@inflexa-ai/harness 0.1.1

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

@@ -0,0 +1,295 @@
+/**
+ * Zod schemas for Cortex chat data parts — validation at boundaries.
+ */
+import { z } from "zod";
+// ── Presentation ────────────────────────────────────────────────────
+export const PlanStepSchema = z.object({
+    id: z.string(),
+    name: z.string(),
+    agent: z.string(),
+    question: z.string(),
+    depends_on: z.array(z.string()),
+    resources: z.object({ cpu: z.number(), memoryGb: z.number() }).optional(),
+    maxSteps: z.number(),
+});
+export const PresentationContentSchema = z.discriminatedUnion("kind", [
+    z.object({
+        kind: z.literal("echart"),
+        spec: z.record(z.string(), z.unknown()),
+        // Analysis-rooted CSV path the host resolves to `dataset.source` at render time; optional
+        // because a self-contained spec may embed its own data.
+        dataPath: z.string().optional(),
+    }),
+    z.object({
+        kind: z.literal("markdown"),
+        body: z.string(),
+    }),
+    z.object({
+        kind: z.literal("code"),
+        code: z.string(),
+        language: z.string(),
+    }),
+    z.object({
+        kind: z.literal("svg"),
+        markup: z.string(),
+    }),
+    z.object({
+        kind: z.literal("table"),
+        headers: z.array(z.string()),
+        rows: z.array(z.array(z.string())),
+        caption: z.string().optional(),
+    }),
+]);
+export const PresentationPartSchema = z.object({
+    type: z.literal("data-presentation"),
+    id: z.string(),
+    title: z.string().optional(),
+    content: PresentationContentSchema,
+});
+// ── Plan reference ──────────────────────────────────────────────────
+export const PlanPartSchema = z.object({
+    type: z.literal("data-plan"),
+    id: z.string(),
+    planId: z.string().regex(/^pln-[a-f0-9]{8}$/),
+    title: z.string().optional(),
+    steps: z.array(PlanStepSchema).optional(),
+    analytical_narrative: z.string().optional(),
+    omicsType: z.string().optional(),
+    omicsSubtype: z.string().optional(),
+});
+// ── Run card ────────────────────────────────────────────────────────
+export const RunCardPartSchema = z.object({
+    type: z.literal("data-run-card"),
+    id: z.string(),
+    runId: z.string(),
+    planId: z.string(),
+    title: z.string(),
+    stepCount: z.number(),
+});
+// ── File reference ──────────────────────────────────────────────────
+export const FileReferenceEntrySchema = z.object({
+    path: z.string().min(1),
+    runId: z.string().optional(),
+    caption: z.string().optional(),
+});
+export const FileReferencePartSchema = z.object({
+    type: z.literal("data-file-reference"),
+    id: z.string(),
+    title: z.string().optional(),
+    files: z.array(FileReferenceEntrySchema).min(1).max(10),
+});
+// ── Run Started ─────────────────────────────────────────────────────
+export const RunStartedPartSchema = z.object({
+    type: z.literal("data-run-started"),
+    runId: z.string(),
+    planSummary: z.string(),
+    stepCount: z.number(),
+});
+// ── DAG State ───────────────────────────────────────────────────────
+export const StepStatusSchema = z.enum(["pending", "running", "completed", "failed"]);
+export const DagStepStateSchema = z
+    .object({
+    id: z.string(),
+    name: z.string(),
+    agent: z.string(),
+    status: StepStatusSchema,
+    level: z.number().int().nonnegative(),
+    dependsOn: z.array(z.string()),
+    durationMs: z.number().optional(),
+    artifactCount: z.number().optional(),
+    summary: z.string().optional(),
+    error: z.string().optional(),
+})
+    .strict();
+export const DagStatePartSchema = z
+    .object({
+    type: z.literal("data-dag-state"),
+    id: z.string(),
+    runId: z.string(),
+    steps: z.array(DagStepStateSchema),
+})
+    .strict();
+// ── Step Activity ───────────────────────────────────────────────────
+export const StepPhaseSchema = z.enum([
+    "sandbox-init",
+    "executing",
+    "generating-metadata",
+    "generating-summary",
+    "indexing",
+    "persisting",
+    "complete",
+    "failed",
+    "retrying",
+    "warning",
+]);
+export const StepActivityPartSchema = z.object({
+    type: z.literal("data-step-activity"),
+    id: z.string(),
+    runId: z.string(),
+    stepId: z.string(),
+    phase: StepPhaseSchema,
+    activity: z.string(),
+});
+// ── Step File Tree ──────────────────────────────────────────────────
+export const FileTreeEntrySchema = z.object({
+    path: z.string(),
+    size: z.number().optional(),
+    type: z.enum(["file", "directory"]),
+});
