@inflexa-ai/harness 0.16.0 → 0.18.0

package/dist/citations/types.js

@@ -0,0 +1,129 @@
+import { z } from "zod";
+export const CitationKindSchema = z.enum(["doi", "pmid", "arxiv", "free_text", "auto"]);
+export const CitationInputSchema = z.object({
+    citation: z.string().trim().min(1).max(5_000),
+    kind: CitationKindSchema.optional(),
+    title: z.string().trim().min(1).max(2_000).optional(),
+    authors: z.array(z.string().trim().min(1).max(500)).max(500).optional(),
+    year: z.number().int().min(1000).max(3000).optional(),
+    venue: z.string().trim().min(1).max(1_000).optional(),
+    volume: z.string().trim().min(1).max(100).optional(),
+    firstPage: z.string().trim().min(1).max(100).optional(),
+});
+export const CitationSourceSchema = z.enum(["doi_registry", "crossref", "pubmed", "arxiv", "semantic_scholar"]);
+export const CitationSourceStatusSchema = z.enum(["ok", "no_data", "unavailable", "not_applicable"]);
+export const CitationVerdictSchema = z.enum(["verified", "metadata_mismatch", "not_found", "unverifiable", "inconclusive"]);
+export const CitationCoverageSchema = z.enum(["complete", "partial", "none"]);
+export const ComparisonStatusSchema = z.enum(["match", "mismatch", "not_compared"]);
+export const CitationFieldSchema = z.enum(["title", "authors", "year", "venue", "volume", "firstPage"]);
+export const UnsupportedWorkKindSchema = z.enum(["personal_communication", "unpublished", "unregistered_in_press"]);
+export const CitationIdentifiersSchema = z.object({
+    doi: z.string().optional(),
+    pmid: z.string().optional(),
+    arxiv: z.string().optional(),
+    corpusId: z.string().optional(),
+});
+export const NormalizedCitationMetadataSchema = z.object({
+    title: z.string().optional(),
+    authors: z.array(z.string()).optional(),
+    year: z.number().int().optional(),
+    venue: z.string().optional(),
+    volume: z.string().optional(),
+    firstPage: z.string().optional(),
+});
+export const NormalizedCitationSchema = z.object({
+    citation: z.string(),
+    query: z.string(),
+    kind: z.enum(["doi", "pmid", "arxiv", "free_text"]),
+    identifiers: CitationIdentifiersSchema,
+    supplied: NormalizedCitationMetadataSchema,
+    unsupportedWorkKind: UnsupportedWorkKindSchema.optional(),
+});
+export const CitationRecordSchema = z.object({
+    source: CitationSourceSchema,
+    sourceRecordId: z.string(),
+    identifiers: CitationIdentifiersSchema,
+    title: z.string().optional(),
+    authors: z.array(z.string()).optional(),
+    year: z.number().int().optional(),
+    venue: z.string().optional(),
+    volume: z.string().optional(),
+    firstPage: z.string().optional(),
+    registrationAgency: z.string().optional(),
+    url: z.string().optional(),
+});
+export const IdentifierEvidenceSchema = z.object({
+    type: z.enum(["doi", "pmid", "arxiv"]),
+    identifier: z.string(),
+    exists: z.boolean(),
+    registrationAgency: z.string().optional(),
+    metadataAvailable: z.boolean(),
+});
+export const CitationSourceOutcomeSchema = z.object({
+    source: CitationSourceSchema,
+    operation: z.string(),
+    status: CitationSourceStatusSchema,
+    requestCount: z.number().int().nonnegative(),
+    records: z.array(CitationRecordSchema),
+    detail: z.string().optional(),
+    identifierEvidence: IdentifierEvidenceSchema.optional(),
+});
+export const CitationFieldComparisonSchema = z.object({
+    field: CitationFieldSchema,
+    status: ComparisonStatusSchema,
+    supplied: z.union([z.string(), z.number(), z.array(z.string())]),
+    sourceValues: z.array(z.object({
+        source: CitationSourceSchema,
+        value: z.union([z.string(), z.number(), z.array(z.string())]),
+    })),
+    ruleVersion: z.string(),
+});
+export const CitationConflictSchema = z.object({
+    field: CitationFieldSchema,
+    values: z.array(z.object({
+        source: CitationSourceSchema,
+        value: z.union([z.string(), z.number(), z.array(z.string())]),
+    })),
+});
+export const CitationClusterRelationSchema = z.object({
+    clusterId: z.string(),
+    kind: z.enum(["preprint_of", "published_as", "related_version"]),
+});
+export const CitationCandidateClusterSchema = z.object({
+    id: z.string(),
+    score: z.number().min(0).max(1),
+    records: z.array(CitationRecordSchema).min(1),
+    relations: z.array(CitationClusterRelationSchema),
+});
+export const CitationResolutionResultSchema = z.object({
+    input: CitationInputSchema,
+    normalized: NormalizedCitationSchema,
+    sourceOutcomes: z.array(CitationSourceOutcomeSchema),
+    candidates: z.array(CitationCandidateClusterSchema),
+    selectedClusterId: z.string().optional(),
+    comparisons: z.array(CitationFieldComparisonSchema),
+    conflicts: z.array(CitationConflictSchema),
+    verdict: CitationVerdictSchema,
+    coverage: CitationCoverageSchema,
+});
+export const CitationSourceOperationSchema = z.enum([
+    "doi_exact",
+    "crossref_doi_if_owned",
+    "crossref_bibliographic",
+    "pubmed_exact",
+    "pubmed_doi",
+    "pubmed_structured",
+    "pubmed_title",
+    "arxiv_exact",
+    "arxiv_bibliographic",
+    "semantic_scholar_identifier",
+    "semantic_scholar_bibliographic",
+    "none",
+]);
+export const CitationSourcePlanItemSchema = z.object({
+    source: CitationSourceSchema,
+    applicable: z.boolean(),
+    operation: CitationSourceOperationSchema,
+    candidateGeneration: z.boolean(),
+    reason: z.string(),
+});

