@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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* Pure async client functions for the ChEMBL REST API.
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*
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* Used directly by target-assessment workflow steps and by tool wrappers.
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*/
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import { z } from "zod";
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import { apiFetchValidated, describeApiError } from "./api-utils.js";
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import { CHEMBL_BASE, CHEMBL_HEADERS as HEADERS } from "./chembl-config.js";
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const TargetComponentSynonymSchema = z.object({
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syn_type: z.string().optional(),
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component_synonym: z.string().optional(),
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});
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const TargetComponentSchema = z.object({
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accession: z.string().optional(),
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target_component_synonyms: z.array(TargetComponentSynonymSchema).optional(),
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});
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const RawTargetSchema = z.object({
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target_chembl_id: z.string().optional(),
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pref_name: z.string().optional(),
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target_type: z.string().optional(),
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organism: z.string().optional(),
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target_components: z.array(TargetComponentSchema).optional(),
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});
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/** A raw activity row from the ChEMBL `activity` endpoint. */
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const RawChemblActivitySchema = z.object({
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activity_id: z.number().optional(),
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molecule_chembl_id: z.string().optional(),
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target_chembl_id: z.string().optional(),
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standard_type: z.string().optional(),
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standard_value: z.union([z.string(), z.number()]).nullable().optional(),
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standard_units: z.string().optional(),
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assay_chembl_id: z.string().optional(),
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assay_type: z.string().optional(),
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pchembl_value: z.union([z.string(), z.number()]).nullable().optional(),
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});
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/** A raw mechanism row from the ChEMBL `mechanism` endpoint. */
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const RawChemblMechanismSchema = z.object({
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mechanism_of_action: z.string().optional(),
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action_type: z.string().optional(),
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target_chembl_id: z.string().optional(),
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molecule_chembl_id: z.string().optional(),
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});
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/** A drug-indication record nested inside a ChEMBL molecule/drug record. */
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const DrugIndicationRecordSchema = z.object({
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mesh_heading: z.string().optional(),
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efo_term: z.string().optional(),
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});
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/** A raw molecule/drug record from the ChEMBL `molecule` / `drug` endpoints. */
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const RawChemblMoleculeSchema = z.object({
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molecule_chembl_id: z.string().optional(),
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pref_name: z.string().optional(),
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max_phase: z.number().nullable().optional(),
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molecule_type: z.string().optional(),
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first_approval: z.number().nullable().optional(),
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drug_indications: z.array(DrugIndicationRecordSchema).optional(),
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molecule_hierarchy: z.object({ parent_chembl_id: z.string().optional() }).optional(),
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});
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// Response envelopes returned by the ChEMBL list/record endpoints, validated at
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// the fetch boundary. Every wrapper field is optional because the API omits it
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// when there is no data (a 404 is handled separately as an expected empty).
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const TargetSearchResponseSchema = z.object({ targets: z.array(RawTargetSchema).optional() });
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const ActivitiesResponseSchema = z.object({ activities: z.array(RawChemblActivitySchema).optional() });
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const MechanismsResponseSchema = z.object({ mechanisms: z.array(RawChemblMechanismSchema).optional() });
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const DrugSearchResponseSchema = z.object({ drugs: z.array(RawChemblMoleculeSchema).optional() });
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const MoleculeSearchResponseSchema = z.object({ molecules: z.array(RawChemblMoleculeSchema).optional() });
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const TargetNameResponseSchema = z.object({ pref_name: z.string().optional() });
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const MoleculeStructuresResponseSchema = z.object({
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molecule_structures: z.object({ standard_inchi_key: z.string().nullable().optional() }).optional(),
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});
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const TargetComponentsResponseSchema = z.object({
