@inflexa-ai/harness 0.35.8 → 0.36.0

package/dist/workflows/target-assessment/lib/impc-organ-map.js

@@ -1,39 +0,0 @@
-/**
- * The IMPC top-level-phenotype vocabulary onto the canonical organ vocabulary.
- *
- * Buckets with no organ system to land in (hearing, growth, mortality,
- * craniofacial) are absent: a phenotype is reported under the organ it affects
- * or not at all, never under an approximate neighbour. The map's values are the
- * canonical tokens, so it declares no enumeration of its own.
- *
- * The endocrine bucket is absent for the same reason: IMPC's
- * "endocrine/exocrine gland phenotype" spans every endocrine organ and the
- * exocrine glands besides, while the only endocrine token names the thyroid.
- * A knockout in that bucket names no canonical organ, so it is dropped and
- * counted rather than read as a thyroid finding.
- */
-const IMPC_ORGAN_SYSTEMS = {
-    cardiovascular: "cardiac",
-    gastrointestinal: "gi",
-    hematologic: "hematologic",
-    metabolic: "metabolic",
-    immune: "immune",
-    skin: "dermatologic",
-    hepatic: "hepatic",
-    musculoskeletal: "musculoskeletal",
-    skeleton: "musculoskeletal",
-    cns: "cns",
-    renal: "renal",
-    reproductive: "reproductive",
-    respiratory: "respiratory",
-    vision: "ocular",
-};
-/** Resolve one IMPC bucket, or null when it denotes no canonical organ. */
-export function resolveImpcOrgan(bucket) {
-    return IMPC_ORGAN_SYSTEMS[bucket] ?? null;
-}
-/** Resolve a set of IMPC buckets, dropping those with no canonical organ. */
-export function toOrganSystems(impcOrganSystems) {
-    const resolved = impcOrganSystems.map((o) => resolveImpcOrgan(o)).filter((o) => o !== null);
-    return [...new Set(resolved)];
-}

package/dist/workflows/target-assessment/lib/intended-polypharm-filter.d.ts

@@ -1,4 +0,0 @@
-export declare function isIntendedCoTarget(modulatorChemblId: string, offTargetChemblId: string): {
-    intended: boolean;
-    reason?: string;
-};

package/dist/workflows/target-assessment/lib/intended-polypharm-filter.js

@@ -1,24 +0,0 @@
-/**
- * Hand-curated catalogue of multi-target peptide agonists. Conservative
- * by design — only well-documented dual/triple agonists where the
- * additional receptor IS the marketed mechanism. Ambiguous cases stay
- * in the off-target panel.
- *
- * Source: ChEMBL triage_rationale strings + class-precedent literature.
- * Extend as new dual/triple agonists appear in chembl-modulators output.
- */
-const INTENDED_PAIRS = [
-    { modulator: "CHEMBL4297839", coTarget: "CHEMBL4383", reason: "tirzepatide is a dual GLP-1R/GIPR agonist" },
-    { modulator: "CHEMBL4297630", coTarget: "CHEMBL1985", reason: "cotadutide is a dual GLP-1R/GCGR agonist" },
-    { modulator: "CHEMBL5095485", coTarget: "CHEMBL4383", reason: "retatrutide is a triple GLP-1R/GIPR/GCGR agonist" },
-    { modulator: "CHEMBL5095485", coTarget: "CHEMBL1985", reason: "retatrutide is a triple GLP-1R/GIPR/GCGR agonist" },
-    { modulator: "CHEMBL5314776", coTarget: "CHEMBL1985", reason: "survodutide is a dual GLP-1R/GCGR agonist" },
-    { modulator: "CHEMBL4297576", coTarget: "CHEMBL1985", reason: "efinopegdutide is a dual GLP-1R/GCGR agonist" },
-    { modulator: "CHEMBL3990012", coTarget: "CHEMBL1985", reason: "pegapamodutide is a dual GLP-1R/GCGR agonist" },
-];
-export function isIntendedCoTarget(modulatorChemblId, offTargetChemblId) {
-    const hit = INTENDED_PAIRS.find((p) => p.modulator === modulatorChemblId && p.coTarget === offTargetChemblId);
-    if (hit)
-        return { intended: true, reason: hit.reason };
-    return { intended: false };
-}

