@inflexa-ai/harness 0.45.0 → 0.46.0

package/dist/schemas/file-metadata.js

@@ -1,6 +1,5 @@
 import { z } from "zod";
-export const FileMetadataSchema = z
-    .object({
+export const FileMetadataSchema = z.looseObject({
     role: z.enum(["input", "step_output"]),
     dataType: z.string(),
     format: z.string(),
@@ -14,8 +13,7 @@ export const FileMetadataSchema = z
     featureType: z.string().optional(),
     tags: z.array(z.string()).optional(),
     warnings: z.array(z.string()).optional(),
-})
-    .passthrough();
+});
 /**
  * One file's metadata as submitted by the describer agent through the
  * `submit_file_metadata` tool. Keyed by `path` — the tool validates each

package/dist/schemas/plan-schemas.d.ts

@@ -7,12 +7,16 @@ import type { AnalysisPlan } from "./workflow-state.js";
 /** Step schema for planner output — omits fields populated at execution time
  *  and the hardcoded sandbox turn budget. */
 export declare const PlanStepSchema: z.ZodObject<{
+    id: z.ZodString;
     name: z.ZodString;
+    track: z.ZodString;
+    step_type: z.ZodString;
+    question: z.ZodString;
     context: z.ZodOptional<z.ZodString>;
-    description: z.ZodOptional<z.ZodString>;
-    id: z.ZodString;
+    constraints: z.ZodOptional<z.ZodArray<z.ZodString>>;
+    acceptance_criteria: z.ZodArray<z.ZodString>;
     caveats: z.ZodOptional<z.ZodArray<z.ZodString>>;
-    question: z.ZodString;
+    packages: z.ZodNonOptional<z.ZodOptional<z.ZodArray<z.ZodString>>>;
     depends_on: z.ZodArray<z.ZodString>;
     resources: z.ZodNonOptional<z.ZodOptional<z.ZodObject<{
         cpu: z.ZodNumber;
@@ -21,11 +25,25 @@ export declare const PlanStepSchema: z.ZodObject<{
             count: z.ZodNumber;
         }, z.core.$strip>>;
     }, z.core.$strip>>>;
-    track: z.ZodString;
-    step_type: z.ZodString;
-    acceptance_criteria: z.ZodArray<z.ZodString>;
-    constraints: z.ZodOptional<z.ZodArray<z.ZodString>>;
-    packages: z.ZodNonOptional<z.ZodOptional<z.ZodArray<z.ZodString>>>;
+    grounding: z.ZodOptional<z.ZodObject<{
+        status: z.ZodEnum<{
+            flagged: "flagged";
+            grounded: "grounded";
+            ungrounded: "ungrounded";
+        }>;
+        snapshot: z.ZodString;
+        claims: z.ZodArray<z.ZodString>;
+        template: z.ZodOptional<z.ZodString>;
+        settings: z.ZodOptional<z.ZodArray<z.ZodObject<{
+            step: z.ZodString;
+            name: z.ZodString;
+            value: z.ZodUnion<readonly [z.ZodString, z.ZodNumber, z.ZodBoolean, z.ZodArray<z.ZodString>]>;
+            source: z.ZodOptional<z.ZodString>;
+        }, z.core.$strip>>>;
+        reason: z.ZodString;
+    }, z.core.$strip>>;
+    capability: z.ZodNonOptional<z.ZodOptional<z.ZodString>>;
+    description: z.ZodOptional<z.ZodString>;
     agent: z.ZodEnum<{
         [x: string]: string;
     }>;
@@ -40,12 +58,16 @@ export declare const PlannerPlanSchema: z.ZodObject<{
     omicsSubtype: z.ZodOptional<z.ZodString>;
     title: z.ZodString;
     steps: z.ZodArray<z.ZodObject<{
+        id: z.ZodString;
         name: z.ZodString;
+        track: z.ZodString;
+        step_type: z.ZodString;
+        question: z.ZodString;
         context: z.ZodOptional<z.ZodString>;
-        description: z.ZodOptional<z.ZodString>;
-        id: z.ZodString;
+        constraints: z.ZodOptional<z.ZodArray<z.ZodString>>;
+        acceptance_criteria: z.ZodArray<z.ZodString>;
         caveats: z.ZodOptional<z.ZodArray<z.ZodString>>;
-        question: z.ZodString;
+        packages: z.ZodNonOptional<z.ZodOptional<z.ZodArray<z.ZodString>>>;
         depends_on: z.ZodArray<z.ZodString>;
         resources: z.ZodNonOptional<z.ZodOptional<z.ZodObject<{
             cpu: z.ZodNumber;
@@ -54,11 +76,25 @@ export declare const PlannerPlanSchema: z.ZodObject<{
                 count: z.ZodNumber;
             }, z.core.$strip>>;
         }, z.core.$strip>>>;
-        track: z.ZodString;
-        step_type: z.ZodString;
-        acceptance_criteria: z.ZodArray<z.ZodString>;
