Attempt at spinning off clientsubmission.
This commit is contained in:
lwark
3
TODO.md
3
TODO.md
@@ -1,3 +1,6 @@
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- [ ] Add in database objects for rsl_run (submission -> run), procedure (run -> procedure), many more things will likely be associated with procedure.
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- [ ] Add in database object for client submission.
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- [ ] Add arbitrary pipette addition to equipment UI.
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- [ ] transfer details template rendering fully into sql objects
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- [ ] transfer details template rendering fully into sql objects
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- [x] Add in connecting links for tips.
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- [x] Add in connecting links for tips.
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- [x] Add in connecting links for equipment/processes.
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- [x] Add in connecting links for equipment/processes.
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@@ -1,428 +0,0 @@
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"""rebuild 20240723
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Revision ID: 0746f7e2c10e
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Revises:
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Create Date: 2024-07-23 14:08:37.436400
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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 = '0746f7e2c10e'
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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('_basicsample',
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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.PrimaryKeyConstraint('id'),
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sa.UniqueConstraint('submitter_id')
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)
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op.create_table('_configitem',
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sa.Column('id', sa.INTEGER(), nullable=False),
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sa.Column('key', sa.String(length=32), nullable=True),
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sa.Column('value', sa.JSON(), nullable=True),
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sa.PrimaryKeyConstraint('id')
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)
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op.create_table('_contact',
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sa.Column('id', sa.INTEGER(), nullable=False),
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sa.Column('sub_type', 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('_controltype',
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sa.Column('id', sa.INTEGER(), nullable=False),
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sa.Column('sub_type', 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('sub_type')
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)
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op.create_table('_equipment',
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sa.Column('id', sa.INTEGER(), nullable=False),
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sa.Column('sub_type', sa.String(length=64), nullable=True),
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sa.Column('nickname', sa.String(length=64), nullable=True),
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sa.Column('asset_number', sa.String(length=16), nullable=True),
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sa.PrimaryKeyConstraint('id')
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)
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op.create_table('_equipmentrole',
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sa.Column('id', sa.INTEGER(), nullable=False),
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sa.Column('sub_type', sa.String(length=32), nullable=True),
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sa.PrimaryKeyConstraint('id')
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)
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op.create_table('_kittype',
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sa.Column('id', sa.INTEGER(), nullable=False),
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sa.Column('sub_type', sa.String(length=64), nullable=True),
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sa.PrimaryKeyConstraint('id'),
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sa.UniqueConstraint('sub_type')