package/dist/contracts/chat-events.d.ts

@@ -84,6 +84,15 @@ export interface ToolFinishedEvent {
     outcome: ToolOutcome;
     /** The same detail the matching `tool-started` carried. */
     detail?: ToolCallDetail;
+    /**
+     * The time in milliseconds around this call's own dispatch. Absent — never
+     * zero — when the harness took no measurement.
+     *
+     * A host must read it as `event.durationMs ?? (its own bracket)`. The bracket
+     * of a host spans the whole round, because the loop emits every start before
+     * it dispatches anything. Thus the fallback is correct only for one call.
+     */
+    durationMs?: number;
     source: EventSource;
 }
 /**

package/dist/contracts/index.d.ts

@@ -1,3 +1,7 @@
+export { ORGAN_SYSTEMS, OrganSystemSchema, ORGAN_SYSTEM_LABELS, organSystemLabel } from "./organ-system.js";
+export type { OrganSystem } from "./organ-system.js";
+export { SEVERITIES, SeveritySchema } from "./severity.js";
+export type { Severity } from "./severity.js";
 export type { PlanStep, PresentationContent, PresentationPart, PlanPart, RunCardPart, FileReferenceEntry, FileReferencePart, AskPart, RunStartedPart, StepStatus, DagStepState, DagStatePart, StepPhase, StepActivityPart, FileTreeEntry, StepFileTreePart, StepOutputFile, StepOutputPart, StepSummaryPart, StepUsagePart, StepBlockedPart, SynthesizedFinding, BiologicalTheme, RunSynthesisPart, SynthesisPhase, SynthesisProgressPart, RunCompletedFinding, RunCompletedPart, RunFailedPart, PreviewPart, DataPreviewFailedPart, CortexChatPart, } from "./chat-parts.js";
 export type { EventSource, TextDeltaEvent, ToolStartedEvent, ToolFinishedEvent, FinishEvent, ChatErrorEvent, CortexChatEvent } from "./chat-events.js";
 export type { TokenUsageRollup } from "./usage.js";
@@ -7,8 +11,8 @@ export { PART_REGISTRY, isTransient, isReconciling, isSidebarPart } from "./part
 export type { CortexChatPartType, PartDescriptor, PartEmitter, PartConsumer } from "./part-registry.js";
 export { AnalogyCoverageSchema, AnalogyReportSchema, AnalogyReportErrorSchema, AnalogicalReasonerOutputSchema } from "./analogy-report.js";
 export type { AnalogyCoverage, AnalogyReport, AnalogyReportError, AnalogicalReasonerOutput } from "./analogy-report.js";
