def test_setting_reaction(self):
widget = ReactionAttributesDisplayWidget()
reaction = Reaction(id="id",
name="name",
subsystem="subsystem",
lower_bound=-1000.,
upper_bound=1000.)
model = Model()
model.add_reactions((reaction, ))
reaction.objective_coefficient = 1.
assert widget.idLineEdit.text() == ""
assert widget.nameLineEdit.text() == ""
assert widget.subsystemLineEdit.text() == ""
assert widget.lowerBoundInput.value() == 0.
assert widget.upperBoundInput.value() == 0.
assert widget.objectiveCoefficientInput.value() == 0.
assert widget.content_changed is False
assert widget.valid_inputs() is False
widget.set_item(reaction, model)
assert widget.idLineEdit.text() == reaction.id
assert widget.nameLineEdit.text() == reaction.name
assert widget.subsystemLineEdit.text() == reaction.subsystem
assert widget.lowerBoundInput.value() == reaction.lower_bound
assert widget.upperBoundInput.value() == reaction.upper_bound
assert widget.objectiveCoefficientInput.value(
) == reaction.objective_coefficient
assert widget.content_changed is False
assert widget.valid_inputs() is True
def copy_reaction(self, move=False):
""" Copy or move reactions between compartmsntes
Parameters
----------
move : bool
Returns
-------
"""
# Get selected items
rows = self.dataView.get_selected_rows()
reactions = [self.dataTable.item_from_row(i) for i in rows]
# Only continue if rows are selected
if not rows:
return
# Collect compartments of metabolites in the selected reactions
compartments = set()
for reaction in reactions:
compartments.update([metabolite.compartment for metabolite in reaction.metabolites])
# Get compartment mapping from user
compartment_mapping = dict()
for compartment in compartments:
value, status = QInputDialog().getItem(self, "Choose target compartment", 'Choose target for compartment "{}":'.format(compartment), list(self.model.gem_compartments.keys()), 0, False)
if not status:
return
else:
compartment_mapping[compartment] = value
progress = QProgressDialog("{} reactions".format("Moving" if move else "Copying"),
"Cancel", 0, len(reactions), self)
# Copy reactions using matching metabolite from other compartment
for n, reaction in enumerate(reactions):
# Check user input and update progress dialog
if progress.wasCanceled():
progress.close()
return
else:
progress.setValue(n)
QApplication.processEvents()
metabolites = dict()
# Collect corresponding metabolites in target compartment
for key, value in reaction.metabolites.items():
target_compartment = compartment_mapping[key.compartment]
putative_target_metabolits = find_duplicate_metabolite(key,
[x for x in self.model.metabolites if x.compartment == target_compartment],
same_compartment=False)
corresponding_metabolite = None
if putative_target_metabolits:
best_hit, score = putative_target_metabolits[0]
if best_hit.compartment == target_compartment and score >= 2.:
corresponding_metabolite = best_hit
if not corresponding_metabolite:
corresponding_metabolite = self.model.copy_metabolite(key, target_compartment)
metabolites[corresponding_metabolite] = value
# Create new reaction if the move flag is false
if not move:
new_reaction = Reaction(id=generate_copy_id(reaction.id, self.model.reactions),
name=reaction.name,
subsystem=reaction.subsystem,
lower_bound=reaction.lower_bound,
upper_bound=reaction.upper_bound,
comment=reaction.comment)
new_reaction.annotation = reaction.annotation.copy()
new_reaction.add_metabolites(metabolites)
self.model.add_reactions([new_reaction])
# Set objective coefficient after adding reaction to model
new_reaction.objective_coefficient = reaction.objective_coefficient
self.model.QtReactionTable.update_row_from_item(new_reaction)
# Update existing reactions with new metabolites if moving
else:
reaction.clear_metabolites()
reaction.add_metabolites(metabolites)
self.model.QtReactionTable.update_row_from_link(rows[n])
progress.close()
