Checking kit integrity on import.

alembic/versions/3d80e4a17a26_added_versions_to_ref_kraken.py

@@ -0,0 +1,59 @@
+"""added versions to ref/kraken
+
+Revision ID: 3d80e4a17a26
+Revises: 785bb1140878
+Create Date: 2023-03-02 13:09:30.750398
+
+"""
+from alembic import op
+import sqlalchemy as sa
+from sqlalchemy.dialects import sqlite
+
+# revision identifiers, used by Alembic.
+revision = '3d80e4a17a26'
+down_revision = '785bb1140878'
+branch_labels = None
+depends_on = None
+
+
+def upgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    # op.drop_table('_alembic_tmp__submissions')
+    with op.batch_alter_table('_control_samples', schema=None) as batch_op:
+        batch_op.add_column(sa.Column('refseq_version', sa.String(length=16), nullable=True))
+        batch_op.add_column(sa.Column('kraken2_version', sa.String(length=16), nullable=True))
+        batch_op.add_column(sa.Column('kraken2_db_version', sa.String(length=32), nullable=True))
+
+    # ### end Alembic commands ###
+
+
+def downgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    
+    with op.batch_alter_table('_control_samples', schema=None) as batch_op:
+        batch_op.drop_column('kraken2_db_version')
+        batch_op.drop_column('kraken2_version')
+        batch_op.drop_column('refseq_version')
+
+    # op.create_table('_alembic_tmp__submissions',
+    # sa.Column('id', sa.INTEGER(), nullable=False),
+    # sa.Column('rsl_plate_num', sa.VARCHAR(length=32), nullable=False),
+    # sa.Column('submitter_plate_num', sa.VARCHAR(length=127), nullable=True),
+    # sa.Column('submitted_date', sa.TIMESTAMP(), nullable=True),
+    # sa.Column('submitting_lab_id', sa.INTEGER(), nullable=True),
+    # sa.Column('sample_count', sa.INTEGER(), nullable=True),
+    # sa.Column('extraction_kit_id', sa.INTEGER(), nullable=True),
+    # sa.Column('submission_type', sa.VARCHAR(length=32), nullable=True),
+    # sa.Column('technician', sa.VARCHAR(length=64), nullable=True),
+    # sa.Column('reagents_id', sa.VARCHAR(), nullable=True),
+    # sa.Column('extraction_info', sqlite.JSON(), nullable=True),
+    # sa.Column('run_cost', sa.FLOAT(), nullable=True),
+    # sa.Column('uploaded_by', sa.VARCHAR(length=32), nullable=True),
+    # sa.ForeignKeyConstraint(['extraction_kit_id'], ['_kits.id'], ondelete='SET NULL'),
+    # sa.ForeignKeyConstraint(['reagents_id'], ['_reagents.id'], ondelete='SET NULL'),
+    # sa.ForeignKeyConstraint(['submitting_lab_id'], ['_organizations.id'], ondelete='SET NULL'),
+    # sa.PrimaryKeyConstraint('id'),
+    # sa.UniqueConstraint('rsl_plate_num'),
+    # sa.UniqueConstraint('submitter_plate_num')
+    # )
+    # ### end Alembic commands ###