@inflexa-ai/harness 0.45.1 → 0.46.0
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 +6 -3
- package/dist/agents/conversation-agent.d.ts +9 -3
- package/dist/agents/conversation-agent.js +34 -33
- package/dist/agents/report-session-agent.d.ts +15 -15
- package/dist/agents/report-session-agent.js +23 -15
- package/dist/agents/sandbox/index.d.ts +1 -1
- package/dist/agents/sandbox/index.js +1 -1
- package/dist/agents/sandbox/shared.d.ts +12 -14
- package/dist/agents/sandbox/shared.js +18 -12
- package/dist/agents/sandbox/types.d.ts +4 -4
- package/dist/agents/sandbox/validate-skills.d.ts +2 -2
- package/dist/agents/sandbox/validate-skills.js +3 -1
- package/dist/agents/sandbox-catalog.d.ts +2 -2
- package/dist/agents/sandbox-catalog.js +3 -3
- package/dist/agents/system-prompt.d.ts +2 -2
- package/dist/app/chat-turn-workflow.d.ts +114 -0
- package/dist/app/chat-turn-workflow.js +307 -0
- package/dist/app/chat-turn.d.ts +85 -57
- package/dist/app/chat-turn.js +123 -100
- package/dist/app/data-profile-orientation.js +10 -8
- package/dist/app/data-profile-view.d.ts +4 -4
- package/dist/app/data-profile-view.js +9 -8
- package/dist/app/in-process-turn.d.ts +42 -0
- package/dist/app/in-process-turn.js +139 -0
- package/dist/app/message-assembly.d.ts +10 -4
- package/dist/app/message-assembly.js +13 -8
- package/dist/app/report-session-runtime.d.ts +4 -4
- package/dist/app/report-session-runtime.js +36 -21
- package/dist/app/spawn-report-session.d.ts +33 -28
- package/dist/app/spawn-report-session.js +25 -40
- package/dist/app/synthesize-run.d.ts +22 -16
- package/dist/app/synthesize-run.js +41 -35
- package/dist/app/work.d.ts +96 -0
- package/dist/app/work.js +147 -0
- package/dist/auth/local-auth-context.d.ts +1 -3
- package/dist/auth/local-auth-context.js +1 -3
- package/dist/auth/local-run-authorizer.d.ts +1 -1
- package/dist/auth/local-run-authorizer.js +5 -3
- package/dist/auth/types.d.ts +26 -26
- package/dist/billing/cached-resolver.d.ts +4 -4
- package/dist/billing/run-charge.d.ts +5 -8
- package/dist/billing/run-charge.js +2 -2
- package/dist/billing/usage-recorder.d.ts +9 -9
- package/dist/citations/aggregate.js +1 -1
- package/dist/citations/clients/arxiv.d.ts +2 -2
- package/dist/citations/clients/arxiv.js +12 -4
- package/dist/citations/clients/common.js +4 -2
- package/dist/citations/clients/crossref.d.ts +2 -2
- package/dist/citations/clients/crossref.js +37 -37
- package/dist/citations/clients/doi-registry.js +15 -16
- package/dist/citations/clients/pubmed.d.ts +2 -2
- package/dist/citations/clients/pubmed.js +20 -13
- package/dist/citations/clients/semantic-scholar.d.ts +2 -2
- package/dist/citations/clients/semantic-scholar.js +9 -9
- package/dist/citations/compare.js +2 -2
- package/dist/citations/match.d.ts +2 -2
- package/dist/citations/match.js +12 -7
- package/dist/citations/normalize.js +35 -26
- package/dist/citations/plan.js +6 -2
- package/dist/citations/resolve.d.ts +6 -6
- package/dist/citations/resolve.js +34 -25
- package/dist/citations/types.d.ts +77 -77
- package/dist/config/environment-stores.d.ts +6 -6
- package/dist/config/resource-limits.js +1 -3
- package/dist/contracts/analogy-report.d.ts +7 -7
- package/dist/contracts/analogy-report.js +2 -2
- package/dist/contracts/chat-events.d.ts +38 -24
- package/dist/contracts/chat-frame.d.ts +15 -5
- package/dist/contracts/chat-frame.js +64 -41
- package/dist/contracts/chat-parts.d.ts +130 -67
- package/dist/contracts/chat-parts.js +1 -0
- package/dist/contracts/content-url.js +16 -2
- package/dist/contracts/data-profile.d.ts +38 -38
- package/dist/contracts/index.d.ts +2 -2
- package/dist/contracts/index.js +1 -1
- package/dist/contracts/message.d.ts +6 -6
- package/dist/contracts/organ-system.d.ts +11 -11
- package/dist/contracts/part-registry.d.ts +5 -4
- package/dist/contracts/part-registry.js +5 -0
- package/dist/contracts/profile-vocabulary.d.ts +11 -10
- package/dist/contracts/profile-vocabulary.js +10 -3
- package/dist/contracts/report-blocks.d.ts +329 -329
- package/dist/contracts/report-reference.d.ts +105 -81
- package/dist/contracts/report-reference.js +30 -13
- package/dist/contracts/schemas/chat-events.d.ts +30 -16
- package/dist/contracts/schemas/chat-events.js +15 -6
- package/dist/contracts/schemas/chat-parts.d.ts +175 -102
- package/dist/contracts/schemas/chat-parts.js +33 -7
- package/dist/contracts/severity.d.ts +1 -1
- package/dist/contracts/structure-source.d.ts +3 -3
- package/dist/contracts/structure-source.js +6 -2
- package/dist/contracts/subagent-activity.d.ts +2 -2
- package/dist/contracts/subagent-activity.js +5 -3
- package/dist/contracts/usage.d.ts +2 -2
- package/dist/data/safety-panel-schema.d.ts +25 -25
- package/dist/data/safety-panel-schema.js +13 -4
- package/dist/execution/artifact-metadata.d.ts +23 -15
- package/dist/execution/artifact-metadata.js +33 -10
- package/dist/execution/artifact-record.d.ts +2 -2
- package/dist/execution/artifact-registration.d.ts +5 -5
- package/dist/execution/artifact-registry.d.ts +8 -8
- package/dist/execution/dbos-run-launcher.d.ts +24 -4
- package/dist/execution/dbos-run-launcher.js +58 -4
- package/dist/execution/dbos-workflow-purger.d.ts +5 -6
