def db_model(pub_model):
# dump the model
start = time()
# take out special characters from model bigg_id
db_model = dump_model(pub_model.id.replace('.', '_'))
print("Dumped %s in %.2f sec" % (pub_model.id, time() - start))
return db_model
def write_static_model(bigg_id, model_polisher_path):
"""Write out static files for a model with the given BiGG ID.
This will output compressed and uncompressed SBML L3 + FBCv2, JSON,
and MAT files.
"""
success = True
print('Dumping model')
t = time.time()
model = dump_model(bigg_id)
print('Dumping finished in %.2f seconds' % (time.time() - t))
sbml_filepath = join(static_dir, bigg_id + '.xml')
try:
print('Writing SBML')
t = time.time()
cobra.io.write_sbml_model(model, sbml_filepath)
print('Writing SBML finished in %.2f seconds' % (time.time() - t))
except Exception as e:
success = False
print('failed to export sbml model "%s": %s' % (bigg_id, e.message))
else:
print('Compressing')
t = time.time()
system('gzip --keep --force --best ' + sbml_filepath)
print('Compressing finished in %.2f seconds' % (time.time() - t))
# else:
# success = False
print('Writing MAT')
t = time.time()
mat_filepath = join(static_dir, bigg_id + '.mat')
cobra.io.save_matlab_model(model, mat_filepath)
system('gzip --keep --force --best ' + mat_filepath)
print('Writing MAT finished in %.2f seconds' % (time.time() - t))
print('Writing JSON')
t = time.time()
json_filepath = join(static_dir, bigg_id + '.json')
cobra.io.save_json_model(model, json_filepath)
system('gzip --keep --force --best ' + json_filepath)
print('Writing JSON finished in %.2f seconds' % (time.time() - t))
return success
def test_cannot_dump_unknown_model(dumped_model, session):
with pytest.raises(Exception):
dump_model('C3PO', session)
def dumped_model(load_models, session):
bigg_id = 'Ecoli_core_model'
model = dump_model(bigg_id)
return model
def write_static_model(bigg_id, model_polisher_path):
"""Write out static files for a model with the given BiGG ID.
This will output compressed and uncompressed SBML L3 + FBCv2, JSON,
and MAT files.
"""
success = True
print('Dumping model')
t = time.time()
model = dump_model(bigg_id)
print('Dumping finished in %.2f seconds' % (time.time() - t))
raw_sbml_filepath = join(static_dir, 'raw', bigg_id + '.xml')
sbml_filepath = join(static_dir, bigg_id + '.xml')
try:
print('Writing SBML')
t = time.time()
cobra.io.write_sbml_model(model, raw_sbml_filepath)
print('Writing SBML finished in %.2f seconds' % (time.time() - t))
except Exception as e:
success = False
print('failed to export sbml model "%s": %s' % (bigg_id, e.message))
else:
# polish
print('Polishing')
t = time.time()
command = [settings.java,
'-jar',
'-Xms8G',
'-Xmx8G',
'-Xss128M',
'-Duser.language=en',
model_polisher_path,
'--user=%s' % settings.postgres_user,
'--passwd=%s' % settings.postgres_password,
'--host=%s' % settings.postgres_host,
'--dbname=%s' % settings.postgres_database,
'--input=%s' % raw_sbml_filepath,
'--output=%s' % static_dir,
'--compression-type=NONE',
'--check-mass-balance=true',
'--omit-generic-terms=false',
'--log-level=OFF',
'--include-any-uri=false',
'--annotate-with-bigg=true']
polish_result = call(command)
print('Polishing finished in %.2f seconds' % (time.time() - t))
if polish_result == 0:
# compress model
print('Compressing')
t = time.time()
system('gzip --keep --force --best ' + sbml_filepath)
print('Compressing finished in %.2f seconds' % (time.time() - t))
else:
success = False
print('Writing MAT')
t = time.time()
mat_filepath = join(static_dir, bigg_id + '.mat')
cobra.io.save_matlab_model(model, mat_filepath)
system('gzip --keep --force --best ' + mat_filepath)
print('Writing MAT finished in %.2f seconds' % (time.time() - t))
print('Writing JSON')
t = time.time()
json_filepath = join(static_dir, bigg_id + '.json')
cobra.io.save_json_model(model, json_filepath)
system('gzip --keep --force --best ' + json_filepath)
print('Writing JSON finished in %.2f seconds' % (time.time() - t))
return success
def test_cannot_dump_unknown_model(dumped_model, session):
with pytest.raises(Exception):
dump_model('C3PO', session)
def dumped_model(load_models, session):
bigg_id = 'Ecoli_core_model'
model = dump_model(bigg_id)
return model