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galaxy.model.migrate package

Subpackages

• galaxy.model.migrate.versions package
  • Submodules
  • galaxy.model.migrate.versions.0001_initial_tables module
  • galaxy.model.migrate.versions.0002_metadata_file_table module
  • galaxy.model.migrate.versions.0003_security_and_libraries module
  • galaxy.model.migrate.versions.0004_indexes_and_defaults module
  • galaxy.model.migrate.versions.0005_cleanup_datasets_fix module
  • galaxy.model.migrate.versions.0006_change_qual_datatype module
  • galaxy.model.migrate.versions.0007_sharing_histories module
  • galaxy.model.migrate.versions.0008_galaxy_forms module
  • galaxy.model.migrate.versions.0009_request_table module
  • galaxy.model.migrate.versions.0010_hda_display_at_authz_table module
  • galaxy.model.migrate.versions.0011_v0010_mysql_index_fix module
  • galaxy.model.migrate.versions.0012_user_address module
  • galaxy.model.migrate.versions.0013_change_lib_item_templates_to_forms module
  • galaxy.model.migrate.versions.0014_pages module
  • galaxy.model.migrate.versions.0015_tagging module
  • galaxy.model.migrate.versions.0016_v0015_mysql_index_fix module
  • galaxy.model.migrate.versions.0017_library_item_indexes module
  • galaxy.model.migrate.versions.0018_ordered_tags_and_page_tags module
  • galaxy.model.migrate.versions.0019_request_library_folder module
  • galaxy.model.migrate.versions.0020_library_upload_job module
  • galaxy.model.migrate.versions.0021_user_prefs module
  • galaxy.model.migrate.versions.0022_visualization_tables module
  • galaxy.model.migrate.versions.0023_page_published_and_deleted_columns module
  • galaxy.model.migrate.versions.0024_page_slug_unique_constraint module
  • galaxy.model.migrate.versions.0025_user_info module
  • galaxy.model.migrate.versions.0026_cloud_tables module
  • galaxy.model.migrate.versions.0027_request_events module
  • galaxy.model.migrate.versions.0028_external_metadata_file_override module
  • galaxy.model.migrate.versions.0029_user_actions module
  • galaxy.model.migrate.versions.0030_history_slug_column module
  • galaxy.model.migrate.versions.0031_community_and_workflow_tags module
  • galaxy.model.migrate.versions.0032_stored_workflow_slug_column module
  • galaxy.model.migrate.versions.0033_published_cols_for_histories_and_workflows module
  • galaxy.model.migrate.versions.0034_page_user_share_association module
  • galaxy.model.migrate.versions.0035_item_annotations_and_workflow_step_tags module
  • galaxy.model.migrate.versions.0036_add_deleted_column_to_library_template_assoc_tables module
  • galaxy.model.migrate.versions.0037_samples_library module
  • galaxy.model.migrate.versions.0038_add_inheritable_column_to_library_template_assoc_tables module
  • galaxy.model.migrate.versions.0039_add_synopsis_column_to_library_table module
  • galaxy.model.migrate.versions.0040_page_annotations module
  • galaxy.model.migrate.versions.0041_workflow_invocation module
  • galaxy.model.migrate.versions.0042_workflow_invocation_fix module
  • galaxy.model.migrate.versions.0043_visualization_sharing_tagging_annotating module
  • galaxy.model.migrate.versions.0044_add_notify_column_to_request_table module
  • galaxy.model.migrate.versions.0045_request_type_permissions_table module
  • galaxy.model.migrate.versions.0046_post_job_actions module
  • galaxy.model.migrate.versions.0047_job_table_user_id_column module
  • galaxy.model.migrate.versions.0048_dataset_instance_state_column module
  • galaxy.model.migrate.versions.0049_api_keys_table module
  • galaxy.model.migrate.versions.0050_drop_cloud_tables module
  • galaxy.model.migrate.versions.0051_imported_col_for_jobs_table module
  • galaxy.model.migrate.versions.0052_sample_dataset_table module
  • galaxy.model.migrate.versions.0053_item_ratings module
  • galaxy.model.migrate.versions.0054_visualization_dbkey module
  • galaxy.model.migrate.versions.0055_add_pja_assoc_for_jobs module
  • galaxy.model.migrate.versions.0056_workflow_outputs module
  • galaxy.model.migrate.versions.0057_request_notify module
  • galaxy.model.migrate.versions.0058_history_import_export module
  • galaxy.model.migrate.versions.0059_sample_dataset_file_path module
  • galaxy.model.migrate.versions.0060_history_archive_import module
  • galaxy.model.migrate.versions.0061_tasks module
  • galaxy.model.migrate.versions.0062_user_openid_table module
  • galaxy.model.migrate.versions.0063_sequencer_table module
