@inflexa-ai/harness 0.35.7 → 0.36.0

package/dist/workflows/target-assessment/steps/phase3-aggregate.js

@@ -1,16 +0,0 @@
-/**
- * Phase 3 aggregator — schema definitions retained for downstream
- * type-checking. The DBOS workflow assembles the Phase-3 bundle inline.
- */
-import { z } from "zod";
-import { Phase2BundleSchema } from "./phase2-aggregate.js";
-import { PerModulatorFaersResultsSchema, PerTrialAEsResultsSchema, PerModulatorPolypharmResultsSchema, PerClassDrugAEsResultsSchema, } from "../sub-workflows/index.js";
-export const Phase3BundleSchema = z.object({
-    phase2: Phase2BundleSchema,
-    fanout: z.object({
-        perModulatorFaers: PerModulatorFaersResultsSchema,
-        perTrialAes: PerTrialAEsResultsSchema,
-        perModulatorPolypharm: PerModulatorPolypharmResultsSchema,
-        perClassDrugAes: PerClassDrugAEsResultsSchema,
-    }),
-});

package/dist/workflows/target-assessment/steps/synthesis/diagnostics.d.ts

@@ -1,28 +0,0 @@
-/**
- * Synthesis diagnostics row builder.
- *
- * Each Phase-5 synthesis step accumulates a single
- * `SynthesisDiagnosticRow` describing its attempt history (model id,
- * attempts, retry critique, output length, probe verdict, final
- * coverage). Phase-5 persist collects the four rows and stamps them
- * into `dossier.analytics.synthesis_diagnostics`.
- *
- * Diagnostics persist even when synthesis fails — that is the point.
- * A reader who sees `executive_recommendation.coverage = queried_no_data`
- * with `error.kind = synthesis-too-shallow` can open the diagnostics
- * row to see exactly which probe rejected the output and why.
- */
-import type { SynthesisDiagnosticRow } from "@inflexa-ai/harness/contracts/target-dossier.js";
-import type { ProbeResult } from "../../synthesis-probes.js";
-export type StepId = SynthesisDiagnosticRow["step_id"];
-export interface BuildDiagnosticsRowInput {
-    stepId: StepId;
-    modelId: string;
-    attemptCount: 1 | 2;
-    retryCritique: string | null;
-    finalProbe: ProbeResult;
-    finalCoverage: "available" | "queried_no_data";
-    errorKind?: "synthesis-too-shallow" | "synthesis-unavailable" | "voice-violation" | null;
-    errorMessage?: string | null;
-}
-export declare function buildDiagnosticsRow(input: BuildDiagnosticsRowInput): SynthesisDiagnosticRow;

package/dist/workflows/target-assessment/steps/synthesis/diagnostics.js

@@ -1,27 +0,0 @@
-/**
- * Synthesis diagnostics row builder.
- *
- * Each Phase-5 synthesis step accumulates a single
- * `SynthesisDiagnosticRow` describing its attempt history (model id,
- * attempts, retry critique, output length, probe verdict, final
- * coverage). Phase-5 persist collects the four rows and stamps them
- * into `dossier.analytics.synthesis_diagnostics`.
- *
- * Diagnostics persist even when synthesis fails — that is the point.
- * A reader who sees `executive_recommendation.coverage = queried_no_data`
- * with `error.kind = synthesis-too-shallow` can open the diagnostics
- * row to see exactly which probe rejected the output and why.
- */
-export function buildDiagnosticsRow(input) {
-    return {
-        step_id: input.stepId,
-        model_id: input.modelId,
-        attempt_count: input.attemptCount,
-        retry_critique: input.retryCritique,
-        output_chars: input.finalProbe.output_chars,
-        probe_verdict: input.finalProbe.verdict,
-        final_coverage: input.finalCoverage,
-        error_kind: input.errorKind ?? null,
-        error_message: input.errorMessage ?? null,
-    };
-}

package/dist/workflows/target-assessment/sub-workflows/index.d.ts

@@ -1,15 +0,0 @@
-/**
- * Phase-3 fan-out result schemas.
- *
- * The DBOS workflow body owns the fan-out itself (`.foreach` is replaced by
- * inline `Promise.all` over `DBOS.runStep`); this module re-exports each
- * sub-workflow's result schema.
- */
-export { PerModulatorFaersResultsSchema } from "./per-modulator-faers.js";
-export type { PerModulatorFaersResults } from "./per-modulator-faers.js";
-export { PerTrialAEsResultsSchema } from "./per-trial-aes.js";
-export type { PerTrialAEsResults } from "./per-trial-aes.js";
-export { PerModulatorPolypharmResultsSchema } from "./per-modulator-polypharm.js";
-export type { PerModulatorPolypharmResults } from "./per-modulator-polypharm.js";
-export { PerClassDrugAEsResultsSchema } from "./per-class-drug-aes.js";
-export type { PerClassDrugAEsResults } from "./per-class-drug-aes.js";

