@inflexa-ai/harness 0.12.0 → 0.14.0

package/dist/agents/sandbox/ephemeral-executor.js

@@ -1,20 +0,0 @@
-/**
- * Ephemeral Executor — read-only sandbox agent for quick computations.
- * Cannot create files; step conventions don't apply.
- */
-import { ephemeralExecutorPrompt } from "../../prompts/sandbox/ephemeral-executor.js";
-import { BASE_SANDBOX_TOOLS, createSandboxAgent } from "./shared.js";
-export const meta = {
-    id: "ephemeral-executor",
-    capabilities: ["data inspection", "quick statistics", "data transformation", "table preview"],
-    suitableFor: ["bulk-rna-seq", "single-cell", "proteomics", "metabolomics", "genomics", "transcriptomics", "general-omics"],
-    skills: ["shared/omics-general"],
-    tools: [...BASE_SANDBOX_TOOLS, "pubmed", "searchGene", "searchPathway", "lookupGoTerm", "searchInteractions"],
-    plannable: false,
-};
-export function createEphemeralExecutorAgent(deps) {
-    return createSandboxAgent(deps, meta, ephemeralExecutorPrompt, {
-        appendAnalysisStepStandards: false,
-        readOnly: true,
-    });
-}

package/dist/execution/ephemeral-runner.d.ts

@@ -1,98 +0,0 @@
-/**
- * Ephemeral runner — read-only sandbox execution for ad-hoc data
- * exploration, run as a turn-scoped DBOS workflow.
- *
- * The `run_ephemeral` conversation tool authorizes the run at the async
- * edge, starts this workflow, and awaits its result inline within the chat
- * turn. The workflow is "bare": it has no run-event stream, so `emit` is a
- * no-op and live sandbox progress events are dropped. It is never recovered
- * — chat disconnect cancels it (`DBOS.cancelWorkflow`), and a boot-time sweep
- * cancels any `ephemeral:`-prefixed PENDING workflow a dead pod left behind.
- *
- * Lifecycle: create sandbox → build the ephemeral-executor with synthetic
- * step coords (`runId = stepId = "ephemeral"`, the literal the host-managed
- * billing rules key on) → drive `runAgent` over the executor with `durableStep` →
- * final text + step count → teardown the sandbox in `finally` on every
- * terminal path.
- *
- * Read-only is enforced, not aspirational: the executor agent is built with
- * `readOnly: true` (no `write_file`/`edit_file` tools) and its sandbox is
- * provisioned with no read-write mount — only the read-only analysis tree.
- * Container-local `/tmp` stays writable (torn down with the sandbox); nothing
- * persists. The prompt's "you physically cannot write files" is now true.
- */
-import type { Pool } from "pg";
-import type { RunSession } from "../auth/types.js";
-import type { EnvironmentStorePaths } from "../config/environment-stores.js";
-import type { ResourcePolicy } from "../config/resource-limits.js";
-import type { ChatProvider, EmbeddingProvider } from "../providers/types.js";
-import type { SandboxClient } from "../sandbox/client.js";
-import type { BioToolKeys } from "../tools/bio/keys.js";
-import type { WorkspaceFilesystem } from "../workspace/filesystem.js";
-import type { ResolveWorkspaceRoot } from "../workspace/paths.js";
-import type { Logger } from "../lib/logger.js";
-/** Sub-agent identity — appended to `callPath`, set as `agentId`. */
