def build_applications(self, args):
if args.files:
files = args.files
else:
files = []
applications = {}
for file in files:
file = os.path.abspath(file)
if os.path.isdir(file):
handler = DirectoryHandler(filename=file)
else:
handler = ScriptHandler(filename=file)
if handler.failed:
die("Error loading %s:\n\n%s\n%s " %
(file, handler.error, handler.error_detail))
application = Application()
application.add(handler)
route = handler.url_path()
if not route:
if '/' in applications:
die("Don't know the URL path to use for %s" % (file))
route = '/'
applications[route] = application
if len(applications) == 0:
# create an empty application by default, used with output_server typically
applications['/'] = Application()
return applications
def build_applications(self, args):
if args.files:
files = args.files
else:
files = []
applications = {}
for file in files:
file = os.path.abspath(file)
if os.path.isdir(file):
handler = DirectoryHandler(filename=file)
else:
handler = ScriptHandler(filename=file)
if handler.failed:
die("Error loading %s:\n\n%s\n%s " % (file, handler.error, handler.error_detail))
application = Application()
application.add(handler)
route = handler.url_path()
if not route:
if '/' in applications:
die("Don't know the URL path to use for %s" % (file))
route = '/'
applications[route] = application
if len(applications) == 0:
# create an empty application by default, used with output_server typically
applications['/'] = Application()
return applications
def load(filename):
handler = DirectoryHandler(filename=filename)
assert handler.safe_to_fork
result['handler'] = handler
handler.modify_document(doc)
if handler.failed:
raise RuntimeError(handler.error)
assert not handler.safe_to_fork
def load(filename):
handler = DirectoryHandler(filename=filename)
assert handler.safe_to_fork
result['handler'] = handler
handler.modify_document(doc)
if handler.failed:
raise RuntimeError(handler.error)
assert not handler.safe_to_fork
def main():
# parse command line arguments
args = parse_args()
# set the logger
log = logging.getLogger("dashmd")
log.setLevel(loglevel.get(args.log))
log.debug(f"Set log level to '{args.log}'")
os.environ['BOKEH_PY_LOG_LEVEL'] = dashmd_loglevel_to_bokeh.get(args.log)
os.environ['BOKEH_LOG_LEVEL'] = dashmd_loglevel_to_bokeh.get(args.log)
log.debug(f"Set Bokeh log level to '{dashmd_loglevel_to_bokeh.get(args.log)}'")
# start the server
try:
log.info("Preparing the Bokeh server")
io_loop = IOLoop.current()
# force bokeh to load resources from CDN
os.environ['BOKEH_RESOURCES'] = 'cdn'
app_dir = os.path.dirname(os.path.realpath(__file__))
bokeh_app = Application(DirectoryHandler(filename=app_dir, argv=[args.default_dir, args.update]))
server = Server(
{'/': bokeh_app}, io_loop=io_loop,
port=args.port, num_procs=1,
allow_websocket_origin=[f'localhost:{args.port}'],
)
except OSError:
log.error(f"[ERROR] Port {args.port} is already in use. Please specify a different one by using the --port flag.")
sys.exit(1)
server.start()
log.info(f"Opening DashMD on http://localhost:{args.port}")
server.io_loop.add_callback(server.show, "/")
server.io_loop.start()
def build_single_handler_application(path):
''' Return a Bokeh application built using a single handler for a file
or directory.
Args:
path (str) : path to a file or directory for creating a Bokeh
application.
Returns:
Application
Raises:
RuntimeError
'''
path = os.path.abspath(path)
if os.path.isdir(path):
handler = DirectoryHandler(filename=path)
else:
handler = ScriptHandler(filename=path)
if handler.failed:
raise RuntimeError("Error loading %s:\n\n%s\n%s " %
(path, handler.error, handler.error_detail))
application = Application(handler)
return application
def main():
"""The photodiag command line interface.
This is a wrapper around bokeh server that provides an interface to launch
applications bundled with the photodiag package.
"""
# Discover photodiag apps
apps_path = os.path.join(os.path.dirname(os.path.abspath(__file__)),
'apps')
available_apps = []
for module_info in pkgutil.iter_modules([apps_path]):
if module_info.ispkg:
available_apps.append(module_info.name)
parser = argparse.ArgumentParser(
prog='photodiag',
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument(
'app',
type=str,
choices=available_apps,
help="photodiag application",
)
parser.add_argument('--port',
type=int,
default=5006,
help="the port to listen on for HTTP requests")
parser.add_argument(
'--allow-websocket-origin',
metavar='HOST[:PORT]',
type=str,
action='append',
default=None,
help="hostname that can connect to the server websocket",
)
parser.add_argument(
'--args',
nargs=argparse.REMAINDER,
default=[],
help="command line arguments for the photodiag application",
)
args = parser.parse_args()
app_path = os.path.join(apps_path, args.app)
logger.info(app_path)
handler = DirectoryHandler(filename=app_path, argv=args.args)
server = Server(
{'/': Application(handler)},
port=args.port,
allow_websocket_origin=args.allow_websocket_origin,
)
server.start()
server.io_loop.start()
def build_single_handler_application(path, argv=None):
''' Return a Bokeh application built using a single handler for a script,
notebook, or directory.