package/dist/workflows/target-assessment/sub-workflows/index.js

@@ -1,11 +0,0 @@
-/**
- * Phase-3 fan-out result schemas.
- *
- * The DBOS workflow body owns the fan-out itself (`.foreach` is replaced by
- * inline `Promise.all` over `DBOS.runStep`); this module re-exports each
- * sub-workflow's result schema.
- */
-export { PerModulatorFaersResultsSchema } from "./per-modulator-faers.js";
-export { PerTrialAEsResultsSchema } from "./per-trial-aes.js";
-export { PerModulatorPolypharmResultsSchema } from "./per-modulator-polypharm.js";
-export { PerClassDrugAEsResultsSchema } from "./per-class-drug-aes.js";

package/dist/workflows/target-assessment/sub-workflows/per-class-drug-aes.d.ts

@@ -1,41 +0,0 @@
-/**
- * Per-class-drug AEs — Phase-3 fan-out result schema.
- *
- * The DBOS workflow body drives the `.foreach` fan-out itself; this module
- * is kept for its result schema.
- */
-import { z } from "zod";
-export declare const PerClassDrugAEsResultsSchema: z.ZodObject<{
-    results: z.ZodArray<z.ZodDiscriminatedUnion<[z.ZodObject<{
-        coverage: z.ZodLiteral<"available">;
-        data: z.ZodObject<{
-            moleculeChemblId: z.ZodString;
-            preferredName: z.ZodString;
-            totalReports: z.ZodNullable<z.ZodNumber>;
-            topReactions: z.ZodArray<z.ZodObject<{
-                reaction: z.ZodString;
-                count: z.ZodNumber;
-            }, z.core.$strip>>;
-            seriousness: z.ZodNullable<z.ZodObject<{
-                totalReports: z.ZodNumber;
-                fatalCount: z.ZodNumber;
-                hospitalizationCount: z.ZodNumber;
-                lifeThreateningCount: z.ZodNumber;
-                disablingCount: z.ZodNumber;
-                congenitalAnomalyCount: z.ZodDefault<z.ZodNumber>;
-                otherSeriousCount: z.ZodDefault<z.ZodNumber>;
-            }, z.core.$strip>>;
-        }, z.core.$strip>;
-    }, z.core.$strip>, z.ZodObject<{
-        coverage: z.ZodLiteral<"queried_no_data">;
-        error: z.ZodOptional<z.ZodObject<{
-            message: z.ZodString;
-            name: z.ZodOptional<z.ZodString>;
-            stack: z.ZodOptional<z.ZodString>;
-        }, z.core.$strip>>;
-    }, z.core.$strip>, z.ZodObject<{
-        coverage: z.ZodLiteral<"not_loaded">;
-        reason: z.ZodOptional<z.ZodString>;
-    }, z.core.$strip>], "coverage">>;
-}, z.core.$strip>;
-export type PerClassDrugAEsResults = z.infer<typeof PerClassDrugAEsResultsSchema>;

package/dist/workflows/target-assessment/sub-workflows/per-class-drug-aes.js

@@ -1,12 +0,0 @@
-/**
- * Per-class-drug AEs — Phase-3 fan-out result schema.
- *
- * The DBOS workflow body drives the `.foreach` fan-out itself; this module
- * is kept for its result schema.
- */
-import { z } from "zod";
-import { PerClassDrugAEsItemSchema } from "../steps/fanout/index.js";
-import { withCoverage } from "../coverage.js";
-export const PerClassDrugAEsResultsSchema = z.object({
-    results: z.array(withCoverage(PerClassDrugAEsItemSchema)),
-});