- package/dist/execution/dbos-workflow-purger.js +8 -7
- package/dist/execution/input-signature.d.ts +2 -2
- package/dist/execution/post-step-pipeline.d.ts +9 -9
- package/dist/execution/post-step-pipeline.js +1 -1
- package/dist/execution/post-step.js +2 -2
- package/dist/execution/reconcile-manifest.d.ts +4 -4
- package/dist/execution/reconcile-manifest.js +3 -2
- package/dist/execution/run-authorizer.d.ts +46 -37
- package/dist/execution/run-authorizer.js +8 -8
- package/dist/execution/run-canceler.d.ts +7 -7
- package/dist/execution/run-canceler.js +14 -7
- package/dist/execution/run-end-record.d.ts +2 -3
- package/dist/execution/run-event-parts.d.ts +0 -8
- package/dist/execution/run-event-parts.js +29 -24
- package/dist/execution/run-event-stream.d.ts +8 -8
- package/dist/execution/run-event-stream.js +3 -4
- package/dist/execution/run-launcher.d.ts +4 -4
- package/dist/execution/run-synthesis.d.ts +49 -48
- package/dist/execution/run-synthesis.js +96 -255
- package/dist/execution/staged-input.d.ts +2 -2
- package/dist/execution/step-summary.d.ts +6 -6
- package/dist/execution/step-summary.js +4 -8
- package/dist/execution/topo-sort.js +4 -3
- package/dist/execution/workflow-purger.d.ts +2 -2
- package/dist/index.d.ts +17 -20
- package/dist/index.js +25 -36
- package/dist/input-sanitization.js +9 -2
- package/dist/input-scan/clustering.d.ts +6 -6
- package/dist/input-scan/clustering.js +11 -5
- package/dist/input-scan/companions.js +3 -2
- package/dist/input-scan/detect-sets.d.ts +2 -2
- package/dist/input-scan/detect-sets.js +25 -21
- package/dist/input-scan/enrich.d.ts +6 -6
- package/dist/input-scan/enrich.js +29 -12
- package/dist/input-scan/formats.d.ts +2 -2
- package/dist/input-scan/formats.js +8 -2
- package/dist/input-scan/markers.d.ts +2 -2
- package/dist/input-scan/markers.js +14 -5
- package/dist/input-scan/menu.d.ts +10 -10
- package/dist/input-scan/menu.js +0 -0
- package/dist/input-scan/quarantine.d.ts +2 -2
- package/dist/input-scan/quarantine.js +23 -18
- package/dist/input-scan/readout-budget.d.ts +2 -2
- package/dist/input-scan/readout-budget.js +1 -1
- package/dist/input-scan/readout.d.ts +2 -2
- package/dist/input-scan/readout.js +47 -34
- package/dist/input-scan/scan.d.ts +2 -2
- package/dist/input-scan/scan.js +7 -5
- package/dist/input-scan/set-types.d.ts +28 -28
- package/dist/input-scan/shapes.d.ts +4 -4
- package/dist/input-scan/shapes.js +0 -0
- package/dist/input-scan/templates.d.ts +10 -10
- package/dist/input-scan/templates.js +30 -22
- package/dist/input-scan/tokens.d.ts +6 -4
- package/dist/input-scan/tokens.js +100 -38
- package/dist/input-scan/types.d.ts +22 -22
- package/dist/lib/async-utils.d.ts +3 -7
- package/dist/lib/async-utils.js +5 -9
- package/dist/lib/cache.js +1 -1
- package/dist/lib/chrome.d.ts +46 -6
- package/dist/lib/console-logger.js +2 -2
- package/dist/lib/db-result.d.ts +22 -6
- package/dist/lib/db-result.js +9 -13
- package/dist/lib/eyes.d.ts +4 -4
- package/dist/lib/eyes.js +1 -1
- package/dist/lib/fs-helpers.js +18 -6
- package/dist/lib/fs-result.d.ts +1 -0
- package/dist/lib/fs-result.js +5 -6
- package/dist/lib/hooks.d.ts +23 -7
- package/dist/lib/hooks.js +17 -3
- package/dist/lib/host-concurrency.js +3 -2
- package/dist/lib/logger.d.ts +2 -2
- package/dist/lib/logger.js +2 -1
- package/dist/lib/metrics.d.ts +1 -1
- package/dist/lib/null-proto.d.ts +6 -0
- package/dist/lib/null-proto.js +17 -0
- package/dist/lib/otel-spans.d.ts +1 -1
- package/dist/lib/otel-spans.js +9 -5
- package/dist/lib/otel.d.ts +4 -2
- package/dist/lib/otel.js +10 -2
- package/dist/lib/page-capture.d.ts +8 -8
- package/dist/lib/page-capture.js +9 -4
- package/dist/lib/parse-json.d.ts +5 -0
- package/dist/lib/parse-json.js +12 -0
- package/dist/lib/present.d.ts +12 -0
- package/dist/lib/present.js +39 -0
- package/dist/lib/rate-limit.d.ts +4 -4
- package/dist/lib/rate-limit.js +12 -13
- package/dist/lib/regulatory-corpus/fetch-fda-guidance.d.ts +4 -4
- package/dist/lib/regulatory-corpus/fetch-fda-guidance.js +4 -10
- package/dist/lib/regulatory-corpus/fetch-ich.d.ts +4 -4
- package/dist/lib/regulatory-corpus/fetch-ich.js +18 -14
- package/dist/lib/regulatory-corpus/normalize-whitespace.d.ts +6 -0
- package/dist/lib/regulatory-corpus/normalize-whitespace.js +41 -0
- package/dist/lib/regulatory-corpus.d.ts +10 -10
- package/dist/lib/regulatory-corpus.js +3 -1
- package/dist/lib/result.d.ts +10 -11
- package/dist/lib/result.js +15 -13
- package/dist/lib/storage.d.ts +2 -2
- package/dist/lib/test/async-iterable.d.ts +9 -0
- package/dist/lib/test/async-iterable.js +28 -0
- package/dist/lib/test/request-url.d.ts +5 -0
- package/dist/lib/test/request-url.js +7 -0
- package/dist/lib/test/result-assert.d.ts +12 -0
- package/dist/lib/test/result-assert.js +17 -0
- package/dist/lib/test/text-shapes.d.ts +24 -0
- package/dist/lib/test/text-shapes.js +63 -0
- package/dist/lib/text.d.ts +22 -0
- package/dist/lib/text.js +68 -0
- package/dist/lib/thrown.d.ts +18 -0
- package/dist/lib/thrown.js +30 -0
- package/dist/lib/unknown-array.d.ts +6 -0
- package/dist/lib/unknown-array.js +8 -0
- package/dist/lib/unknown-containers.d.ts +14 -0
- package/dist/lib/unknown-containers.js +17 -0
- package/dist/lib/unknown-text.d.ts +8 -0
