@inflexa-ai/harness 0.23.0 → 0.25.0

package/dist/contracts/data-profile.d.ts

@@ -24,3 +24,169 @@
  * reporting the profile as an unnamed run — a failure with no red test anywhere.
  */
 export declare const DATA_PROFILE_RUN_LITERAL: "data-profile";
+/**
+ * Where an extracted subject fact came from, so a consumer can judge how much to trust
+ * it. Ordered most-direct first in the profiler's own guidance.
+ */
+export type DataProfileSubjectSource = "metadata" | "document" | "filename" | "user-context" | "inferred";
+/** The subject organism, with its provenance and the profiler's confidence in it. */
+export interface DataProfileOrganism {
+    scientificName: string;
+    /** NCBI Taxonomy ID as a string, e.g. `"9606"`. */
+    taxonId: string;
+    source: DataProfileSubjectSource;
+    confidence: "high" | "medium" | "low";
+    notes?: string;
+}
+/**
+ * One profiled file's persisted record.
+ *
+ * `path` + `description` are the original pair every snapshot carries; everything below
+ * them is optional on read, because a snapshot written before the record was widened
+ * carries only the pair.
+ */
+export interface DataProfileFile {
+    path: string;
+    description: string;
+    /** Semantic data type (count-matrix, variants, clinical-metadata, document, …). */
+    dataType?: string;
+    /** File format (CSV, h5ad, VCF, BAM, …). */
+    format?: string;
+    rows?: number | null;
+    cols?: number | null;
+    /** Searchable labels the profiler attached. */
+    tags?: string[];
+    /** Quality issues specific to this file. */
+    warnings?: string[];
+    /** Flat, identity-establishing facts (sparsity, delimiter, normalizationState, …). */
+    metrics?: Record<string, string | number | boolean>;
+}
+/** Dataset-wide quality findings the profiler recorded. */
+export interface DataProfileQualityAssessment {
+    concerns: string[];
+    strengths: string[];
+}
+/**
+ * One repeating set of files — the dataset's structure, as opposed to its contents.
+ *
+ * A kind is a claim about MEANING, made by the profiler agent: the deterministic input
+ * scan establishes that filenames differ only at one position, and cannot establish that
+ * the files are the same sort of thing. A singleton is a kind of `count` 1, so a
+ * two-file analysis is two kinds and needs no special case.
+ */
+export interface DataProfileKind {
+    name: string;
+    /** What ONE member represents. The grouping decision, stated apart from the description. */
+    memberRepresents: string;
+    description: string;
+    count: number;
+    /** Glob the members match, relative to the analysis root. Coverage is computed from it. */
+    pathPattern: string;
+    format?: string;
+    /** Labels of the `axes` that vary across this set's members. */
+    axisLabels?: string[];
+}
+/**
+ * What varies across a kind's members — the experimental design, as far as it is
+ * observable. The scan reports that a filename position varies and which values it
+ * takes; what the variation IS is the agent's label.
+ */
+export interface DataProfileAxis {
+    label: string;
+    cardinality: number;
+    exampleValues?: string[];
+    description?: string;
+}
+/**
+ * The comparand identifying WHICH files a profile covered and whether the SAME BYTES
+ * were profiled.
+ *
+ * `digest` is a stable hash over the staged inputs' identities, sizes, and mtimes in a
+ * canonical order, so it depends on the set and not on enumeration order. It excludes
+ * content hashes deliberately: enumerating those would mean reading every input in full
+ * on every parity check. An edit preserving both byte length and mtime is therefore not
+ * detected — bounded, and documented.
+ */
+export interface DataProfileInputSignature {
+    count: number;
+    digest: string;
+}
+/**
+ * How much of the scanned tree the profile's kinds describe.
+ *
+ * Computed deterministically by matching the submitted kind patterns against the scanned
+ * file set — never self-reported. Low coverage is a distinct failure from drift: a
+ * profile that classified a fraction of its inputs used to carry the same comparand as
+ * one that classified all of them, so it read as complete and fresh. Coverage does NOT by
+ * itself drive a re-profile, because some input sets legitimately resist classification.
+ */
+export interface DataProfileCoverage {
+    matched: number;
+    unmatched: number;
+    total: number;
+    unmatchedSample?: string[];
+}
+/**
+ * One profiled input file's legacy drift signature. `fileId` is a path identity (two
+ * files at the same path share it regardless of content), so `size` + `mtimeMs` are what
+ * let a consumer notice the bytes behind a path changed. Superseded by
+ * {@link DataProfileInputSignature}, and still readable on older rows.
+ */
+export interface DataProfileInputFile {
+    fileId: string;
+    size: number;
+    mtimeMs: number;
+}
+/**
+ * The profile snapshot stored in `cortex_analysis_state.data_profile_result`.
+ *
+ * It carries the profiler's full finding rather than a summary of it: this row is the
+ * profile's only durable home, so a field dropped on the way in is not "summarized
+ * away", it is destroyed, and the next reader can recover it only by re-reading the raw
+ * inputs.
+ *
+ * It does NOT carry a record per input file. The workspace filesystem is the
+ * authoritative file list — listing, grep, and the vector index all read the live tree —
+ * so a copy here would be a stale duplicate on a row detoasted by every reader,
+ * including the planner's, which reads a few hundred characters of it. `files` holds the
+ * individually notable inputs; `kinds` holds the dataset's structure.
+ */
+export interface DataProfileResult {
+    summary: string;
+    /** Individually described files — notable singletons, not the dataset's contents. */
+    files: DataProfileFile[];
+    /** The repeating sets the tree was grouped into. Absent on a pre-kinds snapshot. */
+    kinds?: DataProfileKind[];
+    /** What varies across those sets. Absent for the same reason as `kinds`. */
+    axes?: DataProfileAxis[];
+    /** The drift comparand. Preferred over `inputFileIds`, which it replaces. */
+    inputSignature?: DataProfileInputSignature;
+    /** How much of the scanned tree the kinds describe. Absent on pre-coverage snapshots. */
+    coverage?: DataProfileCoverage;
+    /** The legacy identity-list comparand, on rows written before the signature existed. */
+    inputFileIds?: string[];
+    /** The legacy per-file drift signature, on rows of the same era. */
+    inputFiles?: DataProfileInputFile[];
+    /** ISO 8601 timestamp of profile completion. */
+    profiledAt: string;
+    /** Scientific domain (transcriptomics, cheminformatics, clinical, …). */
+    domain?: string;
+    /** Specific subtype within the domain (bulk-rna-seq, single-cell, LC-MS/MS, …). */
+    subtype?: string;
+    /**
+     * Explicit `null` is a real, distinct value — the profiler looked and no input
+     * identified an organism — as opposed to absent, which means the snapshot predates
+     * the field.
+     */
+    organism?: DataProfileOrganism | null;
+    tissue?: string | null;
+    cellType?: string | null;
+    condition?: string | null;
+    /** Public dataset accessions found in any input (GSE/SRP/PRJNA/E-MTAB/phs/EGAS). */
+    accessions?: string[];
+    /** Conditions, groups, comparisons, replicates, pairing. */
+    experimentalDesign?: string;
+    qualityAssessment?: DataProfileQualityAssessment;
+}
+/** The profile's lifecycle, as the ledger records it. */
+export type DataProfileLifecycleStatus = "pending" | "running" | "completed" | "failed";

