@inflexa-ai/harness 0.29.0 → 0.30.0

package/dist/tools/research/generate-plan.js

@@ -35,6 +35,12 @@ import { defineTool } from "../define-tool.js";
 import { createListAvailablePackagesTool } from "../sandbox/list-available-packages.js";
 import { createListAvailableRefsTool } from "../sandbox/list-available-refs.js";
 import { createReportBlockerToolFor } from "../sandbox/report-blocker.js";
+import { searchGeoDatasetsTool } from "../bio/search-geo-datasets.js";
+import { createNcbiTools } from "../bio/keys.js";
+import { queryDocsTool, resolveLibraryIdTool } from "./context7-docs.js";
+import { searchArxivTool } from "./search-arxiv.js";
+import { createSearchGithubReposTool } from "./search-github-repos.js";
+import { createSearchSemanticScholarTool } from "./search-semantic-scholar.js";
 import { DATA_PROFILE_ORIENTATION_MAX_CHARS, buildDataProfileOrientation } from "../../app/data-profile-orientation.js";
 import { DEFAULT_SANDBOX_MAX_STEPS } from "../../config/resource-limits.js";
 import { plannerPrompt } from "../../prompts/planner.js";
@@ -49,10 +55,17 @@ import { insertPlan, loadDataProfileStatus, loadPlan } from "../../state/index.j
 /** Sub-agent identity for the planner — provenance only. */
 const PLANNER_AGENT_ID = "planner";
 /**
- * Budget for the planner's internal loop: one draft/submit attempt plus
- * correction retries and headroom.
+ * Budget for the planner's internal loop: the research phase, one draft/submit
+ * attempt, correction retries, and headroom.
+ *
+ * The number is deliberately far above what a plan costs. A well-grounded plan
+ * still costs two or three calls, because the prompt gates the research phase on
+ * what the seed does not already answer. What the ceiling must never do is stop
+ * a planner that is searching correctly. A capped run takes the forced wrap-up
+ * path and submits the plan that it had, not the plan that it was building.
+ * Thus the wall-clock guard, not this number, is what bounds the worst case.
  */
-const PLANNER_MAX_ITERATIONS = 13;
+const PLANNER_MAX_ITERATIONS = 200;
 /** Wall-clock guard for a single plan-generation invocation. */
 const PLAN_TIMEOUT_MS = 600_000;
 // ── Diagnostic bounds ───────────────────────────────────────────────
@@ -71,7 +84,7 @@ const MAX_LOGGED_ISSUE_CHARS = 240;
 const MAX_LOGGED_REJECTIONS = 6;
 /** Excerpt of the planner's last words — the one artifact that explains a run ending on prose. */
 const MAX_LOGGED_PROSE_CHARS = 800;
-/** Tool-call trace length. The planner's whole budget is ~16 turns, so this rarely truncates. */
+/** Tool-call trace length. A long research phase passes it, and `toolCallsTruncated` marks the record when it does. */
 const MAX_LOGGED_TOOL_CALLS = 48;
 /** Trim to `max`, marking the cut so a truncated value never reads as a complete one. */
 function bounded(value, max) {
@@ -629,6 +642,44 @@ const OUTCOME_LEVEL = {
     invalid_parent_plan: "warn",
     parent_plan_load_failed: "error",
 };
+/**
+ * The search tools of the planner — built one time, not per invocation.
+ *
+ * The set answers the two questions that a seed cannot. "What did a study of
+ * this kind do before?" reaches the public dataset records and the literature.
+ * "What does this package actually give me?" reaches the developer docs. The
+ * planner reads its reference and package inventories from the seed, thus the
+ * docs pair is what turns a package name into a real function.
+ *
+ * A tool here never writes and never computes. Thus the worst outcome of a
+ * needless call is latency, and the prompt is what bounds that.
+ */
+function buildPlannerSearchTools(deps) {
+    const bioKeys = deps.bioKeys;
+    const ncbi = createNcbiTools(bioKeys);
+    return [
+        // Comparable public studies — the design, the platform, and the sample
+        // count that a plan for the same assay must answer to.
+        searchGeoDatasetsTool,
+        // Prior methods, in three corpora that do not overlap: the biomedical
+        // literature, the statistics and machine-learning preprints, and the
+        // cross-field index that ranks a method paper best.
+        ncbi.pubmed,
+        searchArxivTool,
+        createSearchSemanticScholarTool({ ...(bioKeys.semanticScholar === undefined ? {} : { apiKey: bioKeys.semanticScholar }) }),
+        // The same approach as running code — a pipeline that someone published.
+        createSearchGithubReposTool({ githubToken: bioKeys.github }),
+        // The API of a staged package, so a step names a function that exists.
+        resolveLibraryIdTool,
+        queryDocsTool,
+        // The environment itself. The seed already carries a rendered census of
+        // both stores. These two tools are for the narrow second look: one
+        // collection of the reference store, or one package name that a step is
+        // about to import.
+        createListAvailableRefsTool(deps.refStorePath === undefined ? {} : { refStorePath: deps.refStorePath }),
+        createListAvailablePackagesTool(deps.packagesFile === undefined ? {} : { packagesFile: deps.packagesFile }),
+    ];
+}
 /** Build the `generate_plan` tool bound to its provider and pool. */
 export function createGeneratePlanTool(deps) {
     const baseLogger = (deps.logger ?? createNoopLogger()).named("generate-plan");
@@ -806,11 +857,19 @@ export function createGeneratePlanTool(deps) {
                 parentPlanId: input.parentPlanId ?? null,
             };
             const innerTools = buildInnerTools(holder, trace, persistCtx, deps.pool, deps.resourcePolicy, logger);
+            // Built here rather than at construction: a `describeCall` hook reads no
+            // dep, thus the tool must stay constructible from an empty bag. The tool
+            // definitions are identical across invocations, thus the request prefix
+            // that the cache keys on does not move.
+            const searchTools = buildPlannerSearchTools(deps);
             const planner = {
                 id: PLANNER_AGENT_ID,
                 systemPrompt: composeSystemPrompt(plannerInstructions(deps.resourcePolicy)),
                 model: deps.conversation.model,
-                tools: innerTools.terminal,
+                // The search tools come first, and the terminal tools come last.
+                // The order is the order of the prompt, and it is stable across
+                // every invocation, thus the cached request prefix holds.
+                tools: [...searchTools, ...innerTools.terminal],
                 maxIterations: PLANNER_MAX_ITERATIONS,
             };
             // Merge the outer abort signal with a wall-clock timeout — either

