def add_operation(self, op_id):
# first, find the matching plugin
plugin = next((x for x in self.op_plugins if x.id == op_id))
# next, get an operation
op = plugin.get_operation()
# make a new workflow item
wi = WorkflowItem(operation = op,
deletable = (op_id != 'edu.mit.synbio.cytoflowgui.op_plugins.import'))
# if the op has a default view, add it to the wi
try:
wi.default_view = op.default_view()
wi.views.append(wi.default_view)
wi.current_view = wi.default_view
except AttributeError:
pass
# figure out where to add it
if self.model.selected:
idx = self.model.workflow.index(self.model.selected) + 1
else:
idx = len(self.model.workflow)
# the add_remove_items handler takes care of updating the linked list
self.model.workflow.insert(idx, wi)
# and make sure to actually select the new wi
self.model.selected = wi
def add_operation(self, op_id):
# first, find the matching plugin
plugin = next((x for x in self.op_plugins if x.id == op_id))
# default to inserting at the end of the list if none selected
after = self.model.selected
if after is None:
after = self.model.workflow[-1]
idx = self.model.workflow.index(after)
wi = WorkflowItem(task = self)
wi.operation = plugin.get_operation()
wi.next = after.next
after.next = wi
wi.previous = after
if wi.next:
wi.next.previous = wi
self.model.workflow.insert(idx+1, wi)
# set up the default view
wi.default_view = plugin.get_default_view(wi.operation)
if wi.default_view is not None:
wi.default_view.handler = \
wi.default_view.handler_factory(model = wi.default_view, wi = wi.previous)
wi.views.append(wi.default_view)
# select (open) the new workflow item
self.model.selected = wi
if wi.default_view:
wi.current_view = wi.default_view
# invalidate everything following
self.operation_parameters_updated()
def setUp(self):
TasbeTest.setUp(self)
plugin = ThresholdPlugin()
op = plugin.get_operation()
op.name = "Morpho"
op.channel = "FSC-A"
op.threshold = 100000
wi = WorkflowItem(operation=op)
self.workflow.workflow.append(wi)
self.assertTrue(wait_for(wi, 'status', lambda v: v == 'valid', 30))
plugin = AutofluorescencePlugin()
self.op = op = plugin.get_operation()
self.cwd = os.path.dirname(os.path.abspath(__file__))
op.blank_file = self.cwd + "/../../cytoflow/tests/data/tasbe/blank.fcs"
op.channels = ["FITC-A", "Pacific Blue-A", "PE-Tx-Red-YG-A"]
op.subset_list.append(BoolSubset(name="Morpho"))
op.subset_list[0].selected_t = True
self.wi = wi = WorkflowItem(operation=op)
wi.default_view = self.op.default_view()
wi.view_error = "Not yet plotted"
wi.views.append(self.wi.default_view)
self.workflow.workflow.append(wi)
self.workflow.selected = self.wi
# run the estimate
op.do_estimate = True
self.assertTrue(wait_for(wi, 'status', lambda v: v == 'valid', 30))
def add_operation(self, operation):
# add the new operation after the selected workflow item or at the end
# of the workflow if no wi is selected
# make a new workflow item
wi = WorkflowItem(operation = operation,
deletable = (operation.id != "edu.mit.synbio.cytoflow.operations.import"))
# they say in Python you should ask for forgiveness instead of permission
try:
wi.default_view = operation.default_view()
wi.views.append(wi.default_view)
except AttributeError:
pass
if self.workflow and self.selected:
idx = self.workflow.index(self.selected) + 1
elif self.workflow:
idx = len(self.workflow)
else:
idx = 0
# the add_remove_items handler takes care of updating the linked list
self.workflow.insert(idx, wi)
# select (open) the new workflow item
self.selected = wi
if wi.default_view:
wi.current_view = wi.default_view
def setUp(self):
TasbeTest.setUp(self)
plugin = ThresholdPlugin()
op = plugin.get_operation()
op.name = "Morpho"
op.channel = "FSC-A"
op.threshold = 100000
wi = WorkflowItem(operation=op)
self.workflow.workflow.append(wi)
self.assertTrue(wait_for(wi, 'status', lambda v: v == 'valid', 30))
plugin = TasbePlugin()
self.op = op = plugin.get_operation()
