proteworks 0.1.0__tar.gz → 0.1.2__tar.gz

{proteworks-0.1.0 → proteworks-0.1.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: proteworks
-Version: 0.1.0
+Version: 0.1.2
 Summary: Sync files with Proteworks using file-browser paths.
 Requires-Python: >=3.11
 Description-Content-Type: text/markdown

{proteworks-0.1.0 → proteworks-0.1.2}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "proteworks"
-version = "0.1.0"
+version = "0.1.2"
 description = "Sync files with Proteworks using file-browser paths."
 readme = "README.md"
 requires-python = ">=3.11"

{proteworks-0.1.0 → proteworks-0.1.2}/src/proteworks/api.py

@@ -105,6 +105,28 @@ class ApiClient:
                 break
         return {"items": items, "total": total or 0, "root_folder_id": root_folder_id}
 
+    def export_page(self, offset: int, limit: int = 500) -> dict:
+        return self.request(
+            "GET",
+            "/api/v1/sync/export",
+            params={"offset": offset, "limit": limit},
+        )
+
+    def export_all(self) -> dict:
+        """Follow export pages. Returns every item for the active organization."""
+        offset = 0
+        items: list[dict] = []
+        total = None
+        while True:
+            page = self.export_page(offset)
+            batch = list(page.get("items") or [])
+            items.extend(batch)
+            total = int(page.get("total") or 0)
+            offset += len(batch)
+            if not batch or offset >= total:
+                break
+        return {"items": items, "total": total or 0}
+
     def content_urls(self, file_ids: list[str]) -> dict[str, dict]:
         """Mint signed download URLs. Retries when the API asks the client to slow down."""
         payload = self._request_with_backoff(

{proteworks-0.1.0 → proteworks-0.1.2}/src/proteworks/auth.py

@@ -4,6 +4,7 @@ from __future__ import annotations
 
 import base64
 import hashlib
+import os
 import secrets
 import webbrowser
 from http.server import BaseHTTPRequestHandler, HTTPServer
@@ -65,6 +66,18 @@ def loopback_redirect_uri(port: int = LOOPBACK_PORT) -> str:
     return f"http://127.0.0.1:{port}{LOOPBACK_REDIRECT_PATH}"
 
 
+def open_browser(url: str) -> bool:
+    """Open the sign-in page. The browser's own startup errors stay hidden."""
+    saved_stderr = os.dup(2)
+    try:
+        with open(os.devnull, "wb") as discarded:
+            os.dup2(discarded.fileno(), 2)
+            return bool(webbrowser.open(url))
+    finally:
+        os.dup2(saved_stderr, 2)
+        os.close(saved_stderr)
+
+
 def login(settings: Settings, token_store: TokenStore, stderr) -> None:
     """Open a browser, receive the loopback redirect, and save the access token."""
     verifier, challenge = pkce_pair()
@@ -77,9 +90,8 @@ def login(settings: Settings, token_store: TokenStore, stderr) -> None:
         ) from exc
     redirect_uri = loopback_redirect_uri()
     url = authorize_url(settings, redirect_uri, state, challenge)
-    print(f"Auth0 must allow this callback URL: {redirect_uri}", file=stderr)
     print("Opening a browser to sign in.", file=stderr)
-    opened = webbrowser.open(url)
+    opened = open_browser(url)
     if not opened:
         print("Open this URL to sign in:", file=stderr)
         print(url, file=stderr)

{proteworks-0.1.0 → proteworks-0.1.2}/src/proteworks/cli.py

@@ -16,7 +16,7 @@ from proteworks.orgs import (
     regular_organizations,
     select_organization,
 )
-from proteworks.pull import pull_path
+from proteworks.pull import export_organization, pull_path
 from proteworks.push import push_directory
 from proteworks.redact import install_redacting_logs
 
@@ -33,6 +33,11 @@ examples:
   proteworks push ./campaigns '~/My Files/campaigns/'
 """
 
+_EXPORT_EXAMPLES = """\
+examples:
+  proteworks export ./backup
+"""
+
 
 def build_parser() -> argparse.ArgumentParser:
     """Build the parser, then describe commands by walking what was registered."""
@@ -70,6 +75,15 @@ def build_parser() -> argparse.ArgumentParser:
     push.add_argument("remote", help="Remote folder path ending with /")
     push.add_argument("--dry-run", action="store_true", help="Print the files that would be uploaded")
 