package/dist/tools/research/resolve-citation.js

@@ -4,10 +4,15 @@ import { defineTool } from "../define-tool.js";
 export function createResolveCitationTool(resolver) {
     return defineTool({
         id: "resolve_citation",
-        description: "Verify one supplied citation against applicable bibliographic authorities. " +
-            "Use this for 'does this reference exist and does its metadata agree?', not for topical literature discovery. " +
+        description: "Verify one supplied citation against the applicable bibliographic authorities — the DOI registry, Crossref, PubMed, arXiv and Semantic " +
+            "Scholar — and report where they agree. " +
+            "Use this for 'does this reference exist and does its metadata agree?', not for topical literature discovery: pubmed, " +
+            "search_semantic_scholar and search_arxiv are the discovery tools.\n" +
+            "ACCEPTED IDENTIFIERS: a DOI ('10.1038/nature12373'), a PMID ('23945592'), an arXiv ID ('2301.00001'), or raw bibliographic text. Each " +
+            "authority that the input cannot address is marked not_applicable rather than queried.\n" +
             "Returns source-labelled records, field comparisons, conflicts, coverage, and one of verified, metadata_mismatch, " +
-            "not_found, unverifiable, or inconclusive. Source failure never becomes not_found.",
+            "not_found, unverifiable, or inconclusive. Source failure never becomes not_found — an unreachable authority reports unavailable, and " +
+            "not_found means the authorities that answered hold no such record.",
         inputSchema: CitationInputSchema,
         describeCall: ({ citation }) => `verify ${citation}`,
         execute: async (input, ctx) => ok(await resolver.resolveOne(input, { signal: ctx.signal })),