- package/dist/lib/unknown-text.js +28 -0
- package/dist/lib/zod-issue-shape.d.ts +1 -1
- package/dist/lib/zod-issue-shape.js +31 -31
- package/dist/lib/zod-issues.d.ts +3 -3
- package/dist/lib/zod-issues.js +30 -17
- package/dist/literature/sources/arxiv.d.ts +6 -6
- package/dist/literature/sources/arxiv.js +92 -35
- package/dist/literature/sources/http.d.ts +2 -2
- package/dist/literature/sources/http.js +16 -15
- package/dist/literature/sources/pubmed.d.ts +16 -16
- package/dist/literature/sources/pubmed.js +96 -61
- package/dist/literature/sources/semantic-scholar.d.ts +8 -8
- package/dist/literature/sources/semantic-scholar.js +22 -13
- package/dist/loop/accounting.d.ts +63 -0
- package/dist/loop/accounting.js +141 -0
- package/dist/loop/call-policy.d.ts +73 -0
- package/dist/loop/call-policy.js +109 -0
- package/dist/loop/chat-stream.d.ts +62 -0
- package/dist/loop/chat-stream.js +237 -0
- package/dist/loop/compaction.d.ts +9 -9
- package/dist/loop/compaction.js +1 -1
- package/dist/loop/metrics.d.ts +12 -15
- package/dist/loop/metrics.js +14 -26
- package/dist/loop/run-loop.d.ts +233 -0
- package/dist/loop/run-loop.js +770 -0
- package/dist/loop/sub-agent.d.ts +61 -0
- package/dist/loop/sub-agent.js +161 -0
- package/dist/loop/tool-adapter.d.ts +98 -0
- package/dist/loop/tool-adapter.js +364 -0
- package/dist/loop/tool-detail.d.ts +1 -1
- package/dist/loop/tool-detail.js +6 -5
- package/dist/loop/tool-outcome.d.ts +1 -1
- package/dist/loop/tool-output.d.ts +4 -4
- package/dist/loop/tool-output.js +2 -2
- package/dist/loop/turn-credentials.d.ts +34 -0
- package/dist/loop/turn-credentials.js +73 -0
- package/dist/loop/types.d.ts +29 -38
- package/dist/loop/types.js +2 -7
- package/dist/memory/ai-sdk-message-storage.d.ts +5 -5
- package/dist/memory/ai-sdk-message-storage.js +13 -11
- package/dist/memory/card-builders.d.ts +14 -14
- package/dist/memory/card-builders.js +19 -15
- package/dist/memory/conversation-display-recorder.d.ts +22 -4
- package/dist/memory/conversation-display-recorder.js +43 -24
- package/dist/memory/conversation-display-replay.js +3 -2
- package/dist/memory/conversation-display-storage.d.ts +15 -7
- package/dist/memory/conversation-display-storage.js +141 -36
- package/dist/memory/conversation-view.d.ts +4 -4
- package/dist/memory/conversation-view.js +5 -4
- package/dist/memory/count-tokens.js +10 -8
- package/dist/memory/derive-thread-title.d.ts +0 -13
- package/dist/memory/derive-thread-title.js +2 -1
- package/dist/memory/message-backfill.d.ts +12 -5
- package/dist/memory/message-backfill.js +5 -3
- package/dist/memory/thread-history.d.ts +36 -21
- package/dist/memory/thread-history.js +78 -54
- package/dist/memory/thread-store.d.ts +26 -17
- package/dist/memory/thread-store.js +15 -9
- package/dist/memory/tool-call-integrity.d.ts +2 -2
- package/dist/memory/tool-call-integrity.js +4 -3
- package/dist/memory/working-memory.d.ts +16 -12
- package/dist/memory/working-memory.js +72 -61
- package/dist/prompts/briefing.d.ts +12 -12
- package/dist/prompts/briefing.js +1 -1
- package/dist/prompts/synthesis-agent.d.ts +1 -1
- package/dist/prompts/synthesis-agent.js +6 -14
- package/dist/provenance/collector.d.ts +6 -6
- package/dist/provenance/collector.js +15 -8
- package/dist/provenance/exec-frame.d.ts +2 -2
- package/dist/provenance/exec-frame.js +6 -1
- package/dist/provenance/seam.d.ts +1 -4
- package/dist/provenance/types.d.ts +6 -6
- package/dist/providers/ai-sdk.d.ts +113 -62
- package/dist/providers/ai-sdk.js +283 -518
- package/dist/providers/embedding.d.ts +2 -2
- package/dist/providers/embedding.js +1 -1
- package/dist/providers/errors.d.ts +22 -2
- package/dist/providers/errors.js +98 -50
- package/dist/providers/prompt-cache.d.ts +8 -8
- package/dist/providers/prompt-cache.js +13 -11
- package/dist/providers/reasoning.d.ts +2 -2
- package/dist/providers/reasoning.js +2 -2
- package/dist/providers/types.d.ts +55 -94
- package/dist/reference-data/catalog.d.ts +2 -15
- package/dist/reference-data/catalog.js +25 -8
- package/dist/reference-data/receipt.d.ts +2 -2
- package/dist/report-model/assert-rules.js +1 -1
- package/dist/report-model/authoring-grammar.d.ts +211 -233
- package/dist/report-model/block-walk.d.ts +10 -10
- package/dist/report-model/block-walk.js +2 -0
- package/dist/report-model/draft-finish.d.ts +8 -8
- package/dist/report-model/draft-finish.js +1 -1
- package/dist/report-model/draft-hash.js +8 -7
- package/dist/report-model/draft-operations.d.ts +22 -10
- package/dist/report-model/draft-operations.js +48 -30
- package/dist/report-model/draft-read.d.ts +19 -7
- package/dist/report-model/draft-read.js +16 -6
- package/dist/report-model/draft.d.ts +844 -2
- package/dist/report-model/draft.js +3 -1
- package/dist/report-model/fixture-resolver.js +39 -16
- package/dist/report-model/pin-snapshot.d.ts +2 -2
- package/dist/report-model/pin-snapshot.js +15 -15
- package/dist/report-model/production-resolver.d.ts +18 -18
- package/dist/report-model/production-resolver.js +50 -42
- package/dist/report-model/reference-resolver.d.ts +26 -10
- package/dist/report-model/reference-resolver.js +68 -5
- package/dist/report-model/reference-stamp.js +30 -38
