proker 2.0.0__tar.gz

proker-2.0.0/MANIFEST.in

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+include pyproject.toml
+include README.md
+recursive-include proteomicsviewer/server/templates *
+recursive-exclude Test\ data *
+exclude proker_logo.jpg
+exclude *.bat
+exclude *.command

proker-2.0.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: proker
+Version: 2.0.0
+Summary: Pro-ker Proteomics Viewer — an interactive browser-based proteomics data visualization tool
+Author-email: Billy Ngo <billy.ngo0108@gmail.com>
+License-Expression: LicenseRef-Proprietary
+Project-URL: Homepage, https://github.com/billy-ngo/proteomics-viewer
+Project-URL: Repository, https://github.com/billy-ngo/proteomics-viewer
+Keywords: proteomics,mass-spectrometry,visualization,MaxQuant,bioinformatics,pro-ker
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+Requires-Dist: fastapi>=0.111.0
+Requires-Dist: uvicorn[standard]>=0.29.0
+Requires-Dist: python-multipart>=0.0.9

proker-2.0.0/proker.egg-info/PKG-INFO

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+Metadata-Version: 2.4
+Name: proker
+Version: 2.0.0
+Summary: Pro-ker Proteomics Viewer — an interactive browser-based proteomics data visualization tool
+Author-email: Billy Ngo <billy.ngo0108@gmail.com>
+License-Expression: LicenseRef-Proprietary
+Project-URL: Homepage, https://github.com/billy-ngo/proteomics-viewer
+Project-URL: Repository, https://github.com/billy-ngo/proteomics-viewer
+Keywords: proteomics,mass-spectrometry,visualization,MaxQuant,bioinformatics,pro-ker
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+Requires-Dist: fastapi>=0.111.0
+Requires-Dist: uvicorn[standard]>=0.29.0
+Requires-Dist: python-multipart>=0.0.9

proker-2.0.0/proker.egg-info/SOURCES.txt

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+MANIFEST.in
+pyproject.toml
+proker.egg-info/PKG-INFO
+proker.egg-info/SOURCES.txt
+proker.egg-info/dependency_links.txt
+proker.egg-info/entry_points.txt
+proker.egg-info/requires.txt
+proker.egg-info/top_level.txt
+proteomicsviewer/__init__.py
+proteomicsviewer/__main__.py
+proteomicsviewer/cli.py
+proteomicsviewer/icon.py
+proteomicsviewer/install_shortcut.py
+proteomicsviewer/server/__init__.py
+proteomicsviewer/server/main.py
+proteomicsviewer/server/parser.py
+proteomicsviewer/server/state.py
+proteomicsviewer/server/templates/index.html
+proteomicsviewer/server/templates/logo.svg

proker-2.0.0/proker.egg-info/dependency_links.txt

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+

proker-2.0.0/proker.egg-info/entry_points.txt

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+[console_scripts]
+proker = proteomicsviewer.cli:main

proker-2.0.0/proker.egg-info/requires.txt

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+fastapi>=0.111.0
+uvicorn[standard]>=0.29.0
+python-multipart>=0.0.9

proker-2.0.0/proker.egg-info/top_level.txt

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+proteomicsviewer

proker-2.0.0/proteomicsviewer/__init__.py

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+"""Pro-ker Proteomics Viewer — an interactive browser-based proteomics data visualization tool."""
+
+__version__ = "2.0.0"

proker-2.0.0/proteomicsviewer/__main__.py

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+"""Entry point for `python -m proteomicsviewer` and the `protview` CLI command."""
+
+import sys
+from proteomicsviewer.cli import main
+
+if __name__ == "__main__":
+    sys.exit(main())