package/dist/contracts/index.d.ts

@@ -2,10 +2,11 @@ export { ORGAN_SYSTEMS, OrganSystemSchema, ORGAN_SYSTEM_LABELS, organSystemLabel
 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, ReportSessionStartedPart, CortexChatPart, } from "./chat-parts.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, ChildSessionStartedPart, ReportRenderedPart, CortexChatPart, } from "./chat-parts.js";
 export type { EventSource, TextDeltaEvent, ToolStartedEvent, ToolFinishedEvent, FinishEvent, ChatErrorEvent, CortexChatEvent } from "./chat-events.js";
 export type { TokenUsageRollup } from "./usage.js";
 export { DATA_PROFILE_RUN_LITERAL } from "./data-profile.js";
+export type { DataProfileAxis, DataProfileCoverage, DataProfileFile, DataProfileInputFile, DataProfileInputSignature, DataProfileKind, DataProfileLifecycleStatus, DataProfileOrganism, DataProfileQualityAssessment, DataProfileResult, DataProfileSubjectSource, } from "./data-profile.js";
 export type { TextPart, ToolCallPart, CortexPart, CortexMessage } from "./message.js";
 export { PART_REGISTRY, isTransient, isReconciling, isSidebarPart } from "./part-registry.js";
 export type { CortexChatPartType, PartDescriptor, PartEmitter, PartConsumer } from "./part-registry.js";
@@ -15,4 +16,4 @@ export { CoverageSchema, RowCoverageSchema, EntitySchema, ClaimSupportSchema, Cl
 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, buildReportSessionUrl, previewResourceId, reportSessionResourceId } from "./content-url.js";
+export { buildReportSessionUrl, reportSessionResourceId } from "./content-url.js";

