GUI app (experimental) (#730)

* add default config

* first pass

* flake8

* cleanup

* first pass at using qthreads

* cleanup

* WIP

* better error handling

* improved UI

* bugfix

* fix merge bugs

* import order

* cleanup

* make gui requirements optional

* pr review requested changes

* Update server/gui/main.py

Co-Authored-By: csweaver <charlottesweaver@gmail.com>

* pr review request

* qt child class methods -> camelCase

* whitespace

.gitignore

@@ -27,6 +27,9 @@ server/app/web/templates/index\.html
 .ipynb_checkpoints
 *.ipynb
 
+# cefpython
+error.log
+
 # misc
 .DS_Store
 npm-debug.log

server/app/app.py

@@ -14,20 +14,25 @@ class Server:
     def __init__(self):
         self.data = None
         self.cache = Cache(config={"CACHE_TYPE": "simple", "CACHE_DEFAULT_TIMEOUT": 860_000})
+        self.app = None
 
     def create_app(self):
-        app = Flask(__name__, static_folder="web/static")
-        app.json_encoder = Float32JSONEncoder
-        self.cache.init_app(app)
-        Compress(app)
-        CORS(app)
+        self.app = Flask(__name__, static_folder="web/static")
+        self.app.json_encoder = Float32JSONEncoder
+        self.cache.init_app(self.app)
+        Compress(self.app)
+        CORS(self.app)
 
         # Config
         SECRET_KEY = os.environ.get("CXG_SECRET_KEY", default="SparkleAndShine")
-        app.config.update(SECRET_KEY=SECRET_KEY)
+        self.app.config.update(SECRET_KEY=SECRET_KEY)
+        self.app.config.update(SCRIPTS=[])
 
         resources = get_api_resources()
-        app.register_blueprint(webapp.bp)
-        app.register_blueprint(resources.blueprint)
-        app.add_url_rule("/", endpoint="index")
-        return app
+        self.app.register_blueprint(webapp.bp)
+        self.app.register_blueprint(resources.blueprint)
+        self.app.add_url_rule("/", endpoint="index")
+
+    def attach_data(self, data, title="Demo"):
+        self.app.config.update(DATASET_TITLE=title)
+        self.app.data = data

server/cli/launch.py

@@ -10,6 +10,7 @@ import click
 from server.app.app import Server
 from server.app.util.errors import ScanpyFileError
 from server.app.util.utils import custom_format_warning
+from server.utils.constants import MODES
 
 
 @click.command()
@@ -17,7 +18,7 @@ from server.app.util.utils import custom_format_warning
 @click.option(
     "--layout",
     "-l",
-    type=click.Choice(["umap", "tsne", "draw_graph_fa", "draw_graph_fr", "diffmap", "phate"]),
+    type=click.Choice(MODES),
     default="umap",
     show_default=True,
     help="Method for layout."
@@ -140,9 +141,8 @@ security risk by including the --scripts flag. Make sure you trust the scripts t
     # Import Flask app
     server = Server()
 
-    app = server.create_app()
-    app.config.update(DATASET_TITLE=title)
-    app.config.update(SCRIPTS=scripts)
+    server.create_app()
+    server.app.config.update(SCRIPTS=scripts)
 
     if not verbose:
         log = logging.getLogger("werkzeug")
@@ -167,7 +167,7 @@ security risk by including the --scripts flag. Make sure you trust the scripts t
     }
 
     try:
-        app.data = ScanpyEngine(data, args)
+        server.attach_data(ScanpyEngine(data, args), title=title)
     except ScanpyFileError as e:
         raise click.ClickException(f"{e}")
 
@@ -183,4 +183,4 @@ security risk by including the --scripts flag. Make sure you trust the scripts t
         f = open(devnull, "w")
         sys.stdout = f
 
-    app.run(host=host, debug=debug, port=port, threaded=True)
+    server.app.run(host=host, debug=debug, port=port, threaded=True)

