@inflexa-ai/harness 0.35.7 → 0.36.0

package/dist/tools/lib/clinical-benchmarks-client.js

@@ -47,7 +47,7 @@ export function getBenchmarks(therapeuticArea) {
         transitions: dataset.phase_transitions[ta],
     };
 }
-/** Return the dataset's metadata for transparency in the dossier. */
+/** Return the dataset's metadata for transparency. */
 export function getDatasetAttribution() {
     const ds = loadDataset();
     return {

package/dist/tools/lib/clinical-trials-client.d.ts

@@ -1,9 +1,6 @@
 /**
  * Pure async client functions for the ClinicalTrials.gov v2 API.
  *
- * Used by target-assessment workflow steps for §2.5 (clinical record),
- * §2.6.3 (trial AEs), §2.5 (failed trials), and §6.5 (discovery trials).
- *
  * Absence policy: the API omits the key of an absent value, and its OpenAPI
  * document marks nothing as nullable. Thus a maybe-absent field carries
  * `.optional()`, not `.nullable()`.

package/dist/tools/lib/clinical-trials-client.js

@@ -1,9 +1,6 @@
 /**
  * Pure async client functions for the ClinicalTrials.gov v2 API.
  *
- * Used by target-assessment workflow steps for §2.5 (clinical record),
- * §2.6.3 (trial AEs), §2.5 (failed trials), and §6.5 (discovery trials).
- *
  * Absence policy: the API omits the key of an absent value, and its OpenAPI
  * document marks nothing as nullable. Thus a maybe-absent field carries
  * `.optional()`, not `.nullable()`.

package/dist/tools/lib/identifier-resolver.d.ts

@@ -2,10 +2,9 @@
  * Identifier resolver — combines HGNC, UniProt, Ensembl, and ChEMBL gene-name
  * fields into a single canonical entity payload with synonyms.
  *
- * Used by Phase 0 of the target-assessment workflow to resolve a user-
- * supplied target string (gene symbol, alias, UniProt accession, Ensembl
- * id, ChEMBL target id) to a canonical entity that downstream collectors
- * can key off.
+ * Resolves a user-supplied target string (gene symbol, alias, UniProt
+ * accession, Ensembl id, ChEMBL target id) to a canonical entity that a
+ * caller can key off.
  *
  * Resolution order:
  *   1. If the input matches a known id pattern (ENSG, UniProt 6-char,
@@ -84,9 +83,8 @@ export interface AutocompleteCandidate {
 /**
  * Resolve a single gene-symbol query for the autocomplete UI by fanning
  * out HGNC + UniProt + Ensembl in parallel and merging into one canonical
- * candidate. Per `target-assessment/spec.md` "Autocomplete returns
- * canonical identifiers" — three identifiers populated on one row, not
- * three separate rows.
+ * candidate: three identifiers populated on one row, not three separate
+ * rows.
  *
  * Returns `null` when none of the upstream sources find a match. Throws
  * never — failures of individual sources degrade to `null` for that field.

package/dist/tools/lib/identifier-resolver.js

@@ -2,10 +2,9 @@
  * Identifier resolver — combines HGNC, UniProt, Ensembl, and ChEMBL gene-name
  * fields into a single canonical entity payload with synonyms.
  *
- * Used by Phase 0 of the target-assessment workflow to resolve a user-
- * supplied target string (gene symbol, alias, UniProt accession, Ensembl
- * id, ChEMBL target id) to a canonical entity that downstream collectors
- * can key off.
+ * Resolves a user-supplied target string (gene symbol, alias, UniProt
+ * accession, Ensembl id, ChEMBL target id) to a canonical entity that a
+ * caller can key off.
  *
  * Resolution order:
  *   1. If the input matches a known id pattern (ENSG, UniProt 6-char,
@@ -272,9 +271,8 @@ export async function resolveTarget(input, logger) {
 /**
  * Resolve a single gene-symbol query for the autocomplete UI by fanning
  * out HGNC + UniProt + Ensembl in parallel and merging into one canonical
- * candidate. Per `target-assessment/spec.md` "Autocomplete returns
- * canonical identifiers" — three identifiers populated on one row, not
- * three separate rows.
+ * candidate: three identifiers populated on one row, not three separate
+ * rows.
  *
  * Returns `null` when none of the upstream sources find a match. Throws
  * never — failures of individual sources degrade to `null` for that field.

