OSError: [WinError 193] %1 is not a valid Win32 application when running owltools on Windows

[shreema26]

Description:

I'm encountering an error when trying to execute the owltools file after cloning the OMOP2OBO repository. The error message is as follows:
OSError: [WinError 193] %1 is not a valid Win32 application

Additional Information:
Operating System: Windows
Python Version: 3.12.6
Error Screenshot(s):

The error seems to indicate that the owltools file is not recognized as a valid executable on Windows. It might be related to compatibility issues or platform-specific requirements.

If there are any suggestions on resolving this issue or if there's a compatible version of owltools for Windows, please advise.

[callahantiff]

Hi @shreema26 -- Sorry for the delay. The code was developed and in tested for OSX and I am not a Windows user, but I will do my best to try and help (especially since I cannot reproduce the error on my end) 🙃😄.

This stack overview post seems particularly relevant and suggests something quick you can try. Can you run the following in your Python console within the project directory?

import os.path
import subprocess

owltools_location  = './omop2obo/libs/owltools'
write_loc = 'resources/ontologies/cl'
source = 'http://purl.obolibrary.org/obo/cl.owl'

subprocess.check_call(
    [os.path.abspath(owltools_location),
     str(source),
     '-o',
     str(write_loc) + '_without_imports.owl'],
    shell=True)

This is the functionality in the method that caused the error with one difference, the addition of shell=True in the subprocess.check_call() function. This may not work but it's worth a try.

[shreema26]

Hi Tiffany, I am Shreema from the OHDSI India chapter.I wanted to let you know that I tried implementing the method you suggested and also made some changes to the .py files to make them compatible with Windows. However, I’m still encountering the same issue, which I’ve attached for reference. Would it be possible to connect over a call, perhaps for 15 minutes, to go through this together? I believe discussing it might help us find a solution more effectively. Thank you very much for your assistance and time. Best regards, Shreema S Rao Junior Data Engineer [cid:b09fcb7c-b11d-4873-95a8-0100b29dd958] Cell IN +91 8277159297 [cid:555ada65-b370-4790-8f1b-6d0ad750d603]<https://global-value-web.com/> Follow us: LinkedIn<https://www.linkedin.com/company/global-value-web> | Website<https://global-value-web.com/>

…

________________________________ From: Tiffany J. Callahan ***@***.***> Sent: Friday, October 25, 2024 10:47 PM To: callahantiff/OMOP2OBO ***@***.***> Cc: Shreema S Rao ***@***.***>; Mention ***@***.***> Subject: Re: [callahantiff/OMOP2OBO] OSError: [WinError 193] %1 is not a valid Win32 application when running owltools on Windows (Issue #82) Hi @shreema26<https://github.com/shreema26> -- Sorry for the delay. The code was developed and in tested for OSX and I am not a Windows user, but I will do my best to try and help (especially since I cannot reproduce the error on my end) 🙃😄. This stack overview<https://stackoverflow.com/questions/25651990/oserror-winerror-193-1-is-not-a-valid-win32-application> post seems particularly relevant and suggests something quick you can try. Can you run the following in your Python console within the project directory? import os.path import subprocess owltools_location = './omop2obo/libs/owltools' write_loc = 'resources/ontologies/cl' source = 'http://purl.obolibrary.org/obo/cl.owl' subprocess.check_call( [os.path.abspath(owltools_location), str(source), '-o', str(write_loc) + '_without_imports.owl'], shell=True) This is the functionality in the method that caused the error with one difference, the addition of shell=True in the subprocess.check_call() function. This may not work but it's worth a try. — Reply to this email directly, view it on GitHub<#82 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/BAGYPXFBFMM6I5HBPWS5E4LZ5J4LDAVCNFSM6AAAAABPUAXHP2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDIMZYGM4DKNZSG4>. You are receiving this because you were mentioned.Message ID: ***@***.***>

[callahantiff]

Hi @shreema26. I received your email but like last time, but similar to last time my responses keep getting bounced. Is there another email address that I can reach you at. Here is the message that I tried to email you:

Hi Shreema-

Thank you for your email and apologies for the delay in responding. OMOP2OBO is not part of my current job so any work to it has to happen outside of work hours.

I’m sorry to hear that my precious suggestion did not resolve your error. As I mentioned in the issue, OMOP2OBO was not developed on windows nor has it been tested on it. It does work without any issues when run on a Mac, which is the system it was developed on. While it would be fantastic if it could run on Windows, it’s not something I am personally able to support at this time. So, I am very sorry but I’m afraid that even if we were to meet, I would not be very helpful as I don’t use Windows nor develop for that operating system. The previous fix I sent was what I found after Googling the error message you described.

What I can suggest is to try to contact the maintainer of OWLTools, https://github.com/owlcollab/owltools (https://github.com/owlcollab/owltools). They should ultimately be able to tell you if/how it can be used on a windows machine. Also make sure your version of Python matches what the omop2obo repo requires (3.6). I don’t think this is what is causing you trouble but it’s always good to check.

If you are able to find a work solution on Windows, I’d be happy to incorporate the changes. Windows support/maintenance is just not something I can provide at this time. 

One final thing I can suggest if you are not able to find a resolution through OWLTools, is that there are ways to use the program without it. You will just have to download the ontologies manually and put them in the correct location. There may be a few more uses of OWLTools throughout the program but they are similarly minor. While this might get you through, please note that there might be other issues as this code was not developed for nor tested on a Windows machine.

Apologies there is not more I can do at this time but I’m afraid I don’t have the right expertise to aid in the use of this program on your operating system.

Are you trying to create mappings using an ontology other than what was used in the paper? If not, I highly recommend downloading the existing mapping set that’s linked through the repo. Maybe you can tell me a little more about your use case?

-Tiffany