⚗️ Try forcing relative paths for FSL Merge

Ref FCP-INDI/app-C-PAC-brainlife.io#13

CPAC/utils/interfaces/fsl.py

@@ -0,0 +1,25 @@
+"""FSL Nipype interfaces with customized functionality"""
+import os
+from nipype.interfaces.fsl.utils import Merge as fslMerge
+
+
+class Merge(fslMerge):
+    """Use relative paths for input files"""
+    def _format_arg(self, name, spec, value):
+        if name == "tr":
+            if self.inputs.dimension != "t":
+                raise ValueError("When TR is specified, dimension must be t")
+            return spec.argstr % value
+        if name == "dimension":
+            if isdefined(self.inputs.tr):
+                return "-tr"
+            return spec.argstr % value
+        # Begin custom code
+        # -----------------
+        if name == "in_files":
+            return ' '.join([
+                os.path.relpath(in_file) for in_file in value.split(' ')
+            ])
+        # ---------------
+        # End custom code
+        return super(Merge, self)._format_arg(name, spec, value)

CPAC/utils/interfaces/tests/test_fsl.py

@@ -0,0 +1,54 @@
+from ..fsl import Merge
+
+
+def test_Merge_inputs():
+    input_map = dict(
+        args=dict(
+            argstr="%s",
+        ),
+        dimension=dict(
+            argstr="-%s",
+            mandatory=True,
+            position=0,
+        ),
+        environ=dict(
+            nohash=True,
+            usedefault=True,
+        ),
+        in_files=dict(
+            argstr="%s",
+            mandatory=True,
+            position=2,
+        ),
+        merged_file=dict(
+            argstr="%s",
+            extensions=None,
+            hash_files=False,
+            name_source="in_files",
+            name_template="%s_merged",
+            position=1,
+        ),
+        output_type=dict(),
+        tr=dict(
+            argstr="%.2f",
+            position=-1,
+        ),
+    )
+    inputs = Merge.input_spec()
+
+    for key, metadata in list(input_map.items()):
+        for metakey, value in list(metadata.items()):
+            assert getattr(inputs.traits()[key], metakey) == value
+
+
+def test_Merge_outputs():
+    output_map = dict(
+        merged_file=dict(
+            extensions=None,
+        ),
+    )
+    outputs = Merge.output_spec()
+
+    for key, metadata in list(output_map.items()):
+        for metakey, value in list(metadata.items()):
+            assert getattr(outputs.traits()[key], metakey) == value