remove superseded and published versions from the staged collection

bioimageio_collection_backoffice/generate_collection_json.py

@@ -1,12 +1,13 @@
 from pathlib import Path
-from typing import Any, Dict, List, Union
+from typing import Any, Dict, List, Optional, Union
 
 from bioimageio.spec import ValidationContext
 from bioimageio.spec._internal.io import (
     get_sha256,  # TODO: use bioimageio.spec.utils.get_sha256
 )
 from bioimageio.spec.common import HttpUrl
 from bioimageio.spec.utils import download
+from loguru import logger
 from ruyaml import YAML
 
 from .remote_resource import PublishedVersion, StagedVersion
@@ -18,7 +19,7 @@
 def create_entry(
     client: Client,
     rv: Union[PublishedVersion, StagedVersion],
-) -> Dict[str, Any]:
+) -> Optional[Dict[str, Any]]:
     with ValidationContext(perform_io_checks=False):
         rdf_url = HttpUrl(rv.rdf_url)
 
@@ -91,6 +92,14 @@ def maybe_swap_with_thumbnail(
         client.get_file_url("").strip("/") + "/" + rv.folder.strip("/") + "/files"
     )
     entry["info"] = rv.info.model_dump(mode="json")
+    if isinstance(rv, StagedVersion) and (
+        status := entry["info"]["status"]["name"]
+    ) in (
+        "superseded",
+        "published",
+    ):
+        logger.debug("skipping {} staged version {} {}", status, rv.id, rv.version)
+        return None
     try:
         old_doi = rdf["config"]["_conceptdoi"]
     except KeyError:

bioimageio_collection_backoffice/remote_collection.py

@@ -66,7 +66,8 @@ def generate_collection_json(
                     )
                     logger.error(error_in_published_entry)
                 else:
-                    collection["collection"].append(entry)
+                    if entry is not None:
+                        collection["collection"].append(entry)
         elif mode == "staged":
             for rv in self.get_all_staged_versions():
                 try:
@@ -76,7 +77,8 @@ def generate_collection_json(
                         "failed to create {} {} entry: {}", rv.id, rv.version, e
                     )
                 else:
-                    collection["collection"].append(entry)
+                    if entry is not None:
+                        collection["collection"].append(entry)
         else:
             assert_never(mode)
         coll_descr = build_description(