-export declare const EPHEMERAL_AGENT_ID = "ephemeral-executor";
-/** Workflow-id prefix — the boot-time never-recover sweep matches on it. */
-export declare const EPHEMERAL_WORKFLOW_PREFIX: "ephemeral:";
-/** The body's construction-time deps — closed over at registration. */
-export interface EphemeralDeps extends EnvironmentStorePaths {
-    /** Operational logging seam; omitted falls back to no-op. */
-    readonly logger?: Logger;
-    readonly provider: ChatProvider;
-    readonly pool: Pool;
-    readonly sandboxClient: SandboxClient;
-    readonly workspaceFs: WorkspaceFilesystem;
-    /** Embedding provider for the executor's in-sandbox `workspace_search`. */
-    readonly embedding: EmbeddingProvider;
-    /** Workspace-root resolution seam (see workspace/paths.ts). */
-    readonly resolveWorkspaceRoot: ResolveWorkspaceRoot;
-    /** Model id — provenance / metric label; the provider owns the wire model. */
-    readonly model: string;
-    /** API keys for the bio/chem tools the ephemeral executor may use. */
-    readonly bioKeys: BioToolKeys;
-    /** Host resource policy — its `ephemeral` spec overrides the default sandbox size. */
-    readonly resourcePolicy?: ResourcePolicy;
-}
-/**
- * Workflow input. JSON-serialisable — the authorized `RunSession` carries the
- * run credential; the body reads it and never re-authorizes.
- */
-export interface EphemeralWorkflowInput {
-    readonly runSession: RunSession;
-    readonly prompt: string;
-    /** Optional cap on the inner agent's tool-call budget. */
-    readonly maxIterations?: number;
-    /** Optional deadline override for sandbox-server execs (unix ms). */
-    readonly deadlineMs?: number;
-}
-export interface EphemeralResult {
-    readonly text: string;
-    readonly durationMs: number;
-    readonly stepsUsed: number;
-}
-/**
- * Register the ephemeral workflow with DBOS. Returns the registered callable
- * so the `run_ephemeral` tool can dispatch via `DBOS.startWorkflow`.
- */
-export declare function registerEphemeralWorkflow(deps: EphemeralDeps): (input: EphemeralWorkflowInput) => Promise<EphemeralResult>;
-/**
- * The executor's seed: its workspace frame, then the caller's ask.
- *
- * An ephemeral run is not scheduled by `executeAnalysis`, so no step briefing is
- * composed for it — and the sandbox system prompt names no paths (it is static
- * per agent type, so the provider's prompt cache can reuse it). The analysis
- * root would otherwise reach the agent nowhere: `run_ephemeral`'s `prompt` is
- * free text authored by the conversation agent.
- *
- * The frame differs from a step's, so this does not reuse `renderWorkspace`:
- * there is no writable directory to name. The read-only tree IS the cwd.
- */
-export declare function ephemeralSeed(analysisId: string, prompt: string): string;
-/**
- * Run the ephemeral-executor agent against a fresh read-only sandbox.
- * Throws on sandbox start failure; otherwise returns the agent's final
- * text plus timing. Sandbox teardown fires on every terminal path —
- * success, error, cancel.
- */
-export declare function runEphemeralBody(input: EphemeralWorkflowInput, deps: EphemeralDeps): Promise<EphemeralResult>;

