def __init__(self, *args):
BaseComponents.BlissWidget.__init__(self, *args)
# Internal members
self.current_cpos = None
self.__collection_stopped = False
self.current_view = None
# Framework 2 hardware objects
self._lims_hwobj = None
self.sample_changer = None
self.plate_manipulator_hwobj = None
self.queue_hwobj = None
# Properties
self.addProperty("holderLengthMotor", "string", "")
self.addProperty("queue", "string", "/queue")
self.addProperty("default_centring_method", "integer", 1)
self.addProperty("queue_model", "string", "/queue-model")
self.addProperty("beamline_setup", "string", "/beamline-setup")
self.addProperty("xml_rpc_server", "string", "/xml_rpc_server")
# Qt - Slots
# From ProposalBrick2
self.defineSlot("logged_in", ())
# Used from TaskToolBoxBrick
self.defineSlot("get_tree_brick",())
self.defineSlot("get_selected_samples", ())
# From SampleChangerBrick3, signal emitted when
# the status of the hwobj changes.
self.defineSlot("status_msg_changed", ())
# From sample changer hwobj, emitted when the
# load state changes.
self.defineSlot("sample_load_state_changed", ())
#self.defineSlot("get_mounted_sample", ())
#self.defineSlot("new_centred_position", ())
#self.defineSlot("add_dcg", ())
#self.defineSlot("add_data_collection", ())
#self.defineSlot("set_session", ())
# Qt - Signals
self.defineSignal("enable_hutch_menu", ())
self.defineSignal("enable_command_menu", ())
self.defineSignal("enable_task_toolbox", ())
# Hiding and showing the tabs
self.defineSignal("hide_sample_tab", ())
self.defineSignal("hide_dc_parameters_tab", ())
self.defineSignal("hide_sample_centring_tab", ())
self.defineSignal("hide_dcg_tab", ())
self.defineSignal("hide_sample_changer_tab", ())
self.defineSignal("hide_edna_tab", ())
self.defineSignal("hide_energy_scan_tab",())
self.defineSignal("hide_xrf_spectrum_tab",())
self.defineSignal("hide_workflow_tab", ())
# Populating the tabs with data
self.defineSignal("populate_parameter_widget", ())
self.defineSignal("populate_edna_parameter_widget",())
self.defineSignal("populate_sample_details",())
self.defineSignal("populate_energy_scan_widget", ())
self.defineSignal("populate_xrf_spectrum_widget", ())
self.defineSignal("populate_workflow_tab", ())
# Handle selection
self.defineSignal("selection_changed",())
self.defineSignal("set_directory", ())
self.defineSignal("set_prefix", ())
self.defineSignal("set_sample", ())
#self.defineSignal("clear_centred_positions", ())
# Layout
#self.setSizePolicy(qt.QSizePolicy(qt.QSizePolicy.Fixed,
# qt.QSizePolicy.Expanding))
widget = qtui.QWidgetFactory.\
create(os.path.join(os.path.dirname(__file__),
'widgets/ui_files/sample_changer_widget_layout.ui'))
widget.reparent(self, qt.QPoint(0, 0))
self.sample_changer_widget = widget
self.refresh_pixmap = Icons.load("Refresh2.png")
self.sample_changer_widget.child('synch_button').\
setIconSet(qt.QIconSet(self.refresh_pixmap))
self.sample_changer_widget.child('synch_button').setText("Synch ISPyB")
self.dc_tree_widget = DataCollectTree(self)
self.dc_tree_widget.selection_changed_cb = self.selection_changed
self.dc_tree_widget.run_cb = self.run
#self.dc_tree_widget.clear_centred_positions_cb = \
# self.clear_centred_positions
qt.QObject.connect(self.sample_changer_widget.child('details_button'),
qt.SIGNAL("clicked()"),
self.toggle_sample_changer_tab)
qt.QObject.connect(self.sample_changer_widget.child('filter_cbox'),
qt.SIGNAL("activated(int)"),
self.dc_tree_widget.filter_sample_list)
qt.QObject.connect(self.sample_changer_widget.child('centring_cbox'),
qt.SIGNAL("activated(int)"),
self.dc_tree_widget.set_centring_method)
qt.QObject.connect(self.sample_changer_widget.child('synch_button'),
qt.SIGNAL("clicked()"),
self.refresh_sample_list)
vlayout = qt.QVBoxLayout(self, 0, 0, 'main_layout')
vlayout.setSpacing(10)
self.layout().addWidget(self.sample_changer_widget)
self.layout().addWidget(self.dc_tree_widget)
self.enable_collect(False)
self.sample_changer_widget.child('centring_cbox').setCurrentItem(1)
self.dc_tree_widget.set_centring_method(1)
class TreeBrick(BaseComponents.BlissWidget):
def __init__(self, *args):
BaseComponents.BlissWidget.__init__(self, *args)
# Internal members
self.current_cpos = None
self.__collection_stopped = False
self.current_view = None
# Framework 2 hardware objects
self._lims_hwobj = None
self.sample_changer = None
self.plate_manipulator_hwobj = None
self.queue_hwobj = None
# Properties
self.addProperty("holderLengthMotor", "string", "")
self.addProperty("queue", "string", "/queue")
self.addProperty("default_centring_method", "integer", 1)
self.addProperty("queue_model", "string", "/queue-model")
self.addProperty("beamline_setup", "string", "/beamline-setup")
self.addProperty("xml_rpc_server", "string", "/xml_rpc_server")
# Qt - Slots
# From ProposalBrick2
self.defineSlot("logged_in", ())
# Used from TaskToolBoxBrick
self.defineSlot("get_tree_brick",())
self.defineSlot("get_selected_samples", ())
# From SampleChangerBrick3, signal emitted when
# the status of the hwobj changes.
self.defineSlot("status_msg_changed", ())
# From sample changer hwobj, emitted when the
# load state changes.
self.defineSlot("sample_load_state_changed", ())
#self.defineSlot("get_mounted_sample", ())
#self.defineSlot("new_centred_position", ())
#self.defineSlot("add_dcg", ())
#self.defineSlot("add_data_collection", ())
#self.defineSlot("set_session", ())
# Qt - Signals
self.defineSignal("enable_hutch_menu", ())
self.defineSignal("enable_command_menu", ())
self.defineSignal("enable_task_toolbox", ())
# Hiding and showing the tabs
self.defineSignal("hide_sample_tab", ())
self.defineSignal("hide_dc_parameters_tab", ())
self.defineSignal("hide_sample_centring_tab", ())
self.defineSignal("hide_dcg_tab", ())
self.defineSignal("hide_sample_changer_tab", ())
self.defineSignal("hide_edna_tab", ())
self.defineSignal("hide_energy_scan_tab",())
self.defineSignal("hide_xrf_spectrum_tab",())
self.defineSignal("hide_workflow_tab", ())
# Populating the tabs with data
self.defineSignal("populate_parameter_widget", ())
self.defineSignal("populate_edna_parameter_widget",())
self.defineSignal("populate_sample_details",())
self.defineSignal("populate_energy_scan_widget", ())
self.defineSignal("populate_xrf_spectrum_widget", ())
self.defineSignal("populate_workflow_tab", ())
# Handle selection
self.defineSignal("selection_changed",())
self.defineSignal("set_directory", ())
self.defineSignal("set_prefix", ())
self.defineSignal("set_sample", ())
#self.defineSignal("clear_centred_positions", ())
# Layout
#self.setSizePolicy(qt.QSizePolicy(qt.QSizePolicy.Fixed,
# qt.QSizePolicy.Expanding))
widget = qtui.QWidgetFactory.\
create(os.path.join(os.path.dirname(__file__),
'widgets/ui_files/sample_changer_widget_layout.ui'))
widget.reparent(self, qt.QPoint(0, 0))
self.sample_changer_widget = widget
self.refresh_pixmap = Icons.load("Refresh2.png")
self.sample_changer_widget.child('synch_button').\
setIconSet(qt.QIconSet(self.refresh_pixmap))
self.sample_changer_widget.child('synch_button').setText("Synch ISPyB")
self.dc_tree_widget = DataCollectTree(self)
self.dc_tree_widget.selection_changed_cb = self.selection_changed
self.dc_tree_widget.run_cb = self.run
#self.dc_tree_widget.clear_centred_positions_cb = \
# self.clear_centred_positions
qt.QObject.connect(self.sample_changer_widget.child('details_button'),
qt.SIGNAL("clicked()"),
self.toggle_sample_changer_tab)
qt.QObject.connect(self.sample_changer_widget.child('filter_cbox'),
qt.SIGNAL("activated(int)"),
self.dc_tree_widget.filter_sample_list)
qt.QObject.connect(self.sample_changer_widget.child('centring_cbox'),
qt.SIGNAL("activated(int)"),
self.dc_tree_widget.set_centring_method)
qt.QObject.connect(self.sample_changer_widget.child('synch_button'),
qt.SIGNAL("clicked()"),
self.refresh_sample_list)
vlayout = qt.QVBoxLayout(self, 0, 0, 'main_layout')
vlayout.setSpacing(10)
self.layout().addWidget(self.sample_changer_widget)
self.layout().addWidget(self.dc_tree_widget)
self.enable_collect(False)
self.sample_changer_widget.child('centring_cbox').setCurrentItem(1)
self.dc_tree_widget.set_centring_method(1)
# Framework 2 method
def run(self):
self.emit(qt.PYSIGNAL("hide_dc_parameters_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_dcg_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_sample_centring_tab"), (False,))
self.emit(qt.PYSIGNAL("hide_edna_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_sample_changer_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_sample_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_energy_scan_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_xrf_spectrum_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_workflow_tab"), (True,))
def eventFilter(self, _object, event):
if event.type() == qt.QEvent.MouseButtonPress:
if event.state() & qt.Qt.ShiftButton:
return True
return False
# Framework 2 method
def propertyChanged(self, property_name, old_value, new_value):
if property_name == 'holder_length_motor':
self.dc_tree_widget.hl_motor_hwobj = self.getHardwareObject(new_value)
elif property_name == 'default_centring_method':
self.sample_changer_widget.child('centring_cbox').setCurrentItem(new_value)
self.dc_tree_widget.set_centring_method(new_value)
elif property_name == 'queue':
self.queue_hwobj = self.getHardwareObject(new_value)
self.dc_tree_widget.queue_hwobj = self.queue_hwobj
self.connect(self.queue_hwobj, 'show_workflow_tab',
self.show_workflow_tab_from_model)
self.connect(self.queue_hwobj, 'queue_paused',
self.dc_tree_widget.queue_paused_handler)
self.connect(self.queue_hwobj, 'queue_execution_finished',
self.dc_tree_widget.queue_execution_completed)
self.connect(self.queue_hwobj, 'queue_stopped',
self.dc_tree_widget.queue_stop_handler)
elif property_name == 'queue_model':
self.queue_model_hwobj = self.getHardwareObject(new_value)
self.dc_tree_widget.queue_model_hwobj = self.queue_model_hwobj
self.dc_tree_widget.confirm_dialog.queue_model_hwobj = self.queue_model_hwobj
self.connect(self.queue_model_hwobj, 'child_added',
self.dc_tree_widget.add_to_view)
elif property_name == 'beamline_setup':
bl_setup = self.getHardwareObject(new_value)
self.beamline_config_hwobj = bl_setup
self.dc_tree_widget.beamline_setup_hwobj = bl_setup
self.sample_changer_hwobj = bl_setup.sample_changer_hwobj
try:
self.plate_manipulator_hwobj = bl_setup.plate_manipulator_hwobj
except AttributeError:
self.plate_manipulator_hwobj = None
self.dc_tree_widget.sample_changer_hwobj = self.sample_changer_hwobj
self.dc_tree_widget.plate_manipulator_hwobj = self.plate_manipulator_hwobj
self.session_hwobj = bl_setup.session_hwobj
self._lims_hwobj = bl_setup.lims_client_hwobj
if self.sample_changer_hwobj is not None:
self.connect(self.sample_changer_hwobj,
SampleChanger.STATE_CHANGED_EVENT,
self.sample_load_state_changed)
self.connect(self.sample_changer_hwobj,
SampleChanger.INFO_CHANGED_EVENT,
self.set_sample_pin_icon)
if self.plate_manipulator_hwobj is not None:
self.connect(self.plate_manipulator_hwobj, SampleChanger.STATE_CHANGED_EVENT,
self.sample_load_state_changed)
self.connect(self.plate_manipulator_hwobj, SampleChanger.INFO_CHANGED_EVENT,
self.set_sample_pin_icon)
has_shutter_less = bl_setup.detector_has_shutterless()
if has_shutter_less:
self.dc_tree_widget.confirm_dialog.disable_dark_current_cbx()
elif property_name == 'xml_rpc_server':
xml_rpc_server_hwobj = self.getHardwareObject(new_value)
if xml_rpc_server_hwobj:
self.connect(xml_rpc_server_hwobj, 'add_to_queue',
self.add_to_queue)
self.connect(xml_rpc_server_hwobj, 'start_queue',
self.dc_tree_widget.collect_items)
def set_session(self, session_id, t_prop_code = None, prop_number = None,
prop_id = None, start_date = None, prop_code = None,
is_inhouse = None):
self.session_hwobj.set_session_start_date(start_date)
def logged_in_old_version(self, logged_in):
"""
Reomve this method if logged_in finalized
Connected to the signal loggedIn of ProposalBrick2.
