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Windows: image file delete impossible after adding it to project when using Bioformats #23

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ap-- opened this issue Jul 29, 2020 · 9 comments
Open
3 tasks

Windows: image file delete impossible after adding it to project when using Bioformats #23

ap-- opened this issue Jul 29, 2020 · 9 comments
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@ap--
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ap-- commented Jul 29, 2020 •
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Update

So it seems as if deleting an image file on windows in the same session that is was added via QuPathProject.add_image causes a Permission exception on Windows.

Causes I'm investigating currently:

  • it's probably just Windows
  • our windows tests on the CI use qupath's bioformats imageserver extension instead of openslide
  • maybe bioformats imageserver .close method is not implemented correctly

Initial issue

So windows had two failing tests (AND loads of thread error messages that might be pytest related...)
1951a56 fixed one of them.

A potential reason why the windows tests fails is, that we don't have a https://anaconda.org/sdvillal/qupath QuPath v0.2.1 pkg for windows. And we're currently testing against 0.2.0-m11...

@sdvillal it looks like you cancelled the CI when it was building the windows packages. the job failed to upload
could you rerun them? ❤️
@sdvillal
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yes, I rerun the job already but it kept refusing the upload; I will package 0.2.2 and let's cross fingers that the CI completes this time

@sdvillal
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0.2.2 is now up in the channel and this time windows upload did not get stuck

Note that while I had been testing both the qupath packages and pimping it from python for a few months in linux and mac, how these things work in windows is terra incognita. If it gets nasty we probably will be better off testing using one of these free VMs from microsoft, or maybe we can use the "mycloud" thingy?

@ap--
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ap-- commented Jul 30, 2020

Okay, So I can reproduce locally. And other than failing one test, we're hitting:
jpype-project/jpype#561

@ap--
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ap-- commented Jul 30, 2020

windows pytest output is now spam free: a5b5cb6

@sdvillal
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windows pytest output is now spam free: a5b5cb6

can we use pyproject.toml instead of pytest.ini?

@ap--
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ap-- commented Jul 30, 2020

pytest-dev/pytest#1556

Now that pytest 6.0 is out: yes 😄

@ap--
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ap-- commented Jul 30, 2020

@sdvillal is there (and if yes what is) the best way to get openslide working with our conda qupath?

@ap--
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ap-- commented Jul 30, 2020

Note: The test's on windows are using the bioformatsimageserver backend.

I believe that some filehandles are still open, because bioformats readers are not explicitly closed here:
https://github.com/qupath/qupath/blob/ecac7c444f8099b288a065dd754025d19e7791d1/qupath-extension-bioformats/src/main/java/qupath/lib/images/servers/bioformats/BioFormatsImageServer.java#L975-L978

@ap-- ap-- mentioned this issue Jul 30, 2020
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@ap-- ap-- changed the title Windows tests fail Windows: deletion of image file impossible after adding it as project entry Jul 30, 2020
@ap-- ap-- added the bug Something isn't working label Jul 30, 2020
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ap-- commented Jul 30, 2020

Ah 💡

https://github.com/bayer-science-for-a-better-life/paquo/blob/b212aea59466893a6773d67db13473a21ac2f18b/paquo/tests/test_images.py#L41-L61

Is probably the difference between openslide and bioformats...

ap-- added a commit that referenced this issue Aug 3, 2020
@ap--
paquo.jpype_backend: remove macos jvm_options
d7df792 
This solves the mystery why macos used a different image backend
which caused the downsampling test to report a different set of
levels...

#23 (comment)
@ap-- ap-- changed the title Windows: deletion of image file impossible after adding it as project entry Windows: image file delete impossible after adding it to project when using Bioformats Aug 5, 2020
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