@inflexa-ai/harness 0.16.0 → 0.18.0

package/dist/workflows/target-assessment/steps/phase2-aggregate.d.ts

@@ -11,68 +11,6 @@
  * compiles, but nothing populates them.
  */
 import { z } from "zod";
-export declare const Phase2AggregateInputSchema: z.ZodObject<{
-    "decision-modulator-triage": z.ZodDiscriminatedUnion<[z.ZodObject<{
-        coverage: z.ZodLiteral<"available">;
-        data: z.ZodObject<{
-            shortlist: z.ZodArray<z.ZodObject<{
-                moleculeChemblId: z.ZodString;
-                preferredName: z.ZodString;
-                maxPhase: z.ZodNullable<z.ZodNumber>;
-                firstApproval: z.ZodNullable<z.ZodNumber>;
-                rationale: z.ZodString;
-            }, z.core.$strip>>;
-            notes: z.ZodString;
-            dropped_synonyms: z.ZodDefault<z.ZodArray<z.ZodObject<{
-                chemblId: z.ZodString;
-                reason: z.ZodEnum<{
-                    same_active_substance: "same_active_substance";
-                    ambiguous_name_synonym: "ambiguous_name_synonym";
-                }>;
-                keptId: z.ZodNullable<z.ZodString>;
-            }, z.core.$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.$strip>], "coverage">;
-    "decision-drugs-in-class": z.ZodDiscriminatedUnion<[z.ZodObject<{
-        coverage: z.ZodLiteral<"available">;
-        data: z.ZodObject<{
-            drugs: z.ZodArray<z.ZodObject<{
-                moleculeChemblId: z.ZodString;
-                preferredName: z.ZodString;
-                maxPhase: z.ZodNullable<z.ZodNumber>;
-                firstApproval: z.ZodNullable<z.ZodNumber>;
-                moleculeType: z.ZodNullable<z.ZodString>;
-                sources: z.ZodArray<z.ZodEnum<{
-                    dgidb: "dgidb";
-                    drugbank: "drugbank";
-                    chembl: "chembl";
-                }>>;
-            }, z.core.$strip>>;
-            total: z.ZodNumber;
-            truncated: z.ZodBoolean;
-        }, 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 declare const Phase2BundleSchema: z.ZodObject<{
     phase1: z.ZodObject<{
         resolved: z.ZodObject<{
@@ -336,10 +274,10 @@ export declare const Phase2BundleSchema: z.ZodObject<{
                         tissues: z.ZodArray<z.ZodObject<{
                             tissue: z.ZodString;
                             rank: z.ZodEnum<{
+                                absent: "absent";
                                 high: "high";
                                 medium: "medium";
                                 low: "low";
-                                absent: "absent";
                             }>;
                             expressionScore: z.ZodNullable<z.ZodNumber>;
                         }, z.core.$strip>>;
@@ -543,6 +481,31 @@ export declare const Phase2BundleSchema: z.ZodObject<{
                 coverage: z.ZodLiteral<"not_loaded">;
                 reason: z.ZodOptional<z.ZodString>;
             }, z.core.$strip>], "coverage">;
+            monarch: z.ZodDiscriminatedUnion<[z.ZodObject<{
+                coverage: z.ZodLiteral<"available">;
+                data: z.ZodObject<{
+                    geneCurie: z.ZodString;
+                    phenotypes: z.ZodArray<z.ZodObject<{
+                        hpoId: z.ZodString;
+                        label: z.ZodString;
+                        ancestorIds: z.ZodArray<z.ZodString>;
+                        publications: z.ZodArray<z.ZodString>;
+                        diseaseContext: z.ZodNullable<z.ZodString>;
+                        frequencyPercent: z.ZodNullable<z.ZodNumber>;
+                        primaryKnowledgeSource: 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">;
             therapeuticPrograms: z.ZodOptional<z.ZodDiscriminatedUnion<[z.ZodObject<{
                 coverage: z.ZodLiteral<"available">;
                 data: z.ZodObject<{
@@ -560,6 +523,7 @@ export declare const Phase2BundleSchema: z.ZodObject<{
                         evidence: z.ZodArray<z.ZodObject<{
                             pmid: z.ZodOptional<z.ZodString>;
                             doi: z.ZodOptional<z.ZodString>;
+                            accession: z.ZodOptional<z.ZodString>;
                             source: z.ZodString;
                             predicate: z.ZodOptional<z.ZodString>;
                             score: z.ZodOptional<z.ZodNumber>;