package/dist/tools/research/search-arxiv.js

@@ -7,9 +7,14 @@ export { parseArxivAtom } from "../../literature/sources/arxiv.js";
 const source = createArxivSource({ maxRetries: 3, retryDelayMs: 1_000, timeoutMs: 90_000 });
 export const searchArxivTool = defineTool({
     id: "search_arxiv",
-    description: "Search arXiv for preprints in ML, physics, math, control theory, " +
-        "economics, and related quantitative fields. Returns id, title, " +
-        "abstract, authors, publication date, arXiv categories, and URLs.",
+    description: "Search arXiv — the open preprint server of Cornell University — for work in machine learning, physics, math, quantitative biology, control " +
+        "theory, economics and the related quantitative fields. Returns id, title, abstract, authors, publication date, arXiv categories, and URLs.\n" +
+        "It carries PREPRINTS, thus a paper here may not be peer reviewed, and it is where a method appears months before a journal holds it. For the " +
+        "clinical and biomedical literature use pubmed, which indexes MEDLINE; for cross-domain coverage of any field use search_semantic_scholar.\n" +
+        "ACCEPTED IDENTIFIERS: free text in `query`, and arXiv category codes in `categories` ('cs.LG', 'q-bio.GN', 'math.OC'). An arXiv ID " +
+        "('2301.00001') also matches as free text.\n" +
+        "ABSENCE IS NORMAL: an empty papers array means arXiv holds nothing for the query, and `success: false` with an `error` string means the service " +
+        "could not be reached. Report either one and continue, do not retry unchanged.",
     inputSchema: z.object({
         query: z.string().describe('Free-text query. Example: "adaptive control feedback stabilization".'),
         categories: z

package/dist/tools/research/search-semantic-scholar.js

@@ -13,10 +13,16 @@ export function createSearchSemanticScholarTool(options = {}) {
     });
     return defineTool({
         id: "search_semantic_scholar",
-        description: "Search Semantic Scholar for academic papers across all sciences " +
-            "(biology, ML, physics, math, economics, engineering, etc.). Returns " +
-            "paper id, title, abstract, year, venue, citation count, authors, and " +
-            "external IDs (DOI, ArXiv). Best for cross-domain analogical search.",
+        description: "Search Semantic Scholar — the cross-disciplinary literature corpus of the Allen Institute for AI, which indexes over 200M papers across " +
+            "biology, medicine, machine learning, physics, math, economics and engineering. Returns paper id, title, abstract, year, venue, citation " +
+            "count, authors, and external IDs (DOI, arXiv). Its citation counts are what rank a field by influence, and its breadth is what makes it the " +
+            "tool for a cross-domain analogical search.\n" +
+            "For the clinical and biomedical literature alone, pubmed indexes MEDLINE more precisely; for preprints in the quantitative fields use " +
+            "search_arxiv.\n" +
+            "ACCEPTED IDENTIFIERS: free text in `query`. A DOI or an arXiv ID also matches as free text, and each result carries its DOI and arXiv ID " +
+            "back for a citation.\n" +
+            "ABSENCE IS NORMAL: an empty papers array means the corpus holds nothing for the query, and `success: false` with an `error` string means the " +
+            "service could not be reached (its unkeyed rate limit lands here). Report either one and continue, do not retry unchanged.",
         inputSchema: z.object({
             query: z
                 .string()

package/dist/workflows/sandbox-step.d.ts

@@ -106,6 +106,12 @@ export interface SandboxStepInput {
  * declare it explicitly.
  */
 export declare const DEFAULT_STEP_TIMEOUT_SECONDS = 3600;
+/**
+ * Deterministic `blocked_reason` for a loop that spent every iteration and
+ * persisted no output files (see the harness-sandbox-agents spec). Fixed prose,
+ * never model output — the summarizer does not run on this path.
+ */
+export declare const CAPPED_OUT_EMPTY_REASON = "The step hit its iteration cap with no output files persisted.";
 export type SandboxStepStatus = "complete" | "failed" | "canceled" | "blocked";
 /**
  * DBOS message topic the child uses to notify the parent that it is