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)
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op.create_table('_organization',
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sa.Column('id', sa.INTEGER(), nullable=False),
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sa.Column('sub_type', sa.String(length=64), nullable=True),
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sa.Column('cost_centre', sa.String(), nullable=True),
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sa.PrimaryKeyConstraint('id')
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)
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op.create_table('_process',
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sa.Column('id', sa.INTEGER(), nullable=False),
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sa.Column('sub_type', sa.String(length=64), nullable=True),
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sa.PrimaryKeyConstraint('id'),
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sa.UniqueConstraint('sub_type')
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)
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op.create_table('_reagentrole',
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sa.Column('id', sa.INTEGER(), nullable=False),
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sa.Column('sub_type', sa.String(length=64), nullable=True),
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sa.Column('eol_ext', sa.Interval(), nullable=True),
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sa.PrimaryKeyConstraint('id')
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)
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op.create_table('_submissiontype',
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sa.Column('id', sa.INTEGER(), nullable=False),
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sa.Column('sub_type', sa.String(length=128), nullable=True),
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sa.Column('info_map', sa.JSON(), nullable=True),
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sa.Column('defaults', sa.JSON(), nullable=True),
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sa.Column('template_file', sa.LargeBinary(), nullable=True),
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sa.Column('sample_map', sa.JSON(), nullable=True),
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sa.PrimaryKeyConstraint('id'),
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sa.UniqueConstraint('sub_type')
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)
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op.create_table('_tiprole',
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sa.Column('id', sa.INTEGER(), nullable=False),
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sa.Column('sub_type', sa.String(length=64), nullable=True),
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sa.PrimaryKeyConstraint('id')
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)
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op.create_table('_bacterialculturesample',
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sa.Column('id', sa.INTEGER(), 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.ForeignKeyConstraint(['id'], ['_basicsample.id'], ),
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sa.PrimaryKeyConstraint('id')
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)
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op.create_table('_discount',
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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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sa.Column('client_id', sa.INTEGER(), nullable=True),
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sa.Column('sub_type', sa.String(length=128), nullable=True),
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sa.Column('amount', sa.FLOAT(precision=2), nullable=True),
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sa.ForeignKeyConstraint(['client_id'], ['_organization.id'], name='fk_org_id', ondelete='SET NULL'),
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sa.ForeignKeyConstraint(['kit_id'], ['_kittype.id'], name='fk_kit_type_id', ondelete='SET NULL'),
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sa.PrimaryKeyConstraint('id')
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)
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op.create_table('_equipment_processes',
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sa.Column('process_id', sa.INTEGER(), nullable=True),
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sa.Column('equipment_id', sa.INTEGER(), nullable=True),
