def on_set_dstat_params_file(self, widget, data=None):
options = self.get_step_options()
form = Form.of(Filepath.named('dstat_params_file')
.using(default=options.get('dstat_params_file', ''),
optional=True,
properties={'patterns':
[('Dstat parameters file (*.yml)',
('*.yml', ))]}))
dialog = FormViewDialog(form, 'Set DStat parameters file')
valid, response = dialog.run()
if valid:
options['dstat_params_file'] = response['dstat_params_file']
self.set_step_values(options)
def __init__(self):
window = gtk.Window(gtk.WINDOW_TOPLEVEL)
window.set_title("Mpeg2-Player")
window.set_default_size(640, 500)
window.connect("destroy", self.on_destroy)
vbox = gtk.VBox()
window.add(vbox)
hbox = gtk.HBox()
vbox.pack_start(hbox, expand=False)
video_mode_enum = Enum.named('video_mode').valued(*self.video_mode_keys)
form = Form.of(
video_mode_enum.using(default=self.video_mode_keys[0]),
Filepath.named('output_path').using(default=''),
Integer.named('bitrate').using(default=150, validators=[ValueAtLeast(
minimum=25)], properties={'step': 25,
'label': 'Bitrate (KB/s)', }),
String.named('transform_string').using(default='1,0,0,0,1,0,0,0,1'),
Boolean.named('draw_cairo').using(default=False),
)
self.video_mode_form_view = create_form_view(form)
for field in ['video_mode', 'output_path', 'bitrate',
'transform_string', 'draw_cairo']:
setattr(self, '%s_field' % field, self.video_mode_form_view.form\
.fields[field])
self.video_mode_field.proxy.connect('changed', self._on_mode_changed)
self.video_source = None
hbox.add(self.video_mode_form_view.widget)
self.button = gtk.Button("Start")
hbox.pack_start(self.button, False)
self.button.connect("clicked", self.start_stop)
self.aframe = gtk.AspectFrame(xalign=0.5, yalign=1.0, ratio=4.0 / 3.0,
obey_child=False)
self.pipeline = None
self._proxy = None
vbox.pack_start(self.aframe, expand=True)
self.movie_view = GtkVideoView()
self.movie_window = self.movie_view.widget
self.aframe.add(self.movie_window)
window.show_all()
self.window = window
def on_select_script(self, widget, data=None):
"""
Handler called when the user clicks on
"PSTrace step config..." in the "Tools" menu.
"""
app = get_app()
options = self.get_step_options()
form = Form.of(Filepath.named('script').using(default=options.script,
optional=True))
dialog = FormViewDialog()
valid, response = dialog.run(form)
step_options_changed = False
if valid and (response['script'] and response['script'] !=
options.script):
options.script = response['script']
step_options_changed = True
if step_options_changed:
emit_signal('on_step_options_changed', [self.name,
app.protocol
.current_step_number],
interface=IPlugin)
class App(SingletonPlugin, AppDataController):
implements(IPlugin)
'''
INFO: <Plugin App 'microdrop.app'>
INFO: <Plugin ConfigController 'microdrop.gui.config_controller'>
INFO: <Plugin DmfDeviceController 'microdrop.gui.dmf_device_controller'>
INFO: <Plugin ExperimentLogController
'microdrop.gui.experiment_log_controller'>
INFO: <Plugin MainWindowController 'microdrop.gui.main_window_controller'>
INFO: <Plugin ProtocolController 'microdrop.gui.protocol_controller'>
INFO: <Plugin ProtocolGridController 'microdrop.gui.protocol_grid_controller'>
'''
core_plugins = [
'microdrop.app', 'microdrop.gui.config_controller',
'microdrop.gui.dmf_device_controller',
'microdrop.gui.experiment_log_controller',
'microdrop.gui.main_window_controller',
'microdrop.gui.protocol_controller',
'microdrop.gui.protocol_grid_controller', 'microdrop.zmq_hub_plugin',
'microdrop.electrode_controller_plugin', 'microdrop.device_info_plugin'
]
AppFields = Form.of(
Integer.named('x').using(default=None,
optional=True,
properties={'show_in_gui': False}),
Integer.named('y').using(default=None,
optional=True,
properties={'show_in_gui': False}),
Integer.named('width').using(default=400,
optional=True,
properties={'show_in_gui': False}),
Integer.named('height').using(default=500,
optional=True,
properties={'show_in_gui': False}),
String.named('server_url').using(
default='http://microfluidics.utoronto.ca/update',
optional=True,
properties=dict(show_in_gui=False)),
Boolean.named('realtime_mode').using(
default=False, optional=True, properties=dict(show_in_gui=False)),
Filepath.named('log_file').using(
default='',
optional=True,
properties={'action': gtk.FILE_CHOOSER_ACTION_SAVE}),
Boolean.named('log_enabled').using(default=False, optional=True),
Enum.named('log_level').using(default='info', optional=True).valued(
'debug', 'info', 'warning', 'error', 'critical'))
def __init__(self):
'''
.. versionchanged:: 2.11.2
Add :attr:`gtk_thread` attribute, holding a reference to the thread
that the GTK main loop is executing in.
.. versionchanged:: 2.17
Remove :attr:`version` attribute. Use
:attr:`microdrop.__version__` instead.
'''
args = parse_args()
print 'Arguments: %s' % args
self.name = "microdrop.app"
#: .. versionadded:: 2.11.2
self.gtk_thread = None
self.realtime_mode = False
self.running = False
self.builder = gtk.Builder()
self.signals = {}
self.plugin_data = {}
# these members are initialized by plugins
self.experiment_log_controller = None
self.config_controller = None
self.dmf_device_controller = None
self.protocol_controller = None
self.main_window_controller = None
# Enable custom logging handler
logging.getLogger().addHandler(CustomHandler())
self.log_file_handler = None
# config model
try:
self.config = Config(args.config)
except IOError:
logging.error(
'Could not read configuration file, `%s`. Make sure'
' it exists and is readable.', args.config)
raise SystemExit(-1)
# set the log level
if self.name in self.config.data and ('log_level'
in self.config.data[self.name]):
self._set_log_level(self.config.data[self.name]['log_level'])
_L().info('MicroDrop version: %s', __version__)
_L().info('Running in working directory: %s', os.getcwd())
# dmf device
self.dmf_device = None
# protocol
self.protocol = None
def get_data(self, plugin_name):
data = self.plugin_data.get(plugin_name)
if data:
return data
else:
return {}
def set_data(self, plugin_name, data):
'''
.. versionchanged:: 2.20
Log data and plugin name to debug level.
'''
logger = _L() # use logger with method context
if logger.getEffectiveLevel() >= logging.DEBUG:
caller = caller_name(skip=2)
logger.debug('%s -> plugin_data:', caller)
map(logger.debug, pprint.pformat(data).splitlines())
self.plugin_data[plugin_name] = data
def on_app_options_changed(self, plugin_name):
if plugin_name == self.name:
data = self.get_data(self.name)
if 'realtime_mode' in data:
if self.realtime_mode != data['realtime_mode']:
self.realtime_mode = data['realtime_mode']
if self.protocol_controller:
self.protocol_controller.run_step()
if 'log_file' in data and 'log_enabled' in data:
self.apply_log_file_config(data['log_file'],
data['log_enabled'])
if 'log_level' in data:
self._set_log_level(data['log_level'])
if 'width' in data and 'height' in data:
self.main_window_controller.view.resize(
data['width'], data['height'])
# allow window to resize before other signals are processed
while gtk.events_pending():
gtk.main_iteration()
if data.get('x') is not None and data.get('y') is not None:
self.main_window_controller.view.move(data['x'], data['y'])
# allow window to resize before other signals are processed
while gtk.events_pending():
gtk.main_iteration()
def apply_log_file_config(self, log_file, enabled):
if enabled and not log_file:
_L().error('Log file can only be enabled if a path is selected.')
return False
self.update_log_file()
return True
@property
def plugins(self):
return set(self.plugin_data.keys())
def plugin_name_lookup(self, name, re_pattern=False):
if not re_pattern:
return name
for plugin_name in self.plugins:
if re.search(name, plugin_name):
return plugin_name
return None
def update_plugins(self):
'''
.. versionchanged:: 2.16.2
Method was deprecated.
'''
raise DeprecationWarning('The `update_plugins` method was deprecated '
'in version 2.16.2.')
def gtk_thread_active(self):
'''
Returns
-------
bool
``True`` if the currently active thread is the GTK thread.
.. versionadded:: 2.11.2
'''
if self.gtk_thread is not None and (threading.current_thread().ident
== self.gtk_thread.ident):
return True
else:
return False
def run(self):
'''
.. versionchanged:: 2.11.2
Set :attr:`gtk_thread` attribute, holding a reference to the thread
that the GTK main loop is executing in.
.. versionchanged:: 2.16.2
Do not attempt to update plugins.
'''
logger = _L() # use logger with method context
self.gtk_thread = threading.current_thread()
# set realtime mode to false on startup
if self.name in self.config.data and \
'realtime_mode' in self.config.data[self.name]:
self.config.data[self.name]['realtime_mode'] = False
plugin_manager.emit_signal('on_plugin_enable')
log_file = self.get_app_values()['log_file']
if not log_file:
self.set_app_values({
'log_file':
ph.path(self.config['data_dir']).joinpath('microdrop.log')
})
pwd = ph.path(os.getcwd()).realpath()
if '' in sys.path and pwd.joinpath('plugins').isdir():
logger.info(
'[warning] Removing working directory `%s` from Python'
' import path.', pwd)
sys.path.remove('')
# Import enabled plugins from Conda environment.
conda_plugins_dir = mpm.api.MICRODROP_CONDA_ETC.joinpath(
'plugins', 'enabled')
if conda_plugins_dir.isdir():
plugin_manager.load_plugins(conda_plugins_dir,
import_from_parent=False)
self.update_log_file()
logger.info('User data directory: %s', self.config['data_dir'])
logger.info('Plugins directory: %s', conda_plugins_dir)
logger.info('Devices directory: %s', self.get_device_directory())
FormViewDialog.default_parent = self.main_window_controller.view
self.builder.connect_signals(self.signals)
observers = {}
plugins_to_disable_by_default = []
# Enable plugins according to schedule requests
for package_name in self.config['plugins']['enabled']:
try:
service = plugin_manager. \
get_service_instance_by_package_name(package_name)
observers[service.name] = service
except KeyError:
logger.warning('No plugin found registered with name `%s`',
package_name)
# Mark plugin to be removed from "enabled" list to prevent
# trying to enable it on future launches.
plugins_to_disable_by_default.append(package_name)
except Exception, exception:
logger.error(exception, exc_info=True)