proker-2.0.0/proteomicsviewer/cli.py

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+"""
+Pro-ker Proteomics Analysis CLI — launch the viewer from the command line.
+
+Usage:
+    proker                      # start on default port 8050
+    proker data.txt             # start and auto-load a file
+    proker --port 9000          # start on a custom port
+    proker --no-browser         # start without opening the browser
+    proker --install            # create a desktop shortcut
+    proker --update             # check for updates and install if available
+    proker --no-update          # skip the automatic update check
+"""
+
+import argparse
+import atexit
+import json
+import os
+import subprocess
+import sys
+import threading
+import time
+import webbrowser
+from pathlib import Path
+
+_CONFIG_DIR = Path.home() / ".proker"
+_LOCK_FILE = _CONFIG_DIR / "server.lock"
+_FIRST_RUN_MARKER = _CONFIG_DIR / ".shortcut_prompted"
+_UPDATE_CHECK_FILE = _CONFIG_DIR / ".last_update_check"
+_VERSION_MARKER = _CONFIG_DIR / ".installed_version"
+
+_UPDATE_CHECK_INTERVAL = 3600  # 1 hour
+
+
+# ── Welcome message ──────────────────────────────────────────────
+def _show_welcome_if_new():
+    ver = _get_installed_version()
+    try:
+        prev = _VERSION_MARKER.read_text().strip() if _VERSION_MARKER.exists() else None
+    except Exception:
+        prev = None
+
+    if prev == ver:
+        return
+
+    try:
+        _CONFIG_DIR.mkdir(parents=True, exist_ok=True)
+        _VERSION_MARKER.write_text(ver)
+    except Exception:
+        pass
+
+    try:
+        if sys.stdout is None:
+            return
+        sys.stdout.write('')
+    except Exception:
+        return
+
+    is_upgrade = prev is not None
+    print()
+    print(f"  {'=' * 44}")
+    if is_upgrade:
+        print(f"    Pro-ker Proteomics Analysis updated to v{ver}")
+    else:
+        print(f"    Pro-ker Proteomics Analysis v{ver} installed")
+    print(f"  {'=' * 44}")
+    print()
+    if not is_upgrade:
+        print("  Supported formats:")
+        print("    MaxQuant proteinGroups.txt (tab-separated)")
+        print()
+        print("  Quick start:")
+        print("    - Upload a proteinGroups.txt file")
+        print("    - Assign samples to groups")
+        print("    - Configure processing options")
+        print("    - Add visualizations to the canvas")
+        print()
+    print("  Commands:")
+    print("    proker                Launch the viewer")
+    print("    proker file.txt       Load a file on start")
+    print("    proker --update       Check for updates")
+    print("    proker --install      Create a desktop shortcut")
+    print("    proker --version      Show installed version")
+    print()
+
+
+# ── Auto-update ──────────────────────────────────────────────────
+def _get_installed_version():
+    try:
+        from proteomicsviewer import __version__
+        return __version__
+    except Exception:
+        return "0.0.0"
+
+
+def _get_pypi_version():
+    try:
+        import urllib.request
+        url = "https://pypi.org/pypi/proker/json"
+        with urllib.request.urlopen(url, timeout=3) as resp:
+            data = json.loads(resp.read())
+            return data["info"]["version"]
+    except Exception:
+        return None
+
+
+def _version_tuple(v):
+    try:
+        return tuple(int(x) for x in v.split(".")[:3])
+    except Exception:
+        return (0, 0, 0)
+
+
+def _should_check_update():
+    try:
+        if _UPDATE_CHECK_FILE.exists():
+            last = float(_UPDATE_CHECK_FILE.read_text().strip())
+            return (time.time() - last) > _UPDATE_CHECK_INTERVAL
+    except Exception:
+        pass
+    return True
+
+
+def _record_update_check():
+    try:
+        _CONFIG_DIR.mkdir(parents=True, exist_ok=True)
+        _UPDATE_CHECK_FILE.write_text(str(time.time()))
+    except Exception:
+        pass
+
+
+def _do_upgrade():
+    cmds = [
+        [sys.executable, "-m", "pip", "install", "--upgrade", "proker"],
+        [sys.executable, "-m", "pip", "install", "--upgrade", "--user", "proker"],
+    ]
+    last_err = None
+    for cmd in cmds:
+        try:
+            result = subprocess.run(cmd, capture_output=True, text=True, timeout=120)
+            if result.returncode == 0:
+                return True
+            last_err = result.stderr.strip()[:200]