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target_components: z.array(z.object({ accession: z.string().optional(), component_type: z.string().optional() })).optional(),
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});
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function extractGeneNames(components) {
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if (!components?.length)
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return [];
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const genes = new Set();
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for (const comp of components) {
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for (const syn of comp.target_component_synonyms ?? []) {
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if (syn.syn_type === "GENE_SYMBOL" && syn.component_synonym) {
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genes.add(syn.component_synonym);
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}
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}
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}
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if (genes.size === 0) {
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for (const comp of components) {
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if (comp.accession)
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genes.add(comp.accession);
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}
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}
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return [...genes];
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}
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function mapTarget(raw) {
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return {
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targetChemblId: raw.target_chembl_id ?? "",
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preferredName: raw.pref_name ?? null,
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targetType: raw.target_type ?? null,
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organism: raw.organism ?? null,
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geneNames: extractGeneNames(raw.target_components),
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};
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}
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function parseNumeric(val) {
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if (val == null)
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return null;
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const n = typeof val === "number" ? val : parseFloat(val);
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return Number.isNaN(n) ? null : n;
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}
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export async function searchTargets(query, limit = 25) {
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const url = `${CHEMBL_BASE}/target/search.json?q=${encodeURIComponent(query)}&limit=${limit}`;
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const res = await apiFetchValidated(url, TargetSearchResponseSchema, { headers: HEADERS });
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if (res.isErr()) {
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if (res.error.type === "http_status" && res.error.status === 404)
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return [];
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throw new Error(describeApiError(res.error));
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}
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return (res.value.targets ?? []).map(mapTarget);
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}
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export async function getBioactivity(chemblId, type, options = {}) {
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const limit = options.limit ?? 500;
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const idParam = type === "compound" ? `molecule_chembl_id=${encodeURIComponent(chemblId)}` : `target_chembl_id=${encodeURIComponent(chemblId)}`;
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let url = `${CHEMBL_BASE}/activity.json?${idParam}&limit=${limit}`;
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if (options.activityType) {
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url += `&standard_type=${encodeURIComponent(options.activityType)}`;
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}
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const res = await apiFetchValidated(url, ActivitiesResponseSchema, { headers: HEADERS });
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if (res.isErr()) {
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if (res.error.type === "http_status" && res.error.status === 404)
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return [];
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throw new Error(describeApiError(res.error));
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}
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return (res.value.activities ?? []).map((raw) => ({
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activityId: raw.activity_id != null ? raw.activity_id : null,
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compoundChemblId: raw.molecule_chembl_id ?? "",
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targetChemblId: raw.target_chembl_id ?? null,
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standardType: raw.standard_type ?? null,
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standardValue: parseNumeric(raw.standard_value),
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standardUnits: raw.standard_units ?? null,
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assayChemblId: raw.assay_chembl_id ?? null,
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assayType: raw.assay_type ?? null,
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pchemblValue: parseNumeric(raw.pchembl_value),
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}));
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}
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async function fetchTargetName(targetChemblId) {
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const res = await apiFetchValidated(`${CHEMBL_BASE}/target/${targetChemblId}.json`, TargetNameResponseSchema, { headers: HEADERS });
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if (res.isErr() || !res.value.pref_name)
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return null;
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return res.value.pref_name;
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}
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export async function getMechanism(chemblId) {
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const url = `${CHEMBL_BASE}/mechanism.json?molecule_chembl_id=${encodeURIComponent(chemblId)}`;
