Documentation of slicer_cli_web to work with DSA?

[pearcetm]

My team and I are struggling to find clear documentation of how to use slicer_cli_web to build image analysis tasks.

Specifically, we discovered by trial and error and looking at other examples that <longflag>outputAnnontationFile</longflag> must be set in order for a json file returned by the job to be used by the DSA as an annotation. <longflag>output_file</longflag> works differently.

Now we understand this (or at least we think we understand), but it would be great to have some official documentation so we know what we are actually doing. Does that exist somewhere? Apologies if I've overlooked it.

[manthey]

The DSA uses the slicer cli execution schema with a few modifications. The reference to this is split (and should definitely be improved). Specifically, much of the girder-specifics are documented here: https://github.com/girder/slicer_cli_web?tab=readme-ov-file#docker-clis including a link to the base schema (https://www.slicer.org/w/index.php?title=Documentation/Nightly/Developers/SlicerExecutionModel). There are some Histomics specific further changes that are documented here: https://github.com/DigitalSlideArchive/HistomicsUI?tab=readme-ov-file#annotations-and-metadata-from-jobs; but looking at that it isn't particularly clear that this modifies the slicer cli execution schema.

I'll add an issue in the HistomicsUI space to make this documentation clearer and to add some illustrative examples.

[pearcetm]

but looking at that it isn't particularly clear that this modifies the slicer cli execution schema.

I'll add an issue in the HistomicsUI space to make this documentation clearer and to add some illustrative examples.

Thanks for the quick reply. The HistomicsUI docs seem to touch on this most directly. It would really be great to get some better examples and clearer (possibly consolidated) documentation. Thanks for opening that new issue!