🗃️ DB migrations for new sample table

migrations/versions/1558052490ff_add_sample_table.py

@@ -0,0 +1,71 @@
+"""
+1.17.0 Add new Sample table
+
+Represents parent specimens of current Biospecimens
+
+Revision ID: 1558052490ff
+Revises: 3b427603af51
+Create Date: 2024-02-02 10:13:44.030498
+
+"""
+from alembic import op
+import sqlalchemy as sa
+from sqlalchemy.dialects import postgresql
+
+from dataservice.api.common.model import KfId
+
+# revision identifiers, used by Alembic.
+revision = '1558052490ff'
+down_revision = '3b427603af51'
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.create_table('sample',
+                    sa.Column('uuid', postgresql.UUID(), nullable=True),
+                    sa.Column('created_at', sa.DateTime(), nullable=True),
+                    sa.Column('modified_at', sa.DateTime(), nullable=True),
+                    sa.Column('visible', sa.Boolean(),
+                              server_default='true', nullable=False),
+                    sa.Column('visibility_reason', sa.Text(), nullable=True),
+                    sa.Column('visibility_comment', sa.Text(), nullable=True),
+                    sa.Column('external_id', sa.Text(), nullable=True),
+                    sa.Column('age_at_event_days',
+                              sa.Integer(), nullable=True),
+                    sa.Column('sample_event_key', sa.Text(), nullable=True),
+                    sa.Column('tissue_type', sa.Text(), nullable=True),
+                    sa.Column('sample_type', sa.Text(), nullable=True),
+                    sa.Column('anatomical_location', sa.Text(), nullable=True),
+                    sa.Column('volume_ul', sa.Float(), nullable=True),
+                    sa.Column('method_of_sample_procurement',
+                              sa.Text(), nullable=True),
+                    sa.Column('preservation_method', sa.Text(), nullable=True),
+                    sa.Column('participant_id', KfId(
+                        length=11), nullable=False),
+                    sa.Column('kf_id', KfId(
+                        length=11), nullable=False),
+                    sa.ForeignKeyConstraint(['participant_id'], [
+                                            'participant.kf_id'], ),
+                    sa.PrimaryKeyConstraint('kf_id'),
+                    sa.UniqueConstraint('external_id', 'participant_id', 'age_at_event_days', 'sample_type', 'anatomical_location',
+                                        'method_of_sample_procurement', 'tissue_type', 'preservation_method', name='sample_unique_constraint'),
+                    sa.UniqueConstraint('uuid')
+                    )
+    op.create_index(op.f('ix_sample_created_at'),
+                    'sample', ['created_at'], unique=False)
+    op.add_column('biospecimen', sa.Column(
+        'sample_id', KfId(length=11), nullable=True))
+    op.create_foreign_key(None, 'biospecimen', 'sample',
+                          ['sample_id'], ['kf_id'])
+    # ### end Alembic commands ###
+
+
+def downgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.drop_constraint(None, 'biospecimen', type_='foreignkey')
+    op.drop_column('biospecimen', 'sample_id')
+    op.drop_index(op.f('ix_sample_created_at'), table_name='sample')
+    op.drop_table('sample')
+    # ### end Alembic commands ###