self.cwd = os.path.dirname(os.path.abspath(__file__))
self.wi = wi = WorkflowItem(operation=op)
wi.default_view = self.op.default_view()
wi.view_error = "Not yet plotted"
wi.views.append(self.wi.default_view)
self.workflow.workflow.append(wi)
self.workflow.selected = self.wi
op.channels = ["FITC-A", "Pacific Blue-A", "PE-Tx-Red-YG-A"]
op.blank_file = self.cwd + "/../../cytoflow/tests/data/tasbe/blank.fcs"
op.bleedthrough_list = [
_BleedthroughControl(channel="FITC-A",
file=self.cwd +
"/../../cytoflow/tests/data/tasbe/eyfp.fcs"),
_BleedthroughControl(channel="Pacific Blue-A",
file=self.cwd +
"/../../cytoflow/tests/data/tasbe/ebfp.fcs"),
_BleedthroughControl(channel="PE-Tx-Red-YG-A",
file=self.cwd +
"/../../cytoflow/tests/data/tasbe/mkate.fcs")
]
op.beads_name = "Spherotech RCP-30-5A Lot AG01, AF02, AD04 and AAE01"
op.beads_file = self.cwd + "/../../cytoflow/tests/data/tasbe/beads.fcs"
op.beads_unit = "MEFL"
op.to_channel = "FITC-A"
self.op.translation_list[
0].file = self.cwd + "/../../cytoflow/tests/data/tasbe/rby.fcs"
self.op.translation_list[
1].file = self.cwd + "/../../cytoflow/tests/data/tasbe/rby.fcs"
op.subset_list.append(BoolSubset(name="Morpho"))
op.subset_list[0].selected_t = True
# run the estimate
op.do_estimate = True
self.assertTrue(wait_for(wi, 'status', lambda v: v == 'valid', 30))
def activated(self):
self.model.backup_workflow = self.model.workflow
self.model.workflow = []
self.model.modified = False
# add the op
self.op = TasbeCalibrationOp()
# make a new workflow item
wi = WorkflowItem(operation=self.op, deletable=False)
wi.default_view = self.op.default_view()
wi.views.append(wi.default_view)
wi.current_view = wi.default_view
self.model.workflow.append(wi)
self.model.selected = wi
self.help_pane.html = self.op.get_help()
def setUp(self):
TasbeTest.setUp(self)
plugin = ThresholdPlugin()
op = plugin.get_operation()
op.name = "Morpho"
op.channel = "FSC-A"
op.threshold = 100000
wi = WorkflowItem(operation = op)
self.workflow.workflow.append(wi)
self.assertTrue(wait_for(wi, 'status', lambda v: v == 'valid', 5))
plugin = BleedthroughLinearPlugin()
self.op = op = plugin.get_operation()
self.cwd = os.path.dirname(os.path.abspath(__file__))
op.controls_list = [_Control(channel = "FITC-A",
file = self.cwd + '/../../cytoflow/tests/data/tasbe/eyfp.fcs'),
_Control(channel = "PE-Tx-Red-YG-A",
file = self.cwd + '/../../cytoflow/tests/data/tasbe/mkate.fcs'),
_Control(channel = "Pacific Blue-A",
file = self.cwd + '/../../cytoflow/tests/data/tasbe/ebfp.fcs')]
op.subset_list.append(BoolSubset(name = "Morpho"))
op.subset_list[0].selected_t = True
self.wi = wi = WorkflowItem(operation = op)
wi.default_view = self.op.default_view()
wi.view_error = "Not yet plotted"
wi.views.append(self.wi.default_view)
self.workflow.workflow.append(wi)
self.workflow.selected = self.wi
# run the estimate
op.do_estimate = True
self.assertTrue(wait_for(wi, 'status', lambda v: v == 'valid', 30))
def add_operation(self, op_id):
# first, find the matching plugin
plugin = next((x for x in self.op_plugins if x.id == op_id))
# default to inserting at the end of the list if none selected
after = self.model.selected
if after is None:
after = self.model.workflow[-1]
idx = self.model.workflow.index(after)
wi = WorkflowItem(task=self)
wi.operation = plugin.get_operation()
wi.next = after.next
after.next = wi
wi.previous = after
if wi.next:
wi.next.previous = wi
self.model.workflow.insert(idx + 1, wi)
# set up the default view
wi.default_view = plugin.get_default_view()
if wi.default_view is not None:
wi.default_view.op = wi.operation
wi.default_view.handler = \
wi.default_view.handler_factory(model = wi.default_view, wi = wi.previous)
wi.views.append(wi.default_view)
# select (open) the new workflow item
self.model.selected = wi
if wi.default_view:
wi.current_view = wi.default_view
# invalidate everything following
self.operation_parameters_updated()