package/dist/workflows/sandbox-step.js

@@ -46,6 +46,12 @@ import { createBlockerHolder } from "../tools/sandbox/report-blocker.js";
  * declare it explicitly.
  */
 export const DEFAULT_STEP_TIMEOUT_SECONDS = 3600;
+/**
+ * Deterministic `blocked_reason` for a loop that spent every iteration and
+ * persisted no output files (see the harness-sandbox-agents spec). Fixed prose,
+ * never model output — the summarizer does not run on this path.
+ */
+export const CAPPED_OUT_EMPTY_REASON = "The step hit its iteration cap with no output files persisted.";
 /**
  * DBOS message topic the child uses to notify the parent that it is
  * about to self-cancel because of a 402 budget-exceeded error. The
@@ -427,20 +433,36 @@ export async function runSandboxStepBody(input, deps) {
             usage: stepUsage,
         });
     }
+    // Manifest walk, hoisted above the blocked branch so the capped-out
+    // predicate can read it. The call is inline (not `DBOS.runStep`-wrapped),
+    // so the hoist shifts no function id (see the harness-durable-runtime spec).
+    const manifest = await safeRunValue(logger, () => walkStepArtifacts({
+        writePrefix,
+        stepId: input.stepId,
+        runId: input.runId,
+    }), "post-step.walk", []);
     // Blocker (see the harness-sandbox-agents spec): the agent declared it cannot fulfil the step. A
     // blocked step has no deliverables — skip the artifact post-step pipeline,
     // mark `blocked` (carrying the reason), emit the blocked part, and return a
     // terminal-failure status so the parent's fail-fast cascade fires.
+    //
+    // The capped-out empty case routes into the same branch: a loop that spent
+    // every iteration and persisted nothing has no deliverables, and a green
+    // status would attest an empty step. A blocker outcome keeps its own
+    // reason. A capped-out step WITH artifacts stays on the completed path,
+    // because partial output is real output.
     const blockerOutcome = blockerHolder.outcome;
-    if (blockerOutcome) {
+    const cappedOutEmpty = hitMaxSteps && manifest.length === 0;
+    if (blockerOutcome || cappedOutEmpty) {
+        const blockedReason = blockerOutcome?.reason ?? CAPPED_OUT_EMPTY_REASON;
         await tryTeardown(logger, deps, sandbox);
         const durationMs = (await DBOS.now()) - startedAt;
         await DBOS.runStep(async () => {
             unwrapOrThrow(await updateStepExecution(deps.pool, input.runId, input.stepId, {
                 status: "blocked",
                 durationMs,
-                error: blockerOutcome.reason,
-                blockedReason: blockerOutcome.reason,
+                error: blockedReason,
+                blockedReason,
                 attempts: 1,
                 lastErrorClass: "blocked",
                 finishReason,
@@ -453,21 +475,21 @@ export async function runSandboxStepBody(input, deps) {
             runId: input.runId,
             stepId: input.stepId,
             agentId: input.agentId,
-            reason: blockerOutcome.reason,
+            reason: blockedReason,
         });
         await emitActivity("failed", "Step blocked");
         return {
             status: "blocked",
             durationMs,
             finishReason,
-            error: blockerOutcome.reason,
+            error: blockedReason,
             ...(stepUsage ? { usage: stepUsage } : {}),
         };
     }
-    // (4-8) post-step — the body is the explicit composition: walk the artifact
-    // tree once, then thread each stage's typed output into the next. Helpers
-    // run inline (not `DBOS.runStep`-wrapped), so a replay re-executes this
-    // section. Each helper is best-effort (`safeRun*` logs + degrades) so a
+    // (4-8) post-step — the body is the explicit composition: the manifest from
+    // the single walk above threads each stage's typed output into the next.
+    // Helpers run inline (not `DBOS.runStep`-wrapped), so a replay re-executes
+    // this section. Each helper is best-effort (`safeRun*` logs + degrades) so a
     // single failure never fails the step.
     const postCtx = {
         input,
@@ -478,11 +500,6 @@ export async function runSandboxStepBody(input, deps) {
         lineageCollector,
     };
     await emitActivity("generating-metadata", "Describing output files");
-    const manifest = await safeRunValue(logger, () => walkStepArtifacts({
-        writePrefix,
-        stepId: input.stepId,
-        runId: input.runId,
-    }), "post-step.walk", []);
     // The two post-step LLM producers are wrapped in `DBOS.runStep` so their
     // outputs are checkpointed (see the harness-durable-runtime spec): the conditional terminal emits they
     // gate (`data-step-summary`, file-tree) stay replay-stable and the billed

