Merge pull request #7 from ArcanaFramework/frametree-refactor

Changes for Frametree refactor

.github/workflows/ci-cd.yml

@@ -59,7 +59,7 @@ jobs:
     - name: Upload coverage to Codecov
       uses: codecov/codecov-action@v4
       with:
-        fail_ci_if_error: true
+        fail_ci_if_error: false
         token: ${{ secrets.CODECOV_TOKEN }}
 
   build:
@@ -81,7 +81,7 @@ jobs:
     - name: Install build tools
       run: python3 -m pip install --break-system-packages build twine
     - name: Build source and wheel distributions
-      run: python3 -m build 
+      run: python3 -m build
     - name: Check distributions
       run: twine check dist/*
     - uses: actions/upload-artifact@v3

.gitignore

@@ -22,4 +22,4 @@ __pycache__
 ~*
 /test-data/dicom-dataset
 *.venv
-/pydra2app/xnat/_version.py
+/pipeline2app/xnat/_version.py

README.md

@@ -1,21 +1,21 @@
-# Pydra2App - XNAT
-[![tests](https://github.com/arcanaframework/pydra2app-xnat/actions/workflows/ci-cd.yml/badge.svg)](https://github.com/ArcanaFramework/pydra2app-xnat/actions/workflows/ci-cd.yml)
-[![codecov](https://codecov.io/gh/arcanaframework/pydra2app-xnat/branch/main/graph/badge.svg?token=UIS0OGPST7)](https://codecov.io/gh/arcanaframework/pydra2app-xnat)
-[![Python versions](https://img.shields.io/pypi/pyversions/pydra2app-xnat.svg)](https://pypi.python.org/pypi/pydra2app-xnat/)
-[![Latest Version](https://img.shields.io/pypi/v/pydra2app-xnat.svg)](https://pypi.python.org/pypi/pydra2app-xnat/)
-[![docs](https://img.shields.io/badge/docs-latest-brightgreen.svg?style=flat)](https://arcanaframework.github.io/pydra2app)
+# Pipeline2App - XNAT
+[![tests](https://github.com/arcanaframework/pipeline2app-xnat/actions/workflows/ci-cd.yml/badge.svg)](https://github.com/ArcanaFramework/pipeline2app-xnat/actions/workflows/ci-cd.yml)
+[![codecov](https://codecov.io/gh/arcanaframework/pipeline2app-xnat/branch/main/graph/badge.svg?token=UIS0OGPST7)](https://codecov.io/gh/arcanaframework/pipeline2app-xnat)
+[![Python versions](https://img.shields.io/pypi/pyversions/pipeline2app-xnat.svg)](https://pypi.python.org/pypi/pipeline2app-xnat/)
+[![Latest Version](https://img.shields.io/pypi/v/pipeline2app-xnat.svg)](https://pypi.python.org/pypi/pipeline2app-xnat/)
+[![docs](https://img.shields.io/badge/docs-latest-brightgreen.svg?style=flat)](https://arcanaframework.github.io/pipeline2app)
 
-An extension for the [Pydra2App](http://arcanaframework.github.io/pydra2app) framework that support for building [XNAT](https://xnat.org) "apps" (container service docker images)
+An extension for the [Pipeline2App](http://arcanaframework.github.io/pipeline2app) framework that support for building [XNAT](https://xnat.org) "apps" (container service docker images)
 
 ## Quick Installation
 
 This extension can be installed for Python 3 using *pip*:
 
 ```
-$ pip3 install pydra2app-xnat
+$ pip3 install pipeline2app-xnat
 ```
 
-This will also install the core Pydra2App package and any required dependencies.
+This will also install the core Pipeline2App package and any required dependencies.
 
