def populate_free_pin(self):
self.queue_model_hwobj.clear_model('free-pin')
self.queue_model_hwobj.select_model('free-pin')
sample = queue_model_objects.Sample()
sample.free_pin_mode = True
sample.set_name('manually-mounted')
self.queue_model_hwobj.add_child(
self.queue_model_hwobj.get_model_root(), sample)
def get_default_prefix(sample_data, generic_name):
sample = qmo.Sample()
sample.code = sample_data.get("code", "")
sample.name = sample_data.get("sampleName", "")
sample.location = sample_data.get("location", "").split(':')
sample.crystals[0].protein_acronym = sample_data.get("proteinAcronym", "")
return mxcube.session.get_default_prefix(sample, generic_name)
def samples_from_sc_content(self, sc_content):
sample_list = []
for sample_info in sc_content:
sample = queue_model_objects.Sample()
sample.init_from_sc_sample(sample_info)
sample_list.append(sample)
return sample_list
def samples_from_sc_content(self, sc_basket_content, sc_sample_content):
basket_list = []
sample_list = []
for basket_info in sc_basket_content:
basket = queue_model_objects.Basket()
basket.init_from_sc_basket(basket_info, "Puck")
basket_list.append(basket)
for sample_info in sc_sample_content:
sample = queue_model_objects.Sample()
sample.init_from_sc_sample(sample_info)
sample_list.append(sample)
return basket_list, sample_list
def get_default_prefix(sample_data, generic_name):
if isinstance(sample_data, dict):
sample = qmo.Sample()
sample.code = sample_data.get("code", "")
sample.name = sample_data.get("sampleName", "")
sample.location = sample_data.get("location", "").split(':')
sample.lims_id = sample_data.get("limsID", -1)
sample.crystals[0].protein_acronym = sample_data.get("proteinAcronym", "")
else:
sample = sample_data
return mxcube.session.get_default_prefix(sample, generic_name)
def samples_from_lims(self, lims_sample_list):
barcode_samples = {}
location_samples = {}
for lims_sample in lims_sample_list:
sample = queue_model_objects.Sample()
sample.init_from_lims_object(lims_sample)
if sample.lims_code:
barcode_samples[sample.lims_code] = sample
if sample.lims_location:
location_samples[sample.lims_location] = sample
return (barcode_samples, location_samples)
def samples_from_plate_content(self, plate_sample_content):
row_list = []
sample_list = []
actual_row_index = -1
for sample_info in plate_sample_content:
if actual_row_index < sample_info[1]:
row = queue_model_objects.Basket()
row_info = [sample_info[1], None]
row.init_from_sc_basket(row_info, "Row")
row_list.append(row)
actual_row_index = sample_info[1]
sample = queue_model_objects.Sample()
sample.init_from_plate_sample(sample_info)
sample_list.append(sample)
return row_list, sample_list
def add_sample(sample_id, item):
"""
Adds a sample with sample id <sample_id> the queue.
:param str sample_id: Sample id (often sample changer location)
:returns: SampleQueueEntry
"""
# Is the sample with location sample_id already in the queue,
# in that case, send error response
for sampleId, sampleData in queue_to_dict().iteritems():
if sampleId == sample_id:
msg = "[QUEUE] sample could not be added, already in the queue"
raise Exception(msg)
sample_model = qmo.Sample()
# We should really use sample_id instead of loc_str
sample_model.loc_str = sample_id
sample_model.free_pin_mode = item['location'] == 'Manual'
sample_model.set_name(item['sampleName'])
sample_model.crystals[0].protein_acronym = item.get('proteinAcronym', '')
if sample_model.free_pin_mode:
sample_model.location = (None, sample_id)
else:
sample_model.location = tuple(map(int, item['location'].split(':')))
sample_entry = qe.SampleQueueEntry(Mock(), sample_model)
sample_entry.set_enabled(True)
mxcube.queue.add_child(mxcube.queue.get_model_root(), sample_model)
mxcube.queue.queue_hwobj.enqueue(sample_entry)
return sample_model._node_id
def __init__(self, *args):
"""
Descript. :
"""
BlissWidget.__init__(self, *args)
# Internal variables ------------------------------------------------
self.sample = queue_model_objects.Sample()
self.crystal = self.sample.crystals[0]
self.sample_mib = DataModelInputBinder(self.sample)
self.crystal_mib = DataModelInputBinder(self.crystal)
# Signals ------------------------------------------------------------
# Slots --------------------------------------------------------------
self.defineSlot("populate_sample_details", ({}))
# Graphic elements ----------------------------------------------------
_info_widget = QWidget(self)
self.crystal_widget = loadUi(\