package/dist/contracts/index.js

@@ -5,4 +5,4 @@ export { PART_REGISTRY, isTransient, isReconciling, isSidebarPart } from "./part
 export { AnalogyCoverageSchema, AnalogyReportSchema, AnalogyReportErrorSchema, AnalogicalReasonerOutputSchema } from "./analogy-report.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, buildReportSessionUrl, previewResourceId, reportSessionResourceId } from "./content-url.js";
+export { buildReportSessionUrl, reportSessionResourceId } from "./content-url.js";

package/dist/contracts/message.d.ts

@@ -3,7 +3,7 @@
  * and the public API for everything the chat path exchanges.
  *
  * No AI SDK types appear here or anywhere else in the package. The
- * discriminant is `type`, so `switch (part.type) { case "data-report-preview": ... }`
+ * discriminant is `type`, so `switch (part.type) { case "data-child-session-started": ... }`
  * narrows the union member without any `as` cast.
  */
 import type { ToolCallDetail, ToolCallOutcome } from "./chat-events.js";

package/dist/contracts/message.js

@@ -3,7 +3,7 @@
  * and the public API for everything the chat path exchanges.
  *
  * No AI SDK types appear here or anywhere else in the package. The
- * discriminant is `type`, so `switch (part.type) { case "data-report-preview": ... }`
+ * discriminant is `type`, so `switch (part.type) { case "data-child-session-started": ... }`
  * narrows the union member without any `as` cast.
  */
 export {};

package/dist/contracts/part-registry.js

@@ -16,9 +16,8 @@ export const PART_REGISTRY = {
     "data-synthesis-progress": { emitter: "workflow", consumer: "sidebar", transient: false, reconciling: true },
     "data-run-completed": { emitter: "workflow", consumer: "sidebar", transient: false, reconciling: false },
     "data-run-failed": { emitter: "workflow", consumer: "sidebar", transient: false, reconciling: false },
-    "data-report-preview": { emitter: "conversation", consumer: "conversation", transient: false, reconciling: false },
-    "data-report-preview-failed": { emitter: "conversation", consumer: "conversation", transient: false, reconciling: false },
-    "data-report-session-started": { emitter: "conversation", consumer: "conversation", transient: false, reconciling: false },
+    "data-child-session-started": { emitter: "conversation", consumer: "conversation", transient: false, reconciling: false },
+    "data-report-rendered": { emitter: "conversation", consumer: "conversation", transient: false, reconciling: false },
 };
 export function isTransient(type) {
     return PART_REGISTRY[type].transient;