-        constraints: z.ZodOptional<z.ZodArray<z.ZodString>>;
-        packages: z.ZodNonOptional<z.ZodOptional<z.ZodArray<z.ZodString>>>;
+        grounding: z.ZodOptional<z.ZodObject<{
+            status: z.ZodEnum<{
+                flagged: "flagged";
+                grounded: "grounded";
+                ungrounded: "ungrounded";
+            }>;
+            snapshot: z.ZodString;
+            claims: z.ZodArray<z.ZodString>;
+            template: z.ZodOptional<z.ZodString>;
+            settings: z.ZodOptional<z.ZodArray<z.ZodObject<{
+                step: z.ZodString;
+                name: z.ZodString;
+                value: z.ZodUnion<readonly [z.ZodString, z.ZodNumber, z.ZodBoolean, z.ZodArray<z.ZodString>]>;
+                source: z.ZodOptional<z.ZodString>;
+            }, z.core.$strip>>>;
+            reason: z.ZodString;
+        }, z.core.$strip>>;
+        capability: z.ZodNonOptional<z.ZodOptional<z.ZodString>>;
+        description: z.ZodOptional<z.ZodString>;
         agent: z.ZodEnum<{
             [x: string]: string;
         }>;
@@ -70,9 +106,9 @@ export declare function hydratePlanSteps(plannerPlan: PlannerPlan): AnalysisPlan
 /** Schema for the planning agent's structured output. */
 export declare const PlanningAgentOutputSchema: z.ZodObject<{
     event: z.ZodEnum<{
+        clarification_needed: "clarification_needed";
         error: "error";
         plan_complete: "plan_complete";
-        clarification_needed: "clarification_needed";
     }>;
     planId: z.ZodOptional<z.ZodString>;
     plan: z.ZodOptional<z.ZodObject<{
@@ -82,12 +118,16 @@ export declare const PlanningAgentOutputSchema: z.ZodObject<{
         omicsSubtype: z.ZodOptional<z.ZodString>;
         title: z.ZodString;
         steps: z.ZodArray<z.ZodObject<{
+            id: z.ZodString;
             name: z.ZodString;
+            track: z.ZodString;
+            step_type: z.ZodString;
+            question: z.ZodString;
             context: z.ZodOptional<z.ZodString>;
-            description: z.ZodOptional<z.ZodString>;
-            id: z.ZodString;
+            constraints: z.ZodOptional<z.ZodArray<z.ZodString>>;
+            acceptance_criteria: z.ZodArray<z.ZodString>;
             caveats: z.ZodOptional<z.ZodArray<z.ZodString>>;
-            question: z.ZodString;
+            packages: z.ZodNonOptional<z.ZodOptional<z.ZodArray<z.ZodString>>>;
             depends_on: z.ZodArray<z.ZodString>;
             resources: z.ZodNonOptional<z.ZodOptional<z.ZodObject<{
                 cpu: z.ZodNumber;
@@ -96,11 +136,25 @@ export declare const PlanningAgentOutputSchema: z.ZodObject<{
                     count: z.ZodNumber;
                 }, z.core.$strip>>;
             }, z.core.$strip>>>;
-            track: z.ZodString;
-            step_type: z.ZodString;
-            acceptance_criteria: z.ZodArray<z.ZodString>;
-            constraints: z.ZodOptional<z.ZodArray<z.ZodString>>;
-            packages: z.ZodNonOptional<z.ZodOptional<z.ZodArray<z.ZodString>>>;
+            grounding: z.ZodOptional<z.ZodObject<{
+                status: z.ZodEnum<{
+                    flagged: "flagged";
+                    grounded: "grounded";
+                    ungrounded: "ungrounded";
+                }>;
+                snapshot: z.ZodString;
+                claims: z.ZodArray<z.ZodString>;
+                template: z.ZodOptional<z.ZodString>;
+                settings: z.ZodOptional<z.ZodArray<z.ZodObject<{
+                    step: z.ZodString;
+                    name: z.ZodString;
+                    value: z.ZodUnion<readonly [z.ZodString, z.ZodNumber, z.ZodBoolean, z.ZodArray<z.ZodString>]>;
+                    source: z.ZodOptional<z.ZodString>;
+                }, z.core.$strip>>>;
+                reason: z.ZodString;
+            }, z.core.$strip>>;
+            capability: z.ZodNonOptional<z.ZodOptional<z.ZodString>>;
+            description: z.ZodOptional<z.ZodString>;
             agent: z.ZodEnum<{
                 [x: string]: string;
             }>;

package/dist/schemas/plan-schemas.js

@@ -17,7 +17,7 @@ export const PlanStepSchema = AnalysisStepSchema.omit({
     error: true,
     maxSteps: true,
 })
-    .required({ agent: true, resources: true, packages: true })
+    .required({ agent: true, resources: true, packages: true, capability: true })
     .extend({
     agent: z.enum(plannableAgentIds).describe("Sandbox agent ID, routed by the step's primary data object. Must be one of the available agents."),
 });

package/dist/schemas/run-synthesis.d.ts

@@ -15,10 +15,10 @@ export declare const LiteratureReferenceSchema: z.ZodObject<{
     citation: z.ZodString;
     relevance: z.ZodString;
     concordance: z.ZodEnum<{
-        supports: "supports";
+        contextualizes: "contextualizes";
         contradicts: "contradicts";
         extends: "extends";
-        contextualizes: "contextualizes";
+        supports: "supports";
     }>;
 }, z.core.$strip>;
 export declare const SynthesizedFindingSchema: z.ZodObject<{
@@ -26,16 +26,16 @@ export declare const SynthesizedFindingSchema: z.ZodObject<{
     title: z.ZodString;
     description: z.ZodString;
     confidence: z.ZodEnum<{
+        high: "high";
         low: "low";
         medium: "medium";
-        high: "high";
     }>;
     noveltyStatus: z.ZodEnum<{
-        novel: "novel";
         confirmed: "confirmed";
-        partially_confirmed: "partially_confirmed";
         contradicted: "contradicted";
         expected: "expected";
+        novel: "novel";
+        partially_confirmed: "partially_confirmed";
     }>;
     literatureInterpretation: z.ZodString;
     references: z.ZodArray<z.ZodObject<{
@@ -43,29 +43,29 @@ export declare const SynthesizedFindingSchema: z.ZodObject<{
         citation: z.ZodString;
         relevance: z.ZodString;
         concordance: z.ZodEnum<{
-            supports: "supports";
+            contextualizes: "contextualizes";
             contradicts: "contradicts";
             extends: "extends";
-            contextualizes: "contextualizes";
+            supports: "supports";
         }>;
     }, z.core.$strip>>;
     translationalRelevance: z.ZodOptional<z.ZodObject<{
         stage: z.ZodEnum<{
-            discovery: "discovery";
-            "preclinical-validation": "preclinical-validation";
             "biomarker-candidate": "biomarker-candidate";
             "clinical-evidence": "clinical-evidence";
+            discovery: "discovery";
+            "preclinical-validation": "preclinical-validation";
         }>;
         actionType: z.ZodOptional<z.ZodEnum<{
+            "mechanism-of-action": "mechanism-of-action";
             none: "none";
-            "therapeutic-target": "therapeutic-target";
+            "patient-stratification": "patient-stratification";
+            "pharmacodynamic-biomarker": "pharmacodynamic-biomarker";
             "predictive-biomarker": "predictive-biomarker";
             "prognostic-biomarker": "prognostic-biomarker";
-            "pharmacodynamic-biomarker": "pharmacodynamic-biomarker";
-            "safety-signal": "safety-signal";
             "resistance-mechanism": "resistance-mechanism";
-            "patient-stratification": "patient-stratification";
-            "mechanism-of-action": "mechanism-of-action";
+            "safety-signal": "safety-signal";
+            "therapeutic-target": "therapeutic-target";
         }>>;
         rationale: z.ZodString;
     }, z.core.$strip>>;
@@ -92,16 +92,16 @@ export declare const RunSynthesisSchema: z.ZodObject<{
         title: z.ZodString;
         description: z.ZodString;
         confidence: z.ZodEnum<{
+            high: "high";
             low: "low";
             medium: "medium";
-            high: "high";
         }>;
         noveltyStatus: z.ZodEnum<{
-            novel: "novel";
             confirmed: "confirmed";
-            partially_confirmed: "partially_confirmed";
             contradicted: "contradicted";
             expected: "expected";
+            novel: "novel";
+            partially_confirmed: "partially_confirmed";
         }>;
         literatureInterpretation: z.ZodString;
         references: z.ZodArray<z.ZodObject<{
@@ -109,29 +109,29 @@ export declare const RunSynthesisSchema: z.ZodObject<{
             citation: z.ZodString;
             relevance: z.ZodString;
             concordance: z.ZodEnum<{
-                supports: "supports";
+                contextualizes: "contextualizes";
                 contradicts: "contradicts";
                 extends: "extends";
-                contextualizes: "contextualizes";
+                supports: "supports";
             }>;
         }, z.core.$strip>>;
         translationalRelevance: z.ZodOptional<z.ZodObject<{
             stage: z.ZodEnum<{
-                discovery: "discovery";
-                "preclinical-validation": "preclinical-validation";
                 "biomarker-candidate": "biomarker-candidate";
                 "clinical-evidence": "clinical-evidence";
+                discovery: "discovery";
+                "preclinical-validation": "preclinical-validation";
             }>;
             actionType: z.ZodOptional<z.ZodEnum<{
+                "mechanism-of-action": "mechanism-of-action";
                 none: "none";
-                "therapeutic-target": "therapeutic-target";
+                "patient-stratification": "patient-stratification";
+                "pharmacodynamic-biomarker": "pharmacodynamic-biomarker";
                 "predictive-biomarker": "predictive-biomarker";
                 "prognostic-biomarker": "prognostic-biomarker";
-                "pharmacodynamic-biomarker": "pharmacodynamic-biomarker";
-                "safety-signal": "safety-signal";
                 "resistance-mechanism": "resistance-mechanism";
-                "patient-stratification": "patient-stratification";
-                "mechanism-of-action": "mechanism-of-action";
+                "safety-signal": "safety-signal";
+                "therapeutic-target": "therapeutic-target";
             }>>;
             rationale: z.ZodString;
         }, z.core.$strip>>;
@@ -156,3 +156,72 @@ export type SynthesizedFinding = z.infer<typeof SynthesizedFindingSchema>;
 export type BiologicalTheme = z.infer<typeof BiologicalThemeSchema>;
 export type LiteratureReference = z.infer<typeof LiteratureReferenceSchema>;
 export type KeyReference = z.infer<typeof KeyReferenceSchema>;
+/** The synthesis that the synthesizer submits. The host stamps the run id, thus the model never types it. */
+export declare const SynthesisDraftSchema: z.ZodObject<{
+    overview: z.ZodString;
+    conclusions: z.ZodString;
+    findings: z.ZodArray<z.ZodObject<{
+        stepId: z.ZodString;
+        title: z.ZodString;
+        description: z.ZodString;
+        confidence: z.ZodEnum<{
+            high: "high";
+            low: "low";
+            medium: "medium";
+        }>;
+        noveltyStatus: z.ZodEnum<{
+            confirmed: "confirmed";
+            contradicted: "contradicted";
+            expected: "expected";
+            novel: "novel";
+            partially_confirmed: "partially_confirmed";
+        }>;
+        literatureInterpretation: z.ZodString;
+        references: z.ZodArray<z.ZodObject<{
+            pmid: z.ZodString;
+            citation: z.ZodString;
+            relevance: z.ZodString;
+            concordance: z.ZodEnum<{
+                contextualizes: "contextualizes";
+                contradicts: "contradicts";
+                extends: "extends";
+                supports: "supports";
+            }>;
+        }, z.core.$strip>>;
+        translationalRelevance: z.ZodOptional<z.ZodObject<{
+            stage: z.ZodEnum<{
+                "biomarker-candidate": "biomarker-candidate";
+                "clinical-evidence": "clinical-evidence";
+                discovery: "discovery";
+                "preclinical-validation": "preclinical-validation";
+            }>;
+            actionType: z.ZodOptional<z.ZodEnum<{
+                "mechanism-of-action": "mechanism-of-action";
+                none: "none";
+                "patient-stratification": "patient-stratification";
+                "pharmacodynamic-biomarker": "pharmacodynamic-biomarker";
+                "predictive-biomarker": "predictive-biomarker";
+                "prognostic-biomarker": "prognostic-biomarker";
+                "resistance-mechanism": "resistance-mechanism";
+                "safety-signal": "safety-signal";
+                "therapeutic-target": "therapeutic-target";
+            }>>;
+            rationale: z.ZodString;
+        }, z.core.$strip>>;
+    }, z.core.$strip>>;
+    themes: z.ZodArray<z.ZodObject<{
+        name: z.ZodString;
+        findings: z.ZodArray<z.ZodObject<{
+            stepId: z.ZodString;
+            title: z.ZodString;
+        }, z.core.$strip>>;
+        narrative: z.ZodString;
+    }, z.core.$strip>>;
+    limitations: z.ZodArray<z.ZodString>;
+    keyReferences: z.ZodArray<z.ZodObject<{
+        pmid: z.ZodString;
+        citation: z.ZodString;
+        description: z.ZodString;
+    }, z.core.$strip>>;
+}, z.core.$strip>;
+export type SynthesisDraft = z.infer<typeof SynthesisDraftSchema>;