- package/dist/report-model/structural-validation.js +12 -4
- package/dist/report-model/validate.d.ts +7 -7
- package/dist/report-model/validate.js +6 -6
- package/dist/report-render/assets.d.ts +2 -2
- package/dist/report-render/assets.js +27 -3
- package/dist/report-render/chart-export.d.ts +10 -2
- package/dist/report-render/chart-export.js +37 -11
- package/dist/report-render/chart-presets.d.ts +8 -8
- package/dist/report-render/chart-presets.js +3 -3
- package/dist/report-render/chart-renderers.d.ts +23 -16
- package/dist/report-render/chart-renderers.js +74 -53
- package/dist/report-render/chart-toolbox.d.ts +2 -2
- package/dist/report-render/chart-toolbox.js +7 -6
- package/dist/report-render/chart.d.ts +15 -16
- package/dist/report-render/chart.js +369 -252
- package/dist/report-render/design.d.ts +36 -297
- package/dist/report-render/design.js +0 -12
- package/dist/report-render/figures/common.d.ts +12 -12
- package/dist/report-render/figures/common.js +42 -31
- package/dist/report-render/figures/dendrogram.d.ts +3 -3
- package/dist/report-render/figures/dendrogram.js +10 -10
- package/dist/report-render/figures/dense.js +15 -8
- package/dist/report-render/figures/dotplot.js +46 -33
- package/dist/report-render/figures/embedding.js +52 -43
- package/dist/report-render/figures/equal-units.d.ts +10 -10
- package/dist/report-render/figures/equal-units.js +27 -27
- package/dist/report-render/figures/forest.js +9 -7
- package/dist/report-render/figures/gsea.js +21 -11
- package/dist/report-render/figures/heatmap.js +13 -9
- package/dist/report-render/figures/index.d.ts +10 -10
- package/dist/report-render/figures/index.js +4 -2
- package/dist/report-render/figures/km.js +10 -9
- package/dist/report-render/figures/label-room.d.ts +12 -12
- package/dist/report-render/figures/label-room.js +7 -2
- package/dist/report-render/figures/locuszoom.d.ts +2 -2
- package/dist/report-render/figures/locuszoom.js +59 -31
- package/dist/report-render/figures/lollipop.js +3 -2
- package/dist/report-render/figures/ma.js +8 -4
- package/dist/report-render/figures/manhattan.d.ts +1 -2
- package/dist/report-render/figures/manhattan.js +52 -34
- package/dist/report-render/figures/oncoprint.js +4 -5
- package/dist/report-render/figures/pca.js +25 -11
- package/dist/report-render/figures/qq.js +20 -9
- package/dist/report-render/figures/roc.js +1 -1
- package/dist/report-render/figures/sankey.d.ts +2 -2
- package/dist/report-render/figures/sankey.js +11 -10
- package/dist/report-render/figures/upset.d.ts +6 -6
- package/dist/report-render/figures/upset.js +7 -4
- package/dist/report-render/figures/volcano.js +12 -10
- package/dist/report-render/hybrid-svg.d.ts +4 -4
- package/dist/report-render/hybrid-svg.js +7 -5
- package/dist/report-render/number-format.d.ts +4 -4
- package/dist/report-render/number-format.js +62 -27
- package/dist/report-render/page.js +2 -1
- package/dist/report-render/provenance-data.d.ts +2 -2
- package/dist/report-render/references.d.ts +4 -4
- package/dist/report-render/render.d.ts +2 -2
- package/dist/report-render/render.js +10 -11
- package/dist/report-render/script-json.js +1 -1
- package/dist/report-render/table-data.d.ts +6 -6
- package/dist/report-render/test/options.d.ts +49 -0
- package/dist/report-render/test/options.js +143 -0
- package/dist/report-render/test/page-function.d.ts +19 -0
- package/dist/report-render/test/page-function.js +33 -0
- package/dist/report-render/types.d.ts +10 -10
- package/dist/report-render/value-bridge.d.ts +4 -4
- package/dist/report-render/value-bridge.js +27 -14
- package/dist/report-render/views/chart-view.d.ts +2 -2
- package/dist/report-render/views/chart-view.js +2 -2
- package/dist/report-render/views/lineage.d.ts +6 -6
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- package/dist/loop/continue-agent.d.ts +0 -40
- package/dist/loop/continue-agent.js +0 -38
- package/dist/loop/genai-spans.d.ts +0 -47
- package/dist/loop/genai-spans.js +0 -134
- package/dist/loop/run-agent.d.ts +0 -245
- package/dist/loop/run-agent.js +0 -1124
- package/dist/loop/run-step.d.ts +0 -29
- package/dist/loop/run-step.js +0 -34
- package/dist/loop/run-to-terminal.d.ts +0 -66
- package/dist/loop/run-to-terminal.js +0 -93
- package/dist/loop/tool-mask.d.ts +0 -23
- package/dist/loop/tool-mask.js +0 -46
- package/dist/providers/streaming-chat.d.ts +0 -32
- package/dist/providers/streaming-chat.js +0 -91
- package/dist/tasks/derive-table-exec.d.ts +0 -54
- package/dist/tasks/derive-table-exec.js +0 -86
- package/dist/workflows/suspension.d.ts +0 -32
- package/dist/workflows/suspension.js +0 -38
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import { z } from "zod";
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export const FileMetadataSchema = z
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.object({
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/** Step schema for planner output — omits fields populated at execution time
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constraints: z.ZodOptional<z.ZodArray<z.ZodString>>;
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caveats: z.ZodOptional<z.ZodArray<z.ZodString>>;