package/dist/workflows/target-assessment/assemblers/safety.d.ts

@@ -319,7 +319,7 @@ export declare function aggregateClassPrecedent(phase2: Phase2Bundle, fanout: Fa
 } | null;
 export declare function buildOrganRollup(faers: ReturnType<typeof aggregateFaersAcrossModulators>, trialAes: ReturnType<typeof aggregateTrialAes>, offTarget: OffTargetPanelRows | null, classP: ReturnType<typeof aggregateClassPrecedent>, regulatoryActions?: RegulatoryActionRow[] | null): {
     organ: "hematologic" | "metabolic" | "immune" | "hepatic" | "musculoskeletal" | "cns" | "renal" | "reproductive" | "respiratory" | "cardiac" | "vascular" | "pns" | "gi" | "pancreas" | "endocrine_thyroid" | "dermatologic" | "ocular" | "oncology";
-    risk_level: "high" | "medium" | "low";
+    risk_level: "low" | "medium" | "high";
     signal_type_count: number;
     signals: {
         chembl_polypharm_count: number;

package/dist/workflows/target-assessment/phase4-assemble.d.ts

@@ -442,9 +442,9 @@ export declare const Phase4OutputSchema: z.ZodObject<{
                         start_date: z.ZodNullable<z.ZodString>;
                         completion_date: z.ZodNullable<z.ZodString>;
                         match_confidence: z.ZodEnum<{
-                            high: "high";
-                            medium: "medium";
                             low: "low";
+                            medium: "medium";
+                            high: "high";
                             off_target: "off_target";
                         }>;
                         attribution: z.ZodObject<{
@@ -499,9 +499,9 @@ export declare const Phase4OutputSchema: z.ZodObject<{
                         start_date: z.ZodNullable<z.ZodString>;
                         completion_date: z.ZodNullable<z.ZodString>;
                         match_confidence: z.ZodEnum<{
-                            high: "high";
-                            medium: "medium";
                             low: "low";
+                            medium: "medium";
+                            high: "high";
                             off_target: "off_target";
                         }>;
                         attribution: z.ZodObject<{
@@ -855,9 +855,9 @@ export declare const Phase4OutputSchema: z.ZodObject<{
                             oncology: "oncology";
                         }>;
                         risk_level: z.ZodEnum<{
-                            high: "high";
-                            medium: "medium";
                             low: "low";
+                            medium: "medium";
+                            high: "high";
                         }>;
                         signal_type_count: z.ZodNumber;
                         signals: z.ZodObject<{
@@ -1409,9 +1409,9 @@ export declare const Phase4OutputSchema: z.ZodObject<{
                         trail: z.ZodString;
                         mechanism_hypothesis: z.ZodOptional<z.ZodNullable<z.ZodString>>;
                         severity: z.ZodEnum<{
-                            high: "high";
-                            medium: "medium";
                             low: "low";
+                            medium: "medium";
+                            high: "high";
                         }>;
                         support: z.ZodDiscriminatedUnion<[z.ZodObject<{
                             state: z.ZodLiteral<"scored">;
@@ -2462,11 +2462,11 @@ export declare const Phase4OutputSchema: z.ZodObject<{
                                 dog: "dog";
                             }>;
                             rank: z.ZodEnum<{
+                                low: "low";
+                                medium: "medium";
+                                high: "high";
                                 no_data: "no_data";
                                 absent: "absent";
-                                high: "high";
-                                medium: "medium";
-                                low: "low";
                                 not_loaded: "not_loaded";
                             }>;
                         }, z.core.$strip>>;
@@ -2800,9 +2800,9 @@ export declare const Phase4OutputSchema: z.ZodObject<{
                         start_date: z.ZodOptional<z.ZodString>;
                         completion_date: z.ZodOptional<z.ZodString>;
                         match_confidence: z.ZodEnum<{
-                            high: "high";
-                            medium: "medium";
                             low: "low";
+                            medium: "medium";
+                            high: "high";
                         }>;
                         relevance_basis: z.ZodDiscriminatedUnion<[z.ZodObject<{
                             kind: z.ZodLiteral<"drug_in_class_match">;
@@ -2869,9 +2869,9 @@ export declare const Phase4OutputSchema: z.ZodObject<{
                         start_date: z.ZodOptional<z.ZodString>;
                         completion_date: z.ZodOptional<z.ZodString>;
                         match_confidence: z.ZodEnum<{
-                            high: "high";
-                            medium: "medium";
                             low: "low";
+                            medium: "medium";
+                            high: "high";
                         }>;
                         relevance_basis: z.ZodDiscriminatedUnion<[z.ZodObject<{
                             kind: z.ZodLiteral<"drug_in_class_match">;
@@ -3122,9 +3122,9 @@ export declare const Phase4OutputSchema: z.ZodObject<{
                     insufficient_evidence: "insufficient_evidence";
                 }>;
                 confidence: z.ZodEnum<{
-                    high: "high";
-                    medium: "medium";
                     low: "low";
+                    medium: "medium";
+                    high: "high";
                 }>;
                 rationale: z.ZodString;
                 key_strengths: z.ZodDefault<z.ZodArray<z.ZodString>>;