package/dist/contracts/schemas/chat-parts.d.ts

@@ -441,36 +441,17 @@ export declare const RunFailedPartSchema: z.ZodObject<{
     error: z.ZodString;
     reason: z.ZodOptional<z.ZodString>;
 }, z.core.$strip>;
-export declare const PreviewPartSchema: z.ZodObject<{
-    type: z.ZodLiteral<"data-report-preview">;
-    id: z.ZodString;
-    previewId: z.ZodString;
-    version: z.ZodNumber;
-    title: z.ZodString;
-    previewPath: z.ZodString;
-    format: z.ZodEnum<{
-        html: "html";
-        pdf: "pdf";
-    }>;
-}, z.core.$strip>;
-export declare const DataPreviewFailedPartSchema: z.ZodObject<{
-    type: z.ZodLiteral<"data-report-preview-failed">;
-    id: z.ZodString;
-    previewId: z.ZodString;
-    version: z.ZodNumber;
-    reason: z.ZodString;
-    errorKind: z.ZodOptional<z.ZodEnum<{
-        timeout: "timeout";
-        render: "render";
-        submit: "submit";
-        build: "build";
-        internal: "internal";
-    }>>;
-}, z.core.$strip>;
-export declare const ReportSessionStartedPartSchema: z.ZodObject<{
-    type: z.ZodLiteral<"data-report-session-started">;
+export declare const ChildSessionStartedPartSchema: z.ZodObject<{
+    type: z.ZodLiteral<"data-child-session-started">;
     threadId: z.ZodString;
     parentThreadId: z.ZodString;
+    threadType: z.ZodString;
+}, z.core.$strip>;
+export declare const ReportRenderedPartSchema: z.ZodObject<{
+    type: z.ZodLiteral<"data-report-rendered">;
+    id: z.ZodString;
+    renderedAt: z.ZodString;
+    title: z.ZodOptional<z.ZodString>;
 }, z.core.$strip>;
 export declare const CortexChatPartSchema: z.ZodDiscriminatedUnion<[z.ZodObject<{
     type: z.ZodLiteral<"data-presentation">;
@@ -745,31 +726,13 @@ export declare const CortexChatPartSchema: z.ZodDiscriminatedUnion<[z.ZodObject<
     error: z.ZodString;
     reason: z.ZodOptional<z.ZodString>;
 }, z.core.$strip>, z.ZodObject<{
-    type: z.ZodLiteral<"data-report-preview">;
-    id: z.ZodString;
-    previewId: z.ZodString;
-    version: z.ZodNumber;
-    title: z.ZodString;
-    previewPath: z.ZodString;
-    format: z.ZodEnum<{
-        html: "html";
-        pdf: "pdf";
-    }>;
-}, z.core.$strip>, z.ZodObject<{
-    type: z.ZodLiteral<"data-report-preview-failed">;
-    id: z.ZodString;
-    previewId: z.ZodString;
-    version: z.ZodNumber;
-    reason: z.ZodString;
-    errorKind: z.ZodOptional<z.ZodEnum<{
-        timeout: "timeout";
-        render: "render";
-        submit: "submit";
-        build: "build";
-        internal: "internal";
-    }>>;
-}, z.core.$strip>, z.ZodObject<{
-    type: z.ZodLiteral<"data-report-session-started">;
+    type: z.ZodLiteral<"data-child-session-started">;
     threadId: z.ZodString;
     parentThreadId: z.ZodString;
+    threadType: z.ZodString;
+}, z.core.$strip>, z.ZodObject<{
+    type: z.ZodLiteral<"data-report-rendered">;
+    id: z.ZodString;
+    renderedAt: z.ZodString;
+    title: z.ZodOptional<z.ZodString>;
 }, z.core.$strip>], "type">;

package/dist/contracts/schemas/chat-parts.js

@@ -275,30 +275,21 @@ export const RunFailedPartSchema = z.object({
     error: z.string(),
     reason: z.string().optional(),
 });
-// ── Preview ────────────────────────────────────────────────────────
-export const PreviewPartSchema = z.object({
-    type: z.literal("data-report-preview"),
-    id: z.string(),
-    previewId: z.string(),
-    version: z.number(),
-    title: z.string(),
-    previewPath: z.string(),
-    format: z.enum(["html", "pdf"]),
-});
-// ── Preview Failed ─────────────────────────────────────────────────
-export const DataPreviewFailedPartSchema = z.object({
-    type: z.literal("data-report-preview-failed"),
-    id: z.string(),
-    previewId: z.string(),
-    version: z.number(),
-    reason: z.string(),
-    errorKind: z.enum(["render", "submit", "build", "timeout", "internal"]).optional(),
-});
-// ── Report Session Started ─────────────────────────────────────────
-export const ReportSessionStartedPartSchema = z.object({
-    type: z.literal("data-report-session-started"),
+// ── Child Session Started ──────────────────────────────────────────
+export const ChildSessionStartedPartSchema = z.object({
+    type: z.literal("data-child-session-started"),
     threadId: z.string(),
     parentThreadId: z.string(),
+    // A plain string, deliberately not an enum: a future session type must
+    // not fail validation in an older consumer.
+    threadType: z.string(),
+});
+// ── Report Rendered ────────────────────────────────────────────────
+export const ReportRenderedPartSchema = z.object({
+    type: z.literal("data-report-rendered"),
+    id: z.string(),
+    renderedAt: z.string(),
+    title: z.string().optional(),
 });
 // ── Union ───────────────────────────────────────────────────────────
 export const CortexChatPartSchema = z.discriminatedUnion("type", [
@@ -319,7 +310,6 @@ export const CortexChatPartSchema = z.discriminatedUnion("type", [
     SynthesisProgressPartSchema,
     RunCompletedPartSchema,
     RunFailedPartSchema,
-    PreviewPartSchema,
-    DataPreviewFailedPartSchema,
-    ReportSessionStartedPartSchema,
+    ChildSessionStartedPartSchema,
+    ReportRenderedPartSchema,
 ]);

