@inflexa-ai/harness 0.1.1 → 0.3.0
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/README.md +48 -0
- package/dist/agents/conversation-agent.d.ts +15 -11
- package/dist/agents/conversation-agent.js +31 -34
- package/dist/agents/report-builder.js +2 -1
- package/dist/agents/sandbox/bulk-transcriptomics-agent.js +1 -1
- package/dist/agents/sandbox/cheminformatics-agent.js +1 -19
- package/dist/agents/sandbox/chromatin-agent.js +1 -10
- package/dist/agents/sandbox/dna-methylation-agent.js +1 -10
- package/dist/agents/sandbox/drug-repurposing-agent.js +4 -14
- package/dist/agents/sandbox/enrichment-agent.js +1 -10
- package/dist/agents/sandbox/ephemeral-executor.js +1 -10
- package/dist/agents/sandbox/genomic-variant-agent.js +1 -3
- package/dist/agents/sandbox/immune-profiling-agent.js +1 -13
- package/dist/agents/sandbox/metabolomics-agent.js +1 -1
- package/dist/agents/sandbox/microbiome-agent.js +1 -1
- package/dist/agents/sandbox/multi-omics-integration-agent.js +1 -12
- package/dist/agents/sandbox/multimodal-sc-agent.js +1 -1
- package/dist/agents/sandbox/network-agent.js +1 -10
- package/dist/agents/sandbox/pkpd-clinical-response-agent.js +2 -8
- package/dist/agents/sandbox/proteomics-agent.js +1 -1
- package/dist/agents/sandbox/scientific-executor.js +1 -10
- package/dist/agents/sandbox/shared.d.ts +20 -6
- package/dist/agents/sandbox/shared.js +50 -39
- package/dist/agents/sandbox/single-cell-agent.js +1 -1
- package/dist/agents/sandbox/spatial-omics-agent.js +1 -1
- package/dist/agents/sandbox/statistical-modeling-agent.js +1 -1
- package/dist/agents/sandbox/translational-safety-agent.js +3 -9
- package/dist/agents/sandbox/types.d.ts +1 -1
- package/dist/agents/system-prompt.d.ts +37 -11
- package/dist/agents/system-prompt.js +35 -12
- package/dist/app/chat-turn.d.ts +3 -0
- package/dist/app/chat-turn.js +3 -1
- package/dist/app/data-profile-orientation.d.ts +34 -0
- package/dist/app/data-profile-orientation.js +117 -0
- package/dist/app/synthesize-run.d.ts +3 -0
- package/dist/app/synthesize-run.js +3 -1
- package/dist/contracts/schemas/chat-parts.d.ts +9 -9
- package/dist/execution/artifact-metadata.d.ts +3 -0
- package/dist/execution/artifact-metadata.js +10 -3
- package/dist/execution/artifact-registration.d.ts +2 -1
- package/dist/execution/artifact-registration.js +8 -2
- package/dist/execution/ephemeral-runner.d.ts +16 -0
- package/dist/execution/ephemeral-runner.js +31 -5
- package/dist/execution/post-step-pipeline.d.ts +3 -0
- package/dist/execution/post-step-pipeline.js +24 -4
- package/dist/execution/reconcile-manifest.d.ts +7 -0
- package/dist/execution/reconcile-manifest.js +19 -5
- package/dist/execution/report-runner.d.ts +3 -0
- package/dist/execution/report-runner.js +4 -4
- package/dist/execution/run-synthesis.js +20 -19
- package/dist/execution/step-summary.d.ts +3 -0
- package/dist/execution/step-summary.js +6 -3
- package/dist/index.d.ts +9 -2
- package/dist/index.js +24 -5
- package/dist/lib/chrome.d.ts +4 -1
- package/dist/lib/chrome.js +10 -7
- package/dist/lib/console-logger.d.ts +19 -0
- package/dist/lib/console-logger.js +62 -0
- package/dist/lib/logger.d.ts +88 -0
- package/dist/lib/logger.js +37 -0
- package/dist/lib/otel.d.ts +2 -1
- package/dist/lib/otel.js +8 -3
- package/dist/loop/__fixtures__/scripted-provider.d.ts +2 -2
- package/dist/loop/__fixtures__/scripted-provider.js +2 -1
- package/dist/loop/metrics.d.ts +33 -1
- package/dist/loop/metrics.js +56 -2
- package/dist/loop/run-agent.d.ts +13 -1