package/dist/workflows/target-assessment/schemas.d.ts

@@ -17,8 +17,8 @@ export declare const ResolvedTargetSchema: z.ZodObject<{
     goal: z.ZodNullable<z.ZodString>;
     canonicalId: z.ZodString;
     canonicalOntology: z.ZodEnum<{
-        ensembl: "ensembl";
         hgnc: "hgnc";
+        ensembl: "ensembl";
     }>;
     geneSymbol: z.ZodString;
     approvedName: z.ZodString;
@@ -249,10 +249,10 @@ export declare const ExpressionMultiSpeciesBundleSchema: z.ZodObject<{
         tissues: z.ZodArray<z.ZodObject<{
             tissue: z.ZodString;
             rank: z.ZodEnum<{
-                absent: "absent";
-                high: "high";
-                medium: "medium";
                 low: "low";
+                medium: "medium";
+                high: "high";
+                absent: "absent";
             }>;
             expressionScore: z.ZodNullable<z.ZodNumber>;
         }, z.core.$strip>>;
@@ -400,9 +400,9 @@ export declare const TherapeuticProgramsBundleSchema: z.ZodObject<{
             }, z.core.$strip>>;
         }, z.core.$strip>>;
         confidence: z.ZodEnum<{
-            high: "high";
-            medium: "medium";
             low: "low";
+            medium: "medium";
+            high: "high";
         }>;
     }, z.core.$strip>>;
 }, z.core.$strip>;
@@ -432,8 +432,8 @@ export declare const Phase1BundleSchema: z.ZodObject<{
         goal: z.ZodNullable<z.ZodString>;
         canonicalId: z.ZodString;
         canonicalOntology: z.ZodEnum<{
-            ensembl: "ensembl";
             hgnc: "hgnc";
+            ensembl: "ensembl";
         }>;
         geneSymbol: z.ZodString;
         approvedName: z.ZodString;
@@ -688,10 +688,10 @@ export declare const Phase1BundleSchema: z.ZodObject<{
                     tissues: z.ZodArray<z.ZodObject<{
                         tissue: z.ZodString;
                         rank: z.ZodEnum<{
-                            absent: "absent";
-                            high: "high";
-                            medium: "medium";
                             low: "low";
+                            medium: "medium";
+                            high: "high";
+                            absent: "absent";
                         }>;
                         expressionScore: z.ZodNullable<z.ZodNumber>;
                     }, z.core.$strip>>;
@@ -954,9 +954,9 @@ export declare const Phase1BundleSchema: z.ZodObject<{
                         }, z.core.$strip>>;
                     }, z.core.$strip>>;
                     confidence: z.ZodEnum<{
-                        high: "high";
-                        medium: "medium";
                         low: "low";
+                        medium: "medium";
+                        high: "high";
                     }>;
                 }, z.core.$strip>>;
             }, z.core.$strip>;

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

@@ -18,8 +18,8 @@ export declare const Phase2BundleSchema: z.ZodObject<{
             goal: z.ZodNullable<z.ZodString>;
             canonicalId: z.ZodString;
             canonicalOntology: z.ZodEnum<{
-                ensembl: "ensembl";
                 hgnc: "hgnc";
+                ensembl: "ensembl";
             }>;
             geneSymbol: z.ZodString;
             approvedName: z.ZodString;
@@ -274,10 +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";
+                                medium: "medium";
+                                high: "high";
+                                absent: "absent";
                             }>;
                             expressionScore: z.ZodNullable<z.ZodNumber>;
                         }, z.core.$strip>>;
@@ -540,9 +540,9 @@ export declare const Phase2BundleSchema: z.ZodObject<{
                             }, z.core.$strip>>;
                         }, z.core.$strip>>;
                         confidence: z.ZodEnum<{
-                            high: "high";
-                            medium: "medium";
                             low: "low";
+                            medium: "medium";
+                            high: "high";
                         }>;
                     }, z.core.$strip>>;
                 }, z.core.$strip>;