+export const StepFileTreePartSchema = z.object({
+    type: z.literal("data-step-file-tree"),
+    id: z.string(),
+    runId: z.string(),
+    stepId: z.string(),
+    files: z.array(FileTreeEntrySchema),
+});
+// ── Step Output ─────────────────────────────────────────────────────
+export const StepOutputFileSchema = z.object({
+    path: z.string(),
+    size: z.number(),
+    fileType: z.enum(["script", "output", "figure", "log", "notebook", "summary"]),
+    description: z.string(),
+});
+export const StepOutputPartSchema = z.object({
+    type: z.literal("data-step-output"),
+    id: z.string(),
+    runId: z.string(),
+    stepId: z.string(),
+    agentId: z.string(),
+    files: z.array(StepOutputFileSchema),
+    artifactCount: z.number(),
+    durationMs: z.number(),
+    finishReason: z.string().optional(),
+    hitMaxSteps: z.boolean().optional(),
+});
+// ── Step Summary ────────────────────────────────────────────────────
+export const StepSummaryPartSchema = z.object({
+    type: z.literal("data-step-summary"),
+    id: z.string(),
+    runId: z.string(),
+    stepId: z.string(),
+    agentId: z.string(),
+    markdown: z.string(),
+});
+export const StepBlockedPartSchema = z.object({
+    type: z.literal("data-step-blocked"),
+    id: z.string(),
+    runId: z.string(),
+    stepId: z.string(),
+    agentId: z.string(),
+    reason: z.string(),
+});
+// ── Run Completed ───────────────────────────────────────────────────
+export const RunCompletedFindingSchema = z.object({
+    title: z.string(),
+    confidence: z.enum(["high", "medium", "low"]),
+});
+export const RunCompletedPartSchema = z.object({
+    type: z.literal("data-run-completed"),
+    runId: z.string(),
+    status: z.enum(["completed", "partial"]),
+    completedSteps: z.number(),
+    totalSteps: z.number(),
+    artifactCount: z.number(),
+    findings: z.array(RunCompletedFindingSchema),
+    note: z.string().optional(),
+});
+// ── Run Synthesis ──────────────────────────────────────────────────
+export const SynthesizedFindingSchema = z.object({
+    stepId: z.string(),
+    title: z.string(),
+    description: z.string(),
+    confidence: z.enum(["high", "medium", "low"]),
+    noveltyStatus: z.enum(["novel", "confirmed", "partially_confirmed", "contradicted", "expected"]),
+    literatureInterpretation: z.string(),
+});
+export const BiologicalThemeSchema = z.object({
+    name: z.string(),
+    findings: z.array(z.object({ stepId: z.string(), title: z.string() })),
+    narrative: z.string(),
+});
+export const RunSynthesisPartSchema = z.object({
+    type: z.literal("data-run-synthesis"),
+    id: z.string(),
+    runId: z.string(),
+    overview: z.string(),
+    conclusions: z.string().optional(),
+    findings: z.array(SynthesizedFindingSchema),
+    themes: z.array(BiologicalThemeSchema),
+    limitations: z.array(z.string()).optional(),
+    keyReferences: z.array(z.object({
+        pmid: z.string(),
+        citation: z.string(),
+        description: z.string(),
+    })),
+});
+// ── Synthesis Progress ─────────────────────────────────────────────
+export const SynthesisPhaseSchema = z.enum([
+    "starting",
+    "researching",
+    "drafting",
+    "validating",
+    "refining",
+    "indexing",
+    "persisting",
+    "complete",
+    "skipped",
+    "failed",
+]);
+export const SynthesisProgressPartSchema = z.object({
+    type: z.literal("data-synthesis-progress"),
+    id: z.string(),
+    runId: z.string(),
+    phase: SynthesisPhaseSchema,
+    activity: z.string(),
+    delegationCount: z.number().int().nonnegative().optional(),
+    validationAttempts: z.number().int().nonnegative().optional(),
+    reason: z.string().optional(),
+    error: z.string().optional(),
+});
+// ── Run Failed ──────────────────────────────────────────────────────
+export const RunFailedPartSchema = z.object({
+    type: z.literal("data-run-failed"),
+    runId: z.string(),
+    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(),
+});
+// ── Union ───────────────────────────────────────────────────────────
+export const CortexChatPartSchema = z.discriminatedUnion("type", [
+    PresentationPartSchema,
+    PlanPartSchema,
+    RunCardPartSchema,
+    FileReferencePartSchema,
+    RunStartedPartSchema,
+    DagStatePartSchema,
+    StepActivityPartSchema,
+    StepFileTreePartSchema,
+    StepOutputPartSchema,
+    StepSummaryPartSchema,
+    StepBlockedPartSchema,
+    RunSynthesisPartSchema,
+    SynthesisProgressPartSchema,
+    RunCompletedPartSchema,
+    RunFailedPartSchema,
+    PreviewPartSchema,
+    DataPreviewFailedPartSchema,
+]);