  • galaxy.model.migrate.versions.0064_add_run_and_sample_run_association_tables module
  • galaxy.model.migrate.versions.0065_add_name_to_form_fields_and_values module
  • galaxy.model.migrate.versions.0066_deferred_job_and_transfer_job_tables module
  • galaxy.model.migrate.versions.0067_populate_sequencer_table module
  • galaxy.model.migrate.versions.0068_rename_sequencer_to_external_services module
  • galaxy.model.migrate.versions.0069_rename_sequencer_form_type module
  • galaxy.model.migrate.versions.0070_add_info_column_to_deferred_job_table module
  • galaxy.model.migrate.versions.0071_add_history_and_workflow_to_sample module
  • galaxy.model.migrate.versions.0072_add_pid_and_socket_columns_to_transfer_job_table module
  • galaxy.model.migrate.versions.0073_add_ldda_to_implicit_conversion_table module
  • galaxy.model.migrate.versions.0074_add_purged_column_to_library_dataset_table module
  • galaxy.model.migrate.versions.0075_add_subindex_column_to_run_table module
  • galaxy.model.migrate.versions.0076_fix_form_values_data_corruption module
  • galaxy.model.migrate.versions.0077_create_tool_tag_association_table module
  • galaxy.model.migrate.versions.0078_add_columns_for_disk_usage_accounting module
  • galaxy.model.migrate.versions.0079_input_library_to_job_table module
  • galaxy.model.migrate.versions.0080_quota_tables module
  • galaxy.model.migrate.versions.0081_add_tool_version_to_hda_ldda module
  • galaxy.model.migrate.versions.0082_add_tool_shed_repository_table module
  • galaxy.model.migrate.versions.0083_add_prepare_files_to_task module
  • galaxy.model.migrate.versions.0084_add_ldda_id_to_implicit_conversion_table module
  • galaxy.model.migrate.versions.0085_add_task_info module
  • galaxy.model.migrate.versions.0086_add_tool_shed_repository_table_columns module
  • galaxy.model.migrate.versions.0087_tool_id_guid_map_table module
  • galaxy.model.migrate.versions.0088_add_installed_changeset_revison_column module
  • galaxy.model.migrate.versions.0089_add_object_store_id_columns module
  • galaxy.model.migrate.versions.0090_add_tool_shed_repository_table_columns module
  • galaxy.model.migrate.versions.0091_add_tool_version_tables module
  • galaxy.model.migrate.versions.0092_add_migrate_tools_table module
  • galaxy.model.migrate.versions.0093_add_job_params_col module
  • galaxy.model.migrate.versions.0094_add_job_handler_col module
  • galaxy.model.migrate.versions.0095_hda_subsets module
  • galaxy.model.migrate.versions.0096_openid_provider module
  • galaxy.model.migrate.versions.0097_add_ctx_rev_column module
  • galaxy.model.migrate.versions.0098_genome_index_tool_data_table module
  • galaxy.model.migrate.versions.0099_add_tool_dependency_table module
  • galaxy.model.migrate.versions.0100_alter_tool_dependency_table_version_column module
  • galaxy.model.migrate.versions.0101_drop_installed_changeset_revision_column module
  • galaxy.model.migrate.versions.0102_add_tool_dependency_status_columns module
  • galaxy.model.migrate.versions.0103_add_tool_shed_repository_status_columns module
  • galaxy.model.migrate.versions.0104_update_genome_downloader_job_parameters module
  • galaxy.model.migrate.versions.0105_add_cleanup_event_table module
  • galaxy.model.migrate.versions.0106_add_missing_indexes module
  • galaxy.model.migrate.versions.0107_add_exit_code_to_job_and_task module
  • galaxy.model.migrate.versions.0108_add_extended_metadata module
  • galaxy.model.migrate.versions.0109_add_repository_dependency_tables module
  • galaxy.model.migrate.versions.0110_add_dataset_uuid module
  • galaxy.model.migrate.versions.0111_add_job_destinations module
  • galaxy.model.migrate.versions.0112_add_data_manager_history_association_and_data_manager_job_association_tables module
  • galaxy.model.migrate.versions.0113_update_migrate_tools_table module
  • galaxy.model.migrate.versions.0114_update_migrate_tools_table_again module
  • galaxy.model.migrate.versions.0115_longer_user_password_field module
  • galaxy.model.migrate.versions.0116_drop_update_available_col_add_tool_shed_status_col module
  • galaxy.model.migrate.versions.0117_add_user_activation module
  • galaxy.model.migrate.versions.0118_add_hda_extended_metadata module
  • galaxy.model.migrate.versions.0119_job_metrics module
  • galaxy.model.migrate.versions.0120_dataset_collections module
  • galaxy.model.migrate.versions.0121_workflow_uuids module
  • galaxy.model.migrate.versions.0122_grow_mysql_blobs module