+        except Exception as e:
+            last_err = str(e)
+    if last_err:
+        _log(f"  pip failed: {last_err}")
+    return False
+
+
+def _log(msg):
+    try:
+        print(msg)
+    except Exception:
+        pass
+    try:
+        log = _CONFIG_DIR / "update.log"
+        _CONFIG_DIR.mkdir(parents=True, exist_ok=True)
+        with open(log, "a") as f:
+            f.write(f"{time.strftime('%Y-%m-%d %H:%M:%S')} {msg}\n")
+    except Exception:
+        pass
+
+
+def check_and_update(force=False):
+    if not force and not _should_check_update():
+        return ('skip', None)
+
+    _record_update_check()
+    installed = _get_installed_version()
+    latest = _get_pypi_version()
+
+    if latest is None:
+        return ('skip', None)
+    if _version_tuple(latest) <= _version_tuple(installed):
+        return ('current', None)
+
+    _log(f"  Updating Pro-ker: {installed} -> {latest} ...")
+    if _do_upgrade():
+        _log(f"  Updated to {latest}.")
+        return ('updated', latest)
+    else:
+        _log(f"  Update failed (retry with: proker --update)")
+        return ('failed', latest)
+
+
+def _check_update_with_prompt():
+    try:
+        _record_update_check()
+        installed = _get_installed_version()
+        latest = _get_pypi_version()
+
+        if latest is None or _version_tuple(latest) <= _version_tuple(installed):
+            return
+
+        has_terminal = False
+        try:
+            if sys.stdout is not None and hasattr(sys.stdout, 'write'):
+                sys.stdout.write('')
+                has_terminal = True
+        except Exception:
+            pass
+
+        should_update = False
+
+        if has_terminal:
+            try:
+                print(f"\n  Update available: {installed} -> {latest}")
+                answer = input("  Install update now? [Y/n]: ").strip()
+                should_update = answer.lower() != 'n'
+            except (EOFError, OSError):
+                should_update = _tk_update_prompt(installed, latest)
+        else:
+            should_update = _tk_update_prompt(installed, latest)
+
+        if should_update:
+            _log(f"  Updating Pro-ker: {installed} -> {latest} ...")
+            if _do_upgrade():
+                _log(f"  Updated to {latest}.")
+                if has_terminal:
+                    print(f"\n  Please run 'proker' again to launch the new version.\n")
+                    sys.exit(0)
+                else:
+                    try:
+                        import tkinter as tk
+                        from tkinter import messagebox
+                        root = tk.Tk(); root.withdraw()
+                        messagebox.showinfo(
+                            "Pro-ker",
+                            f"Updated to v{latest}.\n\nThe viewer will now relaunch."
+                        )
+                        root.destroy()
+                    except Exception:
+                        pass
+                    subprocess.Popen([sys.executable, "-m", "proteomicsviewer", "--no-update"])
+                    sys.exit(0)
+            else:
+                _log(f"  Update failed. Retry with: proker --update")
+    except Exception:
+        pass
+
+
+def _tk_update_prompt(installed, latest):
+    try:
+        import tkinter as tk
+        from tkinter import messagebox
+        root = tk.Tk(); root.withdraw()
+        answer = messagebox.askyesno(
+            "Pro-ker Update",
+            f"A new version is available: {installed} -> {latest}\n\n"
+            f"Install the update now?",
+        )
+        root.destroy()
+        return answer
+    except Exception:
+        return False
+
+
+# ── Instance detection ───────────────────────────────────────────
+def _pid_alive(pid):
+    if sys.platform == "win32":
+        import ctypes
+        kernel32 = ctypes.windll.kernel32
+        handle = kernel32.OpenProcess(0x100000, False, pid)
+        if handle:
+            kernel32.CloseHandle(handle)
+            return True
+        return False
+    try:
+        os.kill(pid, 0)
+        return True
+    except (OSError, ProcessLookupError, PermissionError):
+        return False
+
+
+def _http_check(host, port, timeout=0.5):
+    try:
+        import urllib.request
+        url = f"http://{'localhost' if host in ('0.0.0.0', '127.0.0.1') else host}:{port}/health"