- package/dist/loop/run-agent.js +19 -4
- package/dist/memory/card-builders.d.ts +8 -1
- package/dist/memory/card-builders.js +20 -3
- package/dist/memory/reconstruct-cards.js +4 -3
- package/dist/memory/thread-history.d.ts +27 -2
- package/dist/memory/thread-history.js +45 -5
- package/dist/memory/working-memory.d.ts +93 -10
- package/dist/memory/working-memory.js +220 -84
- package/dist/prompts/SOUL.d.ts +22 -9
- package/dist/prompts/SOUL.js +56 -37
- package/dist/prompts/analogical-reasoner.d.ts +1 -1
- package/dist/prompts/analogical-reasoner.js +2 -2
- package/dist/prompts/briefing.d.ts +100 -0
- package/dist/prompts/briefing.js +166 -0
- package/dist/prompts/conversation.d.ts +1 -1
- package/dist/prompts/conversation.js +94 -440
- package/dist/prompts/literature-reviewer.d.ts +1 -1
- package/dist/prompts/literature-reviewer.js +10 -10
- package/dist/prompts/planner.js +28 -59
- package/dist/prompts/report-builder.d.ts +1 -1
- package/dist/prompts/report-builder.js +71 -24
- package/dist/prompts/sandbox/bulk-transcriptomics-agent.d.ts +1 -1
- package/dist/prompts/sandbox/bulk-transcriptomics-agent.js +2 -7
- package/dist/prompts/sandbox/cheminformatics-agent.d.ts +1 -1
- package/dist/prompts/sandbox/cheminformatics-agent.js +11 -15
- package/dist/prompts/sandbox/chromatin-agent.d.ts +1 -1
- package/dist/prompts/sandbox/chromatin-agent.js +3 -7
- package/dist/prompts/sandbox/data-profiler.d.ts +1 -1
- package/dist/prompts/sandbox/data-profiler.js +13 -8
- package/dist/prompts/sandbox/dna-methylation-agent.d.ts +1 -1
- package/dist/prompts/sandbox/dna-methylation-agent.js +2 -7
- package/dist/prompts/sandbox/drug-repurposing-agent.d.ts +1 -1
- package/dist/prompts/sandbox/drug-repurposing-agent.js +15 -16
- package/dist/prompts/sandbox/enrichment-agent.d.ts +1 -1
- package/dist/prompts/sandbox/enrichment-agent.js +2 -9
- package/dist/prompts/sandbox/genomic-variant-agent.d.ts +1 -1
- package/dist/prompts/sandbox/genomic-variant-agent.js +2 -6
- package/dist/prompts/sandbox/immune-profiling-agent.d.ts +1 -1
- package/dist/prompts/sandbox/immune-profiling-agent.js +3 -8
- package/dist/prompts/sandbox/metabolomics-agent.d.ts +1 -1
- package/dist/prompts/sandbox/metabolomics-agent.js +1 -7
- package/dist/prompts/sandbox/microbiome-agent.d.ts +1 -1
- package/dist/prompts/sandbox/microbiome-agent.js +2 -7
- package/dist/prompts/sandbox/multi-omics-integration-agent.d.ts +1 -1
- package/dist/prompts/sandbox/multi-omics-integration-agent.js +2 -8
- package/dist/prompts/sandbox/multimodal-sc-agent.d.ts +1 -1
- package/dist/prompts/sandbox/multimodal-sc-agent.js +2 -7
- package/dist/prompts/sandbox/network-agent.d.ts +1 -1
- package/dist/prompts/sandbox/network-agent.js +2 -7
- package/dist/prompts/sandbox/proteomics-agent.d.ts +1 -1
- package/dist/prompts/sandbox/proteomics-agent.js +2 -9
- package/dist/prompts/sandbox/single-cell-agent.d.ts +1 -1
- package/dist/prompts/sandbox/single-cell-agent.js +2 -9
- package/dist/prompts/sandbox/spatial-omics-agent.d.ts +1 -1
- package/dist/prompts/sandbox/spatial-omics-agent.js +3 -6
- package/dist/prompts/sandbox/statistical-modeling-agent.d.ts +1 -1
- package/dist/prompts/sandbox/statistical-modeling-agent.js +2 -7
- package/dist/prompts/sandbox/translational-safety-agent.d.ts +1 -1
- package/dist/prompts/sandbox/translational-safety-agent.js +13 -14
- package/dist/prompts/sandbox-standards.d.ts +22 -14
- package/dist/prompts/sandbox-standards.js +91 -71
- package/dist/prompts/synthesis-agent.d.ts +1 -1