package/dist/workflows/target-assessment/steps/phase2-aggregate.js

@@ -23,10 +23,6 @@ const StubOffTargetCuratorSchema = z.object({
     truncated: z.boolean().default(false),
     notes: z.string().default(""),
 });
-export const Phase2AggregateInputSchema = z.object({
-    "decision-modulator-triage": withCoverage(ModulatorTriageOutputSchema),
-    "decision-drugs-in-class": withCoverage(DrugsInClassOutputSchema),
-});
 export const Phase2BundleSchema = z.object({
     phase1: Phase1BundleSchema,
     decisions: z.object({

package/dist/workflows/target-assessment/steps/phase3-aggregate.d.ts

@@ -3,160 +3,6 @@
  * type-checking. The DBOS workflow assembles the Phase-3 bundle inline.
  */
 import { z } from "zod";
-export declare const Phase3AggregateInputSchema: z.ZodObject<{
-    "per-modulator-faers": 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>;
-    "per-trial-aes": 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>;
-    "per-modulator-polypharm": 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>;
-                    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.$strip>;
-    "per-class-drug-aes": z.ZodObject<{
-        results: z.ZodArray<z.ZodDiscriminatedUnion<[z.ZodObject<{
-            coverage: z.ZodLiteral<"available">;
-            data: z.ZodObject<{
-                moleculeChemblId: z.ZodString;
-                preferredName: z.ZodString;
-                totalReports: z.ZodNullable<z.ZodNumber>;
-                topReactions: z.ZodArray<z.ZodObject<{
-                    reaction: z.ZodString;
-                    count: z.ZodNumber;
-                }, z.core.$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.$strip>;
-}, z.core.$strip>;
 export declare const Phase3BundleSchema: z.ZodObject<{
     phase2: z.ZodObject<{
         phase1: z.ZodObject<{
@@ -421,10 +267,10 @@ export declare const Phase3BundleSchema: z.ZodObject<{
                             tissues: z.ZodArray<z.ZodObject<{
                                 tissue: z.ZodString;
                                 rank: z.ZodEnum<{
+                                    absent: "absent";
                                     high: "high";
                                     medium: "medium";
                                     low: "low";
-                                    absent: "absent";
                                 }>;
                                 expressionScore: z.ZodNullable<z.ZodNumber>;
                             }, z.core.$strip>>;
@@ -628,6 +474,31 @@ export declare const Phase3BundleSchema: z.ZodObject<{
                     coverage: z.ZodLiteral<"not_loaded">;
                     reason: z.ZodOptional<z.ZodString>;
                 }, z.core.$strip>], "coverage">;
+                monarch: z.ZodDiscriminatedUnion<[z.ZodObject<{
+                    coverage: z.ZodLiteral<"available">;
+                    data: z.ZodObject<{
+                        geneCurie: z.ZodString;
+                        phenotypes: z.ZodArray<z.ZodObject<{
+                            hpoId: z.ZodString;
+                            label: z.ZodString;
+                            ancestorIds: z.ZodArray<z.ZodString>;
+                            publications: z.ZodArray<z.ZodString>;
+                            diseaseContext: z.ZodNullable<z.ZodString>;
+                            frequencyPercent: z.ZodNullable<z.ZodNumber>;
+                            primaryKnowledgeSource: 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">;
                 therapeuticPrograms: z.ZodOptional<z.ZodDiscriminatedUnion<[z.ZodObject<{
                     coverage: z.ZodLiteral<"available">;
                     data: z.ZodObject<{
@@ -645,6 +516,7 @@ export declare const Phase3BundleSchema: z.ZodObject<{
                             evidence: z.ZodArray<z.ZodObject<{
                                 pmid: z.ZodOptional<z.ZodString>;
                                 doi: z.ZodOptional<z.ZodString>;
+                                accession: z.ZodOptional<z.ZodString>;
                                 source: z.ZodString;
                                 predicate: z.ZodOptional<z.ZodString>;
                                 score: z.ZodOptional<z.ZodNumber>;
@@ -880,6 +752,7 @@ export declare const Phase3BundleSchema: z.ZodObject<{
                     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>;