package/dist/execution/ephemeral-runner.js

@@ -1,189 +0,0 @@
-/**
- * Ephemeral runner — read-only sandbox execution for ad-hoc data
- * exploration, run as a turn-scoped DBOS workflow.
- *
- * The `run_ephemeral` conversation tool authorizes the run at the async
- * edge, starts this workflow, and awaits its result inline within the chat
- * turn. The workflow is "bare": it has no run-event stream, so `emit` is a
- * no-op and live sandbox progress events are dropped. It is never recovered
- * — chat disconnect cancels it (`DBOS.cancelWorkflow`), and a boot-time sweep
- * cancels any `ephemeral:`-prefixed PENDING workflow a dead pod left behind.
- *
- * Lifecycle: create sandbox → build the ephemeral-executor with synthetic
- * step coords (`runId = stepId = "ephemeral"`, the literal the host-managed
- * billing rules key on) → drive `runAgent` over the executor with `durableStep` →
- * final text + step count → teardown the sandbox in `finally` on every
- * terminal path.
- *
- * Read-only is enforced, not aspirational: the executor agent is built with
- * `readOnly: true` (no `write_file`/`edit_file` tools) and its sandbox is
- * provisioned with no read-write mount — only the read-only analysis tree.
- * Container-local `/tmp` stays writable (torn down with the sandbox); nothing
- * persists. The prompt's "you physically cannot write files" is now true.
- */
-import { DBOS, Error as DBOSErrors } from "@dbos-inc/dbos-sdk";
-import { forSubAgent } from "../auth/types.js";
-import { finalText, runAgent } from "../loop/run-agent.js";
-import { durableStep } from "../loop/run-step.js";
-import { generateExecutionId } from "../sandbox/execution-id.js";
-import { mintSandboxIdentity } from "../sandbox/identity.js";
-import { createEphemeralExecutorAgent } from "../agents/sandbox/ephemeral-executor.js";
-import { createNoopLogger } from "../lib/console-logger.js";
-/** Sub-agent identity — appended to `callPath`, set as `agentId`. */
-export const EPHEMERAL_AGENT_ID = "ephemeral-executor";
-/**
- * Synthetic run/step literal stamped into the agent's step coords.
- * Host-managed billing rules key on this literal to recognize chat-turn
- * ephemeral runs (no `cortex_runs` row, no DBOS stream).
- */
-const EPHEMERAL_RUN_LITERAL = "ephemeral";
-/** Workflow-id prefix — the boot-time never-recover sweep matches on it. */
-export const EPHEMERAL_WORKFLOW_PREFIX = "ephemeral:";
-/** Default budget — chat-turn-scoped, no recovery, no checkpointing. */
-const DEFAULT_DEADLINE_MS = 120_000;
-/** Ephemeral runs have no planner estimate, so the sandbox box is chosen here
- *  explicitly — the policy's `ephemeral` spec when supplied, otherwise this
- *  mid-range default; either way clamped to cluster limits at create time. */
-const EPHEMERAL_SANDBOX_RESOURCES = { cpu: 4, memoryGb: 8 };
-/**
- * Register the ephemeral workflow with DBOS. Returns the registered callable
- * so the `run_ephemeral` tool can dispatch via `DBOS.startWorkflow`.
- */
-export function registerEphemeralWorkflow(deps) {
-    return DBOS.registerWorkflow((input) => runEphemeralBody(input, deps), { name: "ephemeral" });
-}
-/**
- * The executor's seed: its workspace frame, then the caller's ask.
- *
- * An ephemeral run is not scheduled by `executeAnalysis`, so no step briefing is
- * composed for it — and the sandbox system prompt names no paths (it is static
- * per agent type, so the provider's prompt cache can reuse it). The analysis
- * root would otherwise reach the agent nowhere: `run_ephemeral`'s `prompt` is
- * free text authored by the conversation agent.
- *
- * The frame differs from a step's, so this does not reuse `renderWorkspace`:
- * there is no writable directory to name. The read-only tree IS the cwd.
- */
-export function ephemeralSeed(analysisId, prompt) {
-    const root = `/${analysisId}`;
-    return [
-        "## Workspace",
-        `- Analysis root (read-only): \`${root}\` — inputs at \`${root}/data/inputs/\`, prior runs at \`${root}/runs/\`.`,
-        `- The analysis root is also your cwd, and what relative paths resolve against. The sandbox is read-only: there is nowhere to write, so return every result inline.`,
-        "",
-        prompt,
-    ].join("\n");
-}
-/**
- * Run the ephemeral-executor agent against a fresh read-only sandbox.
- * Throws on sandbox start failure; otherwise returns the agent's final
- * text plus timing. Sandbox teardown fires on every terminal path —
- * success, error, cancel.
- */
-export async function runEphemeralBody(input, deps) {
-    const { runSession } = input;
-    if (runSession.scope.kind !== "analysis") {
-        throw new Error(`runEphemeralBody requires an analysis-scoped session — got ${runSession.scope.kind}`);
-    }
-    const analysisId = runSession.scope.analysisId;
-    // Bound after the scope guard: `analysisId` comes off the session's scope,
-    // not the workflow input.
