@inflexa-ai/harness 0.1.1 → 0.3.0

package/dist/workflows/target-assessment/steps/phase1-aggregate.js

@@ -1,25 +0,0 @@
-/**
- * Phase 1 aggregator — schema definitions retained for downstream
- * type-checking. The DBOS workflow assembles the Phase-1 bundle inline.
- */
-import { z } from "zod";
-import { Phase1BundleSchema } from "../schemas.js";
-import { withCoverage } from "../coverage.js";
-import { OpenTargetsBundleSchema, ChemblModulatorsBundleSchema, CtgovBundleSchema, FaersByTargetBundleSchema, ExpressionHumanBundleSchema, ExpressionMultiSpeciesBundleSchema, ClinvarBundleSchema, CbioportalBundleSchema, ImpcBundleSchema, PubmedIndexBundleSchema, PathwaysBundleSchema, StringPpiBundleSchema, FamilyComplexesBundleSchema, TherapeuticProgramsBundleSchema, } from "../schemas.js";
-export const Phase1AggregateInputSchema = z.object({
-    "collector-opentargets": withCoverage(OpenTargetsBundleSchema),
-    "collector-chembl-modulators": withCoverage(ChemblModulatorsBundleSchema),
-    "collector-ctgov": withCoverage(CtgovBundleSchema),
-    "collector-faers-by-target": withCoverage(FaersByTargetBundleSchema),
-    "collector-expression-human": withCoverage(ExpressionHumanBundleSchema),
-    "collector-expression-multi-species": withCoverage(ExpressionMultiSpeciesBundleSchema),
-    "collector-clinvar": withCoverage(ClinvarBundleSchema),
-    "collector-cbioportal": withCoverage(CbioportalBundleSchema),
-    "collector-impc": withCoverage(ImpcBundleSchema),
-    "collector-pubmed-index": withCoverage(PubmedIndexBundleSchema),
-    "collector-pathways": withCoverage(PathwaysBundleSchema),
-    "collector-string-ppi": withCoverage(StringPpiBundleSchema),
-    "collector-family-complexes": withCoverage(FamilyComplexesBundleSchema),
-    "collector-therapeutic-programs": withCoverage(TherapeuticProgramsBundleSchema),
-});
-export const phase1OutputSchema = Phase1BundleSchema;

package/dist/workspace/mount-strategy.d.ts

@@ -1,50 +0,0 @@
-/**
- * Mount strategy — single source of truth for workspace/pod mount paths.
- *
- * Single-mount model: one workspace mount covers the full analysis tree.
- * Write protection is enforced via K8s RO volumeMount (execute_command) and
- * by the harness write guard at the workspace-filesystem layer. Pod mounts
- * are nested (K8s handles this fine — most-specific path wins).
- */
-/**
- * Canonical paths for a step.
- *
- * ANALYSIS is the single workspace mount (covers the full analysis tree).
- * ARTIFACTS is a subpath within that mount (the step's writable area, used as CWD).
- */
-export declare function buildMountPaths(resourceId: string, runId: string, stepId: string): {
-    /** Full analysis tree — single workspace mount. */
-    readonly ANALYSIS: `/${string}`;
-    /** Step's writable area — subpath within ANALYSIS, used as CWD. */
-    readonly ARTIFACTS: `/${string}`;
-};
-export interface PodMount {
-    mountPath: string;
-    subPath: string;
-    readOnly: boolean;
-}
-export interface DockerMount {
-    hostPath: string;
-    containerPath: string;
-    readOnly: boolean;
-}
-/**
- * Build pod volumeMount specs — nested: full analysis (RO) + step area (RW).
- * K8s handles nested mounts — the most-specific path wins.
- */
-export declare function buildPodMounts(opts: {
-    resourceId: string;
-    runId: string;
-    stepId: string;
-}): PodMount[];
-/**
- * Build Docker bind mount specs — same nesting logic as buildPodMounts,
- * but with host paths derived from sessionPath.
- * Docker handles nested mounts — the most-specific path wins.
- */
-export declare function buildDockerMounts(opts: {
-    resourceId: string;
-    runId: string;
-    stepId: string;
-    sessionPath: string;
-}): DockerMount[];

