debugging bids apps refactor

Author: tclose

specs/australian-imaging-service/mri/human/neuro/bidsapp/fmriprep.yaml

@@ -95,13 +95,6 @@ commands:
           type: medimage/nifti-gz-x
           help: "Field map - BIDS Case 3: magnitude image used for anatomical reference"
           path: fmap/magnitude
-        fmap_phasediff:
-          type: medimage/nifti-gz-x
-          help: "Field map - BIDS Case 1: phasediff image corresponding to the phase-diff map between echo times"
-        fmap_magnitude:
-          type: medimage/nifti-gz-x
-          help: "Field map - BIDS Case 3: magnitude image used for anatomical reference"
-          path: fmap/magnitude
         fmap_phasediff:
           type: medimage/nifti-gz-x
           help: "Field map - BIDS Case 1: phasediff image corresponding to the phase-diff map between echo times"

specs/australian-imaging-service/mri/human/neuro/bidsapp/mriqc.yaml

@@ -31,15 +31,15 @@ commands:
       inputs:
         t1w:
           type: medimage/nifti-gz-x
-          help: "T1-weighted anatomical scan"
+          help: "T1-weighted anatomical MRI"
           path: anat/T1w
         t2w:
           type: medimage/nifti-gz-x
-          help: "T2-weighted anatomical scan"
+          help: "T2-weighted anatomical MRI"
           path: anat/T2w
-        fMRI:
+        bold:
           type: medimage/nifti-gz-x
-          help: "functional MRI"
+          help: "Resting-state functional MRI"
           path: func/task-rest_bold
       outputs:
         mriqc:

tests/test_bids_apps.py

@@ -1,4 +1,5 @@
 import json
+import itertools
 from pydra2app.core.cli import make
 from pydra2app.xnat import XnatApp
 from frametree.core.utils import show_cli_trace
@@ -23,20 +24,27 @@ def test_bids_app(
     else:
         build_arg = "--build"
 
+    licenses = [["--license", p.stem, str(p)] for p in license_src.glob("*")]
+
     result = cli_runner(
         make,
-        [
-            str(bp.spec_path),
-            "pipelines-core-test",
-            "--build-dir",
-            str(build_dir),
-            build_arg,
-            "--for-localhost",
-            "--use-local-packages",
-            "--raise-errors",
-            "--license-src",
-            str(license_src),
-        ],
+        list(
+            itertools.chain(
+                [
+                    "xnat",
+                    str(bp.spec_path),
+                    "--registry",
+                    "pipelines-core-test",
+                    "--build-dir",
+                    str(build_dir),
+                    build_arg,
+                "--for-localhost",
+                "--use-local-packages",
+                "--raise-errors",
+                ],
+                *licenses,
+            )
+        )
     )
 
     assert result.exit_code == 0, show_cli_trace(result)
@@ -45,36 +53,38 @@ def test_bids_app(
 
     with xnat_connect() as xlogin:
 
+        build_name = image_spec.name.split(".")[-1]
+
         with open(
-            build_dir / image_spec.name / "xnat_commands" / (image_spec.name + ".json")
+            build_dir / "xnat_commands" / (build_name + ".json")
         ) as f:
             xnat_command = json.load(f)
-        xnat_command.name = xnat_command.label = image_spec.name + run_prefix
+        xnat_command['name'] = xnat_command['label'] = image_spec.name + run_prefix
 
         test_xsession = next(iter(xlogin.projects[bp.project_id].experiments.values()))
 
         inputs_json = {}
 
-        for inpt in image_spec.command.inputs:
-            if (bids_app_blueprint.test_data / inpt.name).exists():
+        for inpt in image_spec.command().inputs:
+            if (bids_app_blueprint.test_data / inpt).exists():
                 converter_args_path = (
-                    bids_app_blueprint.test_data / inpt.name / "converter.json"
+                    bids_app_blueprint.test_data / inpt / "converter.json"
                 )
                 converter_args = ""
                 if converter_args_path.exists():
                     with open(converter_args_path) as f:
                         dct = json.load(f)
                     for name, val in dct.items():
                         converter_args += f" converter.{name}={val}"
-                inputs_json[inpt.name] = inpt.name + converter_args
+                inputs_json[inpt] = inpt + converter_args
             else:
-                inputs_json[inpt.name] = ""
+                inputs_json[inpt] = ""
 
         for pname, pval in bp.parameters.items():
             inputs_json[pname] = pval
 
-        inputs_json["Arcana_flags"] = (
-            "--worker serial "
+        inputs_json["pydra_flags"] = (
+            "--worker debug "
             "--work /work "  # NB: work dir moved inside container due to file-locking issue on some mounted volumes (see https://github.com/tox-dev/py-filelock/issues/147)
             "--dataset-name default "
             "--loglevel debug "