Update fetch results (#779)

* 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>

devtools/data/fix_rbfe_results.py

@@ -0,0 +1,57 @@
+"""A script to fix up rbfe_results.tar.gz
+
+Useful if Settings are ever changed in a backwards-incompatible way
+
+Will expect "rbfe_results.tar.gz" in this directory, will overwrite this file
+"""
+from gufe.tokenization import JSON_HANDLER
+import glob
+import json
+from openfe.protocols import openmm_rfe
+import os.path
+import tarfile
+
+
+def untar(fn):
+    """extract tarfile called *fn*"""
+    with tarfile.open(fn) as f:
+        f.extractall()
+
+
+def retar(loc, name):
+    """create tar.gz called *name* of directory *loc*"""
+    with tarfile.open(name, mode='w:gz') as f:
+        f.add(loc, arcname=os.path.basename(loc))
+
+
+def replace_settings(fn, new_settings):
+    """replace settings instances in *fn* with *new_settings*"""
+    with open(fn, 'r') as f:
+        data = json.load(f)
+
+    for k in data['protocol_result']['data']:
+        data['protocol_result']['data'][k][0]['inputs']['settings'] = new_settings
+
+    for k in data['unit_results']:
+        data['unit_results'][k]['inputs']['settings'] = new_settings
+
+    with open(fn, 'w') as f:
+        json.dump(data, f, cls=JSON_HANDLER.encoder)
+
+
+def fix_rbfe_results():
+    untar('rbfe_results.tar.gz')
+
+    # generate valid settings as defaults
+    new_settings = openmm_rfe.RelativeHybridTopologyProtocol.default_settings()
+
+    # walk over all result jsons
+    for fn in glob.glob('./results/*json'):
+        # replace instances of settings within with valid settings
+        replace_settings(fn, new_settings)
+
+    retar('results', 'rbfe_results.tar.gz')
+
+
+if __name__ == '__main__':
+    fix_rbfe_results()