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EstelleDaEstelleDa
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Merge branch 'release-2025.2.0' into improve/estelle/350/surfaceValidationErrors
2 parents 633dcf5 + ce029be commit bc06144

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‎.github/workflows/run-tests-on-push.yml‎

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jobs:
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run-tests-3_9-core-dependencies:
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runs-on: ubuntu-20.04
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name: Pytest on Core Dependencies-- Python 3.9 / Ubuntu 20.04
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runs-on: ubuntu-latest
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name: Pytest on Core Dependencies-- Python 3.9
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steps:
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- uses: actions/checkout@v4
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- uses: actions/setup-python@v5
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- run: poetry run pytest tests/
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run-tests-3_9:
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runs-on: ubuntu-20.04
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name: Pytest on Optional Dependencies-- Python 3.9 / Ubuntu 20.04
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runs-on: ubuntu-latest
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name: Pytest on Optional Dependencies-- Python 3.9
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steps:
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- uses: actions/checkout@v4
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- uses: actions/setup-python@v5

‎alembic/versions/34026092c7f8_clinvar_variant_table.py‎

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"""clinvar variant table
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Revision ID: 34026092c7f8
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Revises: e8a3b5d8f885
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Create Date: 2025-01-28 21:48:42.532346
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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 = "34026092c7f8"
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down_revision = "e8a3b5d8f885"
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branch_labels = None
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depends_on = None
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def upgrade():
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# ### commands auto generated by Alembic - please adjust! ###
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op.create_table(
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"clinvar_variants",
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sa.Column("id", sa.Integer(), nullable=False),
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sa.Column("allele_id", sa.Integer(), nullable=False),
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sa.Column("gene_symbol", sa.String(), nullable=False),
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sa.Column("clinical_significance", sa.String(), nullable=False),
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sa.Column("clinical_review_status", sa.String(), nullable=False),
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sa.Column("clinvar_db_version", sa.String(), nullable=False),
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sa.Column("creation_date", sa.Date(), nullable=False),
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sa.Column("modification_date", sa.Date(), nullable=False),
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sa.PrimaryKeyConstraint("id"),
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)
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op.create_index(op.f("ix_clinvar_variants_allele_id"), "clinvar_variants", ["allele_id"], unique=False)
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op.add_column("mapped_variants", sa.Column("clinvar_variant_id", sa.Integer(), nullable=True))
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op.create_index(
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op.f("ix_mapped_variants_clinvar_variant_id"), "mapped_variants", ["clinvar_variant_id"], unique=False
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)
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op.create_foreign_key(
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"mapped_variant_clinvar_variant_id_foreign_key_constraint",
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"mapped_variants",
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"clinvar_variants",
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["clinvar_variant_id"],
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["id"],
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)
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# ### end Alembic commands ###
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def downgrade():
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# ### commands auto generated by Alembic - please adjust! ###
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op.drop_constraint(
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"mapped_variant_clinvar_variant_id_foreign_key_constraint", "mapped_variants", type_="foreignkey"
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)
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op.drop_index(op.f("ix_mapped_variants_clinvar_variant_id"), table_name="mapped_variants")
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op.drop_column("mapped_variants", "clinvar_variant_id")
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op.drop_index(op.f("ix_clinvar_variants_allele_id"), table_name="clinvar_variants")
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op.drop_table("clinvar_variants")
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# ### end Alembic commands ###

