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Fix MS consumer Code blocks

Open jpfeuffer opened this issue 1 year ago • 0 comments

They are apparently declared as "output" not "python" because they are not working.

---------------------------------------------------------------------------
RuntimeError                              Traceback (most recent call last)
Cell In[8], line 34
     31 consumer = oms.PlainMSDataWritingConsumer(outputfile)
     32 consumer = FilteringConsumer(consumer, filter_string)
---> 34 oms.MzMLFile().transform(inputfile,consumer)

File pyopenms/_pyopenms_7.pyx:10193, in pyopenms._pyopenms_7.MzMLFile.transform()

File pyopenms/_pyopenms_7.pyx:10279, in pyopenms._pyopenms_7.MzMLFile._transform_1()

RuntimeError: - due to that error of type FileNotFound in: /__w/OpenMS/OpenMS/OpenMS/src/openms/source/FORMAT/XMLFile.cpp@107-void OpenMS::Internal::XMLFile::parse_(const OpenMS::String&, OpenMS::Internal::XMLHandler*)

I didn't check but it might be the change from output to python block. Maybe the code is not executable or a file missing. I think a quick fix for your PR would be to change it back to output.

Originally posted by @timosachsenberg in https://github.com/OpenMS/pyopenms-docs/pull/396#issuecomment-1552067570

jpfeuffer avatar May 18 '23 06:05 jpfeuffer