+    export = sub.add_parser(
+        "export",
+        help="Download the active organization's files (organization admins)",
+        formatter_class=argparse.RawDescriptionHelpFormatter,
+        epilog=_EXPORT_EXAMPLES,
+    )
+    export.add_argument("dest", help="Local directory")
+    export.add_argument("--dry-run", action="store_true", help="Print the files that would be downloaded")
+
     commands = "\n".join(f"  {line}" for line in _registered_commands(parser))
     parser.description = (
         f"Commands:\n{commands}\n\n"
@@ -79,6 +93,7 @@ def build_parser() -> argparse.ArgumentParser:
         "  proteworks pull '~/My Files/msa/*.cif' ./msa\n"
         "  proteworks push ./1UBQ.pdb '~/My Files/test/'\n"
         "  proteworks push ./campaigns '~/My Files/campaigns/'\n"
+        "  proteworks export ./backup\n"
     )
     return parser
 
@@ -133,6 +148,8 @@ def main(argv: list[str] | None = None, *, settings: Settings | None = None, tok
         api.organization_id = org["id"]
         if args.command == "pull":
             return pull_path(api, args.remote, Path(args.dest), dry_run=args.dry_run, stderr=sys.stderr)
+        if args.command == "export":
+            return export_organization(api, Path(args.dest), dry_run=args.dry_run, stderr=sys.stderr)
         if args.command == "push":
             return push_directory(api, Path(args.local_dir), args.remote, dry_run=args.dry_run, stderr=sys.stderr)
         parser.print_help(sys.stderr)

{proteworks-0.1.0 → proteworks-0.1.2}/src/proteworks/index.py

@@ -64,6 +64,8 @@ def sha256_bytes(payload: bytes) -> str:
 def local_relative(remote: str, relative_path: str) -> str:
     """Path under the destination, relative to the requested remote prefix."""
     prefix = remote.rstrip("/")
+    if not prefix:
+        return relative_path[2:] if relative_path.startswith("~/") else relative_path
     if relative_path == prefix:
         return Path(relative_path).name
     marker = prefix + "/"

{proteworks-0.1.0 → proteworks-0.1.2}/src/proteworks/pull.py

@@ -29,6 +29,38 @@ def pull_path(api: ApiClient, remote: str, dest: Path, *, dry_run: bool, stderr)
         return 1
     items = list(page.get("items") or [])
     single_file = len(items) == 1 and not remote.endswith("/") and "*" not in remote and "?" not in remote
+    return download_items(api, items, dest, remote=remote, dry_run=dry_run, stderr=stderr, single_file=single_file)
+
+
+def export_organization(api: ApiClient, dest: Path, *, dry_run: bool, stderr) -> int:
+    """Download every live file in the active organization. Returns a process status code."""
+    try:
+        page = api.export_all()
+    except ApiError as exc:
+        print(str(exc), file=stderr)
+        return 1
+    return download_items(
+        api,
+        list(page.get("items") or []),
+        dest,
+        remote="",
+        dry_run=dry_run,
+        stderr=stderr,
+        single_file=False,
+    )
+
+
+def download_items(
+    api: ApiClient,
+    items: list[dict],
+    dest: Path,
+    *,
+    remote: str,
+    dry_run: bool,
+    stderr,
+    single_file: bool,
+) -> int:
+    """Write manifest items under dest. ``remote`` is stripped from each local path."""
     print(f"{len(items)} file(s)", file=stderr)
     if dry_run:
         for item in items:

{proteworks-0.1.0 → proteworks-0.1.2}/src/proteworks.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: proteworks
-Version: 0.1.0
+Version: 0.1.2
 Summary: Sync files with Proteworks using file-browser paths.
 Requires-Python: >=3.11
 Description-Content-Type: text/markdown

{proteworks-0.1.0 → proteworks-0.1.2}/tests/test_cli.py

@@ -5,12 +5,15 @@ from __future__ import annotations
 import hashlib
 import json
 import mimetypes
+import os
+import subprocess
+import sys
 import threading
 from http.server import BaseHTTPRequestHandler, ThreadingHTTPServer
 from pathlib import Path
 from urllib.parse import parse_qs, urlparse
 
-from proteworks.auth import loopback_redirect_uri
+from proteworks.auth import loopback_redirect_uri, open_browser
 from proteworks.cli import main
 from proteworks.config import Settings
 from proteworks.push import _iter_local_files
@@ -34,11 +37,13 @@ class MemoryTokens:
 