In general a Bokeh :class:`~bokeh.application.application.Application` may
have any number of handlers to initialize :class:`~bokeh.document.Document`
objects for new client sessions. However, in many cases only a single
handler is needed. This function examines the ``path`` provided, and
returns an ``Application`` initialized with one of the following handlers:
* :class:`~bokeh.application.handlers.script.ScriptHandler` when ``path``
is to a ``.py`` script.
* :class:`~bokeh.application.handlers.notebook.NotebookHandler` when
``path`` is to an ``.ipynb`` Jupyter notebook.
* :class:`~bokeh.application.handlers.directory.DirectoryHandler` when
``path`` is to a directory containing a ``main.py`` script.
Args:
path (str) : path to a file or directory for creating a Bokeh
application.
argv (seq[str], optional) : command line arguments to pass to the
application handler
Returns:
:class:`~bokeh.application.application.Application`
Raises:
RuntimeError
Notes:
If ``path`` ends with a file ``main.py`` then a warning will be printed
regarding running directory-style apps by passing the directory instead.
'''
argv = argv or []
path = os.path.abspath(path)
if os.path.isdir(path):
handler = DirectoryHandler(filename=path, argv=argv)
else:
if path.endswith(".ipynb"):
handler = NotebookHandler(filename=path, argv=argv)
elif path.endswith(".py"):
if path.endswith("main.py"):
warnings.warn(DIRSTYLE_MAIN_WARNING)
handler = ScriptHandler(filename=path, argv=argv)
else:
raise ValueError(
"Expected a '.py' script or '.ipynb' notebook, got: '%s'" %
path)
if handler.failed:
raise RuntimeError("Error loading %s:\n\n%s\n%s " %
(path, handler.error, handler.error_detail))
application = Application(handler)
return application
def build_single_handler_application(path):
''' Return a Bokeh application built using a single handler for a file
or directory.
Args:
path (str) : path to a file or directory for creating a Bokeh
application.
Returns:
Application
Raises:
RuntimeError
'''
path = os.path.abspath(path)
if os.path.isdir(path):
handler = DirectoryHandler(filename=path)
else:
if path.endswith(".ipynb"):
handler = NotebookHandler(filename=path)
elif path.endswith(".py"):
handler = ScriptHandler(filename=path)
else:
raise ValueError("Expected a '.py' script or '.ipynb' notebook, got: '%s'" % path)
if handler.failed:
raise RuntimeError("Error loading %s:\n\n%s\n%s " % (path, handler.error, handler.error_detail))
application = Application(handler)
return application
def run_viewer(results_path: Union[Path, str], port: int = 5007, starting_index: int = 0):
print(f'Opening viewer on http://localhost:{port}/')
handler = DirectoryHandler(filename=str(Path(__file__).parent), argv=[results_path, starting_index])
application = Application(handler)
server = Server(application, port=port)
server.start()
server.io_loop.add_callback(server.show, "/")
server.io_loop.start()
def main(appnames, applist_file, port, allow_origin):
env = Environment(loader=FileSystemLoader('templates'))
class IndexHandler(RequestHandler):
def get(self):
template = env.get_template('index.html')
#script = server_document('http://localhost:5006/app-base')
self.write(template.render(applist=apps))
if appnames == None:
print(
"No appname provided on command line \n Trying to read app names from: ",
applist_file)
try:
with open(applist_file) as file:
apps = [line.strip() for line in file]
print("found ", len(apps)) #,sep=":")
print(apps)
except:
sys.exit("Not found ! You need to provide appnames")
else:
apps = appnames
serverlist = {}
bokeh_app = []
for i in range(len(apps)):
# libfolder=os.path.join(os.path.abspath(os.path.dirname(__file__)),apps[0])
# print (libfolder)
# sys.path.insert(0, libfolder)
print("adding ", apps[i]) # ,sep=":" )
bokeh_app.append(Application(DirectoryHandler(filename=apps[i])))
rpath = '/' + str(apps[i])
serverlist[rpath] = bokeh_app[i]
#server = Server({'/Qm7b': bokeh_app, '/Arginine-Dipeptide':bokeh_app2 }, num_procs=1,port=5001, extra_patterns=[('/', IndexHandler),("/static", StaticFileHandler, {'path':'static/'})])
server = Server(serverlist,
num_procs=1,
use_xheaders=False,
port=port,
allow_websocket_origin=allow_origin,
extra_patterns=[('/', IndexHandler),
(r"/static/(.*)", StaticFileHandler, {
"path": "./static"
})])
#server = Server({'/app-base': bokeh_app }, num_procs=1, port=5001)
server.start()
return server
def run(self) -> None:
self.settings.setup_elasticsearch_connection()
