Unexpected behaviors in omerotools: parse_url and upload_image_to_omero

Hi all

while testing your OMERO_batch_projection.py script I noticed:

parse_url:

Lines 113-117 should be removed (they do not do anything)

python-imcflibs/src/imcflibs/imagej/omerotools.py

Lines 113 to 117 in 1f6b508

    
           image_ids = ( 
        
               [s.split("%")[0].replace("|", "") for s in omero_str.split("image-")[1:]] 
        
               if "image-" in omero_str 
        
               else omero_str.split(",") 
        
           )

Does not work with plain dataset ID. Running on dataset IDs results in an error.This would require checking if the supplied ID (e.g. 12345) is a Dataset, Project, or Image.

upload_image_to_omero:

It would be nice if it would check if the path exists and if not: raise a FileNotFoundError.

I can do a PR if you like, let me know!

Hi Loïc,

thanks for the report. I have edited your comment above to link to the respective functions and code blocks. Could you double-check this is correct, i.e. is what you meant please?

🤗

Thanks,
Niko

@loicsauteur

Could you double-check this is correct, i.e. is what you meant please?

Ping @loicsauteur

@ehrenfeu

Hi @ehrenfeu & @rohangirishrao

Yes, correct. Thanks for updating & sorry for the delayed answer.

@loicsauteur

Thanks, @loicsauteur

@loicsauteur

@loicsauteur: If you like, go ahead an provide a PR please! 🚀

Lines 113-117 should be removed (they do not do anything)

Not sure that this is true. This splits the string passed by the user and

if it's a link that contains multiple image-ids ("https://omero.biozentrum.unibas.ch/webclient/?show=image-1997093|image-1997094|image-1997095") it will only return the IDs as an array).
if it's just IDs separated by commas then it makes an array

@lguerard

Hi @lguerard

I described a bit clearer in #157 (comment).

if it's a link that contains multiple image-ids ("https://omero.biozentrum.unibas.ch/webclient/?show=image-1997093|image-1997094|image-1997095") it will only return the IDs as an array).

This is taken care of in the elif before.

if it's just IDs separated by commas then it makes an array

Yes, it is only for comma-separated IDs.

Ahh true, I checked the original code and indeed there was redundancy, thanks for spotting it ;)

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Unexpected behaviors in `omerotools`: `parse_url` and `upload_image_to_omero` #154

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	image_ids = (
	[s.split("%")[0].replace("\|", "") for s in omero_str.split("image-")[1:]]
	if "image-" in omero_str
	else omero_str.split(",")
	)

Unexpected behaviors in omerotools: parse_url and upload_image_to_omero #154

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ehrenfeu commented on Sep 16, 2026

ehrenfeu commented on Sep 24, 2026

loicsauteur commented on Sep 28, 2026

ehrenfeu commented on Sep 28, 2026

ehrenfeu commented on Oct 8, 2026

lguerard commented on Oct 12, 2026

loicsauteur commented on Oct 12, 2026

lguerard commented on Oct 12, 2026

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Unexpected behaviors in `omerotools`: `parse_url` and `upload_image_to_omero` #154