package/dist/contracts/schemas/index.d.ts

@@ -1,3 +1,3 @@
-export { PlanStepSchema, PresentationContentSchema, PresentationPartSchema, PlanPartSchema, RunCardPartSchema, FileReferenceEntrySchema, FileReferencePartSchema, RunStartedPartSchema, StepStatusSchema, DagStepStateSchema, DagStatePartSchema, StepPhaseSchema, StepActivityPartSchema, FileTreeEntrySchema, StepFileTreePartSchema, StepOutputFileSchema, StepOutputPartSchema, StepSummaryPartSchema, StepUsagePartSchema, StepBlockedPartSchema, SynthesizedFindingSchema, BiologicalThemeSchema, RunSynthesisPartSchema, SynthesisPhaseSchema, SynthesisProgressPartSchema, RunCompletedFindingSchema, RunCompletedPartSchema, RunFailedPartSchema, PreviewPartSchema, DataPreviewFailedPartSchema, CortexChatPartSchema, } from "./chat-parts.js";
+export { PlanStepSchema, PresentationContentSchema, PresentationPartSchema, PlanPartSchema, RunCardPartSchema, FileReferenceEntrySchema, FileReferencePartSchema, RunStartedPartSchema, StepStatusSchema, DagStepStateSchema, DagStatePartSchema, StepPhaseSchema, StepActivityPartSchema, FileTreeEntrySchema, StepFileTreePartSchema, StepOutputFileSchema, StepOutputPartSchema, StepSummaryPartSchema, StepUsagePartSchema, StepBlockedPartSchema, SynthesizedFindingSchema, BiologicalThemeSchema, RunSynthesisPartSchema, SynthesisPhaseSchema, SynthesisProgressPartSchema, RunCompletedFindingSchema, RunCompletedPartSchema, RunFailedPartSchema, CortexChatPartSchema, } from "./chat-parts.js";
 export { EventSourceSchema, TextDeltaEventSchema, ToolStartedEventSchema, ToolFinishedEventSchema, FinishEventSchema, ChatErrorEventSchema, CortexChatEventSchema, } from "./chat-events.js";
 export { TokenUsageRollupSchema } from "./usage.js";

package/dist/contracts/schemas/index.js

@@ -1,3 +1,3 @@
-export { PlanStepSchema, PresentationContentSchema, PresentationPartSchema, PlanPartSchema, RunCardPartSchema, FileReferenceEntrySchema, FileReferencePartSchema, RunStartedPartSchema, StepStatusSchema, DagStepStateSchema, DagStatePartSchema, StepPhaseSchema, StepActivityPartSchema, FileTreeEntrySchema, StepFileTreePartSchema, StepOutputFileSchema, StepOutputPartSchema, StepSummaryPartSchema, StepUsagePartSchema, StepBlockedPartSchema, SynthesizedFindingSchema, BiologicalThemeSchema, RunSynthesisPartSchema, SynthesisPhaseSchema, SynthesisProgressPartSchema, RunCompletedFindingSchema, RunCompletedPartSchema, RunFailedPartSchema, PreviewPartSchema, DataPreviewFailedPartSchema, CortexChatPartSchema, } from "./chat-parts.js";
+export { PlanStepSchema, PresentationContentSchema, PresentationPartSchema, PlanPartSchema, RunCardPartSchema, FileReferenceEntrySchema, FileReferencePartSchema, RunStartedPartSchema, StepStatusSchema, DagStepStateSchema, DagStatePartSchema, StepPhaseSchema, StepActivityPartSchema, FileTreeEntrySchema, StepFileTreePartSchema, StepOutputFileSchema, StepOutputPartSchema, StepSummaryPartSchema, StepUsagePartSchema, StepBlockedPartSchema, SynthesizedFindingSchema, BiologicalThemeSchema, RunSynthesisPartSchema, SynthesisPhaseSchema, SynthesisProgressPartSchema, RunCompletedFindingSchema, RunCompletedPartSchema, RunFailedPartSchema, CortexChatPartSchema, } from "./chat-parts.js";
 export { EventSourceSchema, TextDeltaEventSchema, ToolStartedEventSchema, ToolFinishedEventSchema, FinishEventSchema, ChatErrorEventSchema, CortexChatEventSchema, } from "./chat-events.js";
 export { TokenUsageRollupSchema } from "./usage.js";