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export declare const SynthesizedFindingSchema: z.ZodObject<{
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expected: "expected";
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"preclinical-validation": "preclinical-validation";
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"biomarker-candidate": "biomarker-candidate";
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"clinical-evidence": "clinical-evidence";
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discovery: "discovery";
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none: "none";
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"
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"patient-stratification": "patient-stratification";
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"pharmacodynamic-biomarker": "pharmacodynamic-biomarker";
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"predictive-biomarker": "predictive-biomarker";
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"prognostic-biomarker": "prognostic-biomarker";
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"pharmacodynamic-biomarker": "pharmacodynamic-biomarker";
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"safety-signal": "safety-signal";
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"resistance-mechanism": "resistance-mechanism";
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"safety-signal": "safety-signal";
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"therapeutic-target": "therapeutic-target";
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}>>;
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}, z.core.$strip>>;
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@@ -92,16 +92,16 @@ export declare const RunSynthesisSchema: z.ZodObject<{
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novel: "novel";
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confirmed: "confirmed";
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partially_confirmed: "partially_confirmed";
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expected: "expected";
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literatureInterpretation: z.ZodString;
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references: z.ZodArray<z.ZodObject<{
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@@ -109,29 +109,29 @@ export declare const RunSynthesisSchema: z.ZodObject<{
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contextualizes: "contextualizes";
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supports: "supports";
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}, z.core.$strip>>;
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stage: z.ZodEnum<{
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discovery: "discovery";
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"preclinical-validation": "preclinical-validation";
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"biomarker-candidate": "biomarker-candidate";
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"clinical-evidence": "clinical-evidence";
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discovery: "discovery";
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}>;
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contradicted: "contradicted";
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novel: "novel";
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}>;
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citation: z.ZodString;
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relevance: z.ZodString;
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supports: "supports";
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discovery: "discovery";
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none: "none";
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rationale: z.ZodString;
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}, z.core.$strip>>;
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}, z.core.$strip>>;
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name: z.ZodString;
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}, z.core.$strip>>;
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narrative: z.ZodString;
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limitations: z.ZodArray<z.ZodString>;
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keyReferences: z.ZodArray<z.ZodObject<{
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description: z.ZodString;
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}, z.core.$strip>>;
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description: z.string().describe("What the paper establishes and why it is key to this run."),
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});
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overview: z
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.string()
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.describe("2-4 sentences: the run's scope, the top-line result, and the most important takeaway. " +
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.array(KeyReferenceSchema)