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const res = await apiFetchValidated(url, MechanismsResponseSchema, { headers: HEADERS });
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if (res.isErr()) {
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if (res.error.type === "http_status" && res.error.status === 404)
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return [];
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throw new Error(describeApiError(res.error));
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}
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const rawMechanisms = res.value.mechanisms ?? [];
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const targetIds = new Set();
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for (const mech of rawMechanisms) {
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if (mech.target_chembl_id)
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targetIds.add(mech.target_chembl_id);
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}
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const targetNames = new Map();
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const targetIdArray = [...targetIds];
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const concurrency = 5;
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for (let i = 0; i < targetIdArray.length; i += concurrency) {
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const batch = targetIdArray.slice(i, i + concurrency);
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const names = await Promise.all(batch.map(fetchTargetName));
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for (const [idx, id] of batch.entries()) {
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const name = names[idx];
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if (name)
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targetNames.set(id, name);
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}
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}
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return rawMechanisms.map((raw) => ({
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mechanismOfAction: raw.mechanism_of_action ?? null,
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actionType: raw.action_type ?? null,
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targetChemblId: raw.target_chembl_id ?? null,
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targetName: targetNames.get(raw.target_chembl_id ?? "") ?? null,
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moleculeChemblId: raw.molecule_chembl_id ?? "",
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}));
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}
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function extractIndication(indications) {
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if (!indications?.length)
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return null;
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const terms = new Set();
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for (const ind of indications) {
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if (ind.mesh_heading)
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terms.add(ind.mesh_heading);
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else if (ind.efo_term)
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terms.add(ind.efo_term);
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}
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return terms.size > 0 ? [...terms].join("; ") : null;
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}
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export async function getDrugInfo(query, limit = 25) {
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const drugUrl = `${CHEMBL_BASE}/drug/search.json?q=${encodeURIComponent(query)}&limit=${limit}`;
|
|
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|
+
const drugRes = await apiFetchValidated(drugUrl, DrugSearchResponseSchema, { headers: HEADERS });
|
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|
+
if (drugRes.isOk() && drugRes.value.drugs?.length) {
|
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|
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return drugRes.value.drugs.map((raw) => ({
|
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|
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moleculeChemblId: raw.molecule_chembl_id ?? "",
|
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|
+
preferredName: raw.pref_name ?? null,
|
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201
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maxPhase: raw.max_phase != null ? Number(raw.max_phase) : null,
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moleculeType: raw.molecule_type ?? null,
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firstApproval: raw.first_approval ?? null,
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indication: extractIndication(raw.drug_indications),
|
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|
+
}));
|
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|
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}
|
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|
+
if (drugRes.isErr() && !(drugRes.error.type === "http_status" && drugRes.error.status === 404)) {
|
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|
+
throw new Error(describeApiError(drugRes.error));
|
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|
+
}
|
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210
|
+
const molUrl = `${CHEMBL_BASE}/molecule/search.json?q=${encodeURIComponent(query)}&limit=${limit}`;
|
|
211
|
+
const molRes = await apiFetchValidated(molUrl, MoleculeSearchResponseSchema, { headers: HEADERS });
|
|
212
|
+
if (molRes.isErr()) {
|
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213
|
+
if (molRes.error.type === "http_status" && molRes.error.status === 404)
|
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214
|
+
return [];
|
|
215
|
+
throw new Error(describeApiError(molRes.error));
|
|
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|
+
}
|
|
217
|
+
const approved = (molRes.value.molecules ?? []).filter((mol) => mol.max_phase != null && mol.max_phase >= 4);
|
|
218
|
+
return approved.map((raw) => ({
|
|
219
|
+
moleculeChemblId: raw.molecule_chembl_id ?? "",
|
|
220
|
+
preferredName: raw.pref_name ?? null,
|
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+
maxPhase: raw.max_phase != null ? Number(raw.max_phase) : null,
|
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|
+
moleculeType: raw.molecule_type ?? null,
|
|
223
|
+
firstApproval: raw.first_approval ?? null,
|
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|
+
indication: null,
|
|
225
|
+
}));
|
|
226
|
+
}
|
|
227
|
+
/**
|
|
228
|
+
* Fetch all clinical-stage modulators (max_phase ≥ 2 by default) for a target.
|
|
229
|
+
* Used for §2.6.6 (class precedent) and as the input to §2.6.4 (off-target panel).
