[galaxy-commits] [galaxyproject/galaxy] 0d21f6: Consolidate exception logging in db migrations

7 Feb 2017


      Branch: refs/heads/dev
  Home:   https://github.com/galaxyproject/galaxy
  Commit: 0d21f657ca4115ce3e309394cff8bdb084de6ef3
      https://github.com/galaxyproject/galaxy/commit/0d21f657ca4115ce3e309394cff8b...
  Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk>
  Date:   2017-02-07 (Tue, 07 Feb 2017)

  Changed paths:
    M lib/galaxy/model/migrate/versions/0003_security_and_libraries.py
    M lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py
    M lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py
    M lib/galaxy/model/migrate/versions/0007_sharing_histories.py
    M lib/galaxy/model/migrate/versions/0008_galaxy_forms.py
    M lib/galaxy/model/migrate/versions/0009_request_table.py
    M lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py
    M lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py
    M lib/galaxy/model/migrate/versions/0012_user_address.py
    M lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py
    M lib/galaxy/model/migrate/versions/0014_pages.py
    M lib/galaxy/model/migrate/versions/0015_tagging.py
    M lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py
    M lib/galaxy/model/migrate/versions/0017_library_item_indexes.py
    M lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py
    M lib/galaxy/model/migrate/versions/0019_request_library_folder.py
    M lib/galaxy/model/migrate/versions/0020_library_upload_job.py
    M lib/galaxy/model/migrate/versions/0021_user_prefs.py
    M lib/galaxy/model/migrate/versions/0022_visualization_tables.py
    M lib/galaxy/model/migrate/versions/0024_page_slug_unique_constraint.py
    M lib/galaxy/model/migrate/versions/0025_user_info.py
    M lib/galaxy/model/migrate/versions/0027_request_events.py
    M lib/galaxy/model/migrate/versions/0028_external_metadata_file_override.py
    M lib/galaxy/model/migrate/versions/0029_user_actions.py
    M lib/galaxy/model/migrate/versions/0031_community_and_workflow_tags.py
    M lib/galaxy/model/migrate/versions/0033_published_cols_for_histories_and_workflows.py
    M lib/galaxy/model/migrate/versions/0034_page_user_share_association.py
    M lib/galaxy/model/migrate/versions/0035_item_annotations_and_workflow_step_tags.py
    M lib/galaxy/model/migrate/versions/0036_add_deleted_column_to_library_template_assoc_tables.py
    M lib/galaxy/model/migrate/versions/0037_samples_library.py
    M lib/galaxy/model/migrate/versions/0038_add_inheritable_column_to_library_template_assoc_tables.py
    M lib/galaxy/model/migrate/versions/0040_page_annotations.py
    M lib/galaxy/model/migrate/versions/0043_visualization_sharing_tagging_annotating.py
    M lib/galaxy/model/migrate/versions/0045_request_type_permissions_table.py
    M lib/galaxy/model/migrate/versions/0046_post_job_actions.py
    M lib/galaxy/model/migrate/versions/0047_job_table_user_id_column.py
    M lib/galaxy/model/migrate/versions/0048_dataset_instance_state_column.py
    M lib/galaxy/model/migrate/versions/0049_api_keys_table.py
    M lib/galaxy/model/migrate/versions/0050_drop_cloud_tables.py
    M lib/galaxy/model/migrate/versions/0051_imported_col_for_jobs_table.py
    M lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py
    M lib/galaxy/model/migrate/versions/0053_item_ratings.py
    M lib/galaxy/model/migrate/versions/0055_add_pja_assoc_for_jobs.py
    M lib/galaxy/model/migrate/versions/0057_request_notify.py
    M lib/galaxy/model/migrate/versions/0058_history_import_export.py
    M lib/galaxy/model/migrate/versions/0059_sample_dataset_file_path.py
    M lib/galaxy/model/migrate/versions/0060_history_archive_import.py
    M lib/galaxy/model/migrate/versions/0062_user_openid_table.py
    M lib/galaxy/model/migrate/versions/0063_sequencer_table.py
    M lib/galaxy/model/migrate/versions/0064_add_run_and_sample_run_association_tables.py
    M lib/galaxy/model/migrate/versions/0065_add_name_to_form_fields_and_values.py
    M lib/galaxy/model/migrate/versions/0066_deferred_job_and_transfer_job_tables.py
    M lib/galaxy/model/migrate/versions/0067_populate_sequencer_table.py
    M lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py
    M lib/galaxy/model/migrate/versions/0069_rename_sequencer_form_type.py
    M lib/galaxy/model/migrate/versions/0070_add_info_column_to_deferred_job_table.py
    M lib/galaxy/model/migrate/versions/0071_add_history_and_workflow_to_sample.py