The signal is emitted when a user was succesfully logged in.
"""
self.enable_collect(logged_in)
if not logged_in:
self.dc_tree_widget.populate_free_pin()
else:
sc_basket_content, sc_sample_content = self.get_sc_content()
if sc_basket_content and sc_sample_content:
sc_basket_list, sc_sample_list = self.dc_tree_widget.samples_from_sc_content(
sc_basket_content, sc_sample_content)
self.dc_tree_widget.populate_list_view(sc_basket_list, sc_sample_list)
self.sample_changer_widget.child('filter_cbox').setCurrentItem(0)
if sc_basket_content:
sc_basket_list, sc_sample_list = self.dc_tree_widget.samples_from_sc_content(
sc_basket_content, sc_sample_content)
self.dc_tree_widget.populate_list_view(sc_basket_list, sc_sample_list)
self.sample_changer_widget.child('filter_cbox').setCurrentItem(0)
else:
self.sample_changer_widget.child('filter_cbox').setCurrentItem(2)
#if self.sample_changer_hwobj:
# if not self.sample_changer_hwobj.hasLoadedSample():
self.dc_tree_widget.sample_list_view_selection()
def logged_in(self, logged_in):
"""
Connected to the signal loggedIn of ProposalBrick2.
The signal is emitted when a user was succesfully logged in.
"""
self.enable_collect(logged_in)
plate_sample_content = None
sc_basket_content = None
sc_sample_content = None
if not logged_in:
self.dc_tree_widget.populate_free_pin()
self.sample_changer_widget.child('filter_cbox').setCurrentItem(2)
self.dc_tree_widget.beamline_setup_hwobj.set_plate_mode(False)
sc_basket_content, sc_sample_content = self.get_sc_content()
if sc_basket_content and sc_sample_content:
sc_basket_list, sc_sample_list = self.dc_tree_widget.samples_from_sc_content(
sc_basket_content, sc_sample_content)
self.dc_tree_widget.populate_list_view(sc_basket_list, sc_sample_list)
self.sample_changer_widget.child('filter_cbox').setCurrentItem(0)
if self.dc_tree_widget.beamline_setup_hwobj.diffractometer_hwobj.in_plate_mode():
plate_sample_content = self.get_plate_content()
self.dc_tree_widget.beamline_setup_hwobj.set_plate_mode(True)
if plate_sample_content:
self.dc_tree_widget.beamline_setup_hwobj.set_plate_mode(True)
plate_row_list, plate_sample_list = self.dc_tree_widget.\
samples_from_plate_content(plate_sample_content)
self.dc_tree_widget.populate_plate_view(plate_row_list, plate_sample_list)
self.sample_changer_widget.child('filter_cbox').setCurrentItem(3)
self.dc_tree_widget.sample_list_view_selection()
self.dc_tree_widget.set_sample_pin_icon()
def enable_collect(self, state):
"""
Enables the collect controls.
:param state: Enable if state is True and disable if False
:type state: bool
:returns: None
"""
self.dc_tree_widget.enable_collect(state)
def enable_hutch_menu(self, state):
self.emit(qt.PYSIGNAL("enable_hutch_menu"), (state,))
def enable_command_menu(self, state):
self.emit(qt.PYSIGNAL("enable_command_menu"), (state,))
def enable_task_toolbox(self, state):
self.emit(qt.PYSIGNAL("enable_task_toolbox"), (state,))
def get_tree_brick(self, tree_brick):
"""
Gets the reference to the tree brick. Used to get a reference from
another brick via the signal get_tree_brick. The attribute tree_brick
of the passed dictionary will contain the reference.
:param tree_brick: A dictonary to contain the reference.
:type tree_brick: dict
:returns: None
"""
tree_brick['tree_brick'] = self
def samples_from_lims(self, samples):
barcode_samples, location_samples = self.dc_tree_widget.samples_from_lims(samples)
l_samples = dict()
if self.sample_changer_hwobj.__class__.__TYPE__ == 'Robodiff':
for location, l_sample in location_samples.iteritems():
if l_sample.lims_location != (None, None):
basket, sample = l_sample.lims_location
cell = int(round((basket+0.5)/3.0))
puck = basket-3*(cell-1)
new_location = (cell, puck, sample)
l_sample.lims_location = new_location
l_samples[new_location] = l_sample
name = l_sample.get_name()
l_sample.init_from_sc_sample([new_location])
l_sample.set_name(name)
else:
l_samples.update(location_samples)
return barcode_samples, l_samples
def refresh_sample_list(self):
"""
Retrives sample information from ISPyB and populates the sample list
accordingly.
"""
lims_client = self._lims_hwobj
samples = lims_client.get_samples(self.session_hwobj.proposal_id,
self.session_hwobj.session_id)
sample_list = []
if samples:
(barcode_samples, location_samples) = self.samples_from_lims(samples)
sc_basket_content, sc_samples_content = self.get_sc_content()
sc_basket_list, sc_sample_list = self.dc_tree_widget.\
samples_from_sc_content(sc_basket_content, sc_samples_content)
basket_list = sc_basket_list
for sc_sample in sc_sample_list:
# Get the sample in lims with the barcode
# sc_sample.code
lims_sample = barcode_samples.get(sc_sample.code)
# There was a sample with that barcode
if lims_sample:
if lims_sample.lims_location == sc_sample.location:
logging.getLogger("user_level_log").\
warning("Found sample in ISPyB for location %s" % str(sc_sample.location))
sample_list.append(lims_sample)
else:
logging.getLogger("user_level_log").\
warning("The sample with the barcode (%s) exists"+\
" in LIMS but the location does not mat" +\
"ch. Sample changer location: %s, LIMS " +\
"location %s" % (sc_sample.code,
sc_sample.location,
lims_sample.lims_location))
sample_list.append(sc_sample)
else: # No sample with that barcode, continue with location
lims_sample = location_samples.get(sc_sample.location)
if lims_sample:
if lims_sample.lims_code:
logging.getLogger("user_level_log").\
warning("The sample has a barcode in LIMS, but "+\
"the SC has no barcode information for "+\
"this sample. For location: %s" % str(sc_sample.location))
sample_list.append(lims_sample)
else:
logging.getLogger("user_level_log").\
warning("Found sample in ISPyB for location %s" % str(sc_sample.location))
sample_list.append(lims_sample)
else:
if lims_sample:
if lims_sample.lims_location != None:
logging.getLogger("user_level_log").\
warning("No barcode was provided in ISPyB "+\
"which makes it impossible to verify if"+\
"the locations are correct, assuming "+\
"that the positions are correct.")
sample_list.append(lims_sample)
else:
logging.getLogger("user_level_log").\
warning("No sample in ISPyB for location %s" % str(sc_sample.location))
sample_list.append(sc_sample)
self.dc_tree_widget.populate_list_view(basket_list, sample_list)
def get_sc_content(self):
"""
Gets the 'raw' data from the sample changer.
:returns: A list with tuples, containing the sample information.
"""
sc_basket_content = []
sc_sample_content = []
try:
for basket in self.sample_changer_hwobj.getBasketList():
basket_index = basket.getIndex()
basket_code = basket.getID() or ""
is_present = basket.isPresent()
sc_basket_content.append((basket_index+1, basket)) #basket_code, is_present))
for sample in self.sample_changer_hwobj.getSampleList():
coords = sample.getCoords()
matrix = sample.getID() or ""
basket_index = str(coords[0])
vial_index = ":".join(map(str, coords[1:]))
basket_code = sample.getContainer().getID() or ""
sc_sample_content.append((matrix, basket_index, vial_index, basket_code, 0, coords))
except:
logging.getLogger("user_level_log").\
info("Could not connect to sample changer," + \
" unable to list contents. Make sure that" + \
" the sample changer is turned on. Using free pin mode")
return sc_basket_content, sc_sample_content
def get_plate_content(self):
"""
"""
plate_sample_content = []
for sample in self.plate_manipulator_hwobj.getSampleList():
row_index = sample.getCell().getRowIndex()
col_index = sample.getCell().getCol()
coords = sample.getCoords()
matrix = sample.getID() or ""
vial_index = ":".join(map(str, coords[1:]))
plate_sample_content.append((matrix, row_index, col_index, coords[1], 0, coords))
return plate_sample_content
def status_msg_changed(self, msg, color):
"""
Status message from the SampleChangerBrick.
:param msg: The message
:type msg: str
:returns: None
"""
logging.getLogger("user_level_log").info(msg)
def set_sample_pin_icon(self):
"""
Updates the location of the sample pin when the
matrix code information changes. The matrix code information
is updated, but not exclusively, when a sample is changed.
"""
self.dc_tree_widget.set_sample_pin_icon()
def sample_load_state_changed(self, state, *args):
"""
The state in the sample loading procedure changed.