package/dist/workflows/target-assessment/lib/llm-step.d.ts

@@ -1,80 +0,0 @@
-/**
- * LLM step wrapper for the target-assessment DBOS workflow body.
- *
- * Each Phase-2 decision and Phase-5 synthesis LLM call goes through
- * `runLlmStep` — it wraps `DBOS.runStep({name})` around the chat provider
- * call and classifies caught errors:
- *
- *   - `isBudgetExceeded(err) === true` (billing-gateway 402): self-send a
- *     `BUDGET_EXCEEDED_TOPIC` marker addressed to this workflow's own
- *     id, then return a sentinel marker. The wrapper does NOT call
- *     `DBOS.cancelWorkflow` itself — the workflow body's terminal block
- *     reads the marker, writes `status = "suspended_insufficient_funds"`
- *     via `DBOS.runStep({name: "ta-terminal-suspended"})`, then issues
- *     `DBOS.cancelWorkflow` + a trailing `runStep` to materialise the
- *     CANCELLED terminal state. Deferring the cancel keeps the terminal
- *     handler's DB writes inside DBOS step boundaries (replay-cached).
- *   - anything else: rethrow so the caller wraps the failure as
- *     `coverage: "queried_no_data"` with `error.kind: "synthesis-unavailable"`
- *     (or `"queried_no_data"` for decisions).
- *
- * The step name is attempt-numbered by the caller — e.g.
- * `"ta-synth:liability-bullets:0"`. On 402 + top-up + `DBOS.resumeWorkflow`
- * the caller bumps the attempt counter so the resumed call lands a fresh
- * DBOS cache slot rather than replaying the cancelled prior attempt.
- */
-import type { Logger } from "../../../lib/logger.js";
-import type { AgentChat, ChatRequest, ChatResponse } from "../../../providers/types.js";
-import type { AgentSession } from "../../../auth/types.js";
-/**
- * DBOS message topic the LLM step uses to mark the workflow as
- * self-cancelled on a billing-gateway 402. The terminal handler drains the topic
- * to dispatch to `markAssessmentSuspended` rather than the generic
- * operator-cancel handler.
- */
-export declare const BUDGET_EXCEEDED_TOPIC = "ta-budget-exceeded";
-export interface BudgetExceededMarker {
-    readonly stepName: string;
-    readonly agentId: string;
-    readonly error: string;
-}
-export interface RunLlmStepOptions {
-    /** Operational logging seam; omitted falls back to no-op. */
-    readonly logger?: Logger;
-    /** Durable-step name — already attempt-numbered by the caller. */
-    readonly stepName: string;
-    /** Agent id stamped in the marker for telemetry. */
-    readonly agentId: string;
-    readonly provider: AgentChat;
-    readonly req: ChatRequest;
-    readonly session: AgentSession;
-    readonly signal?: AbortSignal;
-}
-/**
- * Sentinel returned (NOT thrown) when the wrapper has self-cancelled the
- * workflow. The next `DBOS.runStep` after this point raises
- * `DBOSWorkflowCancelledError`, so call sites only see this value on the
- * synchronous return path before the cancel materialises. Callers MUST NOT
- * wrap this as `coverage: "queried_no_data"` — the workflow is unwinding.
- */
-export declare const BUDGET_EXCEEDED_SENTINEL: unique symbol;
-export type RunLlmStepResult = {
-    readonly kind: "ok";
-    readonly response: ChatResponse;
-} | {
-    readonly kind: "budget-exceeded";
-    readonly sentinel: typeof BUDGET_EXCEEDED_SENTINEL;
-};
-/**
- * Run one LLM call inside a `DBOS.runStep` boundary. On a billing-gateway 402 the
- * workflow self-cancels and the caller receives a sentinel result; on any
- * other throw the original error rethrows.
- */
-export declare function runLlmStep(opts: RunLlmStepOptions): Promise<RunLlmStepResult>;
-/**
- * Drain the budget-exceeded topic for this workflow. Called from the
- * terminal handler (after the body has unwound) to decide whether the
- * workflow cancelled because of a 402 or because of an operator-initiated
- * cancel. Returns the first marker (or `null` if none queued).
- */
-export declare function readBudgetExceededMarker(): Promise<BudgetExceededMarker | null>;

