def convertInputData(self):
"""Convert input data to command-adaptable format data."""
# {system: Data, restraint
self.state.preparing
for socket_name, c in self.inputs.items():
data = c['data']
if data.type in self.__command.type_format_table:
formats = self.__command.type_format_table[data.type]
dc = DataConverter(data, formats, user_command=False)
dc.convert()
datas = dc.get_datas()
rev_formats = dict([ (format, key) for key, format
in self.__command.input_formats.items() ])
for data in datas:
if data.format in rev_formats:
option = rev_formats[data.format]
if option in self.__command.default_options:
filename = self.__command.default_options[option]
file_abspath = os.path.join(self.path, filename)
data.dump(file_abspath)
else:
mes = "option: {0} was not found in default options."
raise OptionNotFound(mes.format(option))
else:
mes = "format: {0} was not found in input formats:"
raise FormatNotFound(mes.format(key))
def __call__(self):
start_time = time.time()
try:
zf = zipfile.ZipFile(self.input_file, 'r')
zf.extractall(self.extract_dir)
zf.close()
# data conversion start
converter = DataConverter(in_dir=self.extract_dir,
out_dir=self.output_dir,
zipfilename=os.path.basename(
self.input_file),
logger=self.logger)
data = converter.run(output_format=self.output_format)
# insert in database if settings were provided (IP and Port)
if self.db_settings['enabled'] is True:
dbconnection = MongoDBConnector(self.db_settings['ip'],
self.db_settings['port'],
self.db_settings['database'])
dbconnection.insert_dataset(datapoints=data,
datasetname='l' + self.logger +
'_' +
os.path.basename(self.input_file))
shutil.rmtree(self.extract_dir)
shutil.move(
self.input_file,
self.processed_dir + '/' + os.path.basename(self.input_file))
except Exception as err:
print(' error: executing conversion task of %s failed: %s' %
(os.path.basename(self.input_file), err))
return
end_time = time.time()
print('converted %s to %s (%s sec)' %
(os.path.basename(self.input_file), self.output_format,
round((end_time - start_time), 2)))
return
def main():
# d = DataConverter()
# for k, f in d.convert_dict.items():
# print k, f
import project
p = project.Project()
d = Data(p, type='System')
p.append_data(d)
print d.context
pdb_path = '~/Dropbox/Office/Nagara/v02-src/examples/structures/1HEW.pdb'
pdb_abspath = os.path.expanduser(pdb_path)
d.set_local_file(filename=pdb_abspath, format='PDB')
print d.context
print d.get_file()
from dataconverter import DataConverter
dc = DataConverter(
input_data_list=[d],
output_format_list=['NagaraData']
)
system_data = dc.get_data_list()[0]
print system_data.context
system = system_data.ndo
# for atom in system.atoms:
# print atom
dc2 = DataConverter(
input_data_list=[system_data], output_format_list=['PDB']
)
pdb_data = dc2.get_data_list()[0]
print 222222222, pdb_data.type
print 33333333333, pdb_data.context