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vjcitn / rhdf5client

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Fix for string-only compounds + add reporting of request errors #6

Closed assaron closed 10 months ago

vjcitn commented 1 year ago

Would you please bump version in DESCRIPTION with any PR? Thanks

assaron commented 1 year ago

Yes, sorry, now it should be with the proper version.

vjcitn commented 11 months ago

I may have missed this. But it looks like the hsdshdflab.hdfgroup.org is not working right now. Do you think it would be possible to emulate the tests in hdf5 data that we could install at our bioconductor service?

assaron commented 11 months ago

@vjcitn Hi, I think hsdshdflab.hdfgroup.org is up right now.

Do you think it would be possible to emulate the tests in hdf5 data that we could install at our bioconductor service?

Not sure what you mean. What exactly is your bioconductor service?

vjcitn commented 11 months ago

hi @assaron -- what I mean is that if you can grab the hdf5 entities that your tests use, from the hdfgroup services that is being shut down, then I can add them to our bioconductor hsds system so that your tests can run against those with the proper URL.

assaron commented 10 months ago

@vjcitn got you. I've committed a generator for test files (not sure where to put the actual files) and changed the test accordingly (but they're failing, as the url is incorrect). Is that what you meant? Is there a public url for bioconductor hsds service?

vjcitn commented 10 months ago

The bioconductor hsds is at https://hsdsdev.bioconductor.org -- i have uploaded your files. I think I have to change the src values in the tests.

  hsload /home/stvjc/HSDS/alexey/inst/test_scalar.h5 /shared/bioconductor/test_scalar.h5
  hsacl /shared/bioconductor/test_scalar.h5 +re default
       username     create      read    update    delete   readACL  updateACL 
--------------------------------------------------------------------------------
        default      False      True     False     False      True     False 
  hsload /home/stvjc/HSDS/alexey/inst/test_string.h5 /shared/bioconductor/test_string.h5
  hsacl /shared/bioconductor/test_string.h5 +re default
       username     create      read    update    delete   readACL  updateACL 
--------------------------------------------------------------------------------
        default      False      True     False     False      True     False 
  hsload /home/stvjc/HSDS/alexey/inst/test_compound.h5 /shared/bioconductor/test_compound.h5
  hsacl /shared/bioconductor/test_compound.h5 +re default
       username     create      read    update    delete   readACL  updateACL 
--------------------------------------------------------------------------------
        default      False      True     False     False      True     False
vjcitn commented 10 months ago

the tests are all revised and passing

assaron commented 10 months ago

Great, thanks!