package/dist/execution/input-signature.d.ts

@@ -0,0 +1,33 @@
+/**
+ * The input signature — the fixed-width comparand a completed profile persists in
+ * place of a per-file identity list.
+ *
+ * `inputFileIds` had exactly one consumer, the staleness comparison, so a set of
+ * several thousand identifiers was persisted, detoasted on every read of the row, and
+ * compared element-wise to answer a question 40 bytes answer. The signature covers
+ * `size` and `mtimeMs` as well, so it also notices that the bytes behind a path
+ * changed — a `fileId` is a path identity and survives an in-place edit unchanged.
+ *
+ * Order independence is a property of the digest, not of the caller: entries are
+ * sorted canonically before hashing, so two enumerations of the same set agree.
+ */
+import type { DataProfileInputSignature } from "../state/data-profile.js";
+import type { StagedInput } from "./staged-input.js";
+/** The fields a signature covers. A manifest entry satisfies it structurally. */
+export interface SignableInput {
+    readonly fileId: string;
+    readonly size: number;
+    readonly mtimeMs?: number;
+}
+/**
+ * Digest a staged input set.
+ *
+ * A workflow input persisted before `StagedInput.mtimeMs` existed deserializes without
+ * it despite the compile-time type; such an entry contributes `-` in the mtime field
+ * rather than omitting the signature entirely. The comparison still notices an added,
+ * removed, or resized file, and one re-profile under the current code restores the full
+ * signature.
+ */
+export declare function computeInputSignature(inputs: readonly SignableInput[]): DataProfileInputSignature;
+/** Convenience over the workflow's own manifest type. */
+export declare function signatureOfStagedInputs(inputs: readonly StagedInput[]): DataProfileInputSignature;

package/dist/execution/run-authorizer.d.ts

@@ -11,7 +11,7 @@
  * `RunSession` with no host call, no jti, no revoke. The harness's tools depend only on
  * this interface and never read a credential.
  *
- * Mirrors the `PreviewPublisher` seam: a narrow interface in the harness, the managed
+ * Mirrors the `SessionPagePublisher` seam: a narrow interface in the harness, the managed
  * realization injected at the composition root.
  */
 import type { AuthContext, Provenance, RunFrame, RunSession, Scope } from "../auth/types.js";

package/dist/execution/run-authorizer.js

@@ -11,7 +11,7 @@
  * `RunSession` with no host call, no jti, no revoke. The harness's tools depend only on
  * this interface and never read a credential.
  *
- * Mirrors the `PreviewPublisher` seam: a narrow interface in the harness, the managed
+ * Mirrors the `SessionPagePublisher` seam: a narrow interface in the harness, the managed
  * realization injected at the composition root.
  */
 export {};

