@inflexa-ai/harness 0.35.8 → 0.36.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/dist/auth/types.d.ts +5 -14
- package/dist/auth/types.js +3 -10
- package/dist/billing/usage-recorder.d.ts +1 -1
- package/dist/contracts/analogy-report.d.ts +1 -1
- package/dist/contracts/analogy-report.js +1 -1
- package/dist/contracts/chat-parts.d.ts +2 -3
- package/dist/contracts/index.d.ts +0 -4
- package/dist/contracts/index.js +0 -2
- package/dist/index.d.ts +0 -7
- package/dist/index.js +0 -21
- package/dist/lib/metrics.d.ts +1 -1
- package/dist/lib/otel-spans.d.ts +0 -2
- package/dist/lib/otel-spans.js +0 -2
- package/dist/loop/run-agent.d.ts +1 -1
- package/dist/runtime/assemble.d.ts +0 -3
- package/dist/runtime/assemble.js +0 -3
- package/dist/state/index.d.ts +0 -2
- package/dist/state/index.js +0 -1
- package/dist/state/init.js +1 -60
- package/dist/state/purge-analysis.d.ts +1 -2
- package/dist/state/purge-analysis.js +1 -2
- package/dist/tasks/regulatory-corpus-boot-refresh.js +1 -1
- package/dist/tools/bio/gene-preclinical-profile.d.ts +1 -3
- package/dist/tools/bio/gene-preclinical-profile.js +1 -3
- package/dist/tools/lib/chembl-client.d.ts +1 -4
- package/dist/tools/lib/chembl-client.js +1 -4
- package/dist/tools/lib/clinical-benchmarks-client.d.ts +1 -1
- package/dist/tools/lib/clinical-benchmarks-client.js +1 -1
- package/dist/tools/lib/clinical-trials-client.d.ts +0 -3
- package/dist/tools/lib/clinical-trials-client.js +0 -3
- package/dist/tools/lib/identifier-resolver.d.ts +5 -7
- package/dist/tools/lib/identifier-resolver.js +5 -7
- package/dist/tools/lib/iuphar-client.d.ts +1 -3
- package/dist/tools/lib/iuphar-client.js +1 -3
- package/dist/tools/lib/opentargets-client.d.ts +1 -1
- package/dist/tools/lib/opentargets-client.js +1 -1
- package/dist/tools/lib/protein-family-normalize.d.ts +5 -7
- package/dist/tools/lib/protein-family-normalize.js +5 -7
- package/dist/tools/lib/uniprot-client.d.ts +0 -7
- package/dist/tools/lib/uniprot-client.js +2 -9
- package/package.json +1 -1
- package/dist/contracts/target-assessment-row.d.ts +0 -85
- package/dist/contracts/target-assessment-row.js +0 -37
- package/dist/contracts/target-dossier.d.ts +0 -12423
- package/dist/contracts/target-dossier.js +0 -1282
- package/dist/prompts/target-assessment/briefs/executive-recommendation.d.ts +0 -1
- package/dist/prompts/target-assessment/briefs/executive-recommendation.js +0 -85
- package/dist/prompts/target-assessment/briefs/index.d.ts +0 -4
- package/dist/prompts/target-assessment/briefs/index.js +0 -4
- package/dist/prompts/target-assessment/briefs/liability-bullets.d.ts +0 -1
- package/dist/prompts/target-assessment/briefs/liability-bullets.js +0 -114
- package/dist/prompts/target-assessment/briefs/target-organ-liabilities.d.ts +0 -1
- package/dist/prompts/target-assessment/briefs/target-organ-liabilities.js +0 -37
- package/dist/prompts/target-assessment/briefs/translational-commentary.d.ts +0 -1
- package/dist/prompts/target-assessment/briefs/translational-commentary.js +0 -23
- package/dist/prompts/target-assessment/drugs-in-class.d.ts +0 -1
- package/dist/prompts/target-assessment/drugs-in-class.js +0 -29
- package/dist/prompts/target-assessment/investigation/adversarial-critique.d.ts +0 -1
- package/dist/prompts/target-assessment/investigation/adversarial-critique.js +0 -67
- package/dist/prompts/target-assessment/investigation/claim-reverification.d.ts +0 -1
- package/dist/prompts/target-assessment/investigation/claim-reverification.js +0 -49
- package/dist/prompts/target-assessment/investigation/index.d.ts +0 -3
- package/dist/prompts/target-assessment/investigation/index.js +0 -3
- package/dist/prompts/target-assessment/investigation/mechanism-proposal.d.ts +0 -1
- package/dist/prompts/target-assessment/investigation/mechanism-proposal.js +0 -49
- package/dist/prompts/target-assessment/modulator-triage.d.ts +0 -1
- package/dist/prompts/target-assessment/modulator-triage.js +0 -31
- package/dist/prompts/target-assessment/off-target-annotator.d.ts +0 -1
- package/dist/prompts/target-assessment/off-target-annotator.js +0 -28
- package/dist/prompts/target-assessment/tox-voice/core.d.ts +0 -1
- package/dist/prompts/target-assessment/tox-voice/core.js +0 -74
- package/dist/prompts/target-assessment/tox-voice/critique.d.ts +0 -7
- package/dist/prompts/target-assessment/tox-voice/critique.js +0 -109
- package/dist/prompts/target-assessment/tox-voice/exemplars.d.ts +0 -8
- package/dist/prompts/target-assessment/tox-voice/exemplars.js +0 -24
- package/dist/prompts/target-assessment/tox-voice/index.d.ts +0 -4
- package/dist/prompts/target-assessment/tox-voice/index.js +0 -4
- package/dist/prompts/target-assessment/tox-voice/vocabulary.d.ts +0 -18
- package/dist/prompts/target-assessment/tox-voice/vocabulary.js +0 -61
- package/dist/state/target-assessments.d.ts +0 -68
- package/dist/state/target-assessments.js +0 -222
- package/dist/workflows/execute-target-assessment.d.ts +0 -118
