Update.

xcp_d/interfaces/bids.py

@@ -93,14 +93,6 @@ def _list_outputs(self):
             f"bids:{self.inputs.dataset_name}:{str(Path(p).relative_to(self.inputs.dataset_path))}"
             for p in raw_paths
         ]
-        if not bids_uris:
-            raise ValueError(
-                "Something's missing:\n"
-                f"\tdataset_name: {self.inputs.dataset_name}\n"
-                f"\tdataset_path: {self.inputs.dataset_path}\n"
-                f"\tvalues: {values}\n"
-                f"\traw_paths: {raw_paths}"
-            )
 
         outputs["bids_uris"] = bids_uris
         return outputs

xcp_d/tests/test_interfaces_bids.py

@@ -25,3 +25,13 @@ def test_infer_bids_uris():
         f"bids:{dataset_name}:sub-01/ses-01/func/sub-01_ses-01_task-rest_run-02_bold.nii.gz",
         f"bids:{dataset_name}:sub-01/ses-01/func/sub-01_ses-01_task-nback_run-01_bold.nii.gz",
     ]
+
+    dataset_name = "ds000001"
+    dataset_path = "/path/to/dset"
+    infer_bids_uris = bids.InferBIDSURIs(
+        numinputs=0,
+        dataset_name=dataset_name,
+        dataset_path=dataset_path,
+    )
+    out = infer_bids_uris.run()
+    assert out.outputs.bids_uris == []

xcp_d/tests/test_utils_bids.py

@@ -294,3 +294,16 @@ def test_group_across_runs():
         "/path/sub-01_task-rest_dir-LR_run-2_bold.nii.gz",
         "/path/sub-01_task-rest_dir-RL_run-2_bold.nii.gz",
     ]
+
+
+def test_make_uri():
+    """Test _make_uri."""
+    in_file = "/path/to/dset/sub-01/func/sub-01_task-rest_bold.nii.gz"
+    dataset_name = "test"
+    dataset_path = "/path/to/dset"
+    uri = xbids._make_uri(in_file, dataset_name=dataset_name, dataset_path=dataset_path)
+    assert uri == "bids:test:sub-01/func/sub-01_task-rest_bold.nii.gz"
+
+    dataset_path = "/another/path/haha"
+    with pytest.raises(ValueError, match="is not in the subpath of"):
+        xbids._make_uri(in_file, dataset_name=dataset_name, dataset_path=dataset_path)

xcp_d/tests/test_utils_utils.py

@@ -450,19 +450,6 @@ def test_make_dictionary():
     assert out_metadata["Sources"] == ["b"]
 
 
-def test_out_file_to_source():
-    """Test _out_file_to_source."""
-    in_file = "/path/to/dset/sub-01/func/sub-01_task-rest_bold.nii.gz"
-    dataset_name = "test"
-    dataset_path = "/path/to/dset"
-    uri = utils._out_file_to_source(in_file, dataset_name=dataset_name, dataset_path=dataset_path)
-    assert uri == "bids:test:sub-01/func/sub-01_task-rest_bold.nii.gz"
-
-    dataset_path = "/another/path/haha"
-    with pytest.raises(ValueError, match="is not in the subpath of"):
-        utils._out_file_to_source(in_file, dataset_name=dataset_name, dataset_path=dataset_path)
-
-
 def test_transpose_lol():
     """Test _transpose_lol."""
     inputs = [

xcp_d/utils/bids.py

@@ -7,6 +7,7 @@
 """
 import os
 import warnings
+from pathlib import Path
 
 import nibabel as nb
 import yaml
@@ -975,3 +976,51 @@ def group_across_runs(in_files):
         out_files[group_idx].append(in_file)
 
