@inflexa-ai/harness 0.1.1

package/dist/agents/sandbox/__fixtures__/deps.js

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+/**
+ * Test-only `SandboxAgentDeps` builder. Hands every dependency a stub so
+ * `createSandboxAgent` builds without touching Postgres, the network, or
+ * a real sandbox.
+ */
+import { okAsync } from "neverthrow";
+export function makeFakeSandboxClient() {
+    const ref = {
+        sandboxId: "sb-test",
+        host: "127.0.0.1",
+        port: 8765,
+        backend: "docker",
+        callbackSecret: "secret",
+    };
+    return {
+        async createSandbox(_meta) {
+            return ref;
+        },
+        async submitExec(_ref, _body) { },
+        async awaitExec(_ref, execId, _emit, _deadline) {
+            return {
+                execId,
+                exitCode: 0,
+                stdout: "",
+                stderr: "",
+                durationMs: 1,
+                timedOut: false,
+            };
+        },
+        async isAlive() {
+            return { alive: true, oomKilled: false };
+        },
+        async teardown() { },
+        async teardownById() { },
+        async listManagedSandboxes() {
+            return [];
+        },
+    };
+}
+export function makeFakeWorkspaceFs() {
+    return {
+        readFile() {
+            return okAsync({ kind: "ok", content: Buffer.alloc(0), truncated: false });
+        },
+        list() {
+            return okAsync({ kind: "ok", entries: [] });
+        },
+        stat() {
+            return okAsync({ kind: "not_found" });
+        },
+    };
+}
+export function makeFakeChatProvider() {
+    return {
+        capabilities: { toolCalling: true },
+        chat() {
+            throw new Error("fake chat provider — not exercised in these tests");
+        },
+        chatStream() {
+            throw new Error("fake chat provider — not exercised in these tests");
+        },
+    };
+}
+export function makeFakePool() {
+    return {};
+}
+export function makeFakeSandboxAgentDeps(over = {}) {
+    return {
+        provider: makeFakeChatProvider(),
+        pool: makeFakePool(),
+        sandboxClient: makeFakeSandboxClient(),
+        workspaceFs: makeFakeWorkspaceFs(),
+        model: over.model ?? "claude-opus-4-7",
+        bioKeys: { drugbank: "", disgenet: "", epaCcte: "" },
+        step: {
+            sandbox: {
+                sandboxId: "sb-test",
+                host: "127.0.0.1",
+                port: 8765,
+                backend: "docker",
+                callbackSecret: "secret",
+            },
+            workspaceRoot: "/tmp/sessions/analysis-001",
+            analysisId: over.analysisId ?? "analysis-001",
+            runId: over.runId ?? "run-001",
+            stepId: over.stepId ?? "step-001",
+            workflowId: over.workflowId ?? "wf-001",
+            allowedWritePrefix: over.allowedWritePrefix ?? "/tmp/sessions/analysis-001/runs/run-001/step-001",
+            nextFunctionId: (() => {
+                let n = 0;
+                return () => `fn-${++n}`;
+            })(),
+            deadlineMs: () => Date.now() + 60_000,
+        },
+    };
+}

package/dist/agents/sandbox/bulk-transcriptomics-agent.d.ts

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+/**
+ * Bulk Transcriptomics Agent — bulk RNA-seq and microarray analysis specialist.
+ */
+import type { AgentDefinition } from "../../loop/types.js";
+import { type SandboxAgentDeps } from "./shared.js";
+import type { AgentMeta } from "./types.js";
+export declare const meta: AgentMeta;
+export declare function createBulkTranscriptomicsAgent(deps: SandboxAgentDeps): AgentDefinition;