Ie from Loading to mounted
:param state: str (Enumerable)
:returns: None
"""
s_color = SC_STATE_COLOR.get(state, "UNKNOWN")
self.sample_changer_widget.child('details_button').\
setPaletteBackgroundColor(qt.QColor(s_color))
def show_sample_centring_tab(self):
self.sample_changer_widget.child('details_button').setText("Show SC-details")
self.emit(qt.PYSIGNAL("hide_dc_parameters_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_dcg_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_sample_centring_tab"), (False,))
self.emit(qt.PYSIGNAL("hide_sample_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_sample_changer_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_edna_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_energy_scan_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_xrf_spectrum_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_workflow_tab"), (True,))
def show_sample_tab(self, item):
self.sample_changer_widget.child('details_button').setText("Show SC-details")
self.emit(qt.PYSIGNAL("hide_dc_parameters_tab"), (True,))
self.emit(qt.PYSIGNAL("populate_sample_details"), (item.get_model(),))
self.emit(qt.PYSIGNAL("hide_dcg_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_sample_centring_tab"), (False,))
self.emit(qt.PYSIGNAL("hide_sample_tab"), (False,))
self.emit(qt.PYSIGNAL("hide_sample_changer_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_edna_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_energy_scan_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_xrf_spectrum_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_workflow_tab"), (True,))
def show_dcg_tab(self):
self.sample_changer_widget.child('details_button').setText("Show SC-details")
self.emit(qt.PYSIGNAL("hide_dc_parameters_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_dcg_tab"), (False,))
self.emit(qt.PYSIGNAL("hide_sample_changer_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_edna_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_sample_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_energy_scan_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_xrf_spectrum_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_workflow_tab"), (True,))
def populate_parameters_tab(self, item = None):
self.emit(qt.PYSIGNAL("populate_parameter_widget"),
(item,))
def show_datacollection_tab(self, item):
self.sample_changer_widget.child('details_button').setText("Show SC-details")
self.emit(qt.PYSIGNAL("hide_dcg_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_dc_parameters_tab"), (False,))
self.emit(qt.PYSIGNAL("hide_sample_changer_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_edna_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_sample_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_energy_scan_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_xrf_spectrum_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_workflow_tab"), (True,))
self.populate_parameters_tab(item)
def show_edna_tab(self, item):
self.sample_changer_widget.child('details_button').setText("Show SC-details")
self.emit(qt.PYSIGNAL("hide_dcg_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_dc_parameters_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_sample_changer_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_edna_tab"), (False,))
self.emit(qt.PYSIGNAL("hide_sample_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_energy_scan_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_xrf_spectrum_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_workflow_tab"), (True,))
self.populate_edna_parameters_tab(item)
def populate_edna_parameters_tab(self, item):
self.emit(qt.PYSIGNAL("populate_edna_parameter_widget"),
(item,))
def show_energy_scan_tab(self, item):
self.sample_changer_widget.child('details_button').setText("Show SC-details")
self.emit(qt.PYSIGNAL("hide_dcg_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_dc_parameters_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_sample_changer_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_edna_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_sample_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_energy_scan_tab"), (False,))
self.emit(qt.PYSIGNAL("hide_xrf_spectrum_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_workflow_tab"), (True,))
self.populate_energy_scan_tab(item)
def populate_energy_scan_tab(self, item):
self.emit(qt.PYSIGNAL("populate_energy_scan_widget"), (item,))
def show_xrf_spectrum_tab(self, item):
self.sample_changer_widget.child('details_button').setText("Show SC")
self.emit(qt.PYSIGNAL("hide_dcg_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_dc_parameters_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_sample_changer_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_edna_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_sample_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_energy_scan_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_xrf_spectrum_tab"), (False,))
self.emit(qt.PYSIGNAL("hide_workflow_tab"), (True,))
self.populate_xrf_spectrum_tab(item)
def populate_xrf_spectrum_tab(self, item):
self.emit(qt.PYSIGNAL("populate_xrf_spectrum_widget"), (item,))
def show_workflow_tab_from_model(self):
self.show_workflow_tab(None)
def show_workflow_tab(self, item):
self.sample_changer_widget.child('details_button').setText("Show SC-details")
self.emit(qt.PYSIGNAL("hide_dcg_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_dc_parameters_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_sample_changer_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_edna_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_sample_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_energy_scan_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_xrf_spectrum_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_workflow_tab"), (False,))
running = self.queue_hwobj.is_executing()
self.populate_workflow_tab(item, running=running)
def populate_workflow_tab(self, item, running = False):
self.emit(qt.PYSIGNAL("populate_workflow_tab"), (item, running))
def toggle_sample_changer_tab(self):
if self.current_view == self.sample_changer_widget:
self.current_view = None
self.emit(qt.PYSIGNAL("hide_sample_changer_tab"), (True,))
self.dc_tree_widget.sample_list_view_selection()
self.sample_changer_widget.child('details_button').setText("Show SC-details")
else:
self.current_view = self.sample_changer_widget
self.emit(qt.PYSIGNAL("hide_dc_parameters_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_dcg_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_sample_changer_tab"), (False,))
self.sample_changer_widget.child('details_button').setText("Hide SC-details")
self.emit(qt.PYSIGNAL("hide_sample_tab"), (True,))
def selection_changed(self, items):
if len(items) == 1:
item = items[0]
if isinstance(item, queue_item.SampleQueueItem):
self.emit(qt.PYSIGNAL("populate_sample_details"), (item.get_model(),))
self.emit_set_sample(item)
self.emit_set_directory()
self.emit_set_prefix(item)
#self.populate_edna_parameter_widget(item)
elif isinstance(item, queue_item.DataCollectionQueueItem):
self.populate_parameters_tab(item)
elif isinstance(item, queue_item.CharacterisationQueueItem):
self.populate_edna_parameters_tab(item)
elif isinstance(item, queue_item.EnergyScanQueueItem):
self.populate_energy_scan_tab(item)
elif isinstance(item, queue_item.XRFSpectrumQueueItem):
self.populate_xrf_spectrum_tab(item)
elif isinstance(item, queue_item.GenericWorkflowQueueItem):
self.populate_workflow_tab(item)
self.emit(qt.PYSIGNAL("selection_changed"), (items,))
def emit_set_directory(self):
directory = self.session_hwobj.get_base_image_directory()
self.emit(qt.PYSIGNAL("set_directory"), (directory,))
def emit_set_prefix(self, item):
prefix = self.session_hwobj.get_default_prefix(item.get_model())
self.emit(qt.PYSIGNAL("set_prefix"), (prefix,))
def emit_set_sample(self, item):
self.emit(qt.PYSIGNAL("set_sample"), (item,))
def get_selected_items(self):
items = self.dc_tree_widget.get_selected_items()
return items
def add_to_queue(self, task_list, parent_tree_item = None, set_on = True):
if not parent_tree_item :
parent_tree_item = self.dc_tree_widget.get_mounted_sample_item()
self.dc_tree_widget.add_to_queue(task_list, parent_tree_item, set_on)
class TreeBrick(BaseComponents.BlissWidget):
def __init__(self, *args):
BaseComponents.BlissWidget.__init__(self, *args)
# Internal members
self.current_cpos = None
self.__collection_stopped = False
self.current_view = None
# Framework 2 hardware objects
self.beamline_config_hwobj = None
self._lims_hwobj = None
self.sample_changer = None
self.queue_hwobj = None
# Properties
self.addProperty("holderLengthMotor", "string", "")
self.addProperty("queue", "string", "/queue")
self.addProperty("queue_model", "string", "/queue-model")
self.addProperty("beamline_setup", "string", "/beamline-setup")
self.addProperty("xml_rpc_server", "string", "/xml_rpc_server")
# Qt - Slots
# From ProposalBrick2
self.defineSlot("logged_in", ())
# Used from TaskToolBoxBrick
self.defineSlot("get_tree_brick",())
self.defineSlot("get_selected_samples", ())
# From SampleChangerBrick3, signal emitted when
# the status of the hwobj changes.
self.defineSlot("status_msg_changed", ())
# From sample changer hwobj, emitted when the
# load state changes.
self.defineSlot("sample_load_state_changed", ())
#self.defineSlot("get_mounted_sample", ())
#self.defineSlot("new_centred_position", ())
#self.defineSlot("add_dcg", ())
#self.defineSlot("add_data_collection", ())
#self.defineSlot("set_session", ())
# Qt - Signals
self.defineSignal("enable_hutch_menu", ())
self.defineSignal("enable_command_menu", ())
self.defineSignal("enable_task_toolbox", ())
# Hiding and showing the tabs
self.defineSignal("hide_sample_tab", ())
self.defineSignal("hide_dc_parameters_tab", ())
self.defineSignal("hide_sample_centring_tab", ())
self.defineSignal("hide_dcg_tab", ())
self.defineSignal("hide_sample_changer_tab", ())
self.defineSignal("hide_edna_tab", ())
self.defineSignal("hide_energy_scan_tab",())
self.defineSignal("hide_workflow_tab", ())
# Populating the tabs with data
self.defineSignal("populate_parameter_widget", ())
self.defineSignal("populate_edna_parameter_widget",())
self.defineSignal("populate_sample_details",())
self.defineSignal("populate_energy_scan_widget", ())
self.defineSignal("populate_workflow_tab", ())
# Handle selection
self.defineSignal("selection_changed",())
self.defineSignal("set_directory", ())
self.defineSignal("set_prefix", ())
self.defineSignal("set_sample", ())
#self.defineSignal("clear_centred_positions", ())
# Layout
self.setSizePolicy(qt.QSizePolicy(qt.QSizePolicy.Fixed,
qt.QSizePolicy.Expanding))
widget = qtui.QWidgetFactory.\
create(os.path.join(os.path.dirname(__file__),
'widgets/ui_files/sample_changer_widget_layout.ui'))
widget.reparent(self, qt.QPoint(0, 0))
self.sample_changer_widget = widget
self.refresh_pixmap = Icons.load("Refresh2.png")
self.sample_changer_widget.child('synch_button').\
setIconSet(qt.QIconSet(self.refresh_pixmap))
self.sample_changer_widget.child('synch_button').setText("Synch ISPyB")
self.dc_tree_widget = DataCollectTree(self)
self.dc_tree_widget.selection_changed_cb = self.selection_changed
self.dc_tree_widget.run_cb = self.run
#self.dc_tree_widget.clear_centred_positions_cb = \
# self.clear_centred_positions
qt.QObject.connect(self.sample_changer_widget.child('details_button'),
qt.SIGNAL("clicked()"),
self.toggle_sample_changer_tab)
qt.QObject.connect(self.sample_changer_widget.child('filter_cbox'),
qt.SIGNAL("activated(int)"),
self.dc_tree_widget.filter_sample_list)
qt.QObject.connect(self.sample_changer_widget.child('centring_cbox'),
qt.SIGNAL("activated(int)"),
self.dc_tree_widget.set_centring_method)
qt.QObject.connect(self.sample_changer_widget.child('synch_button'),
qt.SIGNAL("clicked()"),
self.refresh_sample_list)
vlayout = qt.QVBoxLayout(self, 0, 0, 'main_layout')
vlayout.setSpacing(10)
self.layout().addWidget(self.sample_changer_widget)
self.layout().addWidget(self.dc_tree_widget)
self.enable_collect(False)
self.sample_changer_widget.child('centring_cbox').setCurrentItem(1)
self.dc_tree_widget.set_centring_method(1)
# Framework 2 method
def run(self):
self.emit(qt.PYSIGNAL("hide_dc_parameters_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_dcg_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_sample_centring_tab"), (False,))
self.emit(qt.PYSIGNAL("hide_edna_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_sample_changer_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_sample_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_energy_scan_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_workflow_tab"), (True,))
camera_brick = None
for w in qt.QApplication.allWidgets():
if isinstance(w, BaseComponents.BlissWidget):
if "CameraBrick" in str(w.__class__):
camera_brick = w
camera_brick.installEventFilter(self)
break
# workaround for the remote access problem
# (have to disable video display when DC is running)
if BaseComponents.BlissWidget.isInstanceRoleClient():
# find the video brick, make sure it is hidden when collecting data
# and that it is shown again when DC is finished
def disable_video(w=camera_brick):
w.disable_update()
self.__disable_video=disable_video
def enable_video(w=camera_brick):
w.enable_update()
self.__enable_video=enable_video
dispatcher.connect(self.__disable_video, "collect_started")
dispatcher.connect(self.__enable_video, "collect_finished")
def eventFilter(self, _object, event):
if event.type() == qt.QEvent.MouseButtonPress:
if event.state() & qt.Qt.ShiftButton:
return True
return False
# Framework 2 method
def propertyChanged(self, property_name, old_value, new_value):
if property_name == 'holder_length_motor':
self.dc_tree_widget.hl_motor_hwobj = self.getHardwareObject(new_value)
elif property_name == 'queue':
self.queue_hwobj = self.getHardwareObject(new_value)
self.dc_tree_widget.queue_hwobj = self.queue_hwobj
self.connect(self.queue_hwobj, 'show_workflow_tab',
self.show_workflow_tab_from_model)
self.connect(self.queue_hwobj, 'queue_paused',
self.dc_tree_widget.queue_paused_handler)
self.connect(self.queue_hwobj, 'queue_execution_finished',
self.dc_tree_widget.queue_execution_completed)
self.connect(self.queue_hwobj, 'queue_stopped',
self.dc_tree_widget.queue_stop_handler)
elif property_name == 'queue_model':
self.queue_model_hwobj = self.getHardwareObject(new_value)
self.dc_tree_widget.queue_model_hwobj = self.queue_model_hwobj
self.dc_tree_widget.confirm_dialog.queue_model_hwobj = self.queue_model_hwobj
self.connect(self.queue_model_hwobj, 'child_added',
self.dc_tree_widget.add_to_view)
elif property_name == 'beamline_setup':
bl_setup = self.getHardwareObject(new_value)
self.dc_tree_widget.beamline_setup_hwobj = bl_setup
self.sample_changer_hwobj = bl_setup.sample_changer_hwobj
self.dc_tree_widget.sample_changer_hwobj = self.sample_changer_hwobj
self.session_hwobj = bl_setup.session_hwobj
self._lims_hwobj = bl_setup.lims_client_hwobj
if self.sample_changer_hwobj is not None:
self.connect(self.sample_changer_hwobj, 'matrixCodesUpdate',
self.set_sample_pin_icon)
self.connect(self.sample_changer_hwobj, 'stateChanged',
self.sample_load_state_changed)
has_shutter_less = bl_setup.detector_has_shutterless()
if has_shutter_less:
self.dc_tree_widget.confirm_dialog.disable_dark_current_cbx()
elif property_name == 'xml_rpc_server':
xml_rpc_server_hwobj = self.getHardwareObject(new_value)
if xml_rpc_server_hwobj:
self.connect(xml_rpc_server_hwobj, 'add_to_queue',
self.add_to_queue)
self.connect(xml_rpc_server_hwobj, 'start_queue',
self.dc_tree_widget.collect_items)
def set_session(self, session_id, t_prop_code = None, prop_number = None,
prop_id = None, start_date = None, prop_code = None,
is_inhouse = None):
pass
def logged_in(self, logged_in):
"""
Connected to the signal loggedIn of ProposalBrick2.
The signal is emitted when a user was succesfully logged in.
"""
self.enable_collect(logged_in)
#if not logged_in:
self.dc_tree_widget.populate_free_pin()
sc_content = self.get_sc_content()
sc_sample_list = self.dc_tree_widget.samples_from_sc_content(sc_content)
self.dc_tree_widget.populate_list_view(sc_sample_list)
self.sample_changer_widget.child('filter_cbox').setCurrentItem(0)
#endif
loaded_sample = self.sample_changer_hwobj.\
getLoadedSampleLocation()
if loaded_sample == (None, None):
self.dc_tree_widget.filter_sample_list(2)
self.sample_changer_widget.child('filter_cbox').setCurrentItem(2)
self.dc_tree_widget.sample_list_view_selection()
def enable_collect(self, state):
"""
Enables the collect controls.