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sa.ForeignKeyConstraint(['equipment_id'], ['_equipment.id'], ),
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sa.ForeignKeyConstraint(['process_id'], ['_process.id'], )
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)
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op.create_table('_equipmentroles_equipment',
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sa.Column('equipment_id', sa.INTEGER(), nullable=True),
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sa.Column('equipmentroles_id', sa.INTEGER(), nullable=True),
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sa.ForeignKeyConstraint(['equipment_id'], ['_equipment.id'], ),
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sa.ForeignKeyConstraint(['equipmentroles_id'], ['_equipmentrole.id'], )
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)
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op.create_table('_equipmentroles_processes',
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sa.Column('process_id', sa.INTEGER(), nullable=True),
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sa.Column('equipmentrole_id', sa.INTEGER(), nullable=True),
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sa.ForeignKeyConstraint(['equipmentrole_id'], ['_equipmentrole.id'], ),
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sa.ForeignKeyConstraint(['process_id'], ['_process.id'], )
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)
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op.create_table('_kittypereagentroleassociation',
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sa.Column('reagent_roles_id', sa.INTEGER(), nullable=False),
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sa.Column('kits_id', sa.INTEGER(), nullable=False),
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sa.Column('submission_type_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.Column('last_used', sa.String(length=32), nullable=True),
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sa.ForeignKeyConstraint(['kits_id'], ['_kittype.id'], ),
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sa.ForeignKeyConstraint(['reagent_roles_id'], ['_reagentrole.id'], ),
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sa.ForeignKeyConstraint(['submission_type_id'], ['_submissiontype.id'], ),
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sa.PrimaryKeyConstraint('reagent_roles_id', 'kits_id', 'submission_type_id')
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)
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op.create_table('_kittypes_processes',
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sa.Column('process_id', sa.INTEGER(), nullable=True),
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sa.Column('kit_id', sa.INTEGER(), nullable=True),
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sa.ForeignKeyConstraint(['kit_id'], ['_kittype.id'], ),
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sa.ForeignKeyConstraint(['process_id'], ['_process.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'], ['_contact.id'], ),
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sa.ForeignKeyConstraint(['org_id'], ['_organization.id'], )
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)
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op.create_table('_process_tiprole',
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sa.Column('process_id', sa.INTEGER(), nullable=True),
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sa.Column('tiprole_id', sa.INTEGER(), nullable=True),
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sa.ForeignKeyConstraint(['process_id'], ['_process.id'], ),
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sa.ForeignKeyConstraint(['tiprole_id'], ['_tiprole.id'], )
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)
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op.create_table('_reagent',
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sa.Column('id', sa.INTEGER(), nullable=False),
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sa.Column('role_id', sa.INTEGER(), nullable=True),
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sa.Column('sub_type', 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(['role_id'], ['_reagentrole.id'], name='fk_reagent_role_id', ondelete='SET NULL'),
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sa.PrimaryKeyConstraint('id')
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)
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op.create_table('_submissiontypeequipmentroleassociation',
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sa.Column('equipmentrole_id', sa.INTEGER(), nullable=False),
