fixing output spec for bosh; changing output_file_template so it works for templates with or w/o extensions

Author: djarecka

pydra/engine/boutiques.py

@@ -4,6 +4,7 @@
 import subprocess as sp
 import os
 from pathlib import Path
+from functools import reduce
 
 from ..utils.messenger import AuditFlag
 from ..engine import ShellCommandTask
@@ -110,6 +111,7 @@ def _download_spec(self, zenodo):
     def _prepare_input_spec(self):
         """ creating input spec from the zenodo file"""
         binputs = self.bosh_spec["inputs"]
+        self._input_spec_keys = {}
         fields = []
         for input in binputs:
             name = input["id"]
@@ -133,6 +135,7 @@ def _prepare_input_spec(self):
                 "argstr": input.get("command-line-flag", None),
             }
             fields.append((name, tp, mdata))
+            self._input_spec_keys[input["value-key"]] = "{" + f"{name}" + "}"
 
         spec = SpecInfo(name="Inputs", fields=fields, bases=(ShellSpec,))
         return spec
@@ -143,14 +146,17 @@ def _prepare_output_spec(self):
         fields = []
         for output in boutputs:
             name = output["id"]
+            path_template = reduce(
+                lambda s, r: s.replace(*r),
+                self._input_spec_keys.items(),
+                output["path-template"],
+            )
             mdata = {
                 "help_string": output["description"],
                 "mandatory": not output["optional"],
+                "output_file_template": path_template,
             }
-            # TODO NOW: temp. default value
-            fields.append(
-                (name, attr.ib(type=File, default="test_brain.nii.gz", metadata=mdata))
-            )
+            fields.append((name, attr.ib(type=File, metadata=mdata)))
 
         spec = SpecInfo(name="Outputs", fields=fields, bases=(ShellOutSpec,))
         return spec

pydra/engine/specs.py

@@ -359,9 +359,23 @@ def _field_metadata(self, fld, inputs, output_dir):
         if "value" in fld.metadata:
             return output_dir / fld.metadata["value"]
         elif "output_file_template" in fld.metadata:
-            return output_dir / fld.metadata["output_file_template"].format(
-                **inputs.__dict__
+            sfx_tmpl = (output_dir / fld.metadata["output_file_template"]).suffixes
+            if sfx_tmpl:
+                # removing suffix from input field if template has it's own suffix
+                inputs_templ = {
+                    k: v.split(".")[0]
+                    for k, v in inputs.__dict__.items()
+                    if isinstance(v, str)
+                }
+            else:
+                inputs_templ = {
+                    k: v for k, v in inputs.__dict__.items() if isinstance(v, str)
+                }
+            out_path = output_dir / fld.metadata["output_file_template"].format(
+                **inputs_templ
             )
+            return out_path
+
         elif "callable" in fld.metadata:
             return fld.metadata["callable"](fld.name, output_dir)
         else:

pydra/engine/tests/test_boutiques.py

@@ -13,9 +13,20 @@
 
 
 @need_bosh_docker
-def test_boutiques():
+@pytest.mark.parametrize(
+    "maskfile", ["test_brain.nii.gz", "test_brain", "test_brain.nii"]
+)
+def test_boutiques_1(maskfile):
     btask = BoshTask(name="NA", zenodo="zenodo.1482743")
     btask.inputs.infile = Path(__file__).resolve().parent / "data_tests" / "test.nii.gz"
-    btask.inputs.maskfile = "test_brain.nii.gz"
+    btask.inputs.maskfile = maskfile
     res = btask()
-    # breakpoint()
+
+    assert res.output.return_code == 0
+
+    # checking if the outfile exists and if it has proper name
+    assert res.output.outfile.name == "test_brain.nii.gz"
+    assert res.output.outfile.exists()
+    # other files should also have proper names, but they do not exist
+    assert res.output.out_outskin_off.name == "test_brain_outskin_mesh.off"
+    assert not res.output.out_outskin_off.exists()