Merge pull request #238 from bioimage-io/parent

Add tests for build_model with parent field

Author: FynnBe

bioimageio/core/build_spec/build_model.py

@@ -891,7 +891,6 @@ def build_model(
         kwargs["maintainers"] = [model_spec.raw_nodes.Maintainer(**m) for m in maintainers]
 
     if parent is not None:
-        assert len(parent) == 2
         kwargs["parent"] = parent
 
     if training_data is not None:

bioimageio/core/resource_io/nodes.py

@@ -73,6 +73,11 @@ class CollectionEntry(Node, collection_raw_nodes.CollectionEntry):
     source: URI = missing
 
 
+@dataclass
+class LinkedDataset(Node, model_raw_nodes.LinkedDataset):
+    pass
+
+
 @dataclass
 class ModelParent(Node, model_raw_nodes.ModelParent):
     pass

bioimageio/core/resource_io/utils.py

@@ -67,12 +67,6 @@ def transform_LocalImportableModule(self, node: raw_nodes.LocalImportableModule)
 
         return nodes.ImportedSource(factory=getattr(module, node.callable_name))
 
-    @staticmethod
-    def transform_ImportableModule(node):
-        raise RuntimeError(
-            "Encountered raw_nodes.ImportableModule in _SourceNodeTransformer. Apply _UriNodeTransformer first!"
-        )
-
     @staticmethod
     def transform_ResolvedImportableSourceFile(node: raw_nodes.ResolvedImportableSourceFile) -> nodes.ImportedSource:
         module_path = resolve_source(node.source_file)
@@ -83,12 +77,6 @@ def transform_ResolvedImportableSourceFile(node: raw_nodes.ResolvedImportableSou
         importlib_spec.loader.exec_module(dep)  # type: ignore  # todo: possible to use "loader.load_module"?
         return nodes.ImportedSource(factory=getattr(dep, node.callable_name))
 
-    @staticmethod
-    def transform_ImportablePath(node):
-        raise RuntimeError(
-            "Encountered raw_nodes.ImportableSourceFile in _SourceNodeTransformer. Apply _UriNodeTransformer first!"
-        )
-
 
 class RawNodeTypeTransformer(NodeTransformer):
     def __init__(self, nodes_module: ModuleType):
@@ -117,9 +105,11 @@ def all_sources_available(
         return True
 
 
-def resolve_raw_resource_description(raw_rd: GenericRawRD, nodes_module: typing.Any) -> GenericResolvedNode:
-    """resolve all uris and sources"""
-    rd = UriNodeTransformer(root_path=raw_rd.root_path).transform(raw_rd)
+def resolve_raw_resource_description(
+    raw_rd: GenericRawRD, nodes_module: typing.Any, uri_only_if_in_package: bool = True
+) -> GenericResolvedNode:
+    """resolve all uris and paths (that are included when packaging)"""
+    rd = UriNodeTransformer(root_path=raw_rd.root_path, uri_only_if_in_package=uri_only_if_in_package).transform(raw_rd)
     rd = SourceNodeTransformer().transform(rd)
     rd = RawNodeTypeTransformer(nodes_module).transform(rd)
     return rd

tests/build_spec/test_build_spec.py

@@ -18,6 +18,7 @@ def _test_build_spec(
     use_original_covers=False,
     use_absoloute_arch_path=False,
     training_data=None,
+    parent=None,
 ):
     from bioimageio.core.build_spec import build_model
 
@@ -118,6 +119,8 @@ def _test_build_spec(
         kwargs["covers"] = resolve_source(model_spec.covers, root)
     if training_data is not None:
         kwargs["training_data"] = training_data
+    if parent is not None:
+        kwargs["parent"] = parent
 
     build_model(**kwargs)
     assert out_path.exists()
@@ -211,6 +214,16 @@ def test_build_spec_training_data2(unet2d_nuclei_broad_model, tmp_path):
     _test_build_spec(unet2d_nuclei_broad_model, tmp_path / "model.zip", "torchscript", training_data=training_data)
 
 
+def test_build_spec_parent1(unet2d_nuclei_broad_model, tmp_path):
+    parent = {"uri": "https:/my-parent-model.org"}
+    _test_build_spec(unet2d_nuclei_broad_model, tmp_path / "model.zip", "torchscript", parent=parent)
+
+
+def test_build_spec_parent2(unet2d_nuclei_broad_model, tmp_path):
+    parent = {"id": "10.5281/zenodo.5764892"}
+    _test_build_spec(unet2d_nuclei_broad_model, tmp_path / "model.zip", "torchscript", parent=parent)
+
+
 def test_build_spec_deepimagej_keras(unet2d_keras, tmp_path):
     _test_build_spec(
         unet2d_keras, tmp_path / "model.zip", "keras_hdf5", add_deepimagej_config=True, tensorflow_version="1.12"