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Bugfix for sequence #73

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lakodarmstadt wants to merge 1 commit into from
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Bugfix for sequence #73

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6 changes: 6 additions & 0 deletions lyse/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -246,6 +246,7 @@ def save_result_array(self, name, data, group=None,
if not group:
# Save dataset to results group by default
group = 'results/' + self.group

@philipstarkey philipstarkey Oct 19, 2020

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Could you remove this unnecessary change so that it doesn't clutter up the diff?

elif not group in h5_file:
# Create the group if it doesn't exist
h5_file.create_group(group)
Expand Down Expand Up @@ -422,6 +423,11 @@ def __init__(self, h5_path, run_paths, no_write=False):
run_paths = run_paths['filepath']
self.h5_path = h5_path
self.no_write = no_write
try:
h5py.File(h5_path, 'r')

@philipstarkey philipstarkey Oct 19, 2020

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I think that this may leave an open reference to the h5 file. It would be better to use a context manager like this:

with h5py.File(h5_path, 'r') as f:
    pass

Which ensures that the file is closed appropriately.

except:

@philipstarkey philipstarkey Oct 19, 2020

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It is best to catch a specific exception class here. Could you catch the specific exception raised? (Presumably it is FileNotFoundError?)

h5py.File(h5_path,'w')

@philipstarkey philipstarkey Oct 19, 2020

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Similar to previous comment, use of a context manager here would be preferable. Also, you might want to consider using the 'a' filemode (so that the file doesn't get truncated should it happen to be created by an external process in between the two h5py calls executing - which could conceivably be a significant time should there be contention on the zlock/h5lock lock).

I think it might also be appropriate to wrap the creation call in a check of the no_write argument and raise the FileNotFoundError should the file not exist and the no_write argument be true?


if not self.no_write:
self._create_group_if_not_exists(h5_path, '/', 'results')

Expand Down