mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-19 10:51:34 +08:00
Nicola Soranzo
9d74bba7fb
Upgrade syntax using `pyupgrade --py36-plus` . Manually drop several `six` imports. Also: - Remove broken pr_cache in scripts/bootstrap_history.py - Fix broken prefix removal in lib/galaxy/tool_util/deps/mulled/mulled_build.py
52 lines
1.6 KiB
Python
52 lines
1.6 KiB
Python
#!/usr/bin/env python
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import argparse
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import os
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import sys
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sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, 'lib')))
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import galaxy.config
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from galaxy.objectstore import build_object_store_from_config
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from galaxy.util.script import app_properties_from_args, populate_config_args
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parser = argparse.ArgumentParser()
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populate_config_args(parser)
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args = parser.parse_args()
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def init():
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app_properties = app_properties_from_args(args)
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config = galaxy.config.Configuration(**app_properties)
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object_store = build_object_store_from_config(config)
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model = galaxy.config.init_models_from_config(config, object_store=object_store)
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return model, object_store
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if __name__ == '__main__':
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print('Loading Galaxy model...')
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model, object_store = init()
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sa_session = model.context.current
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set = 0
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dataset_count = sa_session.query(model.Dataset).count()
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print('Processing %i datasets...' % dataset_count)
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percent = 0
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print('Completed %i%%' % percent, end=' ')
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sys.stdout.flush()
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for i, dataset in enumerate(sa_session.query(model.Dataset).enable_eagerloads(False).yield_per(1000)):
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if dataset.total_size is None:
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dataset.set_total_size()
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set += 1
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if not set % 1000:
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sa_session.flush()
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new_percent = int(float(i) / dataset_count * 100)
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if new_percent != percent:
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percent = new_percent
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print('\rCompleted %i%%' % percent, end=' ')
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sys.stdout.flush()
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sa_session.flush()
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print('\rCompleted 100%')
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object_store.shutdown()
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