Initial release: rarelens platform skeleton (AGPL-3.0)

End-to-end variant interpretation platform for rare genetic disease research:
SvelteKit UI, FastAPI + PostgreSQL API, Nextflow/Ensembl VEP pipeline,
LightGBM pathogenicity scoring with MLflow, K8s/ArgoCD/GCP infrastructure.
Public test data only; no clinical claims.

api/alembic/env.py

@@ -0,0 +1,32 @@
+import asyncio
+from logging.config import fileConfig
+
+from alembic import context
+from sqlalchemy.ext.asyncio import async_engine_from_config
+from sqlalchemy import pool
+
+from app.config import settings
+from app.models import Base
+
+config = context.config
+config.set_main_option("sqlalchemy.url", settings.database_url)
+if config.config_file_name:
+    fileConfig(config.config_file_name)
+target_metadata = Base.metadata
+
+
+def run_migrations(connection):
+    context.configure(connection=connection, target_metadata=target_metadata)
+    with context.begin_transaction():
+        context.run_migrations()
+
+
+async def run_async():
+    engine = async_engine_from_config(
+        config.get_section(config.config_ini_section, {}), poolclass=pool.NullPool
+    )
+    async with engine.connect() as conn:
+        await conn.run_sync(run_migrations)
+
+
+asyncio.run(run_async())

api/alembic/script.py.mako

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+"""${message}
+
+Revision ID: ${up_revision}
+Revises: ${down_revision | comma,n}
+Create Date: ${create_date}
+
+"""
+from typing import Sequence, Union
+
+from alembic import op
+import sqlalchemy as sa
+${imports if imports else ""}
+
+# revision identifiers, used by Alembic.
+revision: str = ${repr(up_revision)}
+down_revision: Union[str, None] = ${repr(down_revision)}
+branch_labels: Union[str, Sequence[str], None] = ${repr(branch_labels)}
+depends_on: Union[str, Sequence[str], None] = ${repr(depends_on)}
+
+
+def upgrade() -> None:
+    ${upgrades if upgrades else "pass"}
+
+
+def downgrade() -> None:
+    ${downgrades if downgrades else "pass"}

api/alembic/versions/a3e9ead256a5_initial_schema.py

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+"""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 ###