server/gui/browser.py

@@ -0,0 +1,97 @@
+# flake8: noqa F403, F405
+from cefpython3 import cefpython as cef
+from PyQt5.QtCore import *
+from PyQt5.QtGui import *
+from PyQt5.QtWidgets import *
+
+from server.gui.utils import WINDOWS, LINUX
+
+WindowUtils = cef.WindowUtils()
+
+# OS differences
+# noinspection PyUnresolvedReferences
+CefWidgetParent = QWidget
+if LINUX:
+    # noinspection PyUnresolvedReferences
+    CefWidgetParent = QX11EmbedContainer
+
+
+class CefWidget(CefWidgetParent):
+    def __init__(self, parent=None):
+        super(CefWidget, self).__init__(parent)
+        self.parent = parent
+        self.browser = None
+        # TODO test without this on linux
+        self.hidden_window = None  # Required for PyQt5 on Linux
+        self.show()
+
+    def focusInEvent(self, event):
+        # This event seems to never get called on Linux, as CEF is
+        # stealing all focus due to Issue #284.
+        if self.browser:
+            if WINDOWS:
+                WindowUtils.OnSetFocus(self.getHandle(), 0, 0, 0)
+            self.browser.SetFocus(True)
+
+    def focusOutEvent(self, event):
+        # This event seems to never get called on Linux, as CEF is
+        # stealing all focus due to Issue #284.
+        if self.browser:
+            self.browser.SetFocus(False)
+
+    def embedBrowser(self):
+        if LINUX:
+            self.hidden_window = QWindow()
+        window_info = cef.WindowInfo()
+        rect = [0, 0, self.width(), self.height()]
+        window_info.SetAsChild(self.getHandle(), rect)
+        # TODO better splash
+        self.browser = cef.CreateBrowserSync(window_info)
+
+    def getHandle(self):
+        if self.hidden_window:
+            # PyQt5 on Linux
+            return int(self.hidden_window.winId())
+        else:
+            return int(self.winId())
+
+    def moveEvent(self, _):
+        self.x = 0
+        self.y = 0
+        if self.browser:
+            if WINDOWS:
+                WindowUtils.OnSize(self.getHandle(), 0, 0, 0)
+            elif LINUX:
+                self.browser.SetBounds(self.x, self.y,
+                                       self.width(), self.height())
+            self.browser.NotifyMoveOrResizeStarted()
+
+    def resizeEvent(self, event):
+        size = event.size()
+        if self.browser:
+            if WINDOWS:
+                WindowUtils.OnSize(self.getHandle(), 0, 0, 0)
+            elif LINUX:
+                self.browser.SetBounds(self.x, self.y,
+                                       size.width(), size.height())
+            self.browser.NotifyMoveOrResizeStarted()
+
+
+class CefApplication(QApplication):
+    def __init__(self, args):
+        super(CefApplication, self).__init__(args)
+        if not cef.GetAppSetting("external_message_pump"):
+            self.timer = self.createTimer()
+
+    def createTimer(self):
+        timer = QTimer()
+        timer.timeout.connect(self.onTimer)
+        timer.start(10)
+        return timer
+
+    def onTimer(self):
+        cef.MessageLoopWork()
+
+    def stopTimer(self):
+        # Stop the timer after Qt's message loop has ended
+        self.timer.stop()

