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Lazy loading of medimages4tests imports #18

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merged 4 commits into from
Oct 16, 2024
Merged

Lazy loading of medimages4tests imports #18

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c0eedb3
added dynamic available datasets to add-data help string
tclose Aug 6, 2024
7d8f430
lazily import medimages4tests to speed up cases where it isn't required
tclose Oct 10, 2024
5b2c11a
added type annotations
tclose Oct 16, 2024
f533e44
formatting
tclose Oct 16, 2024
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4 changes: 3 additions & 1 deletion tests/test_base.py
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Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,9 @@ def test_launch(config, launched_xnat):
login.put(f"/data/archive/projects/{PROJECT}")

# Create subject
xsubject = login.classes.SubjectData(label=SUBJECT, parent=login.projects[PROJECT])
xsubject = login.classes.SubjectData(
label=SUBJECT, parent=login.projects[PROJECT]
)
# Create session
xsession = login.classes.MrSessionData(label=SESSION, parent=xsubject)

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4 changes: 2 additions & 2 deletions xnat4tests/cli.py
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Expand Up @@ -139,9 +139,9 @@ def restart_cli(ctx, loglevel):

@cli.command(
name="add-data",
help="""Adds sample data to the XNAT instance
help=f"""Adds sample data to the XNAT instance

DATASET is the name of the dataset to add (out of ['dummydicom'])""",
DATASET is the name of the dataset to add (out of {AVAILABLE_DATASETS})""",
)
@click.argument("dataset", type=click.Choice(AVAILABLE_DATASETS))
@click.option(
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23 changes: 13 additions & 10 deletions xnat4tests/data.py
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Original file line number Diff line number Diff line change
Expand Up @@ -6,16 +6,6 @@
from contextlib import contextmanager
from pathlib import Path
from xnat.exceptions import XNATResponseError
from medimages4tests.dummy.dicom.mri.t1w.siemens.skyra.syngo_d13c import (
get_image as t1w_syngo,
)
from medimages4tests.dummy.dicom.mri.dwi.siemens.skyra.syngo_d13c import (
get_image as dwi_syngo,
)
from medimages4tests.dummy.dicom.mri.fmap.siemens.skyra.syngo_d13c import (
get_image as fmap_syngo,
)
from medimages4tests.mri.neuro.t1w import get_image as openneuro_t1w
from .base import connect
from .config import Config
from .utils import logger
Expand Down Expand Up @@ -64,6 +54,15 @@ def add_data(dataset: str, config_name: str or dict = "default"):
)

if dataset == "dummydicom":
from medimages4tests.dummy.dicom.mri.t1w.siemens.skyra.syngo_d13c import (
get_image as t1w_syngo,
)
from medimages4tests.dummy.dicom.mri.dwi.siemens.skyra.syngo_d13c import (
get_image as dwi_syngo,
)
from medimages4tests.dummy.dicom.mri.fmap.siemens.skyra.syngo_d13c import (
get_image as fmap_syngo,
)

_upload_dicom_data(
[t1w_syngo(), dwi_syngo(), fmap_syngo()],
Expand All @@ -74,6 +73,7 @@ def add_data(dataset: str, config_name: str or dict = "default"):
)

elif dataset == "openneuro-t1w":
from medimages4tests.mri.neuro.t1w import get_image as openneuro_t1w

_upload_directly(
{"t1w": openneuro_t1w()},
Expand Down Expand Up @@ -119,6 +119,9 @@ def add_data(dataset: str, config_name: str or dict = "default"):
)

elif dataset == "user-training":
from medimages4tests.dummy.dicom.mri.fmap.siemens.skyra.syngo_d13c import (
get_image as fmap_syngo,
)

_upload_dicom_data(
[t1w_syngo(), fmap_syngo()],
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6 changes: 3 additions & 3 deletions xnat4tests/registry.py
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Original file line number Diff line number Diff line change
@@ -1,10 +1,10 @@
import docker
import docker.models.containers
from .utils import logger
from .config import Config
from .base import docker_network, connect


def start_registry(config_name="default"):
def start_registry(config_name: str = "default") -> docker.models.containers.Container:

config = Config.load(config_name)

Expand Down Expand Up @@ -38,7 +38,7 @@ def start_registry(config_name="default"):
return container


def stop_registry(config_name="default"):
def stop_registry(config_name: str = "default") -> None:

config = Config.load(config_name)

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