def test_run_tableexport_compounds(self):
with redirected_stdout() as f:
main(args=['--model', self._model_dir, 'tableexport', 'compounds'])
self.assertEqual(
f.getvalue(), '\n'.join(
['id\tin_model', 'A_\u2206\tTrue', 'B\tTrue', 'C\tTrue', '']))
def test_solver_command_main(self):
with self.assertRaises(generic.RequirementsError):
main(MockSolverCommand,
args=[
'--model', self._model_dir, '--solver',
'name=not-an-actual-solver'
])
def test_run_tableexport_compounds(self):
with redirected_stdout() as f:
main(args=[
'--model', self._model_dir, 'tableexport', 'compounds'])
self.assertEqual(f.getvalue(), '\n'.join([
'id', 'A_\u2206', 'B', 'C', ''
]))
def test_run_tableexport_limits(self):
with redirected_stdout() as f:
main(args=['--model', self._model_dir, 'tableexport', 'limits'])
self.assertEqual(
f.getvalue(), '\n'.join([
'Reaction ID\tLower Limits\tUpper Limits',
'rxn_2_\u03c0\tNone\t100', ''
]))
def test_run_tableexport_metadata(self):
with redirected_stdout() as f:
main(args=['--model', self._model_dir, 'tableexport', 'metadata'])
self.assertEqual(
f.getvalue(), '\n'.join([
'Model Name: Test model', 'Biomass Reaction: rxn_1',
'Default Flux Limits: 1000', ''
]))
def run_solver_command(self, args, requirements):
with redirected_stdout() as f:
if self.is_solver_available(**requirements):
main(args=args)
else:
with self.assertRaises(generic.RequirementsError):
main(args=args)
return f
def run_solver_command(self, args, requirements):
with redirected_stdout() as f:
if self.is_solver_available(**requirements):
main(args=args)
else:
with self.assertRaises(generic.RequirementsError):
main(args=args)
return f
def test_run_tableexport_medium(self):
with redirected_stdout() as f:
main(args=['--model', self._model_dir, 'tableexport', 'medium'])
self.assertEqual(
f.getvalue(), '\n'.join([
'Compound ID\tReaction ID\tLower Limit\tUpper Limit',
'A_\u2206[e]\tNone\t-1000\t1000', 'C[e]\tNone\t-1000\t1000', ''
]))
def test_run_tableexport_reactions(self):
with redirected_stdout() as f:
main(args=['--model', self._model_dir, 'tableexport', 'reactions'])
self.assertEqual(
f.getvalue(), '\n'.join([
'id\tequation\tgenes',
"rxn_1\t|A[e]| => |B[c]|\t['gene_1', 'gene_2']",
'rxn_2\t|B[c]| => |C[e]|\tgene_3 or (gene_4 and gene_5)', ''
]))
def test_run_tableexport_limits(self):
with redirected_stdout() as f:
main(args=[
'--model', self._model_dir, 'tableexport', 'limits'])
self.assertEqual(f.getvalue(), '\n'.join([
'Reaction ID\tLower Limits\tUpper Limits',
'rxn_2_\u03c0\tNone\t100',
''
]))
def test_run_tableexport_metadata(self):
with redirected_stdout() as f:
main(args=[
'--model', self._model_dir, 'tableexport', 'metadata'])
self.assertEqual(f.getvalue(), '\n'.join([
'Model Name: Test model',
'Biomass Reaction: rxn_1',
'Default Flux Limits: 1000',
''
]))
def test_run_tableexport_medium(self):
with redirected_stdout() as f:
main(args=[
'--model', self._model_dir, 'tableexport', 'medium'])
self.assertEqual(f.getvalue(), '\n'.join([
'Compound ID\tReaction ID\tLower Limit\tUpper Limit',
'A_\u2206[e]\tNone\t-1000\t1000',
'C[e]\tNone\t-1000\t1000',
''
]))
def test_run_tableexport_reactions(self):
with redirected_stdout() as f:
main(args=[
'--model', self._model_dir, 'tableexport', 'reactions'])
self.assertEqual(f.getvalue(), '\n'.join([
'id\tequation\tgenes',
"rxn_1\t|A_\u2206[e]| => |B[c]|\t['gene_1', 'gene_2']",
'rxn_2_\u03c0\t|B[c]| => |C[e]|\tgene_3 or (gene_4 and gene_5)',
''
]))
def test_run_tableexport_reactions(self):