- package/dist/prompts/synthesis-agent.js +33 -131
- package/dist/provenance/collector.js +1 -1
- package/dist/providers/ai-sdk.js +31 -4
- package/dist/providers/prompt-cache.d.ts +74 -0
- package/dist/providers/prompt-cache.js +77 -0
- package/dist/providers/types.d.ts +33 -0
- package/dist/reference-data/catalog.d.ts +131 -0
- package/dist/reference-data/catalog.js +348 -0
- package/dist/reference-data/receipt.d.ts +41 -0
- package/dist/reference-data/receipt.js +40 -0
- package/dist/runtime/boot.d.ts +2 -2
- package/dist/runtime/boot.js +1 -1
- package/dist/runtime/connection-budget.d.ts +2 -2
- package/dist/runtime/connection-budget.js +5 -3
- package/dist/runtime/dbos.d.ts +7 -7
- package/dist/runtime/dbos.js +14 -11
- package/dist/runtime/shutdown.d.ts +2 -2
- package/dist/runtime/shutdown.js +4 -3
- package/dist/sandbox/create-sandbox.d.ts +2 -2
- package/dist/sandbox/docker-client.d.ts +2 -2
- package/dist/sandbox/docker-client.js +4 -1
- package/dist/sandbox/k8s-client.d.ts +3 -0
- package/dist/sandbox/k8s-client.js +5 -4
- package/dist/sandbox/notification-sweep.d.ts +3 -3
- package/dist/sandbox/notification-sweep.js +4 -2
- package/dist/sandbox/reaper.d.ts +3 -3
- package/dist/sandbox/reaper.js +7 -4
- package/dist/sandbox/watchdog.d.ts +3 -3
- package/dist/sandbox/watchdog.js +8 -2
- package/dist/schemas/data-profile-schemas.js +5 -3
- package/dist/schemas/plan-schemas.d.ts +21 -21
- package/dist/schemas/plan-schemas.js +9 -3
- package/dist/schemas/run-synthesis.d.ts +8 -4
- package/dist/schemas/run-synthesis.js +92 -56
- package/dist/schemas/validate-plan.js +1 -1
- package/dist/schemas/workflow-state.d.ts +7 -1
- package/dist/schemas/workflow-state.js +33 -19
- package/dist/state/artifacts.d.ts +13 -0
- package/dist/state/artifacts.js +27 -0
- package/dist/state/data-profile.d.ts +64 -5
- package/dist/state/index.d.ts +3 -3
- package/dist/state/index.js +1 -1
- package/dist/state/init.d.ts +2 -1
- package/dist/state/init.js +5 -6
- package/dist/tasks/data-profile.d.ts +25 -2
- package/dist/tasks/data-profile.js +95 -39
- package/dist/tools/bio/chembl.d.ts +38 -0
- package/dist/tools/bio/chembl.js +138 -0
- package/dist/tools/bio/comptox.d.ts +50 -0
- package/dist/tools/bio/comptox.js +149 -0
- package/dist/tools/bio/get-impc-ko-profile.js +9 -6
- package/dist/tools/bio/index.d.ts +5 -17
- package/dist/tools/bio/index.js +5 -17
- package/dist/tools/bio/keys.d.ts +14 -9
- package/dist/tools/bio/keys.js +16 -16
- package/dist/tools/bio/opentargets.d.ts +38 -0
- package/dist/tools/bio/opentargets.js +89 -0
- package/dist/tools/bio/pubchem.d.ts +29 -0
- package/dist/tools/bio/pubchem.js +92 -0
- package/dist/tools/bio/pubmed.d.ts +51 -0
- package/dist/tools/bio/pubmed.js +100 -0
- package/dist/tools/bio/search-bgee-expression.js +12 -6
- package/dist/tools/bio/search-clinical-trials.js +16 -5
- package/dist/tools/bio/search-dgidb.d.ts +11 -1
- package/dist/tools/bio/search-dgidb.js +92 -78
- package/dist/tools/bio/search-faers.js +8 -4
- package/dist/tools/bio/search-geo-datasets.js +20 -6
- package/dist/tools/bio/search-gwas-catalog.d.ts +1 -1
- package/dist/tools/bio/search-pharmgkb.js +10 -4
- package/dist/tools/display/index.d.ts +1 -0
- package/dist/tools/display/index.js +1 -0
- package/dist/tools/display/normalize-echart-spec.d.ts +61 -0
- package/dist/tools/display/normalize-echart-spec.js +211 -0
- package/dist/tools/display/show-user.d.ts +6 -1
- package/dist/tools/display/show-user.js +25 -12
- package/dist/tools/execute-plan.js +5 -2