os.path.join(os.path.dirname(__file__),
"widgets/ui_files/Qt4_crystal_widget_layout.ui"))
self.sample_info_widget = loadUi(
os.path.join(os.path.dirname(__file__),
"widgets/ui_files/Qt4_sample_info_widget_layout.ui"))
#self.ispyb_sample_info_widget = ISPyBSampleInfoWidget(self)
# Layout --------------------------------------------------------------
_info_widget_hlayout = QHBoxLayout(_info_widget)
_info_widget_hlayout.addWidget(self.sample_info_widget)
_info_widget_hlayout.addWidget(self.crystal_widget)
_info_widget_hlayout.addStretch(0)
_info_widget_hlayout.setSpacing(0)
_info_widget_hlayout.setContentsMargins(2, 2, 2, 2)
_main_hlayout = QVBoxLayout(self)
_main_hlayout.addWidget(_info_widget)
#_main_hlayout.addWidget(self.ispyb_sample_info_widget)
_main_hlayout.addStretch(0)
_main_hlayout.setSpacing(0)
_main_hlayout.setContentsMargins(2, 2, 2, 2)
# SizePolicies --------------------------------------------------------
# Qt signal/slot connections ------------------------------------------
# Other ---------------------------------------------------------------
self.crystal_mib.bind_value_update(
'space_group', self.crystal_widget.space_group_value_label, str,
None)
self.crystal_mib.bind_value_update(
'protein_acronym', self.crystal_widget.protein_acronym_value_label,
str, None)
self.crystal_mib.bind_value_update('cell_a',
self.crystal_widget.a_value_label,
str, None)
self.crystal_mib.bind_value_update(
'cell_alpha', self.crystal_widget.alpha_value_label, str, None)
self.crystal_mib.bind_value_update('cell_b',
self.crystal_widget.b_value_label,
str, None)
self.crystal_mib.bind_value_update(
'cell_beta', self.crystal_widget.beta_value_label, str, None)
self.crystal_mib.bind_value_update('cell_c',
self.crystal_widget.c_value_label,
str, None)
self.crystal_mib.bind_value_update(
'cell_gamma', self.crystal_widget.gamma_value_label, str, None)
self.sample_mib.bind_value_update(
'name', self.sample_info_widget.name_value_label, str, None)
self.sample_mib.bind_value_update(
'code', self.sample_info_widget.data_matrix_value_label, str, None)
self.sample_mib.bind_value_update(
'holder_length', self.sample_info_widget.holder_length_value_label,
str, None)
self.sample_mib.bind_value_update(
'lims_sample_location',
self.sample_info_widget.sample_location_value_label, str, None)
self.sample_mib.bind_value_update(
'lims_container_location',
self.sample_info_widget.basket_location_value_label, str, None)
def __init__(self, *args):
BaseComponents.BlissWidget.__init__(self, *args)
#
# Data attributes
#
self.sample = queue_model_objects.Sample()
self.crystal = self.sample.crystals[0]
self.sample_mib = DataModelInputBinder(self.sample)
self.crystal_mib = DataModelInputBinder(self.crystal)
#
# Qt - Signals/Slots
#
self.defineSlot("populate_sample_details", ({}))
#
# Layout
#
main_layout = qt.QHBoxLayout(self, 11, 15, "main_layout")
self.crystal_widget = CrystalWidgetLayout(self)
self.sample_info_widget = SampleInfoWidgetLayout(self)
main_layout.addWidget(self.sample_info_widget)
main_layout.addWidget(self.crystal_widget)
main_layout.addStretch(10)
self.crystal_mib.bind_value_update(
'space_group', self.crystal_widget.space_group_value_label, str,
None)
self.crystal_mib.bind_value_update(
'protein_acronym', self.crystal_widget.protein_acronym_value_label,
str, None)
self.crystal_mib.bind_value_update('cell_a',
self.crystal_widget.a_value_label,
str, None)
self.crystal_mib.bind_value_update(
'cell_alpha', self.crystal_widget.alpha_value_label, str, None)
self.crystal_mib.bind_value_update('cell_b',
self.crystal_widget.b_value_label,
str, None)
self.crystal_mib.bind_value_update(
'cell_beta', self.crystal_widget.beta_value_label, str, None)
self.crystal_mib.bind_value_update('cell_c',
self.crystal_widget.c_value_label,
str, None)
self.crystal_mib.bind_value_update(
'cell_gamma', self.crystal_widget.gamma_value_label, str, None)
self.sample_mib.bind_value_update(
'name', self.sample_info_widget.name_value_label, str, None)
self.sample_mib.bind_value_update(
'code', self.sample_info_widget.data_matrix_value_label, str, None)
self.sample_mib.bind_value_update(
'holder_length', self.sample_info_widget.holder_length_value_label,
str, None)
self.sample_mib.bind_value_update(
'lims_sample_location',
self.sample_info_widget.sample_location_value_label, str, None)
self.sample_mib.bind_value_update(
'lims_container_location',
self.sample_info_widget.basket_location_value_label, str, None)