with redirected_stdout() as f:
main(args=['--model', self._model_dir, 'tableexport', 'reactions'])
self.assertEqual(
f.getvalue(),
'\n'.join('\t'.join(row) for row in
[['id', 'equation', 'genes', 'in_model'],
[
'rxn_1', '|A_\u2206[e]| => |B[c]|',
"['gene_1', 'gene_2']", 'True'
],
[
'rxn_2_\u03c0', '|B[c]| => |C[e]|',
'gene_3 or (gene_4 and gene_5)', 'True'
], ['rxn_3', '|D[c]| => |E[c]|', 'None', 'True'], []]))
def test_run_search_reaction(self):
with redirected_stdout():
main(args=[
'--model', self._model_dir, 'search', 'reaction',
'--id', 'rxn_1'])
def test_run_search_compound(self):
with redirected_stdout():
main(args=[
'--model', self._model_dir, 'search', 'compound', '--id', 'A'])
def test_run_sbmlexport(self):
with redirected_stdout(BytesIO()):
main(args=['--model', self._model_dir, 'sbmlexport'])
def test_run_formulacheck(self):
with redirected_stdout():
main(args=['--model', self._model_dir, 'formulacheck'])
def test_run_search_reaction(self):
with redirected_stdout():
main(args=[
'--model', self._model_dir, 'search', 'reaction', '--id',
'rxn_1'
])
def test_run_chargecheck(self):
with redirected_stdout():
main(args=['--model', self._model_dir, 'chargecheck'])
def test_solver_command_main(self):
with self.assertRaises(generic.RequirementsError):
main(MockSolverCommand, args=[
'--model', self._model_dir,
'--solver', 'name=not-an-actual-solver'])
def test_command_main(self):
main(MockCommand, args=['--model', self._model_dir, '--test-argument'])
self.assertTrue(MockCommand.run_called)
self.assertTrue(MockCommand.init_parser_called)
self.assertTrue(MockCommand.has_native_model)
def test_run_excelexport(self):
dest_path = os.path.join(self._model_dir, 'model.xlsx')
with redirected_stdout():
main(args=['--model', self._model_dir, 'excelexport', dest_path])
self.assertTrue(os.path.isfile(dest_path))
def test_run_formulacheck(self):
with redirected_stdout():
main(args=['--model', self._model_dir, 'formulacheck'])
def test_run_sbmlexport(self):
with redirected_stdout(BytesIO()):
main(args=['--model', self._model_dir, 'sbmlexport'])
def test_invoke_version(self):
with redirected_stdout():
with self.assertRaises(SystemExit) as context:
main(args=['--version'])
self.assertEqual(context.exception.code, 0)
def test_invoke_version(self):
with redirected_stdout():
with self.assertRaises(SystemExit) as context:
main(args=['--version'])
self.assertEqual(context.exception.code, 0)
def test_run_chargecheck(self):
with redirected_stdout():
main(args=['--model', self._model_dir, 'chargecheck'])
def test_run_excelexport(self):
dest_path = os.path.join(self._model_dir, 'model.xlsx')
with redirected_stdout():
main(args=['--model', self._model_dir, 'excelexport', dest_path])
self.assertTrue(os.path.isfile(dest_path))
def test_command_main(self):
main(MockCommand, args=[
'--model', self._model_dir, '--test-argument'])
self.assertTrue(MockCommand.run_called)
self.assertTrue(MockCommand.init_parser_called)
self.assertTrue(MockCommand.has_native_model)
def test_run_search_compound(self):
with redirected_stdout():
main(args=[
'--model', self._model_dir, 'search', 'compound', '--id', 'A'
])
def test_metabolic_command_main(self):
main(MockMetabolicCommand, args=[
'--model', self._model_dir])
self.assertTrue(MockMetabolicCommand.has_metabolic_model)
def test_metabolic_command_main(self):
main(MockMetabolicCommand, args=['--model', self._model_dir])
self.assertTrue(MockMetabolicCommand.has_metabolic_model)