Adds in Tutorial

.gitignore

@@ -22,7 +22,8 @@ test.log
 /docker-tests
 ~*
 /docs/source/_static/images/logo-square.png
-/src/australianimagingservice_community/_version.py
+/src/**/_version.py
 *.venv
 .mypy_cache
 .build*
+.ipynb_checkpoints

requirements.txt

@@ -1,8 +1,2 @@
-arcana >=0.10.11
-arcana-xnat >= 0.3.6
-fileformats >= 0.8.6
-fileformats-extras >= 0.2.1
-fileformats-datascience >= 0.1.0
-fileformats-datascience-extras >= 0.1.1
-fileformats-medimage >= 0.4.4
-fileformats-medimage-extras >= 0.1.5
+pydra2app-xnat >=0.51
+

specs/australian-imaging-service-community/au/edu/sydney/sydneyimaging/t1_preproc.yaml

@@ -1,5 +1,5 @@
-arcana_spec_version: 1.0  # the version of the specification format used for this file
-title: 'Preprocess T1-weighted MRI'  # Short name for the pipeline referenced in the UI
+title: "Preprocess T1-weighted MRI" # Short name for the pipeline referenced in the UI
+schema_version: 1.0 # the version of the specification format used for this file
 version:
   # The version of Ubuntu's zip we are using
   package: "1.0"
@@ -24,18 +24,19 @@ packages:
   neurodocker:
     mrtrix3: 3.0.2
 command:
-  task: australianimagingservice.community.au.edu.sydney.sydneyimaging.t1_preproc:t1_preproc  # Use the generic "shell-cmd" task
-  row_frequency: session  # the pipeline is desgined to run on imaging "sessions" as opposed to "subjects" or "projects"
-  inputs:  # List the inputs that are presented to end-user in UI
+  task: australianimagingservice.community.au.edu.sydney.sydneyimaging.t1_preproc:t1_preproc # Use the generic "shell-cmd" task
+  row_frequency: session # the pipeline is desgined to run on imaging "sessions" as opposed to "subjects" or "projects"
+  inputs: # List the inputs that are presented to end-user in UI
     example_input:
-      datatype: medimage/dicom-series  # MIME-type or "MIME-like" format
-      help: "Example Input"  # description of field presented in UI
-  outputs:  # List the outputs generated by the pipeline
+      datatype: medimage/dicom-series # MIME-type or "MIME-like" format
+      help: "Example Input" # description of field presented in UI
+  outputs: # List the outputs generated by the pipeline
     example_output:
-      datatype: medimage/nifti-gz-x  # MIME-type or "MIME-like" format
-      help: Example Output  # description of field presented in UI
-  parameters:  # Parameters exposed to user to UI
+      datatype: medimage/nifti-gz-x # MIME-type or "MIME-like" format
+      help: Example Output # description of field presented in UI
+  parameters: # Parameters exposed to user to UI
     example_param:
-      datatype: field/integer  # Format of the field
-      help: an example parameter  # description of field presented in UI
-      default: 99  # Default value, filled in on the UI
+      datatype: field/integer # Format of the field
+      help: an example parameter # description of field presented in UI
+      default: 99 # Default value, filled in on the UI
+

