8000 Do not overwrite OPENMS_DATA_PATH in PyOpenMS if it is already set by radusuciu · Pull Request #5562 · OpenMS/OpenMS · GitHub
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Do not overwrite OPENMS_DATA_PATH in PyOpenMS if it is already set #5562

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Merged
merged 4 commits into from
Sep 29, 2021
Merged

Do not overwrite OPENMS_DATA_PATH in PyOpenMS if it is already set #5562

merged 4 commits into from
Sep 29, 2021

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radusuciu
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@radusuciu radusuciu commented Sep 27, 2021 •
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Description

I've got a lot of customizations (mostly to unimod.xml ) that I've set in a new directory that is referenced by OPENMS_DATA_PATH but PyOpenMS clobbers that on initialization. This simple modification should prevent it from doing so, if there is a path already set.

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  • Make sure that you are listed in the AUTHORS file
  • Add relevant changes and new features to the CHANGELOG file
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@radusuciu
Do not overwrite OPENMS_DATA_PATH in PyOpenMS if it is already set (#1)
dfe1f8b 
* Do not overwrite OPENMS_DATA_PATH if it is already set
* Update CHANGELOG
* Update AUTHORS
@radusuciu radusuciu changed the title Do not overwrite OPENMS_DATA_PATH in PyOpenMS if it is already set (#1) Do not overwrite OPENMS_DATA_PATH in PyOpenMS if it is already set Sep 27, 2021
@timosachsenberg
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@jpfeuffer looks reasonable. We often have both OpenMS and pyOpenMS installed so if versions differ this might lead to problems. E.g., new OpenMS version with Elements.xml removed and old version of pyOpenMS that expects the file to exist in share. Do you think we need to cover that case?

@jpfeuffer
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Hmm yes, I am not sure. Maybe we should print an info message that the path is set from outside and will be used?

@timosachsenberg
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I agree. Outputting a warning like:
"Warning: OPENMS_DATA_PATH environment variable already exists. pyOpenMS will use it ('" + path + "') to locate data in the OpenMS share folder (e.g., the unimod database)."
Would suffice @radusuciu can you add this?

@radusuciu
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radusuciu commented Sep 28, 2021 •
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That sounds very reasonable, apologies for the accidental merge commit - I didn't mean to push when I did. I have a slight edit to make to make the line length more reasonable if that's okay with you. I also added in the default path in the error message and used variables + str.format() to make things a little cleaner (subjective obviously).

@radusuciu
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Regardless of whether or not you accept my stylistic change, thank you very much for being open to this small contribution! This makes my life just a littttle bit easier :)

@radusuciu
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radusuciu commented Sep 28, 2021 •
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An alternative that I just thought about would be to have a different environment variable that is specific to PyOpenMS eg. PYOPENMS_DATA_PATH or similar.

default_openms_data_path = os.path.join(here, "share/OpenMS")
pyopenms_openms_data_path = os.environ.get("PYOPENMS_DATA_PATH")

os.environ["OPENMS_DATA_PATH"] = pyopenms_openms_data_path or default_openms_data_path

or

default_openms_data_path = os.path.join(here, "share/OpenMS")
os.environ["OPENMS_DATA_PATH"] = os.environ.get("PYOPENMS_DATA_PATH", default_openms_data_path)

This probably wouldn't necessitate a warning, just some documentation about PYOPENMS_DATA_PATH.

@timosachsenberg
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Nice. Thanks for the cleanup. From my side this PR is good to go!

oliveralka
oliveralka approved these changes Sep 29, 2021
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Looks good!

@oliveralka oliveralka merged commit 9163f07 into OpenMS:develop Sep 29, 2021
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@radusuciu @timosachsenberg @jpfeuffer @oliveralka
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