- package/dist/workflows/execute-target-assessment.js +0 -631
- package/dist/workflows/target-assessment/assemblers/index.d.ts +0 -5
- package/dist/workflows/target-assessment/assemblers/index.js +0 -4
- package/dist/workflows/target-assessment/assemblers/literature.d.ts +0 -281
- package/dist/workflows/target-assessment/assemblers/literature.js +0 -971
- package/dist/workflows/target-assessment/assemblers/orchestrator.d.ts +0 -118
- package/dist/workflows/target-assessment/assemblers/orchestrator.js +0 -945
- package/dist/workflows/target-assessment/assemblers/safety.d.ts +0 -374
- package/dist/workflows/target-assessment/assemblers/safety.js +0 -1068
- package/dist/workflows/target-assessment/assemblers/trials.d.ts +0 -30
- package/dist/workflows/target-assessment/assemblers/trials.js +0 -75
- package/dist/workflows/target-assessment/collectors/index.d.ts +0 -114
- package/dist/workflows/target-assessment/collectors/index.js +0 -538
- package/dist/workflows/target-assessment/coverage.d.ts +0 -97
- package/dist/workflows/target-assessment/coverage.js +0 -86
- package/dist/workflows/target-assessment/decisions/index.d.ts +0 -86
- package/dist/workflows/target-assessment/decisions/index.js +0 -127
- package/dist/workflows/target-assessment/fanout/index.d.ts +0 -32
- package/dist/workflows/target-assessment/fanout/index.js +0 -156
- package/dist/workflows/target-assessment/investigation/index.d.ts +0 -97
- package/dist/workflows/target-assessment/investigation/index.js +0 -419
- package/dist/workflows/target-assessment/lib/approval-precedents.d.ts +0 -73
- package/dist/workflows/target-assessment/lib/approval-precedents.js +0 -185
- package/dist/workflows/target-assessment/lib/citation-validator.d.ts +0 -46
- package/dist/workflows/target-assessment/lib/citation-validator.js +0 -316
- package/dist/workflows/target-assessment/lib/clinical-consequence-annotator.d.ts +0 -65
- package/dist/workflows/target-assessment/lib/clinical-consequence-annotator.js +0 -174
- package/dist/workflows/target-assessment/lib/clinical-evidence-attribution.d.ts +0 -44
- package/dist/workflows/target-assessment/lib/clinical-evidence-attribution.js +0 -152
- package/dist/workflows/target-assessment/lib/compute-derived.d.ts +0 -20
- package/dist/workflows/target-assessment/lib/compute-derived.js +0 -261
- package/dist/workflows/target-assessment/lib/compute-selectivity.d.ts +0 -15
- package/dist/workflows/target-assessment/lib/compute-selectivity.js +0 -18
- package/dist/workflows/target-assessment/lib/dedup-modulators.d.ts +0 -37
- package/dist/workflows/target-assessment/lib/dedup-modulators.js +0 -157
- package/dist/workflows/target-assessment/lib/evidence-conflict-detector.d.ts +0 -17
- package/dist/workflows/target-assessment/lib/evidence-conflict-detector.js +0 -100
- package/dist/workflows/target-assessment/lib/expression-constants.d.ts +0 -21
- package/dist/workflows/target-assessment/lib/expression-constants.js +0 -21
- package/dist/workflows/target-assessment/lib/family-complex-supplement.d.ts +0 -20
- package/dist/workflows/target-assessment/lib/family-complex-supplement.js +0 -36
- package/dist/workflows/target-assessment/lib/fda-label-safety.d.ts +0 -72
- package/dist/workflows/target-assessment/lib/fda-label-safety.js +0 -166
- package/dist/workflows/target-assessment/lib/heterodimer-filter.d.ts +0 -30
- package/dist/workflows/target-assessment/lib/heterodimer-filter.js +0 -44
- package/dist/workflows/target-assessment/lib/hpo-organ-map.d.ts +0 -34
- package/dist/workflows/target-assessment/lib/hpo-organ-map.js +0 -63
- package/dist/workflows/target-assessment/lib/impc-organ-map.d.ts +0 -19
- package/dist/workflows/target-assessment/lib/impc-organ-map.js +0 -39
- package/dist/workflows/target-assessment/lib/intended-polypharm-filter.d.ts +0 -4
- package/dist/workflows/target-assessment/lib/intended-polypharm-filter.js +0 -24
- package/dist/workflows/target-assessment/lib/llm-step.d.ts +0 -80
- package/dist/workflows/target-assessment/lib/llm-step.js +0 -101
- package/dist/workflows/target-assessment/lib/meddra-organ-map.d.ts +0 -40
- package/dist/workflows/target-assessment/lib/meddra-organ-map.js +0 -138
- package/dist/workflows/target-assessment/lib/recommendation-quality-gates.d.ts +0 -17
- package/dist/workflows/target-assessment/lib/recommendation-quality-gates.js +0 -99
- package/dist/workflows/target-assessment/lib/recommendation-sanitizer.d.ts +0 -2
- package/dist/workflows/target-assessment/lib/recommendation-sanitizer.js +0 -51
- package/dist/workflows/target-assessment/lib/regulatory-actions.d.ts +0 -25
- package/dist/workflows/target-assessment/lib/regulatory-actions.js +0 -176
- package/dist/workflows/target-assessment/lib/safety-corroboration.d.ts +0 -44
- package/dist/workflows/target-assessment/lib/safety-corroboration.js +0 -273
- package/dist/workflows/target-assessment/lib/structured-llm.d.ts +0 -61
- package/dist/workflows/target-assessment/lib/structured-llm.js +0 -102