-export { CoverageSchema, EntitySchema, SummarySchema, LiabilitySummarySchema, TractabilitySchema, IndicationsSchema, DrugInteractionsSchema, ClinicalDevelopmentSchema, SafetyProfileSchema, OffTissueRiskSchema, EvidenceConflictsSchema, EvidenceTimelineSchema, TranslationalChainSchema, AdditionalEvidenceSchema, DiscoveryTrialsSchema, DossierSchema, DossierSchemaV3Legacy, DossierV4Schema, DossierV5Schema, DossierV5BodySchema, ClinicalTrialAttributionV5Schema, ClinicalDevelopmentV5Schema, RegulatoryActionRowV5Schema, QualityGateStatusSchema, QualityGatesSchema, LiabilitySummaryV4Schema, ClinicalDevelopmentV4Schema, SafetyProfileV4Schema, OrganRiskRowV4Schema, ReferenceBiologyV4Shape, isDossier, dossierJsonSchema, SECTION_BLURBS, TargetAssessmentPhaseSchema, TargetAssessmentProgressEventSchema, } from "./target-dossier.js";
-export type { Coverage, Entity, Summary, LiabilitySummary, TractabilitySection, EvidenceItem, Dossier, DossierV4, DossierV5, DossierV5Body, ClinicalTrialAttributionV5, ClinicalTrialRowV5, FailedTrialRowV5, TrialOutcomeRowV5, RegulatoryActionRowV5, QualityGateStatus, QualityGates, SectionBlurbKey, TargetAssessmentPhase, TargetAssessmentProgressEvent, } from "./target-dossier.js";
+export { CoverageSchema, RowCoverageSchema, EntitySchema, ClaimSupportSchema, ClaimEvidenceSchema, LiabilityBulletSchema, LiabilitySummarySchema, TractabilitySchema, IndicationsSchema, DrugInteractionsSchema, ClinicalTrialAttributionSchema, ClinicalDevelopmentSchema, OrganRiskRowSchema, OffTargetRowSchema, OffTargetPanelSchema, RegulatoryActionRowSchema, SafetyFlagSchema, SafetyProfileSchema, OffTissueRowSchema, OffTissueRiskSchema, ReferenceBiologyShape, EvidenceConflictsSchema, EvidenceTimelineSchema, TranslationalChainSchema, AdditionalEvidenceSchema, DiscoveryTrialsSchema, QualityGateStatusSchema, QualityGatesSchema, DerivedSchema, DossierSchema, DossierBodySchema, isDossier, dossierJsonSchema, SECTION_BLURBS, TargetAssessmentPhaseSchema, TargetAssessmentProgressEventSchema, } from "./target-dossier.js";
+export type { Coverage, RowCoverage, Entity, EvidenceItem, ClaimSupport, ClaimEvidence, LiabilityBullet, LiabilitySummary, TractabilitySection, ClinicalTrialAttribution, ClinicalTrialRow, ClinicalDevelopment, FailedTrialRow, TrialOutcomeRow, OrganRiskRow, OffTargetRow, RegulatoryActionRow, SafetyFlag, SafetyProfile, OffTissueRow, QualityGateStatus, QualityGates, Derived, Dossier, DossierBody, SectionBlurbKey, TargetAssessmentPhase, TargetAssessmentProgressEvent, } from "./target-dossier.js";
 export { TargetAssessmentStatusSchema, TargetAssessmentErrorSchema, TargetAssessmentListRowSchema, TargetAssessmentRowSchema, } from "./target-assessment-row.js";
 export type { TargetAssessmentStatus, TargetAssessmentError, TargetAssessmentListRow, TargetAssessmentRow } from "./target-assessment-row.js";
 export { buildPreviewUrl, previewResourceId } from "./content-url.js";