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sa.Column('submissiontype_id', sa.INTEGER(), nullable=False),
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sa.Column('uses', sa.JSON(), nullable=True),
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sa.Column('static', sa.INTEGER(), nullable=True),
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sa.ForeignKeyConstraint(['equipmentrole_id'], ['_equipmentrole.id'], ),
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sa.ForeignKeyConstraint(['submissiontype_id'], ['_submissiontype.id'], ),
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sa.PrimaryKeyConstraint('equipmentrole_id', 'submissiontype_id')
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)
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op.create_table('_submissiontypekittypeassociation',
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sa.Column('submission_types_id', sa.INTEGER(), nullable=False),
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sa.Column('kits_id', sa.INTEGER(), nullable=False),
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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.ForeignKeyConstraint(['kits_id'], ['_kittype.id'], ),
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sa.ForeignKeyConstraint(['submission_types_id'], ['_submissiontype.id'], ),
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sa.PrimaryKeyConstraint('submission_types_id', 'kits_id')
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)
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op.create_table('_submissiontypes_processes',
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sa.Column('process_id', sa.INTEGER(), nullable=True),
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sa.Column('equipmentroles_id', sa.INTEGER(), nullable=True),
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sa.ForeignKeyConstraint(['equipmentroles_id'], ['_submissiontype.id'], ),
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sa.ForeignKeyConstraint(['process_id'], ['_process.id'], )
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)
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op.create_table('_submissiontypetiproleassociation',
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sa.Column('tiprole_id', sa.INTEGER(), nullable=False),
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sa.Column('submissiontype_id', sa.INTEGER(), nullable=False),
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sa.Column('uses', sa.JSON(), nullable=True),
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sa.Column('static', sa.INTEGER(), nullable=True),
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sa.ForeignKeyConstraint(['submissiontype_id'], ['_submissiontype.id'], ),
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sa.ForeignKeyConstraint(['tiprole_id'], ['_tiprole.id'], ),
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sa.PrimaryKeyConstraint('tiprole_id', 'submissiontype_id')
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)
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op.create_table('_tips',
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sa.Column('id', sa.INTEGER(), nullable=False),
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sa.Column('role_id', sa.INTEGER(), nullable=True),
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sa.Column('sub_type', sa.String(length=64), nullable=True),
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sa.Column('lot', sa.String(length=64), nullable=True),
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sa.ForeignKeyConstraint(['role_id'], ['_tiprole.id'], name='fk_tip_role_id', ondelete='SET NULL'),
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sa.PrimaryKeyConstraint('id')
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)
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op.create_table('_wastewatersample',
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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_full_sample_id', 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('received_date', sa.TIMESTAMP(), nullable=True),
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sa.Column('notes', sa.String(length=2000), nullable=True),
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sa.Column('sample_location', sa.String(length=8), nullable=True),
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sa.ForeignKeyConstraint(['id'], ['_basicsample.id'], ),
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sa.PrimaryKeyConstraint('id')
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)
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op.create_table('_basicsubmission',