|
|
230
|
+
*/
|
|
231
|
+
export async function getTargetModulators(targetChemblId, options = {}) {
|
|
232
|
+
const minPhase = options.minPhase ?? 2;
|
|
233
|
+
const limit = options.limit ?? 200;
|
|
234
|
+
const mechUrl = `${CHEMBL_BASE}/mechanism.json?target_chembl_id=${encodeURIComponent(targetChemblId)}` + `&limit=${limit}`;
|
|
235
|
+
const mechRes = await apiFetchValidated(mechUrl, MechanismsResponseSchema, { headers: HEADERS });
|
|
236
|
+
if (mechRes.isErr()) {
|
|
237
|
+
if (mechRes.error.type === "http_status" && mechRes.error.status === 404)
|
|
238
|
+
return [];
|
|
239
|
+
throw new Error(describeApiError(mechRes.error));
|
|
240
|
+
}
|
|
241
|
+
const moleculeIds = new Set();
|
|
242
|
+
for (const mech of mechRes.value.mechanisms ?? []) {
|
|
243
|
+
if (mech.molecule_chembl_id)
|
|
244
|
+
moleculeIds.add(mech.molecule_chembl_id);
|
|
245
|
+
}
|
|
246
|
+
if (moleculeIds.size === 0)
|
|
247
|
+
return [];
|
|
248
|
+
const modulators = [];
|
|
249
|
+
const ids = [...moleculeIds];
|
|
250
|
+
const concurrency = 5;
|
|
251
|
+
for (let i = 0; i < ids.length; i += concurrency) {
|
|
252
|
+
const batch = ids.slice(i, i + concurrency);
|
|
253
|
+
const results = await Promise.all(batch.map(async (id) => {
|
|
254
|
+
const res = await apiFetchValidated(`${CHEMBL_BASE}/molecule/${id}.json`, RawChemblMoleculeSchema, {
|
|
255
|
+
headers: HEADERS,
|
|
256
|
+
});
|
|
257
|
+
if (res.isErr())
|
|
258
|
+
return null;
|
|
259
|
+
const m = res.value;
|
|
260
|
+
const phase = m.max_phase != null ? Number(m.max_phase) : null;
|
|
261
|
+
if (phase == null || phase < minPhase)
|
|
262
|
+
return null;
|
|
263
|
+
return {
|
|
264
|
+
moleculeChemblId: m.molecule_chembl_id ?? id,
|
|
265
|
+
parentChemblId: m.molecule_hierarchy?.parent_chembl_id ?? null,
|
|
266
|
+
preferredName: m.pref_name ?? null,
|
|
267
|
+
maxPhase: phase,
|
|
268
|
+
moleculeType: m.molecule_type ?? null,
|
|
269
|
+
firstApproval: m.first_approval ?? null,
|
|
270
|
+
};
|
|
271
|
+
}));
|
|
272
|
+
for (const r of results)
|
|
273
|
+
if (r)
|
|
274
|
+
modulators.push(r);
|
|
275
|
+
}
|
|
276
|
+
return modulators;
|
|
277
|
+
}
|
|
278
|
+
/**
|
|
279
|
+
* Fetch off-target binding hits for a modulator: every target the molecule
|
|
280
|
+
* has been measured against (excluding the primary target), with potency.
|
|
281
|
+
* Used for §2.6.4 / §2.8 off-target panel.