-    const logger = (deps.logger ?? createNoopLogger()).named("ephemeral").with({ analysisId });
-    const startedAt = performance.now();
-    const executionId = generateExecutionId(EPHEMERAL_AGENT_ID);
-    const workflowId = DBOS.workflowID ?? `${EPHEMERAL_WORKFLOW_PREFIX}${executionId}`;
-    const childSession = forSubAgent(runSession, EPHEMERAL_AGENT_ID);
-    // Resolver throw = loud workflow failure, per the workspace-root-resolution contract.
-    const workspaceRoot = deps.resolveWorkspaceRoot(analysisId);
-    logger.info("starting sandbox", { executionId });
-    const sandbox = await deps.sandboxClient.createSandbox({
-        runId: EPHEMERAL_RUN_LITERAL,
-        stepId: EPHEMERAL_RUN_LITERAL,
-        analysisId,
-        execId: null,
-        childWorkflowId: workflowId,
-        resources: deps.resourcePolicy?.ephemeral ?? EPHEMERAL_SANDBOX_RESOURCES,
-        // No read-write step mount — only the read-only analysis tree.
-        readOnly: true,
-    }, mintSandboxIdentity(EPHEMERAL_RUN_LITERAL));
-    try {
-        // The fallback reads the CHECKPOINTED clock, not `Date.now()`: `awaitExec`
-        // gates on this absolute deadline, and its recovery-pull is a durable step,
-        // so a wall-clock deadline that grew on replay would shift which loop
-        // iteration crosses the deadline and desynchronise the recorded function-ID
-        // sequence (see the harness-durable-runtime spec; sandbox-step.ts does the
-        // same). `input.deadlineMs`, when present, is already replay-stable.
-        const deadlineAbs = input.deadlineMs ?? (await DBOS.now()) + DEFAULT_DEADLINE_MS;
-        const nextFunctionId = makeNextFunctionId();
-        const sandboxAgentDeps = {
-            provider: deps.provider,
-            pool: deps.pool,
-            sandboxClient: deps.sandboxClient,
-            workspaceFs: deps.workspaceFs,
-            embedding: deps.embedding,
-            model: deps.model,
-            bioKeys: deps.bioKeys,
-            ...(deps.packagesFile ? { packagesFile: deps.packagesFile } : {}),
-            ...(deps.refStorePath ? { refStorePath: deps.refStorePath } : {}),
-            step: {
-                sandbox,
-                workspaceRoot,
-                analysisId,
-                runId: EPHEMERAL_RUN_LITERAL,
-                stepId: EPHEMERAL_RUN_LITERAL,
-                workflowId,
-                // Enforced read-only: the executor agent gets no write_file/edit_file
-                // tools and the sandbox has no read-write mount. This prefix is not a
-                // writable location — it only resolves `execute_command`'s default cwd
-                // to the read-only analysis-tree root (`/{analysisId}`), where reads land.
-                allowedWritePrefix: workspaceRoot,
-                nextFunctionId,
-                deadlineMs: () => deadlineAbs,
-            },
-        };
-        const agentDef = createEphemeralExecutorAgent(sandboxAgentDeps);
-        const agent = input.maxIterations !== undefined ? { ...agentDef, maxIterations: input.maxIterations } : agentDef;
-        const signal = new AbortController().signal;
-        const { messages: finalMessages } = await runAgent(agent, [{ role: "user", content: ephemeralSeed(analysisId, input.prompt) }], childSession, {
-            provider: deps.provider,
-            signal,
-            emit: () => { },
-            runStep: durableStep,
-            isFatalLoopError: (err) => err instanceof DBOSErrors.DBOSWorkflowCancelledError,
-        });
-        const text = finalText(finalMessages);
-        const stepsUsed = countAssistantTurns(finalMessages);
-        const durationMs = Math.round(performance.now() - startedAt);
-        logger.info("completed", { executionId, stepsUsed, durationMs });
-        return { text, stepsUsed, durationMs };
-    }
-    catch (err) {
-        const message = err instanceof Error ? err.message : String(err);
-        logger.error("failed", { executionId, err: message });
-        throw err;
-    }
-    finally {
-        try {
-            await deps.sandboxClient.teardown(sandbox);
-        }
-        catch (teardownErr) {
-            // Teardown is idempotent — "already gone" is success. A failure here
-            // is best-effort logged so the chat turn doesn't fail on cleanup.
-            logger.warn("teardown failed (non-fatal)", { executionId, ...logger.errorFields(teardownErr) });
-        }
-    }
-}
-/** Per-call function-id minter — replay-deterministic. */
-function makeNextFunctionId() {
-    let n = 0;
-    return () => `fn-${(n++).toString(36)}`;
-}
-/** The agent's final assistant turn is the `stepsUsed` proxy — every loop
- *  iteration produces one assistant message. */
-function countAssistantTurns(messages) {
-    let n = 0;
-    for (const m of messages)
-        if (m.role === "assistant")
-            n++;
-    return n;
-}