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

@@ -11,8 +11,8 @@ export declare const Phase3BundleSchema: z.ZodObject<{
                 goal: z.ZodNullable<z.ZodString>;
                 canonicalId: z.ZodString;
                 canonicalOntology: z.ZodEnum<{
-                    ensembl: "ensembl";
                     hgnc: "hgnc";
+                    ensembl: "ensembl";
                 }>;
                 geneSymbol: z.ZodString;
                 approvedName: z.ZodString;
@@ -267,10 +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";
+                                    medium: "medium";
+                                    high: "high";
+                                    absent: "absent";
                                 }>;
                                 expressionScore: z.ZodNullable<z.ZodNumber>;
                             }, z.core.$strip>>;
@@ -533,9 +533,9 @@ export declare const Phase3BundleSchema: z.ZodObject<{
                                 }, z.core.$strip>>;
                             }, z.core.$strip>>;
                             confidence: z.ZodEnum<{
-                                high: "high";
-                                medium: "medium";
                                 low: "low";
+                                medium: "medium";
+                                high: "high";
                             }>;
                         }, z.core.$strip>>;
                     }, z.core.$strip>;

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

@@ -24,9 +24,9 @@ export declare const LiabilityBulletsOutputSchema: z.ZodObject<{
     bullets: z.ZodArray<z.ZodObject<{
         organ_or_axis: z.ZodString;
         severity: z.ZodEnum<{
-            high: "high";
-            medium: "medium";
             low: "low";
+            medium: "medium";
+            high: "high";
         }>;
         text: z.ZodString;
         evidence_pointer: z.ZodString;
@@ -66,9 +66,9 @@ export declare const SafetyFlagsTrailOutputSchema: z.ZodObject<{
             oncology: "oncology";
         }>;
         severity: z.ZodEnum<{
-            high: "high";
-            medium: "medium";
             low: "low";
+            medium: "medium";
+            high: "high";
         }>;
         trail: z.ZodString;
         mechanism_hypothesis: z.ZodNullable<z.ZodString>;
@@ -109,9 +109,9 @@ export declare const DossierRecommendationOutputSchema: z.ZodObject<{
         insufficient_evidence: "insufficient_evidence";
     }>;
     confidence: z.ZodEnum<{
-        high: "high";
-        medium: "medium";
         low: "low";
+        medium: "medium";
+        high: "high";
     }>;
     rationale: z.ZodString;
     key_strengths: z.ZodArray<z.ZodString>;
@@ -146,9 +146,9 @@ export declare const LiabilityBulletsStepOutputSchema: z.ZodDiscriminatedUnion<[
         bullets: z.ZodArray<z.ZodObject<{
             organ_or_axis: z.ZodString;
             severity: z.ZodEnum<{
-                high: "high";
-                medium: "medium";
                 low: "low";
+                medium: "medium";
+                high: "high";
             }>;
             text: z.ZodString;
             evidence_pointer: z.ZodString;
@@ -269,9 +269,9 @@ export declare const SafetyFlagsTrailStepOutputSchema: z.ZodDiscriminatedUnion<[
                 oncology: "oncology";
             }>;
             severity: z.ZodEnum<{
-                high: "high";
-                medium: "medium";
                 low: "low";
+                medium: "medium";
+                high: "high";
             }>;
             trail: z.ZodString;
             mechanism_hypothesis: z.ZodNullable<z.ZodString>;
@@ -461,9 +461,9 @@ export declare const DossierRecommendationStepOutputSchema: z.ZodDiscriminatedUn
             insufficient_evidence: "insufficient_evidence";
         }>;
         confidence: z.ZodEnum<{
-            high: "high";
-            medium: "medium";
             low: "low";
+            medium: "medium";
+            high: "high";
         }>;
         rationale: z.ZodString;
         key_strengths: z.ZodArray<z.ZodString>;

package/package.json

@@ -1,6 +1,6 @@
 {
     "name": "@inflexa-ai/harness",
-    "version": "0.29.0",
+    "version": "0.30.0",
     "description": "Host-agnostic bioinformatics agent harness — hand-rolled agent loop, DBOS-durable workflows, sandboxed compute.",
     "license": "Apache-2.0",
     "type": "module",