Addition of WW artic parsers, large-scale shake-up of parser structure.

alembic/versions/8d32abdafe2b_moved_artic_info_to_ww_samples.py

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+"""moved artic info to ww_samples
+
+Revision ID: 8d32abdafe2b
+Revises: aac569c672de
+Create Date: 2023-06-05 10:10:37.650733
+
+"""
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision = '8d32abdafe2b'
+down_revision = 'aac569c672de'
+branch_labels = None
+depends_on = None
+
+
+def upgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    with op.batch_alter_table('_ww_samples', schema=None) as batch_op:
+        batch_op.add_column(sa.Column('artic_well_number', sa.String(length=8), nullable=True))
+    # ### end Alembic commands ###
+
+
+def downgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    with op.batch_alter_table('_ww_samples', schema=None) as batch_op:
+        batch_op.drop_column('artic_well_number')
+    # ### end Alembic commands ###

alembic/versions/aac569c672de_added_in_artic_information.py

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+"""added in artic information
+
+Revision ID: aac569c672de
+Revises: 64fec6271a50
+Create Date: 2023-06-02 15:14:13.726489
+
+"""
+from alembic import op
+import sqlalchemy as sa
+from sqlalchemy.dialects import sqlite
+
+# revision identifiers, used by Alembic.
+revision = 'aac569c672de'
+down_revision = '64fec6271a50'
+branch_labels = None
+depends_on = None
+
+
+def upgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    # op.create_table('_artic_samples',
+    # sa.Column('id', sa.INTEGER(), nullable=False),
+    # sa.Column('well_number', sa.String(length=8), nullable=True),
+    # sa.Column('rsl_plate_id', sa.INTEGER(), nullable=True),
+    # sa.Column('ww_sample_full_id', sa.String(length=64), nullable=False),
+    # sa.Column('lims_sample_id', sa.String(length=64), nullable=False),
+    # sa.Column('ct_1', sa.FLOAT(precision=2), nullable=True),
+    # sa.Column('ct_2', sa.FLOAT(precision=2), nullable=True),
+    # sa.ForeignKeyConstraint(['rsl_plate_id'], ['_submissions.id'], name='fk_WWA_submission_id', ondelete='SET NULL'),
+    # sa.PrimaryKeyConstraint('id')
+    # )
+    op.drop_table('_alembic_tmp__submissions')
+    
+    # ### end Alembic commands ###
+
+
+def downgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    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.Column('pcr_info', sqlite.JSON(), nullable=True),
+    sa.Column('comment', sqlite.JSON(), 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')
+    )
+    # op.drop_table('_artic_samples')
+    # ### end Alembic commands ###