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FIX: Underspecified regex sets BIDSLayout to ignore data with sesions #1094
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68da3b4
fix: add testing data to avoid regressions
oesteban e2ed100
fix: underspecified regex sets ``BIDSLayout`` to ignore data with ses…
oesteban 2a96710
enh: more programmatic testing
oesteban 18548a3
fix: final improvements
oesteban 6690ced
sty: run black on new test files
oesteban 9ee9f9a
enh: add code suggestion by @effigies
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| 180 |
32,486 changes: 32,486 additions & 0 deletions
32,486
mriqc/data/tests/gh921-dmd-20220428-0.manifest
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1 @@ | ||
| 0 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,58 @@ | ||
| /data/skohut/data/thc2 | ||
| /data/skohut/data/thc2/template_part1_post.fsf | ||
| /data/skohut/data/thc2/sub-ss34F | ||
| /data/skohut/data/thc2/sub-ss34F/ses-21chronic | ||
| /data/skohut/data/thc2/sub-ss34F/ses-21chronic/func | ||
| /data/skohut/data/thc2/sub-ss34F/ses-21chronic/func/sub-ss34F_ses-21chronic_task-rest_bold.nii | ||
| /data/skohut/data/thc2/template_part2.fsf | ||
| /data/skohut/data/thc2/template_part1_pre.fsf | ||
| /data/skohut/data/thc2/sub-ss26 | ||
| /data/skohut/data/thc2/sub-ss26/ses-22chronic | ||
| /data/skohut/data/thc2/sub-ss26/ses-22chronic/func | ||
| /data/skohut/data/thc2/sub-ss26/ses-22chronic/func/sub-ss26_ses-22chronic_task-rest_bold.nii | ||
| /data/skohut/data/thc2/sub-ss26/ses-21chronic | ||
| /data/skohut/data/thc2/sub-ss26/ses-21chronic/func | ||
| /data/skohut/data/thc2/sub-ss26/ses-21chronic/func/sub-ss26_ses-21chronic_task-rest_bold.nii | ||
| /data/skohut/data/thc2/sub-ss22 | ||
| /data/skohut/data/thc2/sub-ss22/ses-21chronic | ||
| /data/skohut/data/thc2/sub-ss22/ses-21chronic/func | ||
| /data/skohut/data/thc2/sub-ss22/ses-21chronic/func/sub-ss22_ses-21chronic_task-rest_bold.nii | ||
| /data/skohut/data/thc2/preproc | ||
| /data/skohut/data/thc2/sub-ss35F | ||
| /data/skohut/data/thc2/sub-ss35F/ses-21chronic | ||
| /data/skohut/data/thc2/sub-ss35F/ses-21chronic/func | ||
| /data/skohut/data/thc2/sub-ss35F/ses-21chronic/func/sub-ss35F_ses-21chronic_task-rest_bold.nii | ||
| /data/skohut/data/thc2/template_part1_pharma.fsf | ||
| /data/skohut/data/thc2/sub-ss32F | ||
| /data/skohut/data/thc2/sub-ss32F/ses-21chronic | ||
| /data/skohut/data/thc2/sub-ss32F/ses-21chronic/func | ||
| /data/skohut/data/thc2/sub-ss32F/ses-21chronic/func/sub-ss32F_ses-21chronic_task-rest_bold.nii | ||
| /data/skohut/data/thc2/sub-ss25 | ||
| /data/skohut/data/thc2/sub-ss25/ses-21chronic | ||
| /data/skohut/data/thc2/sub-ss25/ses-21chronic/func | ||
| /data/skohut/data/thc2/sub-ss25/ses-21chronic/func/sub-ss25_ses-21chronic_task-rest_bold.nii | ||
| /data/skohut/data/thc2/sub-ss27 | ||
| /data/skohut/data/thc2/sub-ss27/ses-21chronic | ||
| /data/skohut/data/thc2/sub-ss27/ses-21chronic/func | ||
| /data/skohut/data/thc2/sub-ss27/ses-21chronic/func/sub-ss27_ses-21chronic_task-rest_bold.nii | ||
| /data/skohut/data/thc2/sub-ss20 | ||
| /data/skohut/data/thc2/sub-ss20/ses-21chronic | ||
| /data/skohut/data/thc2/sub-ss20/ses-21chronic/func | ||
| /data/skohut/data/thc2/sub-ss20/ses-21chronic/func/sub-ss20_ses-21chronic_task-rest_bold.nii | ||
| /data/skohut/data/thc2/sub-ss36F | ||
| /data/skohut/data/thc2/sub-ss36F/ses-21chronic | ||
| /data/skohut/data/thc2/sub-ss36F/ses-21chronic/func | ||
