new parsers/DB objects, pre code cleanup

alembic/versions/3d9a88bd4ecd_added_in_other_ww_techs.py

@@ -0,0 +1,34 @@
+"""added in other ww techs
+
+Revision ID: 3d9a88bd4ecd
+Revises: f7f46e72f057
+Create Date: 2023-08-30 11:03:41.575219
+
+"""
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision = '3d9a88bd4ecd'
+down_revision = 'f7f46e72f057'
+branch_labels = None
+depends_on = None
+
+
+def upgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    with op.batch_alter_table('_submissions', schema=None) as batch_op:
+        batch_op.add_column(sa.Column('ext_technician', sa.String(length=64), nullable=True))
+        batch_op.add_column(sa.Column('pcr_technician', sa.String(length=64), nullable=True))
+
+    # ### end Alembic commands ###
+
+
+def downgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    with op.batch_alter_table('_submissions', schema=None) as batch_op:
+        batch_op.drop_column('pcr_technician')
+        batch_op.drop_column('ext_technician')
+
+    # ### end Alembic commands ###

alembic/versions/9a133efb3ffd_adjusting_reagents_reagenttypes_to_many_.py

@@ -0,0 +1,33 @@
+"""adjusting reagents/reagenttypes to many-to-many
+
+Revision ID: 9a133efb3ffd
+Revises: 3d9a88bd4ecd
+Create Date: 2023-09-01 10:28:22.335890
+
+"""
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision = '9a133efb3ffd'
+down_revision = '3d9a88bd4ecd'
+branch_labels = None
+depends_on = None
+
+
+def upgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.create_table('_reagenttypes_reagents',
+    sa.Column('reagent_id', sa.INTEGER(), nullable=True),
+    sa.Column('reagenttype_id', sa.INTEGER(), nullable=True),
+    sa.ForeignKeyConstraint(['reagent_id'], ['_reagents.id'], ),
+    sa.ForeignKeyConstraint(['reagenttype_id'], ['_reagent_types.id'], )
+    )
+    # ### end Alembic commands ###
+
+
+def downgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.drop_table('_reagenttypes_reagents')
+    # ### end Alembic commands ###

alembic/versions/f7f46e72f057_rebuild_database.py

@@ -1,8 +1,8 @@
 """rebuild database
 
-Revision ID: cac89ced412b
+Revision ID: f7f46e72f057
 Revises: 
-Create Date: 2023-08-25 14:03:48.883090
+Create Date: 2023-08-30 09:47:18.071070
 
 """
 from alembic import op
@@ -10,7 +10,7 @@ import sqlalchemy as sa
 
 
 # revision identifiers, used by Alembic.
-revision = 'cac89ced412b'
+revision = 'f7f46e72f057'
 down_revision = None
 branch_labels = None
 depends_on = None
@@ -168,8 +168,8 @@ def upgrade() -> None:
     op.create_table('_submission_sample',
     sa.Column('sample_id', sa.INTEGER(), nullable=False),
     sa.Column('submission_id', sa.INTEGER(), nullable=False),
-    sa.Column('row', sa.INTEGER(), nullable=True),
-    sa.Column('column', sa.INTEGER(), nullable=True),
+    sa.Column('row', sa.INTEGER(), nullable=False),
+    sa.Column('column', sa.INTEGER(), nullable=False),
     sa.Column('base_sub_type', sa.String(), nullable=True),
     sa.Column('ct_n1', sa.FLOAT(precision=2), nullable=True),
     sa.Column('ct_n2', sa.FLOAT(precision=2), nullable=True),
@@ -178,7 +178,7 @@ def upgrade() -> None:
     sa.Column('pcr_results', sa.JSON(), nullable=True),
     sa.ForeignKeyConstraint(['sample_id'], ['_samples.id'], ),
     sa.ForeignKeyConstraint(['submission_id'], ['_submissions.id'], ),
-    sa.PrimaryKeyConstraint('sample_id', 'submission_id')
+    sa.PrimaryKeyConstraint('submission_id', 'row', 'column')
     )
     # ### end Alembic commands ###