package/dist/agents/sandbox/bulk-transcriptomics-agent.js

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+/**
+ * Bulk Transcriptomics Agent — bulk RNA-seq and microarray analysis specialist.
+ */
+import { bulkTranscriptomicsAgentPrompt } from "../../prompts/sandbox/bulk-transcriptomics-agent.js";
+import { BASE_SANDBOX_TOOLS, createSandboxAgent } from "./shared.js";
+export const meta = {
+    id: "bulk-transcriptomics-agent",
+    capabilities: [
+        "differential expression",
+        "normalization",
+        "batch correction",
+        "quality control",
+        "count-based statistical modeling",
+        "microarray analysis",
+    ],
+    suitableFor: ["bulk-rna-seq", "microarray"],
+    skills: ["bulk-transcriptomics", "shared/omics-general"],
+    tools: [...BASE_SANDBOX_TOOLS, "searchPubMed", "getArticleDetails", "getArticleFullText", "searchGeoDatasets"],
+};
+export function createBulkTranscriptomicsAgent(deps) {
+    return createSandboxAgent(deps, meta, bulkTranscriptomicsAgentPrompt);
+}

package/dist/agents/sandbox/cheminformatics-agent.d.ts

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+/**
+ * Cheminformatics Agent — molecular structure analysis, SAR triage, QSAR
+ * modeling, and chemical tractability assessment.
+ */
+import type { AgentDefinition } from "../../loop/types.js";
+import { type SandboxAgentDeps } from "./shared.js";
+import type { AgentMeta } from "./types.js";
+export declare const meta: AgentMeta;
+export declare function createCheminformaticsAgent(deps: SandboxAgentDeps): AgentDefinition;

package/dist/agents/sandbox/cheminformatics-agent.js

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+/**
+ * Cheminformatics Agent — molecular structure analysis, SAR triage, QSAR
+ * modeling, and chemical tractability assessment.
+ */
+import { cheminformaticsAgentPrompt } from "../../prompts/sandbox/cheminformatics-agent.js";
+import { BASE_SANDBOX_TOOLS, createSandboxAgent } from "./shared.js";
+export const meta = {
+    id: "cheminformatics-agent",
+    capabilities: [
+        "molecular property profiling",
+        "scaffold decomposition",
+        "structural alert filtering",
+        "SAR analysis",
+        "chemical diversity assessment",
+        "compound library characterization",
+        "QSAR modeling",
+        "chemical space visualization",
+        "ADMET prediction",
+        "molecular descriptor calculation",
+        "structure-activity relationship",
+        "target engagement assessment",
+        "occupancy estimation",
+        "drug perturbation signature matching",
+        "CMap-style connectivity scoring",
+        "selectivity profiling",
+        "kinase selectivity analysis",
+    ],
+    suitableFor: [
+        "chemical-structures",
+        "smiles-data",
+        "compound-activity-data",
+        "compound-libraries",
+        "target-compound-queries",
+        "sar-data",
+        "target-engagement-data",
+        "selectivity-panel-data",
+        "perturbation-signatures",
+    ],
+    skills: ["cheminformatics", "shared/omics-general"],
+    tools: [
+        ...BASE_SANDBOX_TOOLS,
+        "searchPubMed",
+        "getArticleDetails",
+        "getArticleFullText",
+        "searchGene",
+        "searchPathway",
+        "lookupGoTerm",
+        "searchInteractions",
+        "searchCompounds",
+        "getBioactivity",
+        "searchTargets",
+        "getMechanism",
+        "getDrugInfo",
+        "searchDgidb",
+        "searchPubchemCompound",
+        "getPubchemCrossRefs",
+        "getPubchemAssays",
+    ],
+};
+export function createCheminformaticsAgent(deps) {
+    return createSandboxAgent(deps, meta, cheminformaticsAgentPrompt);
+}

package/dist/agents/sandbox/chromatin-agent.d.ts

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+/**
+ * Chromatin & Regulation Agent — chromatin accessibility and TF binding specialist.
+ */
+import type { AgentDefinition } from "../../loop/types.js";
+import { type SandboxAgentDeps } from "./shared.js";
+import type { AgentMeta } from "./types.js";
+export declare const meta: AgentMeta;
+export declare function createChromatinAgent(deps: SandboxAgentDeps): AgentDefinition;