package/dist/tools/lib/iuphar-client.d.ts

@@ -5,9 +5,7 @@
  * Used to discover, for any HGNC target or UniProt accession, the obligate
  * heterodimer complexes that share the same primary protein (e.g., AMY1/
  * AMY2/AMY3 amylin receptors share the CT receptor protein with the
- * calcitonin receptor and differ only by their RAMP accessory). Powers
- * data-driven heterodimer filtering in target-assessment so off-target
- * panels never list a sibling receptor-complex as a developable hit.
+ * calcitonin receptor and differ only by their RAMP accessory).
  */
 import { z } from "zod";
 import type { Logger } from "../../lib/logger.js";

package/dist/tools/lib/iuphar-client.js

@@ -5,9 +5,7 @@
  * Used to discover, for any HGNC target or UniProt accession, the obligate
  * heterodimer complexes that share the same primary protein (e.g., AMY1/
  * AMY2/AMY3 amylin receptors share the CT receptor protein with the
- * calcitonin receptor and differ only by their RAMP accessory). Powers
- * data-driven heterodimer filtering in target-assessment so off-target
- * panels never list a sibling receptor-complex as a developable hit.
+ * calcitonin receptor and differ only by their RAMP accessory).
  */
 import { z } from "zod";
 import { createNoopLogger } from "../../lib/console-logger.js";

package/dist/tools/lib/opentargets-client.d.ts

@@ -1,7 +1,7 @@
 /**
  * Pure async client functions for the Open Targets Platform GraphQL API.
  *
- * Used directly by target-assessment workflow steps and by tool wrappers.
+ * Used by tool wrappers.
  *
  * Absence policy: the nullability of the GraphQL SDL encodes an absent value.
  * Open Targets answers each requested field with a key and an explicit `null`,

package/dist/tools/lib/opentargets-client.js

@@ -1,7 +1,7 @@
 /**
  * Pure async client functions for the Open Targets Platform GraphQL API.
  *
- * Used directly by target-assessment workflow steps and by tool wrappers.
+ * Used by tool wrappers.
  *
  * Absence policy: the nullability of the GraphQL SDL encodes an absent value.
  * Open Targets answers each requested field with a key and an explicit `null`,

package/dist/tools/lib/protein-family-normalize.d.ts

@@ -1,12 +1,10 @@
 /**
  * Map free-text protein-family descriptors (UniProt keywords, HGNC names,
- * GraphQL labels) to a single canonical lowercase form so the modality lookup
- * in `protein-family-modality.json` has one pattern set to match against.
+ * GraphQL labels) to a single canonical lowercase form, so a consumer has one
+ * form to match against.
  *
- * Why this exists: UniProt keyword text and the modality-JSON patterns
- * disagreed on hyphenation ("G-protein coupled receptor" vs
- * "G protein-coupled receptor"), causing every GPCR target whose UniProt
- * keyword used the hyphenated variant to fall through to the dataset default
- * modality. See review of dossier 9ad29ba5 (GLP1R) — 2026-05-13.
+ * Why this exists: UniProt keyword text varies in hyphenation
+ * ("G-protein coupled receptor" vs "G protein-coupled receptor"), thus an
+ * exact match on the raw text misses one of the two spellings.
  */
 export declare function normalizeProteinFamily(input: string | null): string | null;

package/dist/tools/lib/protein-family-normalize.js

@@ -1,13 +1,11 @@
 /**
  * Map free-text protein-family descriptors (UniProt keywords, HGNC names,
- * GraphQL labels) to a single canonical lowercase form so the modality lookup
- * in `protein-family-modality.json` has one pattern set to match against.
+ * GraphQL labels) to a single canonical lowercase form, so a consumer has one
+ * form to match against.
  *
- * Why this exists: UniProt keyword text and the modality-JSON patterns
- * disagreed on hyphenation ("G-protein coupled receptor" vs
- * "G protein-coupled receptor"), causing every GPCR target whose UniProt
- * keyword used the hyphenated variant to fall through to the dataset default
- * modality. See review of dossier 9ad29ba5 (GLP1R) — 2026-05-13.
+ * Why this exists: UniProt keyword text varies in hyphenation
+ * ("G-protein coupled receptor" vs "G protein-coupled receptor"), thus an
+ * exact match on the raw text misses one of the two spellings.
  */
 const FAMILIES = [
     {