:param state: Enable if state is True and disable if False
:type state: bool
:returns: None
"""
self.dc_tree_widget.enable_collect(state)
def enable_hutch_menu(self, state):
self.emit(qt.PYSIGNAL("enable_hutch_menu"), (state,))
def enable_command_menu(self, state):
self.emit(qt.PYSIGNAL("enable_command_menu"), (state,))
def enable_task_toolbox(self, state):
self.emit(qt.PYSIGNAL("enable_task_toolbox"), (state,))
def get_tree_brick(self, tree_brick):
"""
Gets the reference to the tree brick. Used to get a reference from
another brick via the signal get_tree_brick. The attribute tree_brick
of the passed dictionary will contain the reference.
:param tree_brick: A dictonary to contain the reference.
:type tree_brick: dict
:returns: None
"""
tree_brick['tree_brick'] = self
def refresh_sample_list(self):
"""
Retrives sample information from ISPyB and populates the sample list
accordingly.
"""
lims_client = self._lims_hwobj
samples = lims_client.get_samples(self.session_hwobj.proposal_id,
self.session_hwobj.session_id)
sample_list = []
if samples:
(barcode_samples, location_samples) = \
self.dc_tree_widget.samples_from_lims(samples)
sc_content = self.get_sc_content()
sc_sample_list = self.dc_tree_widget.\
samples_from_sc_content(sc_content)
for sc_sample in sc_sample_list:
# Get the sample in lims with the barcode
# sc_sample.code
lims_sample = barcode_samples.get(sc_sample.code)
# There was a sample with that barcode
if lims_sample:
if lims_sample.lims_location == sc_sample.location:
logging.getLogger("user_level_log").\
warning("Found sample in ISPyB for location %s" % str(sc_sample.location))
sample_list.append(lims_sample)
else:
logging.getLogger("user_level_log").\
warning("The sample with the barcode (%s) exists"+\
" in LIMS but the location does not mat" +\
"ch. Sample changer location: %s, LIMS " +\
"location %s" % (sc_sample.code,
sc_sample.location,
lims_sample.lims_location))
sample_list.append(sc_sample)
else: # No sample with that barcode, continue with location
lims_sample = location_samples.get(sc_sample.location)
if lims_sample:
if lims_sample.lims_code:
logging.getLogger("user_level_log").\
warning("The sample has a barcode in LIMS, but "+\
"the SC has no barcode information for "+\
"this sample. For location: %s" % str(sc_sample.location))
sample_list.append(lims_sample)
else:
logging.getLogger("user_level_log").\
warning("Found sample in ISPyB for location %s" % str(sc_sample.location))
sample_list.append(lims_sample)
else:
if lims_sample:
if lims_sample.lims_location != (None, None):
logging.getLogger("user_level_log").\
warning("No barcode was provided in ISPyB "+\
"which makes it impossible to verify if"+\
"the locations are correct, assuming "+\
"that the positions are correct.")
sample_list.append(lims_sample)
else:
logging.getLogger("user_level_log").\
warning("No sample in ISPyB for location %s" % str(sc_sample.location))
sample_list.append(sc_sample)
self.dc_tree_widget.populate_list_view(sample_list)
def get_sc_content(self):
"""
Gets the 'raw' data from the sample changer.
:returns: A list with tuples, containing the sample information.
"""
sc_content = []
try:
sc_content = self.sample_changer_hwobj.getMatrixCodes()
except Exception:
logging.getLogger("user_level_log").\
info("Could not connect to sample changer," + \
" unable to list contents. Make sure that" + \
" the sample changer is turned on. Using free pin mode")
sc_content = [('', -1, -1, '', 1)]
#self.dc_tree_widget.init_with_sc_content(sc_content)
#self.dc_tree_widget.filter_sample_list(SC_FILTER_OPTIONS.FREE_PIN)
#self.sample_changer_widget.filter_cbox.\
# setCurrentItem(SC_FILTER_OPTIONS.FREE_PIN)
return sc_content
def status_msg_changed(self, msg, color):
"""
Status message from the SampleChangerBrick.
:param msg: The message
:type msg: str
:returns: None
"""
logging.getLogger("user_level_log").info(msg)
def set_sample_pin_icon(self, matrices):
"""
Updates the location of the sample pin when the
matrix code information changes. The matrix code information
is updated, but not exclusively, when a sample is changed.
"""
self.dc_tree_widget.set_sample_pin_icon()
def sample_load_state_changed(self, state):
"""
The state in the sample loading procedure changed.
Ie from Loading to mounted
:param state: str (Enumerable)
:returns: None
"""
s_color = SC_STATE_COLOR.get(state, "UNKNOWN")
self.sample_changer_widget.child('details_button').\
setPaletteBackgroundColor(qt.QColor(s_color))
def show_sample_centring_tab(self):
self.sample_changer_widget.child('details_button').setText("Show SC-details")
self.emit(qt.PYSIGNAL("hide_dc_parameters_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_dcg_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_sample_centring_tab"), (False,))
self.emit(qt.PYSIGNAL("hide_sample_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_sample_changer_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_edna_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_energy_scan_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_workflow_tab"), (True,))
def show_sample_tab(self, item):
self.sample_changer_widget.child('details_button').setText("Show SC-details")
self.emit(qt.PYSIGNAL("hide_dc_parameters_tab"), (True,))
self.emit(qt.PYSIGNAL("populate_sample_details"), (item.get_model(),))
self.emit(qt.PYSIGNAL("hide_dcg_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_sample_centring_tab"), (False,))
self.emit(qt.PYSIGNAL("hide_sample_tab"), (False,))
self.emit(qt.PYSIGNAL("hide_sample_changer_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_edna_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_energy_scan_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_workflow_tab"), (True,))
def show_dcg_tab(self):
self.sample_changer_widget.child('details_button').setText("Show SC-details")
self.emit(qt.PYSIGNAL("hide_dc_parameters_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_dcg_tab"), (False,))
self.emit(qt.PYSIGNAL("hide_sample_changer_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_edna_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_sample_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_energy_scan_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_workflow_tab"), (True,))
def populate_parameters_tab(self, item = None):
self.emit(qt.PYSIGNAL("populate_parameter_widget"),
(item,))
def show_datacollection_tab(self, item):
self.sample_changer_widget.child('details_button').setText("Show SC-details")
self.emit(qt.PYSIGNAL("hide_dcg_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_dc_parameters_tab"), (False,))
self.emit(qt.PYSIGNAL("hide_sample_changer_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_edna_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_sample_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_energy_scan_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_workflow_tab"), (True,))
self.populate_parameters_tab(item)
def show_edna_tab(self, item):
self.sample_changer_widget.child('details_button').setText("Show SC-details")
self.emit(qt.PYSIGNAL("hide_dcg_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_dc_parameters_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_sample_changer_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_edna_tab"), (False,))
self.emit(qt.PYSIGNAL("hide_sample_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_energy_scan_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_workflow_tab"), (True,))
self.populate_edna_parameters_tab(item)
def populate_edna_parameters_tab(self, item):
self.emit(qt.PYSIGNAL("populate_edna_parameter_widget"),
(item,))
def show_energy_scan_tab(self, item):
self.sample_changer_widget.child('details_button').setText("Show SC-details")
self.emit(qt.PYSIGNAL("hide_dcg_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_dc_parameters_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_sample_changer_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_edna_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_sample_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_energy_scan_tab"), (False,))
self.emit(qt.PYSIGNAL("hide_workflow_tab"), (True,))
self.populate_energy_scan_tab(item)
def populate_energy_scan_tab(self, item):
self.emit(qt.PYSIGNAL("populate_energy_scan_widget"), (item,))
def show_workflow_tab_from_model(self):
self.show_workflow_tab(None)
def show_workflow_tab(self, item):
self.sample_changer_widget.child('details_button').setText("Show SC-details")
self.emit(qt.PYSIGNAL("hide_dcg_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_dc_parameters_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_sample_changer_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_edna_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_sample_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_energy_scan_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_workflow_tab"), (False,))
running = self.queue_hwobj.is_executing()
self.populate_workflow_tab(item, running=running)
def populate_workflow_tab(self, item, running = False):
self.emit(qt.PYSIGNAL("populate_workflow_tab"), (item, running))
def toggle_sample_changer_tab(self):
if self.current_view is self.sample_changer_widget:
self.current_view = None
self.emit(qt.PYSIGNAL("hide_sample_changer_tab"), (True,))
self.dc_tree_widget.sample_list_view_selection()
self.sample_changer_widget.child('details_button').setText("Show SC-details")
else:
self.current_view = self.sample_changer_widget
self.emit(qt.PYSIGNAL("hide_dc_parameters_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_dcg_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_sample_changer_tab"), (False,))
self.sample_changer_widget.child('details_button').setText("Hide SC-details")
self.emit(qt.PYSIGNAL("hide_sample_tab"), (True,))
def selection_changed(self, items):
if len(items) == 1:
item = items[0]
if isinstance(item, queue_item.SampleQueueItem):
self.emit(qt.PYSIGNAL("populate_sample_details"), (item.get_model(),))
self.emit_set_sample(item)
self.emit_set_directory()
self.emit_set_prefix(item)
#self.populate_edna_parameter_widget(item)
elif isinstance(item, queue_item.DataCollectionQueueItem):
self.populate_parameters_tab(item)
elif isinstance(item, queue_item.CharacterisationQueueItem):
self.populate_edna_parameters_tab(item)
elif isinstance(item, queue_item.EnergyScanQueueItem):
self.populate_energy_scan_tab(item)
elif isinstance(item, queue_item.GenericWorkflowQueueItem):
self.populate_workflow_tab(item)
self.emit(qt.PYSIGNAL("selection_changed"), (items,))
def emit_set_directory(self):
directory = self.session_hwobj.get_base_image_directory()
self.emit(qt.PYSIGNAL("set_directory"), (directory,))
def emit_set_prefix(self, item):
prefix = self.session_hwobj.get_default_prefix(item.get_model())
self.emit(qt.PYSIGNAL("set_prefix"), (prefix,))
def emit_set_sample(self, item):
self.emit(qt.PYSIGNAL("set_sample"), (item,))
def get_selected_items(self):
items = self.dc_tree_widget.get_selected_items()
return items
def add_to_queue(self, task_list, parent_tree_item = None, set_on = True):
if not parent_tree_item :
parent_tree_item = self.dc_tree_widget.get_mounted_sample_item()
self.dc_tree_widget.add_to_queue(task_list, parent_tree_item, set_on)
def __init__(self, *args):
BaseComponents.BlissWidget.__init__(self, *args)
# Internal members
self.current_cpos = None
self.__collection_stopped = False
self.current_view = None
# Framework 2 hardware objects
self._lims_hwobj = None
self.sample_changer = None
self.plate_manipulator_hwobj = None
self.queue_hwobj = None
# Properties
self.addProperty("holderLengthMotor", "string", "")
self.addProperty("queue", "string", "/queue")
self.addProperty("default_centring_method", "integer", 1)
self.addProperty("queue_model", "string", "/queue-model")
self.addProperty("beamline_setup", "string", "/beamline-setup")
self.addProperty("xml_rpc_server", "string", "/xml_rpc_server")
# Qt - Slots
# From ProposalBrick2
self.defineSlot("logged_in", ())
# Used from TaskToolBoxBrick
self.defineSlot("get_tree_brick", ())
self.defineSlot("get_selected_samples", ())
# From SampleChangerBrick3, signal emitted when
# the status of the hwobj changes.
self.defineSlot("status_msg_changed", ())
# From sample changer hwobj, emitted when the
# load state changes.
self.defineSlot("sample_load_state_changed", ())
# self.defineSlot("get_mounted_sample", ())
# self.defineSlot("new_centred_position", ())
# self.defineSlot("add_dcg", ())
# self.defineSlot("add_data_collection", ())
# self.defineSlot("set_session", ())
# Qt - Signals
self.defineSignal("enable_hutch_menu", ())
self.defineSignal("enable_command_menu", ())
self.defineSignal("enable_task_toolbox", ())
# Hiding and showing the tabs
self.defineSignal("hide_sample_tab", ())
self.defineSignal("hide_dc_parameters_tab", ())
self.defineSignal("hide_sample_centring_tab", ())
self.defineSignal("hide_dcg_tab", ())
self.defineSignal("hide_sample_changer_tab", ())
self.defineSignal("hide_edna_tab", ())
self.defineSignal("hide_energy_scan_tab", ())
self.defineSignal("hide_xrf_spectrum_tab", ())
self.defineSignal("hide_workflow_tab", ())
# Populating the tabs with data
self.defineSignal("populate_parameter_widget", ())
self.defineSignal("populate_edna_parameter_widget", ())
self.defineSignal("populate_sample_details", ())
self.defineSignal("populate_energy_scan_widget", ())
self.defineSignal("populate_xrf_spectrum_widget", ())
self.defineSignal("populate_workflow_tab", ())
# Handle selection
self.defineSignal("selection_changed", ())
self.defineSignal("set_directory", ())
self.defineSignal("set_prefix", ())
self.defineSignal("set_sample", ())
# self.defineSignal("clear_centred_positions", ())
# Layout
# self.setSizePolicy(qt.QSizePolicy(qt.QSizePolicy.Fixed,
# qt.QSizePolicy.Expanding))
widget = qtui.QWidgetFactory.create(
os.path.join(
os.path.dirname(__file__),
"widgets/ui_files/sample_changer_widget_layout.ui",
))
widget.reparent(self, qt.QPoint(0, 0))
self.sample_changer_widget = widget
self.refresh_pixmap = Icons.load("Refresh2.png")
self.sample_changer_widget.child("synch_button").setIconSet(
qt.QIconSet(self.refresh_pixmap))
self.sample_changer_widget.child("synch_button").setText("Synch ISPyB")
self.dc_tree_widget = DataCollectTree(self)
self.dc_tree_widget.selection_changed_cb = self.selection_changed
self.dc_tree_widget.run_cb = self.run
# self.dc_tree_widget.clear_centred_positions_cb = \
# self.clear_centred_positions
qt.QObject.connect(
self.sample_changer_widget.child("details_button"),
qt.SIGNAL("clicked()"),
self.toggle_sample_changer_tab,
)
qt.QObject.connect(
self.sample_changer_widget.child("filter_cbox"),
qt.SIGNAL("activated(int)"),
self.dc_tree_widget.filter_sample_list,
)
qt.QObject.connect(
self.sample_changer_widget.child("centring_cbox"),
qt.SIGNAL("activated(int)"),
self.dc_tree_widget.set_centring_method,
)
qt.QObject.connect(
self.sample_changer_widget.child("synch_button"),
qt.SIGNAL("clicked()"),
self.refresh_sample_list,
)
vlayout = qt.QVBoxLayout(self, 0, 0, "main_layout")
vlayout.setSpacing(10)
self.layout().addWidget(self.sample_changer_widget)
self.layout().addWidget(self.dc_tree_widget)
self.enable_collect(False)
self.sample_changer_widget.child("centring_cbox").setCurrentItem(1)
self.dc_tree_widget.set_centring_method(1)
class TreeBrick(BaseComponents.BlissWidget):
def __init__(self, *args):
BaseComponents.BlissWidget.__init__(self, *args)
# Internal members
self.current_cpos = None
self.__collection_stopped = False
self.current_view = None
# Framework 2 hardware objects
self._lims_hwobj = None
self.sample_changer = None
self.plate_manipulator_hwobj = None
self.queue_hwobj = None
# Properties
self.addProperty("holderLengthMotor", "string", "")
self.addProperty("queue", "string", "/queue")
self.addProperty("default_centring_method", "integer", 1)
self.addProperty("queue_model", "string", "/queue-model")
self.addProperty("beamline_setup", "string", "/beamline-setup")
self.addProperty("xml_rpc_server", "string", "/xml_rpc_server")
# Qt - Slots
# From ProposalBrick2
self.defineSlot("logged_in", ())
# Used from TaskToolBoxBrick
self.defineSlot("get_tree_brick", ())
self.defineSlot("get_selected_samples", ())
# From SampleChangerBrick3, signal emitted when
# the status of the hwobj changes.
self.defineSlot("status_msg_changed", ())
# From sample changer hwobj, emitted when the
# load state changes.
self.defineSlot("sample_load_state_changed", ())
# self.defineSlot("get_mounted_sample", ())
# self.defineSlot("new_centred_position", ())
# self.defineSlot("add_dcg", ())
# self.defineSlot("add_data_collection", ())
# self.defineSlot("set_session", ())
# Qt - Signals
self.defineSignal("enable_hutch_menu", ())
self.defineSignal("enable_command_menu", ())
self.defineSignal("enable_task_toolbox", ())
# Hiding and showing the tabs
self.defineSignal("hide_sample_tab", ())
self.defineSignal("hide_dc_parameters_tab", ())
self.defineSignal("hide_sample_centring_tab", ())
self.defineSignal("hide_dcg_tab", ())
self.defineSignal("hide_sample_changer_tab", ())
self.defineSignal("hide_edna_tab", ())
self.defineSignal("hide_energy_scan_tab", ())
self.defineSignal("hide_xrf_spectrum_tab", ())
self.defineSignal("hide_workflow_tab", ())
# Populating the tabs with data
self.defineSignal("populate_parameter_widget", ())
self.defineSignal("populate_edna_parameter_widget", ())
self.defineSignal("populate_sample_details", ())
self.defineSignal("populate_energy_scan_widget", ())
self.defineSignal("populate_xrf_spectrum_widget", ())
self.defineSignal("populate_workflow_tab", ())
# Handle selection
self.defineSignal("selection_changed", ())
self.defineSignal("set_directory", ())
self.defineSignal("set_prefix", ())
self.defineSignal("set_sample", ())
# self.defineSignal("clear_centred_positions", ())
# Layout
# self.setSizePolicy(qt.QSizePolicy(qt.QSizePolicy.Fixed,
# qt.QSizePolicy.Expanding))
widget = qtui.QWidgetFactory.create(
os.path.join(
os.path.dirname(__file__),
"widgets/ui_files/sample_changer_widget_layout.ui",
))
widget.reparent(self, qt.QPoint(0, 0))
self.sample_changer_widget = widget
self.refresh_pixmap = Icons.load("Refresh2.png")
self.sample_changer_widget.child("synch_button").setIconSet(
qt.QIconSet(self.refresh_pixmap))
self.sample_changer_widget.child("synch_button").setText("Synch ISPyB")
self.dc_tree_widget = DataCollectTree(self)
self.dc_tree_widget.selection_changed_cb = self.selection_changed
self.dc_tree_widget.run_cb = self.run
# self.dc_tree_widget.clear_centred_positions_cb = \
# self.clear_centred_positions
qt.QObject.connect(
self.sample_changer_widget.child("details_button"),
qt.SIGNAL("clicked()"),
self.toggle_sample_changer_tab,
)
qt.QObject.connect(
self.sample_changer_widget.child("filter_cbox"),
qt.SIGNAL("activated(int)"),
self.dc_tree_widget.filter_sample_list,
)
qt.QObject.connect(
self.sample_changer_widget.child("centring_cbox"),
qt.SIGNAL("activated(int)"),
self.dc_tree_widget.set_centring_method,
)
qt.QObject.connect(
self.sample_changer_widget.child("synch_button"),
qt.SIGNAL("clicked()"),
self.refresh_sample_list,
)
vlayout = qt.QVBoxLayout(self, 0, 0, "main_layout")
vlayout.setSpacing(10)
self.layout().addWidget(self.sample_changer_widget)
self.layout().addWidget(self.dc_tree_widget)
self.enable_collect(False)
self.sample_changer_widget.child("centring_cbox").setCurrentItem(1)
self.dc_tree_widget.set_centring_method(1)
# Framework 2 method
def run(self):
self.emit(qt.PYSIGNAL("hide_dc_parameters_tab"), (True, ))
self.emit(qt.PYSIGNAL("hide_dcg_tab"), (True, ))
self.emit(qt.PYSIGNAL("hide_sample_centring_tab"), (False, ))
self.emit(qt.PYSIGNAL("hide_edna_tab"), (True, ))
self.emit(qt.PYSIGNAL("hide_sample_changer_tab"), (True, ))
self.emit(qt.PYSIGNAL("hide_sample_tab"), (True, ))
self.emit(qt.PYSIGNAL("hide_energy_scan_tab"), (True, ))
self.emit(qt.PYSIGNAL("hide_xrf_spectrum_tab"), (True, ))
self.emit(qt.PYSIGNAL("hide_workflow_tab"), (True, ))
def eventFilter(self, _object, event):
if event.type() == qt.QEvent.MouseButtonPress:
if event.state() & qt.Qt.ShiftButton:
return True
return False
# Framework 2 method
def propertyChanged(self, property_name, old_value, new_value):
if property_name == "holder_length_motor":
self.dc_tree_widget.hl_motor_hwobj = self.getHardwareObject(
new_value)
elif property_name == "default_centring_method":
self.sample_changer_widget.child("centring_cbox").setCurrentItem(
new_value)
self.dc_tree_widget.set_centring_method(new_value)
elif property_name == "queue":
self.queue_hwobj = self.getHardwareObject(new_value)
self.dc_tree_widget.queue_hwobj = self.queue_hwobj
self.connect(self.queue_hwobj, "show_workflow_tab",
self.show_workflow_tab_from_model)
self.connect(
self.queue_hwobj,
"queue_paused",
self.dc_tree_widget.queue_paused_handler,
)
self.connect(
self.queue_hwobj,
"queue_execution_finished",
self.dc_tree_widget.queue_execution_completed,
)
self.connect(
self.queue_hwobj,
"queue_stopped",
self.dc_tree_widget.queue_stop_handler,
)
elif property_name == "queue_model":
self.queue_model_hwobj = self.getHardwareObject(new_value)
self.dc_tree_widget.queue_model_hwobj = self.queue_model_hwobj
self.dc_tree_widget.confirm_dialog.queue_model_hwobj = (
self.queue_model_hwobj)
self.connect(self.queue_model_hwobj, "child_added",
self.dc_tree_widget.add_to_view)
elif property_name == "beamline_setup":
bl_setup = self.getHardwareObject(new_value)
self.beamline_config_hwobj = bl_setup
self.dc_tree_widget.beamline_setup_hwobj = bl_setup
self.sample_changer_hwobj = bl_setup.sample_changer_hwobj
try:
self.plate_manipulator_hwobj = bl_setup.plate_manipulator_hwobj
except AttributeError:
self.plate_manipulator_hwobj = None
self.dc_tree_widget.sample_changer_hwobj = self.sample_changer_hwobj
self.dc_tree_widget.plate_manipulator_hwobj = self.plate_manipulator_hwobj
self.session_hwobj = bl_setup.session_hwobj
self._lims_hwobj = bl_setup.lims_client_hwobj
if self.sample_changer_hwobj is not None:
self.connect(
self.sample_changer_hwobj,
SampleChanger.STATE_CHANGED_EVENT,
self.sample_load_state_changed,
)
self.connect(
self.sample_changer_hwobj,
SampleChanger.INFO_CHANGED_EVENT,
self.set_sample_pin_icon,
)
if self.plate_manipulator_hwobj is not None:
self.connect(
self.plate_manipulator_hwobj,
SampleChanger.STATE_CHANGED_EVENT,
self.sample_load_state_changed,
)
self.connect(
self.plate_manipulator_hwobj,
SampleChanger.INFO_CHANGED_EVENT,
self.set_sample_pin_icon,
)
has_shutter_less = bl_setup.detector_has_shutterless()
if has_shutter_less:
self.dc_tree_widget.confirm_dialog.disable_dark_current_cbx()
elif property_name == "xml_rpc_server":
xml_rpc_server_hwobj = self.getHardwareObject(new_value)
if xml_rpc_server_hwobj:
self.connect(xml_rpc_server_hwobj, "add_to_queue",
self.add_to_queue)
self.connect(
xml_rpc_server_hwobj,
"start_queue",
self.dc_tree_widget.collect_items,
)
def set_session(
self,
session_id,
t_prop_code=None,
prop_number=None,
prop_id=None,
start_date=None,
prop_code=None,
is_inhouse=None,
):
self.session_hwobj.set_session_start_date(start_date)
def logged_in_old_version(self, logged_in):
"""
Reomve this method if logged_in finalized
Connected to the signal loggedIn of ProposalBrick2.
The signal is emitted when a user was succesfully logged in.
"""
self.enable_collect(logged_in)
if not logged_in:
self.dc_tree_widget.populate_free_pin()
else:
sc_basket_content, sc_sample_content = self.get_sc_content()
if sc_basket_content and sc_sample_content:
sc_basket_list, sc_sample_list = self.dc_tree_widget.samples_from_sc_content(
sc_basket_content, sc_sample_content)
self.dc_tree_widget.populate_list_view(sc_basket_list,
sc_sample_list)
self.sample_changer_widget.child("filter_cbox").setCurrentItem(
0)
if sc_basket_content:
sc_basket_list, sc_sample_list = self.dc_tree_widget.samples_from_sc_content(
sc_basket_content, sc_sample_content)
self.dc_tree_widget.populate_list_view(
sc_basket_list, sc_sample_list)
self.sample_changer_widget.child("filter_cbox").setCurrentItem(
0)
else:
self.sample_changer_widget.child("filter_cbox").setCurrentItem(
2)
# if self.sample_changer_hwobj:
# if not self.sample_changer_hwobj.hasLoadedSample():
self.dc_tree_widget.sample_list_view_selection()
def logged_in(self, logged_in):
"""
Connected to the signal loggedIn of ProposalBrick2.
The signal is emitted when a user was succesfully logged in.
"""
self.enable_collect(logged_in)
plate_sample_content = None
sc_basket_content = None
sc_sample_content = None
if not logged_in:
self.dc_tree_widget.populate_free_pin()
self.sample_changer_widget.child("filter_cbox").setCurrentItem(2)
self.dc_tree_widget.beamline_setup_hwobj.set_plate_mode(False)
sc_basket_content, sc_sample_content = self.get_sc_content()
if sc_basket_content and sc_sample_content:
sc_basket_list, sc_sample_list = self.dc_tree_widget.samples_from_sc_content(
sc_basket_content, sc_sample_content)
self.dc_tree_widget.populate_list_view(sc_basket_list,
sc_sample_list)
self.sample_changer_widget.child("filter_cbox").setCurrentItem(0)
if (self.dc_tree_widget.beamline_setup_hwobj.diffractometer_hwobj.
in_plate_mode()):
plate_sample_content = self.get_plate_content()
self.dc_tree_widget.beamline_setup_hwobj.set_plate_mode(True)
if plate_sample_content:
self.dc_tree_widget.beamline_setup_hwobj.set_plate_mode(
True)
plate_row_list, plate_sample_list = self.dc_tree_widget.samples_from_plate_content(
plate_sample_content)
self.dc_tree_widget.populate_plate_view(
plate_row_list, plate_sample_list)
self.sample_changer_widget.child(
"filter_cbox").setCurrentItem(3)
self.dc_tree_widget.sample_list_view_selection()
self.dc_tree_widget.set_sample_pin_icon()
def enable_collect(self, state):
"""
Enables the collect controls.
:param state: Enable if state is True and disable if False
:type state: bool
:returns: None
"""
self.dc_tree_widget.enable_collect(state)
def enable_hutch_menu(self, state):
self.emit(qt.PYSIGNAL("enable_hutch_menu"), (state, ))
def enable_command_menu(self, state):
self.emit(qt.PYSIGNAL("enable_command_menu"), (state, ))
def enable_task_toolbox(self, state):
self.emit(qt.PYSIGNAL("enable_task_toolbox"), (state, ))
def get_tree_brick(self, tree_brick):
"""
Gets the reference to the tree brick. Used to get a reference from
another brick via the signal get_tree_brick. The attribute tree_brick
of the passed dictionary will contain the reference.
:param tree_brick: A dictonary to contain the reference.
:type tree_brick: dict
:returns: None
"""
tree_brick["tree_brick"] = self
def samples_from_lims(self, samples):
barcode_samples, location_samples = self.dc_tree_widget.samples_from_lims(
samples)
l_samples = dict()
if self.sample_changer_hwobj.__class__.__TYPE__ == "Robodiff":
for location, l_sample in location_samples.iteritems():
if l_sample.lims_location != (None, None):
basket, sample = l_sample.lims_location
cell = int(round((basket + 0.5) / 3.0))
puck = basket - 3 * (cell - 1)
new_location = (cell, puck, sample)
l_sample.lims_location = new_location
l_samples[new_location] = l_sample
name = l_sample.get_name()
l_sample.init_from_sc_sample([new_location])
l_sample.set_name(name)
else:
l_samples.update(location_samples)
return barcode_samples, l_samples
def refresh_sample_list(self):
"""
Retrives sample information from ISPyB and populates the sample list
accordingly.
"""
lims_client = self._lims_hwobj
samples = lims_client.get_samples(self.session_hwobj.proposal_id,
self.session_hwobj.session_id)
sample_list = []
if samples:
(barcode_samples,
location_samples) = self.samples_from_lims(samples)
sc_basket_content, sc_samples_content = self.get_sc_content()
sc_basket_list, sc_sample_list = self.dc_tree_widget.samples_from_sc_content(
sc_basket_content, sc_samples_content)
basket_list = sc_basket_list
for sc_sample in sc_sample_list:
# Get the sample in lims with the barcode
# sc_sample.code
lims_sample = barcode_samples.get(sc_sample.code)
# There was a sample with that barcode
if lims_sample:
if lims_sample.lims_location == sc_sample.location:
logging.getLogger("user_level_log").warning(
"Found sample in ISPyB for location %s" %
str(sc_sample.location))
sample_list.append(lims_sample)
else:
logging.getLogger("user_level_log").warning(
"The sample with the barcode (%s) exists" +
" in LIMS but the location does not mat" +
"ch. Sample changer location: %s, LIMS " +
"location %s" % (
sc_sample.code,
sc_sample.location,
lims_sample.lims_location,
))
sample_list.append(sc_sample)
else: # No sample with that barcode, continue with location
lims_sample = location_samples.get(sc_sample.location)
if lims_sample:
if lims_sample.lims_code:
logging.getLogger("user_level_log").warning(
"The sample has a barcode in LIMS, but " +
"the SC has no barcode information for " +
"this sample. For location: %s" %
str(sc_sample.location))
sample_list.append(lims_sample)
else:
logging.getLogger("user_level_log").warning(
"Found sample in ISPyB for location %s" %
str(sc_sample.location))
sample_list.append(lims_sample)
else:
if lims_sample:
if lims_sample.lims_location is not None:
logging.getLogger("user_level_log").warning(
"No barcode was provided in ISPyB " +
"which makes it impossible to verify if" +
"the locations are correct, assuming " +
"that the positions are correct.")
sample_list.append(lims_sample)
else:
logging.getLogger("user_level_log").warning(
"No sample in ISPyB for location %s" %
str(sc_sample.location))
sample_list.append(sc_sample)
self.dc_tree_widget.populate_list_view(basket_list, sample_list)
def get_sc_content(self):
"""
Gets the 'raw' data from the sample changer.
:returns: A list with tuples, containing the sample information.
"""
sc_basket_content = []
sc_sample_content = []
try:
for basket in self.sample_changer_hwobj.getBasketList():
basket_index = basket.getIndex()
basket_code = basket.getID() or ""
is_present = basket.isPresent()
# basket_code, is_present))
sc_basket_content.append((basket_index + 1, basket))
for sample in self.sample_changer_hwobj.getSampleList():
coords = sample.getCoords()
matrix = sample.getID() or ""
basket_index = str(coords[0])
vial_index = ":".join(map(str, coords[1:]))
basket_code = sample.getContainer().getID() or ""
sc_sample_content.append(
(matrix, basket_index, vial_index, basket_code, 0, coords))
except BaseException:
logging.getLogger("user_level_log").info(
"Could not connect to sample changer," +
" unable to list contents. Make sure that" +
" the sample changer is turned on. Using free pin mode")
return sc_basket_content, sc_sample_content
def get_plate_content(self):
"""
"""
plate_sample_content = []
for sample in self.plate_manipulator_hwobj.getSampleList():
row_index = sample.getCell().getRowIndex()
col_index = sample.getCell().getCol()
coords = sample.getCoords()
matrix = sample.getID() or ""
vial_index = ":".join(map(str, coords[1:]))
plate_sample_content.append(
(matrix, row_index, col_index, coords[1], 0, coords))
return plate_sample_content
def status_msg_changed(self, msg, color):
"""
Status message from the SampleChangerBrick.
:param msg: The message
:type msg: str
:returns: None
"""
logging.getLogger("user_level_log").info(msg)
def set_sample_pin_icon(self):
"""
Updates the location of the sample pin when the
matrix code information changes. The matrix code information
is updated, but not exclusively, when a sample is changed.
"""
self.dc_tree_widget.set_sample_pin_icon()
def sample_load_state_changed(self, state, *args):
"""
The state in the sample loading procedure changed.
Ie from Loading to mounted
:param state: str (Enumerable)
:returns: None
"""
s_color = SC_STATE_COLOR.get(state, "UNKNOWN")
self.sample_changer_widget.child(
"details_button").setPaletteBackgroundColor(qt.QColor(s_color))
def show_sample_centring_tab(self):
self.sample_changer_widget.child("details_button").setText(
"Show SC-details")
self.emit(qt.PYSIGNAL("hide_dc_parameters_tab"), (True, ))
self.emit(qt.PYSIGNAL("hide_dcg_tab"), (True, ))
self.emit(qt.PYSIGNAL("hide_sample_centring_tab"), (False, ))
self.emit(qt.PYSIGNAL("hide_sample_tab"), (True, ))
self.emit(qt.PYSIGNAL("hide_sample_changer_tab"), (True, ))
self.emit(qt.PYSIGNAL("hide_edna_tab"), (True, ))
self.emit(qt.PYSIGNAL("hide_energy_scan_tab"), (True, ))
self.emit(qt.PYSIGNAL("hide_xrf_spectrum_tab"), (True, ))
self.emit(qt.PYSIGNAL("hide_workflow_tab"), (True, ))
def show_sample_tab(self, item):
self.sample_changer_widget.child("details_button").setText(
"Show SC-details")
self.emit(qt.PYSIGNAL("hide_dc_parameters_tab"), (True, ))
self.emit(qt.PYSIGNAL("populate_sample_details"), (item.get_model(), ))
self.emit(qt.PYSIGNAL("hide_dcg_tab"), (True, ))
self.emit(qt.PYSIGNAL("hide_sample_centring_tab"), (False, ))
self.emit(qt.PYSIGNAL("hide_sample_tab"), (False, ))
self.emit(qt.PYSIGNAL("hide_sample_changer_tab"), (True, ))
self.emit(qt.PYSIGNAL("hide_edna_tab"), (True, ))
self.emit(qt.PYSIGNAL("hide_energy_scan_tab"), (True, ))
self.emit(qt.PYSIGNAL("hide_xrf_spectrum_tab"), (True, ))
self.emit(qt.PYSIGNAL("hide_workflow_tab"), (True, ))
def show_dcg_tab(self):
self.sample_changer_widget.child("details_button").setText(
"Show SC-details")
self.emit(qt.PYSIGNAL("hide_dc_parameters_tab"), (True, ))
self.emit(qt.PYSIGNAL("hide_dcg_tab"), (False, ))
self.emit(qt.PYSIGNAL("hide_sample_changer_tab"), (True, ))
self.emit(qt.PYSIGNAL("hide_edna_tab"), (True, ))
self.emit(qt.PYSIGNAL("hide_sample_tab"), (True, ))
self.emit(qt.PYSIGNAL("hide_energy_scan_tab"), (True, ))
self.emit(qt.PYSIGNAL("hide_xrf_spectrum_tab"), (True, ))
self.emit(qt.PYSIGNAL("hide_workflow_tab"), (True, ))
def populate_parameters_tab(self, item=None):
self.emit(qt.PYSIGNAL("populate_parameter_widget"), (item, ))
def show_datacollection_tab(self, item):
self.sample_changer_widget.child("details_button").setText(
"Show SC-details")
self.emit(qt.PYSIGNAL("hide_dcg_tab"), (True, ))
self.emit(qt.PYSIGNAL("hide_dc_parameters_tab"), (False, ))
self.emit(qt.PYSIGNAL("hide_sample_changer_tab"), (True, ))
self.emit(qt.PYSIGNAL("hide_edna_tab"), (True, ))
self.emit(qt.PYSIGNAL("hide_sample_tab"), (True, ))
self.emit(qt.PYSIGNAL("hide_energy_scan_tab"), (True, ))
self.emit(qt.PYSIGNAL("hide_xrf_spectrum_tab"), (True, ))
self.emit(qt.PYSIGNAL("hide_workflow_tab"), (True, ))
self.populate_parameters_tab(item)
def show_edna_tab(self, item):
self.sample_changer_widget.child("details_button").setText(
"Show SC-details")
self.emit(qt.PYSIGNAL("hide_dcg_tab"), (True, ))
self.emit(qt.PYSIGNAL("hide_dc_parameters_tab"), (True, ))
self.emit(qt.PYSIGNAL("hide_sample_changer_tab"), (True, ))
self.emit(qt.PYSIGNAL("hide_edna_tab"), (False, ))
self.emit(qt.PYSIGNAL("hide_sample_tab"), (True, ))
self.emit(qt.PYSIGNAL("hide_energy_scan_tab"), (True, ))
self.emit(qt.PYSIGNAL("hide_xrf_spectrum_tab"), (True, ))
self.emit(qt.PYSIGNAL("hide_workflow_tab"), (True, ))
self.populate_edna_parameters_tab(item)
def populate_edna_parameters_tab(self, item):
self.emit(qt.PYSIGNAL("populate_edna_parameter_widget"), (item, ))
def show_energy_scan_tab(self, item):
self.sample_changer_widget.child("details_button").setText(
"Show SC-details")
self.emit(qt.PYSIGNAL("hide_dcg_tab"), (True, ))
self.emit(qt.PYSIGNAL("hide_dc_parameters_tab"), (True, ))
self.emit(qt.PYSIGNAL("hide_sample_changer_tab"), (True, ))
self.emit(qt.PYSIGNAL("hide_edna_tab"), (True, ))
self.emit(qt.PYSIGNAL("hide_sample_tab"), (True, ))
self.emit(qt.PYSIGNAL("hide_energy_scan_tab"), (False, ))
self.emit(qt.PYSIGNAL("hide_xrf_spectrum_tab"), (True, ))
self.emit(qt.PYSIGNAL("hide_workflow_tab"), (True, ))
self.populate_energy_scan_tab(item)
def populate_energy_scan_tab(self, item):
self.emit(qt.PYSIGNAL("populate_energy_scan_widget"), (item, ))
def show_xrf_spectrum_tab(self, item):
