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Galaxy is not recognizing sklearn input 'zip' files #1113

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cat-bro opened this issue Apr 27, 2021 · 0 comments
Open

Galaxy is not recognizing sklearn input 'zip' files #1113

cat-bro opened this issue Apr 27, 2021 · 0 comments

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@cat-bro
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cat-bro commented Apr 27, 2021

sklearn_searchcv and a number of other sklearn tools have input test files that are imported as type 'zip'. Galaxy is throwing an error trying to import these:

For file https://github.com/bgruening/galaxytools/blob/master/tools/sklearn/test-data/pipeline01

 Traceback (most recent call last):                                                            
   File "/mnt/galaxy/galaxy-app/tools/data_source/upload.py", line 339, in <module>            
     __main__()                                                                                
   File "/mnt/galaxy/galaxy-app/tools/data_source/upload.py", line 332, in __main__            
     metadata.append(add_file(dataset, registry, output_path))                                 
   File "/mnt/galaxy/galaxy-app/tools/data_source/upload.py", line 131, in add_file            
     stdout, ext, datatype, is_binary, converted_path = handle_upload(                         
   File "/mnt/galaxy/galaxy-app/lib/galaxy/datatypes/upload_util.py", line 70, in handle_upload
     if check_content and hasattr(datatype, 'sniff') and not datatype.sniff(path):             
   File "/mnt/galaxy/galaxy-app/lib/galaxy/datatypes/binary.py", line 282, in sniff            
     with zipfile.ZipFile(filename) as zf:                                                     
   File "/usr/lib/python3.8/zipfile.py", line 1269, in __init__                                
     self._RealGetContents()                                                                   
   File "/usr/lib/python3.8/zipfile.py", line 1336, in _RealGetContents                        
     raise BadZipFile("File is not a zip file")                                                
 zipfile.BadZipFile: File is not a zip file                  

I'm seeing this error when trying to import it as a zip on Galaxy Australia and Galaxy Europe. These tests passed when we first installed it a year ago so the files must have uploaded without error on Galaxy version 20.01. Could this be a galaxy bug?

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