    M lib/galaxy/model/migrate/versions/0072_add_pid_and_socket_columns_to_transfer_job_table.py
    M lib/galaxy/model/migrate/versions/0073_add_ldda_to_implicit_conversion_table.py
    M lib/galaxy/model/migrate/versions/0074_add_purged_column_to_library_dataset_table.py
    M lib/galaxy/model/migrate/versions/0075_add_subindex_column_to_run_table.py
    M lib/galaxy/model/migrate/versions/0077_create_tool_tag_association_table.py
    M lib/galaxy/model/migrate/versions/0078_add_columns_for_disk_usage_accounting.py
    M lib/galaxy/model/migrate/versions/0079_input_library_to_job_table.py
    M lib/galaxy/model/migrate/versions/0080_quota_tables.py
    M lib/galaxy/model/migrate/versions/0081_add_tool_version_to_hda_ldda.py
    M lib/galaxy/model/migrate/versions/0082_add_tool_shed_repository_table.py
    M lib/galaxy/model/migrate/versions/0083_add_prepare_files_to_task.py
    M lib/galaxy/model/migrate/versions/0084_add_ldda_id_to_implicit_conversion_table.py
    M lib/galaxy/model/migrate/versions/0085_add_task_info.py
    M lib/galaxy/model/migrate/versions/0086_add_tool_shed_repository_table_columns.py
    M lib/galaxy/model/migrate/versions/0087_tool_id_guid_map_table.py
    M lib/galaxy/model/migrate/versions/0088_add_installed_changeset_revison_column.py
    M lib/galaxy/model/migrate/versions/0089_add_object_store_id_columns.py
    M lib/galaxy/model/migrate/versions/0090_add_tool_shed_repository_table_columns.py
    M lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py
    M lib/galaxy/model/migrate/versions/0092_add_migrate_tools_table.py
    M lib/galaxy/model/migrate/versions/0093_add_job_params_col.py
    M lib/galaxy/model/migrate/versions/0094_add_job_handler_col.py
    M lib/galaxy/model/migrate/versions/0095_hda_subsets.py
    M lib/galaxy/model/migrate/versions/0096_openid_provider.py
    M lib/galaxy/model/migrate/versions/0097_add_ctx_rev_column.py
    M lib/galaxy/model/migrate/versions/0098_genome_index_tool_data_table.py
    M lib/galaxy/model/migrate/versions/0099_add_tool_dependency_table.py
    M lib/galaxy/model/migrate/versions/0100_alter_tool_dependency_table_version_column.py
    M lib/galaxy/model/migrate/versions/0101_drop_installed_changeset_revision_column.py
    M lib/galaxy/model/migrate/versions/0102_add_tool_dependency_status_columns.py
    M lib/galaxy/model/migrate/versions/0103_add_tool_shed_repository_status_columns.py
    M lib/galaxy/model/migrate/versions/0105_add_cleanup_event_table.py
    M lib/galaxy/model/migrate/versions/0106_add_missing_indexes.py
    M lib/galaxy/model/migrate/versions/0107_add_exit_code_to_job_and_task.py
    M lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py
    M lib/galaxy/model/migrate/versions/0109_add_repository_dependency_tables.py
    M lib/galaxy/model/migrate/versions/0110_add_dataset_uuid.py
    M lib/galaxy/model/migrate/versions/0111_add_job_destinations.py
    M lib/galaxy/model/migrate/versions/0112_add_data_manager_history_association_and_data_manager_job_association_tables.py
    M lib/galaxy/model/migrate/versions/0113_update_migrate_tools_table.py
    M lib/galaxy/model/migrate/versions/0114_update_migrate_tools_table_again.py
    M lib/galaxy/model/migrate/versions/0116_drop_update_available_col_add_tool_shed_status_col.py
    M lib/galaxy/model/migrate/versions/0117_add_user_activation.py
    M lib/galaxy/model/migrate/versions/0118_add_hda_extended_metadata.py
    M lib/galaxy/model/migrate/versions/0119_job_metrics.py
    M lib/galaxy/model/migrate/versions/0120_dataset_collections.py
    M lib/galaxy/model/migrate/versions/0121_workflow_uuids.py
    M lib/galaxy/model/migrate/versions/0122_grow_mysql_blobs.py
    M lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py
    M lib/galaxy/model/migrate/versions/0124_job_state_history.py
    M lib/galaxy/model/migrate/versions/0125_workflow_step_tracking.py
    M lib/galaxy/model/migrate/versions/0126_password_reset.py
    M lib/galaxy/model/migrate/versions/0127_output_collection_adjustments.py
    M lib/galaxy/model/migrate/versions/0128_session_timeout.py
    M lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py
    M lib/galaxy/model/migrate/versions/0130_change_pref_datatype.py
    M lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py
    M lib/galaxy/model/migrate/versions/0132_add_lastpasswordchange_to_user.py
    M lib/galaxy/model/migrate/versions/0133_add_dependency_column_to_job.py

