@inflexa-ai/harness 0.8.0 → 0.9.0

package/dist/tools/report/submit-report.js

@@ -3,6 +3,7 @@
  * `data-report-preview` until this tool writes the success outcome.
  *
  * Checks:
+ *   - report.html.j2 exists at versionDir/ — the report itself
  *   - index.html exists at versionDir/ with size > 0
  *   - no unrendered `{{ … }}` or `{% … %}` left in the output
  *   - all referenced asset paths resolve to files on disk
@@ -23,26 +24,46 @@ const UNRENDERED_JINJA = /\{\{[^{}]*\}\}|\{%-?\s*\w/;
 export function createSubmitReportTool(state) {
     return defineTool({
         id: "submit_report",
-        description: "Declare the report ready. Validates index.html exists, has no " +
-            "unrendered Jinja, and that all referenced asset paths resolve. " +
+        description: "Declare the report ready. Validates report.html.j2 and index.html " +
+            "exist, that the output has no unrendered Jinja, and that all " +
+            "referenced asset paths resolve. " +
             "You MUST call this to finish — the runner ignores any other claim " +
             "of success. Returns problems[] when checks fail; fix and re-submit. " +
-            "Use `notes` to surface caveats to the caller (e.g. files skipped due " +
-            "to the 50MB asset size limit, sections rendered with partial data, " +
-            "missing inputs that forced a fallback) — these reach the conversation " +
-            "agent and the user in the iteration result.",
+            "Use `notes` to surface caveats to the caller (e.g. sections rendered " +
+            "with partial data, missing inputs that forced a fallback) — these " +
+            "reach the conversation agent and the user in the iteration result.",
         inputSchema: z.object({
             notes: z
                 .array(z.string())
                 .optional()
                 .describe("Caveats / issues to surface to the caller. One short sentence " +
-                "per item. Examples: 'skipped raw_counts.h5ad (1.2GB > 50MB cap)', " +
-                "'pathway-enrichment section omitted — no GSEA output found'. " +
+                "per item. Examples: 'pathway-enrichment section omitted — no " +
+                "GSEA output found', 'cohort table rendered from 8 of 12 " +
+                "samples — the rest had no QC row'. " +
                 "Leave empty when the report shipped cleanly."),
         }),
         execute: async (input) => {
             const problems = [];
-            // 1. index.html exists and is non-empty
+            // 1. report.html.j2 exists — the report itself, as opposed to the
+            // artifact rendered from it. Nothing downstream re-derives this: a
+            // version that is finalized without a template persists as one, and
+            // the next iteration copies a template that isn't there, then tells
+            // the builder to edit it in place. Checked first because an absent
+            // template is the cause the checks below can only report symptoms of.
+            const templatePath = join(state.versionDir, "report.html.j2");
+            let hasTemplate;
+            try {
+                hasTemplate = (await stat(templatePath)).isFile();
+            }
+            catch {
+                hasTemplate = false;
+            }
+            if (!hasTemplate) {
+                problems.push("report.html.j2 is missing — a report is authored as report.html.j2 and " +
+                    "rendered into index.html by build_report; a hand-written index.html is " +
+                    "not a report. Write the template, then call build_report.");
+            }
+            // 2. index.html exists and is non-empty
             const indexPath = join(state.versionDir, "index.html");
             let html;
             try {
@@ -57,13 +78,13 @@ export function createSubmitReportTool(state) {
                 problems.push("index.html does not exist — call build_report first");
                 return ok({ ok: false, problems });
             }
-            // 2. No unrendered Jinja markers
+            // 3. No unrendered Jinja markers
             if (UNRENDERED_JINJA.test(html)) {
                 const match = html.match(UNRENDERED_JINJA);
                 problems.push(`unrendered Jinja in output (e.g. ${JSON.stringify(match?.[0] ?? "")}); ` +
                     "build_report likely failed silently or report.html.j2 was edited after build");
             }
-            // 3. Asset reference resolution
+            // 4. Asset reference resolution
             const refs = extractLocalRefs(html);
             for (const ref of refs) {
                 const resolved = resolveLocalRef(ref, state.versionDir, state.assetsDir);

package/dist/tools/report/version-fs.d.ts

@@ -2,10 +2,10 @@
  * In-process workspace surface for the report-builder agent.
  *
  * Tight read/write/mkdir surface scoped to the version directory.
- * Agent-supplied paths are resolved against `versionDir`; any path that
- * escapes is rejected as `out_of_scope`. Constructed inside the
- * iterate-report runner so it always shares the same `versionDir` as the
- * rest of the report tools.
+ * Agent-supplied paths are relative to `versionDir`; an absolute path, or one
+ * that escapes the directory, is rejected as `out_of_scope`. Constructed
+ * inside the iterate-report runner so it always shares the same `versionDir`
+ * as the rest of the report tools.
  */
 import { type Tool } from "../define-tool.js";
 export interface VersionFsToolsState {

