@inflexa-ai/harness 0.35.8 → 0.36.0

package/dist/workflows/target-assessment/lib/citation-validator.d.ts

@@ -1,46 +0,0 @@
-export type RecommendationAuditEntry = {
-    surface: "rationale" | "key_strengths" | "key_risks" | "modality_choice";
-    path: string;
-    excerpt: string;
-} | {
-    surface: "external_missing";
-    id: string;
-    excerpt: string;
-} | {
-    surface: "organ_claim_without_probe_pass";
-    excerpt: string;
-    bullet_category: string;
-} | {
-    surface: "nct_wrong_class";
-    id: string;
-    excerpt: string;
-} | {
-    surface: "pmid_not_in_key_papers";
-    id: string;
-    excerpt: string;
-};
-export type RecommendationAudit = {
-    citations_total: number;
-    citations_unresolved: RecommendationAuditEntry[];
-    non_dossier_citations: Array<{
-        token: string;
-        source: string;
-    }>;
-};
-type KeyRiskLike = {
-    text: string;
-    category?: string;
-} | string;
-type RecLike = {
-    rationale: string;
-    key_strengths: KeyRiskLike[];
-    key_risks: KeyRiskLike[];
-    modality_choice: {
-        rationale: string;
-    };
-    external_citations?: Array<{
-        id: string;
-    }>;
-};
-export declare function validateRecommendationCitations(rec: RecLike, dossier: unknown): RecommendationAudit;
-export {};

package/dist/workflows/target-assessment/lib/citation-validator.js

@@ -1,316 +0,0 @@
-// The recommendation agent emits citations as `[dossier: path; path; …]`
-// blocks (colon-space, semicolon-separated), sometimes with a trailing
-// `external citation: id; id` segment inside the same bracket. The old
-// `dossier.path` regex never matched this in production — citations_total
-// was always 0. These patterns match the format the agent actually writes.
-// The block content may include array index notation like `[0]`, so we
-// use a pattern that allows `[digits]` inside the outer brackets.
-const DOSSIER_CITE_BLOCK_RE = /\[dossier:\s*((?:[^[\]]|\[\d+\])*)\]/gi;
-// External citation IDs are plain strings — no array-index notation like `[n]` — so the simple [^\]]+ class suffices here instead of the array-index-aware pattern used by DOSSIER_CITE_BLOCK_RE.
-const EXTERNAL_CITE_BLOCK_RE = /\[external citation:\s*([^\]]+)\]/gi;
-// Assumes at most one `external citation:` segment per dossier block (the recommendation prompt produces at most one); a hypothetical second segment in the same block would be parsed imperfectly.
-const EXTERNAL_SEGMENT_RE = /external citation:\s*((?:[^[\]]|\[\d+\])*)/i;
-const NCT_RE = /\bNCT\d{8}\b/g;
-const PMID_RE = /\bPMID[:\s]?(\d{6,9})\b/g;
-// Legacy inline format: `dossier.path.foo` written directly in prose, no
-// brackets. Still emitted by some recommendation outputs and exercised by
-// the regression fixtures, so BOTH this and the `[dossier: …]` block format
-// must be supported. This pattern only matches a bare `dossier.x.y` token —
-// inside a `[dossier: …]` block the word `dossier` is followed by `:`, not
-// `.`/`[`, so the two are disjoint and never double-count.
-const DOSSIER_PATH_RE = /\bdossier(?:\.[A-Za-z_][A-Za-z0-9_]*|\[\d+\])+/g;
-// Legacy bare external reference: `[ANDA215864]` — an all-caps id in
-// brackets. Disjoint from `[dossier: …]` / `[external citation: …]` blocks
-// (those start with a lowercase word) and from `[0]` array indices (digits).