package/dist/prompts/sandbox/ephemeral-executor.d.ts

@@ -1 +0,0 @@
-export declare const ephemeralExecutorPrompt = "# Ephemeral Executor\n\nYou are a read-only compute agent. You execute scripts on the user's data\nand return the results. You **cannot create or save files** \u2014 your sandbox\nis fully read-only.\n\n## What You Do\n\n1. Read data files to understand their structure\n2. Write and execute R or Python scripts via `execute_command`\n3. Return the script output (tables, statistics, plot data) in your response\n\n## Constraints\n\n- **Read-only**: You physically cannot write files. Do not attempt to save\n  output to disk. All results must be returned in your text response.\n- **Inline output**: Print results to stdout. For plots, use base64 encoding\n  and print the encoded string so the caller can display it.\n- **Structured responses**: When returning tabular data, format as markdown\n  tables or JSON arrays. When returning statistics, use clear labeled output.\n\n## Script Execution Pattern\n\nFor Python:\n```\nexecute_command python3 -c \"\nimport pandas as pd\ndf = pd.read_csv('/{resourceId}/data/inputs/{fileId}/data.csv')\nprint(df.describe().to_markdown())\n\"\n```\n\nFor R:\n```\nexecute_command Rscript -e \"\ndf <- read.csv('/{resourceId}/data/inputs/{fileId}/data.csv')\nsummary(df)\n\"\n```\n\nFor plots (base64):\n```\nexecute_command python3 -c \"\nimport matplotlib\nmatplotlib.use('Agg')\nimport matplotlib.pyplot as plt\nimport pandas as pd\nimport base64, io\n\ndf = pd.read_csv('...')\nfig, ax = plt.subplots()\ndf.plot(ax=ax)\nbuf = io.BytesIO()\nfig.savefig(buf, format='png')\nprint(base64.b64encode(buf.getvalue()).decode())\n\"\n```\n\n## Do NOT\n\n- Attempt to write files \u2014 it will fail silently or error\n- Install packages at runtime\n- Return raw binary data without base64 encoding\n- Guess data structure without inspecting the file first\n- Run long-running computations (you have a short timeout)\n";

package/dist/prompts/sandbox/ephemeral-executor.js

@@ -1,66 +0,0 @@
-export const ephemeralExecutorPrompt = `# Ephemeral Executor
-
-You are a read-only compute agent. You execute scripts on the user's data
-and return the results. You **cannot create or save files** — your sandbox
-is fully read-only.
-
-## What You Do
-
-1. Read data files to understand their structure
-2. Write and execute R or Python scripts via \`execute_command\`
-3. Return the script output (tables, statistics, plot data) in your response
-
-## Constraints
-
-- **Read-only**: You physically cannot write files. Do not attempt to save
-  output to disk. All results must be returned in your text response.
-- **Inline output**: Print results to stdout. For plots, use base64 encoding
-  and print the encoded string so the caller can display it.
-- **Structured responses**: When returning tabular data, format as markdown
-  tables or JSON arrays. When returning statistics, use clear labeled output.
-
-## Script Execution Pattern
-
-For Python:
-\`\`\`
-execute_command python3 -c "
-import pandas as pd
-df = pd.read_csv('/{resourceId}/data/inputs/{fileId}/data.csv')
-print(df.describe().to_markdown())
-"
-\`\`\`
-
-For R:
-\`\`\`
-execute_command Rscript -e "
-df <- read.csv('/{resourceId}/data/inputs/{fileId}/data.csv')
-summary(df)
-"
-\`\`\`
-
-For plots (base64):
-\`\`\`
-execute_command python3 -c "
-import matplotlib
-matplotlib.use('Agg')
-import matplotlib.pyplot as plt
-import pandas as pd
-import base64, io
-
-df = pd.read_csv('...')
-fig, ax = plt.subplots()
-df.plot(ax=ax)
-buf = io.BytesIO()
-fig.savefig(buf, format='png')
-print(base64.b64encode(buf.getvalue()).decode())
-"
-\`\`\`
-
-## Do NOT
-
-- Attempt to write files — it will fail silently or error
-- Install packages at runtime
-- Return raw binary data without base64 encoding
-- Guess data structure without inspecting the file first
-- Run long-running computations (you have a short timeout)
-`;

