@tiagojct/subsub 0.9.0 → 0.9.1

package/README.md

@@ -18,7 +18,7 @@ A Zotero librarian and research assistant that runs on your computer, in your br
 * **Code-Enforced Safety Gate**: The model **cannot** modify your library without your explicit approval. Every change is calculated first as a dry-run preview (+added in green, -removed in red) and executed only when you confirm.
 * **Full Journal & Reversible Edits**: Every library modification is recorded with a unique journal ID and can be reverted anytime using `/undo`.
 * **Two Dedicated Roles**:
-  * 📚 **The Librarian**: Cleans tags, imports references (DOI, PMID, ISBN), deduplicates, fixes metadata, retrieves open-access PDFs, creates collections, and checks retractions. *Runs completely offline with no web search access.*
+  * 📚 **The Librarian**: Cleans tags, imports references (DOI, PMID, ISBN), deduplicates, fixes metadata, retrieves open-access PDFs, creates collections, and checks retractions. *Has no web search tools; imports and PDFs come from Crossref, Unpaywall and Open Library.*
   * 🔬 **The Researcher**: Reads items, searches PubMed and OpenAlex, finds gaps, checks citations in manuscripts, and writes structured Markdown notes in your Sub-Sub folder (it can sit inside an Obsidian vault). *Cannot modify library records.*
 * **Local & Private**: Listens strictly on `127.0.0.1` protected by an authenticated single-origin session cookie. Your library contents remain on your computer.
 * **Modern Web Interface & Terminal UI**: Use Sub-Sub in your browser with desktop shortcuts (`~/Applications/Sub-Sub.app`, Start menu, or `.desktop`), or launch it right in your terminal with adaptive color themes.

package/dist/args.js

@@ -65,3 +65,26 @@ export function coerceArgs(original, input) {
     }
     return input;
 }
+/**
+ * Arguments that name a file in the user's working folder (a manuscript, a report
+ * folder, a bibliography to write). The servers run in their own working folder, so
+ * Sub-Sub makes these paths absolute against its own, as pi's file tools read them.
+ * Note paths (tag reviews, the import queue, linked notes) are not here: the servers
+ * read those from the Sub-Sub folder.
+ */
+export const CWD_PATH_ARGS = {
+    scholar_check_manuscript: ["path"],
+    scholar_export_bibliography: ["output_path"],
+    verify_check_manuscript: ["path", "report_dir"],
+    verify_prepare_claims: ["path", "report_dir"],
+    verify_record_claims: ["path", "report_dir"],
+};
+/** Make the working-folder paths of a tool call absolute. Changes input in place. */
+export function resolvePathArgs(tool, input, toAbsolute) {
+    for (const k of CWD_PATH_ARGS[tool] ?? []) {
+        const v = input[k];
+        if (typeof v === "string" && v.trim())
+            input[k] = toAbsolute(v);
+    }
+    return input;
+}

package/dist/config.js

@@ -24,7 +24,7 @@ import { dirname, join, resolve } from "node:path";
 import { isObsidianVault, settingsFile } from "./layout.js";
 export const PROFILES = ["reader", "scholar", "author", "editor"];
 /** The Zotero server release that this Sub-Sub version runs when there is no local server folder. */
-export const SERVER_VERSION = "0.5.0";
+export const SERVER_VERSION = "0.5.1";
 /** The Starbuck release (PyPI) that this Sub-Sub version runs when there is no local Starbuck folder. */
 export const STARBUCK_VERSION = "0.2.0";
 export const STARBUCK_SOURCE = `starbuck==${STARBUCK_VERSION}`;

package/dist/layout.js

@@ -24,6 +24,15 @@ export const SETTINGS_FILES = { tags: "Zotero tags.md", rules: "Zotero agent.md"
 export function isObsidianVault(dir) {
     return existsSync(join(dir, ".obsidian"));
 }
+/** The Obsidian vault that holds a folder: the folder itself or the nearest parent with .obsidian/. */
+export function obsidianRoot(dir) {
+    for (let d = dir;; d = dirname(d)) {
+        if (isObsidianVault(d))
+            return d;
+        if (dirname(d) === d)
+            return undefined;
+    }
+}
 /** The folder that a user's answer means: a vault root becomes <vault>/Sub-Sub. */
 export function subsubFolder(answer) {
     return isObsidianVault(answer) && basename(answer) !== FOLDER_NAME ? join(answer, FOLDER_NAME) : answer;

