Merge pull request #777 from tsalo/dds-config

Pass custom configuration into DerivativesDataSink entity parser

niworkflows/data/nipreps.json

@@ -34,7 +34,7 @@
     },
     {
       "name": "run",
-      "pattern": "[_/\\\\]+run-0*(\\d+)",
+      "pattern": "[_/\\\\]+run-(\\d+)",
       "dtype": "int"
     },
     {

niworkflows/interfaces/bids.py

@@ -55,7 +55,7 @@
 
 regz = re.compile(r"\.gz$")
 _pybids_spec = loads(Path(_pkgres("niworkflows", "data/nipreps.json")).read_text())
-BIDS_DERIV_ENTITIES = frozenset({e["name"] for e in _pybids_spec["entities"]})
+BIDS_DERIV_ENTITIES = _pybids_spec["entities"]
 BIDS_DERIV_PATTERNS = tuple(_pybids_spec["default_path_patterns"])
 
 STANDARD_SPACES = tf.api.templates()
@@ -498,7 +498,8 @@ class DerivativesDataSink(SimpleInterface):
     output_spec = _DerivativesDataSinkOutputSpec
     out_path_base = "niworkflows"
     _always_run = True
-    _config_entities = BIDS_DERIV_ENTITIES
+    _config_entities = frozenset({e["name"] for e in BIDS_DERIV_ENTITIES})
+    _config_entities_dict = BIDS_DERIV_ENTITIES
     _standard_spaces = STANDARD_SPACES
     _file_patterns = BIDS_DERIV_PATTERNS
     _default_dtypes = DEFAULT_DTYPES
@@ -526,7 +527,7 @@ def __init__(self, allowed_entities=None, out_path_base=None, **inputs):
             setattr(self.inputs, k, inputs[k])
 
     def _run_interface(self, runtime):
-        from bids.layout import parse_file_entities
+        from bids.layout import parse_file_entities, Config
         from bids.layout.writing import build_path
         from bids.utils import listify
 
@@ -549,8 +550,16 @@ def _run_interface(self, runtime):
             self._metadata = meta
 
         # Initialize entities with those from the source file.
+        custom_config = Config(
+            name="custom",
+            entities=self._config_entities_dict,
+            default_path_patterns=self._file_patterns,
+        )
         in_entities = [
-            parse_file_entities(str(relative_to_root(source_file)))
+            parse_file_entities(
+                str(relative_to_root(source_file)),
+                config=["bids", "derivatives", custom_config],
+            )
             for source_file in self.inputs.source_file
         ]
         out_entities = {k: v for k, v in in_entities[0].items()

niworkflows/reports/core.py

@@ -63,6 +63,26 @@
 ]
 
 
+class Smallest:
+    """An object that always evaluates smaller than anything else, for sorting
+
+    >>> Smallest() < 1
+    True
+    >>> Smallest() < "epsilon"
+    True
+    >>> sorted([1, None, 2], key=lambda x: x if x is not None else Smallest())
+    [None, 1, 2]
+    """
+    def __lt__(self, other):
+        return not isinstance(other, Smallest)
+
+    def __eq__(self, other):
+        return isinstance(other, Smallest)
+
+    def __gt__(self, other):
+        return False
+
+
 class Element(object):
     """Just a basic component of a report"""
 
@@ -252,7 +272,7 @@ class Report:
     >>> robj.generate_report()
     0
     >>> len((testdir / 'out' / 'fmriprep' / 'sub-01.html').read_text())
-    36693
+    36713
 
     .. testcleanup::
 
@@ -483,7 +503,7 @@ def _process_orderings(orderings, layout):
         # sort the value combinations alphabetically from the first entity to the last entity
         value_combos.sort(
             key=lambda entry: tuple(
-                str(value) if value is not None else "0" for value in entry
+                value if value is not None else Smallest() for value in entry
             )
         )