+        with urllib.request.urlopen(url, timeout=timeout) as resp:
+            return json.loads(resp.read()).get("status") == "ok"
+    except Exception:
+        return False
+
+
+def _check_existing_server(host, port):
+    try:
+        if _LOCK_FILE.exists():
+            data = json.loads(_LOCK_FILE.read_text())
+            lock_host = data.get("host", "127.0.0.1")
+            lock_port = data.get("port", 8050)
+            lock_pid = data.get("pid")
+            if lock_pid and _pid_alive(lock_pid) and _http_check(lock_host, lock_port):
+                h = "localhost" if lock_host in ("0.0.0.0", "127.0.0.1") else lock_host
+                return f"http://{h}:{lock_port}"
+            _LOCK_FILE.unlink(missing_ok=True)
+    except Exception:
+        pass
+
+    if _http_check(host, port):
+        h = "localhost" if host in ("0.0.0.0", "127.0.0.1") else host
+        return f"http://{h}:{port}"
+    return None
+
+
+# ── Lock file helpers ────────────────────────────────────────────
+def _write_lock(host, port):
+    try:
+        _CONFIG_DIR.mkdir(parents=True, exist_ok=True)
+        _LOCK_FILE.write_text(json.dumps({"host": host, "port": port, "pid": os.getpid()}))
+    except Exception:
+        pass
+
+
+def _remove_lock():
+    try:
+        if _LOCK_FILE.exists():
+            data = json.loads(_LOCK_FILE.read_text())
+            if data.get("pid") == os.getpid():
+                _LOCK_FILE.unlink()
+    except Exception:
+        pass
+
+
+# ── First-run shortcut prompt ────────────────────────────────────
+def _offer_shortcut_install():
+    if _FIRST_RUN_MARKER.exists():
+        return
+    try:
+        _CONFIG_DIR.mkdir(parents=True, exist_ok=True)
+        _FIRST_RUN_MARKER.write_text("prompted")
+    except Exception:
+        return
+
+    try:
+        answer = input("  Create a desktop shortcut? [Y/n]: ").strip()
+        if answer.lower() != 'n':
+            try:
+                from proteomicsviewer.install_shortcut import main as install_main
+                install_main()
+            except ImportError:
+                print("  Shortcut creation requires tkinter.")
+                print("  You can create a shortcut later with: proker --install")
+            except Exception as e:
+                print(f"  Shortcut creation failed: {e}")
+                print("  You can try again later with: proker --install")
+        return
+    except (EOFError, OSError):
+        pass
+
+    try:
+        import tkinter as tk
+        from tkinter import messagebox
+        root = tk.Tk(); root.withdraw()
+        answer = messagebox.askyesno(
+            "Pro-ker",
+            "Would you like to create a desktop shortcut?\n\n"
+            "You can also do this later with:  proker --install",
+        )
+        root.destroy()
+        if answer:
+            from proteomicsviewer.install_shortcut import main as install_main
+            install_main()
+    except Exception:
+        pass
+
+
+# ── Browser opener ───────────────────────────────────────────────
+def _open_when_ready(url, timeout=10):
+    import urllib.request
+    deadline = time.monotonic() + timeout
+    while time.monotonic() < deadline:
+        try:
+            urllib.request.urlopen(f"{url}/health", timeout=0.5)
+            break
+        except Exception:
+            time.sleep(0.2)
+    webbrowser.open(url)
+
+
+# ── Entry point ──────────────────────────────────────────────────
+def main():
+    parser = argparse.ArgumentParser(
+        prog="proker",
+        description="Pro-ker Proteomics Analysis — interactive proteomics data visualization",
+    )
+    parser.add_argument("file", nargs="?", default=None,
+                        help="Path to a proteinGroups.txt file to auto-load")
+    parser.add_argument("--port", type=int, default=8050, help="Port (default: 8050)")
+    parser.add_argument("--host", type=str, default="127.0.0.1", help="Host (default: 127.0.0.1)")
+    parser.add_argument("--no-browser", action="store_true", help="Don't open the browser")
+    parser.add_argument("--install", action="store_true", help="Create a desktop shortcut")
+    parser.add_argument("--update", action="store_true", help="Check for updates now")
+    parser.add_argument("--no-update", action="store_true", help="Skip automatic update check")