package/dist/agents/sandbox/chromatin-agent.js

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+/**
+ * Chromatin & Regulation Agent — chromatin accessibility and TF binding specialist.
+ */
+import { chromatinAgentPrompt } from "../../prompts/sandbox/chromatin-agent.js";
+import { BASE_SANDBOX_TOOLS, createSandboxAgent } from "./shared.js";
+export const meta = {
+    id: "chromatin-agent",
+    capabilities: ["peak calling", "differential binding", "differential accessibility", "motif analysis", "footprinting", "signal visualization"],
+    suitableFor: ["atac-seq", "chip-seq", "cut-and-tag", "cut-and-run", "scatac-seq"],
+    skills: ["chromatin-regulation", "shared/omics-general"],
+    tools: [
+        ...BASE_SANDBOX_TOOLS,
+        "searchPubMed",
+        "getArticleDetails",
+        "getArticleFullText",
+        "searchGene",
+        "searchPathway",
+        "lookupGoTerm",
+        "searchInteractions",
+    ],
+};
+export function createChromatinAgent(deps) {
+    return createSandboxAgent(deps, meta, chromatinAgentPrompt);
+}

package/dist/agents/sandbox/data-profiler.d.ts

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+/**
+ * Data Profiler — characterizes datasets for downstream analysis planning.
+ * Produces a JSON summary (no scripts/output/figures), so step conventions
+ * are not appended.
+ */
+import type { AgentDefinition } from "../../loop/types.js";
+import { type SandboxAgentDeps } from "./shared.js";
+import type { AgentMeta } from "./types.js";
+export declare const meta: AgentMeta;
+export declare function createDataProfilerAgent(deps: SandboxAgentDeps): AgentDefinition;

package/dist/agents/sandbox/data-profiler.js

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+/**
+ * Data Profiler — characterizes datasets for downstream analysis planning.
+ * Produces a JSON summary (no scripts/output/figures), so step conventions
+ * are not appended.
+ */
+import { dataProfilerPrompt } from "../../prompts/sandbox/data-profiler.js";
+import { BASE_SANDBOX_TOOLS, createSandboxAgent } from "./shared.js";
+export const meta = {
+    id: "data-profiler",
+    capabilities: ["data profiling", "literature review", "methodology research", "analysis planning", "experimental design analysis"],
+    suitableFor: ["bulk-rna-seq", "single-cell", "proteomics", "metabolomics", "genomics", "transcriptomics", "chemical-structures", "compound-screening"],
+    skills: [],
+    tools: [...BASE_SANDBOX_TOOLS],
+    // Profiling fans out one programmatic pass per input file (head/wc preview +
+    // a Python script + read-back) before the single submit_profile, so a
+    // many-file analysis needs more headroom than the sandbox default.
+    defaultMaxSteps: 85,
+    plannable: false,
+};
+export function createDataProfilerAgent(deps) {
+    return createSandboxAgent(deps, meta, dataProfilerPrompt, {
+        appendAnalysisStepStandards: false,
+    });
+}

package/dist/agents/sandbox/dna-methylation-agent.d.ts

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+/**
+ * DNA Methylation Agent — methylation array and bisulfite sequencing specialist.
+ */
+import type { AgentDefinition } from "../../loop/types.js";
+import { type SandboxAgentDeps } from "./shared.js";
+import type { AgentMeta } from "./types.js";
+export declare const meta: AgentMeta;
+export declare function createDnaMethylationAgent(deps: SandboxAgentDeps): AgentDefinition;