package/dist/tools/report/version-fs.js

@@ -2,10 +2,10 @@
  * In-process workspace surface for the report-builder agent.
  *
  * Tight read/write/mkdir surface scoped to the version directory.
- * Agent-supplied paths are resolved against `versionDir`; any path that
- * escapes is rejected as `out_of_scope`. Constructed inside the
- * iterate-report runner so it always shares the same `versionDir` as the
- * rest of the report tools.
+ * Agent-supplied paths are relative to `versionDir`; an absolute path, or one
+ * that escapes the directory, is rejected as `out_of_scope`. Constructed
+ * inside the iterate-report runner so it always shares the same `versionDir`
+ * as the rest of the report tools.
  */
 import { mkdir as fsMkdir, readFile as fsReadFile, stat as fsStat, writeFile as fsWriteFile } from "node:fs/promises";
 import { dirname, resolve as resolvePath, sep } from "node:path";
@@ -19,13 +19,15 @@ function resolveAgentPath(agentPath, versionDir) {
     if (agentPath.length === 0 || agentPath.includes("\0")) {
         return { kind: "out_of_scope", reason: "empty or null-byte path" };
     }
-    // Strip a leading slash so an agent typing "/index.html" is treated as
-    // "index.html" relative to versionDir (the version dir is the root).
-    const stripped = agentPath.replace(/^\/+/, "");
-    if (!stripped) {
-        return { kind: "out_of_scope", reason: "path resolves to the version dir itself" };
+    // A leading slash is refused rather than trimmed. Trimming it makes the
+    // containment check below unreachable for absolute paths: a deep one such
+    // as "/previews/abc/v1/report.html.j2" would land a real file several
+    // directories below versionDir and report success, and the builder — which
+    // has no directory-listing tool — cannot find where its template went.
+    if (agentPath.startsWith("/")) {
+        return { kind: "out_of_scope", reason: `absolute path rejected, use one relative to the version dir: ${agentPath}` };
     }
-    const absolute = resolvePath(versionDir, stripped);
+    const absolute = resolvePath(versionDir, agentPath);
     if (absolute !== versionDir && !absolute.startsWith(versionDir + sep)) {
         return { kind: "out_of_scope", reason: `path escapes version dir: ${agentPath}` };
     }
@@ -34,9 +36,10 @@ function resolveAgentPath(agentPath, versionDir) {
 export function createVersionFsTools(state) {
     const writeFile = defineTool({
         id: "write_file",
-        description: "Write a UTF-8 text file under the report's version directory. Use " +
-            "relative paths (e.g. `report.html.j2`, `assets/foo.csv`). Returns " +
-            "`out_of_scope` for any path that escapes the version dir.",
+        description: "Write a UTF-8 text file under the report's version directory. Paths " +
+            "are relative to it (e.g. `report.html.j2`, `assets/foo.csv`); an " +
+            "absolute path, or one that escapes the version dir, returns " +
+            "`out_of_scope` and writes nothing.",
         inputSchema: z.object({
             path: z.string().min(1),
             content: z.string(),
@@ -62,8 +65,9 @@ export function createVersionFsTools(state) {
         id: "edit_file",
         description: "Surgical edit of an existing UTF-8 file inside the report's version " +
             "directory: replace the first occurrence of `oldText` with `newText`. " +
-            "Returns `not_found` if the file doesn't exist, `no_match` if " +
-            "`oldText` isn't present.",
+            "Paths are relative to that directory; an absolute or escaping path " +
+            "returns `out_of_scope`. Returns `not_found` if the file doesn't " +
+            "exist, `no_match` if `oldText` isn't present.",
         inputSchema: z.object({
             path: z.string().min(1),
             oldText: z.string().min(1),
@@ -102,7 +106,9 @@ export function createVersionFsTools(state) {
     });
     const readFile = defineTool({
         id: "read_file",
-        description: "Read a UTF-8 file inside the report's version directory. Returns " + "truncated content (capped at 256 KiB) for large files.",
+        description: "Read a UTF-8 file inside the report's version directory. Paths are " +
+            "relative to it; an absolute or escaping path returns `out_of_scope`. " +
+            "Returns truncated content (capped at 256 KiB) for large files.",
         inputSchema: z.object({
             path: z.string().min(1),
         }),
@@ -137,7 +143,8 @@ export function createVersionFsTools(state) {
     });
     const mkdir = defineTool({
         id: "mkdir",
-        description: "Create a directory (recursive) inside the report's version directory.",
+        description: "Create a directory (recursive) inside the report's version directory. " +
+            "Paths are relative to it; an absolute or escaping path returns `out_of_scope`.",
         inputSchema: z.object({
             path: z.string().min(1),
         }),

package/package.json

@@ -1,6 +1,6 @@
 {
     "name": "@inflexa-ai/harness",
-    "version": "0.8.0",
+    "version": "0.9.0",
     "description": "Host-agnostic bioinformatics agent harness \u2014 hand-rolled agent loop, DBOS-durable workflows, sandboxed compute.",
     "license": "Apache-2.0",
     "type": "module",