self.sample_changer_widget.child("details_button").setText("Show SC")
self.emit(qt.PYSIGNAL("hide_dcg_tab"), (True, ))
self.emit(qt.PYSIGNAL("hide_dc_parameters_tab"), (True, ))
self.emit(qt.PYSIGNAL("hide_sample_changer_tab"), (True, ))
self.emit(qt.PYSIGNAL("hide_edna_tab"), (True, ))
self.emit(qt.PYSIGNAL("hide_sample_tab"), (True, ))
self.emit(qt.PYSIGNAL("hide_energy_scan_tab"), (True, ))
self.emit(qt.PYSIGNAL("hide_xrf_spectrum_tab"), (False, ))
self.emit(qt.PYSIGNAL("hide_workflow_tab"), (True, ))
self.populate_xrf_spectrum_tab(item)
def populate_xrf_spectrum_tab(self, item):
self.emit(qt.PYSIGNAL("populate_xrf_spectrum_widget"), (item, ))
def show_workflow_tab_from_model(self):
self.show_workflow_tab(None)
def show_workflow_tab(self, item):
self.sample_changer_widget.child("details_button").setText(
"Show SC-details")
self.emit(qt.PYSIGNAL("hide_dcg_tab"), (True, ))
self.emit(qt.PYSIGNAL("hide_dc_parameters_tab"), (True, ))
self.emit(qt.PYSIGNAL("hide_sample_changer_tab"), (True, ))
self.emit(qt.PYSIGNAL("hide_edna_tab"), (True, ))
self.emit(qt.PYSIGNAL("hide_sample_tab"), (True, ))
self.emit(qt.PYSIGNAL("hide_energy_scan_tab"), (True, ))
self.emit(qt.PYSIGNAL("hide_xrf_spectrum_tab"), (True, ))
self.emit(qt.PYSIGNAL("hide_workflow_tab"), (False, ))
running = self.queue_hwobj.is_executing()
self.populate_workflow_tab(item, running=running)
def populate_workflow_tab(self, item, running=False):
self.emit(qt.PYSIGNAL("populate_workflow_tab"), (item, running))
def toggle_sample_changer_tab(self):
if self.current_view == self.sample_changer_widget:
self.current_view = None
self.emit(qt.PYSIGNAL("hide_sample_changer_tab"), (True, ))
self.dc_tree_widget.sample_list_view_selection()
self.sample_changer_widget.child("details_button").setText(
"Show SC-details")
else:
self.current_view = self.sample_changer_widget
self.emit(qt.PYSIGNAL("hide_dc_parameters_tab"), (True, ))
self.emit(qt.PYSIGNAL("hide_dcg_tab"), (True, ))
self.emit(qt.PYSIGNAL("hide_sample_changer_tab"), (False, ))
self.sample_changer_widget.child("details_button").setText(
"Hide SC-details")
self.emit(qt.PYSIGNAL("hide_sample_tab"), (True, ))
def selection_changed(self, items):
if len(items) == 1:
item = items[0]
if isinstance(item, queue_item.SampleQueueItem):
self.emit(qt.PYSIGNAL("populate_sample_details"),
(item.get_model(), ))
self.emit_set_sample(item)
self.emit_set_directory()
self.emit_set_prefix(item)
# self.populate_edna_parameter_widget(item)
elif isinstance(item, queue_item.DataCollectionQueueItem):
self.populate_parameters_tab(item)
elif isinstance(item, queue_item.CharacterisationQueueItem):
self.populate_edna_parameters_tab(item)
elif isinstance(item, queue_item.EnergyScanQueueItem):
self.populate_energy_scan_tab(item)
elif isinstance(item, queue_item.XRFSpectrumQueueItem):
self.populate_xrf_spectrum_tab(item)
elif isinstance(item, queue_item.GenericWorkflowQueueItem):
self.populate_workflow_tab(item)
self.emit(qt.PYSIGNAL("selection_changed"), (items, ))
def emit_set_directory(self):
directory = self.session_hwobj.get_base_image_directory()
self.emit(qt.PYSIGNAL("set_directory"), (directory, ))
def emit_set_prefix(self, item):
prefix = self.session_hwobj.get_default_prefix(item.get_model())
self.emit(qt.PYSIGNAL("set_prefix"), (prefix, ))
def emit_set_sample(self, item):
self.emit(qt.PYSIGNAL("set_sample"), (item, ))
def get_selected_items(self):
items = self.dc_tree_widget.get_selected_items()
return items
def add_to_queue(self, task_list, parent_tree_item=None, set_on=True):
if not parent_tree_item:
parent_tree_item = self.dc_tree_widget.get_mounted_sample_item()
self.dc_tree_widget.add_to_queue(task_list, parent_tree_item, set_on)
class TreeBrick(BaseComponents.BlissWidget):
def __init__(self, *args):
BaseComponents.BlissWidget.__init__(self, *args)
# Internal members
self.current_cpos = None
self.__collection_stopped = False
self.current_view = None
# Framework 2 hardware objects
self.beamline_config_hwobj = None
self._lims_hwobj = None
self.sample_changer = None
self.queue_hwobj = None
# Properties
self.addProperty("holderLengthMotor", "string", "")
self.addProperty("queue", "string", "/queue")
self.addProperty("queue_model", "string", "/queue-model")
self.addProperty("beamline_setup", "string", "/beamline-setup")
self.addProperty("xml_rpc_server", "string", "/xml_rpc_server")
# Qt - Slots
# From ProposalBrick2
self.defineSlot("logged_in", ())
# Used from TaskToolBoxBrick
self.defineSlot("get_tree_brick",())
self.defineSlot("get_selected_samples", ())
# From SampleChangerBrick3, signal emitted when
# the status of the hwobj changes.
self.defineSlot("status_msg_changed", ())
# From sample changer hwobj, emitted when the
# load state changes.
self.defineSlot("sample_load_state_changed", ())
#self.defineSlot("get_mounted_sample", ())
#self.defineSlot("new_centred_position", ())
#self.defineSlot("add_dcg", ())
#self.defineSlot("add_data_collection", ())
#self.defineSlot("set_session", ())
# Qt - Signals
self.defineSignal("enable_hutch_menu", ())
self.defineSignal("enable_command_menu", ())
self.defineSignal("enable_task_toolbox", ())
# Hiding and showing the tabs
self.defineSignal("hide_sample_tab", ())
self.defineSignal("hide_dc_parameters_tab", ())
self.defineSignal("hide_sample_centring_tab", ())
self.defineSignal("hide_dcg_tab", ())
self.defineSignal("hide_sample_changer_tab", ())
self.defineSignal("hide_edna_tab", ())
self.defineSignal("hide_energy_scan_tab",())
self.defineSignal("hide_workflow_tab", ())
# Populating the tabs with data
self.defineSignal("populate_parameter_widget", ())
self.defineSignal("populate_edna_parameter_widget",())
self.defineSignal("populate_sample_details",())
self.defineSignal("populate_energy_scan_widget", ())
self.defineSignal("populate_workflow_tab", ())
# Handle selection
self.defineSignal("selection_changed",())
self.defineSignal("set_directory", ())
self.defineSignal("set_prefix", ())
self.defineSignal("set_sample", ())
#self.defineSignal("clear_centred_positions", ())
# Layout
#self.setSizePolicy(qt.QSizePolicy(qt.QSizePolicy.Fixed,
# qt.QSizePolicy.Expanding))
widget = qtui.QWidgetFactory.\
create(os.path.join(os.path.dirname(__file__),
'widgets/ui_files/sample_changer_widget_layout.ui'))
widget.reparent(self, qt.QPoint(0, 0))
self.sample_changer_widget = widget
self.refresh_pixmap = Icons.load("Refresh2.png")
self.sample_changer_widget.child('synch_button').\
setIconSet(qt.QIconSet(self.refresh_pixmap))
self.sample_changer_widget.child('synch_button').setText("Synch ISPyB")
self.dc_tree_widget = DataCollectTree(self)
self.dc_tree_widget.selection_changed_cb = self.selection_changed
self.dc_tree_widget.run_cb = self.run
#self.dc_tree_widget.clear_centred_positions_cb = \
# self.clear_centred_positions
qt.QObject.connect(self.sample_changer_widget.child('details_button'),
qt.SIGNAL("clicked()"),
self.toggle_sample_changer_tab)
qt.QObject.connect(self.sample_changer_widget.child('filter_cbox'),
qt.SIGNAL("activated(int)"),
self.dc_tree_widget.filter_sample_list)
qt.QObject.connect(self.sample_changer_widget.child('centring_cbox'),
qt.SIGNAL("activated(int)"),
self.dc_tree_widget.set_centring_method)
qt.QObject.connect(self.sample_changer_widget.child('synch_button'),
qt.SIGNAL("clicked()"),
self.refresh_sample_list)
vlayout = qt.QVBoxLayout(self, 0, 0, 'main_layout')
vlayout.setSpacing(10)
self.layout().addWidget(self.sample_changer_widget)
self.layout().addWidget(self.dc_tree_widget)
self.enable_collect(False)
self.sample_changer_widget.child('centring_cbox').setCurrentItem(1)
self.dc_tree_widget.set_centring_method(1)
# Framework 2 method
def run(self):
self.emit(qt.PYSIGNAL("hide_dc_parameters_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_dcg_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_sample_centring_tab"), (False,))
self.emit(qt.PYSIGNAL("hide_edna_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_sample_changer_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_sample_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_energy_scan_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_workflow_tab"), (True,))
camera_brick = None
for w in qt.QApplication.allWidgets():
if isinstance(w, BaseComponents.BlissWidget):
if "CameraBrick" in str(w.__class__):
camera_brick = w
camera_brick.installEventFilter(self)
break
# workaround for the remote access problem
# (have to disable video display when DC is running)
if BaseComponents.BlissWidget.isInstanceRoleClient():
# find the video brick, make sure it is hidden when collecting data
# and that it is shown again when DC is finished
def disable_video(w=camera_brick):
w.disable_update()
self.__disable_video=disable_video
def enable_video(w=camera_brick):
w.enable_update()
self.__enable_video=enable_video
dispatcher.connect(self.__disable_video, "collect_started")
dispatcher.connect(self.__enable_video, "collect_finished")
def eventFilter(self, _object, event):
if event.type() == qt.QEvent.MouseButtonPress:
if event.state() & qt.Qt.ShiftButton:
return True
return False
# Framework 2 method
def propertyChanged(self, property_name, old_value, new_value):
if property_name == 'holder_length_motor':
self.dc_tree_widget.hl_motor_hwobj = self.getHardwareObject(new_value)
elif property_name == 'queue':
self.queue_hwobj = self.getHardwareObject(new_value)
self.dc_tree_widget.queue_hwobj = self.queue_hwobj
self.connect(self.queue_hwobj, 'show_workflow_tab',
self.show_workflow_tab_from_model)
self.connect(self.queue_hwobj, 'queue_paused',
self.dc_tree_widget.queue_paused_handler)
self.connect(self.queue_hwobj, 'queue_execution_finished',
self.dc_tree_widget.queue_execution_completed)
self.connect(self.queue_hwobj, 'queue_stopped',
self.dc_tree_widget.queue_stop_handler)
elif property_name == 'queue_model':
self.queue_model_hwobj = self.getHardwareObject(new_value)
self.dc_tree_widget.queue_model_hwobj = self.queue_model_hwobj
self.dc_tree_widget.confirm_dialog.queue_model_hwobj = self.queue_model_hwobj
self.connect(self.queue_model_hwobj, 'child_added',
self.dc_tree_widget.add_to_view)
elif property_name == 'beamline_setup':
bl_setup = self.getHardwareObject(new_value)
self.dc_tree_widget.beamline_setup_hwobj = bl_setup
self.sample_changer_hwobj = bl_setup.sample_changer_hwobj
self.dc_tree_widget.sample_changer_hwobj = self.sample_changer_hwobj
self.session_hwobj = bl_setup.session_hwobj
self._lims_hwobj = bl_setup.lims_client_hwobj
if self.sample_changer_hwobj is not None:
self.connect(self.sample_changer_hwobj, SampleChanger.STATE_CHANGED_EVENT,
self.sample_load_state_changed)
self.connect(self.sample_changer_hwobj, SampleChanger.INFO_CHANGED_EVENT,
self.set_sample_pin_icon)
has_shutter_less = bl_setup.detector_has_shutterless()
if has_shutter_less:
self.dc_tree_widget.confirm_dialog.disable_dark_current_cbx()
elif property_name == 'xml_rpc_server':
xml_rpc_server_hwobj = self.getHardwareObject(new_value)
if xml_rpc_server_hwobj:
self.connect(xml_rpc_server_hwobj, 'add_to_queue',
self.add_to_queue)
self.connect(xml_rpc_server_hwobj, 'start_queue',
self.dc_tree_widget.collect_items)
def set_session(self, session_id, t_prop_code = None, prop_number = None,
prop_id = None, start_date = None, prop_code = None,
is_inhouse = None):
self.session_hwobj.set_session_start_date(start_date)
def logged_in(self, logged_in):
"""
Connected to the signal loggedIn of ProposalBrick2.