| /data/skohut/data/thc2/sub-ss36F/ses-21chronic/func/sub-ss36F_ses-21chronic_task-rest_bold.nii | ||
| /data/skohut/data/thc2/sub-ss24 | ||
| /data/skohut/data/thc2/sub-ss24/ses-21chronic | ||
| /data/skohut/data/thc2/sub-ss24/ses-21chronic/func | ||
| /data/skohut/data/thc2/sub-ss24/ses-21chronic/func/sub-ss24_ses-21chronic_task-rest_bold.nii | ||
| /data/skohut/data/thc2/sub-ss24/ses-22chronic | ||
| /data/skohut/data/thc2/sub-ss24/ses-22chronic/func | ||
| /data/skohut/data/thc2/sub-ss24/ses-22chronic/func/sub-ss24_ses-22chronic_task-rest_bold.nii | ||
| /data/skohut/data/thc2/template_part1.fsf | ||
| /data/skohut/data/thc2/sub-ss37F | ||
| /data/skohut/data/thc2/sub-ss37F/ses-21chronic | ||
| /data/skohut/data/thc2/sub-ss37F/ses-21chronic/func | ||
| /data/skohut/data/thc2/sub-ss37F/ses-21chronic/func/sub-ss37F_ses-21chronic_task-rest_bold.nii | ||
| /data/skohut/data/thc2/template_part1_rest.fsf |
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| @@ -0,0 +1 @@ | ||
| 13 |
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|---|---|---|
| @@ -0,0 +1,83 @@ | ||
| # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- | ||
| # vi: set ft=python sts=4 ts=4 sw=4 et: | ||
| # | ||
| # Copyright 2021 The NiPreps Developers <nipreps@gmail.com> | ||
| # | ||
| # Licensed under the Apache License, Version 2.0 (the "License"); | ||
| # you may not use this file except in compliance with the License. | ||
| # You may obtain a copy of the License at | ||
| # | ||
| # http://www.apache.org/licenses/LICENSE-2.0 | ||
| # | ||
| # Unless required by applicable law or agreed to in writing, software | ||
| # distributed under the License is distributed on an "AS IS" BASIS, | ||
| # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. | ||
| # See the License for the specific language governing permissions and | ||
| # limitations under the License. | ||
| # | ||
| # We support and encourage derived works from this project, please read | ||
| # about our expectations at | ||
| # | ||
| # https://www.nipreps.org/community/licensing/ | ||
| # | ||
| """py.test configuration""" | ||
| import os | ||
| from sys import version_info | ||
| from pathlib import Path | ||
| import numpy as np | ||
| import nibabel as nb | ||
| import pandas as pd | ||
| import pytest | ||
| import tempfile | ||
|
|
||
| # disable ET | ||
| os.environ['NO_ET'] = '1' | ||
|
|
||
| _datadir = (Path(__file__).parent.parent / "data" / "tests").resolve(strict=True) | ||
| niprepsdev_path = os.getenv("TEST_DATA_HOME", str(Path.home() / ".cache" / "mriqc")) | ||
| test_output_dir = os.getenv("TEST_OUTPUT_DIR") | ||
| test_workdir = os.getenv("TEST_WORK_DIR") | ||
|
|
||
|
|
||
| @pytest.fixture(autouse=True) | ||
| def expand_namespace(doctest_namespace): | ||
| doctest_namespace["PY_VERSION"] = version_info | ||
| doctest_namespace["np"] = np | ||
| doctest_namespace["nb"] = nb | ||
| doctest_namespace["pd"] = pd | ||
| doctest_namespace["os"] = os | ||
| doctest_namespace["pytest"] = pytest | ||
| doctest_namespace["Path"] = Path | ||
| doctest_namespace["testdata_path"] = _datadir | ||
| doctest_namespace["niprepsdev_path"] = niprepsdev_path | ||
|
|
||
| doctest_namespace["os"] = os | ||
| doctest_namespace["Path"] = Path | ||
|
|
||
| tmpdir = tempfile.TemporaryDirectory() | ||
| doctest_namespace["tmpdir"] = tmpdir.name | ||
|
|
||
| doctest_namespace["output_dir"] = ( | ||
| Path(test_output_dir) if test_output_dir is not None else Path(tmpdir.name) | ||
