|
69
|
+
export declare const BiologicalThemeSchema: z.ZodObject<{
|
|
70
|
+
name: z.ZodString;
|
|
71
|
+
findings: z.ZodArray<z.ZodObject<{
|
|
72
|
+
stepId: z.ZodString;
|
|
73
|
+
title: z.ZodString;
|
|
74
|
+
}, z.core.$strip>>;
|
|
75
|
+
narrative: z.ZodString;
|
|
76
|
+
}, z.core.$strip>;
|
|
77
|
+
export declare const RunSynthesisSchema: z.ZodObject<{
|
|
78
|
+
runId: z.ZodString;
|
|
79
|
+
overview: z.ZodString;
|
|
80
|
+
conclusions: z.ZodString;
|
|
81
|
+
findings: z.ZodArray<z.ZodObject<{
|
|
82
|
+
stepId: z.ZodString;
|
|
83
|
+
title: z.ZodString;
|
|
84
|
+
description: z.ZodString;
|
|
85
|
+
confidence: z.ZodEnum<{
|
|
86
|
+
high: "high";
|
|
87
|
+
medium: "medium";
|
|
88
|
+
low: "low";
|
|
89
|
+
}>;
|
|
90
|
+
noveltyStatus: z.ZodEnum<{
|
|
91
|
+
expected: "expected";
|
|
92
|
+
novel: "novel";
|
|
93
|
+
confirmed: "confirmed";
|
|
94
|
+
partially_confirmed: "partially_confirmed";
|
|
95
|
+
contradicted: "contradicted";
|
|
96
|
+
}>;
|
|
97
|
+
literatureInterpretation: z.ZodString;
|
|
98
|
+
references: z.ZodArray<z.ZodObject<{
|
|
99
|
+
pmid: z.ZodString;
|
|
100
|
+
citation: z.ZodString;
|
|
101
|
+
relevance: z.ZodString;
|
|
102
|
+
concordance: z.ZodEnum<{
|
|
103
|
+
supports: "supports";
|
|
104
|
+
contradicts: "contradicts";
|
|
105
|
+
extends: "extends";
|
|
106
|
+
contextualizes: "contextualizes";
|
|
107
|
+
}>;
|
|
108
|
+
}, z.core.$strip>>;
|
|
109
|
+
translationalRelevance: z.ZodOptional<z.ZodObject<{
|
|
110
|
+
stage: z.ZodEnum<{
|
|
111
|
+
discovery: "discovery";
|
|
112
|
+
"preclinical-validation": "preclinical-validation";
|
|
113
|
+
"biomarker-candidate": "biomarker-candidate";
|
|
114
|
+
"clinical-evidence": "clinical-evidence";
|
|
115
|
+
}>;
|
|
116
|
+
actionType: z.ZodOptional<z.ZodEnum<{
|
|
117
|
+
none: "none";
|
|
118
|
+
"therapeutic-target": "therapeutic-target";
|
|
119
|
+
"predictive-biomarker": "predictive-biomarker";
|
|
120
|
+
"prognostic-biomarker": "prognostic-biomarker";
|
|
121
|
+
"pharmacodynamic-biomarker": "pharmacodynamic-biomarker";
|
|
122
|
+
"safety-signal": "safety-signal";
|
|
123
|
+
"resistance-mechanism": "resistance-mechanism";
|
|
124
|
+
"patient-stratification": "patient-stratification";
|
|
125
|
+
"mechanism-of-action": "mechanism-of-action";
|
|
126
|
+
}>>;
|
|
127
|
+
rationale: z.ZodString;
|
|
128
|
+
}, z.core.$strip>>;
|
|
129
|
+
}, z.core.$strip>>;
|
|
130
|
+
themes: z.ZodArray<z.ZodObject<{
|
|
131
|
+
name: z.ZodString;
|
|
132
|
+
findings: z.ZodArray<z.ZodObject<{
|
|
133
|
+
stepId: z.ZodString;
|
|
134
|
+
title: z.ZodString;
|
|
135
|
+
}, z.core.$strip>>;
|
|
136
|
+
narrative: z.ZodString;
|
|
137
|
+
}, z.core.$strip>>;
|
|
138
|
+
limitations: z.ZodArray<z.ZodString>;
|
|
139
|
+
keyReferences: z.ZodArray<z.ZodObject<{
|
|
140
|
+
pmid: z.ZodString;
|
|
141
|
+
citation: z.ZodString;
|
|
142
|
+
description: z.ZodString;
|
|
143
|
+
}, z.core.$strip>>;
|
|
144
|
+
}, z.core.$strip>;
|
|
145
|
+
export type RunSynthesis = z.infer<typeof RunSynthesisSchema>;
|
|
146
|
+
export type SynthesizedFinding = z.infer<typeof SynthesizedFindingSchema>;
|
|
147
|
+
export type BiologicalTheme = z.infer<typeof BiologicalThemeSchema>;
|
|
148
|
+
export type LiteratureReference = z.infer<typeof LiteratureReferenceSchema>;
|
|
@@ -0,0 +1,87 @@
|
|
|
1
|
+
/**
|
|
2
|
+
* Run synthesis schema — cross-step findings grounded in literature.