     return out_files
+
+
+def _make_uri(in_file, dataset_name, dataset_path):
+    """Convert a filename to a BIDS URI.
+
+    Raises
+    ------
+    ValueError
+        If ``in_file`` is not relative to ``dataset_path``.
+    """
+    bids_uri = [f"bids:{dataset_name}:{str(Path(in_file).relative_to(dataset_path))}"]
+    return bids_uri
+
+
+def _make_xcpd_uri(out_file, output_dir):
+    """Convert postprocessing derivative's path to BIDS URI."""
+    import os
+
+    from xcp_d.utils.bids import _make_uri
+
+    dataset_path = os.path.join(output_dir, "xcp_d")
+
+    if isinstance(out_file, list):
+        return [_make_uri(of, "xcp_d", dataset_path) for of in out_file]
+    else:
+        return _make_uri(out_file, "xcp_d", dataset_path)
+
+
+def _make_preproc_uri(out_file, fmri_dir):
+    """Convert preprocessing derivative's path to BIDS URI."""
+    from xcp_d.utils.bids import _make_uri
+
+    if isinstance(out_file, list):
+        return [_make_uri(of, "preprocessed", fmri_dir) for of in out_file]
+    else:
+        return _make_uri(out_file, "preprocessed", fmri_dir)
+
+
+def _make_custom_uri(out_file):
+    """Convert custom confound's path to BIDS URI."""
+    import os
+
+    from xcp_d.utils.bids import _make_uri
+
+    if isinstance(out_file, list):
+        return [_make_uri(of, "custom_confounds", os.path.dirname(of)) for of in out_file]
+    else:
+        return _make_uri(out_file, "custom_confounds", os.path.dirname(out_file))

xcp_d/utils/utils.py

@@ -2,7 +2,6 @@
 # -*- coding: utf-8 -*-
 """Miscellaneous utility functions for xcp_d."""
 import warnings
-from pathlib import Path
 
 import nibabel as nb
 import numpy as np
@@ -565,12 +564,6 @@ def _make_dictionary(metadata=None, **kwargs):
         return dict(kwargs)
 
 
-def _out_file_to_source(in_file, dataset_name, dataset_path):
-    """Convert a filename to a BIDS URI."""
-    bids_uri = [f"bids:{dataset_name}:{str(Path(in_file).relative_to(dataset_path))}"]
-    return bids_uri
-
-
 def _transpose_lol(lol):
     """Transpose list of lists."""
     return list(map(list, zip(*lol)))

xcp_d/workflows/outputs.py

@@ -9,7 +9,12 @@
 
 from xcp_d.interfaces.bids import DerivativesDataSink, InferBIDSURIs
 from xcp_d.interfaces.utils import FilterUndefined
-from xcp_d.utils.bids import get_entity
+from xcp_d.utils.bids import (
+    _make_custom_uri,
+    _make_preproc_uri,
+    _make_xcpd_uri,
+    get_entity,
+)
 from xcp_d.utils.doc import fill_doc
 from xcp_d.utils.utils import _make_dictionary
 
@@ -282,39 +287,6 @@ def init_postproc_derivatives_wf(
         name="outputnode",
     )
 
-    def _postproc_to_source(out_file, output_dir):
-        import os
-
-        from xcp_d.utils.utils import _out_file_to_source
-
-        if isinstance(out_file, list):
-            return [
-                _out_file_to_source(of, "xcp_d", os.path.join(output_dir, "xcp_d"))
-                for of in out_file
-            ]
-        else:
-            return _out_file_to_source(out_file, "xcp_d", os.path.join(output_dir, "xcp_d"))
-
-    def _preproc_to_source(out_file, fmri_dir):
-        from xcp_d.utils.utils import _out_file_to_source
-
-        if isinstance(out_file, list):
-            return [_out_file_to_source(of, "preprocessed", fmri_dir) for of in out_file]
-        else:
-            return _out_file_to_source(out_file, "preprocessed", fmri_dir)
-
-    def _custom_to_source(out_file):
-        import os
-
-        from xcp_d.utils.utils import _out_file_to_source
-
-        if isinstance(out_file, list):
-            return [
-                _out_file_to_source(of, "custom_confounds", os.path.dirname(of)) for of in out_file
-            ]
-        else:
-            return _out_file_to_source(out_file, "custom_confounds", os.path.dirname(out_file))
-
     # Create dictionary of basic information
     cleaned_data_dictionary = {
         "nuisance parameters": params,
@@ -343,7 +315,7 @@ def _custom_to_source(out_file):
     # Determine cohort (if there is one) in the original data
     cohort = get_entity(name_source, "cohort")
 
