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0a64694fa5
* update rbfe_results.tar.gz for new settings schema * re-enable test_gather tests * devscript for updating rbfe_results.tar.gz * cli: gather: rework raw gather to work off protocol_result dict this allows us to later deduplicate and remove the unit_results key from results dicts * cli: gather: update expected gather results current raw results are only one replicate, should probably have multiple repeats to test raw output * cli: gather: use \t escape code in gather raw test could instead normalise the whitespace to be more permissive... * Apply suggestions from code review Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com> * rerun ci --------- Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com>
58 lines
1.5 KiB
Python
58 lines
1.5 KiB
Python
"""A script to fix up rbfe_results.tar.gz
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Useful if Settings are ever changed in a backwards-incompatible way
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Will expect "rbfe_results.tar.gz" in this directory, will overwrite this file
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"""
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from gufe.tokenization import JSON_HANDLER
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import glob
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import json
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from openfe.protocols import openmm_rfe
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import os.path
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import tarfile
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def untar(fn):
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"""extract tarfile called *fn*"""
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with tarfile.open(fn) as f:
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f.extractall()
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def retar(loc, name):
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"""create tar.gz called *name* of directory *loc*"""
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with tarfile.open(name, mode='w:gz') as f:
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f.add(loc, arcname=os.path.basename(loc))
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def replace_settings(fn, new_settings):
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"""replace settings instances in *fn* with *new_settings*"""
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with open(fn, 'r') as f:
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data = json.load(f)
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for k in data['protocol_result']['data']:
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data['protocol_result']['data'][k][0]['inputs']['settings'] = new_settings
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for k in data['unit_results']:
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data['unit_results'][k]['inputs']['settings'] = new_settings
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with open(fn, 'w') as f:
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json.dump(data, f, cls=JSON_HANDLER.encoder)
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def fix_rbfe_results():
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untar('rbfe_results.tar.gz')
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# generate valid settings as defaults
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new_settings = openmm_rfe.RelativeHybridTopologyProtocol.default_settings()
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# walk over all result jsons
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for fn in glob.glob('./results/*json'):
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# replace instances of settings within with valid settings
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replace_settings(fn, new_settings)
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retar('results', 'rbfe_results.tar.gz')
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if __name__ == '__main__':
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fix_rbfe_results()
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