|
|
3
|
+
*
|
|
4
|
+
* Produced by the synthesis step after all sandbox steps complete.
|
|
5
|
+
* Combines computational findings from step summaries with literature
|
|
6
|
+
* evidence from the literature-reviewer agent.
|
|
7
|
+
*/
|
|
8
|
+
import { z } from "zod";
|
|
9
|
+
export const LiteratureReferenceSchema = z.object({
|
|
10
|
+
pmid: z.string(),
|
|
11
|
+
citation: z.string(),
|
|
12
|
+
relevance: z.string(),
|
|
13
|
+
concordance: z.enum(["supports", "contradicts", "extends", "contextualizes"]),
|
|
14
|
+
});
|
|
15
|
+
export const SynthesizedFindingSchema = z.object({
|
|
16
|
+
/** Which step produced this finding. */
|
|
17
|
+
stepId: z.string(),
|
|
18
|
+
/** Finding title from the step summary. */
|
|
19
|
+
title: z.string(),
|
|
20
|
+
/** Finding description from the step summary. */
|
|
21
|
+
description: z.string(),
|
|
22
|
+
/** Confidence from the step summary. */
|
|
23
|
+
confidence: z.enum(["high", "medium", "low"]),
|
|
24
|
+
/** Novelty assessment based on literature review. */
|
|
25
|
+
noveltyStatus: z.enum(["novel", "confirmed", "partially_confirmed", "contradicted", "expected"]),
|
|
26
|
+
/** How this finding relates to existing literature. */
|
|
27
|
+
literatureInterpretation: z.string(),
|
|
28
|
+
/** Supporting or contradicting references. */
|
|
29
|
+
references: z.array(LiteratureReferenceSchema),
|
|
30
|
+
/** Translational proximity and actionability assessment. */
|
|
31
|
+
translationalRelevance: z
|
|
32
|
+
.object({
|
|
33
|
+
/** How close this finding is to clinical application. */
|
|
34
|
+
stage: z.enum(["discovery", "preclinical-validation", "biomarker-candidate", "clinical-evidence"]),
|
|
35
|
+
/** What type of translational action this finding supports. */
|
|
36
|
+
actionType: z
|
|
37
|
+
.enum([
|
|
38
|
+
"therapeutic-target",
|
|
39
|
+
"predictive-biomarker",
|
|
40
|
+
"prognostic-biomarker",
|
|
41
|
+
"pharmacodynamic-biomarker",
|
|
42
|
+
"safety-signal",
|
|
43
|
+
"resistance-mechanism",
|
|
44
|
+
"patient-stratification",
|
|
45
|
+
"mechanism-of-action",
|
|
46
|
+
"none",
|
|
47
|
+
])
|
|
48
|
+
.optional(),
|
|
49
|
+
/** Brief rationale for the stage and action type. */
|
|
50
|
+
rationale: z.string(),
|
|
51
|
+
})
|
|
52
|
+
.optional(),
|
|
53
|
+
});
|
|
54
|
+
export const BiologicalThemeSchema = z.object({
|
|
55
|
+
/** Theme name, e.g. "Immune dysregulation", "Metabolic reprogramming". */
|
|
56
|
+
name: z.string(),
|
|
57
|
+
/** Findings that contribute to this theme (by stepId + title). */
|
|
58
|
+
findings: z.array(z.object({ stepId: z.string(), title: z.string() })),
|
|
59
|
+
/** How these findings connect into a coherent biological story. */
|
|
60
|
+
narrative: z.string(),
|
|
61
|
+
});
|
|
62
|
+
export const RunSynthesisSchema = z.object({
|
|
63
|
+
runId: z.string(),
|
|
64
|
+
/** Brief (2-4 sentence) summary of the run's scope and top-line result. */
|
|
65
|
+
overview: z.string(),
|
|
66
|
+
/**
|
|
67
|
+
* Integrated interpretation: what the run establishes, what is novel,
|
|
68
|
+
* what is actionable from a translational perspective. This is the
|
|
69
|
+
* primary interpretive section — the "so what" of the analysis.