|
|
282
|
+
*/
|
|
283
|
+
export async function getModulatorPolypharmacology(moleculeChemblId, options = {}) {
|
|
284
|
+
const minPchembl = options.minPchembl ?? 5;
|
|
285
|
+
const limit = options.limit ?? 200;
|
|
286
|
+
const url = `${CHEMBL_BASE}/activity.json?molecule_chembl_id=${encodeURIComponent(moleculeChemblId)}` + `&limit=${limit}&pchembl_value__gte=${minPchembl}`;
|
|
287
|
+
const res = await apiFetchValidated(url, ActivitiesResponseSchema, { headers: HEADERS });
|
|
288
|
+
if (res.isErr()) {
|
|
289
|
+
if (res.error.type === "http_status" && res.error.status === 404)
|
|
290
|
+
return [];
|
|
291
|
+
throw new Error(describeApiError(res.error));
|
|
292
|
+
}
|
|
293
|
+
const byTarget = new Map();
|
|
294
|
+
for (const raw of res.value.activities ?? []) {
|
|
295
|
+
const tid = raw.target_chembl_id;
|
|
296
|
+
if (!tid)
|
|
297
|
+
continue;
|
|
298
|
+
if (options.excludeTargetChemblId && tid === options.excludeTargetChemblId)
|
|
299
|
+
continue;
|
|
300
|
+
const pchembl = parseNumeric(raw.pchembl_value);
|
|
301
|
+
const existing = byTarget.get(tid);
|
|
302
|
+
if (!existing || (pchembl != null && (existing.pchemblValue == null || pchembl > existing.pchemblValue))) {
|
|
303
|
+
byTarget.set(tid, {
|
|
304
|
+
moleculeChemblId,
|
|
305
|
+
targetChemblId: tid,
|
|
306
|
+
targetName: null,
|
|
307
|
+
standardType: raw.standard_type ?? null,
|
|
308
|
+
standardValue: parseNumeric(raw.standard_value),
|
|
309
|
+
standardUnits: raw.standard_units ?? null,
|
|
310
|
+
pchemblValue: pchembl,
|
|
311
|
+
});
|
|
312
|
+
}
|
|
313
|
+
}
|
|
314
|
+
const hits = [...byTarget.values()];
|
|
315
|
+
const tids = hits.map((h) => h.targetChemblId);
|
|
316
|
+
const concurrency = 5;
|
|
317
|
+
for (let i = 0; i < tids.length; i += concurrency) {
|
|
318
|
+
const batch = tids.slice(i, i + concurrency);
|
|
319
|
+
const names = await Promise.all(batch.map(fetchTargetName));
|
|
320
|
+
for (const [idx, id] of batch.entries()) {
|
|
321
|
+
const hit = hits.find((h) => h.targetChemblId === id);
|
|
322
|
+
if (hit)
|
|
323
|
+
hit.targetName = names[idx];
|
|
324
|
+
}
|
|
325
|
+
}
|
|
326
|
+
return hits.sort((a, b) => (b.pchemblValue ?? 0) - (a.pchemblValue ?? 0));
|
|
327
|
+
}
|
|
328
|
+
/**
|
|
329
|
+
* Fetch the median pChEMBL value for a modulator measured against its primary
|
|
330
|
+
* on-target. Filters to activities with non-null pchembl_value against the
|
|
331
|
+
* specified target ChEMBL ID. Returns null when no activities are found.
|
|
332
|
+
*
|
|
333
|
+
* Used by the polypharm fanout step so the assembler's computeSelectivity
|
|
334
|
+
* can produce real fold values instead of selectivity_unknown.
|
|
335
|
+
*/
|
|
336
|
+
export async function getModulatorOnTargetPchembl(modulatorChemblId, targetChemblId) {
|
|
337
|
+
const url = `${CHEMBL_BASE}/activity.json?molecule_chembl_id=${encodeURIComponent(modulatorChemblId)}` +
|
|
338
|
+
`&target_chembl_id=${encodeURIComponent(targetChemblId)}` +
|
|
339
|
+
`&pchembl_value__isnull=false&limit=10`;
|
|
340
|
+
const res = await apiFetchValidated(url, ActivitiesResponseSchema, { headers: HEADERS });
|
|
341
|
+
if (res.isErr())
|
|
342
|
+
return null;
|
|
343
|
+
const values = (res.value.activities ?? []).map((a) => parseNumeric(a.pchembl_value)).filter((v) => v !== null);
|
|
344
|
+
if (values.length === 0)
|
|
345
|
+
return null;
|
|
346
|
+
values.sort((a, b) => a - b);
|
|
347
|
+
const mid = Math.floor(values.length / 2);
|
|
348
|
+
return values.length % 2 === 1 ? values[mid] : (values[mid - 1] + values[mid]) / 2;
|
|
349
|
+
}
|
|
350
|
+
/**
|
|
351
|
+
* Secondary path: fetch clinical-stage small molecules via the activity table.