# The following is a simpler `bokeh serve src/nasty_analysis/visualization`.
# Code for that is in `bokeh.commands.subcommands.serve.Serve.invoke`.
# Also Bokeh provides this example:
# https://github.com/bokeh/bokeh/blob/2.0.2/examples/howto/server_embed/standalone_embed.py
address = self.settings.analysis.serve.address
port = self.settings.analysis.serve.port
num_procs = self.settings.analysis.num_procs
autoreload = False
if self.develop:
num_procs = 1
autoreload = True
watch(str(self.settings.find_settings_file()))
for file in Path(nasty_analysis.__file__).parent.glob("**/*.js"):
watch(str(file))
application = ParameterPassingApplication(
DirectoryHandler(filename=Path(serve.__file__).parent),
server_context_params={"settings": self.settings},
)
with report_server_init_errors(address=address, port=port):
server = Server(
{"/": application},
address=address,
port=port,
allow_websocket_origin=[f"{address}:{port}"],
num_procs=num_procs,
autoreload=autoreload,
)
server.start()
if self.show:
server.io_loop.add_callback(server.show, "/")
server.run_until_shutdown()
def build_single_handler_application(path, argv=None):
''' Return a Bokeh application built using a single handler for a file
or directory.
Args:
path (str) : path to a file or directory for creating a Bokeh
application.
argv (seq[str], optional) : command line arguments to pass to the
application handler
Returns:
Application
Raises:
RuntimeError
'''
argv = argv or []
path = os.path.abspath(path)
if os.path.isdir(path):
handler = DirectoryHandler(filename=path, argv=argv)
else:
if path.endswith(".ipynb"):
handler = NotebookHandler(filename=path, argv=argv)
elif path.endswith(".py"):
if path.endswith("main.py"):
warnings.warn(DIRSTYLE_MAIN_WARNING)
handler = ScriptHandler(filename=path, argv=argv)
else:
raise ValueError(
"Expected a '.py' script or '.ipynb' notebook, got: '%s'" %
path)
if handler.failed:
raise RuntimeError("Error loading %s:\n\n%s\n%s " %
(path, handler.error, handler.error_detail))
application = Application(handler)
return application
def start_bokeh_server():
"""
Create and start a bokeh server with a series of
applications.
"""
# Declare the absolute path to the demo application.
demo_path = os.path.abspath("project/server/bokeh_apps/bokehDemo")
# Declare the dictionary of applications to launch.
apps = {
'/bokehDemo': Application(DirectoryHandler(filename=demo_path)),
}
# Instantiate the Bokeh server.
# Allow connections from the Flask application.
server = Server(
applications=apps,
allow_websocket_origin=["127.0.0.1:5000"],
# port=5006
)
server.start()
server.io_loop.start()
def load(filename):
handler = DirectoryHandler(filename=filename)
handler.modify_document(doc)
if handler.failed:
raise RuntimeError(handler.error)
if args.thiel:
show_thiel = True
if args.file is not None:
ulog_file = os.path.abspath(args.file)
show_ulog_file = True
args.show = True
show_3d_page = args.threed
show_pid_analysis_page = args.pid_analysis
applications = {}
if args.show:
thiel_path = os.path.join(os.path.dirname(os.path.realpath(__file__)),
'thiel_app')
print("this is the main file path", thiel_path)
handler = DirectoryHandler(filename=thiel_path)
applications['/thiel_app'] = Application(handler)
set_log_id_is_filename(show_ulog_file)
# additional request handlers
extra_patterns = [
(r'/upload', UploadHandler),
(r'/browse', BrowseHandler),
(r'/browse_data_retrieval', BrowseDataRetrievalHandler),
(r'/3d', ThreeDHandler),
(r'/radio_controller', RadioControllerHandler),
(r'/edit_entry', EditEntryHandler),
(r'/download', DownloadHandler),
(r'/dbinfo', DBInfoHandler),
(r'/error_label', UpdateErrorLabelHandler),
'--allow-websocket-origin',
action='append',
type=str,
metavar='HOST[:PORT]',
help="""Public hostnames which may connect to the Bokeh websocket""",
default=None)
args = parser.parse_args()
# This should remain here until --host is removed entirely
_fixup_deprecated_host_args(args)
applications = {}
main_path = os.path.join(os.path.dirname(os.path.realpath(__file__)),
'plot_app')
handler = DirectoryHandler(filename=main_path)
applications['/plot_app'] = Application(handler)
server_kwargs = {}
if args.port != None: server_kwargs['port'] = args.port
if args.use_xheaders: server_kwargs['use_xheaders'] = args.use_xheaders
server_kwargs['num_procs'] = args.numprocs
if args.address != None: server_kwargs['address'] = args.address
if args.host != None: server_kwargs['host'] = args.host
if args.allow_websocket_origin != None:
server_kwargs['allow_websocket_origin'] = args.allow_websocket_origin
# increase the maximum upload size (default is 100MB)
server_kwargs['http_server_kwargs'] = {'max_buffer_size': 300 * 1024 * 1024}
show_ulog_file = False
def build_single_handler_application(path: str,
argv: List[str] | None = None
) -> Application:
''' Return a Bokeh application built using a single handler for a script,
notebook, or directory.
In general a Bokeh :class:`~bokeh.application.application.Application` may
have any number of handlers to initialize |Document| objects for new client
sessions. However, in many cases only a single handler is needed. This
function examines the ``path`` provided, and returns an ``Application``
initialized with one of the following handlers:
* :class:`~bokeh.application.handlers.script.ScriptHandler` when ``path``
is to a ``.py`` script.
* :class:`~bokeh.application.handlers.notebook.NotebookHandler` when
``path`` is to an ``.ipynb`` Jupyter notebook.
* :class:`~bokeh.application.handlers.directory.DirectoryHandler` when
``path`` is to a directory containing a ``main.py`` script.
Args:
path (str) : path to a file or directory for creating a Bokeh
application.
argv (seq[str], optional) : command line arguments to pass to the
application handler
Returns:
:class:`~bokeh.application.application.Application`
Raises:
RuntimeError
Notes:
If ``path`` ends with a file ``main.py`` then a warning will be printed
regarding running directory-style apps by passing the directory instead.
'''
argv = argv or []
path = os.path.abspath(os.path.expanduser(path))
handler: Handler
# There are certainly race conditions here if the file/directory is deleted
# in between the isdir/isfile tests and subsequent code. But it would be a
# failure if they were not there to begin with, too (just a different error)
if os.path.isdir(path):
handler = DirectoryHandler(filename=path, argv=argv)
elif os.path.isfile(path):
if path.endswith(".ipynb"):
handler = NotebookHandler(filename=path, argv=argv)
elif path.endswith(".py"):
if path.endswith("main.py"):
warnings.warn(DIRSTYLE_MAIN_WARNING)
handler = ScriptHandler(filename=path, argv=argv)
else:
raise ValueError(
"Expected a '.py' script or '.ipynb' notebook, got: '%s'" %
path)
else:
raise ValueError(
"Path for Bokeh server application does not exist: %s" % path)
if handler.failed:
raise RuntimeError("Error loading %s:\n\n%s\n%s " %
(path, handler.error, handler.error_detail))
application = Application(handler)
return application
# in the app
model_map = Model.model_class_reverse_map
for _, cm in CUSTOM_BOKEH_MODELS:
if cm in model_map:
del model_map[cm]
return js_code
if __name__ == '__main__':
os.environ['BOKEH_RESOURCES'] = 'cdn'
loglevel = os.getenv('ADVI_LOGLEVEL', 'INFO')
logging.basicConfig(level=loglevel, format='%(asctime)s %(message)s')
custom_js = compile_custom_models()
apps = {
make_url(arg):
Application(DirectoryHandler(filename='app', argv=[arg, custom_js]))
for _, arg in MENU_VARS
}
extra_patterns = [(make_url('?'), IndexHandler),
(make_url('(favicon.ico)'), StaticFileHandler, {
'path': "app/static"
}), (make_url('static/(.*)'), StaticHandler)]
paths = [a[0] for a in extra_patterns]
paths.extend(list(apps.keys()))
logging.info('Running on localhost:5006 with paths:\n%s', '\n'.join(paths))
server = Server(
apps,
allow_websocket_origin=[WS_ORIGIN],
use_xheaders=True,
extra_patterns=extra_patterns,
def load(filename):
handler = DirectoryHandler(filename=filename)
handler.modify_document(doc)
if handler.failed:
raise RuntimeError(handler.error)
def test_missing_filename_raises():
with pytest.raises(ValueError):
DirectoryHandler()