-const EXTERNAL_ID_RE = /\[([A-Z]{2,}[A-Z0-9_-]+)\]/g;
-// Path prefixes the agent uses that are NOT part of the persisted dossier
-// body — they refer to the per-section synthesis inputs the agent was
-// shown. Citing them is legitimate; resolving them against the dossier is
-// not, so they go to `non_dossier_citations` instead of `unresolved`.
-const NON_DOSSIER_PREFIXES = ["per_section_synthesis"];
-const ORGAN_CATEGORIES = new Set(["high_safety_organ_expression", "broad_expression", "class_liability"]);
-/**
- * Keyword fallback for detecting organ-level claims when the bullet has
- * no structural `category` field (the production
- * DossierRecommendationOutputSchema types key_risks as z.array(z.string())
- * with no category metadata, so a category check alone would be dead
- * code). Matches the regression-test approach in
- * [C4] of calcr-target-assessment.test.ts.
- */
-const ORGAN_KEYWORDS_RE = /\b(kidney|kidneys|renal|nephro\w*|cns|central\s+nervous|brain|hypothalam\w*|cardiac|cardiovascular|hepatic|liver|hepato\w*|pulmonary|respiratory|gastrointestinal)\b/i;
-/**
- * Bullet-keyword → canonical organ class. The keys mirror the alternatives
- * in `ORGAN_KEYWORDS_RE`; values match `target_organ_liabilities[i].organ`,
- * which the assembler emits using the canonical safety-panel set
- * (`cardiac` | `cns` | `hepatic` | `renal` | `gi` | `respiratory` | ...).
- *
- * Used to cross-match an organ-level key_risk bullet against the TOL probe
- * pass without depending on the bullet text containing the literal JSON
- * path `dossier.safety_profile.target_organ_liabilities` — LLM bullets are
- * plain English so the path-based check from earlier never matched in
- * production.
- */
-const BULLET_KEYWORD_TO_ORGAN = [
-    { rx: /\b(kidney|kidneys|renal|nephro\w*)\b/i, organ: "renal" },
-    { rx: /\b(cns|central\s+nervous|brain|hypothalam\w*)\b/i, organ: "cns" },
-    { rx: /\b(cardiac|cardiovascular)\b/i, organ: "cardiac" },
-    { rx: /\b(hepatic|liver|hepato\w*)\b/i, organ: "hepatic" },
-    { rx: /\b(pulmonary|respiratory)\b/i, organ: "respiratory" },
-    { rx: /\b(gastrointestinal)\b/i, organ: "gi" },
-];
-function extractOrganClassesFromText(text) {
-    const result = new Set();
-    for (const { rx, organ } of BULLET_KEYWORD_TO_ORGAN) {
-        if (rx.test(text))
-            result.add(organ);
-    }
-    return result;
-}
-function resolvePath(root, path) {
-    if (!path.startsWith("dossier"))
-        return undefined;
-    const stripped = path.replace(/^dossier\.?/, "");
-    if (stripped === "")
-        return root;
-    const parts = stripped.split(/\.|\[(\d+)\]/).filter(Boolean);
-    return walkWithDataFallback(root, parts);
-}
-function walkWithDataFallback(root, parts) {
-    let cur = root;
-    for (const p of parts) {
-        if (cur == null)
-            return undefined;
-        const next = readPart(cur, p);
-        if (next !== undefined) {
-            cur = next;
-            continue;
-        }
-        // The dossier wraps every section as { coverage, data: {...} }. When a
-        // lookup misses and the current node has a `data` child, descend through
-        // it transparently — the LLM consistently writes paths without the wrapper
-        // (e.g. "translational_chain.peak_evidence_tier" instead of
-        // "translational_chain.data.peak_evidence_tier"). This mirrors how a human
-        // reader refers to the field; flagging it as unresolved produces noise.