# Remove marked plugins from "enabled" list to prevent trying to enable
# it on future launches.
for package_name_i in plugins_to_disable_by_default:
self.config['plugins']['enabled'].remove(package_name_i)
schedule = plugin_manager.get_schedule(observers, "on_plugin_enable")
# Load optional plugins marked as enabled in config
for p in schedule:
try:
plugin_manager.enable(p)
except KeyError:
logger.warning('Requested plugin (%s) is not available.\n\n'
'Please check that it exists in the plugins '
'directory:\n\n %s' %
(p, self.config['plugins']['directory']),
exc_info=True)
plugin_manager.log_summary()
self.experiment_log = None
# save the protocol name from the config file because it is
# automatically overwritten when we load a new device
protocol_name = self.config['protocol']['name']
# if there is no device specified in the config file, try choosing one
# from the device directory by default
device_directory = ph.path(self.get_device_directory())
if not self.config['dmf_device']['name']:
try:
self.config['dmf_device']['name'] = \
device_directory.dirs()[0].name
except Exception:
pass
# load the device from the config file
if self.config['dmf_device']['name']:
if device_directory:
device_path = os.path.join(device_directory,
self.config['dmf_device']['name'],
DEVICE_FILENAME)
self.dmf_device_controller.load_device(device_path)
# if we successfully loaded a device
if self.dmf_device:
# reapply the protocol name to the config file
self.config['protocol']['name'] = protocol_name
# load the protocol
if self.config['protocol']['name']:
directory = self.get_device_directory()
if directory:
filename = os.path.join(directory,
self.config['dmf_device']['name'],
"protocols",
self.config['protocol']['name'])
self.protocol_controller.load_protocol(filename)
data = self.get_data("microdrop.app")
x = data.get('x', None)
y = data.get('y', None)
width = data.get('width', 400)
height = data.get('height', 600)
self.main_window_controller.view.resize(width, height)
if x is not None and y is not None:
self.main_window_controller.view.move(x, y)
plugin_manager.emit_signal('on_gui_ready')
self.main_window_controller.main()
class App(SingletonPlugin, AppDataController):
implements(IPlugin)
'''
INFO: <Plugin App 'microdrop.app'>
INFO: <Plugin ConfigController 'microdrop.gui.config_controller'>
INFO: <Plugin DmfDeviceController 'microdrop.gui.dmf_device_controller'>
INFO: <Plugin ExperimentLogController
'microdrop.gui.experiment_log_controller'>
INFO: <Plugin MainWindowController 'microdrop.gui.main_window_controller'>
INFO: <Plugin ProtocolController 'microdrop.gui.protocol_controller'>
INFO: <Plugin ProtocolGridController 'microdrop.gui.protocol_grid_controller'>
'''
core_plugins = [
'microdrop.app', 'microdrop.gui.config_controller',
'microdrop.gui.dmf_device_controller',
'microdrop.gui.experiment_log_controller',
'microdrop.gui.main_window_controller',
'microdrop.gui.protocol_controller',
'microdrop.gui.protocol_grid_controller', 'wheelerlab.zmq_hub_plugin',
'wheelerlab.electrode_controller_plugin',
'wheelerlab.device_info_plugin'
]
AppFields = Form.of(
Integer.named('x').using(default=None,
optional=True,
properties={'show_in_gui': False}),
Integer.named('y').using(default=None,
optional=True,
properties={'show_in_gui': False}),
Integer.named('width').using(default=400,
optional=True,
properties={'show_in_gui': False}),
Integer.named('height').using(default=500,
optional=True,
properties={'show_in_gui': False}),
Enum.named('update_automatically' #pylint: disable-msg=E1101,E1120
).using(default=1, optional=True).valued(
'auto-update',
'check for updates, but ask before installing',
'''don't check for updates'''),
String.named('server_url').using( #pylint: disable-msg=E1120
default='http://microfluidics.utoronto.ca/update',
optional=True,
properties=dict(show_in_gui=False)),
Boolean.named('realtime_mode').using( #pylint: disable-msg=E1120
default=False,
optional=True,
properties=dict(show_in_gui=False)),
Filepath.named('log_file').using( #pylint: disable-msg=E1120
default='',
optional=True,
properties={'action': gtk.FILE_CHOOSER_ACTION_SAVE}),