package/dist/schemas/run-synthesis.js

@@ -97,7 +97,7 @@ export const KeyReferenceSchema = z.object({
     description: z.string().describe("What the paper establishes and why it is key to this run."),
 });
 export const RunSynthesisSchema = z.object({
-    runId: z.string().describe("The run being synthesized. Must equal the runId given in the prompt."),
+    runId: z.string().describe("The run being synthesized."),
     overview: z
         .string()
         .describe("2-4 sentences: the run's scope, the top-line result, and the most important takeaway. " +
@@ -122,3 +122,5 @@ export const RunSynthesisSchema = z.object({
         .array(KeyReferenceSchema)
         .describe("The 5-10 most important papers across all findings. Prioritize those that directly validate, contradict, or extend the findings — do not pad with background citations."),
 });
+/** The synthesis that the synthesizer submits. The host stamps the run id, thus the model never types it. */
+export const SynthesisDraftSchema = RunSynthesisSchema.omit({ runId: true });

package/dist/schemas/validate-plan.d.ts

@@ -13,11 +13,11 @@
  */
 import type { ResourceLimits } from "../config/resource-limits.js";
 import type { AnalysisPlan } from "./workflow-state.js";
-export interface ValidationResult {
+export type ValidationResult = {
     valid: boolean;
     errors: string[];
-}
-export interface ValidatePlanOptions {
+};
+export type ValidatePlanOptions = {
     /**
      * Host per-step resource ceilings. When present, a step whose declared
      * `resources` exceed them is an error — the planner gets actionable
@@ -27,7 +27,7 @@ export interface ValidatePlanOptions {
      * sandbox-creation clamp remains their backstop).
      */
     readonly perStepCeiling?: ResourceLimits;
-}
+};
 /** Derive a filesystem-safe output prefix from a step ID. */
 export declare function deriveOutputPrefix(stepId: string): string;
 /**

package/dist/schemas/validate-plan.js

@@ -11,6 +11,8 @@
  * 3. All agent assignments exist in the agent catalog
  * 4. All steps have resources defined
  */
+import { errorMessageOf } from "../lib/thrown.js";
+import { textOf } from "../lib/unknown-text.js";
 import { KNOWN_AGENT_IDS } from "../agents/sandbox-catalog.js";
 import { CycleError, DependencyError, topoSortIntoWaves } from "../execution/topo-sort.js";
 import { parseQuery } from "../sandbox/package-identity.js";
@@ -52,10 +54,20 @@ function describeParseError(stepId, entry, error) {
 }
 /** Derive a filesystem-safe output prefix from a step ID. */
 export function deriveOutputPrefix(stepId) {
-    return stepId
-        .toLowerCase()
-        .replace(/[^a-z0-9]+/g, "-")
-        .replace(/^-|-$/g, "");
+    let out = "";
+    let inRun = false;
+    for (const char of stepId.toLowerCase()) {
+        const isSlugChar = (char >= "a" && char <= "z") || (char >= "0" && char <= "9");
+        if (!isSlugChar) {
+            inRun = true;
+            continue;
+        }
+        if (inRun && out.length > 0)
+            out += "-";
+        inRun = false;
+        out += char;
+    }
+    return out;
 }
 /**
  * Validate an analysis plan for structural correctness.
@@ -80,7 +92,7 @@ export function validatePlan(plan, options) {
             errors.push(`Step "${err.stepId}" depends on "${err.missingDependency}" which does not exist in the plan`);
         }
         else {
-            errors.push(`Topological sort failed: ${err instanceof Error ? err.message : String(err)}`);
+            errors.push(`Topological sort failed: ${errorMessageOf(err) ?? textOf(err)}`);
         }
     }
     // 2. Output prefix uniqueness