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 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):
ImportedDataTest.setUp(self)
plugin = ChannelStatisticPlugin()
op = plugin.get_operation()
op.name = "MeanByDox"
op.channel = "Y2-A"
op.statistic_name = "Geom.SD"
op.by = ['Dox']
wi = WorkflowItem(operation=op)
self.workflow.workflow.append(wi)
op = plugin.get_operation()
op.name = "MeanByDoxAndWell"
op.channel = "Y2-A"
op.statistic_name = "Geom.SD"
op.by = ['Dox', 'Well']
wi = WorkflowItem(operation=op)
self.workflow.workflow.append(wi)
op = plugin.get_operation()
op.name = "MeanByDox"
op.channel = "Y2-A"
op.statistic_name = "Geom.Mean"
op.by = ['Dox']
self.wi = wi = WorkflowItem(operation=op)
self.workflow.workflow.append(wi)
op = plugin.get_operation()
op.name = "MeanByDoxAndWell"
op.channel = "Y2-A"
op.statistic_name = "Geom.Mean"
op.by = ['Dox', 'Well']
self.wi = wi = WorkflowItem(operation=op)
self.workflow.workflow.append(wi)
self.workflow.selected = wi
self.assertTrue(wait_for(wi, 'status', lambda v: v == 'valid', 10))
plugin = TablePlugin()
self.view = view = plugin.get_view()
view.statistic = ("MeanByDox", "Geom.Mean")
view.row_facet = "Dox"
self.workflow.remote_exec("self.workflow[-1].view_error = 'waiting'")
self.assertTrue(
wait_for(self.wi, 'view_error', lambda v: v == "waiting", 30))
wi.views.append(view)
wi.current_view = view
self.workflow.selected = wi
self.assertTrue(wait_for(self.wi, 'view_error', lambda v: v == "", 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):
ImportedDataTest.setUp(self)
plugin = ChannelStatisticPlugin()
op = plugin.get_operation()
op.name = "MeanByDox"
op.channel = "Y2-A"
op.statistic_name = "Geom.SD"
op.by = ['Dox', 'Well']
wi = WorkflowItem(operation=op)
self.workflow.workflow.append(wi)
op = plugin.get_operation()
op.name = "MeanByDox"
op.channel = "Y2-A"
op.statistic_name = "Geom.Mean"
op.by = ['Dox', 'Well']
op.subset_list.append(CategorySubset(name="Well", values=["A", "B"]))
self.wi = wi = WorkflowItem(operation=op)
self.workflow.workflow.append(wi)
self.workflow.selected = wi
self.assertTrue(wait_for(wi, 'status', lambda v: v == 'valid', 10))
plugin = Stats1DPlugin()
self.view = view = plugin.get_view()
view.statistic = ("MeanByDox", "Geom.Mean")
view.variable = "Dox"
view.huefacet = "Well"
self.workflow.remote_exec("self.workflow[-1].view_error = 'waiting'")
self.assertTrue(
wait_for(self.wi, 'view_error', lambda v: v == "waiting", 5))
wi.views.append(view)
wi.current_view = view
self.workflow.selected = wi
self.assertTrue(wait_for(self.wi, 'view_error', lambda v: v == "", 5))
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()
def setUp(self):
super().setUp()
plugin = ChannelStatisticPlugin()
op = plugin.get_operation()
op.name = "MeanByDox"
op.channel = "Y2-A"
op.statistic_name = "Geom.SD"
op.by = ['Dox']
wi = WorkflowItem(operation = op,
status = 'waiting',
view_error = "Not yet plotted")
self.workflow.workflow.append(wi)
op = plugin.get_operation()
op.name = "MeanByDoxAndWell"
op.channel = "Y2-A"
op.statistic_name = "Geom.SD"
op.by = ['Dox', 'Well']
wi = WorkflowItem(operation = op,
status = 'waiting',
view_error = "Not yet plotted")
self.workflow.workflow.append(wi)
op = plugin.get_operation()
op.name = "MeanByDox"
op.channel = "Y2-A"
op.statistic_name = "Geom.Mean"
op.by = ['Dox']
wi = WorkflowItem(operation = op,
status = 'waiting',
view_error = "Not yet plotted")
self.workflow.workflow.append(wi)
op = plugin.get_operation()
op.name = "MeanByDoxAndWell"
op.channel = "Y2-A"
op.statistic_name = "Geom.Mean"
op.by = ['Dox', 'Well']
self.wi = wi = WorkflowItem(operation = op,
status = 'waiting',
view_error = "Not yet plotted")
self.workflow.workflow.append(wi)
self.workflow.selected = wi
self.workflow.wi_waitfor(wi, 'status', "valid")
plugin = TablePlugin()
self.view = view = plugin.get_view()
view.statistic = ("MeanByDox", "Geom.Mean")
view.row_facet = "Dox"
self.workflow.wi_sync(self.wi, 'view_error', 'waiting')
wi.views.append(view)
wi.current_view = view
self.workflow.selected = wi
self.workflow.wi_waitfor(self.wi, 'view_error', '')
