コード例 #1
0
    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))
コード例 #2
0
    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
コード例 #3
0
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