 ## License
 

codecov.yml

@@ -1,8 +1,8 @@
 coverage:
   range: "50...100"
-  ignore:          # files and folders that will be removed during processing
+  ignore: # files and folders that will be removed during processing
     - "**/tests"
-    - "arcana/xnat/_version.py"
+    - "pipeline2app/xnat/_version.py"
   status:
     project:
       default:

conftest.py

@@ -20,9 +20,9 @@
 import xnat4tests
 import medimages4tests.dummy.nifti
 import medimages4tests.dummy.dicom.mri.fmap.siemens.skyra.syngo_d13c
-from pydra2app.core.image.base import BaseImage
+from pipeline2app.core.image.base import BaseImage
 from frametree.common import Clinical
-from frametree.core.set import Dataset
+from frametree.core.frameset import FrameSet
 from fileformats.medimage import NiftiGzX, NiftiGz, DicomSeries, NiftiX
 from fileformats.text import Plain as Text
 from fileformats.image import Png
@@ -129,7 +129,7 @@ def arcana_home(work_dir):
 
 TEST_XNAT_DATASET_BLUEPRINTS = {
     "basic": TestXnatDatasetBlueprint(  # dataset name
-        dim_lengths=[1, 1, 3],  # number of timepoints, groups and members respectively
+        dim_lengths=[1, 1, 3],  # number of visits, groups and members respectively
         scans=[
             ScanBP(
                 name="scan1",  # scan type (ID is index)
@@ -190,7 +190,7 @@ def arcana_home(work_dir):
         derivatives=[
             FileBP(
                 path="deriv1",
-                row_frequency=Clinical.timepoint,
+                row_frequency=Clinical.visit,
                 datatype=Text,
                 filenames=["file.txt"],
             ),
@@ -202,20 +202,20 @@ def arcana_home(work_dir):
             ),
             FileBP(
                 path="deriv3",
-                row_frequency=Clinical.batch,
+                row_frequency=Clinical.groupedvisit,
                 datatype=Directory,
                 filenames=["dir"],
             ),
             FileBP(
                 path="deriv4",
-                row_frequency=Clinical.dataset,
+                row_frequency=Clinical.constant,
                 datatype=Text,
                 filenames=["file.txt"],
             ),
         ],
     ),
     "multi": TestXnatDatasetBlueprint(  # dataset name
-        dim_lengths=[2, 2, 2],  # number of timepoints, groups and members respectively
+        dim_lengths=[2, 2, 2],  # number of visits, groups and members respectively
         scans=[
             ScanBP(
                 name="scan1",
@@ -225,7 +225,7 @@ def arcana_home(work_dir):
         id_patterns={
             "group": r"subject::group(\d+)member\d+",
             "member": r"subject::group\d+member(\d+)",
-            "timepoint": r"session::timepoint(\d+).*",
+            "visit": r"session::visit(\d+).*",
         },
         derivatives=[
             FileBP(
@@ -242,7 +242,7 @@ def arcana_home(work_dir):
             ),
             FileBP(
                 path="deriv3",
-                row_frequency=Clinical.timepoint,
+                row_frequency=Clinical.visit,
                 datatype=Directory,
                 filenames=["doubledir"],
             ),
@@ -254,19 +254,19 @@ def arcana_home(work_dir):
             ),
             FileBP(
                 path="deriv5",
-                row_frequency=Clinical.dataset,
+                row_frequency=Clinical.constant,
                 datatype=Text,
                 filenames=["file.txt"],
             ),
             FileBP(
                 path="deriv6",
-                row_frequency=Clinical.batch,
+                row_frequency=Clinical.groupedvisit,
                 datatype=Text,
                 filenames=["file.txt"],
             ),
             FileBP(
                 path="deriv7",
-                row_frequency=Clinical.matchedpoint,
+                row_frequency=Clinical.matchedvisit,
                 datatype=Text,
                 filenames=["file.txt"],
             ),
@@ -380,23 +380,23 @@ def access_dataset(
     access_method: str,
     xnat_repository: Xnat,
     xnat_archive_dir: Path,
-) -> Dataset:
+) -> FrameSet:
     if access_method == "cs":
         proj_dir = xnat_archive_dir / project_id / "arc001"
         store = XnatViaCS(
             server=xnat_repository.server,
             user=xnat_repository.user,
             password=xnat_repository.password,
             cache_dir=xnat_repository.cache_dir,
-            row_frequency=Clinical.dataset,
+            row_frequency=Clinical.constant,
             input_mount=proj_dir,
             output_mount=Path(mkdtemp()),
         )
     elif access_method == "api":
         store = xnat_repository
     else:
         assert False, f"unrecognised access method {access_method}"
-    return store.load_dataset(project_id, name="")
+    return store.load_frameset(project_id, name="")
 