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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=False),
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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_name', sa.String(), nullable=True),
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sa.Column('technician', sa.String(length=64), nullable=True),
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sa.Column('reagents_id', sa.INTEGER(), nullable=True),
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sa.Column('extraction_info', sa.JSON(), nullable=True),
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sa.Column('run_cost', sa.FLOAT(precision=2), nullable=True),
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sa.Column('signed_by', sa.String(length=32), nullable=True),
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sa.Column('comment', sa.JSON(), nullable=True),
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sa.Column('submission_category', sa.String(length=64), nullable=True),
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sa.Column('cost_centre', sa.String(length=64), nullable=True),
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sa.Column('contact_id', sa.INTEGER(), nullable=True),
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sa.ForeignKeyConstraint(['contact_id'], ['_contact.id'], name='fk_BS_contact_id', ondelete='SET NULL'),
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sa.ForeignKeyConstraint(['extraction_kit_id'], ['_kittype.id'], name='fk_BS_extkit_id', ondelete='SET NULL'),
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sa.ForeignKeyConstraint(['reagents_id'], ['_reagent.id'], name='fk_BS_reagents_id', ondelete='SET NULL'),
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||||||
sa.ForeignKeyConstraint(['submission_type_name'], ['_submissiontype.sub_type'], name='fk_BS_subtype_name', ondelete='SET NULL'),
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sa.ForeignKeyConstraint(['submitting_lab_id'], ['_organization.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('_equipment_tips',
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sa.Column('equipment_id', sa.INTEGER(), nullable=True),
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sa.Column('tips_id', sa.INTEGER(), nullable=True),
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sa.ForeignKeyConstraint(['equipment_id'], ['_equipment.id'], ),
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sa.ForeignKeyConstraint(['tips_id'], ['_tips.id'], )
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)
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op.create_table('_reagentroles_reagents',
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sa.Column('reagent_id', sa.INTEGER(), nullable=True),
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sa.Column('reagentrole_id', sa.INTEGER(), nullable=True),
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sa.ForeignKeyConstraint(['reagent_id'], ['_reagent.id'], ),
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sa.ForeignKeyConstraint(['reagentrole_id'], ['_reagentrole.id'], )
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)
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op.create_table('_tiproles_tips',
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sa.Column('tiprole_id', sa.INTEGER(), nullable=True),
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sa.Column('tips_id', sa.INTEGER(), nullable=True),
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sa.ForeignKeyConstraint(['tiprole_id'], ['_tiprole.id'], ),
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sa.ForeignKeyConstraint(['tips_id'], ['_tips.id'], )
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)
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op.create_table('_bacterialculture',
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sa.Column('id', sa.INTEGER(), nullable=False),
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sa.ForeignKeyConstraint(['id'], ['_basicsubmission.id'], ),
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sa.PrimaryKeyConstraint('id')
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)
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op.create_table('_control',
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sa.Column('id', sa.INTEGER(), nullable=False),
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sa.Column('parent_id', sa.INTEGER(), nullable=True),
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sa.Column('sub_type', 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.Column('submission_id', sa.INTEGER(), nullable=True),