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.describe("The 5-10 most important papers across all findings. Prioritize those that directly validate, contradict, or extend the findings — do not pad with background citations."),
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});
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/** The synthesis that the synthesizer submits. The host stamps the run id, thus the model never types it. */
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export const SynthesisDraftSchema = RunSynthesisSchema.omit({ runId: true });
|
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@@ -13,11 +13,11 @@
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*/
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import type { ResourceLimits } from "../config/resource-limits.js";
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import type { AnalysisPlan } from "./workflow-state.js";
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export
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export type ValidationResult = {
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valid: boolean;
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errors: string[];
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}
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export
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};
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export type ValidatePlanOptions = {
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/**
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* Host per-step resource ceilings. When present, a step whose declared
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* `resources` exceed them is an error — the planner gets actionable
|
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* sandbox-creation clamp remains their backstop).
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*/
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}
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+
};
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/** Derive a filesystem-safe output prefix from a step ID. */
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/**
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@@ -11,6 +11,8 @@
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* 3. All agent assignments exist in the agent catalog
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* 4. All steps have resources defined
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*/
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+
import { errorMessageOf } from "../lib/thrown.js";
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+
import { textOf } from "../lib/unknown-text.js";
|
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import { KNOWN_AGENT_IDS } from "../agents/sandbox-catalog.js";
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import { CycleError, DependencyError, topoSortIntoWaves } from "../execution/topo-sort.js";
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import { parseQuery } from "../sandbox/package-identity.js";
|
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@@ -52,10 +54,20 @@ function describeParseError(stepId, entry, error) {
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|
}
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/** Derive a filesystem-safe output prefix from a step ID. */
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|
export function deriveOutputPrefix(stepId) {
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|
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let out = "";
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|
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let inRun = false;
|
|
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|
+
for (const char of stepId.toLowerCase()) {
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|
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|
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const isSlugChar = (char >= "a" && char <= "z") || (char >= "0" && char <= "9");
|
|
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|
+
if (!isSlugChar) {
|
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|
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inRun = true;
|
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|
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continue;
|
|
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|
+
}
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|
+
if (inRun && out.length > 0)
|
|
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|
+
out += "-";
|
|
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|
+
inRun = false;
|
|
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|
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out += char;
|
|
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|
+
}
|
|
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|
+
return out;
|
|
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|
}
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|
/**
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* Validate an analysis plan for structural correctness.