package/dist/index.d.ts

@@ -33,8 +33,6 @@ export { createNoopArtifactRegistry } from "./execution/noop-artifact-registry.j
 export type { ArtifactRegistry, ArtifactRegistrationInput, ArtifactSyncInput, ExternalRegistrationResult } from "./execution/artifact-registry.js";
 export type { ArtifactManifestEntry } from "./schemas/artifact-manifest.js";
 export type { ProvenanceCollector } from "./provenance/collector.js";
-export { UnavailablePreviewPublisher } from "./tools/report/preview-publisher.js";
-export type { PreviewPublisher, PreviewMintResult } from "./tools/report/preview-publisher.js";
 export { UnavailableSessionPagePublisher } from "./tools/report-session/session-page-publisher.js";
 export type { MakeSessionPagePublisher, SessionPagePublisher, SessionPageMintResult } from "./tools/report-session/session-page-publisher.js";
 export type { ResolvePageUrl, SessionPageAccess } from "./tools/report-session/index.js";
@@ -88,7 +86,7 @@ export type { ConversationDisplayMetadata, ConversationUIData, ConversationUIMes
 export { storedMessagesToCortex } from "./memory/conversation-display-replay.js";
 export type { CortexChatEvent, TextDeltaEvent, ToolStartedEvent, ToolFinishedEvent, ToolOutcome, ToolCallOutcome, ToolCallDetail, FinishEvent, ChatErrorEvent, } from "./contracts/chat-events.js";
 export type { TokenUsageRollup } from "./contracts/usage.js";
-export type { CortexChatPart, PresentationPart, PresentationContent, PlanPart, RunCardPart, FileReferencePart, FileReferenceEntry, RunStartedPart, DagStatePart, DagStepState, StepStatus, StepActivityPart, StepPhase, StepFileTreePart, FileTreeEntry, StepOutputPart, StepOutputFile, StepSummaryPart, StepUsagePart, StepBlockedPart, RunSynthesisPart, SynthesizedFinding, BiologicalTheme, SynthesisProgressPart, SynthesisPhase, RunCompletedPart, RunCompletedFinding, RunFailedPart, PreviewPart, DataPreviewFailedPart, } from "./contracts/chat-parts.js";
+export type { CortexChatPart, PresentationPart, PresentationContent, PlanPart, RunCardPart, FileReferencePart, FileReferenceEntry, RunStartedPart, DagStatePart, DagStepState, StepStatus, StepActivityPart, StepPhase, StepFileTreePart, FileTreeEntry, StepOutputPart, StepOutputFile, StepSummaryPart, StepUsagePart, StepBlockedPart, RunSynthesisPart, SynthesizedFinding, BiologicalTheme, SynthesisProgressPart, SynthesisPhase, RunCompletedPart, RunCompletedFinding, RunFailedPart, } from "./contracts/chat-parts.js";
 export { PART_REGISTRY, isTransient, isReconciling, isSidebarPart } from "./contracts/part-registry.js";
 export type { CortexChatPartType, PartDescriptor, PartEmitter, PartConsumer } from "./contracts/part-registry.js";
 export { launchDbos, shutdownDbos, sweepEphemeralWorkflows } from "./runtime/dbos.js";
@@ -117,10 +115,13 @@ export { DATA_PROFILE_RUN_LITERAL } from "./contracts/data-profile.js";
 export { initCortexState } from "./state/init.js";
 export { upsertAnalysis } from "./state/analyses.js";
 export { clearDataProfile, loadDataProfileStatus, tryRetryDataProfile, reconcileOrphanedDataProfile } from "./state/data-profile.js";
-export type { DataProfileInputFile, DataProfileResult, DataProfileStatus } from "./state/data-profile.js";
+export type { DataProfileAxis, DataProfileCoverage, DataProfileFile, DataProfileInputFile, DataProfileInputSignature, DataProfileKind, DataProfileLifecycleStatus, DataProfileOrganism, DataProfileQualityAssessment, DataProfileResult, DataProfileSubjectSource, } from "./contracts/data-profile.js";
+export type { DataProfileStatus } from "./state/data-profile.js";
 export { createAnalysisPurge } from "./state/purge-analysis.js";
 export type { AnalysisPurge, AnalysisPurgeDeps, AnalysisPurgeOutcome } from "./state/purge-analysis.js";
 export type { StagedInput } from "./execution/staged-input.js";
+export { computeInputSignature } from "./execution/input-signature.js";
+export type { SignableInput } from "./execution/input-signature.js";
 export type { ResolveWorkspaceRoot } from "./workspace/paths.js";
 export { createSandboxClient } from "./sandbox/create-sandbox.js";
 export type { CreateSandboxClientConfig, SandboxBackendConfig } from "./sandbox/create-sandbox.js";

package/dist/index.js

@@ -40,8 +40,6 @@ export { createNoopRunCharge } from "./billing/noop-run-charge.js";
 export { createNoopUsageRecorder } from "./billing/noop-usage-recorder.js";
 // Seam: artifact registration.
 export { createNoopArtifactRegistry } from "./execution/noop-artifact-registry.js";
-// Seam: report preview publishing.
-export { UnavailablePreviewPublisher } from "./tools/report/preview-publisher.js";
 // Seam: the hosted view of a report-session page. A managed host serves the URL space
 // `report-sessions/{analysisId}/{threadId}` and mints access through its own publisher,
 // thus the seam belongs on the front door. Both seams bind per call over the auth of the
@@ -207,6 +205,11 @@ export { clearDataProfile, loadDataProfileStatus, tryRetryDataProfile, reconcile
 // Analysis reclamation — `purgeAnalysis` reclaims an analysis's whole Postgres
 // footprint from its id alone; workspace files stay the embedder's to dispose of.
 export { createAnalysisPurge } from "./state/purge-analysis.js";
+// The input signature a completed profile persists. Exported because the embedder owns
+// the OTHER side of the comparison — it enumerates the current input set — and a second
+// implementation of the digest would silently disagree with the one on the row, which is
+// the failure a fixed-width comparand exists to prevent.
+export { computeInputSignature } from "./execution/input-signature.js";
 export { createSandboxClient } from "./sandbox/create-sandbox.js";
 export { MachineBudgetSchema, ResourceLimitsSchema, ResourcePolicySchema, ResourceSpecSchema, parseResourcePolicy } from "./config/resource-limits.js";
 export { createWorkspaceFilesystem } from "./workspace/filesystem.js";

