initial commit
This commit is contained in:
Landon Wark
1
alembic/README
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1
alembic/README
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Generic single-database configuration.
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85
alembic/env.py
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85
alembic/env.py
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from logging.config import fileConfig
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from sqlalchemy import engine_from_config
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from sqlalchemy import pool
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from alembic import context
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import sys
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from pathlib import Path
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sys.path.append(Path(__file__).parents[1].joinpath("src").resolve().__str__())
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print(sys.path)
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# this is the Alembic Config object, which provides
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# access to the values within the .ini file in use.
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config = context.config
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# Interpret the config file for Python logging.
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# This line sets up loggers basically.
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if config.config_file_name is not None:
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fileConfig(config.config_file_name)
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# add your model's MetaData object here
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# for 'autogenerate' support
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# from myapp import mymodel
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# target_metadata = mymodel.Base.metadata
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from submissions.backend.db.models import Base
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target_metadata = [Base.metadata]
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# other values from the config, defined by the needs of env.py,
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# can be acquired:
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# my_important_option = config.get_main_option("my_important_option")
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# ... etc.
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def run_migrations_offline() -> None:
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"""Run migrations in 'offline' mode.
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This configures the context with just a URL
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and not an Engine, though an Engine is acceptable
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here as well. By skipping the Engine creation
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we don't even need a DBAPI to be available.
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Calls to context.execute() here emit the given string to the
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script output.
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"""
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url = config.get_main_option("sqlalchemy.url")
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context.configure(
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url=url,
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target_metadata=target_metadata,
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literal_binds=True,
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dialect_opts={"paramstyle": "named"},
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# must be set to true for sqlite workaround
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render_as_batch=True,
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)
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with context.begin_transaction():
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context.run_migrations()
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def run_migrations_online() -> None:
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"""Run migrations in 'online' mode.
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In this scenario we need to create an Engine
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and associate a connection with the context.
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"""
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connectable = engine_from_config(
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config.get_section(config.config_ini_section),
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prefix="sqlalchemy.",
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poolclass=pool.NullPool,
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)
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with connectable.connect() as connection:
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context.configure(
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connection=connection, target_metadata=target_metadata,
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render_as_batch=True,
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)
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with context.begin_transaction():
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context.run_migrations()
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if context.is_offline_mode():
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run_migrations_offline()
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else:
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run_migrations_online()
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24
alembic/script.py.mako
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alembic/script.py.mako
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"""${message}
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Revision ID: ${up_revision}
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Revises: ${down_revision | comma,n}
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Create Date: ${create_date}
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"""
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from alembic import op
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import sqlalchemy as sa
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${imports if imports else ""}
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# revision identifiers, used by Alembic.
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revision = ${repr(up_revision)}
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down_revision = ${repr(down_revision)}
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branch_labels = ${repr(branch_labels)}
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depends_on = ${repr(depends_on)}
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def upgrade() -> None:
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${upgrades if upgrades else "pass"}
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def downgrade() -> None:
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${downgrades if downgrades else "pass"}
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155
alembic/versions/4cba0c1ffe03_initial_commit.py
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alembic/versions/4cba0c1ffe03_initial_commit.py
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"""initial commit
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Revision ID: 4cba0c1ffe03
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Revises:
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Create Date: 2023-01-18 08:59:34.382715
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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 = '4cba0c1ffe03'
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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('_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=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('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.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.Column('sample_id', sa.String(), 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'], 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(['sample_id'], ['_ww_samples.id'], name='fk_WW_sample_id', ondelete='SET NULL'),
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sa.ForeignKeyConstraint(['submitting_lab_id'], ['_organizations.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('_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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# ### 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('_reagents_submissions')
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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('_ww_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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