 
 @pytest.fixture(scope="session")

pydra2app/xnat/cli/base.py → pipeline2app/xnat/cli/base.py

@@ -1,4 +1,4 @@
-from pydra2app.core.cli import ext
+from pipeline2app.core.cli import ext
 
 
 @ext.group(name="xnat")

pydra2app/xnat/cli/entrypoint.py → pipeline2app/xnat/cli/entrypoint.py

@@ -1,6 +1,6 @@
 import click
-from pydra2app.core.command import entrypoint_opts
-from pydra2app.xnat import XnatApp
+from pipeline2app.core.command import entrypoint_opts
+from pipeline2app.xnat import XnatApp
 from .base import xnat_group
 
 
@@ -10,27 +10,27 @@
 launches a pipeline in a single command. To be used within the command configuration
 of an XNAT Container Service ready Docker image.
 
-DATASET_LOCATOR string containing the nickname of the data store, the ID of the
+ADDRESS string containing the nickname of the data store, the ID of the
 dataset (e.g. XNAT project ID or file-system directory) and the dataset's name
 in the format <store-nickname>//<dataset-id>[@<dataset-name>]
 
 """,
 )
-@click.argument("dataset_locator")
+@click.argument("address")
 @entrypoint_opts.data_columns
 @entrypoint_opts.parameterisation
 @entrypoint_opts.execution
 @entrypoint_opts.debugging
 @entrypoint_opts.dataset_config
 def cs_entrypoint(
-    dataset_locator,
+    address,
     spec_path,
     **kwargs,
 ):
 
     image_spec = XnatApp.load(spec_path)
 
     image_spec.command.execute(
-        dataset_locator,
+        address,
         **kwargs,
     )

pydra2app/xnat/cli/release.py → pipeline2app/xnat/cli/release.py

@@ -17,7 +17,7 @@
 XNAT_USER_KEY = "XNAT_USER"
 XNAT_PASS_KEY = "XNAT_PASS"
 XNAT_AUTH_FILE_KEY = "XNAT_AUTH_FILE"
-XNAT_AUTH_FILE_DEFAULT = Path("~/.pydra2app_xnat_user_token.json").expanduser()
+XNAT_AUTH_FILE_DEFAULT = Path("~/.pipeline2app_xnat_user_token.json").expanduser()
 
 
 def load_auth(server, user, password, auth_file):
@@ -30,7 +30,7 @@ def load_auth(server, user, password, auth_file):
         if auth_file == XNAT_AUTH_FILE_DEFAULT and not Path(auth_file).exists():
             raise RuntimeError(
                 "An auth file must be provided if no server is. "
-                "Use pydra2app ext xnat save-token to create one"
+                "Use pipeline2app ext xnat save-token to create one"
             )
         click.echo(f"Reading existing alias/token pair from '{str(auth_file)}")
         with open(auth_file) as fp:
@@ -284,7 +284,7 @@ def save_token(auth_file, server, user, password):
 JSON file using the XNAT instance's REST API.
 
 MANIFEST_FILE is a JSON file containing a list of container images built in a release
-created by `pydra2app deploy xnat build`
+created by `pipeline2app deploy xnat build`
 
 Authentication credentials can be passed through the {XNAT_USER_KEY}
 and {XNAT_PASS_KEY} environment variables. Otherwise, tokens can be saved

pydra2app/xnat/command.py → pipeline2app/xnat/command.py

@@ -3,7 +3,7 @@
 import re
 import attrs
 from fileformats.core import FileSet, to_mime
-from pydra2app.core.command.base import ContainerCommand
+from pipeline2app.core.command.base import ContainerCommand
 from frametree.xnat import XnatViaCS
 from frametree.common import Clinical
 