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

@@ -5,12 +5,6 @@
 import { z } from "zod";
 import { Phase2BundleSchema } from "./phase2-aggregate.js";
 import { PerModulatorFaersResultsSchema, PerTrialAEsResultsSchema, PerModulatorPolypharmResultsSchema, PerClassDrugAEsResultsSchema, } from "../sub-workflows/index.js";
-export const Phase3AggregateInputSchema = z.object({
-    "per-modulator-faers": PerModulatorFaersResultsSchema,
-    "per-trial-aes": PerTrialAEsResultsSchema,
-    "per-modulator-polypharm": PerModulatorPolypharmResultsSchema,
-    "per-class-drug-aes": PerClassDrugAEsResultsSchema,
-});
 export const Phase3BundleSchema = z.object({
     phase2: Phase2BundleSchema,
     fanout: z.object({

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

@@ -26,9 +26,3 @@ export interface BuildDiagnosticsRowInput {
     errorMessage?: string | null;
 }
 export declare function buildDiagnosticsRow(input: BuildDiagnosticsRowInput): SynthesisDiagnosticRow;
-/**
- * Build a "skipped" diagnostics row for the case where the step never
- * even attempted an LLM call (e.g., upstream coverage was not_loaded
- * and the step short-circuited).
- */
-export declare function buildSkippedDiagnosticsRow(stepId: StepId, modelId: string, reason: string): SynthesisDiagnosticRow;

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

@@ -25,21 +25,3 @@ export function buildDiagnosticsRow(input) {
         error_message: input.errorMessage ?? null,
     };
 }
-/**
- * Build a "skipped" diagnostics row for the case where the step never
- * even attempted an LLM call (e.g., upstream coverage was not_loaded
- * and the step short-circuited).
- */
-export function buildSkippedDiagnosticsRow(stepId, modelId, reason) {
-    return {
-        step_id: stepId,
-        model_id: modelId,
-        attempt_count: 1,
-        retry_critique: null,
-        output_chars: 0,
-        probe_verdict: "skipped",
-        final_coverage: "queried_no_data",
-        error_kind: null,
-        error_message: reason,
-    };
-}

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

@@ -15,6 +15,7 @@ export declare const PerModulatorPolypharmResultsSchema: z.ZodObject<{
             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>;

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

@@ -16,7 +16,7 @@
  * post-402 call lands a fresh cache slot.
  */
 import { z } from "zod";
-import { type DossierV4Body } from "@inflexa-ai/harness/contracts/target-dossier.js";
+import { type DossierBody } from "@inflexa-ai/harness/contracts/target-dossier.js";
 import type { AgentSession } from "../../../auth/types.js";
 import type { AgentChat } from "../../../providers/types.js";
 import { BUDGET_EXCEEDED_SENTINEL } from "../lib/llm-step.js";
@@ -45,7 +45,31 @@ export declare const LiabilityBulletsOutputSchema: z.ZodObject<{
 export type LiabilityBulletsOutput = z.infer<typeof LiabilityBulletsOutputSchema>;
 export declare const SafetyFlagsTrailOutputSchema: z.ZodObject<{
     flags: z.ZodArray<z.ZodObject<{
-        organ: z.ZodString;
+        organ: 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";
+        }>;
+        severity: z.ZodEnum<{
+            high: "high";
+            medium: "medium";
+            low: "low";
+        }>;
         trail: z.ZodString;
         mechanism_hypothesis: z.ZodNullable<z.ZodString>;
     }, z.core.$strip>>;
@@ -77,7 +101,6 @@ export declare const ExternalCitationSchema: z.ZodObject<{
     fetched_at: z.ZodOptional<z.ZodString>;
     excerpt: z.ZodString;
 }, z.core.$strip>;
-export type ExternalCitation = z.infer<typeof ExternalCitationSchema>;
 export declare const DossierRecommendationOutputSchema: z.ZodObject<{
     disposition: z.ZodEnum<{
         pursue: "pursue";
@@ -225,7 +248,31 @@ export declare const SafetyFlagsTrailStepOutputSchema: z.ZodDiscriminatedUnion<[
     coverage: z.ZodLiteral<"available">;
     data: z.ZodObject<{
         flags: z.ZodArray<z.ZodObject<{
-            organ: z.ZodString;
+            organ: 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";
+            }>;
+            severity: z.ZodEnum<{
+                high: "high";
+                medium: "medium";
+                low: "low";
+            }>;
             trail: z.ZodString;
             mechanism_hypothesis: z.ZodNullable<z.ZodString>;
         }, z.core.$strip>>;
@@ -543,7 +590,7 @@ declare function isBudgetExceeded<T>(v: SynthesisStepResult<T>): v is {
 };
 interface Phase4Output {
     readonly assessmentId: string;
-    readonly dossier: DossierV4Body;
+    readonly dossier: DossierBody;
 }
 export declare function liabilityBullets(phase4: Phase4Output, deps: SynthesisAgentDeps): Promise<SynthesisStepResult<LiabilityBulletsStepOutput>>;
 export declare function safetyFlagsTrail(phase4: Phase4Output, deps: SynthesisAgentDeps): Promise<SynthesisStepResult<SafetyFlagsTrailStepOutput>>;