package/dist/tools/lib/uniprot-client.d.ts

@@ -2,13 +2,6 @@
  * Pure async client functions for the UniProt REST API
  * (https://rest.uniprot.org/uniprotkb/).
  *
- * Used by target-assessment as the source of truth for:
- *   - ChEMBL cross-references — every ChEMBL target id linked to a UniProt
- *     accession (replaces the hand-curated ALTERNATE_CHEMBL_IDS map).
- *   - Protein family text — used together with IUPHAR family-target
- *     resolution to identify sibling receptors in the same pharmacological
- *     family (replaces the hand-curated RELATED_FAMILY_UNIPROTS map).
- *
  * Absence policy: the OpenAPI document of UniProt marks no field as required,
  * and the API omits the key of an absent value. Thus a maybe-absent field
  * carries `.optional()`, not `.nullable()`.

package/dist/tools/lib/uniprot-client.js

@@ -2,13 +2,6 @@
  * Pure async client functions for the UniProt REST API
  * (https://rest.uniprot.org/uniprotkb/).
  *
- * Used by target-assessment as the source of truth for:
- *   - ChEMBL cross-references — every ChEMBL target id linked to a UniProt
- *     accession (replaces the hand-curated ALTERNATE_CHEMBL_IDS map).
- *   - Protein family text — used together with IUPHAR family-target
- *     resolution to identify sibling receptors in the same pharmacological
- *     family (replaces the hand-curated RELATED_FAMILY_UNIPROTS map).
- *
  * Absence policy: the OpenAPI document of UniProt marks no field as required,
  * and the API omits the key of an absent value. Thus a maybe-absent field
  * carries `.optional()`, not `.nullable()`.
@@ -107,8 +100,8 @@ export async function getReactomePathwaysByUniProt(accession) {
 }
 /**
  * The field list of the search. It is separate from `FIELDS` on purpose:
- * `FIELDS` feeds `getUniProtRecord` and the target-assessment dossier, thus a
- * widening of it would change what that workflow reads.
+ * `FIELDS` feeds `getUniProtRecord`, thus a widening of it would change what
+ * that function reads.
  */
 const SEARCH_FIELDS = ["accession", "id", "protein_name", "gene_names", "length", "cc_function", "cc_subcellular_location"].join(",");
 /** A FUNCTION comment runs to several hundred words; this is what one answer carries. */

package/package.json

@@ -1,6 +1,6 @@
 {
     "name": "@inflexa-ai/harness",
-    "version": "0.35.7",
+    "version": "0.36.0",
     "description": "Host-agnostic bioinformatics agent harness — hand-rolled agent loop, DBOS-durable workflows, sandboxed compute.",
     "license": "Apache-2.0",
     "type": "module",
@@ -47,11 +47,12 @@
         "typecheck": "tsc --noEmit"
     },
     "dependencies": {
-        "@ai-sdk/anthropic": "^4.0.38",
-        "@ai-sdk/openai": "^4.0.39",
-        "@ai-sdk/openai-compatible": "^3.0.30",
-        "@ai-sdk/provider": "^4.0.7",
-        "@ai-sdk/provider-utils": "5.0.27",
+        "@ai-sdk/anthropic": "^4.0.53",
+        "@ai-sdk/openai": "^4.0.66",
+        "@ai-sdk/openai-compatible": "^3.0.48",
+        "@ai-sdk/otel": "^1.0.99",
+        "@ai-sdk/provider": "^4.0.14",
+        "@ai-sdk/provider-utils": "5.0.40",
         "@anthropic-ai/sdk": "^0.116.0",
         "@dbos-inc/dbos-sdk": "^4.23.6",
         "@fontsource-variable/space-grotesk": "5.1.1",
@@ -68,7 +69,7 @@
         "@opentelemetry/sdk-trace-node": "^2.9.0",
         "@opentelemetry/semantic-conventions": "^1.43.0",
         "ag-grid-community": "36.1.0",
-        "ai": "^7.0.61",
+        "ai": "^7.0.99",
         "cheerio": "^1.2.0",
         "dockerode": "^4.0.12",
         "echarts": "6.1.0",
@@ -94,7 +95,7 @@
         "uuid": "^11.1.1"
     },
     "devDependencies": {
-        "@ai-sdk/amazon-bedrock": "^5.0.74",
+        "@ai-sdk/amazon-bedrock": "^5.0.82",
         "@eslint/js": "^10.0.1",
         "@types/bun": "latest",
         "@types/dockerode": "^3.3.47",

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

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

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

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