Mercurial > repos > iuc > data_manager_gtdbtk_database_installer

comparison data_manager/gtdbtk_database_installer.py @ 6:df84aaed4769 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit a7a73e892ade5f3cb5207c411b8ac27b684316ff
author iuc
date Mon, 09 Sep 2024 09:01:39 +0000
parents 10232d2b5062
children 3b1d503c6260
comparison
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5:e7b39a7e0024 6:df84aaed4769
102 os.remove(tarball) 102 os.remove(tarball)
103 else: 103 else:
104 # handle the test case for the DB 104 # handle the test case for the DB
105 return tarball 105 return tarball
106 106
107 fh.extractall(target_directory)
108 fh.close()
109 os.remove(tarball)
110 # The tarball extraction will create a directory named 107 # The tarball extraction will create a directory named
111 # something like release202 in the target_directory, so 108 # something like release202 in the target_directory, so
112 # we need to move the items in that directory to the 109 # we need to move the items in that directory to the
113 # target directory. 110 # target directory.
114 subdir = next(os.walk(target_directory))[1][0] 111 subdir = next(os.walk(target_directory))[1][0]
131 128
132 if test: 129 if test:
133 # switch the DB to use the test case 130 # switch the DB to use the test case
134 urls[release][ 131 urls[release][
135 "full" 132 "full"
136 ] = "https://data.gtdb.ecogenomic.org/releases/release220/220.0/VERSION.txt" 133 ] = "https://zenodo.org/records/13734217/files/release220-test.tar.gz"
137 134
138 # make use of the test to check if all urls exists 135 # make use of the test to check if all urls exists
139 for _version, items in urls.items(): 136 for _version, items in urls.items():
140 for url in items.values(): 137 for url in items.values():
141 assert is_urlfile(url) 138 assert is_urlfile(url)