Merge pull request #178 from VariantEffect/jstone-uw/bug/score-set-deletion-fails

Add missing indices; fix score set deletion failure.

Author: jstone-dev

alembic/versions/8bcb2b4edc60_add_foreign_key_indices.py

@@ -0,0 +1,94 @@
+"""Add foreign key indices
+
+Revision ID: 8bcb2b4edc60
+Revises: 8e26f1a1160d
+Create Date: 2024-05-14 22:36:47.095490
+
+"""
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision = '8bcb2b4edc60'
+down_revision = '8e26f1a1160d'
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    op.create_index(op.f('ix_access_keys_user_id'), 'access_keys', ['user_id'], unique=False)
+    op.drop_index('ix_doi_identifiers_id', table_name='doi_identifiers')
+    op.drop_index('ix_ensembl_identifiers_id', table_name='ensembl_identifiers')
+    op.drop_index('ix_experiment_sets_id', table_name='experiment_sets')
+    op.create_index(op.f('ix_experiment_sets_created_by_id'), 'experiment_sets', ['created_by_id'], unique=False)
+    op.create_index(op.f('ix_experiment_sets_modified_by_id'), 'experiment_sets', ['modified_by_id'], unique=False)
+    op.drop_index('ix_experiments_id', table_name='experiments')
+    op.create_index(op.f('ix_experiments_created_by_id'), 'experiments', ['created_by_id'], unique=False)
+    op.create_index(op.f('ix_experiments_experiment_set_id'), 'experiments', ['experiment_set_id'], unique=False)
+    op.create_index(op.f('ix_experiments_modified_by_id'), 'experiments', ['modified_by_id'], unique=False)
+    op.drop_index('ix_genome_identifiers_id', table_name='genome_identifiers')
+    op.drop_index('ix_keywords_id', table_name='keywords')
+    op.drop_index('ix_licenses_id', table_name='licenses')
+    op.drop_index('ix_mapped_variants_id', table_name='mapped_variants')
+    op.create_index(op.f('ix_mapped_variants_variant_id'), 'mapped_variants', ['variant_id'], unique=False)
+    op.drop_index('ix_publication_identifiers_id', table_name='publication_identifiers')
+    op.drop_index('ix_refseq_identifiers_id', table_name='refseq_identifiers')
+    op.drop_index('ix_roles_name', table_name='roles')
+    op.drop_index('ix_scoresets_id', table_name='scoresets')
+    op.create_index(op.f('ix_scoresets_created_by_id'), 'scoresets', ['created_by_id'], unique=False)
+    op.create_index(op.f('ix_scoresets_experiment_id'), 'scoresets', ['experiment_id'], unique=False)
+    op.create_index(op.f('ix_scoresets_licence_id'), 'scoresets', ['licence_id'], unique=False)
+    op.create_index(op.f('ix_scoresets_modified_by_id'), 'scoresets', ['modified_by_id'], unique=False)
+    op.create_index(op.f('ix_scoresets_replaces_id'), 'scoresets', ['replaces_id'], unique=False)
+    op.drop_index('ix_sra_identifiers_id', table_name='sra_identifiers')
+    op.drop_index('ix_target_genes_id', table_name='target_genes')
+    op.create_index(op.f('ix_target_genes_accession_id'), 'target_genes', ['accession_id'], unique=False)
+    op.create_index(op.f('ix_target_genes_scoreset_id'), 'target_genes', ['scoreset_id'], unique=False)
+    op.create_index(op.f('ix_target_genes_target_sequence_id'), 'target_genes', ['target_sequence_id'], unique=False)
+    op.drop_index('ix_target_sequences_id', table_name='target_sequences')
+    op.create_index(op.f('ix_target_sequences_taxonomy_id'), 'target_sequences', ['taxonomy_id'], unique=False)
+    op.drop_index('ix_taxonomies_id', table_name='taxonomies')