package/dist/contracts/index.js

@@ -1,6 +1,8 @@
+export { ORGAN_SYSTEMS, OrganSystemSchema, ORGAN_SYSTEM_LABELS, organSystemLabel } from "./organ-system.js";
+export { SEVERITIES, SeveritySchema } from "./severity.js";
 export { DATA_PROFILE_RUN_LITERAL } from "./data-profile.js";
 export { PART_REGISTRY, isTransient, isReconciling, isSidebarPart } from "./part-registry.js";
 export { AnalogyCoverageSchema, AnalogyReportSchema, AnalogyReportErrorSchema, AnalogicalReasonerOutputSchema } from "./analogy-report.js";
-export { CoverageSchema, EntitySchema, SummarySchema, LiabilitySummarySchema, TractabilitySchema, IndicationsSchema, DrugInteractionsSchema, ClinicalDevelopmentSchema, SafetyProfileSchema, OffTissueRiskSchema, EvidenceConflictsSchema, EvidenceTimelineSchema, TranslationalChainSchema, AdditionalEvidenceSchema, DiscoveryTrialsSchema, DossierSchema, DossierSchemaV3Legacy, DossierV4Schema, DossierV5Schema, DossierV5BodySchema, ClinicalTrialAttributionV5Schema, ClinicalDevelopmentV5Schema, RegulatoryActionRowV5Schema, QualityGateStatusSchema, QualityGatesSchema, LiabilitySummaryV4Schema, ClinicalDevelopmentV4Schema, SafetyProfileV4Schema, OrganRiskRowV4Schema, ReferenceBiologyV4Shape, isDossier, dossierJsonSchema, SECTION_BLURBS, TargetAssessmentPhaseSchema, TargetAssessmentProgressEventSchema, } from "./target-dossier.js";
+export { CoverageSchema, RowCoverageSchema, EntitySchema, ClaimSupportSchema, ClaimEvidenceSchema, LiabilityBulletSchema, LiabilitySummarySchema, TractabilitySchema, IndicationsSchema, DrugInteractionsSchema, ClinicalTrialAttributionSchema, ClinicalDevelopmentSchema, OrganRiskRowSchema, OffTargetRowSchema, OffTargetPanelSchema, RegulatoryActionRowSchema, SafetyFlagSchema, SafetyProfileSchema, OffTissueRowSchema, OffTissueRiskSchema, ReferenceBiologyShape, EvidenceConflictsSchema, EvidenceTimelineSchema, TranslationalChainSchema, AdditionalEvidenceSchema, DiscoveryTrialsSchema, QualityGateStatusSchema, QualityGatesSchema, DerivedSchema, DossierSchema, DossierBodySchema, isDossier, dossierJsonSchema, SECTION_BLURBS, TargetAssessmentPhaseSchema, TargetAssessmentProgressEventSchema, } from "./target-dossier.js";
 export { TargetAssessmentStatusSchema, TargetAssessmentErrorSchema, TargetAssessmentListRowSchema, TargetAssessmentRowSchema, } from "./target-assessment-row.js";
 export { buildPreviewUrl, previewResourceId } from "./content-url.js";

