Mercurial > repos > iuc > data_manager_interproscan
comparison data_manager/interproscan.py @ 1:0db4f153d86d draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 7fbeae66de8617e525cd968a2ef89b0be448a618"
author | iuc |
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date | Wed, 17 Nov 2021 19:16:17 +0000 |
parents | e93e32359b67 |
children | 0df47f8552f6 |
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0:e93e32359b67 | 1:0db4f153d86d |
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95 print("Downloading data tarball...") | 95 print("Downloading data tarball...") |
96 dest_tar = os.path.join(output_directory, DATA_URL.format(version=tag).split('/')[-1]) | 96 dest_tar = os.path.join(output_directory, DATA_URL.format(version=tag).split('/')[-1]) |
97 download_file(DATA_URL.format(version=tag), dest_tar) | 97 download_file(DATA_URL.format(version=tag), dest_tar) |
98 | 98 |
99 print("Finished, now checking md5...") | 99 print("Finished, now checking md5...") |
100 md5_computed = hashlib.md5(open(dest_tar, 'rb').read()).hexdigest() | 100 m = hashlib.md5() |
101 blocksize = 2**20 | |
102 with open(dest_tar, 'rb') as tarball: | |
103 while True: | |
104 buf = tarball.read(blocksize) | |
105 if not buf: | |
106 break | |
107 m.update(buf) | |
108 md5_computed = m.hexdigest() | |
101 if not md5.startswith(md5_computed): | 109 if not md5.startswith(md5_computed): |
102 raise RuntimeError("MD5 check failed: computed '%s', expected '%s'" % (md5_computed, md5)) | 110 raise RuntimeError("MD5 check failed: computed '%s', expected '%s'" % (md5_computed, md5)) |
103 | 111 |
104 print("Ok, now extracting data...") | 112 print("Ok, now extracting data...") |
105 tar = tarfile.open(dest_tar, "r:gz") | 113 tar = tarfile.open(dest_tar, "r:gz") |
109 if args.partial: | 117 if args.partial: |
110 print("Moving partial data files around...") | 118 print("Moving partial data files around...") |
111 shutil.move(os.path.join(output_directory, 'interproscan-%s' % tag, 'core/jms-implementation/support-mini-x86-32/data/'), os.path.join(output_directory, 'data')) | 119 shutil.move(os.path.join(output_directory, 'interproscan-%s' % tag, 'core/jms-implementation/support-mini-x86-32/data/'), os.path.join(output_directory, 'data')) |
112 else: | 120 else: |
113 print("Moving data files around...") | 121 print("Moving data files around...") |
114 shutil.move(os.path.join(output_directory, 'interproscan-%s' % tag), os.path.join(output_directory, 'data')) | 122 shutil.move(os.path.join(output_directory, 'interproscan-%s' % tag, 'data'), os.path.join(output_directory, 'data')) |
115 | 123 |
116 print("Done, removing tarball and unneeded files...") | 124 print("Done, removing tarball and unneeded files...") |
117 os.remove(dest_tar) | 125 os.remove(dest_tar) |
118 shutil.rmtree(os.path.join(output_directory, 'interproscan-%s' % tag)) | 126 shutil.rmtree(os.path.join(output_directory, 'interproscan-%s' % tag)) |
119 | 127 |