package/dist/subsub.js

@@ -20,7 +20,7 @@ import { fileURLToPath } from "node:url";
 import { Bridge } from "./bridge.js";
 import { expand, findUv, isProfile, loadConfig, parseEnvFile, saveConfig, serverCommand, starbuckCommand, starbuckEnabled, who, } from "./config.js";
 import { profileList, profileSpec, promptBlocked } from "./profiles.js";
-import { coerceArgs, loosenArrays } from "./args.js";
+import { coerceArgs, loosenArrays, resolvePathArgs } from "./args.js";
 import { applyEdits, checkLiteratureNote } from "./notes.js";
 import { buildPolicy, judgePath, normalizeToolPath, realish, within } from "./paths.js";
 import { describeArgs, formatPreview } from "./preview.js";
@@ -291,6 +291,7 @@ export async function createSubsub(pi, deps = {}) {
         const schema = schemas.get(name);
         if (schema)
             coerceArgs(schema, input);
+        resolvePathArgs(name, input, (p) => normalizeToolPath(p, ctx.cwd));
         if (SERVER_PREFIXES.some((p) => name.startsWith(p))) {
             const why = unavailableReason(name, mode, registered(), profile);
             if (why) {

package/dist/web.js

@@ -23,6 +23,7 @@ import { StringDecoder } from "node:string_decoder";
 import { agentDirFor, chooseCwd, PACKAGE_DIR, packageVersion } from "./cli.js";
 import { expand, loadConfig, saveConfig, withStarbuck } from "./config.js";
 import { TESTED_MODELS } from "./init.js";
+import { obsidianRoot } from "./layout.js";
 import { realish, within } from "./paths.js";
 export function parseWebArgs(args) {
     const o = { port: 0, open: true, librarian: false, here: false, idleMinutes: 10, piArgs: [] };
@@ -599,7 +600,7 @@ export async function startWeb(opts, env = process.env, log = () => { }) {
                     // Documents only: a file that the model wrote must never be run.
                     if (!OPENABLE.has(extname(target).toLowerCase()))
                         return send(res, 403, { error: "Sub-Sub opens only notes and documents (.md, .txt, .pdf, .bib, .csv, .qmd)." });
-                    if (vault && within(target, vault) && existsSync(join(vault, ".obsidian")))
+                    if (vault && within(target, vault) && obsidianRoot(vault))
                         openExternal(`obsidian://open?path=${encodeURIComponent(target)}`);
                     else
                         openExternal(target);

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@tiagojct/subsub",
-  "version": "0.9.0",
+  "version": "0.9.1",
   "description": "Sub-Sub: a Zotero librarian and research assistant in the browser or the terminal, built on pi",
   "type": "module",
   "license": "MIT",

package/src/args.ts

@@ -62,3 +62,27 @@ export function coerceArgs(original: Schema, input: Record<string, unknown>): Re
 	}
 	return input;
 }
+
+/**
+ * Arguments that name a file in the user's working folder (a manuscript, a report
+ * folder, a bibliography to write). The servers run in their own working folder, so
+ * Sub-Sub makes these paths absolute against its own, as pi's file tools read them.
+ * Note paths (tag reviews, the import queue, linked notes) are not here: the servers
+ * read those from the Sub-Sub folder.
+ */
+export const CWD_PATH_ARGS: Record<string, string[]> = {
+	scholar_check_manuscript: ["path"],
+	scholar_export_bibliography: ["output_path"],
+	verify_check_manuscript: ["path", "report_dir"],
+	verify_prepare_claims: ["path", "report_dir"],
+	verify_record_claims: ["path", "report_dir"],
+};
+
+/** Make the working-folder paths of a tool call absolute. Changes input in place. */
+export function resolvePathArgs(tool: string, input: Record<string, unknown>, toAbsolute: (p: string) => string): Record<string, unknown> {
+	for (const k of CWD_PATH_ARGS[tool] ?? []) {
+		const v = input[k];
+		if (typeof v === "string" && v.trim()) input[k] = toAbsolute(v);
+	}
+	return input;
+}

package/src/config.ts

@@ -29,7 +29,7 @@ export type Profile = "reader" | "scholar" | "author" | "editor";
 export const PROFILES: Profile[] = ["reader", "scholar", "author", "editor"];
 