-        if (typeof cur === "object" && "data" in cur) {
-            const viaData = readPart(cur.data, p);
-            if (viaData !== undefined) {
-                cur = viaData;
-                continue;
-            }
-        }
-        return undefined;
-    }
-    return cur;
-}
-function readPart(node, p) {
-    if (node == null)
-        return undefined;
-    if (/^\d+$/.test(p))
-        return Array.isArray(node) ? node[parseInt(p, 10)] : undefined;
-    return typeof node === "object" ? node[p] : undefined;
-}
-/**
- * Extract dossier-path citations from `text`, supporting two formats:
- *   - New `[dossier: path; path]` blocks — `;`-separated bare paths, a
- *     trailing `/ID-list` suffix dropped, `external citation:` segment
- *     excluded (picked up by `findExternalIds`).
- *   - Legacy inline `dossier.path.foo` tokens written directly in prose.
- *
- * Returns `{ path, resolvable }` pairs: `path` is what surfaces in an
- * unresolved-citation entry (bare for block tokens, `dossier.`-prefixed for
- * legacy tokens — matching what each format's callers expect); `resolvable`
- * is always `dossier.`-prefixed so `resolvePath` can walk it.
- */
-function findPathTokens(text) {
-    const tokens = [];
-    // New `[dossier: …]` block format.
-    for (const block of text.matchAll(DOSSIER_CITE_BLOCK_RE)) {
-        const dossierPart = block[1].split(/external citation:/i)[0];
-        for (const raw of dossierPart.split(";")) {
-            const token = raw.trim().split("/")[0].trim();
-            if (token.length > 0)
-                tokens.push({ path: token, resolvable: `dossier.${token}` });
-        }
-    }
-    // Legacy inline `dossier.path.foo` format. The match already carries the
-    // `dossier.` prefix — keep it in `path` (callers expect the prefixed form
-    // for this format) and use it directly as `resolvable`.
-    for (const m of text.matchAll(DOSSIER_PATH_RE)) {
-        tokens.push({ path: m[0], resolvable: m[0] });
-    }
-    return tokens;
-}
-/**
- * Extract external-citation ids. The agent writes them either as a
- * standalone `[external citation: id; id]` block or as a trailing segment
- * inside a `[dossier: …; external citation: id]` block.
- */
-function findExternalIds(text) {
-    const ids = [];
-    const push = (segment) => {
-        for (const raw of segment.split(";")) {
-            const id = raw.trim();
-            if (id.length > 0)
-                ids.push(id);
-        }
-    };
-    for (const block of text.matchAll(EXTERNAL_CITE_BLOCK_RE))
-        push(block[1]);
-    for (const block of text.matchAll(DOSSIER_CITE_BLOCK_RE)) {
-        const m = block[1].match(EXTERNAL_SEGMENT_RE);
-        if (m)
-            push(m[1]);
-    }
-    // Legacy bare `[UPPERCASE_ID]` external reference (e.g. `[ANDA215864]`).
-    // NCT and PMID references in bracket form are already handled by NCT_RE /
-    // PMID_RE in the main loop — skip them here to avoid double-processing.
-    for (const m of text.matchAll(EXTERNAL_ID_RE)) {
-        const id = m[1];
-        if (/^NCT\d/.test(id) || /^PMID\d/.test(id))
-            continue;
-        ids.push(id);
-    }
-    return ids;
-}
-function normaliseBullet(b) {
-    return typeof b === "string" ? { text: b } : { text: b.text, category: b.category };
-}
-function collectClassDrugNames(dossier) {
-    const rows = dossier?.drug_interactions?.data?.rows ?? [];
-    return new Set(rows.map((r) => String(r.drug_name ?? "").toUpperCase()).filter(Boolean));
-}
-function collectKeyPaperPmids(dossier) {
-    const rows = dossier?.reference_biology?.key_papers?.data?.rows ?? [];
-    return new Set(rows.map((r) => String(r.pmid)).filter(Boolean));
-}
-/**
- * Extract intervention names from a trial row. Handles two shapes:
- * - Flat `interventions: string[]` — the production dossier shape assembled by
- *   `partitionTrialsByAttribution`.