- package/dist/tools/iterate-report.d.ts +171 -118
- package/dist/tools/iterate-report.js +336 -96
- package/dist/tools/lib/chembl-client.d.ts +12 -0
- package/dist/tools/lib/chembl-client.js +127 -0
- package/dist/tools/lib/ctx-ops.d.ts +224 -0
- package/dist/tools/lib/ctx-ops.js +450 -0
- package/dist/tools/lib/iuphar-client.js +10 -1
- package/dist/tools/lib/openfda-client.js +11 -3
- package/dist/tools/lib/pathway-client.js +10 -4
- package/dist/tools/lib/pubchem-ops.d.ts +74 -0
- package/dist/tools/lib/pubchem-ops.js +224 -0
- package/dist/tools/memory/update-working-memory.d.ts +45 -7
- package/dist/tools/memory/update-working-memory.js +111 -41
- package/dist/tools/report/index.d.ts +3 -2
- package/dist/tools/report/index.js +3 -2
- package/dist/tools/research/generate-analogy-report.js +25 -12
- package/dist/tools/research/generate-plan.d.ts +12 -5
- package/dist/tools/research/generate-plan.js +168 -37
- package/dist/tools/research/index.d.ts +1 -0
- package/dist/tools/research/index.js +1 -0
- package/dist/tools/research/inspect-data-profile.d.ts +85 -0
- package/dist/tools/research/inspect-data-profile.js +161 -0
- package/dist/tools/research/literature-reviewer.d.ts +3 -0
- package/dist/tools/research/literature-reviewer.js +5 -6
- package/dist/tools/sandbox/list-available-packages.d.ts +79 -5
- package/dist/tools/sandbox/list-available-packages.js +152 -10
- package/dist/tools/sandbox/list-available-refs.d.ts +141 -5
- package/dist/tools/sandbox/list-available-refs.js +647 -134
- package/dist/tools/sandbox/report-blocker.d.ts +39 -9
- package/dist/tools/sandbox/report-blocker.js +43 -20
- package/dist/tools/workspace/execute-command.d.ts +3 -0
- package/dist/tools/workspace/execute-command.js +3 -1
- package/dist/tools/workspace/read-file.js +4 -5
- package/dist/tools/workspace/run-exec.d.ts +4 -4
- package/dist/tools/workspace/run-exec.js +4 -4
- package/dist/tools/workspace/show-file.js +10 -6
- package/dist/tools/workspace/show-plan.js +12 -6
- package/dist/tools/workspace/workspace-search.d.ts +1 -1
- package/dist/tools/workspace/workspace-search.js +11 -5
- package/dist/workflows/execute-analysis.d.ts +46 -4
- package/dist/workflows/execute-analysis.js +118 -13
- package/dist/workflows/execute-target-assessment.d.ts +3 -0
- package/dist/workflows/execute-target-assessment.js +19 -15
- package/dist/workflows/sandbox-step.d.ts +9 -0
- package/dist/workflows/sandbox-step.js +39 -17
- package/dist/workflows/target-assessment/lib/citation-validator.js +2 -2
- package/dist/workflows/target-assessment/lib/clinical-consequence-annotator.js +2 -1
- package/dist/workflows/target-assessment/lib/llm-step.d.ts +3 -0
- package/dist/workflows/target-assessment/lib/llm-step.js +3 -1
- package/dist/workflows/target-assessment/lib/structured-llm.d.ts +3 -0
- package/dist/workflows/target-assessment/lib/structured-llm.js +1 -0
- package/dist/workflows/target-assessment/phase5-persist.d.ts +3 -0
- package/dist/workflows/target-assessment/phase5-persist.js +8 -3
- package/dist/workflows/target-assessment/progress.d.ts +2 -1
- package/dist/workflows/target-assessment/progress.js +4 -3
- package/dist/workspace/filesystem.js +163 -74
- package/dist/workspace/paths.d.ts +2 -2
- package/dist/workspace/paths.js +2 -2
- package/package.json +95 -96
- package/dist/execution/filesystem-artifact-registry.d.ts +0 -57
- package/dist/execution/filesystem-artifact-registry.js +0 -92
- package/dist/lib/identifiers.d.ts +0 -8
- package/dist/lib/identifiers.js +0 -10
