Database updates, scraping samples from excel sheets
This commit is contained in:
Landon Wark
167
alembic/versions/03da9270e51f_initial_commit.py
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167
alembic/versions/03da9270e51f_initial_commit.py
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"""initial commit
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Revision ID: 03da9270e51f
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Revises:
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Create Date: 2023-01-19 09:01:03.022482
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"""
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from alembic import op
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import sqlalchemy as sa
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# revision identifiers, used by Alembic.
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revision = '03da9270e51f'
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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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def upgrade() -> None:
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# ### commands auto generated by Alembic - please adjust! ###
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op.create_table('_contacts',
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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('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.PrimaryKeyConstraint('id')
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)
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op.create_table('_control_types',
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sa.Column('id', sa.INTEGER(), nullable=False),
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sa.Column('name', sa.String(length=255), nullable=True),
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sa.Column('targets', sa.JSON(), nullable=True),
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sa.PrimaryKeyConstraint('id'),
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sa.UniqueConstraint('name')
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)
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op.create_table('_kits',
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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('used_for', sa.JSON(), nullable=True),
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sa.Column('cost_per_run', 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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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.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('_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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sa.Column('name', sa.String(length=255), nullable=True),
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sa.Column('submitted_date', sa.TIMESTAMP(), nullable=True),
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sa.Column('contains', sa.JSON(), nullable=True),
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sa.Column('matches', sa.JSON(), nullable=True),
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sa.Column('kraken', sa.JSON(), nullable=True),
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sa.ForeignKeyConstraint(['parent_id'], ['_control_types.id'], name='fk_control_parent_id'),
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sa.PrimaryKeyConstraint('id'),
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sa.UniqueConstraint('name')
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)
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op.create_table('_organizations',
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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('_reagents',
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sa.Column('id', sa.INTEGER(), nullable=False),
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sa.Column('type_id', sa.INTEGER(), nullable=True),
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sa.Column('name', sa.String(length=64), nullable=True),
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sa.Column('lot', sa.String(length=64), nullable=True),
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sa.Column('expiry', sa.TIMESTAMP(), nullable=True),
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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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sa.ForeignKeyConstraint(['kits_id'], ['_kits.id'], ),
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sa.ForeignKeyConstraint(['reagent_types_id'], ['_reagent_types.id'], )
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)
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op.create_table('_orgs_contacts',
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sa.Column('org_id', sa.INTEGER(), nullable=True),
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sa.Column('contact_id', sa.INTEGER(), nullable=True),
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sa.ForeignKeyConstraint(['contact_id'], ['_contacts.id'], ),
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sa.ForeignKeyConstraint(['org_id'], ['_organizations.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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sa.Column('rsl_plate_num', sa.String(length=32), nullable=True),
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sa.Column('submitter_plate_num', sa.String(length=127), nullable=True),
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sa.Column('submitted_date', sa.TIMESTAMP(), nullable=True),
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sa.Column('submitting_lab_id', sa.INTEGER(), nullable=True),
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sa.Column('sample_count', sa.INTEGER(), nullable=True),
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sa.Column('extraction_kit_id', sa.INTEGER(), nullable=True),
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sa.Column('submission_type', sa.String(length=32), nullable=True),
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sa.Column('technician', sa.String(length=64), nullable=True),
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sa.Column('reagents_id', sa.String(), nullable=True),
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sa.Column('control_id', sa.INTEGER(), nullable=True),
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sa.ForeignKeyConstraint(['control_id'], ['_control_samples.id'], name='fk_BC_control_id', ondelete='SET NULL'),
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sa.ForeignKeyConstraint(['extraction_kit_id'], ['_kits.id'], name='fk_BS_extkit_id', ondelete='SET NULL'),
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sa.ForeignKeyConstraint(['reagents_id'], ['_reagents.id'], name='fk_BS_reagents_id', ondelete='SET NULL'),
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sa.ForeignKeyConstraint(['submitting_lab_id'], ['_organizations.id'], name='fk_BS_sublab_id', ondelete='SET NULL'),
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sa.PrimaryKeyConstraint('id'),
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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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)
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op.create_table('_reagents_submissions',
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sa.Column('reagent_id', sa.INTEGER(), nullable=True),
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sa.Column('submission_id', sa.INTEGER(), nullable=True),
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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('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('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('well_number', sa.String(length=8), nullable=True),
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sa.ForeignKeyConstraint(['rsl_plate_id'], ['_submissions.id'], name='fk_WWS_sample_id', ondelete='SET NULL'),
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sa.PrimaryKeyConstraint('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('_reagents_submissions')
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op.drop_table('_bc_samples')
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op.drop_table('_submissions')
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op.drop_table('_orgs_contacts')
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op.drop_table('_reagentstypes_kittypes')
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op.drop_table('_reagents')
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op.drop_table('_organizations')
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op.drop_table('_control_samples')
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op.drop_table('_reagent_types')
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op.drop_table('_kits')
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op.drop_table('_control_types')
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op.drop_table('_contacts')
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# ### end Alembic commands ###
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