- * - Nested `armsInterventionsModule.interventions: Array<{ name: string }>` — the
- *   raw CT.gov v2 JSON shape that may appear in test fixtures or future collector
- *   output before the assembler flattens it.
- */
-function extractInterventionNames(row) {
-    // Production flat shape (priority)
-    if (Array.isArray(row.interventions)) {
-        return row.interventions.map((iv) => (typeof iv === "string" ? iv.toUpperCase() : String(iv?.name ?? "").toUpperCase()));
-    }
-    // Raw CT.gov nested shape fallback
-    const nested = row?.armsInterventionsModule?.interventions;
-    if (Array.isArray(nested)) {
-        return nested.map((iv) => String(iv?.name ?? "").toUpperCase());
-    }
-    return [];
-}
-function findTrialInterventions(dossier, nctId) {
-    const trialSets = [
-        dossier?.clinical_development?.trials?.data?.rows ?? [],
-        dossier?.clinical_development?.failed_trials?.data?.rows ?? [],
-        dossier?.analytics?.discovery_trials?.data?.rows ?? [],
-    ];
-    for (const set of trialSets) {
-        const row = set.find((t) => t.nct_id === nctId);
-        if (!row)
-            continue;
-        return extractInterventionNames(row);
-    }
-    return [];
-}
-export function validateRecommendationCitations(rec, dossier) {
-    const dossierView = dossier;
-    const unresolved = [];
-    const nonDossier = [];
-    let total = 0;
-    const externalIds = new Set((rec.external_citations ?? []).map((c) => c.id));
-    const surfaces = [
-        { surface: "rationale", text: rec.rationale },
-        { surface: "modality_choice", text: rec.modality_choice.rationale },
-        ...rec.key_strengths.map((b) => ({ surface: "key_strengths", text: normaliseBullet(b).text })),
-        ...rec.key_risks.map((b) => ({ surface: "key_risks", text: normaliseBullet(b).text })),
-    ];
-    const classDrugNames = collectClassDrugNames(dossierView);
-    const keyPmids = collectKeyPaperPmids(dossierView);
-    for (const { surface, text } of surfaces) {
-        for (const { path, resolvable } of findPathTokens(text)) {
-            total += 1;
-            // Legacy-format tokens carry a `dossier.` prefix; block-format tokens
-            // are bare. Strip the prefix so the non-dossier-prefix check works for
-            // both formats.
-            const barePath = path.startsWith("dossier.") ? path.slice("dossier.".length) : path;
-            if (NON_DOSSIER_PREFIXES.some((p) => barePath === p || barePath.startsWith(`${p}.`) || barePath.startsWith(`${p}[`))) {
-                nonDossier.push({ token: path, source: surface });
-                continue;
-            }
-            const resolved = resolvePath(dossier, resolvable);
-            if (resolved === undefined || resolved === null) {
-                unresolved.push({ surface, path, excerpt: text.slice(0, 200) });
-            }
-        }
-        for (const id of findExternalIds(text)) {
-            if (!externalIds.has(id)) {
-                unresolved.push({ surface: "external_missing", id, excerpt: text.slice(0, 200) });
-            }
-        }
-        for (const m of text.matchAll(NCT_RE)) {
-            const nctId = m[0];
-            const interventions = findTrialInterventions(dossierView, nctId);
-            // Only flag wrong-class when the trial IS present in the dossier
-            // and its interventions don't reference the class. Trials absent
-            // from the collected sets are unverifiable — flagging them would
-            // produce false positives for any on-class trial that the
-            // synthesis agent cited but the discovery collector missed.
-            if (interventions.length === 0)
-                continue;
-            // Skip when no class-drug catalog is available — without a reference
-            // set (early-stage / first-in-class targets, or drug_interactions
-            // collector returning queried_no_data) every cited trial would
-            // otherwise flag as wrong-class regardless of its actual class.
