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57 lines
1.7 KiB
Python
Executable File
57 lines
1.7 KiB
Python
Executable File
#!/usr/bin/env python
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"""
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Updates dataset.size column.
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Remember to backup your database before running.
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Deprecated - this doesn't work with modern Galaxy configurations options.
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"""
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from __future__ import print_function
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import os
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import sys
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from six.moves import configparser
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sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, os.pardir, 'lib')))
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import galaxy.app
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assert sys.version_info[:2] >= (2, 6)
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def usage(prog):
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print("usage: %s galaxy.ini" % prog)
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print("""
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Updates the dataset.size column. Users are advised to backup the database before
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running.
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""")
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def main():
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if len(sys.argv) != 2 or sys.argv[1] == "-h" or sys.argv[1] == "--help":
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usage(sys.argv[0])
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sys.exit()
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ini_file = sys.argv.pop(1)
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conf_parser = configparser.ConfigParser({'here': os.getcwd()})
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conf_parser.read(ini_file)
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configuration = {}
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for key, value in conf_parser.items("app:main"):
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configuration[key] = value
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app = galaxy.app.UniverseApplication(global_conf=ini_file, **configuration)
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# Step through Datasets, determining size on disk for each.
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print("Determining the size of each dataset...")
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for row in app.model.Dataset.table.select().execute():
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purged = app.model.Dataset.get(row.id).purged
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file_size = app.model.Dataset.get(row.id).file_size
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if file_size is None and not purged:
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size_on_disk = app.model.Dataset.get(row.id).get_size()
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print("Updating Dataset.%d with file_size: %d" % (row.id, size_on_disk))
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app.model.Dataset.table.update(app.model.Dataset.table.c.id == row.id).execute(file_size=size_on_disk)
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app.shutdown()
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sys.exit(0)
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if __name__ == "__main__":
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main()
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