package/dist/workspace/mount-strategy.js

@@ -1,67 +0,0 @@
-/**
- * Mount strategy — single source of truth for workspace/pod mount paths.
- *
- * Single-mount model: one workspace mount covers the full analysis tree.
- * Write protection is enforced via K8s RO volumeMount (execute_command) and
- * by the harness write guard at the workspace-filesystem layer. Pod mounts
- * are nested (K8s handles this fine — most-specific path wins).
- */
-import { runStepDir } from "./paths.js";
-import { join } from "node:path";
-// ── Mount Path Builders ──────────────────────────────────────────────────
-/**
- * Canonical paths for a step.
- *
- * ANALYSIS is the single workspace mount (covers the full analysis tree).
- * ARTIFACTS is a subpath within that mount (the step's writable area, used as CWD).
- */
-export function buildMountPaths(resourceId, runId, stepId) {
-    return {
-        /** Full analysis tree — single workspace mount. */
-        ANALYSIS: `/${resourceId}`,
-        /** Step's writable area — subpath within ANALYSIS, used as CWD. */
-        ARTIFACTS: `/${runStepDir(resourceId, runId, stepId)}`,
-    };
-}
-// ── Pod mounts ──────────────────────────────────────────────────────────
-/**
- * Build pod volumeMount specs — nested: full analysis (RO) + step area (RW).
- * K8s handles nested mounts — the most-specific path wins.
- */
-export function buildPodMounts(opts) {
-    const mp = buildMountPaths(opts.resourceId, opts.runId, opts.stepId);
-    return [
-        {
-            mountPath: mp.ANALYSIS,
-            subPath: opts.resourceId,
-            readOnly: true,
-        },
-        {
-            mountPath: mp.ARTIFACTS,
-            subPath: runStepDir(opts.resourceId, opts.runId, opts.stepId),
-            readOnly: false,
-        },
-    ];
-}
-// ── Docker bind mounts ─────────────────────────────────────────────────
-/**
- * Build Docker bind mount specs — same nesting logic as buildPodMounts,
- * but with host paths derived from sessionPath.
- * Docker handles nested mounts — the most-specific path wins.
- */
-export function buildDockerMounts(opts) {
-    const mp = buildMountPaths(opts.resourceId, opts.runId, opts.stepId);
-    const stepRelPath = runStepDir(opts.resourceId, opts.runId, opts.stepId);
-    return [
-        {
-            hostPath: join(opts.sessionPath, opts.resourceId),
-            containerPath: mp.ANALYSIS,
-            readOnly: true,
-        },
-        {
-            hostPath: join(opts.sessionPath, stepRelPath),
-            containerPath: mp.ARTIFACTS,
-            readOnly: false,
-        },
-    ];
-}

package/dist/workspace/provenance-collector.d.ts

@@ -1,34 +0,0 @@
-/**
- * Provenance collector seam — the mutate surface records a SHA-256 content
- * snapshot at each write. Construction-time dependency (see the harness-durable-runtime spec): the
- * composition root builds a `ProvenanceCollector` and passes it to the
- * mutate tool factories.
- *
- * Captured here are *harness-side* writes (`write_file`, `edit_file`). The
- * harness does NOT hash in-sandbox writes produced by `execute_command`'s
- * arbitrary commands — sandbox-server emits its own provenance frames per
- * `sandbox-provenance-tracking` and artifact registration reconciles them.
- *
- * `recordSnapshot` is best-effort metadata: collector failures SHALL NOT
- * fail the write. The mutate tools catch and log internally; this contract
- * does not require the collector to be non-throwing.
- */
-export interface ProvenanceSnapshot {
-    readonly analysisId: string;
-    readonly runId: string;
-    readonly stepId: string;
-    /**
-     * The resolved workspace path of the written file — the sandbox-visible
-     * path (e.g. `/{analysisId}/runs/{runId}/{stepId}/output/x.csv`), which is
-     * the same path the read surface uses.
-     */
-    readonly path: string;
-    /** Lowercase hex SHA-256 of the *written* content (post-edit for edit_file). */
-    readonly sha256: string;
-    readonly bytes: number;
-    /** Unix milliseconds at the time of recording. */
-    readonly timestamp: number;
-}
-export interface ProvenanceCollector {
-    recordSnapshot(snapshot: ProvenanceSnapshot): Promise<void>;
-}