package/dist/agents/sandbox/dna-methylation-agent.js

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+/**
+ * DNA Methylation Agent — methylation array and bisulfite sequencing specialist.
+ */
+import { dnaMethylationAgentPrompt } from "../../prompts/sandbox/dna-methylation-agent.js";
+import { BASE_SANDBOX_TOOLS, createSandboxAgent } from "./shared.js";
+export const meta = {
+    id: "dna-methylation-agent",
+    capabilities: ["methylation array analysis", "bisulfite-seq analysis", "DMP detection", "DMR detection", "methylation clocks", "cell type deconvolution"],
+    suitableFor: ["methylation-array", "wgbs", "rrbs", "epic", "450k"],
+    skills: ["dna-methylation", "shared/omics-general"],
+    tools: [
+        ...BASE_SANDBOX_TOOLS,
+        "searchPubMed",
+        "getArticleDetails",
+        "getArticleFullText",
+        "searchGene",
+        "searchPathway",
+        "lookupGoTerm",
+        "searchInteractions",
+    ],
+};
+export function createDnaMethylationAgent(deps) {
+    return createSandboxAgent(deps, meta, dnaMethylationAgentPrompt);
+}

package/dist/agents/sandbox/drug-repurposing-agent.d.ts

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+/**
+ * Drug Repurposing Agent — multi-evidence drug-indication mapping specialist.
+ */
+import type { AgentDefinition } from "../../loop/types.js";
+import { type SandboxAgentDeps } from "./shared.js";
+import type { AgentMeta } from "./types.js";
+export declare const meta: AgentMeta;
+export declare function createDrugRepurposingAgent(deps: SandboxAgentDeps): AgentDefinition;

package/dist/agents/sandbox/drug-repurposing-agent.js

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+/**
+ * Drug Repurposing Agent — multi-evidence drug-indication mapping specialist.
+ */
+import { drugRepurposingAgentPrompt } from "../../prompts/sandbox/drug-repurposing-agent.js";
+import { BASE_SANDBOX_TOOLS, createSandboxAgent } from "./shared.js";
+export const meta = {
+    id: "drug-repurposing-agent",
+    capabilities: [
+        "signature-based drug repurposing",
+        "target-based drug repurposing",
+        "genetics-based drug repurposing",
+        "network proximity analysis",
+        "multi-evidence candidate ranking",
+        "clinical evidence mining",
+        "drug-indication mapping",
+        "preclinical target intelligence (KO + expression)",
+    ],
+    suitableFor: ["drug-repurposing", "drug-repositioning", "indication-expansion", "target-drug-mapping", "therapeutic-candidates", "perturbation-signatures"],
+    skills: ["drug-repurposing", "cheminformatics", "shared/omics-general"],
+    tools: [
+        ...BASE_SANDBOX_TOOLS,
+        "checkSafetyPanel",
+        "searchPubMed",
+        "getArticleDetails",
+        "getArticleFullText",
+        "searchGene",
+        "searchPathway",
+        "lookupGoTerm",
+        "searchInteractions",
+        "searchCompounds",
+        "getBioactivity",
+        "searchTargets",
+        "getMechanism",
+        "getDrugInfo",
+        "searchOpenTargets",
+        "getTargetSafety",
+        "searchClinicalTrials",
+        "searchFaers",
+        "searchGwasCatalog",
+        "searchClinvar",
+        "searchDisgenet",
+        "searchDrugbank",
+        "searchDgidb",
+        "searchBgeeExpression",
+        "getImpcKoProfile",
+        "searchToxcast",
+        "searchCtxHazard",
+        "searchCtxChemical",
+        "searchCtxExposure",
+    ],
+};
+export function createDrugRepurposingAgent(deps) {
+    return createSandboxAgent(deps, meta, drugRepurposingAgentPrompt);
+}

package/dist/agents/sandbox/enrichment-agent.d.ts

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+/**
+ * Enrichment Agent — pathway and gene set enrichment specialist.
+ */
+import type { AgentDefinition } from "../../loop/types.js";
+import { type SandboxAgentDeps } from "./shared.js";
+import type { AgentMeta } from "./types.js";
+export declare const meta: AgentMeta;
+export declare function createEnrichmentAgent(deps: SandboxAgentDeps): AgentDefinition;