The signal is emitted when a user was succesfully logged in.
"""
self.enable_collect(logged_in)
if not logged_in:
self.dc_tree_widget.populate_free_pin()
sc_content = self.get_sc_content()
if sc_content:
sc_sample_list = self.dc_tree_widget.samples_from_sc_content(sc_content)
self.dc_tree_widget.populate_list_view(sc_sample_list)
self.sample_changer_widget.child('filter_cbox').setCurrentItem(0)
if not self.sample_changer_hwobj.hasLoadedSample():
self.dc_tree_widget.filter_sample_list(2)
self.sample_changer_widget.child('filter_cbox').setCurrentItem(2)
self.dc_tree_widget.sample_list_view_selection()
def enable_collect(self, state):
"""
Enables the collect controls.
:param state: Enable if state is True and disable if False
:type state: bool
:returns: None
"""
self.dc_tree_widget.enable_collect(state)
def enable_hutch_menu(self, state):
self.emit(qt.PYSIGNAL("enable_hutch_menu"), (state,))
def enable_command_menu(self, state):
self.emit(qt.PYSIGNAL("enable_command_menu"), (state,))
def enable_task_toolbox(self, state):
self.emit(qt.PYSIGNAL("enable_task_toolbox"), (state,))
def get_tree_brick(self, tree_brick):
"""
Gets the reference to the tree brick. Used to get a reference from
another brick via the signal get_tree_brick. The attribute tree_brick
of the passed dictionary will contain the reference.
:param tree_brick: A dictonary to contain the reference.
:type tree_brick: dict
:returns: None
"""
tree_brick['tree_brick'] = self
def refresh_sample_list(self):
"""
Retrives sample information from ISPyB and populates the sample list
accordingly.
"""
lims_client = self._lims_hwobj
samples = lims_client.get_samples(self.session_hwobj.proposal_id,
self.session_hwobj.session_id)
sample_list = []
if samples:
(barcode_samples, location_samples) = \
self.dc_tree_widget.samples_from_lims(samples)
sc_content = self.get_sc_content()
sc_sample_list = self.dc_tree_widget.\
samples_from_sc_content(sc_content)
for sc_sample in sc_sample_list:
# Get the sample in lims with the barcode
# sc_sample.code
lims_sample = barcode_samples.get(sc_sample.code)
# There was a sample with that barcode
if lims_sample:
if lims_sample.lims_location == sc_sample.location:
logging.getLogger("user_level_log").\
warning("Found sample in ISPyB for location %s" % str(sc_sample.location))
sample_list.append(lims_sample)
else:
logging.getLogger("user_level_log").\
warning("The sample with the barcode (%s) exists"+\
" in LIMS but the location does not mat" +\
"ch. Sample changer location: %s, LIMS " +\
"location %s" % (sc_sample.code,
sc_sample.location,
lims_sample.lims_location))
sample_list.append(sc_sample)
else: # No sample with that barcode, continue with location
lims_sample = location_samples.get(sc_sample.location)
if lims_sample:
if lims_sample.lims_code:
logging.getLogger("user_level_log").\
warning("The sample has a barcode in LIMS, but "+\
"the SC has no barcode information for "+\
"this sample. For location: %s" % str(sc_sample.location))
sample_list.append(lims_sample)
else:
logging.getLogger("user_level_log").\
warning("Found sample in ISPyB for location %s" % str(sc_sample.location))
sample_list.append(lims_sample)
else:
if lims_sample:
if lims_sample.lims_location != (None, None):
logging.getLogger("user_level_log").\
warning("No barcode was provided in ISPyB "+\
"which makes it impossible to verify if"+\
"the locations are correct, assuming "+\
"that the positions are correct.")
sample_list.append(lims_sample)
else:
logging.getLogger("user_level_log").\
warning("No sample in ISPyB for location %s" % str(sc_sample.location))
sample_list.append(sc_sample)
self.dc_tree_widget.populate_list_view(sample_list)
def get_sc_content(self):
"""
Gets the 'raw' data from the sample changer.
:returns: A list with tuples, containing the sample information.
"""
sc_content = []
try:
for sample in self.sample_changer_hwobj.getSampleList():
matrix = sample.getID() or ""
basket_index = sample.getContainer().getIndex()
vial_index = sample.getIndex()
basket_code = sample.getContainer().getID() or ""
sc_content.append((matrix, basket_index+1, vial_index+1, basket_code, 0))
except Exception:
logging.getLogger("user_level_log").\
info("Could not connect to sample changer," + \
" unable to list contents. Make sure that" + \
" the sample changer is turned on. Using free pin mode")
sc_content = [('', -1, -1, '', 1)]
return sc_content
def status_msg_changed(self, msg, color):
"""
Status message from the SampleChangerBrick.
:param msg: The message
:type msg: str
:returns: None
"""
logging.getLogger("user_level_log").info(msg)
def set_sample_pin_icon(self):
"""
Updates the location of the sample pin when the
matrix code information changes. The matrix code information
is updated, but not exclusively, when a sample is changed.
"""
self.dc_tree_widget.set_sample_pin_icon()
def sample_load_state_changed(self, state, *args):
"""
The state in the sample loading procedure changed.
Ie from Loading to mounted
:param state: str (Enumerable)
:returns: None
"""
s_color = SC_STATE_COLOR.get(state, "UNKNOWN")
self.sample_changer_widget.child('details_button').\
setPaletteBackgroundColor(qt.QColor(s_color))
def show_sample_centring_tab(self):
self.sample_changer_widget.child('details_button').setText("Show SC-details")
self.emit(qt.PYSIGNAL("hide_dc_parameters_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_dcg_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_sample_centring_tab"), (False,))
self.emit(qt.PYSIGNAL("hide_sample_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_sample_changer_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_edna_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_energy_scan_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_workflow_tab"), (True,))
def show_sample_tab(self, item):
self.sample_changer_widget.child('details_button').setText("Show SC-details")
self.emit(qt.PYSIGNAL("hide_dc_parameters_tab"), (True,))
self.emit(qt.PYSIGNAL("populate_sample_details"), (item.get_model(),))
self.emit(qt.PYSIGNAL("hide_dcg_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_sample_centring_tab"), (False,))
self.emit(qt.PYSIGNAL("hide_sample_tab"), (False,))
self.emit(qt.PYSIGNAL("hide_sample_changer_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_edna_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_energy_scan_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_workflow_tab"), (True,))
def show_dcg_tab(self):
self.sample_changer_widget.child('details_button').setText("Show SC-details")
self.emit(qt.PYSIGNAL("hide_dc_parameters_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_dcg_tab"), (False,))
self.emit(qt.PYSIGNAL("hide_sample_changer_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_edna_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_sample_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_energy_scan_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_workflow_tab"), (True,))
def populate_parameters_tab(self, item = None):
self.emit(qt.PYSIGNAL("populate_parameter_widget"),
(item,))
def show_datacollection_tab(self, item):
self.sample_changer_widget.child('details_button').setText("Show SC-details")
self.emit(qt.PYSIGNAL("hide_dcg_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_dc_parameters_tab"), (False,))
self.emit(qt.PYSIGNAL("hide_sample_changer_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_edna_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_sample_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_energy_scan_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_workflow_tab"), (True,))
self.populate_parameters_tab(item)
def show_edna_tab(self, item):
self.sample_changer_widget.child('details_button').setText("Show SC-details")
self.emit(qt.PYSIGNAL("hide_dcg_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_dc_parameters_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_sample_changer_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_edna_tab"), (False,))
self.emit(qt.PYSIGNAL("hide_sample_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_energy_scan_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_workflow_tab"), (True,))
self.populate_edna_parameters_tab(item)
def populate_edna_parameters_tab(self, item):
self.emit(qt.PYSIGNAL("populate_edna_parameter_widget"),
(item,))
def show_energy_scan_tab(self, item):
self.sample_changer_widget.child('details_button').setText("Show SC-details")
self.emit(qt.PYSIGNAL("hide_dcg_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_dc_parameters_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_sample_changer_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_edna_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_sample_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_energy_scan_tab"), (False,))
self.emit(qt.PYSIGNAL("hide_workflow_tab"), (True,))
self.populate_energy_scan_tab(item)
def populate_energy_scan_tab(self, item):
self.emit(qt.PYSIGNAL("populate_energy_scan_widget"), (item,))
def show_workflow_tab_from_model(self):
self.show_workflow_tab(None)
def show_workflow_tab(self, item):
self.sample_changer_widget.child('details_button').setText("Show SC-details")
self.emit(qt.PYSIGNAL("hide_dcg_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_dc_parameters_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_sample_changer_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_edna_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_sample_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_energy_scan_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_workflow_tab"), (False,))
running = self.queue_hwobj.is_executing()
self.populate_workflow_tab(item, running=running)
def populate_workflow_tab(self, item, running = False):
self.emit(qt.PYSIGNAL("populate_workflow_tab"), (item, running))
def toggle_sample_changer_tab(self):
if self.current_view is self.sample_changer_widget:
self.current_view = None
self.emit(qt.PYSIGNAL("hide_sample_changer_tab"), (True,))
self.dc_tree_widget.sample_list_view_selection()
self.sample_changer_widget.child('details_button').setText("Show SC-details")
else:
self.current_view = self.sample_changer_widget
self.emit(qt.PYSIGNAL("hide_dc_parameters_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_dcg_tab"), (True,))
self.emit(qt.PYSIGNAL("hide_sample_changer_tab"), (False,))
self.sample_changer_widget.child('details_button').setText("Hide SC-details")
self.emit(qt.PYSIGNAL("hide_sample_tab"), (True,))
def selection_changed(self, items):
if len(items) == 1:
item = items[0]
if isinstance(item, queue_item.SampleQueueItem):
self.emit(qt.PYSIGNAL("populate_sample_details"), (item.get_model(),))
self.emit_set_sample(item)
self.emit_set_directory()
self.emit_set_prefix(item)
#self.populate_edna_parameter_widget(item)
elif isinstance(item, queue_item.DataCollectionQueueItem):
self.populate_parameters_tab(item)
elif isinstance(item, queue_item.CharacterisationQueueItem):
self.populate_edna_parameters_tab(item)
elif isinstance(item, queue_item.EnergyScanQueueItem):
self.populate_energy_scan_tab(item)
elif isinstance(item, queue_item.GenericWorkflowQueueItem):
self.populate_workflow_tab(item)
self.emit(qt.PYSIGNAL("selection_changed"), (items,))
def emit_set_directory(self):
directory = self.session_hwobj.get_base_image_directory()
self.emit(qt.PYSIGNAL("set_directory"), (directory,))
def emit_set_prefix(self, item):
prefix = self.session_hwobj.get_default_prefix(item.get_model())
self.emit(qt.PYSIGNAL("set_prefix"), (prefix,))
def emit_set_sample(self, item):
self.emit(qt.PYSIGNAL("set_sample"), (item,))
def get_selected_items(self):
items = self.dc_tree_widget.get_selected_items()
return items
def add_to_queue(self, task_list, parent_tree_item = None, set_on = True):
if not parent_tree_item :
parent_tree_item = self.dc_tree_widget.get_mounted_sample_item()
self.dc_tree_widget.add_to_queue(task_list, parent_tree_item, set_on)