| ) | ||
|
|
||
| cwd = os.getcwd() | ||
| os.chdir(tmpdir.name) | ||
| yield | ||
| os.chdir(cwd) | ||
| tmpdir.cleanup() | ||
|
|
||
|
|
||
| @pytest.fixture | ||
| def testdata_path(): | ||
| return _datadir | ||
|
|
||
|
|
||
| @pytest.fixture | ||
| def workdir(): | ||
| return None if test_workdir is None else Path(test_workdir) | ||
|
|
||
|
|
||
| @pytest.fixture | ||
| def outdir(): | ||
| return None if test_output_dir is None else Path(test_output_dir) |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,80 @@ | ||
| # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- | ||
| # vi: set ft=python sts=4 ts=4 sw=4 et: | ||
| # | ||
| # Copyright 2021 The NiPreps Developers <nipreps@gmail.com> | ||
| # | ||
| # Licensed under the Apache License, Version 2.0 (the "License"); | ||
| # you may not use this file except in compliance with the License. | ||
| # You may obtain a copy of the License at | ||
| # | ||
| # http://www.apache.org/licenses/LICENSE-2.0 | ||
| # | ||
| # Unless required by applicable law or agreed to in writing, software | ||
| # distributed under the License is distributed on an "AS IS" BASIS, | ||
| # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. | ||
| # See the License for the specific language governing permissions and | ||
| # limitations under the License. | ||
| # | ||
| # We support and encourage derived works from this project, please read | ||
| # about our expectations at | ||
| # | ||
| # https://www.nipreps.org/community/licensing/ | ||
| # | ||
| """Exercise config module.""" | ||
| from pathlib import Path | ||
| import pytest | ||
|
|
||
|
|
||
| def _expand_bids(tmp_path, testdata_path, testcase): | ||
| """Expand manifest file into a temporal folder.""" | ||
|
|
||
| text = (testdata_path / f"{testcase}.manifest").read_text().splitlines() | ||
| root = Path(text[0].strip()) | ||
| out_path = tmp_path / testcase | ||
|
|
||
| for path in reversed(text[1:]): | ||
| relpath = Path(path).relative_to(root) | ||
| if "." in relpath.name or relpath in ("CHANGES", "README", "LICENSE"): | ||
| (out_path / relpath.parent).mkdir(parents=True, exist_ok=True) | ||
| if not (out_path / relpath).exists(): | ||
| contents = "{}" if relpath.name.endswith(".json") else "" | ||
| (out_path / relpath).write_text(contents) | ||
| else: | ||
| (out_path / relpath).mkdir(parents=True, exist_ok=True) | ||
|
|
||
| if ( | ||
| not (out_path / "dataset_description.json").exists() | ||
| or "Name" not in (out_path / "dataset_description.json").read_text() | ||
| ): | ||
| (out_path / "dataset_description.json").write_text( | ||
| '{"Name": "Example dataset", "BIDSVersion": "1.0.2"}' | ||
| ) | ||
|
|
||
| return out_path | ||
|
|
||
|
|
||
| @pytest.mark.parametrize( | ||
| "testcase", | ||
| ( | ||
| "gh921-dmd-20220428-0", | ||
| "gh921-dmd-20230319-0", | ||
| "gh1086-ds004134", | ||
| ), | ||
| ) | ||
| def test_bids_indexing_manifest(tmp_path, testdata_path, testcase): | ||
| """Check ``BIDSLayout`` is indexing what it should.""" | ||
|
|
||
| from mriqc import config | ||
| from importlib import reload | ||
|
|
||
| reload(config) | ||
|
|
||
| config.execution.bids_dir = _expand_bids( | ||
| tmp_path, | ||
| testdata_path, | ||
| testcase, | ||
| ) | ||
| config.execution.init() | ||
| assert len(config.execution.layout.get()) == int( | ||
| (testdata_path / f"{testcase}.oracle").read_text().strip() | ||
| ) |
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