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

@@ -17,6 +17,8 @@
  */
 import { z } from "zod";
 import { SynthesisDiagnosticRowSchema } from "@inflexa-ai/harness/contracts/target-dossier.js";
+import { OrganSystemSchema } from "../../../contracts/organ-system.js";
+import { SeveritySchema } from "../../../contracts/severity.js";
 import { executiveRecommendationBrief, liabilityBulletsBrief, targetOrganLiabilitiesBrief, translationalCommentaryBrief, } from "../../../prompts/target-assessment/briefs/index.js";
 import { toxVoiceCore, toxVoiceExemplars } from "../../../prompts/target-assessment/tox-voice/index.js";
 import { SerializedErrorSchema } from "../coverage.js";
@@ -37,7 +39,8 @@ export const LiabilityBulletsOutputSchema = z.object({
 });
 export const SafetyFlagsTrailOutputSchema = z.object({
     flags: z.array(z.object({
-        organ: z.string(),
+        organ: OrganSystemSchema,
+        severity: SeveritySchema,
         trail: z.string(),
         mechanism_hypothesis: z.string().nullable(),
     })),

package/dist/workflows/target-assessment/synthesis-probes.d.ts

@@ -17,7 +17,7 @@
  * Threshold tuning: the constants block at the top of this file is the
  * single source of truth. Adjust there, never inline.
  */
-import type { DossierV4Body, DossierV5Body } from "@inflexa-ai/harness/contracts/target-dossier.js";
+import type { DossierBody } from "@inflexa-ai/harness/contracts/target-dossier.js";
 import type { DossierRecommendationOutput, LiabilityBulletsOutput, SafetyFlagsTrailOutput, TranslationalCommentaryOutput } from "./synthesis/index.js";
 export declare const PROBE_THRESHOLDS: {
     readonly recommendation: {
@@ -50,7 +50,7 @@ export declare function countSectionReferences(text: string): {
 export declare function countSourceReferences(text: string): {
     matchedSources: string[];
 };
-export declare function probeRecommendation(out: DossierRecommendationOutput, dossier: DossierV4Body | DossierV5Body): ProbeResult;
-export declare function probeLiabilityBullets(out: LiabilityBulletsOutput, dossier?: DossierV4Body | DossierV5Body): ProbeResult;
+export declare function probeRecommendation(out: DossierRecommendationOutput, dossier: DossierBody): ProbeResult;
+export declare function probeLiabilityBullets(out: LiabilityBulletsOutput, dossier?: DossierBody): ProbeResult;
 export declare function probeSafetyFlags(out: SafetyFlagsTrailOutput): ProbeResult;
 export declare function probeTranslationalCommentary(out: TranslationalCommentaryOutput): ProbeResult;

package/package.json

@@ -1,6 +1,6 @@
 {
     "name": "@inflexa-ai/harness",
-    "version": "0.16.0",
+    "version": "0.18.0",
     "description": "Host-agnostic bioinformatics agent harness \u2014 hand-rolled agent loop, DBOS-durable workflows, sandboxed compute.",
     "license": "Apache-2.0",
     "type": "module",
@@ -71,6 +71,7 @@
         "neverthrow": "^8.2.0",
         "nunjucks": "^3.2.4",
         "openai": "^4.104.0",
+        "p-queue": "^9.3.3",
         "pdf-parse": "^2.4.5",
         "pg": "^8.22.0",
         "puppeteer-core": "^23.11.1",
@@ -84,9 +85,11 @@
         "@types/nunjucks": "^3.2.6",
         "@types/pdf-parse": "^1.1.5",
         "@types/pg": "^8.20.0",
+        "csstree-validator": "^4.0.1",
         "eslint": "^10.7.0",
         "eslint-plugin-neverthrow": "^1.1.4",
         "globals": "^17.7.0",
+        "html-validate": "^11.6.2",
         "prettier": "^3.9.5",
         "testcontainers": "^10.28.0",
         "typescript": "^6.0.3",