|
|
352
|
+
*
|
|
353
|
+
* ChEMBL's mechanism table can lag behind for newer programmes (e.g.,
|
|
354
|
+
* orforglipron for GLP1R). Querying the activity table with
|
|
355
|
+
* `max_phase__gte` catches these molecules earlier. The activity table
|
|
356
|
+
* carries `molecule_chembl_id` but not `max_phase` or `molecule_type` —
|
|
357
|
+
* those require a follow-up molecule lookup. We batch unique molecule IDs
|
|
358
|
+
* and fetch molecule records in slices of 5.
|
|
359
|
+
*
|
|
360
|
+
* Returns one `ChemblModulator` per unique molecule that passes the
|
|
361
|
+
* min-phase and molecule-type filters.
|
|
362
|
+
*/
|
|
363
|
+
export async function getModulatorsViaActivity(args) {
|
|
364
|
+
const { target_chembl_id, max_phase_min = 2, molecule_type, limit = 50 } = args;
|
|
365
|
+
let url = `${CHEMBL_BASE}/activity.json?target_chembl_id=${encodeURIComponent(target_chembl_id)}` + `&max_phase__gte=${max_phase_min}&limit=${limit}`;
|
|
366
|
+
if (molecule_type) {
|
|
367
|
+
url += `&molecule_type=${encodeURIComponent(molecule_type)}`;
|
|
368
|
+
}
|
|
369
|
+
const res = await apiFetchValidated(url, ActivitiesResponseSchema, { headers: HEADERS });
|
|
370
|
+
if (res.isErr()) {
|
|
371
|
+
if (res.error.type === "http_status" && res.error.status === 404)
|
|
372
|
+
return [];
|
|
373
|
+
throw new Error(describeApiError(res.error));
|
|
374
|
+
}
|
|
375
|
+
// Collect unique molecule IDs from activity rows.
|
|
376
|
+
const moleculeIds = new Set();
|
|
377
|
+
for (const row of res.value.activities ?? []) {
|
|
378
|
+
if (row.molecule_chembl_id)
|
|
379
|
+
moleculeIds.add(row.molecule_chembl_id);
|
|
380
|
+
}
|
|
381
|
+
if (moleculeIds.size === 0)
|
|
382
|
+
return [];
|
|
383
|
+
const modulators = [];
|
|
384
|
+
const ids = [...moleculeIds];
|
|
385
|
+
const concurrency = 5;
|
|
386
|
+
for (let i = 0; i < ids.length; i += concurrency) {
|
|
387
|
+
const batch = ids.slice(i, i + concurrency);
|
|
388
|
+
const results = await Promise.all(batch.map(async (id) => {
|
|
389
|
+
const molRes = await apiFetchValidated(`${CHEMBL_BASE}/molecule/${id}.json`, RawChemblMoleculeSchema, {
|
|
390
|
+
headers: HEADERS,
|
|
391
|
+
});
|
|
392
|
+
if (molRes.isErr())
|
|
393
|
+
return null;
|
|
394
|
+
const m = molRes.value;
|
|
395
|
+
const phase = m.max_phase != null ? Number(m.max_phase) : null;
|
|
396
|
+
if (phase == null || phase < max_phase_min)
|
|
397
|
+
return null;
|
|
398
|
+
const molType = m.molecule_type ?? null;
|
|
399
|
+
if (molecule_type && molType !== molecule_type)
|
|
400
|
+
return null;
|
|
401
|
+
return {
|
|
402
|
+
moleculeChemblId: m.molecule_chembl_id ?? id,
|
|
403
|
+
parentChemblId: m.molecule_hierarchy?.parent_chembl_id ?? null,
|
|
404
|
+
preferredName: m.pref_name ?? null,
|
|
405
|
+
maxPhase: phase,
|
|
406
|
+
moleculeType: molType,
|
|
407
|
+
firstApproval: m.first_approval ?? null,
|
|
408
|
+
};
|
|
409
|
+
}));
|
|
410
|
+
for (const r of results)
|
|
411
|
+
if (r)
|
|
412
|
+
modulators.push(r);
|
|
413
|
+
}
|
|
414
|
+
return modulators;
|
|
415
|
+
}
|
|
416
|
+
/**
|
|
417
|
+
* Fetch the canonical InChI key for a ChEMBL molecule. Returns null when
|
|
418
|
+
* ChEMBL has no recorded structure (typical for peptide/protein entries
|
|
419
|
+
* with `molecule_type: "Unknown"`).