package/dist/input-scan/coverage.d.ts

@@ -0,0 +1,22 @@
+/**
+ * Profile coverage — how much of the scanned tree the agent's kinds actually describe.
+ *
+ * Measured against the SUBMITTED kinds, never against the scan's own shapes. Computed
+ * from the shapes it would report only whether the scan grouped its own observations,
+ * which is always yes; measured against the kinds it is a real check, and it is the
+ * check that was missing when a profile covering 49 of 3513 files read as complete and
+ * fresh.
+ *
+ * Deterministic by construction: matching declared patterns against a known file set
+ * requires no judgement, and a coverage figure a model self-reported would not be a
+ * check at all.
+ */
+export interface ProfileCoverage {
+    /** Files matching at least one declared kind pattern. */
+    readonly matched: number;
+    readonly unmatched: number;
+    readonly total: number;
+    readonly unmatchedSample: string[];
+}
+/** Coverage of a scanned file set by a set of declared kind patterns. */
+export declare function computeCoverage(paths: readonly string[], patterns: readonly string[]): ProfileCoverage;

package/dist/input-scan/coverage.js

@@ -0,0 +1,85 @@
+/**
+ * Profile coverage — how much of the scanned tree the agent's kinds actually describe.
+ *
+ * Measured against the SUBMITTED kinds, never against the scan's own shapes. Computed
+ * from the shapes it would report only whether the scan grouped its own observations,
+ * which is always yes; measured against the kinds it is a real check, and it is the
+ * check that was missing when a profile covering 49 of 3513 files read as complete and
+ * fresh.
+ *
+ * Deterministic by construction: matching declared patterns against a known file set
+ * requires no judgement, and a coverage figure a model self-reported would not be a
+ * check at all.
+ */
+/** Unmatched paths carried on the snapshot, so a shortfall names examples rather than a bare count. */
+const MAX_UNMATCHED_SAMPLE = 10;
+/**
+ * Compile a kind's path pattern to a matcher.
+ *
+ * `**` crosses directory separators, `*` and `?` do not, and `<0>`-style placeholders —
+ * the syntax the manifest renders variable positions in, which an agent may reasonably
+ * copy — match one token. Everything else is literal.
+ */
+function compilePattern(pattern) {
+    let out = "";
+    for (let i = 0; i < pattern.length; i++) {
+        const char = pattern[i];
+        if (char === "*") {
+            if (pattern[i + 1] === "*") {
+                out += ".*";
+                i++;
+                // `**/` should also match zero directories, so the slash is optional.
+                if (pattern[i + 1] === "/")
+                    i++;
+                continue;
+            }
+            out += "[^/]*";
+            continue;
+        }
+        if (char === "?") {
+            out += "[^/]";
+            continue;
+        }
+        if (char === "<") {
+            const close = pattern.indexOf(">", i);
+            if (close > i) {
+                out += "[^/]*";
+                i = close;
+                continue;
+            }
+        }
+        out += char.replace(/[.+^${}()|[\]\\]/g, "\\$&");
+    }
+    return new RegExp(`^${out}$`);
+}
+function normalize(path) {
+    return path.replace(/^\.\//, "").replace(/^\/+/, "").replace(/\/+/g, "/");
+}
+/**
+ * Whether a path falls under a pattern. A pattern naming a directory covers everything
+ * beneath it — agents write `data/inputs/vcf` as often as `data/inputs/vcf/*.vcf.gz`,
+ * and reading the first as a zero-file kind would report a coverage failure that is an
+ * artefact of notation.
+ */
+function matches(path, pattern, compiled) {
+    if (compiled.test(path))
+        return true;
+    const bare = pattern.replace(/\/+$/, "");
+    return bare.length > 0 && !/[*?<]/.test(bare) && path.startsWith(`${bare}/`);
+}
+/** Coverage of a scanned file set by a set of declared kind patterns. */
+export function computeCoverage(paths, patterns) {
+    const compiled = patterns.map((pattern) => ({ pattern, regex: compilePattern(pattern) }));
+    const unmatchedSample = [];
+    let matched = 0;
+    for (const raw of paths) {
+        const path = normalize(raw);
+        if (compiled.some(({ pattern, regex }) => matches(path, pattern, regex))) {
+            matched++;
+            continue;
+        }
+        if (unmatchedSample.length < MAX_UNMATCHED_SAMPLE)
+            unmatchedSample.push(path);
+    }
+    return { matched, unmatched: paths.length - matched, total: paths.length, unmatchedSample };
+}