‎alembic/versions/695b73abe581_genericize_clinvar_variants_table.py‎

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"""genericize clinvar variants table
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Revision ID: 695b73abe581
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Revises: 34026092c7f8
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Create Date: 2025-02-18 11:54:15.243078
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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 = "695b73abe581"
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down_revision = "34026092c7f8"
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branch_labels = None
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depends_on = None
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def upgrade():
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op.rename_table("clinvar_variants", "clinical_controls")
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op.execute("ALTER SEQUENCE clinvar_variants_id_seq RENAME TO clinical_controls_id_seq")
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op.execute("ALTER INDEX clinvar_variants_pkey RENAME TO clinical_controls_pkey")
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op.alter_column("clinical_controls", "clinvar_db_version", nullable=False, new_column_name="db_version")
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op.alter_column("clinical_controls", "allele_id", nullable=False, new_column_name="db_identifier")
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op.add_column("clinical_controls", sa.Column("db_name", sa.String(), nullable=True))
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op.create_index("ix_clinical_controls_gene_symbol", "clinical_controls", ["gene_symbol"])
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op.create_index("ix_clinical_controls_db_name", "clinical_controls", ["db_name"])
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op.create_index("ix_clinical_controls_db_identifier", "clinical_controls", ["db_identifier"])
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op.create_index("ix_clinical_controls_db_version", "clinical_controls", ["db_version"])
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op.create_table(
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"mapped_variants_clinical_controls",
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sa.Column("mapped_variant_id", sa.Integer(), nullable=False),
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sa.Column("clinical_control_id", sa.Integer(), nullable=False),
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sa.ForeignKeyConstraint(
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["mapped_variant_id"],
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["mapped_variants.id"],
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),
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sa.ForeignKeyConstraint(
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["clinical_control_id"],
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["clinical_controls.id"],
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),
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sa.PrimaryKeyConstraint("mapped_variant_id", "clinical_control_id"),
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)
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# Convert any existing ClinVar variants into clinical control variants. Since
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# this table is being update from a clinvar specific table, we assume all existing
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# controls are from ClinVar.
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op.execute(
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"""
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INSERT INTO mapped_variants_clinical_controls (
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mapped_variant_id,
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clinical_control_id
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)
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SELECT id, clinvar_variant_id
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FROM mapped_variants
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WHERE clinvar_variant_id IS NOT NULL
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"""
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)
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op.execute("UPDATE clinical_controls SET db_name='ClinVar'")
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op.alter_column("clinical_controls", "db_name", nullable=False)
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op.drop_index("ix_mapped_variants_clinvar_variant_id", "mapped_variants")
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op.drop_column("mapped_variants", "clinvar_variant_id")
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def downgrade():
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op.rename_table("clinical_controls", "clinvar_variants")
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op.execute("ALTER SEQUENCE clinical_controls_id_seq RENAME TO clinvar_variants_id_seq")
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op.execute("ALTER INDEX clinical_controls_pkey RENAME TO clinvar_variants_pkey")
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op.drop_index("ix_clinical_controls_gene_symbol", "clinical_controls")
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op.drop_index("ix_clinical_controls_db_name", "clinical_controls")
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op.drop_index("ix_clinical_controls_db_identifier", "clinical_controls")
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op.drop_index("ix_clinical_controls_db_version", "clinical_controls")
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op.alter_column("clinvar_variants", "db_version", nullable=False, new_column_name="clinvar_db_version")
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op.alter_column("clinvar_variants", "db_identifier", nullable=False, new_column_name="allele_id")
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op.drop_column("clinvar_variants", "db_name")
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op.add_column(
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"mapped_variants",
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sa.Column("clinvar_variant_id", sa.Integer(), sa.ForeignKey("clinvar_variants.id"), nullable=True),
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)
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# Downgrades a many-to-many relationship to a one to many. This will result in data loss.
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op.execute(
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"""
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UPDATE mapped_variants
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SET clinvar_variant_id=mapped_variants_clinical_controls.clinical_control_id
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FROM mapped_variants_clinical_controls
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WHERE mapped_variants_clinical_controls.mapped_variant_id=mapped_variants.id
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"""
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)
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op.create_index("ix_mapped_variants_clinvar_variant_id", "mapped_variants", ["clinvar_variant_id"])
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op.drop_table("mapped_variants_clinical_controls")

‎alembic/versions/d6e5a9fde3c9_move_clingen_allele_id_to_mapped_.py‎

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"""move clingen allele id to mapped variants table
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Revision ID: d6e5a9fde3c9
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Revises: 695b73abe581
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Create Date: 2025-02-19 10:51:07.319962
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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 = "d6e5a9fde3c9"
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down_revision = "695b73abe581"
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branch_labels = None
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depends_on = None
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def upgrade():
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# ### commands auto generated by Alembic - please adjust! ###
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op.drop_index("ix_variants_clingen_allele_id", table_name="variants")
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op.add_column("mapped_variants", sa.Column("clingen_allele_id", sa.String(), nullable=True))
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op.execute(
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"""
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UPDATE mapped_variants
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SET clingen_allele_id=variants.clingen_allele_id
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FROM variants
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WHERE variants.id=mapped_variants.variant_id
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"""
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)
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op.drop_column("variants", "clingen_allele_id")
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op.create_index(
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op.f("ix_mapped_variants_clingen_allele_id"), "mapped_variants", ["clingen_allele_id"], unique=False
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)
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# ### end Alembic commands ###
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def downgrade():
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# ### commands auto generated by Alembic - please adjust! ###
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op.drop_index(op.f("ix_mapped_variants_clingen_allele_id"), table_name="mapped_variants")
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op.add_column("variants", sa.Column("clingen_allele_id", sa.String(), nullable=True))
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op.execute(
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"""
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UPDATE variants
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SET clingen_allele_id=mapped_variants.clingen_allele_id
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FROM mapped_variants
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WHERE variants.id=mapped_variants.variant_id
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"""
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)
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op.drop_column("mapped_variants", "clingen_allele_id")
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op.create_index("ix_variants_clingen_allele_id", "variants", ["clingen_allele_id"], unique=False)
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# ### end Alembic commands ###

‎alembic/versions/e8a3b5d8f885_add_clingen_allele_ids.py‎

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"""Add ClinGen allele IDs
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Revision ID: e8a3b5d8f885
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Revises: 4726e4dddde8
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Create Date: 2025-01-27 18:55:09.283855
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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 = "e8a3b5d8f885"
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down_revision = "4726e4dddde8"
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branch_labels = None
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depends_on = None
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def upgrade():
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op.add_column("variants", sa.Column("clingen_allele_id", sa.String(), nullable=True))
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op.create_index(op.f("ix_variants_clingen_allele_id"), "variants", ["clingen_allele_id"], unique=False)
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def downgrade():
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op.drop_index(op.f("ix_variants_clingen_allele_id"), table_name="variants")
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op.drop_column("variants", "clingen_allele_id")

‎alembic/versions/f69b4049bc3b_add_is_base_editor_column_to_target_.py‎

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"""Add is_base_editor column to target_accessions
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Revision ID: f69b4049bc3b
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Revises: c404b6719110
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Revises: d6e5a9fde3c9
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Create Date: 2025-03-02 14:06:52.217554
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"""
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# revision identifiers, used by Alembic.
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revision = "f69b4049bc3b"
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down_revision = "c404b6719110"
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down_revision = "d6e5a9fde3c9"
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branch_labels = None
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depends_on = None
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