package/dist/workflows/target-assessment/sub-workflows/per-modulator-faers.d.ts

@@ -1,41 +0,0 @@
-/**
- * Per-modulator FAERS — Phase-3 fan-out result schema.
- *
- * The DBOS workflow body drives the `.foreach` fan-out itself; this module
- * is kept for its result schema.
- */
-import { z } from "zod";
-export declare const PerModulatorFaersResultsSchema: z.ZodObject<{
-    results: z.ZodArray<z.ZodDiscriminatedUnion<[z.ZodObject<{
-        coverage: z.ZodLiteral<"available">;
-        data: z.ZodObject<{
-            moleculeChemblId: z.ZodString;
-            preferredName: z.ZodString;
-            totalReports: z.ZodNullable<z.ZodNumber>;
-            topReactions: z.ZodArray<z.ZodObject<{
-                reaction: z.ZodString;
-                count: z.ZodNumber;
-            }, z.core.$strip>>;
-            seriousness: z.ZodNullable<z.ZodObject<{
-                totalReports: z.ZodNumber;
-                fatalCount: z.ZodNumber;
-                hospitalizationCount: z.ZodNumber;
-                lifeThreateningCount: z.ZodNumber;
-                disablingCount: z.ZodNumber;
-                congenitalAnomalyCount: z.ZodDefault<z.ZodNumber>;
-                otherSeriousCount: z.ZodDefault<z.ZodNumber>;
-            }, z.core.$strip>>;
-        }, z.core.$strip>;
-    }, z.core.$strip>, z.ZodObject<{
-        coverage: z.ZodLiteral<"queried_no_data">;
-        error: z.ZodOptional<z.ZodObject<{
-            message: z.ZodString;
-            name: z.ZodOptional<z.ZodString>;
-            stack: z.ZodOptional<z.ZodString>;
-        }, z.core.$strip>>;
-    }, z.core.$strip>, z.ZodObject<{
-        coverage: z.ZodLiteral<"not_loaded">;
-        reason: z.ZodOptional<z.ZodString>;
-    }, z.core.$strip>], "coverage">>;
-}, z.core.$strip>;
-export type PerModulatorFaersResults = z.infer<typeof PerModulatorFaersResultsSchema>;

package/dist/workflows/target-assessment/sub-workflows/per-modulator-faers.js

@@ -1,12 +0,0 @@
-/**
- * Per-modulator FAERS — Phase-3 fan-out result schema.
- *
- * The DBOS workflow body drives the `.foreach` fan-out itself; this module
- * is kept for its result schema.
- */
-import { z } from "zod";
-import { PerModulatorFaersItemSchema } from "../steps/fanout/index.js";
-import { withCoverage } from "../coverage.js";
-export const PerModulatorFaersResultsSchema = z.object({
-    results: z.array(withCoverage(PerModulatorFaersItemSchema)),
-});

package/dist/workflows/target-assessment/sub-workflows/per-modulator-polypharm.d.ts

@@ -1,37 +0,0 @@
-/**
- * Per-modulator polypharmacology — Phase-3 fan-out result schema.
- *
- * The DBOS workflow body drives the `.foreach` fan-out itself; this module
- * is kept for its result schema.
- */
-import { z } from "zod";
-export declare const PerModulatorPolypharmResultsSchema: z.ZodObject<{
-    results: z.ZodArray<z.ZodDiscriminatedUnion<[z.ZodObject<{
-        coverage: z.ZodLiteral<"available">;
-        data: z.ZodObject<{
-            moleculeChemblId: z.ZodString;
-            preferredName: z.ZodString;
-            primaryPchembl: z.ZodNullable<z.ZodNumber>;
-            hits: z.ZodArray<z.ZodObject<{
-                targetChemblId: z.ZodString;
-                targetName: z.ZodNullable<z.ZodString>;
-                assayChemblId: z.ZodNullable<z.ZodString>;
-                pchemblValue: z.ZodNullable<z.ZodNumber>;
-                standardType: z.ZodNullable<z.ZodString>;
-                standardValue: z.ZodNullable<z.ZodNumber>;
-                standardUnits: z.ZodNullable<z.ZodString>;
-            }, z.core.$strip>>;
-        }, z.core.$strip>;
-    }, z.core.$strip>, z.ZodObject<{
-        coverage: z.ZodLiteral<"queried_no_data">;
-        error: z.ZodOptional<z.ZodObject<{
-            message: z.ZodString;
-            name: z.ZodOptional<z.ZodString>;
-            stack: z.ZodOptional<z.ZodString>;
-        }, z.core.$strip>>;
-    }, z.core.$strip>, z.ZodObject<{
-        coverage: z.ZodLiteral<"not_loaded">;
-        reason: z.ZodOptional<z.ZodString>;
-    }, z.core.$strip>], "coverage">>;
-}, z.core.$strip>;
-export type PerModulatorPolypharmResults = z.infer<typeof PerModulatorPolypharmResultsSchema>;

package/dist/workflows/target-assessment/sub-workflows/per-modulator-polypharm.js

