Mercurial > repos > iuc > data_manager_mitos

comparison data_manager/data_manager.py @ 1:1ff9996995ee draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
author iuc
date Sun, 22 Nov 2020 12:51:27 +0000
parents 26a6f95e82c8
children 19d9be08560c
comparison
equal deleted inserted replaced
0:26a6f95e82c8 1:1ff9996995ee
69 data_manager_entry['name'] = NAMES[db] 69 data_manager_entry['name'] = NAMES[db]
70 data_manager_entry['type'] = tpe 70 data_manager_entry['type'] = tpe
71 data_manager_entry['path'] = path 71 data_manager_entry['path'] = path
72 data_manager_json = dict(data_tables=dict(mitos=data_manager_entry)) 72 data_manager_json = dict(data_tables=dict(mitos=data_manager_entry))
73 73
74 with open(outjson) as f: 74 with open(outjson) as fh:
75 params = json.loads(f.read()) 75 params = json.load(fh)
76 target_directory = params['output_data'][0]['extra_files_path'] 76 target_directory = params['output_data'][0]['extra_files_path']
77 os.mkdir(target_directory) 77 os.mkdir(target_directory)
78 # output_path = os.path.abspath(os.path.join(os.getcwd(), 'mitos')) 78 # output_path = os.path.abspath(os.path.join(os.getcwd(), 'mitos'))
79 shutil.move(os.path.join(workdir, path), target_directory) 79 shutil.move(os.path.join(workdir, path), target_directory)
80 with open(outjson, 'w') as fh: 80 with open(outjson, 'w') as fh:
81 fh.write(json.dumps(data_manager_json, sort_keys=True)) 81 json.dump(data_manager_json, fh, sort_keys=True)
82 82
83 83
84 if __name__ == '__main__': 84 if __name__ == '__main__':
85 parser = argparse.ArgumentParser(description='Create data manager json.') 85 parser = argparse.ArgumentParser(description='Create data manager json.')
86 parser.add_argument('--out', action='store', help='JSON filename') 86 parser.add_argument('--out', action='store', help='JSON filename')