@@ -16,8 +16,8 @@ class XnatCommand(ContainerCommand):
 
     image: ty.Optional[XnatApp] = None
 
-    # Hard-code the data_space of XNAT commands to be clinical
-    DATA_SPACE = Clinical
+    # Hard-code the axes of XNAT commands to be clinical
+    AXES = Clinical
 
     def make_json(self):
         """Constructs the XNAT CS "command" JSON config, which specifies how XNAT
@@ -39,13 +39,13 @@ def make_json(self):
 
         output_args = self.add_output_fields(cmd_json)
 
-        flag_arg = self.add_pydra2app_flags_field(cmd_json)
+        flag_arg = self.add_pipeline2app_flags_field(cmd_json)
 
         xnat_input_args = self.add_inputs_from_xnat(cmd_json)
 
         cmd_json["command-line"] = " ".join(
             self.image.activate_conda()
-            + ["pydra2app", "ext", "xnat", "cs-entrypoint", "xnat-cs//[PROJECT_ID]"]
+            + ["pipeline2app", "ext", "xnat", "cs-entrypoint", "xnat-cs//[PROJECT_ID]"]
             + input_args
             + output_args
             + param_args
@@ -205,14 +205,14 @@ def add_output_fields(self, cmd_json):
 
         return cmd_args
 
-    def add_pydra2app_flags_field(self, cmd_json):
+    def add_pipeline2app_flags_field(self, cmd_json):
 
         # Add input for dataset name
         FLAGS_KEY = "#PYDRA2APP_FLAGS#"
         cmd_json["inputs"].append(
             {
                 "name": "Pydra2App_flags",
-                "description": "Flags passed to `run-pydra2app-pipeline` command",
+                "description": "Flags passed to `run-pipeline2app-pipeline` command",
                 "type": "string",
                 "default-value": (
                     "--plugin serial "
@@ -342,4 +342,4 @@ def path2xnatname(cls, path):
         return re.sub(r"[^a-zA-Z0-9_]+", "_", path)
 
     COMMAND_INPUT_TYPES = {bool: "bool", str: "string", int: "number", float: "number"}
-    VALID_FREQUENCIES = (Clinical.session, Clinical.dataset)
+    VALID_FREQUENCIES = (Clinical.session, Clinical.constant)

pydra2app/xnat/deploy.py → pipeline2app/xnat/deploy.py

@@ -3,11 +3,11 @@
 import logging
 import json
 import xnat
-from pydra2app.core.exceptions import Pydra2AppError
-from pydra2app.core.utils import extract_file_from_docker_image
+from pipeline2app.core.exceptions import Pydra2AppError
+from pipeline2app.core.utils import extract_file_from_docker_image
 
 
-logger = logging.getLogger("pydra2app-xnat")
+logger = logging.getLogger("pipeline2app-xnat")
 
 INTERNAL_INPUTS = ("Pydra2App_flags", "PROJECT_ID", "SUBJECT_LABEL", "SESSION_LABEL")
 

pydra2app/xnat/image.py → pipeline2app/xnat/image.py

@@ -6,16 +6,16 @@
 from neurodocker.reproenv import DockerRenderer
 from frametree.xnat import XnatViaCS
 from frametree.core.serialize import ClassResolver, ObjectConverter
-from frametree.core.store import DataStore
-from pydra2app.core.image import App
+from frametree.core.store import Store
+from pipeline2app.core.image import App
 from .command import XnatCommand
 
 
 @attrs.define(kw_only=True)
 class XnatApp(App):
 
     PIP_DEPENDENCIES = (
-        "pydra2app-xnat",
+        "pipeline2app-xnat",
         "fileformats-medimage",
         "fileformats-medimage-extras",
     )
@@ -121,10 +121,10 @@ def save_store_config(
             else:
                 ip_address = "host.docker.internal"  # Mac/Windows local debug
             xnat_cs_store_entry["server"] = "http://" + ip_address + ":8080"
-        DataStore.save_configs(
+        Store.save_configs(
             {"xnat-cs": xnat_cs_store_entry}, config_path=build_dir / "stores.yaml"
         )
-        dockerfile.run(command="mkdir -p /root/.pydra2app")
+        dockerfile.run(command="mkdir -p /root/.pipeline2app")
         dockerfile.run(command=f"mkdir -p {str(XnatViaCS.CACHE_DIR)}")
         dockerfile.copy(
             source=["./stores.yaml"],