- package/dist/lib/mime-detect.d.ts +0 -17
- package/dist/lib/mime-detect.js +0 -29
- package/dist/lib/streamed-download.d.ts +0 -28
- package/dist/lib/streamed-download.js +0 -111
- package/dist/lib/trace-context.d.ts +0 -11
- package/dist/lib/trace-context.js +0 -49
- package/dist/providers/llm-capabilities.d.ts +0 -33
- package/dist/providers/llm-capabilities.js +0 -58
- package/dist/schemas/render-step-prompt.d.ts +0 -32
- package/dist/schemas/render-step-prompt.js +0 -76
- package/dist/tools/bio/find-approval-precedent.d.ts +0 -32
- package/dist/tools/bio/find-approval-precedent.js +0 -72
- package/dist/tools/bio/get-article-details.d.ts +0 -11
- package/dist/tools/bio/get-article-details.js +0 -20
- package/dist/tools/bio/get-article-full-text.d.ts +0 -19
- package/dist/tools/bio/get-article-full-text.js +0 -32
- package/dist/tools/bio/get-bioactivity.d.ts +0 -11
- package/dist/tools/bio/get-bioactivity.js +0 -23
- package/dist/tools/bio/get-drug-info.d.ts +0 -9
- package/dist/tools/bio/get-drug-info.js +0 -22
- package/dist/tools/bio/get-mechanism.d.ts +0 -8
- package/dist/tools/bio/get-mechanism.js +0 -18
- package/dist/tools/bio/get-pubchem-assays.d.ts +0 -22
- package/dist/tools/bio/get-pubchem-assays.js +0 -107
- package/dist/tools/bio/get-pubchem-cross-refs.d.ts +0 -15
- package/dist/tools/bio/get-pubchem-cross-refs.js +0 -68
- package/dist/tools/bio/get-target-safety.d.ts +0 -18
- package/dist/tools/bio/get-target-safety.js +0 -26
- package/dist/tools/bio/search-compounds.d.ts +0 -22
- package/dist/tools/bio/search-compounds.js +0 -160
- package/dist/tools/bio/search-ctx-chemical.d.ts +0 -50
- package/dist/tools/bio/search-ctx-chemical.js +0 -130
- package/dist/tools/bio/search-ctx-exposure.d.ts +0 -55
- package/dist/tools/bio/search-ctx-exposure.js +0 -176
- package/dist/tools/bio/search-ctx-hazard.d.ts +0 -111
- package/dist/tools/bio/search-ctx-hazard.js +0 -178
- package/dist/tools/bio/search-opentargets.d.ts +0 -11
- package/dist/tools/bio/search-opentargets.js +0 -25
- package/dist/tools/bio/search-pubchem-compound.d.ts +0 -26
- package/dist/tools/bio/search-pubchem-compound.js +0 -110
- package/dist/tools/bio/search-pubmed.d.ts +0 -17
- package/dist/tools/bio/search-pubmed.js +0 -31
- package/dist/tools/bio/search-targets.d.ts +0 -9
- package/dist/tools/bio/search-targets.js +0 -20
- package/dist/tools/bio/search-toxcast.d.ts +0 -36
- package/dist/tools/bio/search-toxcast.js +0 -141
- package/dist/workflows/register-workflows.d.ts +0 -51
- package/dist/workflows/register-workflows.js +0 -48
- package/dist/workflows/resume-execute-analysis.d.ts +0 -70
- package/dist/workflows/resume-execute-analysis.js +0 -80
- package/dist/workflows/target-assessment/correction-loop.d.ts +0 -45
- package/dist/workflows/target-assessment/correction-loop.js +0 -62
- package/dist/workflows/target-assessment/steps/phase0-resolve.d.ts +0 -71
- package/dist/workflows/target-assessment/steps/phase0-resolve.js +0 -21
- package/dist/workflows/target-assessment/steps/phase1-aggregate.d.ts +0 -1018
- package/dist/workflows/target-assessment/steps/phase1-aggregate.js +0 -25
- package/dist/workspace/mount-strategy.d.ts +0 -50
- package/dist/workspace/mount-strategy.js +0 -67
- package/dist/workspace/provenance-collector.d.ts +0 -34
- package/dist/workspace/provenance-collector.js +0 -16
- package/dist/workspace/workspace-paths.d.ts +0 -26
- package/dist/workspace/workspace-paths.js +0 -31
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