|
|
70
|
+
*/
|
|
71
|
+
conclusions: z.string(),
|
|
72
|
+
/**
|
|
73
|
+
* Selective findings — only novel, contradicted, or high-impact results
|
|
74
|
+
* that warrant individual attention. NOT a per-step catalog.
|
|
75
|
+
*/
|
|
76
|
+
findings: z.array(SynthesizedFindingSchema),
|
|
77
|
+
/** Cross-step biological themes. */
|
|
78
|
+
themes: z.array(BiologicalThemeSchema),
|
|
79
|
+
/** Methodological and translational caveats. */
|
|
80
|
+
limitations: z.array(z.string()),
|
|
81
|
+
/** Key references across all findings. */
|
|
82
|
+
keyReferences: z.array(z.object({
|
|
83
|
+
pmid: z.string(),
|
|
84
|
+
citation: z.string(),
|
|
85
|
+
description: z.string(),
|
|
86
|
+
})),
|
|
87
|
+
});
|
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/**
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* Step summary schema — plain markdown.
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*
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* Each sandbox step produces a free-form markdown summary at the end of its
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* execution. The schema intentionally carries no structured fields — the
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* markdown body is the single source of truth, rendered verbatim by the UI
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* and embedded verbatim into the vector search index with `type: "summary"`.
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*
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* Literature grounding is handled separately by the run synthesis step
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* (see run-synthesis.ts).
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*/
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import { z } from "zod";
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export declare const StepSummarySchema: z.ZodObject<{
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stepId: z.ZodString;
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agentId: z.ZodString;
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markdown: z.ZodString;
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}, z.core.$strip>;
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export type StepSummary = z.infer<typeof StepSummarySchema>;
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/**
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* Step summary schema — plain markdown.
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3
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*
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4
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* Each sandbox step produces a free-form markdown summary at the end of its
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* execution. The schema intentionally carries no structured fields — the
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* markdown body is the single source of truth, rendered verbatim by the UI
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* and embedded verbatim into the vector search index with `type: "summary"`.
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*
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* Literature grounding is handled separately by the run synthesis step
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* (see run-synthesis.ts).
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*/
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import { z } from "zod";
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export const StepSummarySchema = z.object({
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/** Step ID this summary belongs to. */
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stepId: z.string(),
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/** Agent that produced this summary. */
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agentId: z.string(),
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/** Free-form markdown body. Rendered directly by the UI. */
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markdown: z.string(),
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});
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/**
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* Plan validation — pure structural checks on an AnalysisPlan.
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*
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* Depends only on the plan schema types, the topological sorter, and the
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* agent id list. No framework dependencies. The `generatePlan` tool imports
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* this directly.
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*
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* Checks:
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* 1. Topological sort succeeds (no cycles, no missing deps)
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* 2. Output prefix uniqueness
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* 3. All agent assignments exist in the agent catalog
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* 4. All steps have resources defined
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*/
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import type { ResourceLimits } from "../config/resource-limits.js";
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import type { AnalysisPlan } from "./workflow-state.js";
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export interface ValidationResult {
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valid: boolean;
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errors: string[];
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}
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export interface ValidatePlanOptions {
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/**
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* Host per-step resource ceilings. When present, a step whose declared
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* `resources` exceed them is an error — the planner gets actionable
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* feedback at plan time instead of a silent clamp at sandbox creation.
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* The plan-generation path passes this; `execute_plan` deliberately does
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* not, so stored plans that predate the policy keep running (the
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* sandbox-creation clamp remains their backstop).
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*/
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readonly perStepCeiling?: ResourceLimits;
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}
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/** Derive a filesystem-safe output prefix from a step ID. */
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export declare function deriveOutputPrefix(stepId: string): string;
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/**
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* Validate an analysis plan for structural correctness.
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*
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* Returns `valid: true` if the plan passes all checks, or `valid: false`
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* with a list of human-readable error strings.
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*/
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export declare function validatePlan(plan: AnalysisPlan, options?: ValidatePlanOptions): ValidationResult;
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