-            if (classDrugNames.size === 0)
-                continue;
-            const referencesClassDrug = interventions.some((iv) => [...classDrugNames].some((name) => iv.includes(name)));
-            if (!referencesClassDrug) {
-                unresolved.push({ surface: "nct_wrong_class", id: nctId, excerpt: text.slice(0, 200) });
-            }
-        }
-        for (const m of text.matchAll(PMID_RE)) {
-            const pmid = m[1];
-            if (!keyPmids.has(pmid)) {
-                unresolved.push({ surface: "pmid_not_in_key_papers", id: pmid, excerpt: text.slice(0, 200) });
-            }
-        }
-    }
-    const organLiabilities = dossierView?.safety_profile?.target_organ_liabilities?.data?.rows ?? [];
-    const tolOrgans = new Set(organLiabilities
-        .map((t) => String(t?.organ ?? "")
-        .toLowerCase()
-        .trim())
-        .filter((o) => o.length > 0));
-    for (const b of rec.key_risks ?? []) {
-        const norm = normaliseBullet(b);
-        // Detect organ-level claims by structural category when available
-        // (typed bullets) OR by keyword match on the text (plain-string
-        // bullets — the production shape).
-        const isOrganClaim = (norm.category != null && ORGAN_CATEGORIES.has(norm.category)) || ORGAN_KEYWORDS_RE.test(norm.text);
-        if (!isOrganClaim)
-            continue;
-        // "Probe pass" = the TOL section has an entry whose organ matches the
-        // organ class mentioned in the bullet. Production bullets are plain
-        // English so we extract the organ class via keyword matching and
-        // cross-reference against the canonical TOL organ field.
-        const bulletOrgans = extractOrganClassesFromText(norm.text);
-        const citesTOL = bulletOrgans.size > 0 && [...bulletOrgans].some((o) => tolOrgans.has(o));
-        if (!citesTOL) {
-            unresolved.push({
-                surface: "organ_claim_without_probe_pass",
-                excerpt: norm.text.slice(0, 200),
-                bullet_category: norm.category ?? "inferred_from_text",
-            });
-        }
-    }
-    return {
-        citations_total: total,
-        citations_unresolved: unresolved,
-        non_dossier_citations: nonDossier,
-    };
-}

package/dist/workflows/target-assessment/lib/clinical-consequence-annotator.d.ts

@@ -1,65 +0,0 @@
-/**
- * Per-row LLM clinical-consequence annotator with Postgres caching.
- *
- * Any off-target row missing a `clinical_consequence` gets annotated by a
- * focused tool-less LLM specialist that returns ONE sentence + provenance.
- * Results are cached in `cortex_off_target_annotations` keyed by
- * (primary_target_gene, off_target_key) so repeat assessments reuse prior
- * work.
- *
- * Cache miss path: when a `deps` bundle is supplied, build a compact JSON
- * prompt, run a single-shot harness agent loop (no tools, max 2 iterations),
- * parse JSON out of the final assistant text, INSERT on success, return the
- * consequence. With no `deps`, the function returns null on cache miss
- * (no LLM call). Cache hit path: a single primary-key lookup, no LLM call.
- * Per-row failures (LLM, schema validation, DB) are swallowed — annotation
- * is supplementary; the dossier renders fine with null.
