Mercurial > repos > iuc > data_manager_dada2

comparison data_manager/data_manager.py @ 4:739943802404 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
author iuc
date Sun, 22 Nov 2020 12:43:42 +0000
parents d17e5d13b86c
children
comparison
equal deleted inserted replaced
3:d17e5d13b86c 4:739943802404
98 shutil.copyfileobj(f_in, f_out) 98 shutil.copyfileobj(f_in, f_out)
99 99
100 100
101 def remote_dataset(dataset, outjson): 101 def remote_dataset(dataset, outjson):
102 102
103 with open(outjson) as jf: 103 with open(outjson) as fh:
104 params = json.loads(jf.read()) 104 params = json.load(fh)
105 105
106 workdir = params['output_data'][0]['extra_files_path'] 106 workdir = params['output_data'][0]['extra_files_path']
107 os.mkdir(workdir) 107 os.mkdir(workdir)
108 url_download(FILE2TAXURL[dataset], dataset + ".taxonomy", workdir) 108 url_download(FILE2TAXURL[dataset], dataset + ".taxonomy", workdir)
109 109
121 data_manager_entry['value'] = dataset 121 data_manager_entry['value'] = dataset
122 data_manager_entry['name'] = FILE2NAME[dataset] 122 data_manager_entry['name'] = FILE2NAME[dataset]
123 data_manager_entry['path'] = dataset + ".species" 123 data_manager_entry['path'] = dataset + ".species"
124 data_manager_json["data_tables"]["dada2_species"] = data_manager_entry 124 data_manager_json["data_tables"]["dada2_species"] = data_manager_entry
125 125
126 with open(outjson, 'w') as jf: 126 with open(outjson, 'w') as fh:
127 jf.write(json.dumps(data_manager_json, sort_keys=True)) 127 json.dump(data_manager_json, fh, sort_keys=True)
128 128
129 129
130 if __name__ == '__main__': 130 if __name__ == '__main__':
131 parser = argparse.ArgumentParser(description='Create data manager json.') 131 parser = argparse.ArgumentParser(description='Create data manager json.')
132 parser.add_argument('--out', action='store', help='JSON filename') 132 parser.add_argument('--out', action='store', help='JSON filename')