package/dist/contracts/organ-system.d.ts

@@ -0,0 +1,49 @@
+/**
+ * The canonical organ-system vocabulary.
+ *
+ * This is the ONLY organ vocabulary in the package. Per-organ evidence is
+ * joined by equality on these tokens, so a second enumeration — even a
+ * "temporary" or deprecated one — reintroduces the string matching this
+ * exists to remove. Producers resolve external and model-supplied organ
+ * names onto these tokens at their own boundary.
+ *
+ * Membership is anatomical, with one deliberate exception: `oncology` is a
+ * therapeutic area rather than an organ system, so grouping by it does not
+ * denote a site. It is retained because malignancy signals — MedDRA neoplasm
+ * SOC terms, and regulatory findings matched on malignancy keywords — have
+ * no other channel to arrive on, and dropping the member would discard them.
+ * Known debt: the honest fix is a separate non-organ signal channel.
+ */
+import { z } from "zod";
+export declare const ORGAN_SYSTEMS: readonly ["cardiac", "vascular", "hepatic", "renal", "cns", "pns", "gi", "pancreas", "endocrine_thyroid", "metabolic", "hematologic", "immune", "respiratory", "reproductive", "musculoskeletal", "dermatologic", "ocular", "oncology"];
+export declare const OrganSystemSchema: z.ZodEnum<{
+    hematologic: "hematologic";
+    metabolic: "metabolic";
+    immune: "immune";
+    hepatic: "hepatic";
+    musculoskeletal: "musculoskeletal";
+    cns: "cns";
+    renal: "renal";
+    reproductive: "reproductive";
+    respiratory: "respiratory";
+    cardiac: "cardiac";
+    vascular: "vascular";
+    pns: "pns";
+    gi: "gi";
+    pancreas: "pancreas";
+    endocrine_thyroid: "endocrine_thyroid";
+    dermatologic: "dermatologic";
+    ocular: "ocular";
+    oncology: "oncology";
+}>;
+export type OrganSystem = (typeof ORGAN_SYSTEMS)[number];
+/**
+ * Reader-facing prose for each canonical token.
+ *
+ * Narrative surfaces (agent voice, rendered dossiers) read these; structured
+ * fields always carry the token. Keeping the prose a projection of the token
+ * — rather than its own list — is what stops the two drifting into the
+ * separate vocabularies this module replaces.
+ */
+export declare const ORGAN_SYSTEM_LABELS: Record<OrganSystem, string>;
+export declare const organSystemLabel: (organ: OrganSystem) => string;

package/dist/contracts/organ-system.js

@@ -0,0 +1,67 @@
+/**
+ * The canonical organ-system vocabulary.
+ *
+ * This is the ONLY organ vocabulary in the package. Per-organ evidence is
+ * joined by equality on these tokens, so a second enumeration — even a
+ * "temporary" or deprecated one — reintroduces the string matching this
+ * exists to remove. Producers resolve external and model-supplied organ
+ * names onto these tokens at their own boundary.
+ *
+ * Membership is anatomical, with one deliberate exception: `oncology` is a
+ * therapeutic area rather than an organ system, so grouping by it does not
+ * denote a site. It is retained because malignancy signals — MedDRA neoplasm
+ * SOC terms, and regulatory findings matched on malignancy keywords — have
+ * no other channel to arrive on, and dropping the member would discard them.
+ * Known debt: the honest fix is a separate non-organ signal channel.
+ */
+import { z } from "zod";
+export const ORGAN_SYSTEMS = [
+    "cardiac",
+    "vascular",
+    "hepatic",
+    "renal",
+    "cns",
+    "pns",
+    "gi",
+    "pancreas",
+    "endocrine_thyroid",
+    "metabolic",
+    "hematologic",
+    "immune",
+    "respiratory",
+    "reproductive",
+    "musculoskeletal",
+    "dermatologic",
+    "ocular",
+    "oncology",
+];
+export const OrganSystemSchema = z.enum(ORGAN_SYSTEMS);
+/**
+ * Reader-facing prose for each canonical token.
+ *
+ * Narrative surfaces (agent voice, rendered dossiers) read these; structured
+ * fields always carry the token. Keeping the prose a projection of the token
+ * — rather than its own list — is what stops the two drifting into the
+ * separate vocabularies this module replaces.
+ */
+export const ORGAN_SYSTEM_LABELS = {
+    cardiac: "cardiac",
+    vascular: "vascular",
+    hepatic: "hepatobiliary",
+    renal: "renal",
+    cns: "central nervous system",
+    pns: "peripheral nervous system",
+    gi: "gastrointestinal",
+    pancreas: "pancreatic",
+    endocrine_thyroid: "endocrine (thyroid)",
+    metabolic: "metabolic",
+    hematologic: "haematologic",
+    immune: "immunologic",
+    respiratory: "respiratory",
+    reproductive: "reproductive",
+    musculoskeletal: "musculoskeletal",
+    dermatologic: "dermatologic",
+    ocular: "ocular",
+    oncology: "oncology",
+};
+export const organSystemLabel = (organ) => ORGAN_SYSTEM_LABELS[organ];