|
|
420
|
+
*/
|
|
421
|
+
export async function getMoleculeInChIKey(moleculeChemblId) {
|
|
422
|
+
const res = await apiFetchValidated(`${CHEMBL_BASE}/molecule/${moleculeChemblId}.json`, MoleculeStructuresResponseSchema, { headers: HEADERS });
|
|
423
|
+
if (res.isErr())
|
|
424
|
+
return null;
|
|
425
|
+
return res.value.molecule_structures?.standard_inchi_key ?? null;
|
|
426
|
+
}
|
|
427
|
+
/**
|
|
428
|
+
* Resolve a drug's mechanism-of-action targets to UniProt accessions.
|
|
429
|
+
* Returns deduplicated accessions across all mechanism rows.
|
|
430
|
+
* Empty array on no mechanism, missing target, or non-protein target.
|
|
431
|
+
*
|
|
432
|
+
* Used by target-identity-filter to detect off-target trials (e.g., a
|
|
433
|
+
* trial of a CALCRL drug being surfaced under a CALCR assessment).
|
|
434
|
+
*/
|
|
435
|
+
export async function getDrugPrimaryTargetUniprots(moleculeChemblId) {
|
|
436
|
+
const mechRes = await apiFetchValidated(`${CHEMBL_BASE}/mechanism.json?molecule_chembl_id=${encodeURIComponent(moleculeChemblId)}&limit=20`, MechanismsResponseSchema, { headers: HEADERS });
|
|
437
|
+
if (mechRes.isErr())
|
|
438
|
+
return [];
|
|
439
|
+
const targetIds = new Set();
|
|
440
|
+
for (const m of mechRes.value.mechanisms ?? []) {
|
|
441
|
+
if (m.target_chembl_id)
|
|
442
|
+
targetIds.add(m.target_chembl_id);
|
|
443
|
+
}
|
|
444
|
+
if (targetIds.size === 0)
|
|
445
|
+
return [];
|
|
446
|
+
const accessions = new Set();
|
|
447
|
+
for (const targetId of targetIds) {
|
|
448
|
+
const tRes = await apiFetchValidated(`${CHEMBL_BASE}/target/${targetId}.json`, TargetComponentsResponseSchema, { headers: HEADERS });
|
|
449
|
+
if (tRes.isErr())
|
|
450
|
+
continue;
|
|
451
|
+
for (const c of tRes.value.target_components ?? []) {
|
|
452
|
+
if (c.accession && (c.component_type ?? "").toUpperCase() === "PROTEIN") {
|
|
453
|
+
accessions.add(c.accession);
|
|
454
|
+
}
|
|
455
|
+
}
|
|
456
|
+
}
|
|
457
|
+
return [...accessions];
|
|
458
|
+
}
|
|
@@ -0,0 +1,33 @@
|
|
|
1
|
+
export interface PhaseTransitions {
|
|
2
|
+
phase1_to_phase2: number;
|
|
3
|
+
phase2_to_phase3: number;
|
|
4
|
+
phase3_to_nda: number;
|
|
5
|
+
nda_to_approval: number;
|
|
6
|
+
phase1_to_approval: number;
|
|
7
|
+
}
|
|
8
|
+
export interface BenchmarkResult {
|
|
9
|
+
therapeutic_area: string;
|
|
10
|
+
source: "available" | "fallback";
|
|
11
|
+
data_version: string;
|
|
12
|
+
data_window: string;
|
|
13
|
+
attribution: string;
|
|
14
|
+
transitions: PhaseTransitions;
|
|
15
|
+
}
|
|
16
|
+
/**
|
|
17
|
+
* Infer therapeutic area from a list of indication labels using the
|
|
18
|
+
* dataset's pattern map. First match wins.
