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1104 gather check json files #1112

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1104 gather check json files #1112

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a45f4b5
adding output for failed edges
atravitz Jan 30, 2025
51e1905
adding print statements, tests don't pass yet because of extra output
atravitz Jan 30, 2025
87668e6
Merge branch 'main' of github.com:OpenFreeEnergy/openfe into 1104-gat…
atravitz Jan 31, 2025
44e5d1c
remove straggler
atravitz Jan 31, 2025
33498c0
Update openfecli/commands/gather.py
atravitz Feb 10, 2025
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26 changes: 20 additions & 6 deletions openfecli/commands/gather.py
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Original file line number Diff line number Diff line change
Expand Up @@ -79,7 +79,7 @@ def is_results_json(fpath:os.PathLike|str)->bool:
return 'estimate' in open(fpath, 'r').read(20)


def load_results(fpath:os.PathLike|str)->dict:
def load_and_check_result(fpath:os.PathLike|str)->dict:
"""Load the data from a results JSON into a dict

Parameters
Expand All @@ -96,8 +96,25 @@ def load_results(fpath:os.PathLike|str)->dict:
import json
from gufe.tokenization import JSON_HANDLER

return json.load(open(fpath, 'r'), cls=JSON_HANDLER.decoder)
try:
result = json.load(open(fpath, 'r'), cls=JSON_HANDLER.decoder)
except FileNotFoundError:
click.echo(f"Error: {fpath} does not exist. Skipping.")
return None

if "unit_results" not in result.keys():
click.echo(f"{fpath}: No 'unit_results' found, assuming to be a failed simulation.", err=True)

if all('exception' in u for u in result['unit_results'].values()):
click.echo(f"{fpath}: Exception found in 'unit_results', assuming to be a failed simulation.", err=True)

if result['estimate'] is None:
click.echo(f"No{fpath}: No 'estimate' found, assuming to be a failed simulation", err=True)
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if result['uncertainty'] is None:
click.echo(f"{fpath}: No 'uncertainty' found, assuming to be a failed simulation", err=True)
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If an edge has failed this will print all of these messages for that edge? It would be best to have a single message per edge indicating if it has failed.


return result

def get_names(result:dict) -> tuple[str, str]:
"""Get the ligand names from a unit's results data.
Expand Down Expand Up @@ -397,12 +414,9 @@ def gather(rootdir:os.PathLike|str,
legs = defaultdict(lambda: defaultdict(list))

for result_fn in result_fns:
result = load_results(result_fn)
result = load_and_check_result(result_fn)
if result is None:
continue
elif result['estimate'] is None or result['uncertainty'] is None:
click.echo(f"WARNING: Calculations for {result_fn} did not finish successfully!",
err=True)

try:
names = get_names(result)
Expand Down
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