package/dist/tools/bio/check-safety-panel.d.ts

@@ -1,35 +0,0 @@
-/**
- * checkSafetyPanel — look up identifiers against the curated
- * secondary-pharmacology safety target panel.
- */
-export declare const checkSafetyPanelTool: import("../define-tool.js").Tool<{
-    identifiers: string[];
-    identifier_type: "auto" | "gene_symbol" | "uniprot" | "chembl_id";
-    filter_organ?: "hematologic" | "metabolic" | "immune" | "hepatic" | "cns" | "renal" | "respiratory" | "cardiac" | "gi" | undefined;
-}, {
-    matches: {
-        input: string;
-        matched_entry: {
-            chembl_id: string;
-            gene_symbol: string;
-            uniprot: string;
-            name: string;
-            organ_system: "hematologic" | "metabolic" | "immune" | "hepatic" | "cns" | "renal" | "respiratory" | "cardiac" | "gi";
-            clinical_consequence: string;
-            severity: "high" | "medium" | "low";
-            references: string[];
-            ensembl_gene_id?: string | undefined;
-        } | null;
-    }[];
-    summary: {
-        total_input: number;
-        matched: number;
-        by_severity: {
-            high: number;
-            medium: number;
-            low: number;
-        };
-        by_organ: Record<string, number>;
-    };
-    panel_version: string;
-}>;

package/dist/tools/bio/check-safety-panel.js

@@ -1,76 +0,0 @@
-/**
- * checkSafetyPanel — look up identifiers against the curated
- * secondary-pharmacology safety target panel.
- */
-import { ok } from "neverthrow";
-import { z } from "zod";
-import { CHEMBL_RE, ORGAN_SYSTEMS, SafetyPanelFileSchema, UNIPROT_RE } from "../../data/safety-panel-schema.js";
-import panelData from "../../data/safety-panel.json" with { type: "json" };
-import { defineTool } from "../define-tool.js";
-const PANEL = SafetyPanelFileSchema.parse(panelData);
-const BY_CHEMBL = new Map(PANEL.targets.map((t) => [t.chembl_id, t]));
-const BY_GENE = new Map(PANEL.targets.map((t) => [t.gene_symbol, t]));
-const BY_UNIPROT = new Map(PANEL.targets.map((t) => [t.uniprot, t]));
-function detectType(id) {
-    if (CHEMBL_RE.test(id))
-        return "chembl_id";
-    if (UNIPROT_RE.test(id))
-        return "uniprot";
-    return "gene_symbol";
-}
-function lookup(id, type) {
-    switch (type) {
-        case "chembl_id":
-            return BY_CHEMBL.get(id) ?? null;
-        case "gene_symbol":
-            return BY_GENE.get(id.toUpperCase()) ?? null;
-        case "uniprot":
-            return BY_UNIPROT.get(id) ?? null;
-    }
-}
-export const checkSafetyPanelTool = defineTool({
-    id: "check_safety_panel",
-    description: "Look up identifiers (ChEMBL ID, gene symbol, or UniProt accession) against the curated " +
-        "secondary-pharmacology safety target panel. Returns organ system, severity, and clinical " +
-        "consequence for each matched target. Use as a fast first-pass off-target liability check; " +
-        "for comprehensive assessment also call get-target-safety and search-toxcast.",
-    inputSchema: z.object({
-        identifiers: z.array(z.string().min(1)).min(0).max(200).describe("0-200 identifiers (ChEMBL IDs, gene symbols, or UniProt accessions)."),
-        identifier_type: z
-            .enum(["chembl_id", "gene_symbol", "uniprot", "auto"])
-            .default("auto")
-            .describe("Identifier interpretation. 'auto' detects per-input."),
-        filter_organ: z.enum(ORGAN_SYSTEMS).optional().describe("Restrict matches to this organ system."),
-    }),
-    execute: async ({ identifiers, identifier_type = "auto", filter_organ }) => {
-        const matches = identifiers.map((input) => {
-            const type = identifier_type === "auto" ? detectType(input) : identifier_type;
-            let entry = lookup(input, type);
-            if (entry && filter_organ && entry.organ_system !== filter_organ) {
-                entry = null;
-            }
-            return { input, matched_entry: entry };
-        });
-        const bySeverity = { high: 0, medium: 0, low: 0 };
-        const byOrgan = {};
-        let matched = 0;
-        for (const m of matches) {
-            if (!m.matched_entry)
-                continue;
-            matched++;
-            bySeverity[m.matched_entry.severity]++;
-            const o = m.matched_entry.organ_system;
-            byOrgan[o] = (byOrgan[o] ?? 0) + 1;
-        }
-        return ok({
-            matches,
-            summary: {
-                total_input: identifiers.length,
-                matched,
-                by_severity: bySeverity,
-                by_organ: byOrgan,
-            },
-            panel_version: PANEL.panel_version,
-        });
-    },
-});