- package/dist/workflows/target-assessment/lib/target-identity-filter.d.ts +0 -59
- package/dist/workflows/target-assessment/lib/target-identity-filter.js +0 -95
- package/dist/workflows/target-assessment/lib/therapeutic-programs.d.ts +0 -20
- package/dist/workflows/target-assessment/lib/therapeutic-programs.js +0 -68
- package/dist/workflows/target-assessment/metrics.d.ts +0 -16
- package/dist/workflows/target-assessment/metrics.js +0 -30
- package/dist/workflows/target-assessment/phase4-assemble.d.ts +0 -3182
- package/dist/workflows/target-assessment/phase4-assemble.js +0 -39
- package/dist/workflows/target-assessment/phase5-persist.d.ts +0 -59
- package/dist/workflows/target-assessment/phase5-persist.js +0 -349
- package/dist/workflows/target-assessment/progress-stream.d.ts +0 -75
- package/dist/workflows/target-assessment/progress-stream.js +0 -110
- package/dist/workflows/target-assessment/progress.d.ts +0 -39
- package/dist/workflows/target-assessment/progress.js +0 -77
- package/dist/workflows/target-assessment/schemas.d.ts +0 -970
- package/dist/workflows/target-assessment/schemas.js +0 -318
- package/dist/workflows/target-assessment/steps/collectors/pathways.d.ts +0 -15
- package/dist/workflows/target-assessment/steps/collectors/pathways.js +0 -58
- package/dist/workflows/target-assessment/steps/fanout/aes-for-one-class-drug-step.d.ts +0 -34
- package/dist/workflows/target-assessment/steps/fanout/aes-for-one-class-drug-step.js +0 -31
- package/dist/workflows/target-assessment/steps/fanout/aes-for-one-trial-step.d.ts +0 -57
- package/dist/workflows/target-assessment/steps/fanout/aes-for-one-trial-step.js +0 -54
- package/dist/workflows/target-assessment/steps/fanout/faers-for-one-modulator-step.d.ts +0 -35
- package/dist/workflows/target-assessment/steps/fanout/faers-for-one-modulator-step.js +0 -32
- package/dist/workflows/target-assessment/steps/fanout/index.d.ts +0 -14
- package/dist/workflows/target-assessment/steps/fanout/index.js +0 -10
- package/dist/workflows/target-assessment/steps/fanout/polypharm-for-one-modulator-step.d.ts +0 -29
- package/dist/workflows/target-assessment/steps/fanout/polypharm-for-one-modulator-step.js +0 -29
- package/dist/workflows/target-assessment/steps/phase2-aggregate.d.ts +0 -657
- package/dist/workflows/target-assessment/steps/phase2-aggregate.js +0 -34
- package/dist/workflows/target-assessment/steps/phase3-aggregate.d.ts +0 -806
- package/dist/workflows/target-assessment/steps/phase3-aggregate.js +0 -16
- package/dist/workflows/target-assessment/steps/synthesis/diagnostics.d.ts +0 -28
- package/dist/workflows/target-assessment/steps/synthesis/diagnostics.js +0 -27
- package/dist/workflows/target-assessment/sub-workflows/index.d.ts +0 -15
- package/dist/workflows/target-assessment/sub-workflows/index.js +0 -11
- package/dist/workflows/target-assessment/sub-workflows/per-class-drug-aes.d.ts +0 -41
- package/dist/workflows/target-assessment/sub-workflows/per-class-drug-aes.js +0 -12
- package/dist/workflows/target-assessment/sub-workflows/per-modulator-faers.d.ts +0 -41
- package/dist/workflows/target-assessment/sub-workflows/per-modulator-faers.js +0 -12
- package/dist/workflows/target-assessment/sub-workflows/per-modulator-polypharm.d.ts +0 -37
- package/dist/workflows/target-assessment/sub-workflows/per-modulator-polypharm.js +0 -12
- package/dist/workflows/target-assessment/sub-workflows/per-trial-aes.d.ts +0 -66
- package/dist/workflows/target-assessment/sub-workflows/per-trial-aes.js +0 -12
- package/dist/workflows/target-assessment/synthesis/index.d.ts +0 -607
- package/dist/workflows/target-assessment/synthesis/index.js +0 -354
- package/dist/workflows/target-assessment/synthesis-probes.d.ts +0 -56
- package/dist/workflows/target-assessment/synthesis-probes.js +0 -320
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/**
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* Progress emission for the target-assessment DBOS workflow.
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*
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* Emits a typed `data-target-assessment-progress` part via
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* `DBOS.writeStream("progress", part)` and updates `cortex_target_assessments.progress`.
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* Both writes happen inside a `DBOS.runStep` so a recovered workflow does not
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* duplicate the event.
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*
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* Wire shape: `TargetAssessmentProgressEventSchema` in
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* `harness/src/contracts/target-dossier.ts`. The SSE route reads via
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* `DBOS.readStream(workflowId, "progress")` and folds-on-read by `phase`.
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*/