package/dist/workspace/provenance-collector.js

@@ -1,16 +0,0 @@
-/**
- * Provenance collector seam — the mutate surface records a SHA-256 content
- * snapshot at each write. Construction-time dependency (see the harness-durable-runtime spec): the
- * composition root builds a `ProvenanceCollector` and passes it to the
- * mutate tool factories.
- *
- * Captured here are *harness-side* writes (`write_file`, `edit_file`). The
- * harness does NOT hash in-sandbox writes produced by `execute_command`'s
- * arbitrary commands — sandbox-server emits its own provenance frames per
- * `sandbox-provenance-tracking` and artifact registration reconciles them.
- *
- * `recordSnapshot` is best-effort metadata: collector failures SHALL NOT
- * fail the write. The mutate tools catch and log internally; this contract
- * does not require the collector to be non-throwing.
- */
-export {};

package/dist/workspace/workspace-paths.d.ts

@@ -1,26 +0,0 @@
-/**
- * Workspace paths — single source of truth for all agent-visible paths.
- *
- * Composes mount points (buildMountPaths()) with step subdirectory types
- * (STEP_SUBDIRS) into the full paths that agents use in workspace tools.
- *
- * Import from here — not from mount-strategy or paths directly — when
- * you need paths that agents will see.
- */
-import { buildMountPaths } from "./mount-strategy.js";
-import { STEP_SUBDIRS, type StepSubdirType } from "./paths.js";
-export { buildMountPaths };
-export { STEP_SUBDIRS, type StepSubdirType };
-/**
- * Build artifact subdirectory paths for a step using canonical mount paths.
- * Agents see these paths in workspace tools and prompts.
- */
-export declare function buildArtifactDirs(resourceId: string, runId: string, stepId: string): {
-    readonly OUTPUT: `/${string}/output`;
-    readonly SCRIPTS: `/${string}/scripts`;
-    readonly FIGURES: `/${string}/figures`;
-    readonly LOGS: `/${string}/logs`;
-    readonly NOTEBOOKS: `/${string}/notebooks`;
-};
-/** Resolved sessions base path. */
-export declare function sessionsBasePath(sessionsBasePath: string): string;

package/dist/workspace/workspace-paths.js

@@ -1,31 +0,0 @@
-/**
- * Workspace paths — single source of truth for all agent-visible paths.
- *
- * Composes mount points (buildMountPaths()) with step subdirectory types
- * (STEP_SUBDIRS) into the full paths that agents use in workspace tools.
- *
- * Import from here — not from mount-strategy or paths directly — when
- * you need paths that agents will see.
- */
-import { buildMountPaths } from "./mount-strategy.js";
-import { STEP_SUBDIRS } from "./paths.js";
-export { buildMountPaths };
-export { STEP_SUBDIRS };
-/**
- * Build artifact subdirectory paths for a step using canonical mount paths.
- * Agents see these paths in workspace tools and prompts.
- */
-export function buildArtifactDirs(resourceId, runId, stepId) {
-    const mp = buildMountPaths(resourceId, runId, stepId);
-    return {
-        OUTPUT: `${mp.ARTIFACTS}/output`,
-        SCRIPTS: `${mp.ARTIFACTS}/scripts`,
-        FIGURES: `${mp.ARTIFACTS}/figures`,
-        LOGS: `${mp.ARTIFACTS}/logs`,
-        NOTEBOOKS: `${mp.ARTIFACTS}/notebooks`,
-    };
-}
-/** Resolved sessions base path. */
-export function sessionsBasePath(sessionsBasePath) {
-    return sessionsBasePath;
-}