package/dist/workflows/target-assessment/lib/llm-step.js

@@ -1,101 +0,0 @@
-/**
- * LLM step wrapper for the target-assessment DBOS workflow body.
- *
- * Each Phase-2 decision and Phase-5 synthesis LLM call goes through
- * `runLlmStep` — it wraps `DBOS.runStep({name})` around the chat provider
- * call and classifies caught errors:
- *
- *   - `isBudgetExceeded(err) === true` (billing-gateway 402): self-send a
- *     `BUDGET_EXCEEDED_TOPIC` marker addressed to this workflow's own
- *     id, then return a sentinel marker. The wrapper does NOT call
- *     `DBOS.cancelWorkflow` itself — the workflow body's terminal block
- *     reads the marker, writes `status = "suspended_insufficient_funds"`
- *     via `DBOS.runStep({name: "ta-terminal-suspended"})`, then issues
- *     `DBOS.cancelWorkflow` + a trailing `runStep` to materialise the
- *     CANCELLED terminal state. Deferring the cancel keeps the terminal
- *     handler's DB writes inside DBOS step boundaries (replay-cached).
- *   - anything else: rethrow so the caller wraps the failure as
- *     `coverage: "queried_no_data"` with `error.kind: "synthesis-unavailable"`
- *     (or `"queried_no_data"` for decisions).
- *
- * The step name is attempt-numbered by the caller — e.g.
- * `"ta-synth:liability-bullets:0"`. On 402 + top-up + `DBOS.resumeWorkflow`
- * the caller bumps the attempt counter so the resumed call lands a fresh
- * DBOS cache slot rather than replaying the cancelled prior attempt.
- */
-import { DBOS } from "@dbos-inc/dbos-sdk";
-import { createNoopLogger } from "../../../lib/console-logger.js";
-import { unwrapOrThrow } from "../../../lib/result.js";
-import { isBudgetExceeded } from "../../../loop/budget-exceeded.js";
-/**
- * DBOS message topic the LLM step uses to mark the workflow as
- * self-cancelled on a billing-gateway 402. The terminal handler drains the topic
- * to dispatch to `markAssessmentSuspended` rather than the generic
- * operator-cancel handler.
- */
-export const BUDGET_EXCEEDED_TOPIC = "ta-budget-exceeded";
-/**
- * Sentinel returned (NOT thrown) when the wrapper has self-cancelled the
- * workflow. The next `DBOS.runStep` after this point raises
- * `DBOSWorkflowCancelledError`, so call sites only see this value on the
- * synchronous return path before the cancel materialises. Callers MUST NOT
- * wrap this as `coverage: "queried_no_data"` — the workflow is unwinding.
- */
-export const BUDGET_EXCEEDED_SENTINEL = Symbol.for("ta.budget-exceeded");
-/**
- * Run one LLM call inside a `DBOS.runStep` boundary. On a billing-gateway 402 the
- * workflow self-cancels and the caller receives a sentinel result; on any
- * other throw the original error rethrows.
- */
-export async function runLlmStep(opts) {
-    const { stepName, agentId, provider, req, session, signal } = opts;
-    try {
-        const response = await DBOS.runStep(async () => unwrapOrThrow(await provider.chat(req, session, signal)), { name: stepName });
-        return { kind: "ok", response };
-    }
-    catch (err) {
-        if (!isBudgetExceeded(err)) {
-            throw err;
-        }
-        const workflowId = DBOS.workflowID;
-        if (!workflowId) {
-            // Should not happen — the wrapper is only callable from inside a
-            // workflow body. Surface as a generic throw so the caller does not
-            // misclassify as coverage failure.
-            throw err;
-        }
-        const marker = {
-            stepName,
-            agentId,
-            error: err instanceof Error ? err.message : String(err),
-        };
-        // Self-send a marker so the terminal handler's `DBOS.recv(topic, 0)`
-        // drain sees it before the body unwinds. DBOS persists the send under
-        // (workflowID, function_id), so replay does not duplicate the
-        // marker. The send is wrapped in `DBOS.runStep` to own the slot.
-        //
-        // The workflow is NOT cancelled here — the body propagates the
-        // sentinel through phase outputs, the terminal block runs its DB
-        // writes inside DBOS step boundaries, and the cancel materialises at
-        // the very end via the terminal block's trailing
-        // `DBOS.cancelWorkflow` + `DBOS.runStep("self-cancel-budget-exceeded")`.
-        try {
-            await DBOS.runStep(() => DBOS.send(workflowId, marker, BUDGET_EXCEEDED_TOPIC), { name: `${stepName}:notify-budget-exceeded` });
-        }
-        catch (sendErr) {
-            const logger = (opts.logger ?? createNoopLogger()).named("ta-llm-step");
-            logger.warn("notify-budget-exceeded send failed (non-fatal)", { stepName, ...logger.errorFields(sendErr) });
-        }
-        return { kind: "budget-exceeded", sentinel: BUDGET_EXCEEDED_SENTINEL };
-    }
-}
-/**
- * Drain the budget-exceeded topic for this workflow. Called from the
- * terminal handler (after the body has unwound) to decide whether the
- * workflow cancelled because of a 402 or because of an operator-initiated
- * cancel. Returns the first marker (or `null` if none queued).
- */
-export async function readBudgetExceededMarker() {
-    const msg = await DBOS.recv(BUDGET_EXCEEDED_TOPIC, 0);
-    return msg ?? null;
-}