specs/australian-imaging-service-community/examples/bet.yaml

@@ -1,5 +1,5 @@
-arcana_spec_version: 1.0  # the version of the specification format used for this file
-title: 'Example BET pipeline'  # Short name for the pipeline referenced in the UI
+schema_version: 1.0 # the version of the specification format used for this file
+title: "Example BET pipeline" # Short name for the pipeline referenced in the UI
 version:
   # Define a version for the pipeline in combination of the underlying package version (e.g. FSL)
   # and the "build" of the pipeline
@@ -8,8 +8,8 @@ version:
 base_image:
   # Chose a NeuroDesk FSL container as the base
   name: vnmd/fsl_6.0.6.4
-  package_manager: apt  # It is not obvious from the base image what the package manager is
-  tag: '20230618'
+  package_manager: apt # It is not obvious from the base image what the package manager is
+  tag: "20230618"
 packages:
   # Install dependencies for DICOM->NIfTI conversion
   pip:
@@ -22,29 +22,27 @@ authors:
   - name: Thomas G. Close
     email: [email protected]
 docs:
-  info_url: https://fsl.fmrib.ox.ac.uk/fsl/fslwiki  # Link to external documentation for underlying tool
-  description: |  # Description of tool for auto-docs
+  info_url: https://fsl.fmrib.ox.ac.uk/fsl/fslwiki # Link to external documentation for underlying tool
+  description: | # Description of tool for auto-docs
     An example wrapping BET in a XNAT pipeline
 command:
-  task: arcana.common:shell_cmd  # Use the generic "shell-cmd" task
-  row_frequency: session  # the pipeline is desgined to run on imaging "sessions" as opposed to "subjects" or "projects"
-  inputs:  # List the inputs that are presented to end-user in UI
-    T1w:
-      datatype: medimage/nifti-gz  # MIME-type or "MIME-like" format
-      help: "T1-weighted anatomical scan"  # description of field presented in UI
-      configuration:  # Additional configuration parameters that are passed to the arcana.common:shell_cmd task in the "inputs" dict
-        position: -2  # Position of field when printed to command line call. Negative numbers are indexed from the end backwards
-        argstr: ''  # prefix for field when printed to command line
-      column_defaults:
-        datatype: medimage/dicom-series  # the default 
-  outputs:  # List the outputs generated by the pipeline
+  task: common:shell # Use the generic "shell-cmd" task
+  row_frequency: session # the pipeline is desgined to run on imaging "sessions" as opposed to "subjects" or "projects"
+  inputs: # List the inputs that are presented to end-user in UI
+    t1w:
+      datatype: medimage/nifti-gz # MIME-type or "MIME-like" format
+      help: "T1-weighted anatomical scan" # description of field presented in UI
+      configuration: # Additional configuration parameters that are passed to the pydra2app.common:shell task in the "inputs" dict
+        position: -2 # Position of field when printed to command line call. Negative numbers are indexed from the end backwards
+        argstr: "" # prefix for field when printed to command line
+  outputs: # List the outputs generated by the pipeline
     brain:
-      datatype: medimage/nifti-gz  # MIME-type or "MIME-like" format
-      help: Brain-extracted data  # description of field presented in UI
-      configuration:  # Additional configuration parameters that are passed to the arcana.common:shell_cmd task in the "outputs" dict
-        position: -1  # Position of field when printed to command line call. Negative numbers are indexed from the end backwards
-        argstr: ''  # prefix for field when printed to command line
+      datatype: medimage/nifti-gz # MIME-type or "MIME-like" format
+      help: Brain-extracted data # description of field presented in UI
+      configuration: # Additional configuration parameters that are passed to the pydra2app.common:shell task in the "outputs" dict
+        position: -1 # Position of field when printed to command line call. Negative numbers are indexed from the end backwards
+        argstr: "" # prefix for field when printed to command line
   parameters: {}
-  configuration: # Additional args passed to arcana.common:shell_cmd
+  configuration: # Additional args passed to pydra2app.common:shell
     name: bet
     executable: bet

