mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-01 15:37:32 +08:00
John Davis
69 lines
2.6 KiB
Python
69 lines
2.6 KiB
Python
import argparse
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import difflib
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import logging
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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
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import galaxy.app
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import galaxy.config
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from galaxy.managers.pages import (
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PageContentProcessor,
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placeholderRenderForSave,
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)
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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.security.idencoding import IdEncodingHelper
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from galaxy.util import unicodify
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from galaxy.util.bunch import Bunch
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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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def main(argv):
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parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter)
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parser.add_argument("-k", "--secret-key", help="Key to convert pages with", default="")
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parser.add_argument("-d", "--dry-run", help="No changes, just test it.", action="store_true")
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populate_config_args(parser)
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args = parser.parse_args()
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properties = app_properties_from_args(args)
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config = galaxy.config.Configuration(**properties)
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secret = args.secret_key or config.id_secret
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security_helper = IdEncodingHelper(id_secret=secret)
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object_store = build_object_store_from_config(config)
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if not config.database_connection:
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print(
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"The database connection is empty. If you are using the default value, please uncomment that in your galaxy.yml"
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)
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model = init_models_from_config(config, object_store=object_store)
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session = model.context.current()
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pagerevs = session.query(model.PageRevision).all()
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mock_trans = Bunch(app=Bunch(security=security_helper), model=model, user_is_admin=lambda: True, sa_session=session)
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for p in pagerevs:
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try:
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processor = PageContentProcessor(mock_trans, placeholderRenderForSave)
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processor.feed(p.content)
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newcontent = unicodify(processor.output(), "utf-8")
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if p.content != newcontent:
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if not args.dry_run:
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p.content = unicodify(processor.output(), "utf-8")
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session.add(p)
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session.commit()
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else:
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print(f"Modifying revision {p.id}.")
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print(difflib.unified_diff(p.content, newcontent))
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except Exception:
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logging.exception(
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"Error parsing page, rolling changes back and skipping revision %s. Please report this error.", p.id
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)
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session.rollback()
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if __name__ == "__main__":
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main(sys.argv)
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