|
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@@ -80,7 +92,7 @@ export function validatePlan(plan, options) {
|
|
|
80
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|
errors.push(`Step "${err.stepId}" depends on "${err.missingDependency}" which does not exist in the plan`);
|
|
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|
}
|
|
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|
else {
|
|
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|
-
errors.push(`Topological sort failed: ${err
|
|
95
|
+
errors.push(`Topological sort failed: ${errorMessageOf(err) ?? textOf(err)}`);
|
|
84
96
|
}
|
|
85
97
|
}
|
|
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|
// 2. Output prefix uniqueness
|
|
@@ -30,9 +30,9 @@ export type GroundingSetting = z.infer<typeof GroundingSettingSchema>;
|
|
|
30
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|
*/
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|
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|
export declare const GroundingSchema: z.ZodObject<{
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|
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flagged: "flagged";
|
|
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grounded: "grounded";
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|
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ungrounded: "ungrounded";
|
|
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|
-
flagged: "flagged";
|
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|
}>;
|
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|
snapshot: z.ZodString;
|
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|
|
@@ -65,10 +65,10 @@ export declare const AnalysisStepSchema: z.ZodObject<{
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depends_on: z.ZodArray<z.ZodString>;
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status: z.ZodDefault<z.ZodEnum<{
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running: "running";
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completed: "completed";
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skipped: "skipped";
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}>>;
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|
|
@@ -80,9 +80,9 @@ export declare const AnalysisStepSchema: z.ZodObject<{
|
|
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80
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}, z.core.$strip>>;
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grounding: z.ZodOptional<z.ZodObject<{
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flagged: "flagged";
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grounded: "grounded";
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flagged: "flagged";
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|
}>;
|
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snapshot: z.ZodString;
|
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|
|
@@ -120,10 +120,10 @@ export declare const AnalysisPlanSchema: z.ZodObject<{
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depends_on: z.ZodArray<z.ZodString>;
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completed: "completed";
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pending: "pending";
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running: "running";
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completed: "completed";
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skipped: "skipped";
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}>>;
|
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|
|
@@ -135,9 +135,9 @@ export declare const AnalysisPlanSchema: z.ZodObject<{
|
|
|
135
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|
}, z.core.$strip>>;
|
|
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grounding: z.ZodOptional<z.ZodObject<{
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flagged: "flagged";
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grounded: "grounded";
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flagged: "flagged";
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|
}>;
|
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snapshot: z.ZodString;
|
|
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claims: z.ZodArray<z.ZodString>;
|
|
@@ -210,10 +210,10 @@ export declare const ContentBlockSchema: z.ZodDiscriminatedUnion<[z.ZodObject<{
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|
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packages: z.ZodOptional<z.ZodArray<z.ZodString>>;
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depends_on: z.ZodArray<z.ZodString>;
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|
+
completed: "completed";
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|
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pending: "pending";
|
|
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running: "running";
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|
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completed: "completed";
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skipped: "skipped";
|
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|
}>>;
|
|
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|
|
@@ -225,9 +225,9 @@ export declare const ContentBlockSchema: z.ZodDiscriminatedUnion<[z.ZodObject<{
|
|
|
225
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|
}, z.core.$strip>>;
|
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|
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|
+
flagged: "flagged";
|
|
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grounded: "grounded";
|
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|
ungrounded: "ungrounded";
|
|
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|
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flagged: "flagged";
|
|
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|
}>;
|
|
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|
snapshot: z.ZodString;
|
|
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|
|
@@ -255,7 +255,7 @@ export declare const ContentBlockSchema: z.ZodDiscriminatedUnion<[z.ZodObject<{
|
|
|
255
255
|
}, z.core.$strip>;
|
|
256
256
|
}, z.core.$strip>, z.ZodObject<{
|
|
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|
type: z.ZodLiteral<"json">;
|
|
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|
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data: z.ZodRecord<z.ZodString, z.
|
|
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|
+
data: z.ZodRecord<z.ZodString, z.ZodJSONSchema>;
|
|
259
259
|
label: z.ZodOptional<z.ZodString>;
|
|
260
260
|
}, z.core.$strip>, z.ZodObject<{
|
|
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261
|
type: z.ZodLiteral<"text">;
|
|
@@ -271,16 +271,16 @@ export declare const ContentBlockSchema: z.ZodDiscriminatedUnion<[z.ZodObject<{
|
|
|
271
271
|
*/
|
|
272
272
|
export declare const SuspensionActionSchema: z.ZodObject<{
|
|
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273
|
label: z.ZodString;
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|
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value: z.ZodRecord<z.ZodString, z.