package/dist/workflows/target-assessment/lib/meddra-organ-map.d.ts

@@ -1,40 +0,0 @@
-/**
- * MedDRA terms and CT.gov system-organ classes onto the canonical organ
- * vocabulary.
- *
- * The values are the canonical tokens, so this module declares no organ
- * enumeration of its own. Every token in the vocabulary is reachable through
- * the rules below, so nothing a producer may legitimately attribute is
- * unreachable by accident.
- *
- * A term resolves onto the organ it names, or onto nothing. A term whose
- * compartment is genuinely ambiguous — "Paraesthesia" and the other nervous
- * system terms that name no compartment, "Adrenal insufficiency" and the other
- * endocrine terms outside the thyroid — matches no rule, so the caller drops
- * and counts it rather than filing it under a neighbour.
- */
-import type { OrganSystem } from "../../../contracts/organ-system.js";
-export declare function classifyOrgan(meddraTerm: string): OrganSystem | null;
-/**
- * MedDRA SOC (System Organ Class) names as they appear in CT.gov structured
- * AE tables → canonical organ. SOC strings (e.g. "Gastrointestinal disorders")
- * do not contain MedDRA PT stems, so `classifyOrgan` returns null for them —
- * the SOC map is the primary path; `classifyOrgan(term)` is the fallback when
- * the SOC string isn't in the map.
- *
- * A SOC that spans more than one canonical organ is absent: "Nervous system
- * disorders" covers both nervous-system tokens and "Endocrine disorders" is
- * broader than the thyroid, so a row under either resolves by its preferred
- * term or not at all.
- */
-export declare const TRIAL_AE_ORGAN_MAP: Record<string, OrganSystem>;
-/**
- * Classify a trial AE row by its SOC (preferred) or its individual MedDRA
- * preferred term (fallback). Shared between the Phase-4 assembler's
- * organ_rollup builder and the derived-completeness validator so both
- * agree on which organ a trial AE belongs to.
- */
-export declare function classifyTrialAe(ae: {
-    term?: string | null;
-    organ?: string | null;
-}): OrganSystem | null;

