Bugfixes/retro compatibility

src/ensembl/production/metadata/api/models/genome.py

@@ -53,7 +53,7 @@ def get_public_path(self, type='all', release=None):
             raise ValueError("Genebuild annotation source attribute not found for the dataset")
 
         genebuild_source_name = genebuild_annotation_source_attribute.value
-        common_path = f"{self.organism.scientific_name}/{self.assembly.accession}/{genebuild_source_name}"
+        common_path = f"{self.organism.scientific_name.replace(' ', '_')}/{self.assembly.accession}/{genebuild_source_name}"
 
         if type in ['genebuild', 'assembly', 'homology', 'regulation', 'variation', 'all']:
             if type == 'genebuild':

src/ensembl/production/metadata/api/models/organism.py

@@ -10,12 +10,12 @@
 #   See the License for the specific language governing permissions and
 #   limitations under the License.
 import uuid
+import warnings
 
 from sqlalchemy import Column, Integer, String, Index, ForeignKey
 from sqlalchemy.dialects.mysql import TINYINT
 from sqlalchemy.ext.hybrid import hybrid_property
-from sqlalchemy.orm import relationship
-from sqlalchemy.testing.plugin.plugin_base import warnings
+from sqlalchemy.orm import relationship, synonym
 
 from ensembl.production.metadata.api.models.base import Base, LoadAble
 
@@ -37,7 +37,7 @@ class Organism(LoadAble, Base):
     genomes = relationship("Genome", back_populates="organism", cascade="all, delete, delete-orphan")
     organism_group_members = relationship("OrganismGroupMember", back_populates="organism")
     strain_type = Column(String(128), nullable=True, unique=False)
-
+    ensembl_name = synonym("biosample_id")
     #This is the code for ensembl_name. It should be considered temporary and be removed well before 2025
     @hybrid_property
     def ensembl_name(self):

src/tests/test_api.py

@@ -0,0 +1,64 @@
+# See the NOTICE file distributed with this work for additional information
+#   regarding copyright ownership.
+#   Licensed under the Apache License, Version 2.0 (the "License");
+#   you may not use this file except in compliance with the License.
+#   You may obtain a copy of the License at
+#       http://www.apache.org/licenses/LICENSE-2.0
+#   Unless required by applicable law or agreed to in writing, software
+#   distributed under the License is distributed on an "AS IS" BASIS,
+#   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+#   See the License for the specific language governing permissions and
+#   limitations under the License.
+from pathlib import Path
+from unittest import mock
+from unittest.mock import Mock, patch
+
+import pytest
+import re
+
+import sqlalchemy
+from ensembl.database import UnitTestDB, DBConnection
+
+from ensembl.production.metadata.api.exceptions import UpdateBackCoreException
+from ensembl.production.metadata.api.factory import meta_factory
+from ensembl.production.metadata.api.models import Organism, Assembly, Dataset, AssemblySequence, DatasetAttribute, \
+    DatasetSource, DatasetType, Attribute, Genome
+from ensembl.core.models import Meta
+
+from ensembl.production.metadata.updater.core import CoreMetaUpdater
+
+db_directory = Path(__file__).parent / 'databases'
+db_directory = db_directory.resolve()
+
+
+@pytest.mark.parametrize("multi_dbs", [[{'src': 'ensembl_metadata'}, {'src': 'ncbi_taxonomy'}]], indirect=True)
+class TestApi:
+    dbc = None  # type: UnitTestDB
+
+    def test_get_public_path_genebuild(self, multi_dbs):
+        metadata_db = DBConnection(multi_dbs['ensembl_metadata'].dbc.url)
+        with metadata_db.session_scope() as session:
+            genome = session.query(Genome).filter(Genome.genome_uuid == 'a733574a-93e7-11ec-a39d-005056b38ce3').first()
+            paths = genome.get_public_path(type='all')
+            assert len(paths) == 5
+            # assert all("/genebuild/" in path for path in paths)
+            path = genome.get_public_path(type='genebuild')
+            assert path[0] == 'Saccharomyces_cerevisiae_S288c/GCA_000146045.2/test_anno_source/genebuild/test_version'
+            path = genome.get_public_path(type='assembly')
+            assert path[0] == 'Saccharomyces_cerevisiae_S288c/GCA_000146045.2/test_anno_source/genome'
+            path = genome.get_public_path(type='variation')
+            assert path[0] == 'Saccharomyces_cerevisiae_S288c/GCA_000146045.2/test_anno_source/variation'
+            path = genome.get_public_path(type='homology')
+            assert path[0] == 'Saccharomyces_cerevisiae_S288c/GCA_000146045.2/test_anno_source/homology'
+            path = genome.get_public_path(type='regulation')
+            assert path[0] == 'Saccharomyces_cerevisiae_S288c/GCA_000146045.2/test_anno_source/regulation'
+
+    def test_organism_ensembl_name_compat(self, multi_dbs):
+        """ Validate that we can still yse ensembl_name in queries from SQLAlchemy
+        This test will fail when we remove the ORM column for good
+        """
+        metadata_db = DBConnection(multi_dbs['ensembl_metadata'].dbc.url)
+        with metadata_db.session_scope() as session:
+            ensembl_name = session.query(Organism).filter(Organism.ensembl_name == 'homo_sapiens').first()
+            biosample_id = session.query(Organism).filter(Organism.biosample_id == 'homo_sapiens').first()
+            assert ensembl_name.organism_uuid == biosample_id.organism_uuid

src/tests/test_updater.py

@@ -266,25 +266,4 @@ def test_update_released_force(self, multi_dbs):
             ).count()
             assert count > 0
 
-    def test_get_public_path_genebuild(self, multi_dbs):
-        metadata_db = DBConnection(multi_dbs['ensembl_metadata'].dbc.url)
-        with metadata_db.session_scope() as session:
-            genome = session.query(Genome).filter(Genome.genome_uuid == 'a733574a-93e7-11ec-a39d-005056b38ce3').first()
-            paths = genome.get_public_path(type='all')
-            assert len(paths) == 5
-            # assert all("/genebuild/" in path for path in paths)
-            path = genome.get_public_path(type='genebuild')
-            assert path[
-                       0] == 'Saccharomyces cerevisiae S288c/GCA_000146045.2/test_anno_source/genebuild/test_version'
-            path = genome.get_public_path(type='assembly')
-            assert path[
-                       0] == 'Saccharomyces cerevisiae S288c/GCA_000146045.2/test_anno_source/genome'
-            path = genome.get_public_path(type='variation')
-            assert path[
-                       0] == 'Saccharomyces cerevisiae S288c/GCA_000146045.2/test_anno_source/variation'
-            path = genome.get_public_path(type='homology')
-            assert path[
-                       0] == 'Saccharomyces cerevisiae S288c/GCA_000146045.2/test_anno_source/homology'
-            path = genome.get_public_path(type='regulation')
-            assert path[
-                       0] == 'Saccharomyces cerevisiae S288c/GCA_000146045.2/test_anno_source/regulation'
+