Mercurial > repos > iuc > data_manager_manual

comparison data_manager/data_manager_manual.py @ 7:f0d1db0ce33c draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit dddd6cf3ff59f2a877d03930fcf0563240fb40d8"
author iuc
date Wed, 06 Jan 2021 14:15:37 +0000
parents 7f1bac9c4478
children
comparison
equal deleted inserted replaced
6:bfe6e9a80082 7:f0d1db0ce33c
56 data_table_filename = data_table.get_filename_for_source(data_manager, None) 56 data_table_filename = data_table.get_filename_for_source(data_manager, None)
57 if not data_table_filename: 57 if not data_table_filename:
58 if tdtm is None: 58 if tdtm is None:
59 from tool_shed.tools import data_table_manager 59 from tool_shed.tools import data_table_manager
60 tdtm = data_table_manager.ToolDataTableManager(app) 60 tdtm = data_table_manager.ToolDataTableManager(app)
61 target_dir, tool_path, relative_target_dir = tdtm.get_target_install_dir(tool_shed_repository) 61 target_dir = tool_shed_repository.repo_path(app)
62 # Dynamically add this data table 62 # Dynamically add this data table
63 log.debug("Attempting to dynamically create a missing Tool Data Table named %s." % data_table_name) 63 log.debug("Attempting to dynamically create a missing Tool Data Table named %s." % data_table_name)
64 repo_info = tdtm.generate_repository_info_elem_from_repository(tool_shed_repository, parent_elem=None) 64 repo_info = tdtm.generate_repository_info_elem_from_repository(tool_shed_repository, parent_elem=None)
65 if repo_info is not None: 65 if repo_info is not None:
66 repo_info = tostring(repo_info) 66 repo_info = tostring(repo_info)
160 (options, args) = parser.parse_args() 160 (options, args) = parser.parse_args()
161 161
162 filename = args[0] 162 filename = args[0]
163 163
164 with open(filename) as fh: 164 with open(filename) as fh:
165 params = json.loads(fh.read()) 165 params = json.load(fh)
166 target_directory = params['output_data'][0]['extra_files_path'] 166 target_directory = params['output_data'][0]['extra_files_path']
167 167
168 data_table_entries = get_data_table_entries(params['param_dict'], options.galaxy_data_manager_data_path) 168 data_table_entries = get_data_table_entries(params['param_dict'], options.galaxy_data_manager_data_path)
169 169
170 # save info to json file 170 # save info to json file
171 with open(filename, 'w') as fh: 171 with open(filename, 'w') as fh:
172 fh.write(json.dumps({"data_tables": data_table_entries}, sort_keys=True)) 172 json.dump({"data_tables": data_table_entries}, fh, sort_keys=True)
173 173
174 get_file_content(params['param_dict'], target_directory) 174 get_file_content(params['param_dict'], target_directory)
175 175
176 176
177 if __name__ == "__main__": 177 if __name__ == "__main__":