Mercurial > repos > iuc > data_manager_mitos

comparison data_manager/data_manager.py @ 1:58bcd38cecb6 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 2db6284f6077d80d05227180a809b921b4975c60"
author iuc
date Sun, 22 Nov 2020 18:02:48 +0000
parents c25855a79671
children 5408a9225788
comparison
equal deleted inserted replaced
0:c25855a79671 1:58bcd38cecb6
10 # Fall back to Python 2 imports 10 # Fall back to Python 2 imports
11 from urllib2 import Request, urlopen 11 from urllib2 import Request, urlopen
12 12
13 ZENODO = { 13 ZENODO = {
14 "mitos": "2683856", 14 "mitos": "2683856",
15 "mitos2": "3685310" 15 "mitos2": "4284483"
16 } 16 }
17 NAMES = { 17 NAMES = {
18 "mitos1-refdata": "RefSeq39 + MiTFi tRNA models", 18 "mitos1-refdata": "RefSeq39 + MiTFi tRNA models",
19 "refseq39": "RefSeq39 (equivalent to MITOS1 data)", 19 "refseq39": "RefSeq39 (equivalent to MITOS1 data)",
20 "refseq63m": "RefSeq63 Metazoa", 20 "refseq63m": "RefSeq63 Metazoa",
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')