Merge pull request #102 from VariantEffect/ashsny/unique-urns

Enforce unique URNs at schema level for URN-having entities.

Author: ashsny

alembic/versions/fecb3e0d181d_make_urns_unique.py

@@ -0,0 +1,34 @@
+"""empty message
+
+Revision ID: fecb3e0d181d
+Revises: c6154dd7d9b9
+Create Date: 2023-11-15 19:45:42.769529
+
+"""
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision = 'fecb3e0d181d'
+down_revision = 'c6154dd7d9b9'
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.create_index(op.f('ix_experiment_sets_urn'), 'experiment_sets', ['urn'], unique=True)
+    op.create_index(op.f('ix_experiments_urn'), 'experiments', ['urn'], unique=True)
+    op.create_index(op.f('ix_scoresets_urn'), 'scoresets', ['urn'], unique=True)
+    op.create_index(op.f('ix_variants_urn'), 'variants', ['urn'], unique=True)
+    # ### end Alembic commands ###
+
+
+def downgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.drop_index(op.f('ix_variants_urn'), table_name='variants')
+    op.drop_index(op.f('ix_scoresets_urn'), table_name='scoresets')
+    op.drop_index(op.f('ix_experiments_urn'), table_name='experiments')
+    op.drop_index(op.f('ix_experiment_sets_urn'), table_name='experiment_sets')
+    # ### end Alembic commands ###

src/mavedb/models/experiment.py

@@ -44,7 +44,7 @@ class Experiment(Base):
 
     id = Column(Integer, primary_key=True, index=True)
 
-    urn = Column(String(64), nullable=True, default=generate_temp_urn)  # index=True, nullable=True
+    urn = Column(String(64), nullable=True, default=generate_temp_urn, unique=True, index=True)
     title = Column(String, nullable=False)
     short_description = Column(String, nullable=False)
     abstract_text = Column(String, nullable=False)

src/mavedb/models/experiment_set.py

@@ -43,7 +43,7 @@ class ExperimentSet(Base):
 
     id = Column(Integer, primary_key=True, index=True)
 
-    urn = Column(String(64), nullable=True, default=generate_temp_urn)  # index=True, nullable=True
+    urn = Column(String(64), nullable=True, default=generate_temp_urn, unique=True, index=True)
     extra_metadata = Column(JSONB, nullable=False)
 
     private = Column(Boolean, nullable=False, default=True)

src/mavedb/models/score_set.py

@@ -53,7 +53,7 @@ class ScoreSet(Base):
 
     id = Column(Integer, primary_key=True, index=True)
 
-    urn = Column(String(64), nullable=True, default=generate_temp_urn)  # index=True, nullable=True
+    urn = Column(String(64), nullable=True, default=generate_temp_urn, unique=True, index=True)
     title = Column(String, nullable=False)
     method_text = Column(String, nullable=False)
     abstract_text = Column(String, nullable=False)

src/mavedb/models/variant.py

@@ -12,7 +12,7 @@ class Variant(Base):
 
     id = Column(Integer, primary_key=True, index=True)
 
-    urn = Column(String(64), nullable=True)  # index=True, nullable=True
+    urn = Column(String(64), nullable=True, unique=True, index=True)
     data = Column(JSONB, nullable=False)
 
     score_set_id = Column("scoreset_id", Integer, ForeignKey("scoresets.id"), nullable=False)