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|
||||||
sa.Column('refseq_version', sa.String(length=16), nullable=True),
|
|
||||||
sa.Column('kraken2_version', sa.String(length=16), nullable=True),
|
|
||||||
sa.Column('kraken2_db_version', sa.String(length=32), nullable=True),
|
|
||||||
sa.Column('sample_id', sa.INTEGER(), nullable=True),
|
|
||||||
sa.ForeignKeyConstraint(['parent_id'], ['_controltype.id'], name='fk_control_parent_id'),
|
|
||||||
sa.ForeignKeyConstraint(['sample_id'], ['_basicsample.id'], name='cont_BCS_id', ondelete='SET NULL'),
|
|
||||||
sa.ForeignKeyConstraint(['submission_id'], ['_basicsubmission.id'], ),
|
|
||||||
sa.PrimaryKeyConstraint('id'),
|
|
||||||
sa.UniqueConstraint('sub_type')
|
|
||||||
)
|
|
||||||
op.create_table('_submissionequipmentassociation',
|
|
||||||
sa.Column('equipment_id', sa.INTEGER(), nullable=False),
|
|
||||||
sa.Column('submission_id', sa.INTEGER(), nullable=False),
|
|
||||||
sa.Column('role', sa.String(length=64), nullable=False),
|
|
||||||
sa.Column('process_id', sa.INTEGER(), nullable=True),
|
|
||||||
sa.Column('start_time', sa.TIMESTAMP(), nullable=True),
|
|
||||||
sa.Column('end_time', sa.TIMESTAMP(), nullable=True),
|
|
||||||
sa.Column('comments', sa.String(length=1024), nullable=True),
|
|
||||||
sa.ForeignKeyConstraint(['equipment_id'], ['_equipment.id'], ),
|
|
||||||
sa.ForeignKeyConstraint(['process_id'], ['_process.id'], name='SEA_Process_id', ondelete='SET NULL'),
|
|
||||||
sa.ForeignKeyConstraint(['submission_id'], ['_basicsubmission.id'], ),
|
|
||||||
sa.PrimaryKeyConstraint('equipment_id', 'submission_id', 'role')
|
|
||||||
)
|
|
||||||
op.create_table('_submissionreagentassociation',
|
|
||||||
sa.Column('reagent_id', sa.INTEGER(), nullable=False),
|
|
||||||
sa.Column('submission_id', sa.INTEGER(), nullable=False),
|
|
||||||
sa.Column('comments', sa.String(length=1024), nullable=True),
|
|
||||||
sa.ForeignKeyConstraint(['reagent_id'], ['_reagent.id'], ),
|
|
||||||
sa.ForeignKeyConstraint(['submission_id'], ['_basicsubmission.id'], ),
|
|
||||||
sa.PrimaryKeyConstraint('reagent_id', 'submission_id')
|
|
||||||
)
|
|
||||||
op.create_table('_submissionsampleassociation',
|
|
||||||
sa.Column('id', sa.INTEGER(), nullable=False),
|
|
||||||
sa.Column('sample_id', sa.INTEGER(), nullable=False),
|
|
||||||
sa.Column('submission_id', sa.INTEGER(), nullable=False),
|
|
||||||
sa.Column('row', sa.INTEGER(), nullable=False),
|
|
||||||
sa.Column('column', sa.INTEGER(), nullable=False),
|
|
||||||
sa.Column('submission_rank', sa.INTEGER(), nullable=False),
|
|
||||||
sa.Column('base_sub_type', sa.String(), nullable=True),
|
|
||||||
sa.ForeignKeyConstraint(['sample_id'], ['_basicsample.id'], ),
|
|
||||||
sa.ForeignKeyConstraint(['submission_id'], ['_basicsubmission.id'], ),
|
|
||||||
sa.PrimaryKeyConstraint('submission_id', 'row', 'column'),
|
|
||||||
sa.UniqueConstraint('id')
|
|
||||||
)
|
|
||||||
op.create_table('_submissiontipsassociation',
|
|
||||||
sa.Column('tip_id', sa.INTEGER(), nullable=False),
|
|
||||||
sa.Column('submission_id', sa.INTEGER(), nullable=False),
|
|
||||||
sa.Column('role_name', sa.String(length=32), nullable=False),
|
|
||||||
sa.ForeignKeyConstraint(['submission_id'], ['_basicsubmission.id'], ),
|
|
||||||
sa.ForeignKeyConstraint(['tip_id'], ['_tips.id'], ),
|
|
||||||
sa.PrimaryKeyConstraint('tip_id', 'submission_id', 'role_name')
|
|
||||||
)
|
|
||||||
op.create_table('_wastewater',
|
|
||||||
sa.Column('id', sa.INTEGER(), nullable=False),
|
|
||||||
sa.Column('ext_technician', sa.String(length=64), nullable=True),
|
|
||||||
sa.Column('pcr_technician', sa.String(length=64), nullable=True),
|
|
||||||
sa.Column('pcr_info', sa.JSON(), nullable=True),
|
|
||||||
sa.ForeignKeyConstraint(['id'], ['_basicsubmission.id'], ),
|
|
||||||
sa.PrimaryKeyConstraint('id')
|
|
||||||
)
|
|
||||||
op.create_table('_wastewaterartic',
|
|
||||||
sa.Column('id', sa.INTEGER(), nullable=False),
|
|
||||||
sa.Column('artic_technician', sa.String(length=64), nullable=True),
|
|
||||||
sa.Column('dna_core_submission_number', sa.String(length=64), nullable=True),
|
|
||||||
sa.Column('pcr_info', sa.JSON(), nullable=True),
|
|
||||||
sa.Column('gel_image', sa.String(length=64), nullable=True),
|
|
||||||
sa.Column('gel_info', sa.JSON(), nullable=True),
|
|
||||||
sa.Column('gel_controls', sa.JSON(), nullable=True),
|
|
||||||
sa.Column('source_plates', sa.JSON(), nullable=True),
|
|
||||||
sa.Column('artic_date', sa.TIMESTAMP(), nullable=True),
|
|
||||||
sa.Column('ngs_date', sa.TIMESTAMP(), nullable=True),
|
|
||||||
sa.Column('gel_date', sa.TIMESTAMP(), nullable=True),
|
|
||||||
sa.Column('gel_barcode', sa.String(length=16), nullable=True),
|
|
||||||
sa.ForeignKeyConstraint(['id'], ['_basicsubmission.id'], ),
