use enrich_partial_rdf_with_imjoy_plugin from bioimageio.spec.partner

Author: FynnBe

scripts/utils.py

@@ -19,8 +19,7 @@
 )
 from bioimageio.spec.collection.v0_2.utils import resolve_collection_entries
 from bioimageio.spec.io_ import serialize_raw_resource_description
-from bioimageio.spec.partner.imjoy_plugin_parser import get_plugin_as_rdf
-from bioimageio.spec.shared import resolve_rdf_source
+from bioimageio.spec.partner.utils import enrich_partial_rdf_with_imjoy_plugin
 
 
 # todo: use MyYAML from bioimageio.spec. see comment below
@@ -194,36 +193,6 @@ def rec_sort(obj):
         return obj
 
 
-def enrich_partial_rdf_with_imjoy_plugin(partial_rdf: Dict[str, Any]) -> Dict[str, Any]:
-    """
-    a (partial) rdf may have 'rdf_resource' or 'source' which resolve to rdf data that may be overwritten.
-    Due to resolving imjoy plugins this is not done in bioimageio.spec.collection atm
-    """
-    enriched_rdf = {}
-    if "rdf_source" in partial_rdf:
-        rdf_source = partial_rdf["rdf_source"]
-        if isinstance(rdf_source, str) and rdf_source.split("?")[0].endswith(".imjoy.html"):
-            # rdf_source is an imjoy plugin
-            rdf_source = dict(get_plugin_as_rdf(rdf_source))
-
-        else:
-            # rdf_source is an actual rdf
-            if not isinstance(rdf_source, dict):
-                rdf_source, rdf_source_name, rdf_source_root = resolve_rdf_source(rdf_source)
-                rdf_source["root_path"] = rdf_source_root  # enables remote source content to be resolved
-
-        assert isinstance(rdf_source, dict)
-        enriched_rdf.update(rdf_source)
-
-    if "source" in partial_rdf:
-        if partial_rdf["source"].split("?")[0].endswith(".imjoy.html"):
-            rdf_from_source = get_plugin_as_rdf(partial_rdf["source"])
-            enriched_rdf.update(rdf_from_source)
-
-    enriched_rdf.update(partial_rdf)  # initial partial rdf overwrites fields from rdf_source or source
-    return enriched_rdf
-
-
 def write_rdfs_for_resource(resource: dict, dist: Path, only_for_version_id: Optional[str] = None) -> List[str]:
     """write updated version rdfs for the given resource to dist
 
@@ -237,7 +206,7 @@ def write_rdfs_for_resource(resource: dict, dist: Path, only_for_version_id: Opt
     """
     resource_id = resource["id"]
     updated_versions = []
-    resource_info = enrich_partial_rdf_with_imjoy_plugin(resource)
+    resource_info = enrich_partial_rdf_with_imjoy_plugin(resource, pathlib.Path())
     for version_info in resource["versions"]:
         version_id = version_info["version_id"]
         if (
@@ -248,7 +217,7 @@ def write_rdfs_for_resource(resource: dict, dist: Path, only_for_version_id: Opt
         ):
             continue
 
-        version_info = enrich_partial_rdf_with_imjoy_plugin(version_info)
+        version_info = enrich_partial_rdf_with_imjoy_plugin(version_info, pathlib.Path())
 
         rdf = dict(resource_info)  # rdf is based on resource info
         rdf.update(version_info)  # version specific info overwrites resource info