server/gui/main.py

@@ -0,0 +1,212 @@
+# flake8: noqa F403, F405
+import sys
+from os.path import splitext, basename
+
+from cefpython3 import cefpython as cef
+from PyQt5.QtCore import *
+from PyQt5.QtWidgets import *
+
+from server.app.app import Server
+from server.gui.browser import CefWidget, CefApplication
+from server.gui.workers import DataLoadWorker, ServerRunWorker
+from server.gui.utils import WINDOWS, LINUX, MAC
+from server.utils.constants import MODES
+
+
+# Configuration
+# TODO remember this or calculate it?
+
+WIDTH = 1024
+HEIGHT = 768
+
+
+# noinspection PyUnresolvedReferences
+class MainWindow(QMainWindow):
+    def __init__(self):
+        super(MainWindow, self).__init__(None)
+        self.thread_pool = QThreadPool()
+        self.cef_widget = None
+        self.data_widget = None
+        self.server = Server()
+        self.server.create_app()
+        self.runServer()
+        self.setWindowTitle("cellxgene")
+
+        # Strong focus - accepts focus by tab & click
+        self.setFocusPolicy(Qt.StrongFocus)
+        self.setupLayout()
+        self.setupMenu()
+
+    def setupLayout(self):
+        self.resize(WIDTH, HEIGHT)
+        self.cef_widget = CefWidget(self)
+        self.data_widget = LoadWidget(self)
+        self.stacked_layout = QStackedLayout()
+        self.stacked_layout.addWidget(self.data_widget)
+        self.stacked_layout.addWidget(self.cef_widget)
+        main_layout = QVBoxLayout()
+        main_layout.setContentsMargins(0, 0, 0, 0)
+        main_layout.setSpacing(0)
+        main_layout.addLayout(self.stacked_layout)
+        frame = QFrame()
+        frame.setLayout(main_layout)
+        self.setCentralWidget(frame)
+
+        if WINDOWS:
+            # On Windows with PyQt5 main window must be shown first
+            # before CEF browser is embedded, otherwise window is
+            # not resized and application hangs during resize.
+            self.show()
+
+        # Browser can be embedded only after layout was set up
+        self.cef_widget.embedBrowser()
+
+        if LINUX:
+            # On Linux with PyQt5 the QX11EmbedContainer widget is
+            # no longer available. An equivalent in Qt5 is to create
+            # a hidden window, embed CEF browser in it and then
+            # create a container for that hidden window and replace
+            # cef widget in the layout with the container.
+            self.container = QWidget.createWindowContainer(
+                self.cef_widget.hidden_window, parent=self)
+            stacked_layout.addWidget(self.container, 1, 0)
+
+    def setupMenu(self):
+        main_menu = self.menuBar()
+        file_menu = main_menu.addMenu('File')
+        load_action = QAction("Load file...", self)
+        load_action.setStatusTip("Load file")
+        load_action.setShortcut("Ctrl+O")
+        load_action.triggered.connect(self.showLoad)
+        file_menu.addAction(load_action)
+
+    def showLoad(self):
+        self.stacked_layout.setCurrentIndex(0)
+
+    def closeEvent(self, event):
+        # Close browser (force=True) and free CEF reference
+        if self.cef_widget.browser:
+            self.cef_widget.browser.CloseBrowser(True)
+            self.clearBrowserReferences()
+
+    def runServer(self):
+        worker = ServerRunWorker(self.server.app, host="127.0.0.1", port=8000)
+        self.thread_pool.start(worker)
+
+    def clearBrowserReferences(self):
+        # Clear browser references that you keep anywhere in your
+        # code. All references must be cleared for CEF to shutdown cleanly.
+        self.cef_widget.browser = None
+
+
+class LoadWidget(QFrame):
+    def __init__(self, parent):
+        super(LoadWidget, self).__init__(parent=parent)
+
+        # Init layout
+        self.MAX_CONTENT_WIDTH = 500
+        load_ui_layout = QVBoxLayout()
+        h_margin = (WIDTH - self.MAX_CONTENT_WIDTH) // 2
+        if h_margin < 10:
+            h_margin = 10
+        load_ui_layout.setContentsMargins(h_margin, 20, h_margin, 20)
+        logo_layout = QHBoxLayout()
+        logo_layout.setContentsMargins(0, 0, 0, 20)
+
+        load_layout = QGridLayout()
+        load_layout.setContentsMargins(0, 0, 0, 0)
+        load_layout.setSpacing(0)
+        message_layout = QHBoxLayout()
+        message_layout.setContentsMargins(0, 0, 0, 0)
+
+        self.title = ""
+        self.label = QLabel("cellxgene")
+        logo_layout.addWidget(self.label)
+
+        # UI section
+        # TODO add load spinner
+        # TODO add cancel button to send back to browser (if available)
+        self.embedding_label = QLabel("embedding: ")
+        load_layout.addWidget(self.embedding_label, 0, 0)
+        self.file_label = QLabel("file: ")
+        load_layout.addWidget(self.file_label, 0, 1)
+        self.embeddings = QComboBox(self)
+        self.embeddings.currentIndexChanged.connect(self.updateEmbedding)
+        self.embeddings.addItems(MODES)
+        self.embedding_selection = MODES[0]
+        load_layout.addWidget(self.embeddings, 1, 0)
+
+        self.load = QPushButton("Open...")
+        self.load.clicked.connect(self.onLoad)
+        load_layout.addWidget(self.load, 1, 1)
+
+        # Error section
+        self.error_label = QLabel("")
+        self.error_label.setWordWrap(True)
+        self.error_label.setFixedWidth(self.MAX_CONTENT_WIDTH)
+        message_layout.addWidget(self.error_label, alignment=Qt.AlignTop)
+
+        # Layout
+        for l in [logo_layout, load_layout, message_layout ]:
+            load_ui_layout.addLayout(l)
+
+        load_ui_layout.setStretch(2, 10)
+        self.setLayout(load_ui_layout)
+
+    def updateEmbedding(self, idx):
+        self.embedding_selection = MODES[idx]
+
+    def onLoad(self):
+        options = QFileDialog.Options()
+        # options |= QFileDialog.DontUseNativeDialog
+        file_name, _ = QFileDialog.getOpenFileName(self,
+                                                  "Open H5AD File", "", "H5AD Files (*.h5ad)", options=options)
+        self.title = splitext(basename(file_name))[0]
+        worker = DataLoadWorker(file_name, self.embedding_selection)
+        worker.signals.result.connect(self.onDataSuccess)
+        worker.signals.error.connect(self.onDataError)
+        self.window().thread_pool.start(worker)
+
+    def onDataSuccess(self, data):
+        self.window().server.attach_data(data, self.title)
+        self.navigateToLocation()
+        # Reveal browser
+        self.window().stacked_layout.setCurrentIndex(1)
+
+    def onDataError(self, err):
+        self.error_label.setText(f"Error: {err}")
+        self.error_label.resize(self.MAX_CONTENT_WIDTH, self.error_label.height())
+
+    def navigateToLocation(self, location="http://localhost:8000/"):
+        self.window().cef_widget.browser.Navigate(location)
+
+
+def main():
+    # This generates an error.log file on error
+    sys.excepthook = cef.ExceptHook  # To shutdown all CEF processes on error
+    settings = {}
+    # Instead of timer loop
+    if MAC:
+        settings["external_message_pump"] = True
+
+    # Create and launch cef browser and qt window
+    cef.Initialize(settings)
+    app = CefApplication(sys.argv)
+    main_window = MainWindow()
+    main_window.show()
+    main_window.activateWindow()
+    main_window.raise_()
+    app.exec_()
+
+    # Clean up on close
+    if not cef.GetAppSetting("external_message_pump"):
+        app.stopTimer()
+    # TODO clean up threads when we switch threading model
+    del main_window  # Just to be safe, similarly to "del app"
+    del app  # Must destroy app object before calling Shutdown
+    cef.Shutdown()
+    sys.exit(0)
+
+
+if __name__ == '__main__':
+    main()

