Merge pull request #290 from bioimage-io/fix_source_node_checker

Fix source node checker

Author: constantinpape

bioimageio/core/resource_io/utils.py

@@ -28,7 +28,7 @@ class SourceNodeChecker(NodeVisitor):
     """raises FileNotFoundError for unavailable URIs and paths"""
 
     def __init__(self, *, root_path: os.PathLike):
-        self.root_path = pathlib.Path(root_path).resolve()
+        self.root_path = root_path if isinstance(root_path, raw_nodes.URI) else pathlib.Path(root_path).resolve()
 
     def _visit_source(self, leaf: typing.Union[pathlib.Path, raw_nodes.URI]):
         if not source_available(leaf, self.root_path):

bioimageio/core/resource_tests.py

@@ -228,7 +228,7 @@ def _test_expected_resource_type(rd: ResourceDescription, expected_type: str) ->
     return dict(
         name="has expected resource type",
         status="passed" if has_expected_type else "failed",
-        error=f"expected type {expected_type}, found {rd.type}",
+        error=None if has_expected_type else f"expected type {expected_type}, found {rd.type}",
         traceback=None,
         source_name=rd.id or rd.name if hasattr(rd, "id") else rd.name,
     )

tests/test_resource_tests/test_test_model.py

@@ -56,3 +56,14 @@ def test_validation_section_warning(unet2d_nuclei_broad_model, tmp_path: pathlib
     assert summary["name"] == "Test documentation completeness."
     assert summary["warnings"] == {}
     assert summary["status"] == "passed"
+
+
+def test_issue289():
+    """test for failure case from https://github.com/bioimage-io/core-bioimage-io-python/issues/289"""
+    import bioimageio.core
+    from bioimageio.core.resource_tests import test_model
+
+    doi = "10.5281/zenodo.6287342"
+    model_resource = bioimageio.core.load_resource_description(doi)
+    test_result = test_model(model_resource)
+    assert all([t["status"] == "passed" for t in test_result])