|
|
||||||
sa.PrimaryKeyConstraint('id')
|
|
||||||
)
|
|
||||||
op.create_table('_wastewaterarticassociation',
|
|
||||||
sa.Column('id', sa.INTEGER(), nullable=False),
|
|
||||||
sa.Column('source_plate', sa.String(length=16), nullable=True),
|
|
||||||
sa.Column('source_plate_number', sa.INTEGER(), nullable=True),
|
|
||||||
sa.Column('source_well', sa.String(length=8), nullable=True),
|
|
||||||
sa.Column('ct', sa.String(length=8), nullable=True),
|
|
||||||
sa.ForeignKeyConstraint(['id'], ['_submissionsampleassociation.id'], ),
|
|
||||||
sa.PrimaryKeyConstraint('id')
|
|
||||||
)
|
|
||||||
op.create_table('_wastewaterassociation',
|
|
||||||
sa.Column('id', sa.INTEGER(), nullable=False),
|
|
||||||
sa.Column('ct_n1', sa.FLOAT(precision=2), nullable=True),
|
|
||||||
sa.Column('ct_n2', sa.FLOAT(precision=2), nullable=True),
|
|
||||||
sa.Column('n1_status', sa.String(length=32), nullable=True),
|
|
||||||
sa.Column('n2_status', sa.String(length=32), nullable=True),
|
|
||||||
sa.Column('pcr_results', sa.JSON(), nullable=True),
|
|
||||||
sa.ForeignKeyConstraint(['id'], ['_submissionsampleassociation.id'], ),
|
|
||||||
sa.PrimaryKeyConstraint('id')
|
|
||||||
)
|
|
||||||
# ### end Alembic commands ###
|
|
||||||
|
|
||||||
|
|
||||||
def downgrade() -> None:
|
|
||||||
# ### commands auto generated by Alembic - please adjust! ###
|
|
||||||
op.drop_table('_wastewaterassociation')
|
|
||||||
op.drop_table('_wastewaterarticassociation')
|
|
||||||
op.drop_table('_wastewaterartic')
|
|
||||||
op.drop_table('_wastewater')
|
|
||||||
op.drop_table('_submissiontipsassociation')
|
|
||||||
op.drop_table('_submissionsampleassociation')
|
|
||||||
op.drop_table('_submissionreagentassociation')
|
|
||||||
op.drop_table('_submissionequipmentassociation')
|
|
||||||
op.drop_table('_control')
|
|
||||||
op.drop_table('_bacterialculture')
|
|
||||||
op.drop_table('_tiproles_tips')
|
|
||||||
op.drop_table('_reagentroles_reagents')
|
|
||||||
op.drop_table('_equipment_tips')
|
|
||||||
op.drop_table('_basicsubmission')
|
|
||||||
op.drop_table('_wastewatersample')
|
|
||||||
op.drop_table('_tips')
|
|
||||||
op.drop_table('_submissiontypetiproleassociation')
|
|
||||||
op.drop_table('_submissiontypes_processes')
|
|
||||||
op.drop_table('_submissiontypekittypeassociation')
|
|
||||||
op.drop_table('_submissiontypeequipmentroleassociation')
|
|
||||||
op.drop_table('_reagent')
|
|
||||||
op.drop_table('_process_tiprole')
|
|
||||||
op.drop_table('_orgs_contacts')
|
|
||||||
op.drop_table('_kittypes_processes')
|
|
||||||
op.drop_table('_kittypereagentroleassociation')
|
|
||||||
op.drop_table('_equipmentroles_processes')
|
|
||||||
op.drop_table('_equipmentroles_equipment')
|
|
||||||
op.drop_table('_equipment_processes')
|
|
||||||
op.drop_table('_discount')
|
|
||||||
op.drop_table('_bacterialculturesample')
|
|
||||||
op.drop_table('_tiprole')
|
|
||||||
op.drop_table('_submissiontype')
|
|
||||||
op.drop_table('_reagentrole')
|
|
||||||
op.drop_table('_process')
|
|
||||||
op.drop_table('_organization')
|
|
||||||
op.drop_table('_kittype')
|
|
||||||
op.drop_table('_equipmentrole')
|
|
||||||
op.drop_table('_equipment')
|
|
||||||
op.drop_table('_controltype')
|
|
||||||
op.drop_table('_contact')
|
|
||||||
op.drop_table('_configitem')
|
|
||||||
op.drop_table('_basicsample')
|
|
||||||
# ### end Alembic commands ###
|
|
||||||
@@ -1,56 +0,0 @@
|
|||||||
"""Add custom info column to _basicsubmission
|
|
||||||
|
|
||||||
Revision ID: 25b86f5ac2d9
|
|
||||||
Revises: 0746f7e2c10e
|
|
||||||
Create Date: 2024-09-24 09:09:15.223556
|
|
||||||
|
|
||||||
"""
|
|
||||||
from alembic import op
|
|
||||||
import sqlalchemy as sa
|
|
||||||
|
|
||||||
|
|
||||||
# revision identifiers, used by Alembic.
|
|
||||||
revision = '25b86f5ac2d9'
|
|
||||||
down_revision = '0746f7e2c10e'
|
|
||||||
branch_labels = None
|
|
||||||
depends_on = None
|
|
||||||
|
|
||||||
|
|
||||||
def upgrade() -> None:
|
|
||||||
# ### commands auto generated by Alembic - please adjust! ###
|
|
||||||
with op.batch_alter_table('_basicsubmission', schema=None) as batch_op:
|
|
||||||
batch_op.add_column(sa.Column('custom', sa.JSON(), nullable=True))
|
|
||||||
|
|
||||||
# with op.batch_alter_table('_process', schema=None) as batch_op:
|
|
||||||
# batch_op.create_unique_constraint(None, ['name'])
|
|
||||||
#
|
|
||||||
# with op.batch_alter_table('_submissionsampleassociation', schema=None) as batch_op:
|
|
||||||
# batch_op.create_unique_constraint(None, ['id'])
|
|
||||||
|
|
||||||
with op.batch_alter_table('_wastewaterarticassociation', schema=None) as batch_op:
|
|
||||||
batch_op.alter_column('source_plate',
|
|
||||||
existing_type=sa.VARCHAR(length=16),
|
|
||||||
type_=sa.String(length=32),