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|
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value: z.ZodRecord<z.ZodString, z.ZodJSONSchema>;
|
|
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275
|
variant: z.ZodOptional<z.ZodEnum<{
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|
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|
default: "default";
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|
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|
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outline: "outline";
|
|
278
277
|
destructive: "destructive";
|
|
278
|
+
outline: "outline";
|
|
279
279
|
}>>;
|
|
280
280
|
icon: z.ZodOptional<z.ZodEnum<{
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|
+
"alert-circle": "alert-circle";
|
|
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282
|
check: "check";
|
|
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283
|
x: "x";
|
|
283
|
-
"alert-circle": "alert-circle";
|
|
284
284
|
}>>;
|
|
285
285
|
}, z.core.$strip>;
|
|
286
286
|
/**
|
|
@@ -297,9 +297,9 @@ export declare const SuspensionInputSchema: z.ZodObject<{
|
|
|
297
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|
key: z.ZodString;
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|
298
298
|
label: z.ZodString;
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|
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299
|
type: z.ZodEnum<{
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|
+
select: "select";
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|
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|
text: "text";
|
|
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302
|
textarea: "textarea";
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|
-
select: "select";
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|
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|
}>;
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|
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304
|
placeholder: z.ZodOptional<z.ZodString>;
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|
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required: z.ZodOptional<z.ZodBoolean>;
|
|
@@ -348,10 +348,10 @@ export declare const SuspensionPayloadSchema: z.ZodObject<{
|
|
|
348
348
|
packages: z.ZodOptional<z.ZodArray<z.ZodString>>;
|
|
349
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|
depends_on: z.ZodArray<z.ZodString>;
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|
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|
status: z.ZodDefault<z.ZodEnum<{
|
|
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|
+
completed: "completed";
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|
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|
failed: "failed";
|
|
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|
pending: "pending";
|
|
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|
running: "running";
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|
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|
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completed: "completed";
|
|
355
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|
skipped: "skipped";
|
|
356
356
|
}>>;
|
|
357
357
|
resources: z.ZodOptional<z.ZodObject<{
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@@ -363,9 +363,9 @@ export declare const SuspensionPayloadSchema: z.ZodObject<{
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}, z.core.$strip>>;
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grounding: z.ZodOptional<z.ZodObject<{
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status: z.ZodEnum<{
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+
flagged: "flagged";
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grounded: "grounded";
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ungrounded: "ungrounded";
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-
flagged: "flagged";
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}>;
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snapshot: z.ZodString;
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claims: z.ZodArray<z.ZodString>;
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@@ -393,7 +393,7 @@ export declare const SuspensionPayloadSchema: z.ZodObject<{
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}, z.core.$strip>;
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}, z.core.$strip>, z.ZodObject<{
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type: z.ZodLiteral<"json">;
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data: z.ZodRecord<z.ZodString, z.
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+
data: z.ZodRecord<z.ZodString, z.ZodJSONSchema>;
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label: z.ZodOptional<z.ZodString>;
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}, z.core.$strip>, z.ZodObject<{
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type: z.ZodLiteral<"text">;
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@@ -401,25 +401,25 @@ export declare const SuspensionPayloadSchema: z.ZodObject<{
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}, z.core.$strip>], "type">>>;
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actions: z.ZodArray<z.ZodObject<{
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label: z.ZodString;
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value: z.ZodRecord<z.ZodString, z.
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value: z.ZodRecord<z.ZodString, z.ZodJSONSchema>;
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variant: z.ZodOptional<z.ZodEnum<{
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default: "default";
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outline: "outline";
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destructive: "destructive";
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+
outline: "outline";
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}>>;
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icon: z.ZodOptional<z.ZodEnum<{
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+
"alert-circle": "alert-circle";
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check: "check";
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x: "x";
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-
"alert-circle": "alert-circle";
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}>>;
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}, z.core.$strip>>;
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inputs: z.ZodOptional<z.ZodArray<z.ZodObject<{
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key: z.ZodString;
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label: z.ZodString;
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type: z.ZodEnum<{
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+
select: "select";
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text: "text";
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textarea: "textarea";
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-
select: "select";
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}>;
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placeholder: z.ZodOptional<z.ZodString>;
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required: z.ZodOptional<z.ZodBoolean>;
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@@ -161,7 +161,7 @@ export const ContentBlockSchema = z.discriminatedUnion("type", [
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z.object({ type: z.literal("plan"), plan: AnalysisPlanSchema }),
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z.object({
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type: z.literal("json"),
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data: z.record(z.string(), z.
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+
data: z.record(z.string(), z.json()),
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label: z.string().optional(),
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}),
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z.object({ type: z.literal("text"), text: z.string() }),
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@@ -176,7 +176,7 @@ export const ContentBlockSchema = z.discriminatedUnion("type", [
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*/
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export const SuspensionActionSchema = z.object({
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label: z.string(),
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value: z.record(z.string(), z.
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+
value: z.record(z.string(), z.json()),
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variant: z.enum(["default", "outline", "destructive"]).optional(),
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icon: z.enum(["check", "x", "alert-circle"]).optional(),
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});
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