package/dist/workflows/target-assessment/lib/meddra-organ-map.js

@@ -1,138 +0,0 @@
-/**
- * MedDRA terms and CT.gov system-organ classes onto the canonical organ
- * vocabulary.
- *
- * The values are the canonical tokens, so this module declares no organ
- * enumeration of its own. Every token in the vocabulary is reachable through
- * the rules below, so nothing a producer may legitimately attribute is
- * unreachable by accident.
- *
- * A term resolves onto the organ it names, or onto nothing. A term whose
- * compartment is genuinely ambiguous — "Paraesthesia" and the other nervous
- * system terms that name no compartment, "Adrenal insufficiency" and the other
- * endocrine terms outside the thyroid — matches no rule, so the caller drops
- * and counts it rather than filing it under a neighbour.
- */
-/**
- * Order matters: more-specific patterns first. GI is matched before
- * "metabolic" because terms like "blood glucose" should land in
- * metabolic, but "nausea" / "vomiting" must not be reclassified by
- * later metabolic glucose rules.
- *
- * Patterns are stem-based (e.g. "nause" matches "NAUSEA"), so trailing
- * \b is omitted — the stem does not end at a word boundary inside the
- * full MedDRA term. A leading \b is kept to prevent mid-word false matches.
- */
-const RULES = [
-    // pancreas (specific) — must come before generic GI
-    { rx: /\bpancreatit|\bamylase|\blipase/i, organ: "pancreas" },
-    // thyroid / C-cell. The token names the thyroid, not the endocrine system,
-    // so a non-thyroid endocrine term deliberately matches nothing here.
-    { rx: /thyroid|\b(c[-\s]?cell|calcitonin|goit[re]+|medullar[a-z]*\s*carcinoma)/i, organ: "endocrine_thyroid" },
-    // gastrointestinal
-    { rx: /\b(nause|vomit|diarrhoe|diarrhea|constipat|ileus|gastropares|abdominal\s*pain|cholecystit|cholelithias|gallbladder|colit|heartburn)/i, organ: "gi" },
-    // hepatic — liver/alt/ast forms added; alt/ast pinned to "increased" to avoid
-    // over-firing on terms like "ALTERED MENTAL STATUS"
-    {
-        rx: /\b(hepatit|hepato|jaundic|cholestas|transaminas|bilirubin|liver|alt\s+increased|ast\s+increased|alanine\s+aminotransferase|aspartate\s+aminotransferase)/i,
-        organ: "hepatic",
-    },
-    // renal — haematur/hematur explicitly placed here (above hematologic) to prevent
-    // the broad \bhaemat stem from misclassifying HAEMATURIA as hematologic
-    { rx: /\b(renal|kidney|nephro|creatinin|glomerul|dialys|haematur|hematur)/i, organ: "renal" },
-    // cardiac — cardi(ac|al|o) covers CARDIOMYOPATHY/CARDIOVASCULAR/CARDIOTOXICITY;
-    // bare heart covers HEART FAILURE, HEART RATE INCREASED, etc.
-    { rx: /\b(cardi(?:ac|al|o)|heart|myocard|tachycard|brady\w*card|arrhythm|atrial\s+fibrillat|qt\s+prolong|torsade)/i, organ: "cardiac" },
-    // vascular — placed after cardiac so a myocardial event stays cardiac.
-    // `thrombos` rather than the `thrombo` stem, which would swallow
-    // THROMBOCYTOPENIA; `\bvascul` never matches inside CEREBROVASCULAR.
-    { rx: /\b(hypertens|hypotens|vasculit|vascular|thrombos|thromboemboli|thrombophleb|embolism|aneurysm|varicose|phlebit)/i, organ: "vascular" },
-    // metabolic (glucose, weight, lipid)
-    // triglyc has no leading \b because it appears mid-word in HYPERTRIGLYCERIDAEMIA
-    { rx: /\b(glucose|glycaemi|hba1c|insulin|weight\s+(?:decreased|increased)|lipid|cholester|dehydration)|triglyc/i, organ: "metabolic" },
-    // respiratory — above the neurological rules so RESPIRATORY DEPRESSION is
-    // read as a respiratory event rather than by the bare "depression" stem
-    { rx: /\b(nasopharyng|pharyng|bronch|pneumon|dyspnoe|dyspnea|cough|respiratory|sinusit|pulmonary)/i, organ: "respiratory" },
-    // hematologic — above the neurological rules for the same reason, so
-    // BONE MARROW DEPRESSION is read as haematologic
-    { rx: /\b(haemoglobin|hemoglobin|haematocrit|leuko|neutro|thrombocyt|anaemi|haemat|platelet|marrow)/i, organ: "hematologic" },
-    // ocular — above the nerve rules so OPTIC NEUROPATHY stays ocular.
-    // `macular` is pinned to its ocular compounds so it never matches
-    // MACULOPAPULAR RASH.
-    {
