childmindresearch / niwrap

https://childmindresearch.github.io/niwrap/
0 stars 8 forks source link

[DONT MERGE] Fix fsl FNIRT #79

Closed e-kenneally closed 2 months ago

e-kenneally commented 2 months ago

Fixes #50

Error with boutiques validator:


(eliz) [kenneall@r001 kenneall]$ bosh exec simulate -j -c /ocean/projects/med220004p/kenneall/boutiquethon/nopype/descriptors/fsl/fnirt.json
Traceback (most recent call last):
  File "/ocean/projects/med220004p/kenneall/.conda/envs/eliz/bin/bosh", line 8, in <module>
    sys.exit(bosh())
             ^^^^^^
  File "/ocean/projects/med220004p/kenneall/.conda/envs/eliz/lib/python3.11/site-packages/boutiques/bosh.py", line 452, in bosh
    out = execute(*params)
          ^^^^^^^^^^^^^^^^
  File "/ocean/projects/med220004p/kenneall/.conda/envs/eliz/lib/python3.11/site-packages/boutiques/bosh.py", line 126, in execute
    valid = invocation(*arguments)
            ^^^^^^^^^^^^^^^^^^^^^^
  File "/ocean/projects/med220004p/kenneall/.conda/envs/eliz/lib/python3.11/site-packages/boutiques/bosh.py", line 254, in invocation
    validate(*arguments)
  File "/ocean/projects/med220004p/kenneall/.conda/envs/eliz/lib/python3.11/site-packages/boutiques/bosh.py", line 59, in validate
    descriptor = validate_descriptor(descriptor,
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/ocean/projects/med220004p/kenneall/.conda/envs/eliz/lib/python3.11/site-packages/boutiques/validator.py", line 422, in validate_descriptor
    errors += [msg_template.format(grp["id"], member)
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/ocean/projects/med220004p/kenneall/.conda/envs/eliz/lib/python3.11/site-packages/boutiques/validator.py", line 424, in <listcomp>
    if not inById(member)["optional"]]
           ~~~~~~~~~~~~~~^^^^^^^^^^^^
KeyError: 'optional'