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

@@ -0,0 +1,2 @@
+export { PlanStepSchema, PresentationContentSchema, PresentationPartSchema, PlanPartSchema, RunCardPartSchema, FileReferenceEntrySchema, FileReferencePartSchema, RunStartedPartSchema, StepStatusSchema, DagStepStateSchema, DagStatePartSchema, StepPhaseSchema, StepActivityPartSchema, FileTreeEntrySchema, StepFileTreePartSchema, StepOutputFileSchema, StepOutputPartSchema, StepSummaryPartSchema, StepBlockedPartSchema, SynthesizedFindingSchema, BiologicalThemeSchema, RunSynthesisPartSchema, SynthesisPhaseSchema, SynthesisProgressPartSchema, RunCompletedFindingSchema, RunCompletedPartSchema, RunFailedPartSchema, PreviewPartSchema, DataPreviewFailedPartSchema, CortexChatPartSchema, } from "./chat-parts.js";
+export { EventSourceSchema, TextDeltaEventSchema, ToolStartedEventSchema, ToolFinishedEventSchema, FinishEventSchema, ChatErrorEventSchema, CortexChatEventSchema, } from "./chat-events.js";

package/dist/contracts/schemas/index.js

@@ -0,0 +1,2 @@
+export { PlanStepSchema, PresentationContentSchema, PresentationPartSchema, PlanPartSchema, RunCardPartSchema, FileReferenceEntrySchema, FileReferencePartSchema, RunStartedPartSchema, StepStatusSchema, DagStepStateSchema, DagStatePartSchema, StepPhaseSchema, StepActivityPartSchema, FileTreeEntrySchema, StepFileTreePartSchema, StepOutputFileSchema, StepOutputPartSchema, StepSummaryPartSchema, StepBlockedPartSchema, SynthesizedFindingSchema, BiologicalThemeSchema, RunSynthesisPartSchema, SynthesisPhaseSchema, SynthesisProgressPartSchema, RunCompletedFindingSchema, RunCompletedPartSchema, RunFailedPartSchema, PreviewPartSchema, DataPreviewFailedPartSchema, CortexChatPartSchema, } from "./chat-parts.js";
+export { EventSourceSchema, TextDeltaEventSchema, ToolStartedEventSchema, ToolFinishedEventSchema, FinishEventSchema, ChatErrorEventSchema, CortexChatEventSchema, } from "./chat-events.js";