package/dist/tools/bio/get-impc-ko-profile.d.ts

@@ -1,9 +0,0 @@
-/**
- * getImpcKoProfile tool — mouse knockout phenotype profile via IMPC Solr.
- */
-import { buildViabilityCalls, derivedViability, parsePhenotypeResponse } from "../lib/impc-client.js";
-export type { PhenotypeProfile, ViabilityCall, ViabilityCategory } from "../lib/impc-client.js";
-export { buildViabilityCalls, derivedViability, parsePhenotypeResponse };
-export declare const getImpcKoProfileTool: import("../define-tool.js").Tool<{
-    geneSymbol: string;
-}, import("../lib/impc-client.js").KoPhenotypeProfile>;

package/dist/tools/bio/get-impc-ko-profile.js

@@ -1,23 +0,0 @@
-/**
- * getImpcKoProfile tool — mouse knockout phenotype profile via IMPC Solr.
- */
-import { ok } from "neverthrow";
-import { z } from "zod";
-import { defineTool } from "../define-tool.js";
-import { buildViabilityCalls, derivedViability, getKoPhenotypeProfile, parsePhenotypeResponse } from "../lib/impc-client.js";
-export { buildViabilityCalls, derivedViability, parsePhenotypeResponse };
-export const getImpcKoProfileTool = defineTool({
-    id: "get_impc_ko_profile",
-    description: "Get the mouse-knockout phenotype profile for a gene from IMPC — the in-vivo loss-of-function evidence for target tractability and essentiality " +
-        "('what happens to PAX5 knockout mice?', 'is loss of CASP8 lethal?'). " +
-        "Takes a human gene symbol and maps it to the mouse ortholog itself. Returns a top-line pre-weaning viability call (lethal_pre_weaning | subviable | viable | null) with its " +
-        "per-zygosity breakdown, the significant MP phenotype terms ordered by best p-value, the affected organ systems ranked by phenotype count, and a sex-dimorphism flag. " +
-        "An all-empty profile (null mouseMarkerSymbol, null viability, no phenotype terms) means the gene has not been IMPC-phenotyped — common and valid. Do NOT retry on empty output.",
-    inputSchema: z.object({
-        geneSymbol: z
-            .string()
-            .min(1)
-            .describe("HUMAN gene symbol, e.g. 'BRCA1' — one gene per call. The mouse ortholog is resolved internally; do not pass a mouse symbol or an MGI ID."),
-    }),
-    execute: async ({ geneSymbol }) => ok(await getKoPhenotypeProfile(geneSymbol)),
-});

package/dist/tools/bio/lookup-go-term.d.ts

@@ -1,31 +0,0 @@
-/**
- * lookupGoTerm — look up Gene Ontology terms via the QuickGO API (EBI).
- *
- * Supports direct ID lookup, keyword search, and gene annotation retrieval.
- * Multiple modes can be combined in a single call.
- */
-interface GoTerm {
-    id: string;
-    name: string;
-    definition?: string;
-    aspect?: string;
-}
-interface GoAnnotation {
-    geneProductId: string;
-    goId: string;
-    goName: string;
-    aspect?: string;
-    evidenceCode?: string;
-    qualifier?: string;
-}
-export declare const lookupGoTermTool: import("../define-tool.js").Tool<{
-    limit: number;
-    goId?: string | undefined;
-    query?: string | undefined;
-    geneProductId?: string | undefined;
-    taxonId?: number | undefined;
-}, {
-    terms: GoTerm[] | undefined;
-    annotations: GoAnnotation[] | undefined;
-}>;
-export {};