@@ -1,12 +0,0 @@
-/**
- * Per-modulator polypharmacology — Phase-3 fan-out result schema.
- *
- * The DBOS workflow body drives the `.foreach` fan-out itself; this module
- * is kept for its result schema.
- */
-import { z } from "zod";
-import { PerModulatorPolypharmItemSchema } from "../steps/fanout/index.js";
-import { withCoverage } from "../coverage.js";
-export const PerModulatorPolypharmResultsSchema = z.object({
-    results: z.array(withCoverage(PerModulatorPolypharmItemSchema)),
-});

package/dist/workflows/target-assessment/sub-workflows/per-trial-aes.d.ts

@@ -1,66 +0,0 @@
-/**
- * Per-trial AEs — Phase-3 fan-out result schema.
- *
- * The DBOS workflow body drives the `.foreach` fan-out itself; this module
- * is kept for its result schema.
- */
-import { z } from "zod";
-export declare const PerTrialAEsResultsSchema: z.ZodObject<{
-    results: z.ZodArray<z.ZodDiscriminatedUnion<[z.ZodObject<{
-        coverage: z.ZodLiteral<"available">;
-        data: z.ZodObject<{
-            nctId: z.ZodString;
-            title: z.ZodString;
-            whyStopped: z.ZodNullable<z.ZodString>;
-            outcomes: z.ZodDefault<z.ZodArray<z.ZodObject<{
-                type: z.ZodEnum<{
-                    other: "other";
-                    primary: "primary";
-                    secondary: "secondary";
-                }>;
-                measure: z.ZodString;
-                description: z.ZodNullable<z.ZodString>;
-                timeFrame: z.ZodNullable<z.ZodString>;
-                effect: z.ZodDiscriminatedUnion<[z.ZodObject<{
-                    kind: z.ZodLiteral<"quantitative">;
-                    value: z.ZodNumber;
-                    units: z.ZodString;
-                    ci_low: z.ZodOptional<z.ZodNumber>;
-                    ci_high: z.ZodOptional<z.ZodNumber>;
-                }, z.core.$strip>, z.ZodObject<{
-                    kind: z.ZodLiteral<"not_extracted">;
-                    reason: z.ZodEnum<{
-                        ctgov_no_numeric_result: "ctgov_no_numeric_result";
-                        ctgov_no_result_groups: "ctgov_no_result_groups";
-                    }>;
-                }, z.core.$strip>], "kind">;
-            }, z.core.$strip>>>;
-            groups: z.ZodArray<z.ZodObject<{
-                groupId: z.ZodString;
-                title: z.ZodString;
-                description: z.ZodNullable<z.ZodString>;
-            }, z.core.$strip>>;
-            events: z.ZodArray<z.ZodObject<{
-                serious: z.ZodBoolean;
-                term: z.ZodString;
-                organSystem: z.ZodNullable<z.ZodString>;
-                counts: z.ZodArray<z.ZodObject<{
-                    groupId: z.ZodString;
-                    numAffected: z.ZodNullable<z.ZodNumber>;
-                    numAtRisk: z.ZodNullable<z.ZodNumber>;
-                }, z.core.$strip>>;
-            }, z.core.$strip>>;
-        }, z.core.$strip>;
-    }, z.core.$strip>, z.ZodObject<{
-        coverage: z.ZodLiteral<"queried_no_data">;
-        error: z.ZodOptional<z.ZodObject<{
-            message: z.ZodString;
-            name: z.ZodOptional<z.ZodString>;
-            stack: z.ZodOptional<z.ZodString>;
-        }, z.core.$strip>>;
-    }, z.core.$strip>, z.ZodObject<{
-        coverage: z.ZodLiteral<"not_loaded">;
-        reason: z.ZodOptional<z.ZodString>;
-    }, z.core.$strip>], "coverage">>;
-}, z.core.$strip>;
-export type PerTrialAEsResults = z.infer<typeof PerTrialAEsResultsSchema>;

package/dist/workflows/target-assessment/sub-workflows/per-trial-aes.js

@@ -1,12 +0,0 @@
-/**
- * Per-trial AEs — Phase-3 fan-out result schema.
- *
- * The DBOS workflow body drives the `.foreach` fan-out itself; this module
- * is kept for its result schema.
- */
-import { z } from "zod";
-import { PerTrialAEsItemSchema } from "../steps/fanout/index.js";
-import { withCoverage } from "../coverage.js";
-export const PerTrialAEsResultsSchema = z.object({
-    results: z.array(withCoverage(PerTrialAEsItemSchema)),
-});