  • galaxy.model.migrate.versions.0123_add_workflow_request_tables module
  • galaxy.model.migrate.versions.0124_job_state_history module
  • galaxy.model.migrate.versions.0125_workflow_step_tracking module
  • galaxy.model.migrate.versions.0126_password_reset module
  • galaxy.model.migrate.versions.0127_output_collection_adjustments module
  • galaxy.model.migrate.versions.0128_session_timeout module
  • galaxy.model.migrate.versions.0129_job_external_output_metadata_validity module
  • galaxy.model.migrate.versions.0130_change_pref_datatype module
  • galaxy.model.migrate.versions.0131_subworkflow_and_input_parameter_modules module
  • galaxy.model.migrate.versions.0132_add_lastpasswordchange_to_user module
  • galaxy.model.migrate.versions.0133_add_dependency_column_to_job module
  • galaxy.model.migrate.versions.0134_hda_set_deleted_if_purged module
  • galaxy.model.migrate.versions.0135_add_library_tags module
  • galaxy.model.migrate.versions.0136_collection_and_workflow_state module
  • galaxy.model.migrate.versions.0137_add_copied_from_job_id_column module
  • galaxy.model.migrate.versions.0138_add_hda_version module
  • galaxy.model.migrate.versions.0139_add_history_dataset_association_history_table module
  • galaxy.model.migrate.versions.0140_add_dataset_version_to_job_to_input_dataset_association_table module
  • galaxy.model.migrate.versions.0141_add_oidc_tables module
  • galaxy.model.migrate.versions.0142_change_numeric_metric_precision module
  • galaxy.model.migrate.versions.0143_add_cloudauthz_tables module
  • galaxy.model.migrate.versions.0144_add_cleanup_event_user_table module
  • galaxy.model.migrate.versions.0145_add_workflow_step_input module
  • galaxy.model.migrate.versions.0146_workflow_paths module
  • galaxy.model.migrate.versions.0147_job_messages module
  • galaxy.model.migrate.versions.0148_add_checksum_table module
  • galaxy.model.migrate.versions.0149_dynamic_tools module
  • galaxy.model.migrate.versions.0150_add_create_time_field_for_cloudauthz module
  • galaxy.model.migrate.versions.0151_add_worker_process module
  • galaxy.model.migrate.versions.0152_add_metadata_file_uuid module
  • galaxy.model.migrate.versions.0153_add_custos_authnz_token_table module
  • galaxy.model.migrate.versions.0154_created_from_basename module
  • galaxy.model.migrate.versions.0155_job_galaxy_version module
  • galaxy.model.migrate.versions.0156_add_interactivetools module
  • galaxy.model.migrate.versions.0157_rework_dataset_validation module
  • galaxy.model.migrate.versions.0158_workflow_reports module
  • galaxy.model.migrate.versions.0159_add_job_external_id_index module
  • galaxy.model.migrate.versions.0160_hda_set_deleted_if_purged_again module
  • galaxy.model.migrate.versions.0161_add_workflow_invocation_output_table module
  • galaxy.model.migrate.versions.0162_job_only_pjas module
  • galaxy.model.migrate.versions.0163_worker_process_pid module
  • galaxy.model.migrate.versions.0164_page_format module
  • galaxy.model.migrate.versions.0165_add_content_update_time module
  • galaxy.model.migrate.versions.0166_job_state_summary_view module
  • galaxy.model.migrate.versions.0167_add_job_to_input_dataset_collection_element_association module
  • galaxy.model.migrate.versions.0168_stored_workflow_hidden_col module
  • galaxy.model.migrate.versions.0169_add_missing_indexes module
  • galaxy.model.migrate.versions.0170_add_more_missing_indexes module
  • galaxy.model.migrate.versions.0171_schemaorg_metadata module
  • galaxy.model.migrate.versions.0172_it_entrypoint_requires_domain module
  • galaxy.model.migrate.versions.util module

Submodules

galaxy.model.migrate.check module

galaxy.model.migrate.check.create_or_verify_database(url, galaxy_config_file, engine_options=None, app=None, map_install_models=False)

Check that the database is use-able, possibly creating it if empty (this is the only time we automatically create tables, otherwise we force the user to do it using the management script so they can create backups).

1. Empty database –> initialize with latest version and return

2. Database older than migration support –> fail and require manual update

3. Database at state where migrate support introduced –> add version control information but make no changes (might still require manual update)

4. Database versioned but out of date –> fail with informative message, user must run “sh manage_db.sh upgrade”

galaxy.model.migrate.check.migrate_to_current_version(engine, schema)