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import { DBOS } from "@dbos-inc/dbos-sdk";
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import { describeDbError } from "../../lib/db-result.js";
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import { updateProgress } from "../../state/target-assessments.js";
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/** DBOS stream key the SSE route reads via `DBOS.readStream(wfId, "progress")`. */
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export const TA_PROGRESS_STREAM_KEY = "progress";
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export const PROGRESS_PERCENTS = {
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resolving: 5,
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collecting: 25,
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deciding: 55,
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fanning_out: 70,
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assembling: 85,
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synthesizing: 90,
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completed: 100,
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failed: 100,
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suspended: 100,
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};
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export const PROGRESS_MESSAGES = {
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resolving: "Resolving target identity",
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collecting: "Collecting evidence from 14 data sources",
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deciding: "Triaging modulators and classifying trials",
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fanning_out: "Building per-modulator and per-trial detail",
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assembling: "Assembling dossier sections",
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synthesizing: "Drafting safety and translational commentary",
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completed: "Completed",
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failed: "Failed",
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suspended: "Suspended — insufficient funds",
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};
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/**
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* Emit one progress transition. MUST be called from inside the workflow
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* body — the `DBOS.runStep` wrapper makes it replay-safe (DBOS persists
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* the stream-write offset under `(workflowID, function_id)`; replay
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* returns cached without re-writing the part).
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*
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* Best-effort: a DB or stream failure logs and continues — progress
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* emission MUST NOT block the workflow.
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*/
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export async function emitProgress(pool, logger, assessmentId, phase) {
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const log = logger.named("ta-progress").with({ assessmentId, phase });
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const message = PROGRESS_MESSAGES[phase];
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const percent = PROGRESS_PERCENTS[phase];
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await DBOS.runStep(async () => {
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const part = {
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type: "data-target-assessment-progress",
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payload: { phase, message, percent, at: new Date().toISOString() },
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};
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log.warn("writeStream failed", log.errorFields(err));
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}
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const rowStatus = phase === "completed" ? "completed" : phase === "failed" ? "failed" : "running";
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(await updateProgress(pool, assessmentId, message, rowStatus)).match(() => { }, (error) => {
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log.warn("updateProgress failed", { err: describeDbError(error) });
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});
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}
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}, { name: `ta-progress:${phase}` });
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}
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