- */
-import { z } from "zod";
-import type { Pool } from "pg";
-import type { AgentSession } from "../../../auth/types.js";
-import type { AgentChat } from "../../../providers/types.js";
-import type { UsageRecorder } from "../../../billing/usage-recorder.js";
-export declare const OffTargetAnnotationSchema: z.ZodObject<{
-    clinical_consequence: z.ZodString;
-    provenance: z.ZodString;
-}, z.core.$strip>;
-export type OffTargetAnnotation = z.infer<typeof OffTargetAnnotationSchema>;
-export interface ClinicalConsequenceAnnotatorDeps {
-    readonly provider: AgentChat;
-    readonly session: AgentSession;
-    readonly model: string;
-    /** LLM usage-accounting seam for the annotator loop; omitted falls back to the no-op recorder. */
-    readonly usageRecorder?: UsageRecorder;
-}
-export interface AnnotationInput {
-    primaryTargetGene: string;
-    offTargetId: string | null;
-    offTargetName: string;
-    offTargetAccession: string | null;
-    pchembl: number;
-    /** Optional one-line family-relationship hint (e.g., "obligate cofactor"). */
-    context?: string;
-}
-/**
- * Annotate a single off-target row. Returns null on any failure (cache
- * miss + no deps, cache miss + LLM unavailable, schema validation failure,
- * DB unreachable, etc.) — callers must treat null as "no annotation" and
- * leave `clinical_consequence` as their original fallback.
- */
-export declare function annotateClinicalConsequence(pool: Pool, input: AnnotationInput, deps?: ClinicalConsequenceAnnotatorDeps): Promise<OffTargetAnnotation | null>;
-/**
- * Annotate every row in an off-target panel whose `clinical_consequence`
- * is currently null. Mutates the supplied arrays in-place. Pure assembly-
- * time helper — no return value.
- *
- * Per-row LLM calls are bounded by the "annotation-llm" host budget (4 in
- * flight). Cache hits skip the LLM entirely and consume only a cheap
- * Postgres lookup, so the budget gate is held briefly for those rows.
- * Without `deps`, the panel is annotated cache-only — rows missing a
- * cached entry remain with their original fallback.
- */
-export declare function annotateOffTargetPanel(pool: Pool, panel: {
-    rows: Array<Record<string, unknown>>;
-    excluded_rows: Array<Record<string, unknown>>;
-}, primaryTargetGene: string, deps?: ClinicalConsequenceAnnotatorDeps): Promise<void>;

package/dist/workflows/target-assessment/lib/clinical-consequence-annotator.js

@@ -1,174 +0,0 @@
-/**
- * Per-row LLM clinical-consequence annotator with Postgres caching.
- *
- * Any off-target row missing a `clinical_consequence` gets annotated by a
- * focused tool-less LLM specialist that returns ONE sentence + provenance.
- * Results are cached in `cortex_off_target_annotations` keyed by
- * (primary_target_gene, off_target_key) so repeat assessments reuse prior
- * work.
- *
- * Cache miss path: when a `deps` bundle is supplied, build a compact JSON
- * prompt, run a single-shot harness agent loop (no tools, max 2 iterations),
- * parse JSON out of the final assistant text, INSERT on success, return the
- * consequence. With no `deps`, the function returns null on cache miss
- * (no LLM call). Cache hit path: a single primary-key lookup, no LLM call.
- * Per-row failures (LLM, schema validation, DB) are swallowed — annotation
- * is supplementary; the dossier renders fine with null.
- */
-import { z } from "zod";
-import { withHost } from "../../../lib/host-concurrency.js";
-import { tryQuery, tryMutation } from "../../../lib/db-result.js";
-import { offTargetAnnotatorPrompt } from "../../../prompts/target-assessment/off-target-annotator.js";
-import { composeSystemPrompt } from "../../../agents/system-prompt.js";
-import { forSubAgent } from "../../../auth/types.js";
-import { finalText, runAgent } from "../../../loop/run-agent.js";
-import { passthroughStep } from "../../../loop/run-step.js";
-export const OffTargetAnnotationSchema = z.object({
-    clinical_consequence: z.string().min(10),
-    provenance: z.string().min(3),
-});
-function cacheKey(input) {
-    const id = input.offTargetId?.trim();
-    if (id)
-        return id;
-    const name = input.offTargetName.trim().toLowerCase();
-    return name ? `name:${name}` : null;
-}
-async function readCache(pool, primaryTargetGene, key) {
-    // Annotation is supplementary — a cache-read failure must NOT surface. The
-    // `DbError` is collapsed to `null` (treated as a cache miss) via `.unwrapOr`.
-    return tryQuery("offTargetAnnotations.readCache", async () => {
-        const res = await pool.query(`SELECT clinical_consequence, provenance
-       FROM cortex_off_target_annotations
-       WHERE primary_target_gene = $1 AND off_target_key = $2
-       LIMIT 1`, [primaryTargetGene, key]);
-        if (res.rows.length === 0)
-            return null;
-        const row = res.rows[0];
-        return {
-            clinical_consequence: row.clinical_consequence,
-            provenance: row.provenance ?? "",
-        };
-    }).unwrapOr(null);
-}
-async function writeCache(pool, primaryTargetGene, key, offTargetName, annotation, model) {
-    // Cache-write failures must not affect the assembly result — the `DbError`
-    // is swallowed (both branches no-op) so annotation never surfaces a DB fault.
-    await tryMutation("offTargetAnnotations.writeCache", async () => {
-        await pool.query(`INSERT INTO cortex_off_target_annotations
-         (primary_target_gene, off_target_key, off_target_name, clinical_consequence, provenance, model)
-       VALUES ($1, $2, $3, $4, $5, $6)
-       ON CONFLICT (primary_target_gene, off_target_key) DO NOTHING`, [primaryTargetGene, key, offTargetName, annotation.clinical_consequence, annotation.provenance, model]);
-    }).match(() => { }, () => { });
-}
-function buildPrompt(input) {
-    return JSON.stringify({
-        primary_target_gene: input.primaryTargetGene,
-        off_target_id: input.offTargetId,
-        off_target_name: input.offTargetName,
-        off_target_accession: input.offTargetAccession,
-        pchembl: input.pchembl,
-        context: input.context ?? null,
-    }, null, 2);
-}
-/**
- * Best-effort JSON extraction from an LLM text response. Strips fenced
- * code blocks and surrounding prose so a slightly-out-of-spec reply still
- * parses.
- */
-function extractJsonObject(text) {
-    const fenced = text.match(/```(?:json)?\s*([\s\S]*?)```/);
-    const candidate = fenced ? fenced[1] : text;
-    const start = candidate.indexOf("{");
-    const end = candidate.lastIndexOf("}");
-    if (start === -1 || end === -1 || end < start)
-        return null;
-    try {
-        return JSON.parse(candidate.slice(start, end + 1));
-    }
-    catch {
-        return null;
-    }
-}
-const ANNOTATOR_AGENT_ID = "off-target-annotator";
-function buildAnnotatorAgent(model) {
-    return {
-        id: ANNOTATOR_AGENT_ID,
-        systemPrompt: composeSystemPrompt(offTargetAnnotatorPrompt),
-        model,
-        tools: [],
-        maxIterations: 2,
-    };
-}
-/**
- * Annotate a single off-target row. Returns null on any failure (cache
- * miss + no deps, cache miss + LLM unavailable, schema validation failure,
- * DB unreachable, etc.) — callers must treat null as "no annotation" and
- * leave `clinical_consequence` as their original fallback.
- */
-export async function annotateClinicalConsequence(pool, input, deps) {
-    if (!input.primaryTargetGene)
-        return null;
-    const key = cacheKey(input);
-    if (!key)
-        return null;
-    const cached = await readCache(pool, input.primaryTargetGene, key);
-    if (cached)
-        return cached;
-    if (!deps)
-        return null;
-    try {
-        const agent = buildAnnotatorAgent(deps.model);
-        const session = forSubAgent(deps.session, ANNOTATOR_AGENT_ID);
-        const controller = new AbortController();
-        const { messages } = await runAgent(agent, [{ role: "user", content: buildPrompt(input) }], session, {
-            provider: deps.provider,
-            signal: controller.signal,
-            emit: () => { },
-            runStep: passthroughStep,
-            usageRecorder: deps.usageRecorder,
-        });
-        const raw = extractJsonObject(finalText(messages));
-        if (raw === null)
-            return null;
-        const parsed = OffTargetAnnotationSchema.safeParse(raw);
-        if (!parsed.success)
-            return null;
-        await writeCache(pool, input.primaryTargetGene, key, input.offTargetName, parsed.data, deps.model);
-        return parsed.data;
-    }
-    catch {
-        return null;
-    }
-}
-/**
- * Annotate every row in an off-target panel whose `clinical_consequence`
- * is currently null. Mutates the supplied arrays in-place. Pure assembly-
- * time helper — no return value.