+    parser.add_argument("--version", action="store_true", help="Show version and exit")
+    args = parser.parse_args()
+
+    if args.version:
+        print(f"Pro-ker Proteomics Analysis {_get_installed_version()}")
+        return 0
+
+    if args.install:
+        try:
+            from proteomicsviewer.install_shortcut import main as install_main
+            install_main()
+        except ImportError:
+            print("  Shortcut creation requires tkinter.")
+            print("  Install it with: conda install tk  (or)  sudo apt install python3-tk")
+        except Exception as e:
+            print(f"  Shortcut creation failed: {e}")
+        return 0
+
+    # Manual update command
+    if args.update:
+        status, ver = check_and_update(force=True)
+        if status == 'updated':
+            print(f"  Pro-ker updated to {ver}.")
+            print(f"  Run 'proker' to launch the new version.")
+        elif status == 'failed':
+            print(f"  Update to {ver} failed.")
+            print(f"  Check ~/.proker/update.log for details.")
+            print(f"  Or update manually: pip install --upgrade proker")
+        elif status == 'skip':
+            print(f"  Could not reach PyPI. Check your internet connection.")
+        else:
+            print(f"  Pro-ker {_get_installed_version()} is up to date.")
+        return 0
+
+    # Welcome message on first run / upgrade
+    _show_welcome_if_new()
+
+    # Pre-launch update check
+    has_terminal = False
+    try:
+        if sys.stdout is not None and hasattr(sys.stdout, 'write'):
+            sys.stdout.write('')
+            has_terminal = True
+    except Exception:
+        pass
+
+    if not args.no_update and has_terminal:
+        _check_update_with_prompt()
+
+    # Single-instance check
+    existing = _check_existing_server(args.host, args.port)
+    if existing:
+        if not args.no_browser:
+            webbrowser.open(existing)
+        return 0
+
+    # First launch — offer desktop shortcut
+    _offer_shortcut_install()
+
+    # Store file path for auto-load
+    if args.file:
+        filepath = Path(args.file).resolve()
+        if not filepath.exists():
+            print(f"Error: file not found: {filepath}", file=sys.stderr)
+            return 1
+        os.environ["PROTVIEW_AUTOLOAD"] = str(filepath)
+
+    url = f"http://{'localhost' if args.host in ('0.0.0.0',) else args.host}:{args.port}"
+
+    if not args.no_browser:
+        threading.Thread(target=_open_when_ready, args=(url,), daemon=True).start()
+
+    # Heavy imports
+    backend_dir = os.path.join(os.path.dirname(__file__), "server")
+    sys.path.insert(0, backend_dir)
+    os.environ["PROTVIEW_AUTO_SHUTDOWN"] = "1"
+
+    from proteomicsviewer.server.main import app  # noqa: E402
+
+    _write_lock(args.host, args.port)
+    atexit.register(_remove_lock)
+
+    # Background update check for pythonw launches
+    if not args.no_update and not has_terminal:
+        def _bg_update_check():
+            time.sleep(3)
+            try:
+                installed = _get_installed_version()
+                latest = _get_pypi_version()
+                if latest and _version_tuple(latest) > _version_tuple(installed):
+                    _log(f"  Update available: {installed} -> {latest}. Run 'proker --update'.")
+                    if _tk_update_prompt(installed, latest):
+                        if _do_upgrade():
+                            _log(f"  Updated to {latest}.")
+                            try:
+                                import tkinter as tk
+                                from tkinter import messagebox
+                                root = tk.Tk(); root.withdraw()
+                                messagebox.showinfo("Pro-ker", f"Updated to v{latest}.\n\nRestart to use the new version.")
+                                root.destroy()
+                            except Exception:
+                                pass
+            except Exception:
+                pass
+        threading.Thread(target=_bg_update_check, daemon=True).start()
+
+    # Start server
+    if sys.platform == "win32":
+        import asyncio
+        asyncio.set_event_loop_policy(asyncio.WindowsSelectorEventLoopPolicy())
+
+    import uvicorn
+    uvicorn.run(app, host=args.host, port=args.port, log_level="warning")
+    return 0