-        rx: /\b(ocular|ophthalm|retinopath|retinal|glaucoma|cataract|uveit|conjunctivit|blindness|vision|visual|keratit|scleriti|blephariti|eye\s|macular\s+(?:oedema|edema|degenerat)|optic\s+(?:neuropath|neurit|atroph))/i,
-        organ: "ocular",
-    },
-    // peripheral nervous system — a neuropathy is a disease of the peripheral
-    // nerves; a central lesion is named by the terms in the cns rule below
-    // `neuropath` carries no leading \b so POLYNEUROPATHY and MONONEUROPATHY
-    // resolve as well as NEUROPATHY PERIPHERAL
-    { rx: /neuropath|neurit|\b(radiculopath|neuralg|carpal\s+tunnel|guillain|plexopath|peripheral\s+(?:motor|sensory))/i, organ: "pns" },
-    // central nervous system
-    {
-        rx: /\b(headache|dizz|seizure|convuls|suici|depression|anxiet|encephalo|migrain|myelopath|meningit|cerebr|intracranial|somnolen|ataxi|tremor|stroke)/i,
-        organ: "cns",
-    },
-    // dermatologic
-    { rx: /\b(rash|eczem|prurit|urticari|injection\s+site\s+(?:pain|haemorrhag|erythem))/i, organ: "dermatologic" },
-    // musculoskeletal — malignant hyperthermia is a skeletal-muscle crisis and
-    // is matched here so the malignancy stem below never claims it
-    { rx: /\b(arthralg|myalg|musculoskel|fracture|bone\s+pain|rhabdomyol|malignant\s+hyperthermi)/i, organ: "musculoskeletal" },
-    // immune
-    { rx: /\b(hypersensitiv|anaphyl|autoimmune|cytokine\s+release)/i, organ: "immune" },
-    // reproductive
-    { rx: /\b(menstrual|menorrhag|ovari|endometr|prostat|erectile)/i, organ: "reproductive" },
-    // oncology — last, so a malignancy that names its site is filed under that
-    // site and only a term whose content is the malignancy itself lands here
-    { rx: /\b(neoplasm|malignan|carcinoma|sarcoma|lymphoma|leukaemi|leukemi|myeloma|myelodysplas|melanoma|metastas|tumour|tumor|cancer)/i, organ: "oncology" },
-];
-const UNINFORMATIVE_RE = /\b(incorrect\s+dose|off\s+label|drug\s+ineffective|product\s+(?:use|storage|administration)|accidental\s+exposure|inappropriate\s+schedule|exposure\s+via\s+skin|extra\s+dose|wrong\s+technique)\b/i;
-export function classifyOrgan(meddraTerm) {
-    if (UNINFORMATIVE_RE.test(meddraTerm))
-        return null;
-    for (const { rx, organ } of RULES) {
-        if (rx.test(meddraTerm))
-            return organ;
-    }
-    return null;
-}
-/**
- * MedDRA SOC (System Organ Class) names as they appear in CT.gov structured
- * AE tables → canonical organ. SOC strings (e.g. "Gastrointestinal disorders")
- * do not contain MedDRA PT stems, so `classifyOrgan` returns null for them —
- * the SOC map is the primary path; `classifyOrgan(term)` is the fallback when
- * the SOC string isn't in the map.
- *
- * A SOC that spans more than one canonical organ is absent: "Nervous system
- * disorders" covers both nervous-system tokens and "Endocrine disorders" is
- * broader than the thyroid, so a row under either resolves by its preferred
- * term or not at all.
- */
-export const TRIAL_AE_ORGAN_MAP = {
-    "Gastrointestinal disorders": "gi",
-    "Cardiac disorders": "cardiac",
-    "Vascular disorders": "vascular",
-    "Hepatobiliary disorders": "hepatic",
-    "Renal and urinary disorders": "renal",
-    "Respiratory, thoracic and mediastinal disorders": "respiratory",
-    "Skin and subcutaneous tissue disorders": "dermatologic",
-    "Musculoskeletal and connective tissue disorders": "musculoskeletal",
-    "Metabolism and nutrition disorders": "metabolic",
-    "Blood and lymphatic system disorders": "hematologic",
-    "Reproductive system and breast disorders": "reproductive",
-    "Immune system disorders": "immune",
-    "Eye disorders": "ocular",
-    "Neoplasms benign, malignant and unspecified (incl cysts and polyps)": "oncology",
-};
-/**
- * Classify a trial AE row by its SOC (preferred) or its individual MedDRA
- * preferred term (fallback). Shared between the Phase-4 assembler's
- * organ_rollup builder and the derived-completeness validator so both
- * agree on which organ a trial AE belongs to.
- */
-export function classifyTrialAe(ae) {
-    const fromSoc = TRIAL_AE_ORGAN_MAP[ae.organ ?? ""];
-    if (fromSoc)
-        return fromSoc;
-    return classifyOrgan(ae.term ?? "");
-}