package/dist/contracts/target-assessment-row.d.ts

@@ -0,0 +1,85 @@
+/**
+ * Zod schemas for the `cortex_target_assessments` row shape.
+ *
+ * Single source of truth for both Cortex (DB row mappers, HTTP routes) and
+ * downstream consumers that need to validate the row shape at runtime.
+ *
+ * The HTTP API response types in `../api/types.ts` are TypeScript-only
+ * interfaces tailored to the frontend render path; these Zod schemas describe
+ * the full DB row including DBOS workflow tracking fields.
+ */
+import { z } from "zod";
+export declare const TargetAssessmentStatusSchema: z.ZodEnum<{
+    running: "running";
+    completed: "completed";
+    failed: "failed";
+    suspended_insufficient_funds: "suspended_insufficient_funds";
+    queued: "queued";
+    deleted: "deleted";
+}>;
+export type TargetAssessmentStatus = z.infer<typeof TargetAssessmentStatusSchema>;
+export declare const TargetAssessmentErrorSchema: z.ZodObject<{
+    kind: z.ZodString;
+    message: z.ZodString;
+    details: z.ZodOptional<z.ZodUnknown>;
+}, z.core.$strip>;
+export type TargetAssessmentError = z.infer<typeof TargetAssessmentErrorSchema>;
+export declare const TargetAssessmentListRowSchema: z.ZodObject<{
+    id: z.ZodString;
+    organizationId: z.ZodString;
+    targetId: z.ZodString;
+    targetLabel: z.ZodString;
+    goal: z.ZodNullable<z.ZodString>;
+    status: z.ZodEnum<{
+        running: "running";
+        completed: "completed";
+        failed: "failed";
+        suspended_insufficient_funds: "suspended_insufficient_funds";
+        queued: "queued";
+        deleted: "deleted";
+    }>;
+    progress: z.ZodNullable<z.ZodString>;
+    billingContextId: z.ZodString;
+    error: z.ZodNullable<z.ZodObject<{
+        kind: z.ZodString;
+        message: z.ZodString;
+        details: z.ZodOptional<z.ZodUnknown>;
+    }, z.core.$strip>>;
+    requestedBy: z.ZodString;
+    workflowRunId: z.ZodNullable<z.ZodString>;
+    workflowId: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+    createdAt: z.ZodString;
+    updatedAt: z.ZodString;
+    completedAt: z.ZodNullable<z.ZodString>;
+}, z.core.$strip>;
+export type TargetAssessmentListRow = z.infer<typeof TargetAssessmentListRowSchema>;
+export declare const TargetAssessmentRowSchema: z.ZodObject<{
+    id: z.ZodString;
+    organizationId: z.ZodString;
+    targetId: z.ZodString;
+    targetLabel: z.ZodString;
+    goal: z.ZodNullable<z.ZodString>;
+    status: z.ZodEnum<{
+        running: "running";
+        completed: "completed";
+        failed: "failed";
+        suspended_insufficient_funds: "suspended_insufficient_funds";
+        queued: "queued";
+        deleted: "deleted";
+    }>;
+    progress: z.ZodNullable<z.ZodString>;
+    billingContextId: z.ZodString;
+    error: z.ZodNullable<z.ZodObject<{
+        kind: z.ZodString;
+        message: z.ZodString;
+        details: z.ZodOptional<z.ZodUnknown>;
+    }, z.core.$strip>>;
+    requestedBy: z.ZodString;
+    workflowRunId: z.ZodNullable<z.ZodString>;
+    workflowId: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+    createdAt: z.ZodString;
+    updatedAt: z.ZodString;
+    completedAt: z.ZodNullable<z.ZodString>;
+    dossier: z.ZodNullable<z.ZodRecord<z.ZodString, z.ZodUnknown>>;
+}, z.core.$strip>;
+export type TargetAssessmentRow = z.infer<typeof TargetAssessmentRowSchema>;

package/dist/contracts/target-assessment-row.js

@@ -0,0 +1,37 @@
+/**
+ * Zod schemas for the `cortex_target_assessments` row shape.
+ *
+ * Single source of truth for both Cortex (DB row mappers, HTTP routes) and
+ * downstream consumers that need to validate the row shape at runtime.
+ *
+ * The HTTP API response types in `../api/types.ts` are TypeScript-only
+ * interfaces tailored to the frontend render path; these Zod schemas describe
+ * the full DB row including DBOS workflow tracking fields.
+ */
+import { z } from "zod";
+export const TargetAssessmentStatusSchema = z.enum(["queued", "running", "completed", "failed", "deleted", "suspended_insufficient_funds"]);
+export const TargetAssessmentErrorSchema = z.object({
+    kind: z.string(),
+    message: z.string(),
+    details: z.unknown().optional(),
+});
+export const TargetAssessmentListRowSchema = z.object({
+    id: z.string().uuid(),
+    organizationId: z.string(),
+    targetId: z.string(),
+    targetLabel: z.string(),
+    goal: z.string().nullable(),
+    status: TargetAssessmentStatusSchema,
+    progress: z.string().nullable(),
+    billingContextId: z.string(),
+    error: TargetAssessmentErrorSchema.nullable(),
+    requestedBy: z.string(),
+    workflowRunId: z.string().nullable(),
+    workflowId: z.string().nullable().optional(),
+    createdAt: z.string(),
+    updatedAt: z.string(),
+    completedAt: z.string().nullable(),
+});
+export const TargetAssessmentRowSchema = TargetAssessmentListRowSchema.extend({
+    dossier: z.record(z.string(), z.unknown()).nullable(),
+});