|
|
19
|
+
*/
|
|
20
|
+
export declare function inferTherapeuticArea(indicationLabels: string[]): string | null;
|
|
21
|
+
/**
|
|
22
|
+
* Get phase-transition benchmarks for a therapeutic area. Falls back to
|
|
23
|
+
* the all-areas baseline when the requested area is unknown — the
|
|
24
|
+
* `source` field discloses whether the fallback was used.
|
|
25
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+
*/
|
|
26
|
+
export declare function getBenchmarks(therapeuticArea: string | null): BenchmarkResult;
|
|
27
|
+
/** Return the dataset's metadata for transparency in the dossier. */
|
|
28
|
+
export declare function getDatasetAttribution(): {
|
|
29
|
+
data_version: string;
|
|
30
|
+
data_window: string;
|
|
31
|
+
source: string;
|
|
32
|
+
url: string;
|
|
33
|
+
};
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|
@@ -0,0 +1,54 @@
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|
1
|
+
import benchmarksData from "../../data/clinical-benchmarks.json" with { type: "json" };
|
|
2
|
+
const dataset = benchmarksData;
|
|
3
|
+
if (!dataset.phase_transitions || !dataset.phase_transitions.all) {
|
|
4
|
+
throw new Error("clinical-benchmarks.json is missing phase_transitions.all baseline");
|
|
5
|
+
}
|
|
6
|
+
function loadDataset() {
|
|
7
|
+
return dataset;
|
|
8
|
+
}
|
|
9
|
+
/**
|
|
10
|
+
* Infer therapeutic area from a list of indication labels using the
|
|
11
|
+
* dataset's pattern map. First match wins.
|
|
12
|
+
*/
|
|
13
|
+
export function inferTherapeuticArea(indicationLabels) {
|
|
14
|
+
const dataset = loadDataset();
|
|
15
|
+
for (const label of indicationLabels) {
|
|
16
|
+
const lower = label.toLowerCase();
|
|
17
|
+
for (const entry of dataset.indication_to_therapeutic_area) {
|
|
18
|
+
for (const pattern of entry.patterns) {
|
|
19
|
+
if (lower.includes(pattern.toLowerCase())) {
|
|
20
|
+
return entry.therapeutic_area;
|
|
21
|
+
}
|
|
22
|
+
}
|
|
23
|
+
}
|
|
24
|
+
}
|
|
25
|
+
return null;
|
|
26
|
+
}
|
|
27
|
+
/**
|
|
28
|
+
* Get phase-transition benchmarks for a therapeutic area. Falls back to
|
|
29
|
+
* the all-areas baseline when the requested area is unknown — the
|
|
30
|
+
* `source` field discloses whether the fallback was used.
|
|
31
|
+
*/
|
|
32
|
+
export function getBenchmarks(therapeuticArea) {
|
|
33
|
+
const dataset = loadDataset();
|
|
34
|
+
const useFallback = !therapeuticArea || !dataset.phase_transitions[therapeuticArea];
|
|
35
|
+
const ta = useFallback ? "all" : therapeuticArea;
|
|
36
|
+
return {
|
|
37
|
+
therapeutic_area: ta,
|
|
38
|
+
source: useFallback ? "fallback" : "available",
|
|
39
|
+
data_version: dataset.data_version,
|
|
40
|
+
data_window: dataset.data_window,
|
|
41
|
+
attribution: dataset.source,
|
|
42
|
+
transitions: dataset.phase_transitions[ta],
|
|
43
|
+
};
|
|
44
|
+
}
|
|
45
|
+
/** Return the dataset's metadata for transparency in the dossier. */
|
|
46
|
+
export function getDatasetAttribution() {
|
|
47
|
+
const ds = loadDataset();
|
|
48
|
+
return {
|
|
49
|
+
data_version: ds.data_version,
|
|
50
|
+
data_window: ds.data_window,
|
|
51
|
+
source: ds.source,
|
|
52
|
+
url: ds.url,
|
|
53
|
+
};
|
|
54
|
+
}
|