server/gui/utils.py

@@ -0,0 +1,21 @@
+import platform
+
+from PyQt5.QtCore import QObject, pyqtSignal
+
+# Detect OS
+WINDOWS = (platform.system() == "Windows")
+LINUX = (platform.system() == "Linux")
+MAC = (platform.system() == "Darwin")
+
+
+class WorkerSignals(QObject):
+    """
+    Defines the signals available from a running worker thread.
+    Supported signals are:
+        finished
+        error - `str` error message
+        result - `object` data returned from processing, anything
+    """
+    finished = pyqtSignal()
+    error = pyqtSignal(str)
+    result = pyqtSignal(object)

server/gui/workers.py

@@ -0,0 +1,51 @@
+import traceback
+
+from PyQt5.QtCore import QRunnable, pyqtSlot
+
+from server.gui.utils import WorkerSignals
+
+
+class DataLoadWorker(QRunnable):
+    def __init__(self, data_file, layout="umap", *args, **kwargs):
+        super(DataLoadWorker, self).__init__()
+        self.data_file = data_file
+        self.layout = layout
+        self.signals = WorkerSignals()
+
+    @pyqtSlot()
+    def run(self):
+        if not self.data_file:
+            self.signals.finished.emit()
+            return
+
+        # delayed import to speed load
+        from server.app.scanpy_engine.scanpy_engine import ScanpyEngine
+        args = {
+            "layout": self.layout,
+            "diffexp": "ttest",
+            "max_category_items": 100,
+            "diffexp_lfc_cutoff": 0.01,
+            "obs_names": None,
+            "var_names": None,
+        }
+        try:
+            data_results = ScanpyEngine(self.data_file, args)
+        except Exception as e:
+            traceback.print_exc()
+            self.signals.error.emit(str(e))
+        else:
+            self.signals.result.emit(data_results)
+        finally:
+            self.signals.finished.emit()
+
+
+class ServerRunWorker(QRunnable):
+    def __init__(self, app, host, port, *args, **kwargs):
+        super(ServerRunWorker, self).__init__()
+        self.app = app
+        self.host = host
+        self.port = port
+
+    @pyqtSlot()
+    def run(self):
+        self.app.run(host=self.host, debug=False, port=self.port, threaded=True)

server/utils/constants.py

@@ -0,0 +1 @@
+MODES = ["umap", "tsne", "draw_graph_fa", "draw_graph_fr", "diffmap", "phate"]

setup.py

@@ -36,5 +36,5 @@ setup(
         "Topic :: Scientific/Engineering :: Bio-Informatics",
     ],
     entry_points={"console_scripts": ["cellxgene = server.cli.cli:cli"]},
-    extras_require=dict(louvain=["python-igraph", "louvain>=0.6"]),
+    extras_require=dict(louvain=["python-igraph", "louvain>=0.6"], gui=["PyQt5>=5.12.1", "cefpython3>=66"]),
 )