Mercurial > repos > pimarin > data_manager_bakta

comparison data_manager/bakta_build_database.py @ 15:ac4d5e1d1421 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit b082e89a0090f9c4b2a257bb06b7c6f141b42650-dirty
author pimarin
date Wed, 02 Nov 2022 16:21:11 +0000
parents bcac3aa1f494
children 718080c30a76
comparison
equal deleted inserted replaced
14:bcac3aa1f494 15:ac4d5e1d1421
7 import tarfile 7 import tarfile
8 from datetime import datetime 8 from datetime import datetime
9 from pathlib import Path 9 from pathlib import Path
10 10
11 import requests 11 import requests
12 from alive_progress import alive_bar
13
14 class GetBaktaDatabaseInfo: 12 class GetBaktaDatabaseInfo:
15 """ 13 """
16 Extract bakta database information to make a json file for data_manager 14 Extract bakta database information to make a json file for data_manager
17 """ 15 """
18 16
136 try: 134 try:
137 with bakta_path.open('wb') as fh_out, \ 135 with bakta_path.open('wb') as fh_out, \
138 requests.get(self.db_url, stream=True) as resp: 136 requests.get(self.db_url, stream=True) as resp:
139 total_length = resp.headers.get('content-length') 137 total_length = resp.headers.get('content-length')
140 if total_length is None: # no content length header 138 if total_length is None: # no content length header
141 with alive_bar() as bar: 139 for data in resp.iter_content(chunk_size=1024 * 1024):
142 for data in resp.iter_content(chunk_size=1024 * 1024): 140 fh_out.write(data)
143 fh_out.write(data)
144 bar()
145 else: 141 else:
146 total_length = int(int(total_length) / 1024) 142 for data in resp.iter_content(chunk_size=1024 * 1024):
147 with alive_bar(total=total_length) as bar: 143 fh_out.write(data)
148 for data in resp.iter_content(chunk_size=1024 * 1024):
149 fh_out.write(data)
150 bar(incr=len(data) / 1024)
151 print(f'Download bakta database {self.db_version}') 144 print(f'Download bakta database {self.db_version}')
152 self.tarball_path = bakta_path 145 self.tarball_path = bakta_path
153 except IOError: 146 except IOError:
154 print(f'ERROR: Could not download file from Zenodo!' 147 print(f'ERROR: Could not download file from Zenodo!'
155 f' url={self.db_url}, path={self.tarball_name}') 148 f' url={self.db_url}, path={self.tarball_name}')