-    preproc_bold_src = _preproc_to_source(name_source, fmri_dir)
+    preproc_bold_src = _make_preproc_uri(name_source, fmri_dir)
 
     atlas_src = pe.MapNode(
         InferBIDSURIs(
@@ -389,7 +361,7 @@ def _custom_to_source(out_file):
         (inputnode, ds_filtered_motion, [
             ("motion_metadata", "meta_dict"),
             ("filtered_motion", "in_file"),
-            (("fmriprep_confounds_file", _preproc_to_source, fmri_dir), "Sources"),
+            (("fmriprep_confounds_file", _make_preproc_uri, fmri_dir), "Sources"),
         ]),
         (ds_filtered_motion, outputnode, [("out_file", "filtered_motion")]),
     ])
@@ -425,11 +397,11 @@ def _custom_to_source(out_file):
                 ("temporal_mask", "in_file"),
             ]),
             (ds_filtered_motion, ds_temporal_mask, [
-                (("out_file", _postproc_to_source, output_dir), "Sources"),
+                (("out_file", _make_xcpd_uri, output_dir), "Sources"),
             ]),
             (ds_temporal_mask, outputnode, [("out_file", "temporal_mask")]),
             (ds_temporal_mask, merge_dense_src, [
-                (("out_file", _postproc_to_source, output_dir), "in2"),
+                (("out_file", _make_xcpd_uri, output_dir), "in2"),
             ]),
         ])
         # fmt:on
@@ -448,16 +420,16 @@ def _custom_to_source(out_file):
             # fmt:off
             workflow.connect([
                 (ds_temporal_mask, confounds_src, [
-                    (("out_file", _postproc_to_source, output_dir), "in2"),
+                    (("out_file", _make_xcpd_uri, output_dir), "in2"),
                 ]),
             ])
             # fmt:on
 
             if custom_confounds_file:
-                confounds_src.inputs.in3 = _custom_to_source(custom_confounds_file)
+                confounds_src.inputs.in3 = _make_custom_uri(custom_confounds_file)
 
         elif custom_confounds_file:
-            confounds_src.inputs.in2 = _custom_to_source(custom_confounds_file)
+            confounds_src.inputs.in2 = _make_custom_uri(custom_confounds_file)
 
