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https://github.com/galaxyproject/galaxy.git
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John Chilton
528497f7c4
I want to be able to use this class in galaxy.model and it doesn't have any dependnecies on "web" stuff so I'd like to move it out of galaxy.model and into galaxy.security. galaxy.model shouldn't have dependencies on galaxy.web (and doesn't after the recent 976f5ad367), so this pre-emptively ensures it doesn't require these dependencies for https://github.com/galaxyproject/galaxy/pull/7367.
This has the benefit of also eliminating any galaxy.web dependencies from the generic test base file (test/base/testcase.py) which has long been a goal of mine as well.
There are places we legimately use ID encoding and decoding for security (i.e. job files API) but for the most part it doesn't provide security for API endpoints and this causes confusion repeatedly, so I've started the process of renaming the contained class SecurityHelper to something I feel makes it clearer this is just about encoding and decoding IDs.
58 lines
2.5 KiB
Python
58 lines
2.5 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.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 app_properties_from_args, populate_config_args
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from galaxy.webapps.galaxy.controllers.page import _PageContentProcessor, _placeholderRenderForSave
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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("The database connection is empty. If you are using the default value, please uncomment that in your galaxy.yml")
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model = galaxy.config.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.flush()
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else:
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print("Modifying revision %s." % 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("Error parsing page, rolling changes back and skipping revision %s. Please report this error." % p.id)
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session.rollback()
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if __name__ == '__main__':
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main(sys.argv)
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