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FIX: DerivativesDataSink dismissing entity writing reportlet #638

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merged 2 commits into from
May 17, 2021
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FIX: DerivativesDataSink dismissing entity writing reportlet #638

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f0afdbb
FIX: ``DerivativesDataSink`` dismissing entity writing reportlet
oesteban May 16, 2021
d1367b5
fix #637: default patterns discarding 'fmapid-' entity
oesteban May 17, 2021
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2 changes: 1 addition & 1 deletion niworkflows/data/nipreps.json
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Original file line number Diff line number Diff line change
Expand Up @@ -153,7 +153,7 @@
"sub-{subject}[/ses-{session}]/{datatype<dwi>|dwi}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_res-{resolution}]_desc-{desc}_{suffix<mask>}{extension<.json|.nii.gz|.nii>|.nii.gz}",
"sub-{subject}[/ses-{session}]/{datatype<dwi>|dwi}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_res-{resolution}][_desc-{desc}]_{suffix<dwi>}{extension<.tsv|.bval|.bvec>|.tsv}",
"sub-{subject}[/ses-{session}]/{datatype<fmap>|fmap}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_dir-{direction}][_run-{run}][_space-{space}][_cohort-{cohort}][_res-{resolution}][_fmapid-{fmapid}][_desc-{desc}]_{suffix<fieldmap>}{extension<.nii|.nii.gz|.json>|.nii.gz}",
"sub-{subject}/{datatype<figures>}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_desc-{desc}]_{suffix<T1w|T2w|T1rho|T1map|T2map|T2star|FLAIR|FLASH|PDmap|PD|PDT2|inplaneT[12]|angio|dseg|mask|dwi|epiref|fieldmap|T2starw|MTw|TSE>}{extension<.html|.svg>|.svg}",
"sub-{subject}/{datatype<figures>}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_desc-{desc}]_{suffix<T1w|T2w|T1rho|T1map|T2map|T2star|FLAIR|FLASH|PDmap|PD|PDT2|inplaneT[12]|angio|dseg|mask|dwi|epiref|T2starw|MTw|TSE>}{extension<.html|.svg>|.svg}",
"sub-{subject}/{datatype<figures>}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_fmapid-{fmapid}][_desc-{desc}]_{suffix<fieldmap>}{extension<.html|.svg>|.svg}",
"sub-{subject}/{datatype<figures>}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_space-{space}][_cohort-{cohort}][_desc-{desc}]_{suffix<bold>}{extension<.html|.svg>|.svg}"
]
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32 changes: 32 additions & 0 deletions niworkflows/interfaces/tests/test_bids.py
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Expand Up @@ -490,6 +490,38 @@ def make_empty_nii_with_dtype(fname, dtype):
assert nii.get_data_dtype() == np.dtype(source_dtype)


def test_DerivativesDataSink_fmapid(tmp_path):
"""Ascertain #637 is not regressing."""
source_file = [
(tmp_path / s)
for s in [
"sub-36/fmap/sub-36_dir-1_run-1_epi.nii.gz",
"sub-36/fmap/sub-36_dir-1_run-2_epi.nii.gz",
"sub-36/fmap/sub-36_dir-2_run-1_epi.nii.gz",
"sub-36/fmap/sub-36_dir-2_run-2_epi.nii.gz",
]
]
for fname in source_file:
fname.parent.mkdir(exist_ok=True, parents=True)
fname.write_text("")

in_file = tmp_path / "report.svg"
in_file.write_text("")

dds = bintfs.DerivativesDataSink(
base_directory=str(tmp_path),
datatype="figures",
suffix="fieldmap",
desc="pepolar",
dismiss_entities=("fmap",),
allowed_entities=("fmapid",),
fmapid="auto00000",
source_file=[str(s.absolute()) for s in source_file],
in_file=str(in_file),
).run()
assert dds.outputs.out_file.endswith("sub-36_fmapid-auto00000_desc-pepolar_fieldmap.svg")


@pytest.mark.parametrize("field", ["RepetitionTime", "UndefinedField"])
def test_ReadSidecarJSON_connection(testdata_dir, field):
"""
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