Merge pull request #56 from bioimage-io/maintainers

block new version upload for non-maintainers

bioimageio_collection_backoffice/_backoffice.py

@@ -110,7 +110,7 @@ def request_changes(
                 f"Requesting changes of already published  {resource_id} {version} is not implemented"
             )
 
-        rv.request_changes(reviewer=reviewer, reason=reason)
+        rv.request_changes(reviewer, reason=reason)
         notify_uploader(
             rv,
             "needs changes 📑",
@@ -129,7 +129,7 @@ def publish(self, resource_id: str, version: str, reviewer: str):
 
         try:
             rv.lock_publish()
-            published: PublishedVersion = rv.publish(reviewer=reviewer)
+            published: PublishedVersion = rv.publish(reviewer)
             assert isinstance(published, PublishedVersion)
             self.generate_collection_json()
             notify_uploader(

bioimageio_collection_backoffice/db_structure/log.py

@@ -22,6 +22,14 @@ class _LogEntryBaseWithDefaults(_LogEntryBase, frozen=True):
     """creation of log entry"""
 
 
+class CollectionLog(_LogEntryBase, frozen=True):
+    log: str
+
+
+class CollectionLogWithDefaults(_LogEntryBaseWithDefaults, CollectionLog, frozen=True):
+    pass
+
+
 class BioimageioLog(_LogEntryBase, frozen=True):
     log: ValidationSummary
 
@@ -37,6 +45,7 @@ class Log(Node, frozen=True, extra="allow"):
 
     bioimageio_spec: Sequence[BioimageioLog]
     bioimageio_core: Sequence[BioimageioLog]
+    collection: Sequence[CollectionLog]
 
     def get_updated(self, update: Log):
         v: Union[Any, Sequence[Any]]
@@ -59,3 +68,4 @@ class LogWithDefaults(Log, frozen=True, extra="allow"):
 
     bioimageio_spec: Sequence[BioimageioLogWithDefaults] = Field(default_factory=list)
     bioimageio_core: Sequence[BioimageioLogWithDefaults] = Field(default_factory=list)
+    collection: Sequence[CollectionLogWithDefaults] = Field(default_factory=list)

bioimageio_collection_backoffice/generate_collection_json.py

@@ -3,6 +3,9 @@
 from typing import Any, Dict, List, Union
 
 from bioimageio.spec import ValidationContext, build_description
+from bioimageio.spec._internal.io import (
+    get_sha256,  # TODO: use bioimageio.spec.utils.get_sha256
+)
 from bioimageio.spec.collection import CollectionDescr
 from bioimageio.spec.common import HttpUrl
 from bioimageio.spec.utils import download
@@ -48,7 +51,8 @@ def create_entry(
     with ValidationContext(perform_io_checks=False):
         rdf_url = HttpUrl(p.rdf_url)
 
-    rdf = yaml.load(download(rdf_url).path)
+    rdf_path = download(rdf_url).path
+    rdf = yaml.load(rdf_path)
     entry = {
         k: rdf[k]
         for k in (
@@ -102,6 +106,7 @@ def maybe_swap_with_thumbnail(
     entry["nickname"] = entry["id"]
     entry["nickname_icon"] = entry["id_emoji"]
     entry["entry_source"] = p.rdf_url
+    entry["entry_sha256"] = get_sha256(rdf_path)
     entry["rdf_source"] = entry["entry_source"]
     entry["version_number"] = p.number
     entry["versions"] = list(p.concept.versions.published)

bioimageio_collection_backoffice/mailroom/_send_email.py

@@ -1,4 +1,5 @@
 import smtplib
+import sys
 from email.mime.text import MIMEText
 from typing import List, Union
 
@@ -23,8 +24,8 @@ def notify_uploader(
 ):
     email, name = rv.get_uploader()
     if email is None:
-        logger.error("missing uploader email for {} {}", rv.id, rv.version)
-        return
+        rv.report_error(f"missing uploader email for {rv.id} {rv.version}")
+        sys.exit(1)
 
     subject = f"{STATUS_UPDATE_SUBJECT}{rv.id} {rv.version} {subject_end.strip()}"
     if email == BOT_EMAIL: