Before creating info and reagent parser classes.
This commit is contained in:
Landon Wark
@@ -1,8 +1,8 @@
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"""database_rebuild
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"""rebuild database
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Revision ID: 06e2c8dc4889
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Revision ID: b879020f2a91
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Revises:
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Create Date: 2023-07-26 14:08:18.809998
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Create Date: 2023-08-02 09:16:12.792995
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"""
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from alembic import op
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@@ -10,7 +10,7 @@ import sqlalchemy as sa
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# revision identifiers, used by Alembic.
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revision = '06e2c8dc4889'
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revision = 'b879020f2a91'
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down_revision = None
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branch_labels = None
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depends_on = None
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@@ -23,8 +23,6 @@ def upgrade() -> None:
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sa.Column('name', sa.String(length=64), nullable=True),
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sa.Column('email', sa.String(length=64), nullable=True),
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sa.Column('phone', sa.String(length=32), nullable=True),
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sa.Column('organization_id', sa.INTEGER(), nullable=True),
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sa.ForeignKeyConstraint(['organization_id'], ['_organizations.id'], name='fk_contact_org_id', ondelete='SET NULL'),
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sa.PrimaryKeyConstraint('id')
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)
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op.create_table('_control_types',
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@@ -42,8 +40,6 @@ def upgrade() -> None:
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sa.Column('mutable_cost_column', sa.FLOAT(precision=2), nullable=True),
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sa.Column('mutable_cost_sample', sa.FLOAT(precision=2), nullable=True),
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sa.Column('constant_cost', sa.FLOAT(precision=2), nullable=True),
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sa.Column('reagent_types_id', sa.INTEGER(), nullable=True),
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sa.ForeignKeyConstraint(['reagent_types_id'], ['_reagent_types.id'], name='fk_KT_reagentstype_id', ondelete='SET NULL', use_alter=True),
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sa.PrimaryKeyConstraint('id'),
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sa.UniqueConstraint('name')
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)
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@@ -51,20 +47,38 @@ def upgrade() -> None:
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sa.Column('id', sa.INTEGER(), nullable=False),
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sa.Column('name', sa.String(length=64), nullable=True),
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sa.Column('cost_centre', sa.String(), nullable=True),
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sa.Column('contact_ids', sa.INTEGER(), nullable=True),
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sa.ForeignKeyConstraint(['contact_ids'], ['_contacts.id'], name='fk_org_contact_id', ondelete='SET NULL'),
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sa.PrimaryKeyConstraint('id')
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)
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op.create_table('_reagent_types',
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sa.Column('id', sa.INTEGER(), nullable=False),
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sa.Column('name', sa.String(length=64), nullable=True),
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sa.Column('kit_id', sa.INTEGER(), nullable=True),
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sa.Column('eol_ext', sa.Interval(), nullable=True),
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sa.Column('required', sa.INTEGER(), server_default='1', nullable=True),
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sa.Column('last_used', sa.String(length=32), nullable=True),
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sa.ForeignKeyConstraint(['kit_id'], ['_kits.id'], name='fk_RT_kits_id', ondelete='SET NULL', use_alter=True),
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sa.PrimaryKeyConstraint('id')
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)
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op.create_table('_samples',
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sa.Column('id', sa.INTEGER(), nullable=False),
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sa.Column('submitter_id', sa.String(length=64), nullable=False),
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sa.Column('sample_type', sa.String(length=32), nullable=True),
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sa.Column('ww_processing_num', sa.String(length=64), nullable=True),
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sa.Column('rsl_number', sa.String(length=64), nullable=True),
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sa.Column('collection_date', sa.TIMESTAMP(), nullable=True),
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sa.Column('testing_type', sa.String(length=64), nullable=True),
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sa.Column('site_status', sa.String(length=64), nullable=True),
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sa.Column('notes', sa.String(length=2000), nullable=True),
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sa.Column('ct_n1', sa.FLOAT(precision=2), nullable=True),
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sa.Column('ct_n2', sa.FLOAT(precision=2), nullable=True),
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sa.Column('n1_status', sa.String(length=32), nullable=True),
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sa.Column('n2_status', sa.String(length=32), nullable=True),
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sa.Column('seq_submitted', sa.BOOLEAN(), nullable=True),
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sa.Column('ww_seq_run_id', sa.String(length=64), nullable=True),
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sa.Column('pcr_results', sa.JSON(), nullable=True),
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sa.Column('well_24', sa.String(length=8), nullable=True),
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sa.Column('organism', sa.String(length=64), nullable=True),
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sa.Column('concentration', sa.String(length=16), nullable=True),
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sa.PrimaryKeyConstraint('id'),
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sa.UniqueConstraint('submitter_id')
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)
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op.create_table('_discounts',
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sa.Column('id', sa.INTEGER(), nullable=False),
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sa.Column('kit_id', sa.INTEGER(), nullable=True),
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@@ -90,11 +104,14 @@ def upgrade() -> None:
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sa.ForeignKeyConstraint(['type_id'], ['_reagent_types.id'], name='fk_reagent_type_id', ondelete='SET NULL'),
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sa.PrimaryKeyConstraint('id')
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)
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op.create_table('_reagentstypes_kittypes',
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sa.Column('reagent_types_id', sa.INTEGER(), nullable=True),
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sa.Column('kits_id', sa.INTEGER(), nullable=True),
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op.create_table('_reagenttypes_kittypes',
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sa.Column('reagent_types_id', sa.INTEGER(), nullable=False),
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sa.Column('kits_id', sa.INTEGER(), nullable=False),
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sa.Column('uses', sa.JSON(), nullable=True),
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sa.Column('required', sa.INTEGER(), nullable=True),
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sa.ForeignKeyConstraint(['kits_id'], ['_kits.id'], ),
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sa.ForeignKeyConstraint(['reagent_types_id'], ['_reagent_types.id'], )
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sa.ForeignKeyConstraint(['reagent_types_id'], ['_reagent_types.id'], ),
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sa.PrimaryKeyConstraint('reagent_types_id', 'kits_id')
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)
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op.create_table('_submissions',
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sa.Column('id', sa.INTEGER(), nullable=False),
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@@ -119,17 +136,6 @@ def upgrade() -> None:
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sa.UniqueConstraint('rsl_plate_num'),
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sa.UniqueConstraint('submitter_plate_num')
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)
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op.create_table('_bc_samples',
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sa.Column('id', sa.INTEGER(), nullable=False),
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sa.Column('well_number', sa.String(length=8), nullable=True),
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sa.Column('sample_id', sa.String(length=64), nullable=False),
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sa.Column('organism', sa.String(length=64), nullable=True),
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sa.Column('concentration', sa.String(length=16), nullable=True),
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sa.Column('rsl_plate_id', sa.INTEGER(), nullable=True),
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sa.ForeignKeyConstraint(['rsl_plate_id'], ['_submissions.id'], name='fk_BCS_sample_id', ondelete='SET NULL'),
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sa.PrimaryKeyConstraint('id'),
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sa.UniqueConstraint('sample_id')
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)
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op.create_table('_control_samples',
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sa.Column('id', sa.INTEGER(), nullable=False),
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sa.Column('parent_id', sa.String(), nullable=True),
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@@ -153,45 +159,29 @@ def upgrade() -> None:
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sa.ForeignKeyConstraint(['reagent_id'], ['_reagents.id'], ),
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sa.ForeignKeyConstraint(['submission_id'], ['_submissions.id'], )
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)
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op.create_table('_ww_samples',
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sa.Column('id', sa.INTEGER(), nullable=False),
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sa.Column('ww_processing_num', sa.String(length=64), nullable=True),
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sa.Column('ww_sample_full_id', sa.String(length=64), nullable=False),
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sa.Column('rsl_number', sa.String(length=64), nullable=True),
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sa.Column('rsl_plate_id', sa.INTEGER(), nullable=True),
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sa.Column('collection_date', sa.TIMESTAMP(), nullable=True),
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sa.Column('well_number', sa.String(length=8), nullable=True),
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sa.Column('testing_type', sa.String(length=64), nullable=True),
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sa.Column('site_status', sa.String(length=64), nullable=True),
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sa.Column('notes', sa.String(length=2000), nullable=True),
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sa.Column('ct_n1', sa.FLOAT(precision=2), nullable=True),
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sa.Column('ct_n2', sa.FLOAT(precision=2), nullable=True),
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sa.Column('n1_status', sa.String(length=32), nullable=True),
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sa.Column('n2_status', sa.String(length=32), nullable=True),
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sa.Column('seq_submitted', sa.BOOLEAN(), nullable=True),
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sa.Column('ww_seq_run_id', sa.String(length=64), nullable=True),
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sa.Column('sample_type', sa.String(length=8), nullable=True),
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sa.Column('pcr_results', sa.JSON(), nullable=True),
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sa.Column('well_24', sa.String(length=8), nullable=True),
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sa.Column('artic_well_number', sa.String(length=8), nullable=True),
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sa.ForeignKeyConstraint(['rsl_plate_id'], ['_submissions.id'], name='fk_WWS_submission_id', ondelete='SET NULL'),
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sa.PrimaryKeyConstraint('id'),
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sa.UniqueConstraint('ww_sample_full_id')
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op.create_table('_submission_sample',
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sa.Column('sample_id', sa.INTEGER(), nullable=False),
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sa.Column('submission_id', sa.INTEGER(), nullable=False),
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sa.Column('row', sa.INTEGER(), nullable=True),
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sa.Column('column', sa.INTEGER(), nullable=True),
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sa.ForeignKeyConstraint(['sample_id'], ['_samples.id'], ),
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sa.ForeignKeyConstraint(['submission_id'], ['_submissions.id'], ),
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sa.PrimaryKeyConstraint('sample_id', 'submission_id')
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)
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# ### end Alembic commands ###
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def downgrade() -> None:
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# ### commands auto generated by Alembic - please adjust! ###
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op.drop_table('_ww_samples')
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op.drop_table('_submission_sample')
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op.drop_table('_reagents_submissions')
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op.drop_table('_control_samples')
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op.drop_table('_bc_samples')
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op.drop_table('_submissions')
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op.drop_table('_reagentstypes_kittypes')
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op.drop_table('_reagenttypes_kittypes')
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op.drop_table('_reagents')
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op.drop_table('_orgs_contacts')
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op.drop_table('_discounts')
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op.drop_table('_samples')
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op.drop_table('_reagent_types')
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op.drop_table('_organizations')
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op.drop_table('_kits')
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@@ -0,0 +1,56 @@
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"""polymorpherizing associations
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Revision ID: da94eca9d381
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Revises: b879020f2a91
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Create Date: 2023-08-03 13:30:34.056316
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"""
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from alembic import op
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import sqlalchemy as sa
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from sqlalchemy.dialects import sqlite
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# revision identifiers, used by Alembic.
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revision = 'da94eca9d381'
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down_revision = 'b879020f2a91'
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branch_labels = None
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depends_on = None
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def upgrade() -> None:
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# ### commands auto generated by Alembic - please adjust! ###
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with op.batch_alter_table('_samples', schema=None) as batch_op:
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batch_op.drop_column('ct_n2')
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batch_op.drop_column('n1_status')
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batch_op.drop_column('pcr_results')
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batch_op.drop_column('n2_status')
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batch_op.drop_column('ct_n1')
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with op.batch_alter_table('_submission_sample', schema=None) as batch_op:
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batch_op.add_column(sa.Column('base_sub_type', sa.String(), nullable=True))
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batch_op.add_column(sa.Column('ct_n1', sa.FLOAT(precision=2), nullable=True))
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batch_op.add_column(sa.Column('ct_n2', sa.FLOAT(precision=2), nullable=True))
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batch_op.add_column(sa.Column('n1_status', sa.String(length=32), nullable=True))
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batch_op.add_column(sa.Column('n2_status', sa.String(length=32), nullable=True))
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batch_op.add_column(sa.Column('pcr_results', sa.JSON(), nullable=True))
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# ### end Alembic commands ###
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def downgrade() -> None:
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# ### commands auto generated by Alembic - please adjust! ###
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with op.batch_alter_table('_submission_sample', schema=None) as batch_op:
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batch_op.drop_column('pcr_results')
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batch_op.drop_column('n2_status')
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batch_op.drop_column('n1_status')
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batch_op.drop_column('ct_n2')
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batch_op.drop_column('ct_n1')
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batch_op.drop_column('base_sub_type')
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with op.batch_alter_table('_samples', schema=None) as batch_op:
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batch_op.add_column(sa.Column('ct_n1', sa.FLOAT(), nullable=True))
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batch_op.add_column(sa.Column('n2_status', sa.VARCHAR(length=32), nullable=True))
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batch_op.add_column(sa.Column('pcr_results', sqlite.JSON(), nullable=True))
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batch_op.add_column(sa.Column('n1_status', sa.VARCHAR(length=32), nullable=True))
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batch_op.add_column(sa.Column('ct_n2', sa.FLOAT(), nullable=True))
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# ### end Alembic commands ###
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