Boolean.named('log_enabled').using( #pylint: disable-msg=E1120
default=False, optional=True),
Enum.named('log_level').using( #pylint: disable-msg=E1101, E1120
default='info', optional=True).valued('debug', 'info', 'warning',
'error', 'critical'),
)
def __init__(self):
args = parse_args()
print 'Arguments: %s' % args
self.name = "microdrop.app"
# get the version number
self.version = ""
try:
raise Exception
version = subprocess.Popen(
['git', 'describe'],
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
stdin=subprocess.PIPE).communicate()[0].rstrip()
m = re.match('v(\d+)\.(\d+)-(\d+)', version)
self.version = "%s.%s.%s" % (m.group(1), m.group(2), m.group(3))
branch = subprocess.Popen(
['git', 'rev-parse', '--abbrev-ref', 'HEAD'],
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
stdin=subprocess.PIPE).communicate()[0].rstrip()
if branch.strip() != 'master':
self.version += "-%s" % branch
except:
import pkg_resources
version = pkg_resources.get_distribution('microdrop').version
dev = ('dev' in version)
self.version = re.sub('\.dev.*', '', re.sub('post', '', version))
if dev:
self.version += "-dev"
self.realtime_mode = False
self.running = False
self.builder = gtk.Builder()
self.signals = {}
self.plugin_data = {}
# these members are initialized by plugins
self.experiment_log_controller = None
self.config_controller = None
self.dmf_device_controller = None
self.protocol_controller = None
self.main_window_controller = None
# Enable custom logging handler
logging.getLogger().addHandler(CustomHandler())
self.log_file_handler = None
# config model
try:
self.config = Config(args.config)
except IOError:
logging.error(
'Could not read configuration file, `%s`. Make sure'
' it exists and is readable.', args.config)
raise SystemExit(-1)
# set the log level
if self.name in self.config.data and ('log_level'
in self.config.data[self.name]):
self._set_log_level(self.config.data[self.name]['log_level'])
logger.info('MicroDrop version: %s', self.version)
logger.info('Running in working directory: %s', os.getcwd())
# Run post install hooks for freshly installed plugins.
# It is necessary to delay the execution of these hooks here due to
# Windows file locking preventing the deletion of files that are in use.
post_install_queue_path = \
path(self.config.data['plugins']['directory']) \
.joinpath('post_install_queue.yml')
if post_install_queue_path.isfile():
post_install_queue = yaml.load(post_install_queue_path.bytes())
post_install_queue = map(path, post_install_queue)
logger.info('[App] processing post install hooks.')
for p in post_install_queue[:]:
try:
info = get_plugin_info(p)
logger.info(" running post install hook for %s" %
info.plugin_name)
plugin_manager.post_install(p)
except Exception:
logging.info(''.join(traceback.format_exc()))
logging.error('Error running post-install hook for %s.',
p.name,
exc_info=True)
finally:
post_install_queue.remove(p)
post_install_queue_path.write_bytes(yaml.dump(post_install_queue))
# Delete paths that were marked during the uninstallation of a plugin.
# It is necessary to delay the deletion until here due to Windows file
# locking preventing the deletion of files that are in use.
deletions_path = path(self.config.data['plugins']['directory'])\
.joinpath('requested_deletions.yml')
if deletions_path.isfile():
requested_deletions = yaml.load(deletions_path.bytes())
requested_deletions = map(path, requested_deletions)
logger.info('[App] processing requested deletions.')
for p in requested_deletions[:]:
try:
if p != p.abspath():
logger.info(
' (warning) ignoring path %s since it '
'is not absolute', p)
continue
if p.isdir():
info = get_plugin_info(p)
if info:
logger.info(' deleting %s' % p)
cwd = os.getcwd()
os.chdir(p.parent)
try:
path(p.name).rmtree() #ignore_errors=True)
except Exception, why:
logger.warning('Error deleting path %s (%s)',
p, why)
raise
os.chdir(cwd)
requested_deletions.remove(p)
else: # if the directory doesn't exist, remove it from the
# list
requested_deletions.remove(p)
except (AssertionError, ):
logger.info(' NOT deleting %s' % (p))
continue
except (Exception, ):
logger.info(' NOT deleting %s' % (p))
continue