def validate_equation(self):
ok = False
test_reaction = cobra.Reaction(
"xxxx_cnapy_test_reaction", name="cnapy test reaction")
with self.parent.appdata.project.cobra_py_model as model:
model.add_reaction(test_reaction)
try:
eqtxt = self.equation.text().rstrip()
if len(eqtxt) > 0 and eqtxt[-1] == '+':
turn_red(self.equation)
else:
test_reaction.build_reaction_from_string(eqtxt)
turn_white(self.equation)
ok = True
except ValueError:
turn_red(self.equation)
try:
test_reaction = self.parent.appdata.project.cobra_py_model.reactions.get_by_id(
"xxxx_cnapy_test_reaction")
self.parent.appdata.project.cobra_py_model.remove_reactions(
[test_reaction], remove_orphans=True)
except KeyError:
pass
return ok
def apply(self):
try:
self.reaction.id = self.id.text()
except ValueError:
turn_red(self.id)
QMessageBox.information(
self, 'Invalid id', 'Could not apply changes identifier ' +
self.id.text() + ' already used.')
else:
self.reaction.name = self.name.text()
self.reaction.build_reaction_from_string(self.equation.text())
self.reaction.lower_bound = float(self.lower_bound.text())
self.reaction.upper_bound = float(self.upper_bound.text())
self.reaction.objective_coefficient = float(self.coefficent.text())
self.reaction.gene_reaction_rule = self.gene_reaction_rule.text()
self.reaction.annotation = {}
rows = self.annotation.rowCount()
for i in range(0, rows):
key = self.annotation.item(i, 0).text()
if self.annotation.item(i, 1) is None:
value = ""
else:
value = self.annotation.item(i, 1).text()
self.reaction.annotation[key] = value
self.changed = False
self.reactionChanged.emit(self.reaction)
def apply(self):
try:
self.metabolite.id = self.id.text()
except ValueError:
turn_red(self.id)
QMessageBox.information(
self, 'Invalid id', 'Could not apply changes identifier ' +
self.id.text()+' already used.')
else:
self.metabolite.name = self.name.text()
self.metabolite.formula = self.formula.text()
if self.charge.text() == "":
self.metabolite.charge = None
else:
self.metabolite.charge = int(self.charge.text())
self.metabolite.compartment = self.compartment.text()
self.metabolite.annotation = {}
rows = self.annotation.rowCount()
for i in range(0, rows):
key = self.annotation.item(i, 0).text()
if self.annotation.item(i, 1) is None:
value = ""
else:
value = self.annotation.item(i, 1).text()
self.metabolite.annotation[key] = value
self.changed = False
self.metaboliteChanged.emit(self.metabolite)
def validate_gene_reaction_rule(self):
try:
_x = float(self.gene_reaction_rule.text())
except ValueError:
turn_red(self.gene_reaction_rule)
return False
else:
turn_white(self.gene_reaction_rule)
return True
def validate_coefficient(self):
try:
_x = float(self.coefficent.text())
except ValueError:
turn_red(self.coefficent)
return False
else:
turn_white(self.coefficent)
return True
def validate_upperbound(self):
try:
_x = float(self.upper_bound.text())
except ValueError:
turn_red(self.upper_bound)
return False
else:
turn_white(self.upper_bound)
return True
def validate_charge(self):
try:
if self.charge.text() != "":
_x = int(self.charge.text())
except ValueError:
turn_red(self.charge)
return False
else:
turn_white(self.charge)
return True
def validate_name(self):
with self.parent.appdata.project.cobra_py_model as model:
try:
r = cobra.Reaction(id="testid", name=self.name.text())
model.add_reaction(r)
except ValueError:
turn_red(self.name)
return False
else:
turn_white(self.name)
return True
def validate_name(self):
with self.appdata.project.cobra_py_model as model:
try:
m = cobra.Metabolite(id="test_id", name=self.name.text())
model.add_metabolites([m])
except ValueError:
turn_red(self.name)
return False
else:
turn_white(self.name)
return True
def validate_compartment(self):
try:
if ' ' in self.compartment.text():
turn_red(self.compartment)
return False
if '-' in self.compartment.text():
turn_red(self.compartment)
return False
_m = cobra.Metabolite(id="test_id", name=self.compartment.text())
except ValueError:
turn_red(self.compartment)
return False
else:
turn_white(self.compartment)
return True
def validate_id(self):
with self.appdata.project.cobra_py_model as model:
text = self.id.text()
if text == "":
turn_red(self.id)
return False
if ' ' in text:
turn_red(self.id)
return False
try:
m = cobra.Metabolite(id=self.id.text())
model.add_metabolites([m])
except ValueError:
turn_red(self.id)
return False
else:
turn_white(self.id)
return True