         ds_confounds = pe.Node(
             DerivativesDataSink(
@@ -476,7 +448,7 @@ def _custom_to_source(out_file):
             (inputnode, ds_confounds, [("confounds_file", "in_file")]),
             (confounds_src, ds_confounds, [("out", "Sources")]),
             (ds_confounds, merge_dense_src, [
-                (("out_file", _postproc_to_source, output_dir), f"in{3 if fd_thresh > 0 else 2}"),
+                (("out_file", _make_xcpd_uri, output_dir), f"in{3 if fd_thresh > 0 else 2}"),
             ]),
         ])
         # fmt:on
@@ -529,7 +501,7 @@ def _custom_to_source(out_file):
                 ("interpolated_filtered_bold", "in_file"),
             ]),
             (ds_denoised_bold, ds_interpolated_denoised_bold, [
-                (("out_file", _postproc_to_source, output_dir), "Sources"),
+                (("out_file", _make_xcpd_uri, output_dir), "Sources"),
             ]),
             (ds_interpolated_denoised_bold, outputnode, [
                 ("out_file", "interpolated_filtered_bold"),
@@ -579,7 +551,7 @@ def _custom_to_source(out_file):
     workflow.connect([
         (make_atlas_dict, add_denoised_to_src, [("metadata", "metadata")]),
         (ds_denoised_bold, add_denoised_to_src, [
-            (("out_file", _postproc_to_source, output_dir), "Sources"),
+            (("out_file", _make_xcpd_uri, output_dir), "Sources"),
         ]),
     ])
     # fmt:on
@@ -608,7 +580,7 @@ def _custom_to_source(out_file):
         workflow.connect([
             (inputnode, ds_smoothed_bold, [("smoothed_denoised_bold", "in_file")]),
             (ds_denoised_bold, ds_smoothed_bold, [
-                (("out_file", _postproc_to_source, output_dir), "Sources"),
+                (("out_file", _make_xcpd_uri, output_dir), "Sources"),
             ]),
             (ds_smoothed_bold, outputnode, [("out_file", "smoothed_denoised_bold")]),
         ])
@@ -655,7 +627,7 @@ def _custom_to_source(out_file):
     workflow.connect([
         (add_denoised_to_src, add_coverage_to_src, [("metadata", "metadata")]),
         (ds_coverage, add_coverage_to_src, [
-            (("out_file", _postproc_to_source, output_dir), "Sources"),
+            (("out_file", _make_xcpd_uri, output_dir), "Sources"),
         ]),
     ])
     # fmt:on
@@ -764,7 +736,7 @@ def _custom_to_source(out_file):
         workflow.connect([
             (add_denoised_to_src, add_ccoverage_to_src, [("metadata", "metadata")]),
             (ds_coverage_ciftis, add_ccoverage_to_src, [
-                (("out_file", _postproc_to_source, output_dir), "Sources"),
+                (("out_file", _make_xcpd_uri, output_dir), "Sources"),
             ]),
         ])
         # fmt:on
@@ -897,7 +869,7 @@ def _custom_to_source(out_file):
     # fmt:off
     workflow.connect([
         (inputnode, ds_reho, [("reho", "in_file")]),
-        (ds_denoised_bold, ds_reho, [(("out_file", _postproc_to_source, output_dir), "Sources")]),
+        (ds_denoised_bold, ds_reho, [(("out_file", _make_xcpd_uri, output_dir), "Sources")]),
     ])
     # fmt:on
 
@@ -915,7 +887,7 @@ def _custom_to_source(out_file):
     # fmt:off
     workflow.connect([
         (make_atlas_dict, add_reho_to_src, [("metadata", "metadata")]),
-        (ds_reho, add_reho_to_src, [(("out_file", _postproc_to_source, output_dir), "Sources")]),
+        (ds_reho, add_reho_to_src, [(("out_file", _make_xcpd_uri, output_dir), "Sources")]),
     ])
     # fmt:on
 
@@ -968,7 +940,7 @@ def _custom_to_source(out_file):
         workflow.connect([
             (inputnode, ds_alff, [("alff", "in_file")]),
             (ds_denoised_bold, ds_alff, [
-                (("out_file", _postproc_to_source, output_dir), "Sources"),
+                (("out_file", _make_xcpd_uri, output_dir), "Sources"),
             ]),
         ])
         # fmt:on
@@ -997,7 +969,7 @@ def _custom_to_source(out_file):
             workflow.connect([
                 (inputnode, ds_smoothed_alff, [("smoothed_alff", "in_file")]),
                 (ds_alff, ds_smoothed_alff, [
-                    (("out_file", _postproc_to_source, output_dir), "Sources"),
+                    (("out_file", _make_xcpd_uri, output_dir), "Sources"),
                 ]),
             ])
             # fmt:on
@@ -1017,7 +989,7 @@ def _custom_to_source(out_file):
         workflow.connect([
             (make_atlas_dict, add_alff_to_src, [("metadata", "metadata")]),
             (ds_alff, add_alff_to_src, [
-                (("out_file", _postproc_to_source, output_dir), "Sources"),
+                (("out_file", _make_xcpd_uri, output_dir), "Sources"),
             ]),
         ])
         # fmt:on