"""initial schema

Revision ID: a3e9ead256a5
Revises: 
Create Date: 2026-09-11 15:36:04.335440

"""
from typing import Sequence, Union

from alembic import op
import sqlalchemy as sa
from sqlalchemy.dialects import postgresql

# revision identifiers, used by Alembic.
revision: str = 'a3e9ead256a5'
down_revision: Union[str, None] = None
branch_labels: Union[str, Sequence[str], None] = None
depends_on: Union[str, Sequence[str], None] = None


def upgrade() -> None:
    # ### commands auto generated by Alembic - please adjust! ###
    op.create_table('samples',
    sa.Column('id', sa.UUID(), nullable=False),
    sa.Column('name', sa.String(length=120), nullable=False),
    sa.Column('vcf_uri', sa.Text(), nullable=False),
    sa.Column('assembly', sa.String(length=10), nullable=False),
    sa.Column('created_at', sa.DateTime(timezone=True), server_default=sa.text('now()'), nullable=False),
    sa.PrimaryKeyConstraint('id'),
    sa.UniqueConstraint('name')
    )
    op.create_table('jobs',
    sa.Column('id', sa.UUID(), nullable=False),
    sa.Column('sample_id', sa.UUID(), nullable=False),
    sa.Column('status', sa.Enum('queued', 'running', 'succeeded', 'failed', name='jobstatus'), nullable=False),
    sa.Column('workflow_ref', sa.String(length=200), nullable=True),
    sa.Column('vep_version', sa.String(length=40), nullable=True),
    sa.Column('log', sa.Text(), nullable=True),
    sa.Column('created_at', sa.DateTime(timezone=True), server_default=sa.text('now()'), nullable=False),
    sa.Column('finished_at', sa.DateTime(timezone=True), nullable=True),
    sa.ForeignKeyConstraint(['sample_id'], ['samples.id'], ondelete='CASCADE'),
    sa.PrimaryKeyConstraint('id')
    )
    op.create_table('variants',
    sa.Column('id', sa.Integer(), autoincrement=True, nullable=False),
    sa.Column('job_id', sa.UUID(), nullable=False),
    sa.Column('chrom', sa.String(length=10), nullable=False),
    sa.Column('pos', sa.Integer(), nullable=False),
    sa.Column('ref', sa.Text(), nullable=False),
    sa.Column('alt', sa.Text(), nullable=False),
    sa.Column('gene', sa.String(length=60), nullable=True),
    sa.Column('consequence', sa.String(length=120), nullable=True),
    sa.Column('impact', sa.String(length=20), nullable=True),
    sa.Column('hgvsc', sa.Text(), nullable=True),
    sa.Column('hgvsp', sa.Text(), nullable=True),
    sa.Column('gnomad_af', sa.Float(), nullable=True),
    sa.Column('clinvar_sig', sa.String(length=120), nullable=True),
    sa.Column('annotations', postgresql.JSONB(astext_type=sa.Text()), nullable=False),
    sa.ForeignKeyConstraint(['job_id'], ['jobs.id'], ondelete='CASCADE'),
    sa.PrimaryKeyConstraint('id')
    )
    op.create_index(op.f('ix_variants_chrom'), 'variants', ['chrom'], unique=False)
    op.create_index(op.f('ix_variants_gene'), 'variants', ['gene'], unique=False)
    op.create_index(op.f('ix_variants_job_id'), 'variants', ['job_id'], unique=False)
    op.create_index(op.f('ix_variants_pos'), 'variants', ['pos'], unique=False)
    op.create_table('predictions',
    sa.Column('id', sa.Integer(), autoincrement=True, nullable=False),
    sa.Column('variant_id', sa.Integer(), nullable=False),
    sa.Column('model_name', sa.String(length=80), nullable=False),
    sa.Column('model_version', sa.String(length=40), nullable=False),
    sa.Column('score', sa.Float(), nullable=False),
    sa.Column('created_at', sa.DateTime(timezone=True), server_default=sa.text('now()'), nullable=False),
    sa.ForeignKeyConstraint(['variant_id'], ['variants.id'], ondelete='CASCADE'),
    sa.PrimaryKeyConstraint('id'),
    sa.UniqueConstraint('variant_id')
    )
    # ### end Alembic commands ###


def downgrade() -> None:
    # ### commands auto generated by Alembic - please adjust! ###
    op.drop_table('predictions')
    op.drop_index(op.f('ix_variants_pos'), table_name='variants')
    op.drop_index(op.f('ix_variants_job_id'), table_name='variants')
    op.drop_index(op.f('ix_variants_gene'), table_name='variants')
    op.drop_index(op.f('ix_variants_chrom'), table_name='variants')
    op.drop_table('variants')
    op.drop_table('jobs')
    op.drop_table('samples')
    # ### end Alembic commands ###