package/dist/agents/sandbox/enrichment-agent.js

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+/**
+ * Enrichment Agent — pathway and gene set enrichment specialist.
+ */
+import { enrichmentAgentPrompt } from "../../prompts/sandbox/enrichment-agent.js";
+import { BASE_SANDBOX_TOOLS, createSandboxAgent } from "./shared.js";
+export const meta = {
+    id: "enrichment-agent",
+    capabilities: ["pathway enrichment", "gene set enrichment", "GO analysis", "functional annotation"],
+    suitableFor: ["gene-lists", "ranked-lists", "score-matrices", "general-omics"],
+    skills: ["enrichment", "shared/omics-general"],
+    tools: [
+        ...BASE_SANDBOX_TOOLS,
+        "searchPubMed",
+        "getArticleDetails",
+        "getArticleFullText",
+        "searchGene",
+        "searchPathway",
+        "lookupGoTerm",
+        "searchInteractions",
+    ],
+};
+export function createEnrichmentAgent(deps) {
+    return createSandboxAgent(deps, meta, enrichmentAgentPrompt);
+}

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

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+/**
+ * Ephemeral Executor — read-only sandbox agent for quick computations.
+ * Cannot create files; step conventions don't apply.
+ */
+import type { AgentDefinition } from "../../loop/types.js";
+import { type SandboxAgentDeps } from "./shared.js";
+import type { AgentMeta } from "./types.js";
+export declare const meta: AgentMeta;
+export declare function createEphemeralExecutorAgent(deps: SandboxAgentDeps): AgentDefinition;

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

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+/**
+ * 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,
+        "searchPubMed",
+        "getArticleDetails",
+        "getArticleFullText",
+        "searchGene",
+        "searchPathway",
+        "lookupGoTerm",
+        "searchInteractions",
+    ],
+    plannable: false,
+};
+export function createEphemeralExecutorAgent(deps) {
+    return createSandboxAgent(deps, meta, ephemeralExecutorPrompt, {
+        appendAnalysisStepStandards: false,
+        readOnly: true,
+    });
+}

package/dist/agents/sandbox/genomic-variant-agent.d.ts

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+/**
+ * Genomic Variant Agent — variant calling, annotation, and GWAS specialist.
+ */
+import type { AgentDefinition } from "../../loop/types.js";
+import { type SandboxAgentDeps } from "./shared.js";
+import type { AgentMeta } from "./types.js";
+export declare const meta: AgentMeta;
+export declare function createGenomicVariantAgent(deps: SandboxAgentDeps): AgentDefinition;

package/dist/agents/sandbox/genomic-variant-agent.js

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+/**
+ * Genomic Variant Agent — variant calling, annotation, and GWAS specialist.
+ */
+import { genomicVariantAgentPrompt } from "../../prompts/sandbox/genomic-variant-agent.js";
+import { BASE_SANDBOX_TOOLS, createSandboxAgent } from "./shared.js";
+export const meta = {
+    id: "genomic-variant-agent",
+    capabilities: ["variant calling", "variant annotation", "GWAS", "CNV detection", "structural variant detection", "variant filtering"],
+    suitableFor: ["wgs", "wes", "gwas", "cnv-sv", "targeted-panels"],
+    skills: ["genomic-variants", "shared/omics-general"],
+    tools: [
+        ...BASE_SANDBOX_TOOLS,
+        "searchPubMed",
+        "getArticleDetails",
+        "getArticleFullText",
+        "searchGene",
+        "searchPathway",
+        "lookupGoTerm",
+        "searchInteractions",
+        "searchClinvar",
+        "searchDgidb",
+        "searchGwasCatalog",
+    ],
+};
+export function createGenomicVariantAgent(deps) {
+    return createSandboxAgent(deps, meta, genomicVariantAgentPrompt);
+}

