Mercurial > repos > devteam > data_manager_fetch_ncbi_taxonomy

comparison data_manager/data_manager.py @ 5:9de2fb1ce1fb draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
author iuc
date Sun, 22 Nov 2020 12:48:48 +0000
parents d6acd5cd497b
children 6dd9e00dea95
comparison
equal deleted inserted replaced
4:d6acd5cd497b 5:9de2fb1ce1fb
3 import json 3 import json
4 import os 4 import os
5 import shutil 5 import shutil
6 import tarfile 6 import tarfile
7 import zipfile 7 import zipfile
8 try: 8 from urllib.request import Request, urlopen
9 # For Python 3.0 and later
10 from urllib.request import Request, urlopen
11 except ImportError:
12 # Fall back to Python 2 imports
13 from urllib2 import Request, urlopen
14 9
15 10
16 def url_download(url, workdir): 11 def url_download(url, workdir):
17 file_path = os.path.join(workdir, 'download.dat') 12 file_path = os.path.join(workdir, 'download.dat')
18 if not os.path.exists(workdir): 13 if not os.path.exists(workdir):
48 data_manager_entry = {} 43 data_manager_entry = {}
49 data_manager_entry['value'] = args.name.lower() 44 data_manager_entry['value'] = args.name.lower()
50 data_manager_entry['name'] = args.name 45 data_manager_entry['name'] = args.name
51 data_manager_entry['path'] = '.' 46 data_manager_entry['path'] = '.'
52 data_manager_json = dict(data_tables=dict(ncbi_taxonomy=data_manager_entry)) 47 data_manager_json = dict(data_tables=dict(ncbi_taxonomy=data_manager_entry))
53 params = json.loads(open(args.output).read()) 48 with open(args.output) as fh:
49 params = json.load(fh)
54 target_directory = params['output_data'][0]['extra_files_path'] 50 target_directory = params['output_data'][0]['extra_files_path']
55 os.mkdir(target_directory) 51 os.mkdir(target_directory)
56 output_path = os.path.abspath(os.path.join(os.getcwd(), 'taxonomy')) 52 output_path = os.path.abspath(os.path.join(os.getcwd(), 'taxonomy'))
57 for filename in os.listdir(workdir): 53 for filename in os.listdir(workdir):
58 shutil.move(os.path.join(output_path, filename), target_directory) 54 shutil.move(os.path.join(output_path, filename), target_directory)
59 with open(args.output, 'w') as out: 55 with open(args.output, 'w') as fh:
60 out.write(json.dumps(data_manager_json, sort_keys=True)) 56 json.dump(data_manager_json, fh, sort_keys=True)
61 57
62 58
63 if __name__ == '__main__': 59 if __name__ == '__main__':
64 parser = argparse.ArgumentParser(description='Create data manager json.') 60 parser = argparse.ArgumentParser(description='Create data manager json.')
65 parser.add_argument('--out', dest='output', action='store', help='JSON filename') 61 parser.add_argument('--out', dest='output', action='store', help='JSON filename')