 /** The Zotero server release that this Sub-Sub version runs when there is no local server folder. */
-export const SERVER_VERSION = "0.5.0";
+export const SERVER_VERSION = "0.5.1";
 
 /** The Starbuck release (PyPI) that this Sub-Sub version runs when there is no local Starbuck folder. */
 export const STARBUCK_VERSION = "0.2.0";

package/src/layout.ts

@@ -30,6 +30,14 @@ export function isObsidianVault(dir: string): boolean {
 	return existsSync(join(dir, ".obsidian"));
 }
 
+/** The Obsidian vault that holds a folder: the folder itself or the nearest parent with .obsidian/. */
+export function obsidianRoot(dir: string): string | undefined {
+	for (let d = dir; ; d = dirname(d)) {
+		if (isObsidianVault(d)) return d;
+		if (dirname(d) === d) return undefined;
+	}
+}
+
 /** The folder that a user's answer means: a vault root becomes <vault>/Sub-Sub. */
 export function subsubFolder(answer: string): string {
 	return isObsidianVault(answer) && basename(answer) !== FOLDER_NAME ? join(answer, FOLDER_NAME) : answer;

package/src/subsub.ts

@@ -36,7 +36,7 @@ import {
 	who,
 } from "./config.ts";
 import { profileList, profileSpec, promptBlocked } from "./profiles.ts";
-import { coerceArgs, loosenArrays } from "./args.ts";
+import { coerceArgs, loosenArrays, resolvePathArgs } from "./args.ts";
 import { applyEdits, checkLiteratureNote } from "./notes.ts";
 import { buildPolicy, judgePath, normalizeToolPath, realish, within } from "./paths.ts";
 import { describeArgs, formatPreview } from "./preview.ts";
@@ -321,6 +321,7 @@ export async function createSubsub(pi: ExtensionAPI, deps: SubsubDeps = {}): Pro
 		// Previews and the real call must see the same, repaired arguments.
 		const schema = schemas.get(name);
 		if (schema) coerceArgs(schema, input);
+		resolvePathArgs(name, input, (p) => normalizeToolPath(p, ctx.cwd));
 		if (SERVER_PREFIXES.some((p) => name.startsWith(p))) {
 			const why = unavailableReason(name, mode, registered(), profile);
 			if (why) {

package/src/web.ts

@@ -24,6 +24,7 @@ import { StringDecoder } from "node:string_decoder";
 import { agentDirFor, chooseCwd, PACKAGE_DIR, packageVersion } from "./cli.ts";
 import { expand, loadConfig, saveConfig, type SubsubConfig, withStarbuck } from "./config.ts";
 import { TESTED_MODELS } from "./init.ts";
+import { obsidianRoot } from "./layout.ts";
 import { realish, within } from "./paths.ts";
 
 // ---------------------------------------------------------------- options
@@ -610,7 +611,7 @@ export async function startWeb(opts: WebOptions, env: NodeJS.ProcessEnv = proces
 					if (!inside || !existsSync(target)) return send(res, 404, { error: "not found in the Sub-Sub folder" });
 					// Documents only: a file that the model wrote must never be run.
 					if (!OPENABLE.has(extname(target).toLowerCase())) return send(res, 403, { error: "Sub-Sub opens only notes and documents (.md, .txt, .pdf, .bib, .csv, .qmd)." });
-					if (vault && within(target, vault) && existsSync(join(vault, ".obsidian"))) openExternal(`obsidian://open?path=${encodeURIComponent(target)}`);
+					if (vault && within(target, vault) && obsidianRoot(vault)) openExternal(`obsidian://open?path=${encodeURIComponent(target)}`);
 					else openExternal(target);
 					return send(res, 200, { ok: true });
 				}