specs/australian-imaging-service-community/examples/zip.yaml

@@ -1,5 +1,7 @@
-arcana_spec_version: 1.0  # the version of the specification format used for this file
-title: 'Zip up a directory'  # Short name for the pipeline referenced in the UI
+# The version of the specification format used for this file
+schema_version: 1.0
+# Short name for the pipeline referenced in the UI
+title: "Zips up a file or directory"
 version:
   # The version of Ubuntu's zip we are using
   package: "3.0"
@@ -21,34 +23,53 @@ docs:
 packages:
   # Install the zip command in the Ubuntu image
   system:
-  - zip
+    - zip
 command:
-  task: arcana.common:shell_cmd  # Use the generic "shell-cmd" task
-  row_frequency: session  # the pipeline is desgined to run on imaging "sessions" as opposed to "subjects" or "projects"
-  inputs:  # List the inputs that are presented to end-user in UI
+  # Use the generic "shell-command" task
+  task: common:shell
+  # the pipeline is desgined to run on imaging "sessions" as opposed to "subjects" or "projects"
+  row_frequency: session
+  # List the inputs that are presented to end-user in UI
+  inputs:
     to_zip:
-      datatype: generic/fs-object  # MIME-type or "MIME-like" format
-      help: "Input file-system object to zip"  # description of field presented in UI
-      configuration:  # Additional configuration args that are passed to the arcana.common:shell_cmd task as part of the "inputs" dict
-        argstr: ''  # Position of field when printed to command line call. Negative numbers are indexed from the end backwards
-        position: -1  # prefix for field when printed to command line
-  outputs:  # List the outputs generated by the pipeline
+      # MIME-type or "MIME-like" format, generic/fs-object corresponds a file or directory
+      datatype: generic/fs-object
+      # description of field presented in UI
+      help: "Input file-system object to zip"
+      # Additional config args that are passed to the shell task as part of the "inputs" dict
+      configuration:
+        # Position of field on command line call. Negative numbers are indexed backwards from the end
+        argstr: ""
+        # prefix for field when printed to command line
+        position: -1
+  # List the outputs generated by the pipeline
+  outputs:
     zipped:
-      datatype: application/zip  # MIME-type or "MIME-like" format
-      help: Zipped FS Object  # description of field presented in UI
+      # MIME-type or "MIME-like" format
+      datatype: application/zip
+      # description of field presented in UI
+      help: Zipped file-system Object
+      # Additional config args that are passed to the shell task as part of the "outputs" dict
       configuration:
-        argstr: ''  # Position of field when printed to command line call. Negative numbers are indexed from the end backwards
-        position: -2  # prefix for field when printed to command line
-  parameters:  # Parameters exposed to user to UI
+        # Position of field on command line call. Negative numbers are indexed backwards from the end
+        argstr: ""
+        # prefix for field when printed to command line
+        position: -2
+  # Parameters exposed to user to UI
+  parameters:
     compression:
-      datatype: field/integer  # Format of the field
-      help: the level of compression applied  # description of field presented in UI
-      default: 5  # Default value, filled in on the UI
-      configuration: # Additional configuration parameter args that are passed to the arcana.common:shell_cmd task in the "parameters" dict
+      # Format of the field
+      datatype: field/integer
+      # description of field presented in UI
+      help: the level of compression applied
+      # Default value, filled in on the UI
+      default: 5
+      # Additional config args that are passed to the shell task in the "parameters" dict
+      configuration:
         # string template for field when printed to command line. "{field-name}" are
         # replaced by the value provided to the field name
         argstr: -{compression}
-  configuration:  # Additional args passed to arcana.common:shell_cmd
-    name: zip_dir
+  # Additional args passed to shell
+  configuration:
+    # the command to run
     executable: zip
-

tests/test_bet.py

@@ -1,13 +1,13 @@
-
 from pathlib import Path
 import tempfile
-from arcana.common import Clinical
+from frametree.common import Clinical
 from fileformats.medimage import NiftiGz
-from arcana.common import DirTree
+from frametree.common import DirTree
 from arcana.testing.data.blueprint import (
-    TestDatasetBlueprint, FileSetEntryBlueprint as FileBP
+    TestDatasetBlueprint,
+    FileSetEntryBlueprint as FileBP,
 )
-from arcana.core.deploy.command import ContainerCommand
+from pydra2app.core.command import ContainerCommand
 from medimages4tests.mri.neuro.t1w import get_image
 
