Merge pull request #531 from bioimage-io/fix_root_path

Fix root path issue related to new zenodo api

Author: FynnBe

bioimageio/spec/VERSION

@@ -1,3 +1,3 @@
 {
-    "version": "0.4.9post3"
+    "version": "0.4.9post4"
 }

bioimageio/spec/shared/_resolve_source.py

@@ -106,8 +106,6 @@ def resolve_rdf_source(
             # source is bioimageio id or bioimageio nickname
             source = bioimageio_rdf_source
         elif re.fullmatch(DOI_REGEX, source):  # turn doi into url
-            import requests  # not available in pyodide
-
             zenodo_prefix = "10.5281/zenodo."
             zenodo_record_api = "https://zenodo.org/api/records"
             zenodo_sandbox_prefix = "10.5072/zenodo."
@@ -136,23 +134,7 @@ def resolve_rdf_source(
 
                     record_id = record_id.split("/")[-1]
 
-                response = requests.get(f"{zenodo_record_api}/{record_id}")
-                if not response.ok:
-                    raise RuntimeError(response.status_code)
-
-                zenodo_record = response.json()
-                for rdf_name in RDF_NAMES:
-                    for f in zenodo_record["files"]:
-                        if f["key"] == rdf_name:
-                            source = f["links"]["self"]
-                            break
-                    else:
-                        continue
-
-                    break
-                else:
-                    raise ValidationError(f"No RDF found; looked for {RDF_NAMES}")
-
+                source = f"{zenodo_record_api}/{record_id}/files/rdf.yaml/content"
             else:
                 # resolve doi
                 # todo: make sure the resolved url points to a rdf.yaml or a zipped package

bioimageio/spec/shared/raw_nodes.py

@@ -87,8 +87,13 @@ def __truediv__(self, other):
 
     @property
     def parent(self):
-        path_parent = pathlib.PurePosixPath(self.path).parent.as_posix()
-        return dataclasses.replace(self, path=path_parent, uri_string=None)
+        path = pathlib.PurePosixPath(self.path)
+        if self.authority == "zenodo.org" and self.path.startswith("/api/records/") and self.path.endswith("/content"):
+            parent_path = (path.parent.parent / "content").as_posix()
+        else:
+            parent_path = path.parent.as_posix()
+
+        return dataclasses.replace(self, path=parent_path, uri_string=None)
 
     def __post_init__(self):
         uri_string = self.uri_string  # should be InitVar, see comment at definition above

tests/test_commands.py

@@ -11,7 +11,7 @@
 from bioimageio.spec.model import format_version, raw_nodes
 from bioimageio.spec.shared import yaml
 
-SKIP_ZENODO = True
+SKIP_ZENODO = False
 SKIP_ZENODO_REASON = "zenodo api changes"
 
 
@@ -46,14 +46,6 @@ def test_validate_model_as_url():
     )["error"]
 
 
-@pytest.mark.skipif(SKIP_ZENODO, reason=SKIP_ZENODO_REASON)
-def test_validate_model_as_zenodo_sandbox_doi():
-    from bioimageio.spec.commands import validate
-
-    doi = "10.5281/zenodo.5744489"
-    assert not validate(doi, update_format=False, update_format_inner=False)["error"]
-
-
 @pytest.mark.skipif(SKIP_ZENODO, reason=SKIP_ZENODO_REASON)
 def test_validate_model_as_zenodo_doi():
     from bioimageio.spec.commands import validate

tests/test_io.py

@@ -4,7 +4,7 @@
 
 from bioimageio.spec.shared import yaml
 
-SKIP_ZENODO = True
+SKIP_ZENODO = False
 SKIP_ZENODO_REASON = "zenodo api changes"
 
 

tests/test_schema_model.py

@@ -6,7 +6,7 @@
 from bioimageio.spec.model.v0_4 import raw_nodes as raw_nodes_m04
 from bioimageio.spec.shared import yaml
 
-SKIP_ZENODO = True
+SKIP_ZENODO = False
 SKIP_ZENODO_REASON = "zenodo api changes"