package/dist/workflows/target-assessment/lib/recommendation-quality-gates.d.ts

@@ -1,17 +0,0 @@
-import type { ExecutiveRecommendation, QualityGateStatus, RecommendationAudit, SynthesisDiagnosticRow } from "@inflexa-ai/harness/contracts/target-dossier.js";
-type ApplyRecommendationQualityGatesInput = {
-    executive_recommendation: ExecutiveRecommendation;
-    synthesis_diagnostics: Array<Partial<SynthesisDiagnosticRow> & {
-        step_id?: string;
-    }>;
-    recommendation_audit: Extract<RecommendationAudit, {
-        coverage: "available";
-    }>["data"] | null | undefined;
-    has_direct_clinical_evidence: boolean;
-};
-type ApplyRecommendationQualityGatesResult = {
-    executive_recommendation: ExecutiveRecommendation;
-    quality_gates: QualityGateStatus[];
-};
-export declare function applyRecommendationQualityGates(input: ApplyRecommendationQualityGatesInput): ApplyRecommendationQualityGatesResult;
-export {};

package/dist/workflows/target-assessment/lib/recommendation-quality-gates.js

@@ -1,99 +0,0 @@
-const ORGAN_CLAIM_RE = /\b(renal|kidney|nephro\w*|cns|brain|hypothalam\w*|cardiac|cardiovascular|hepatic|liver|pulmonary|respiratory|gastrointestinal|gi|oncology|malignan\w*)\b/i;
-function appendNote(current, addition) {
-    const trimmed = current.trim();
-    return trimmed ? `${trimmed} ${addition}` : addition;
-}
-export function applyRecommendationQualityGates(input) {
-    const quality_gates = [];
-    const executive_recommendation = structuredClone(input.executive_recommendation);
-    const unresolved = input.recommendation_audit?.citations_unresolved ?? [];
-    const visibleRecommendationText = input.executive_recommendation.coverage === "available"
-        ? [
-            input.executive_recommendation.data.rationale,
-            input.executive_recommendation.data.modality_choice.rationale,
-            ...input.executive_recommendation.data.key_strengths,
-            ...input.executive_recommendation.data.key_risks,
-        ].join("\n")
-        : "";
-    const blockingCitationCount = unresolved.filter((u) => {
-        // The unresolved-citation entries are an untyped audit payload narrowed
-        // here to the fields these gates read; `excerpt` exists only on some
-        // surfaces, guarded by the `in` presence check.
-        if (u.surface === "organ_claim_without_probe_pass" && "excerpt" in u) {
-            const excerpt = String(u.excerpt ?? "");
-            return excerpt.length > 0 && visibleRecommendationText.includes(excerpt.slice(0, Math.min(80, excerpt.length)));
-        }
-        return ["external_missing", "nct_wrong_class", "organ_claim_without_probe_pass", "off_topic_citation"].includes(u.surface);
-    }).length;
-    if (blockingCitationCount > 0) {
-        quality_gates.push({
-            gate_id: "recommendation-citations",
-            status: "blocked",
-            message: "Recommendation contains unresolved or unsafe citation references.",
-            affected_sections: ["executive_recommendation"],
-            unresolved_count: blockingCitationCount,
-        });
-        return {
-            executive_recommendation: {
-                coverage: "queried_no_data",
-                error: {
-                    message: "executive recommendation blocked because unresolved citation audit findings remain",
-                    source: "recommendation-quality-gates",
-                },
-            },
-            quality_gates,
-        };
-    }
-    const safetyFlags = input.synthesis_diagnostics.find((row) => row.step_id === "safety-flags-trail");
-    const safetyFlagsAvailable = safetyFlags?.final_coverage === "available";
-    if (!safetyFlagsAvailable && executive_recommendation.coverage === "available") {
-        const rec = executive_recommendation.data;
-        const unverified = rec.key_risks
-            .filter((risk) => ORGAN_CLAIM_RE.test(risk))
-            .map((risk) => ({
-            text: risk,
-            bullet_category: "organ_claim_without_probe_pass",
-            surface: "organ_claim_without_probe_pass",
-        }));
-        if (unverified.length > 0) {
-            rec.key_risks = rec.key_risks.filter((risk) => !ORGAN_CLAIM_RE.test(risk));
-            rec.coverage_qualifier = {
-                ...rec.coverage_qualifier,
-                unverified_bullets: [...(rec.coverage_qualifier.unverified_bullets ?? []), ...unverified],
-                note: appendNote(rec.coverage_qualifier.note, "Organ-level risk bullets were demoted because the safety-flags audit trail did not pass validation."),
-            };
-            quality_gates.push({
-                gate_id: "safety-flags-trail",
-                status: "blocked",
-                message: "Organ-level executive risk claims were demoted because safety-flags-trail was unavailable or failed validation.",
-                affected_sections: ["executive_recommendation.key_risks"],
-                unresolved_count: unverified.length,
-            });
-        }
-    }
-    if (!input.has_direct_clinical_evidence && executive_recommendation.coverage === "available") {
-        const rec = executive_recommendation.data;
-        if (rec.confidence !== "low") {
-            rec.confidence = "low";
-        }
-        rec.coverage_qualifier = {
-            ...rec.coverage_qualifier,
-            note: appendNote(rec.coverage_qualifier.note, "No direct target-modulator clinical evidence was available; recommendation confidence is capped at low."),
-        };
-        quality_gates.push({
-            gate_id: "direct-clinical-evidence",
-            status: "warning",
-            message: "No direct target-modulator clinical evidence is available, so confidence is capped at low.",
-            affected_sections: ["executive_recommendation"],
-        });
-    }
-    if (!quality_gates.some((g) => g.status === "blocked")) {
-        quality_gates.push({
-            gate_id: "recommendation-quality",
-            status: "pass",
-            message: "No blocking recommendation quality issues detected.",
-            affected_sections: ["executive_recommendation"],
-        });
-    }
-    return { executive_recommendation, quality_gates };
-}