 
 class FakeApi(threading.Thread):
-    def __init__(self, orgs, items, root_folder_id="folder-1"):
+    def __init__(self, orgs, items, root_folder_id="folder-1", export_items=None, export_error=None):
         super().__init__(daemon=True)
         self.orgs = orgs
         self.items = items
         self.root_folder_id = root_folder_id
+        self.export_items = export_items
+        self.export_error = export_error
         self.requests = []
         self.signed_hits = []
         self.put_content_types = []
@@ -100,6 +105,23 @@ class FakeApi(threading.Thread):
                     parent.last_manifest_org = query.get("organization_id", [None])[0]
                     parent.last_manifest_path = query.get("path", [None])[0]
                     return
+                if parsed.path == "/api/v1/sync/export":
+                    if parent.export_error is not None:
+                        status, payload = parent.export_error
+                        self._send(status, payload)
+                        return
+                    exported = parent.export_items or []
+                    self._send(
+                        200,
+                        {
+                            "items": exported,
+                            "total": len(exported),
+                            "limit": 500,
+                            "offset": 0,
+                            "cloud_storage_url": GS_URL,
+                        },
+                    )
+                    return
                 if parsed.path == "/api/v1/folders/":
                     self._send(200, {"folders": [{"id": "child-1", "name": "nested"}]})
                     return
@@ -201,6 +223,31 @@ def test_login_callback_url_is_fixed():
     assert loopback_redirect_uri() == "http://127.0.0.1:8765/callback"
 
 
+def test_open_browser_hides_child_stderr(monkeypatch):
+    def noisy_open(_url: str) -> bool:
+        subprocess.run(
+            [sys.executable, "-c", "import os; os.write(2, b'zygote broken pipe\\n')"],
+            check=False,
+        )
+        return True
+
+    monkeypatch.setattr("proteworks.auth.webbrowser.open", noisy_open)
+    read_fd, write_fd = os.pipe()
+    saved = os.dup(2)
+    os.dup2(write_fd, 2)
+    os.close(write_fd)
+    try:
+        assert open_browser("https://example.test/authorize") is True
+        os.write(2, b"still open\n")
+    finally:
+        os.dup2(saved, 2)
+        os.close(saved)
+    captured = os.read(read_fd, 1024)
+    os.close(read_fd)
+    assert b"zygote" not in captured
+    assert b"still open" in captured
+
+
 def test_root_help_lists_commands(capsys):
     try:
         main(["--help"])
@@ -216,12 +263,14 @@ def test_root_help_lists_commands(capsys):
     assert "proteworks pull '~/My Files/campaigns/' ./campaigns" in text
     assert "proteworks pull '~/My Files/msa/*.cif' ./msa" in text
     assert "proteworks push ./campaigns '~/My Files/campaigns/'" in text
+    assert "proteworks export ./backup" in text
 
 
 def test_pull_and_push_help_show_examples(capsys):
     for command, example in (
         ("pull", "proteworks pull '~/My Files/campaigns/' ./campaigns"),
         ("push", "proteworks push ./campaigns '~/My Files/campaigns/'"),
+        ("export", "proteworks export ./backup"),
     ):
         try:
             main([command, "--help"])
@@ -361,6 +410,56 @@ def test_second_pull_skips_file_without_checksum_when_size_matches(tmp_path, cap
     assert "skip designs.studio" in err
 
 
+def test_export_dry_run_lists_users_and_shared_spaces_without_signed_urls(tmp_path, capsys):
+    personal = _item("users/Member/member.cif")
+    shared = _item("shared/Lab Share/shared.cif")
+    shared["file_id"] = "file-2"
+    server = FakeApi(
+        [_org("reg", "Research")],
+        [],
+        export_items=[personal, shared],
+    ).start()
+    try:
+        code = main(
+            ["export", str(tmp_path / "backup"), "--dry-run"],
+            settings=_settings(tmp_path, server.url),
+            token_store=MemoryTokens(),
+        )
+    finally:
+        server.stop()
+    err = capsys.readouterr().err
+    assert code == 0
+    assert "users/Member/member.cif" in err
+    assert "shared/Lab Share/shared.cif" in err
+    assert server.signed_hits == []
+    assert not any(path == "/api/v1/files/content-urls" for method, path, _body in server.requests if method == "POST")
+    assert "gs://" not in err
+    assert "secret-bucket" not in err
+    assert "storage.googleapis.com" not in err
+
+
+def test_export_not_found_hides_storage_locations(tmp_path, capsys):
+    server = FakeApi(
+        [_org("reg", "Research")],
+        [],
+        export_error=(404, {"detail": "gs://secret-bucket/org/users/file", "cloud_storage_url": GS_URL}),
+    ).start()
+    try:
+        code = main(
+            ["export", str(tmp_path / "backup")],
+            settings=_settings(tmp_path, server.url),
+            token_store=MemoryTokens(),
+        )
+    finally:
+        server.stop()
+    err = capsys.readouterr().err
+    assert code == 1
+    assert "gs://" not in err
+    assert "secret-bucket" not in err
+    assert "storage.googleapis.com" not in err
+    assert "cloud_storage_url" not in err
+
+
 def test_pull_hash_mismatch_deletes_partial(tmp_path, capsys):
     bad = dict(_item())
     bad["sha256"] = "0" * 64