Fix get_journal() when journal is a KGProxy (issue + volume case)

Author: apdavison

builder/additional_methods/ScholarlyArticle.py.txt

@@ -9,7 +9,8 @@
                 volume = issue_or_volume
                 issue = None
             journal = volume.is_part_of
-            assert isinstance(journal, Periodical)
+            if not isinstance(journal, Periodical):
+                journal = journal.resolve(client, release_status=self.release_status)
         retval = [journal]
         if with_volume:
             retval.append(volume)
@@ -38,6 +39,5 @@
             title += "."
         journal_name = journal.name if journal else ""
         volume_number = f"{volume.volume_number}: " if (volume and volume.volume_number != "placeholder") else ""
-        return (
-            f"{author_str} ({self.publication_date.year}). {title} {journal_name}, {volume_number}{self.pagination or ''}."
-        )
+        year = self.publication_date.year if self.publication_date else "unpublished?"
+        return f"{author_str} ({year}). {title} {journal_name}, {volume_number}{self.pagination or ''}."

fairgraph/openminds/publications/scholarly_article.py

@@ -114,7 +114,8 @@ def get_journal(self, client, with_volume=False, with_issue=False):
                 volume = issue_or_volume
                 issue = None
             journal = volume.is_part_of
-            assert isinstance(journal, Periodical)
+            if not isinstance(journal, Periodical):
+                journal = journal.resolve(client, release_status=self.release_status)
         retval = [journal]
         if with_volume:
             retval.append(volume)
@@ -143,4 +144,5 @@ def get_citation_string(self, client):
             title += "."
         journal_name = journal.name if journal else ""
         volume_number = f"{volume.volume_number}: " if (volume and volume.volume_number != "placeholder") else ""
-        return f"{author_str} ({self.publication_date.year}). {title} {journal_name}, {volume_number}{self.pagination or ''}."
+        year = self.publication_date.year if self.publication_date else "unpublished?"
+        return f"{author_str} ({year}). {title} {journal_name}, {volume_number}{self.pagination or ''}."

test/test_openminds_publication.py

@@ -1,6 +1,9 @@
 import datetime
+import pytest
 import fairgraph.openminds.core as omcore
 import fairgraph.openminds.publications as ompub
+from fairgraph.kgproxy import KGProxy
+from fairgraph.caching import object_cache
 
 
 def test_get_journal():
@@ -25,6 +28,34 @@ def test_get_journal():
     assert article.get_citation_string(client=None) == expected
 
 
+def test_get_journal_with_issue_proxy_journal():
+    """When data comes from the KG, volume.is_part_of is a KGProxy, not a resolved Periodical.
+    get_journal() should resolve the proxy rather than failing the isinstance assertion."""
+    periodical_id = "https://kg.ebrains.eu/api/instances/00000000-0000-0000-0000-000000000001"
+    jphysiol = ompub.Periodical(name="The Journal of Physiology", id=periodical_id)
+    object_cache[periodical_id] = jphysiol
+
+    try:
+        journal_proxy = KGProxy(ompub.Periodical, periodical_id)
+        volume = ompub.PublicationVolume(is_part_of=journal_proxy, volume_number="117")
+        issue = ompub.PublicationIssue(is_part_of=volume, issue_number="4")
+        article = ompub.ScholarlyArticle(
+            name="A quantitative description of membrane current and its application to conduction and excitation in nerve",
+            authors=[
+                omcore.Person(given_name="AL", family_name="Hodgkin"),
+                omcore.Person(given_name="AF", family_name="Huxley"),
+            ],
+            is_part_of=issue,
+            publication_date=datetime.date(1952, 8, 1),
+            pagination="500–44",
+        )
+        assert article.get_journal(client=None) == jphysiol
+        assert article.get_journal(client=None, with_volume=True) == (jphysiol, volume)
+        assert article.get_journal(client=None, with_volume=True, with_issue=True) == (jphysiol, volume, issue)
+    finally:
+        del object_cache[periodical_id]
+
+
 def test_get_journal_no_issue():
     jphysiol = ompub.Periodical(name="The Journal of Physiology")
     volume = ompub.PublicationVolume(is_part_of=jphysiol, volume_number="117")