package/dist/workflows/target-assessment/lib/recommendation-sanitizer.d.ts

@@ -1,2 +0,0 @@
-import type { DossierRecommendationOutput } from "../synthesis/index.js";
-export declare function sanitizeRecommendation(rec: DossierRecommendationOutput): DossierRecommendationOutput;

package/dist/workflows/target-assessment/lib/recommendation-sanitizer.js

@@ -1,51 +0,0 @@
-/**
- * Strip pipeline scaffold tokens from user-visible recommendation prose.
- *
- * The Phase-5 dossier-recommendation agent occasionally echoes internal
- * indexing paths it saw in its delegation prompt — strings like
- * `per_section_synthesis.liability_bullets[0]` and parenthetical lists
- * containing them. These are scaffolding for the build pipeline; a
- * toxicologist reading the final dossier should never see them.
- *
- * The sanitizer removes the tokens and their parenthetical wrappers,
- * collapses the resulting double whitespace, and preserves surrounding
- * sentence punctuation.
- */
-const SCAFFOLD_TOKEN_RE = /per_section_synthesis\.[A-Za-z_][\w.]*(?:\[[\d–-]+\])?(?:\s+row\s+\d+)?/g;
-// Citations to dossier.per_section_synthesis.* — this namespace doesn't exist
-// in the dossier schema. The synthesis prompt occasionally emits these paths;
-// strip them to prevent non-resolvable citations in recommendation prose.
-const INVALID_PATH_RE = /\(?dossier\.per_section_synthesis\.[a-z_.[\]0-9]*\)?/gi;
-// Dangling "dossier." with no path suffix is leftover templating; strip it.
-const DANGLING_DOSSIER_RE = /\bdossier\.(?=\s|$|[.,;])/g;
-function stripScaffold(text) {
-    if (!text)
-        return text;
-    let out = text;
-    // First pass: remove a parenthetical that contains a scaffold token,
-    // along with its trailing punctuation if it directly precedes one.
-    out = out.replace(/\s*\([^()]*per_section_synthesis\.[^()]*\)/g, "");
-    // Second pass: any leftover scaffold tokens not inside parens.
-    out = out.replace(SCAFFOLD_TOKEN_RE, "");
-    // Strip dossier.per_section_synthesis.* invalid paths and dangling dossier. placeholders.
-    out = out.replace(INVALID_PATH_RE, "").replace(DANGLING_DOSSIER_RE, "");
-    // Collapse double whitespace.
-    out = out.replace(/\s{2,}/g, " ").replace(/\s+([,.;:])/g, "$1");
-    return out.trim();
-}
-export function sanitizeRecommendation(rec) {
-    return {
-        ...rec,
-        rationale: stripScaffold(rec.rationale),
-        key_strengths: rec.key_strengths.map(stripScaffold),
-        key_risks: rec.key_risks.map(stripScaffold),
-        modality_choice: {
-            ...rec.modality_choice,
-            rationale: stripScaffold(rec.modality_choice.rationale),
-        },
-        coverage_qualifier: {
-            ...rec.coverage_qualifier,
-            note: stripScaffold(rec.coverage_qualifier.note),
-        },
-    };
-}

package/dist/workflows/target-assessment/lib/regulatory-actions.d.ts

@@ -1,25 +0,0 @@
-/**
- * Per-drug regulatory-action collector. Queries openFDA Structured Product
- * Labels (boxed warning, Section 5 warnings_and_cautions, REMS indicator)
- * and the EMA referrals catalogue (Article 31 / Article 20 procedures)
- * for each drug, then maps both into the dossier's RegulatoryActionRow
- * shape.
- *
- * Coverage that legitimately has no
- * machine-readable source (e.g., EMA assessment-report procedure codes like
- * EMEA/H/A-31/1291) is omitted rather than backfilled with curation — the
- * source_url points at the canonical document where the human reader can
- * extract the additional context.
- */
-import type { RegulatoryActionRow } from "@inflexa-ai/harness/contracts/target-dossier.js";
-export interface DrugForRegulatoryActions {
-    chemblId: string;
-    name: string;
-}
-/**
- * Fetch regulatory actions (FDA label + EMA referrals) for a set of drugs.
- * Per-drug failures are isolated — one drug throwing does not blank out
- * the rest. Returns an empty array when no drugs are provided or no source
- * returned any actions.
- */
-export declare function fetchRegulatoryActions(drugs: DrugForRegulatoryActions[]): Promise<RegulatoryActionRow[]>;