Source code for galaxy.model.migrate.versions.0106_add_missing_indexes

"""
Migration script to create missing indexes.  Adding new columns to existing tables via SQLAlchemy does not create the index, even if the column definition includes index=True.
"""

import logging

from sqlalchemy import MetaData

from galaxy.model.migrate.versions.util import (
    add_index,
    drop_index
)

log = logging.getLogger(__name__)
metadata = MetaData()

indexes = (
    ("ix_metadata_file_lda_id", 'metadata_file', 'lda_id'),                                   # 0003
    ("ix_history_importable", 'history', 'importable'),                                       # 0007
    ("ix_sample_bar_code", 'sample', 'bar_code'),                                             # 0009
    ("ix_request_type_deleted", 'request_type', 'deleted'),                                   # 0012
    ("ix_galaxy_user_username", 'galaxy_user', 'username'),                                   # 0014
    ("ix_form_definition_type", 'form_definition', 'type'),                                   # 0019
    ("ix_form_definition_layout", 'form_definition', 'layout'),                               # 0019
    ("ix_job_library_folder_id", 'job', 'library_folder_id'),                                 # 0020
    ("ix_page_published", 'page', 'published'),                                               # 0023
    ("ix_page_deleted", 'page', 'deleted'),                                                   # 0023
    ("ix_galaxy_user_form_values_id", 'galaxy_user', 'form_values_id'),                       # 0025
    ("ix_lia_deleted", 'library_info_association', 'deleted'),                                # 0036
    ("ix_lfia_deleted", 'library_folder_info_association', 'deleted'),                        # 0036
    ("ix_lddia_deleted", 'library_dataset_dataset_info_association', 'deleted'),              # 0036
    ("ix_sample_library_id", 'sample', 'library_id'),                                         # 0037
    ("ix_sample_folder_id", 'sample', 'folder_id'),                                           # 0037
    ("ix_lia_inheritable", 'library_info_association', 'inheritable'),                        # 0038
    ("ix_lfia_inheritable", 'library_folder_info_association', 'inheritable'),                # 0038
    ("ix_job_imported", 'job', 'imported'),                                                   # 0051
    ("ix_request_notification", 'request', 'notification'),                                   # 0057
    ("ix_sd_external_service_id", 'sample_dataset', 'external_service_id'),                   # 0068
    ("ix_icda_ldda_parent_id", 'implicitly_converted_dataset_association', 'ldda_parent_id'),  # 0073
    ("ix_library_dataset_purged", 'library_dataset', 'purged'),                               # 0074
    ("ix_run_subindex", 'run', 'subindex'),                                                   # 0075
    ("ix_history_dataset_association_purged", 'history_dataset_association', 'purged'),       # 0078
    ("ix_galaxy_user_disk_usage", 'galaxy_user', 'disk_usage'),                               # 0078
    ("ix_galaxy_session_disk_usage", 'galaxy_session', 'disk_usage'),                         # 0078
    ("ix_icda_ldda_id", 'implicitly_converted_dataset_association', 'ldda_id'),               # 0084
    ("ix_tsr_includes_datatypes", 'tool_shed_repository', 'includes_datatypes'),              # 0086
    ("ix_dataset_object_store_id", 'dataset', 'object_store_id'),                             # 0089
    ("ix_job_object_store_id", 'job', 'object_store_id'),                                     # 0089
    ("ix_metadata_file_object_store_id", 'metadata_file', 'object_store_id'),                 # 0089
    ("ix_job_handler", 'job', 'handler'),                                                     # 0094
    ("ix_galaxy_user_email", 'galaxy_user', 'email')                                          # 0106
)


[docs]def upgrade(migrate_engine):
    print(__doc__)
    metadata.bind = migrate_engine
    metadata.reflect()

    for ix, table, col in indexes:
        add_index(ix, table, col, metadata)


[docs]def downgrade(migrate_engine):
    metadata.bind = migrate_engine
    metadata.reflect()

    # TODO: Dropping a column used in a foreign key fails in MySQL, need to remove the FK first.
    for ix, table, col in indexes:
        drop_index(ix, table, col, metadata)