+    op.create_index(op.f('ix_taxonomies_genome_identifier_id'), 'taxonomies', ['genome_identifier_id'], unique=False)
+    op.drop_index('ix_uniprot_identifiers_id', table_name='uniprot_identifiers')
+    op.drop_index('ix_variants_id', table_name='variants')
+    op.create_index(op.f('ix_variants_scoreset_id'), 'variants', ['scoreset_id'], unique=False)
+
+
+def downgrade():
+    op.drop_index(op.f('ix_variants_scoreset_id'), table_name='variants')
+    op.create_index('ix_variants_id', 'variants', ['id'], unique=False)
+    op.create_index('ix_uniprot_identifiers_id', 'uniprot_identifiers', ['id'], unique=False)
+    op.drop_index(op.f('ix_taxonomies_genome_identifier_id'), table_name='taxonomies')
+    op.create_index('ix_taxonomies_id', 'taxonomies', ['id'], unique=False)
+    op.drop_index(op.f('ix_target_sequences_taxonomy_id'), table_name='target_sequences')
+    op.create_index('ix_target_sequences_id', 'target_sequences', ['id'], unique=False)
+    op.drop_index(op.f('ix_target_genes_target_sequence_id'), table_name='target_genes')
+    op.drop_index(op.f('ix_target_genes_scoreset_id'), table_name='target_genes')
+    op.drop_index(op.f('ix_target_genes_accession_id'), table_name='target_genes')
+    op.create_index('ix_target_genes_id', 'target_genes', ['id'], unique=False)
+    op.create_index('ix_sra_identifiers_id', 'sra_identifiers', ['id'], unique=False)
+    op.drop_index(op.f('ix_scoresets_replaces_id'), table_name='scoresets')
+    op.drop_index(op.f('ix_scoresets_modified_by_id'), table_name='scoresets')
+    op.drop_index(op.f('ix_scoresets_licence_id'), table_name='scoresets')
+    op.drop_index(op.f('ix_scoresets_experiment_id'), table_name='scoresets')
+    op.drop_index(op.f('ix_scoresets_created_by_id'), table_name='scoresets')
+    op.create_index('ix_scoresets_id', 'scoresets', ['id'], unique=False)
+    op.create_index('ix_roles_name', 'roles', ['name'], unique=False)
+    op.create_index('ix_refseq_identifiers_id', 'refseq_identifiers', ['id'], unique=False)
+    op.create_index('ix_publication_identifiers_id', 'publication_identifiers', ['id'], unique=False)
+    op.drop_index(op.f('ix_mapped_variants_variant_id'), table_name='mapped_variants')
+    op.create_index('ix_mapped_variants_id', 'mapped_variants', ['id'], unique=False)
+    op.create_index('ix_licenses_id', 'licenses', ['id'], unique=False)
+    op.create_index('ix_keywords_id', 'keywords', ['id'], unique=False)
+    op.create_index('ix_genome_identifiers_id', 'genome_identifiers', ['id'], unique=False)
+    op.drop_index(op.f('ix_experiments_modified_by_id'), table_name='experiments')
+    op.drop_index(op.f('ix_experiments_experiment_set_id'), table_name='experiments')
+    op.drop_index(op.f('ix_experiments_created_by_id'), table_name='experiments')
+    op.create_index('ix_experiments_id', 'experiments', ['id'], unique=False)
+    op.drop_index(op.f('ix_experiment_sets_modified_by_id'), table_name='experiment_sets')
+    op.drop_index(op.f('ix_experiment_sets_created_by_id'), table_name='experiment_sets')
+    op.create_index('ix_experiment_sets_id', 'experiment_sets', ['id'], unique=False)
+    op.create_index('ix_ensembl_identifiers_id', 'ensembl_identifiers', ['id'], unique=False)
+    op.create_index('ix_doi_identifiers_id', 'doi_identifiers', ['id'], unique=False)
+    op.drop_index(op.f('ix_access_keys_user_id'), table_name='access_keys')