|
|
||||||
existing_nullable=True)
|
|
||||||
|
|
||||||
# ### end Alembic commands ###
|
|
||||||
|
|
||||||
|
|
||||||
def downgrade() -> None:
|
|
||||||
# ### commands auto generated by Alembic - please adjust! ###
|
|
||||||
with op.batch_alter_table('_wastewaterarticassociation', schema=None) as batch_op:
|
|
||||||
batch_op.alter_column('source_plate',
|
|
||||||
existing_type=sa.String(length=32),
|
|
||||||
type_=sa.VARCHAR(length=16),
|
|
||||||
existing_nullable=True)
|
|
||||||
|
|
||||||
# with op.batch_alter_table('_submissionsampleassociation', schema=None) as batch_op:
|
|
||||||
# batch_op.drop_constraint(None, type_='unique')
|
|
||||||
#
|
|
||||||
# with op.batch_alter_table('_process', schema=None) as batch_op:
|
|
||||||
# batch_op.drop_constraint(None, type_='unique')
|
|
||||||
|
|
||||||
with op.batch_alter_table('_basicsubmission', schema=None) as batch_op:
|
|
||||||
batch_op.drop_column('custom')
|
|
||||||
|
|
||||||
# ### end Alembic commands ###
|
|
||||||
@@ -94,6 +94,14 @@ equipment_tips = Table(
|
|||||||
extend_existing=True
|
extend_existing=True
|
||||||
)
|
)
|
||||||
|
|
||||||
|
kittypes_submissions = Table(
|
||||||
|
"_kittypes_submissions",
|
||||||
|
Base.metadata,
|
||||||
|
Column("_basicsubmission_id", INTEGER, ForeignKey("_basicsubmission.id")),
|
||||||
|
Column("kittype_id", INTEGER, ForeignKey("_kittype.id")),
|
||||||
|
extend_existing=True
|
||||||
|
)
|
||||||
|
|
||||||
|
|
||||||
class KitType(BaseClass):
|
class KitType(BaseClass):
|
||||||
"""
|
"""
|
||||||
@@ -104,7 +112,8 @@ class KitType(BaseClass):
|
|||||||
|
|
||||||
id = Column(INTEGER, primary_key=True) #: primary key
|
id = Column(INTEGER, primary_key=True) #: primary key
|
||||||
name = Column(String(64), unique=True) #: name of kit
|
name = Column(String(64), unique=True) #: name of kit
|
||||||
submissions = relationship("BasicSubmission", back_populates="extraction_kit") #: submissions this kit was used for
|
submissions = relationship("BasicSubmission", back_populates="kittypes",
|
||||||
|
secondary=kittypes_submissions) #: submissions this kit was used for
|
||||||
processes = relationship("Process", back_populates="kit_types",
|
processes = relationship("Process", back_populates="kit_types",
|
||||||
secondary=kittypes_processes) #: equipment processes used by this kit
|
secondary=kittypes_processes) #: equipment processes used by this kit
|
||||||
|
|
||||||
@@ -1039,9 +1048,9 @@ class SubmissionType(BaseClass):
|
|||||||
}
|
}
|
||||||
"""
|
"""
|
||||||
|
|
||||||
submissiontype_kit_associations = relationship(
|
runtype_kit_associations = relationship(
|
||||||
"SubmissionTypeKitTypeAssociation",
|
"RunTypeKitTypeAssociation",
|
||||||
back_populates="submission_type",
|
back_populates="runtype",
|
||||||
cascade="all, delete-orphan",
|
cascade="all, delete-orphan",
|
||||||
) #: Association of kittypes
|
) #: Association of kittypes
|
||||||
|
|
||||||
|
|||||||
@@ -31,7 +31,7 @@ class Organization(BaseClass):
|
|||||||
|
|
||||||
id = Column(INTEGER, primary_key=True) #: primary key
|
id = Column(INTEGER, primary_key=True) #: primary key
|
||||||
name = Column(String(64)) #: organization name
|
name = Column(String(64)) #: organization name
|
||||||
submissions = relationship("BasicSubmission",
|
submissions = relationship("ClientSubmission",
|
||||||
back_populates="submitting_lab") #: submissions this organization has submitted
|
back_populates="submitting_lab") #: submissions this organization has submitted
|
||||||
cost_centre = Column(String()) #: cost centre used by org for payment
|
cost_centre = Column(String()) #: cost centre used by org for payment
|
||||||
contacts = relationship("Contact", back_populates="organization",
|
contacts = relationship("Contact", back_populates="organization",
|
||||||
@@ -103,7 +103,7 @@ class Contact(BaseClass):
|
|||||||
phone = Column(String(32)) #: contact phone number
|
phone = Column(String(32)) #: contact phone number
|
||||||
organization = relationship("Organization", back_populates="contacts", uselist=True,
|
organization = relationship("Organization", back_populates="contacts", uselist=True,
|
||||||
secondary=orgs_contacts) #: relationship to joined organization
|
secondary=orgs_contacts) #: relationship to joined organization
|
||||||
submissions = relationship("BasicSubmission", back_populates="contact") #: submissions this contact has submitted
|
submissions = relationship("ClientSubmission", back_populates="contact") #: submissions this contact has submitted
|
||||||
|
|
||||||
@classproperty
|
@classproperty
|
||||||
def searchables(cls):
|
def searchables(cls):
|
||||||
|
|||||||
File diff suppressed because it is too large
Load Diff
Reference in New Issue
Block a user