 
@@ -19,21 +19,21 @@
 NiftiGz(get_image()).copy(source_dir, new_stem="t1w")
 
 bp = TestDatasetBlueprint(
-        hierarchy=["session"],
-        space=Clinical,
-        dim_lengths=[1, 1, 1],
-        entries=[
-            FileBP(path="t1_weighted", datatype=NiftiGz, filenames=["t1w.nii.gz"]),
-        ],
-    )
+    hierarchy=["session"],
+    space=Clinical,
+    dim_lengths=[1, 1, 1],
+    entries=[
+        FileBP(path="t1_weighted", datatype=NiftiGz, filenames=["t1w.nii.gz"]),
+    ],
+)
 
 work_dir = Path(tempfile.mkdtemp())
 
 dataset_id = work_dir / "saved-dataset"
 saved_dataset = bp.make_dataset(DirTree(), dataset_id, name="", source_data=source_dir)
 
 command_spec = ContainerCommand(
-    task="arcana.common:shell_cmd",
+    task="common:shell",
     row_frequency=Clinical.session,
     inputs=[
         {
@@ -43,7 +43,7 @@
             "configuration": {
                 "argstr": "",
                 "position": -2,
-            }
+            },
         },
     ],
     outputs=[
@@ -54,12 +54,12 @@
             "configuration": {
                 "argstr": "",
                 "position": -1,
-            }
+            },
         }
     ],
     configuration={
         "executable": "bet",
-    }
+    },
 )
 # Start generating the arguments for the CLI
 # Add source to loaded dataset

tests/test_build.py

@@ -1,14 +1,14 @@
 from pathlib import Path
 from click.testing import CliRunner
-from arcana.core.cli.deploy import make_app
-from arcana.core.utils.misc import show_cli_trace
+from pydra2app.core.cli import make
+from frametree.core.utils import show_cli_trace
 
 PKG_PATH = Path(__file__).parent.parent.absolute()
 
 runner = CliRunner()
 
 results = runner.invoke(
-    make_app,
+    make,
     [
         f"{PKG_PATH}/australian-imaging-service-community/",
         "xnat:XnatApp",

tests/test_zip.py

@@ -1,36 +1,36 @@
-
 from pathlib import Path
 import tempfile
 import operator as op
 import functools
 from fileformats.generic import Directory
 from fileformats.application import Zip
-from arcana.common import DirTree
-from arcana.testing import TestDataSpace
-from arcana.testing.data.blueprint import (
-    TestDatasetBlueprint, FileSetEntryBlueprint as FileBP
+from frametree.common import DirTree
+from frametree.testing import TestDataSpace
+from frametree.testing.blueprint import (
+    TestDatasetBlueprint,
+    FileSetEntryBlueprint as FileBP,
 )
-from arcana.core.deploy.command import ContainerCommand
+from pydra2app.core.command import ContainerCommand
 
 
 bp = TestDatasetBlueprint(
-        hierarchy=[
-            "abcd"
-        ],  # e.g. XNAT where session ID is unique in project but final layer is organised by timepoint
-        space=TestDataSpace,
-        dim_lengths=[1, 1, 1, 1],
-        entries=[
-            FileBP(path="dir1", datatype=Directory, filenames=["dir"]),
-        ],
-    )
+    hierarchy=[
+        "abcd"
+    ],  # e.g. XNAT where session ID is unique in project but final layer is organised by timepoint
+    space=TestDataSpace,
+    dim_lengths=[1, 1, 1, 1],
+    entries=[
+        FileBP(path="dir1", datatype=Directory, filenames=["dir"]),
+    ],
+)
 
 work_dir = Path(tempfile.mkdtemp())
 
 dataset_id = work_dir / "saved-dataset"
 saved_dataset = bp.make_dataset(DirTree(), dataset_id, name="")
 
 command_spec = ContainerCommand(
-    task="arcana.common:shell_cmd",
+    task="arcana.common:shell",
     row_frequency=bp.space.default(),
     inputs=[
         {
@@ -40,7 +40,7 @@
             "configuration": {
                 "argstr": "",
                 "position": -1,
-            }
+            },
         },
     ],
     outputs=[
@@ -51,7 +51,7 @@
             "configuration": {
                 "argstr": "",
                 "position": -2,
-            }
+            },
         }
     ],
     parameters=[
@@ -67,7 +67,7 @@
     ],
     configuration={
         "executable": "zip",
-    }
+    },
 )
 # Start generating the arguments for the CLI
 # Add source to loaded dataset