Error when trying to submit plugin to chrisstore.co

[grdryn]

Hi!

I've just tried submitting my first plugin through the chrisstore.co UI, and it's giving me an error that something is not a valid string.

Here's the POST Data of the request:

-----------------------------727047094977636124258969607
Content-Disposition: form-data; name="name"

pl-heudiconv
-----------------------------727047094977636124258969607
Content-Disposition: form-data; name="dock_image"

quay.io/rh-impact/pl-heudiconv:0.1
-----------------------------727047094977636124258969607
Content-Disposition: form-data; name="public_repo"

https://github.com/rh-impact/pl-heudiconv
-----------------------------727047094977636124258969607
Content-Disposition: form-data; name="descriptor_file"; filename="blob"
Content-Type: application/json

{"type":"ds","parameters":[{"name":"inputdir_type","type":"str","optional":true,"flag":"--inputdir-type","short_flag":"--inputdir-type","action":"store","help":"For input, heudiconv accepts EITHER a \"--files\"\n            argument, or a \"--dicom_dir_template\" argument. This\n            option specifies which to use for the positional\n            \"inputdir\" argument to this plugin.","default":"files","ui_exposed":true},{"name":"heuristic","type":"str","optional":true,"flag":"--heuristic","short_flag":"-f","action":"store","help":"Name of a known heuristic or path to the Python\n            script containing heuristic.","default":"reproin","ui_exposed":true},{"name":"bids","type":"bool","optional":true,"flag":"--bids","short_flag":"-b","action":"store_true","help":"Flag for output into BIDS structure. Can also take\n            BIDS-specific options by using --bids-options, e.g.,\n            --bids-options notop.","default":false,"ui_exposed":true},{"name":"bids_options","type":"str","optional":true,"flag":"--bids-options","short_flag":"--bids-options","action":"store","help":"The only currently supported bids options is\n             \"notop\", which skips creation of top-level BIDS\n             files. This is useful when running in batch mode to\n             prevent possible race conditions.","default":[],"ui_exposed":true},{"name":"overwrite","type":"bool","optional":true,"flag":"--overwrite","short_flag":"--overwrite","action":"store_true","help":"Overwrite existing converted files.","default":false,"ui_exposed":true},{"name":"datalad","type":"bool","optional":true,"flag":"--datalad","short_flag":"--datalad","action":"store_true","help":"Store the entire collection as DataLad\n            dataset(s). Small files will be committed directly to git,\n            while large to annex. New version (6) of annex\n            repositories will be used in a \"thin\" mode so it would\n            look to mortals as just any other regular directory\n            (i.e. no symlinks to under .git/annex). For now just for\n            BIDS mode.","default":false,"ui_exposed":true},{"name":"minmeta","type":"bool","optional":true,"flag":"--minmeta","short_flag":"--minmeta","action":"store_true","help":"Exclude dcmstack meta information in sidecar jsons.","default":false,"ui_exposed":true},{"name":"random_seed","type":"int","optional":true,"flag":"--random-seed","short_flag":"--random-seed","action":"store","help":"Random seed to initialize RNG.","default":[],"ui_exposed":true},{"name":"locator","type":"str","optional":true,"flag":"--locator","short_flag":"-l","action":"store","help":"Study path under outdir. If provided, it overloads\n            the value provided by the heuristic. If --datalad is\n            enabled, every directory within locator becomes a\n            super-dataset thus establishing a hierarchy. Setting to\n            \"unknown\" will skip that dataset.","default":[],"ui_exposed":true},{"name":"session","type":"str","optional":true,"flag":"--ses","short_flag":"-ss","action":"store","help":"Session for longitudinal study_sessions. Default is\n            None.","default":[],"ui_exposed":true},{"name":"with_prov","type":"bool","optional":true,"flag":"--with-prov","short_flag":"-p","action":"store_true","help":"Store additional provenance information.","default":false,"ui_exposed":true},{"name":"command","type":"str","optional":true,"flag":"--command","short_flag":"--command","action":"store","help":"Custom action to be performed on provided files\n            instead of regular operation.","default":[],"ui_exposed":true},{"name":"anon_cmd","type":"str","optional":true,"flag":"--anon-cmd","short_flag":"--anon-cmd","action":"store","help":"Command to run to convert subject IDs used for DICOMs to anonymized IDs. Such command must take a single argument and return a single anonymized ID.","default":[],"ui_exposed":true},{"name":"subjects","type":"str","optional":true,"flag":"--subjects","short_flag":"-s","action":"store","help":"List of subjects - required for dicom template. If\n            not provided, DICOMS would first be \"sorted\" and subject\n            IDs deduced by the heuristic.","default":[],"ui_exposed":true},{"name":"grouping","type":"str","optional":true,"flag":"--grouping","short_flag":"-g","action":"store","help":"How to group dicoms (default: by studyUID)","default":[],"ui_exposed":true},{"name":"dcmconfig","type":"str","optional":true,"flag":"--dcmconfig","short_flag":"--dcmconfig","action":"store","help":"JSON file for additional dcm2niix configuration.","default":[],"ui_exposed":true}],"icon":"","authors":"grdryn <[email protected]>","title":"A ChRIS plugin for heudiconv","category":"","description":"An app to organize brain imaging data into structured directory layouts","documentation":"https://github.com/rh-impact/pl-heudiconv","license":"MIT","version":"0.1","selfpath":"/usr/local/bin","selfexec":"pl-heudiconv","execshell":"/usr/local/bin/python","max_number_of_workers":1,"min_number_of_workers":1,"max_memory_limit":"","min_memory_limit":8000,"max_cpu_limit":"","min_cpu_limit":2000,"max_gpu_limit":0,"min_gpu_limit":0}
-----------------------------727047094977636124258969607--

and here's the response:

{"collection":{"version":"1.0","href":"https://chrisstore.co/api/v1/plugins/","error":{"message":"{\"value\": [\"Not a valid string.\"]}"}}}

1. Where am I going wrong?
2. Would this error message be more useful if it was more specific?

Thanks!

[grdryn]

I've gotten the store running locally now so that I can test it, and I believe I've narrowed down the problem to invalid defaults that I've set for some typed arguments in the argparse in the plugin. E.g. [] as the default for string or int args rather than, say '' or 0 respectively. The argparse module in the plugin app seems fine with those, but the validation on the JSON produced by --savejson that happens on submission to the store doesn't like it.

[jennydaman]

Ah, sounds like some Python weak-typing fun. This could be a bug in https://github.com/fnndsc/chrisapp, though we have some newer, more sparkly machinery, https://github.com/fnndsc/chris_plugin

It still stands that the ChRIS_store_ui (and perhaps the ChRIS_store backend) could be more helpful here in displaying validation error messages. Thanks for digging around @grdryn

[grdryn]

This could be a bug in https://github.com/fnndsc/chrisapp, though we have some newer, more sparkly machinery, https://github.com/fnndsc/chris_plugin

Thanks @jennydaman, I have a TODO item () to convert my plugin to the new structure of https://github.com/FNNDSC/python-chrisapp-template. Can you tell me how python-chrisapp-template is related to the chris_plugin project that you mention? Should I be looking instead at chris_plugin, or is it a separate concern?

It still stands that the ChRIS_store_ui (and perhaps the ChRIS_store backend) could be more helpful here in displaying validation error messages.

Yes, a list of error messages in the response might be a good approach: one for each validation failure 🤔

[jennydaman]

@grdryn chris_plugin is a Python module, python-chrisapp-template is starter code which uses the chris_plugin module. I recommend you look at python-chrisapp-template (which might lead you to reading the documentation on chris_plugin)