- *
- * Per-row LLM calls are bounded by the "annotation-llm" host budget (4 in
- * flight). Cache hits skip the LLM entirely and consume only a cheap
- * Postgres lookup, so the budget gate is held briefly for those rows.
- * Without `deps`, the panel is annotated cache-only — rows missing a
- * cached entry remain with their original fallback.
- */
-export async function annotateOffTargetPanel(pool, panel, primaryTargetGene, deps) {
-    if (!primaryTargetGene)
-        return;
-    const allRows = [...panel.rows, ...panel.excluded_rows];
-    const needsAnnotation = allRows.filter((r) => r && (r.clinical_consequence == null || r.clinical_consequence === ""));
-    if (needsAnnotation.length === 0)
-        return;
-    await Promise.all(needsAnnotation.map((r) => withHost("annotation-llm", async () => {
-        const annotation = await annotateClinicalConsequence(pool, {
-            primaryTargetGene,
-            offTargetId: typeof r.off_target_id === "string" ? r.off_target_id : null,
-            offTargetName: typeof r.off_target_name === "string" ? r.off_target_name : "",
-            offTargetAccession: typeof r.accession === "string" ? r.accession : null,
-            pchembl: typeof r.pchembl === "number" ? r.pchembl : 0,
-            context: r.relationship === "obligate_cofactor" ? "obligate cofactor with the primary protein" : undefined,
-        }, deps);
-        if (annotation)
-            r.clinical_consequence = annotation.clinical_consequence;
-    })));
-}

package/dist/workflows/target-assessment/lib/clinical-evidence-attribution.d.ts

@@ -1,44 +0,0 @@
-import type { ClinicalTrialAttribution } from "@inflexa-ai/harness/contracts/target-dossier.js";
-type TrialLike = {
-    nctId: string;
-    title: string;
-    officialTitle?: string | null;
-    conditions?: string[];
-    interventions?: string[];
-    interventionDetails?: Array<{
-        name: string;
-        type?: string | null;
-        description?: string | null;
-        otherNames?: string[];
-    }>;
-    studyType?: string | null;
-    primaryPurpose?: string | null;
-    briefSummary?: string | null;
-    detailedDescription?: string | null;
-};
-export type KnownClassDrug = {
-    name: string;
-    moleculeChemblId?: string | null;
-    targetUniprots?: string[];
-};
-export type TherapeuticProgram = {
-    programId: string;
-    name: string;
-    targetSymbol: string;
-    targetUniprot?: string | null;
-    modality?: string | null;
-    nctIds?: string[];
-};
-export type ClinicalEvidenceAttributionContext = {
-    assessmentSymbol: string;
-    assessmentUniprot: string;
-    familyUniprots: string[];
-    knownClassDrugs: KnownClassDrug[];
-    therapeuticPrograms: TherapeuticProgram[];
-};
-export type ClinicalEvidenceAttributionResult = {
-    attribution: ClinicalTrialAttribution;
-    eligible_for_toxicology_aggregation: boolean;
-};
-export declare function classifyClinicalEvidenceTrial(trial: TrialLike, ctx: ClinicalEvidenceAttributionContext): ClinicalEvidenceAttributionResult;
-export {};