Merge pull request #601 from bioimage-io/rm_version_number

Remove version_number field

README.md

@@ -105,9 +105,13 @@ Made with [contrib.rocks](https://contrib.rocks).
 
 ### bioimageio.spec Python package
 
-#### bioimageio.spec 0.5.2post6 (to be released)
+#### bioimageio.spec 0.5.3
 
+* remove collection description
 * update SPDX license list
+* update generic description to 0.3.1
+* update model description to 0.5.3
+* add timeout argument to all requests.get calls
 
 #### bioimageio.spec 0.5.2post5
 
@@ -283,6 +287,11 @@ Made with [contrib.rocks](https://contrib.rocks).
 
 ### Resource Description Format Versions
 
+#### general 0.3.1 and model 0.5.3
+
+* Non-breaking changes
+  * remove `version_number` in favor of using `version`
+
 #### model 0.5.2
 
 * Non-breaking changes

bioimageio/spec/VERSION

@@ -1,3 +1,3 @@
 {
-    "version": "0.5.2post5"
+    "version": "0.5.3"
 }

bioimageio/spec/__init__.py

@@ -3,7 +3,6 @@
 """
 
 from . import application as application
-from . import collection as collection
 from . import dataset as dataset
 from . import generic as generic
 from . import model as model
@@ -31,8 +30,6 @@
 )
 from .application import AnyApplicationDescr as AnyApplicationDescr
 from .application import ApplicationDescr as ApplicationDescr
-from .collection import AnyCollectionDescr as AnyCollectionDescr
-from .collection import CollectionDescr as CollectionDescr
 from .dataset import AnyDatasetDescr as AnyDatasetDescr
 from .dataset import DatasetDescr as DatasetDescr
 from .generic import AnyGenericDescr as AnyGenericDescr

bioimageio/spec/_description.py

@@ -13,9 +13,6 @@
 from .application import AnyApplicationDescr, ApplicationDescr
 from .application.v0_2 import ApplicationDescr as ApplicationDescr02
 from .application.v0_3 import ApplicationDescr as ApplicationDescr03
-from .collection import AnyCollectionDescr, CollectionDescr
-from .collection.v0_2 import CollectionDescr as CollectionDescr02
-from .collection.v0_3 import CollectionDescr as CollectionDescr03
 from .dataset import AnyDatasetDescr, DatasetDescr
 from .dataset.v0_2 import DatasetDescr as DatasetDescr02
 from .dataset.v0_3 import DatasetDescr as DatasetDescr03
@@ -38,7 +35,6 @@
     Annotated[
         Union[
             ApplicationDescr,
-            CollectionDescr,
             DatasetDescr,
             ModelDescr,
             NotebookDescr,
@@ -53,7 +49,6 @@
 SpecificResourceDescr = Annotated[
     Union[
         AnyApplicationDescr,
-        AnyCollectionDescr,
         AnyDatasetDescr,
         AnyModelDescr,
         AnyNotebookDescr,
@@ -99,13 +94,6 @@ def dump_description(
                 None: ApplicationDescr,
             }
         ),
-        "collection": MappingProxyType(
-            {
-                "0.2": CollectionDescr02,
-                "0.3": CollectionDescr03,
-                None: CollectionDescr,
-            }
-        ),
         "dataset": MappingProxyType(
             {
                 "0.2": DatasetDescr02,

bioimageio/spec/_internal/_settings.py

@@ -23,18 +23,19 @@ class Settings(BaseSettings, extra="ignore"):
     """url to bioimageio collection.json to resolve collection specific resource IDs.
     """
 
-    collection_staged: str = (
-        "https://uk1s3.embassy.ebi.ac.uk/public-datasets/bioimage.io/collection_staged.json"
+    collection_draft: str = (
+        "https://uk1s3.embassy.ebi.ac.uk/public-datasets/bioimage.io/collection_draft.json"
     )
-    """url to bioimageio collection_staged.json to resolve collection specific, staged
-    resource IDs."""
-
-    resolve_staged: bool = True
-    """Flag to resolve staged resource versions following the pattern
-    <resource id>/staged/<stage number>.
-    Note that anyone may stage a new resource version and that such a staged version
-    may not have been reviewed.
-    Set this flag to False to avoid this potential security risk."""
+    """url to bioimageio collection_draft.json to resolve collection specific draft
+    versions of resources ending with '/draft'."""
+
+    resolve_draft: bool = True
+    """Flag to resolve draft resource versions following the pattern
+    <resource id>/draft.
+    Note that anyone may stage a new draft and that such a draft version
+    may not have been reviewed yet.
+    Set this flag to False to avoid this potential security risk
+    and disallow loading draft versions."""
 
     perform_io_checks: bool = True
     """wether or not to perform validation that requires file io,

bioimageio/spec/_internal/io_utils.py

@@ -96,13 +96,13 @@ def open_bioimageio_yaml(
 
         collection = get_collection()
         if source not in collection:
-            if "/staged/" in source:
-                if settings.resolve_staged:
-                    collection_url = settings.collection_staged
+            if isinstance(source, str) and source.endswith("/draft"):
+                if settings.resolve_draft:
+                    collection_url = settings.collection_draft
                 else:
                     collection_url = ""
                     logger.error(
-                        "Did not try to resolve '{}' as BIOIMAGEIO_RESOLVE_STAGED is set to False",
+                        "Did not try to resolve '{}' as BIOIMAGEIO_RESOLVE_DRAFT is set to False",
                         source,
                     )
             else:
@@ -115,7 +115,7 @@ def open_bioimageio_yaml(
         logger.info(
             "{} loading {} {} from {}",
             entry.emoji,
-            entry.id,
+            f"{entry.id}/{entry.version}",
             entry.version,
             entry.url,
         )
@@ -142,6 +142,7 @@ class _CollectionEntry(NamedTuple):
     url: str
     sha256: Optional[Sha256]
     version: str
+    doi: Optional[str]
 
 
 def _get_one_collection(url: str):
@@ -160,81 +161,49 @@ def _get_one_collection(url: str):
         logger.error("`collection` field of {} has type {}", url, type(collection))
         return ret
 