package/dist/agents/sandbox/immune-profiling-agent.d.ts

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+/**
+ * Immune Profiling Agent — immune deconvolution and IO biomarker specialist.
+ */
+import type { AgentDefinition } from "../../loop/types.js";
+import { type SandboxAgentDeps } from "./shared.js";
+import type { AgentMeta } from "./types.js";
+export declare const meta: AgentMeta;
+export declare function createImmuneProfilingAgent(deps: SandboxAgentDeps): AgentDefinition;

package/dist/agents/sandbox/immune-profiling-agent.js

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+/**
+ * Immune Profiling Agent — immune deconvolution and IO biomarker specialist.
+ */
+import { immuneProfilingAgentPrompt } from "../../prompts/sandbox/immune-profiling-agent.js";
+import { BASE_SANDBOX_TOOLS, createSandboxAgent } from "./shared.js";
+export const meta = {
+    id: "immune-profiling-agent",
+    capabilities: [
+        "immune cell deconvolution",
+        "immune signature scoring",
+        "checkpoint expression analysis",
+        "tumor microenvironment classification",
+        "TCR/BCR repertoire analysis",
+        "immune-clinical outcome correlation",
+        "IO response prediction",
+    ],
+    suitableFor: [
+        "bulk-immune-profiling",
+        "tumor-microenvironment",
+        "io-biomarkers",
+        "immune-deconvolution",
+        "checkpoint-expression",
+        "tcr-bcr-data",
+        "immune-cell-composition",
+    ],
+    skills: ["immune-profiling", "shared/omics-general"],
+    tools: [
+        ...BASE_SANDBOX_TOOLS,
+        "searchPubMed",
+        "getArticleDetails",
+        "getArticleFullText",
+        "searchGene",
+        "searchPathway",
+        "lookupGoTerm",
+        "searchInteractions",
+        "searchGeoDatasets",
+        "searchOpenTargets",
+        "getTargetSafety",
+    ],
+};
+export function createImmuneProfilingAgent(deps) {
+    return createSandboxAgent(deps, meta, immuneProfilingAgentPrompt);
+}

package/dist/agents/sandbox/index.d.ts

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+/**
+ * Sandbox agent catalog + composition root.
+ *
+ * `createSandboxAgents(deps)` returns one `AgentDefinition` per sandbox
+ * agent — the harness loop's substrate. `SANDBOX_AGENT_META` exposes the
+ * meta record the planner-facing catalog (`harness/agents/sandbox-catalog.ts`)
+ * derives from.
+ *
+ * Adding a new sandbox agent: add the per-agent file under
+ * `harness/agents/sandbox/`, import its `meta` + `create*` factory below,
+ * and add one entry to each of the two arrays. Both wire-ups type-check
+ * against `SandboxToolName`, so any inconsistency surfaces at compile time.
+ */
+import type { AgentDefinition } from "../../loop/types.js";
+import { type SandboxAgentDeps } from "./shared.js";
+import type { AgentMeta } from "./types.js";
+export { BASE_SANDBOX_TOOLS, createSandboxAgent } from "./shared.js";
+export type { SandboxAgentDeps, SandboxStepCoords } from "./shared.js";
+export type { AgentMeta, SandboxToolName } from "./types.js";
+export { SANDBOX_AGENT_DEFAULT_MAX_ITERATIONS } from "./types.js";
+/**
+ * Per-agent meta — id, planner-facing description, tool allowlist. The
+ * source of truth that `harness/agents/sandbox-catalog.ts`'s planner
+ * catalog derives from.
+ */
+export declare const SANDBOX_AGENT_META: Readonly<Record<string, AgentMeta>>;
+/**
+ * Build every sandbox `AgentDefinition` from the shared deps. The returned
+ * record's keys are the agent ids; `runAgent` consumes each value.
+ */
+export declare function createSandboxAgents(deps: SandboxAgentDeps): Record<string, AgentDefinition>;