mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-08-31 01:02:04 +08:00
Nicola Soranzo
60 lines
1.8 KiB
Python
60 lines
1.8 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.model.base import transaction
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from galaxy.model.mapping import init_models_from_config
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from galaxy.objectstore import build_object_store_from_config
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from galaxy.util.script import (
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app_properties_from_args,
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populate_config_args,
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)
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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 = 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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session = sa_session()
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set = 0
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dataset_count = sa_session.query(model.Dataset).count()
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print(f"Processing {dataset_count} datasets...")
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percent = 0
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print(f"Completed {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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with transaction(session):
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session.commit()
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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(f"\rCompleted {percent}%", end=" ")
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sys.stdout.flush()
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with transaction(session):
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session.commit()
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print("\rCompleted 100%")
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object_store.shutdown()
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