-    for entry in collection:
-        if entry["entry_sha256"] is None:
-            logger.debug("skipping {} with entry_sha256=None", entry["id"])
-            continue
-
-        if not isinstance(entry, dict):
-            logger.error("entry has type {}", type(entry))
-            continue
-        if not isinstance(entry["id"], str):
-            logger.error("entry['id'] has type {}", type(entry["id"]))
-            continue
-        if not isinstance(entry["id_emoji"], str):
-            logger.error(
-                "{}.id_emoji has type {}", entry["id"], type(entry["id_emoji"])
+    for raw_entry in collection:
+        try:
+            for i, (v, d) in enumerate(zip(raw_entry["versions"], raw_entry["dois"])):
+                entry = _CollectionEntry(
+                    id=raw_entry["id"],
+                    emoji=raw_entry.get("id_emoji", raw_entry.get("nickname_icon", "")),
+                    url=raw_entry["rdf_source"],
+                    sha256=raw_entry["rdf_sha256"],
+                    version=v,
+                    doi=d,
+                )
+                ret[f"{raw_entry['id']}/{v}"] = entry
+                if i == 0:
+                    # latest version
+                    ret[raw_entry["id"]] = entry
+                    if (concept_doi := raw_entry.get("concept_doi")) is not None:
+                        ret[concept_doi] = entry
+
+                    if (nickname := raw_entry.get("nickname")) is not None:
+                        ret[nickname] = entry
+
+                if d is not None:
+                    ret[d] = entry
+
+        except Exception as e:
+            entry_id = (
+                raw_entry.get("id", "unknown")
+                if isinstance(raw_entry, dict)
+                else "unknown"
             )
-            continue
-        if not isinstance(entry["entry_source"], str):
-            logger.error(
-                "{}.entry_source has type {}", entry["id"], type(entry["entry_source"])
-            )
-            continue
-        if not isinstance(entry["entry_sha256"], str):
             logger.error(
-                "{}.entry_sha256 has type {}", entry["id"], type(entry["entry_sha256"])
+                "failed to parse collection entry with `id={}`: {}", entry_id, e
             )
             continue
 
-        c_entry = _CollectionEntry(
-            entry["id"],
-            entry["id_emoji"],
-            entry["entry_source"],
-            (
-                None
-                if entry.get("entry_sha256") is None
-                else Sha256(entry["entry_sha256"])
-            ),
-            version=str(entry["version_number"]),
-        )
-        # set version specific entry
-        ret[c_entry.id + "/" + str(entry["version_number"])] = c_entry
-
-        # set doi entry
-        doi = entry.get("doi")
-        if doi is not None:
-            ret[doi] = c_entry
-
-        # update 'latest version' entry
-        if c_entry.id not in ret:
-            update = True
-        else:
-            old_v = ret[c_entry.id].version
-            v = c_entry.version
-
-            if old_v.startswith("staged"):
-                update = not v.startswith("staged") or int(
-                    v.replace("staged/", "")
-                ) > int(old_v.replace("staged/", ""))
-            else:
-                update = not v.startswith("staged") and int(v) > int(old_v)
-
-        if update:
-            ret[c_entry.id] = c_entry
-            # set concept doi entry
-            concept_doi = entry.get("concept_doi")
-            if concept_doi is not None:
-                ret[concept_doi] = c_entry
-
     return ret
 
 
 @lru_cache
 def get_collection() -> Mapping[str, _CollectionEntry]:
     try:
-        if settings.resolve_staged:
-            ret = _get_one_collection(settings.collection_staged)
+        if settings.resolve_draft:
+            ret = _get_one_collection(settings.collection_draft)
         else:
             ret = {}
 

bioimageio/spec/application/v0_3.py

@@ -3,7 +3,6 @@
 from pydantic import Field
 from typing_extensions import Annotated
 
-from .._internal.common_nodes import Node
 from .._internal.io import FileDescr as FileDescr
 from .._internal.io_basics import AbsoluteFilePath as AbsoluteFilePath
 from .._internal.io_basics import Sha256 as Sha256
@@ -14,7 +13,7 @@
 from ..generic.v0_3 import BadgeDescr as BadgeDescr
 from ..generic.v0_3 import CiteEntry as CiteEntry
 from ..generic.v0_3 import Doi as Doi
-from ..generic.v0_3 import GenericDescrBase, ResourceId
+from ..generic.v0_3 import GenericDescrBase, LinkedResourceNode, ResourceId
 from ..generic.v0_3 import LinkedResource as LinkedResource
 from ..generic.v0_3 import Maintainer as Maintainer
 from ..generic.v0_3 import OrcidId as OrcidId
@@ -45,11 +44,8 @@ class ApplicationDescr(GenericDescrBase, title="bioimage.io application specific
     """The primary source of the application"""
 
 
-class LinkedApplication(Node):
+class LinkedApplication(LinkedResourceNode):
     """Reference to a bioimage.io application."""
 
     id: ApplicationId
     """A valid application `id` from the bioimage.io collection."""
-
-    version_number: int
-    """version number (n-th published version, not the semantic version) of linked application"""