  Log Message:
  -----------
  Consolidate exception logging in db migrations

Also:
- align engine_true() and engine_false() methods
- remove unused 'now' variables


  Commit: cb4fbe7a1caba8195ac8ec4965c702a58378f592
      https://github.com/galaxyproject/galaxy/commit/cb4fbe7a1caba8195ac8ec4965c70...
  Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk>
  Date:   2017-02-07 (Tue, 07 Feb 2017)

  Changed paths:
    M lib/galaxy/model/migrate/versions/0026_cloud_tables.py
    M lib/galaxy/model/migrate/versions/0036_add_deleted_column_to_library_template_assoc_tables.py
    M lib/galaxy/model/migrate/versions/0038_add_inheritable_column_to_library_template_assoc_tables.py
    M lib/galaxy/model/migrate/versions/0039_add_synopsis_column_to_library_table.py
    M lib/galaxy/model/migrate/versions/0041_workflow_invocation.py
    M lib/galaxy/model/migrate/versions/0044_add_notify_column_to_request_table.py
    M lib/galaxy/model/migrate/versions/0045_request_type_permissions_table.py
    M lib/galaxy/model/migrate/versions/0047_job_table_user_id_column.py
    M lib/galaxy/model/migrate/versions/0050_drop_cloud_tables.py
    M lib/galaxy/model/migrate/versions/0057_request_notify.py
    M lib/galaxy/model/migrate/versions/0063_sequencer_table.py
    M lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py
    M lib/galaxy/model/migrate/versions/0086_add_tool_shed_repository_table_columns.py
    M lib/galaxy/model/migrate/versions/0090_add_tool_shed_repository_table_columns.py
    M lib/galaxy/model/migrate/versions/0104_update_genome_downloader_job_parameters.py
    M lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py
    M lib/galaxy/model/migrate/versions/0115_longer_user_password_field.py
    M lib/galaxy/model/migrate/versions/0117_add_user_activation.py
    M lib/galaxy/model/migrate/versions/0120_dataset_collections.py
    M lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py
    M lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py

  Log Message:
  -----------
  Fix a bunch of database migration bugs


  Commit: 68752b7db0c6328d1d88e657ad21b2e4312f4401
      https://github.com/galaxyproject/galaxy/commit/68752b7db0c6328d1d88e657ad21b...
  Author: Dannon Baker <dannon.baker@gmail.com>
  Date:   2017-02-07 (Tue, 07 Feb 2017)

  Changed paths:
    M lib/galaxy/model/migrate/versions/0003_security_and_libraries.py
    M lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py
    M lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py
    M lib/galaxy/model/migrate/versions/0007_sharing_histories.py
    M lib/galaxy/model/migrate/versions/0008_galaxy_forms.py
    M lib/galaxy/model/migrate/versions/0009_request_table.py
    M lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py
    M lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py
    M lib/galaxy/model/migrate/versions/0012_user_address.py
    M lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py
    M lib/galaxy/model/migrate/versions/0014_pages.py
    M lib/galaxy/model/migrate/versions/0015_tagging.py
    M lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py
    M lib/galaxy/model/migrate/versions/0017_library_item_indexes.py
    M lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py
    M lib/galaxy/model/migrate/versions/0019_request_library_folder.py
    M lib/galaxy/model/migrate/versions/0020_library_upload_job.py
    M lib/galaxy/model/migrate/versions/0021_user_prefs.py
    M lib/galaxy/model/migrate/versions/0022_visualization_tables.py
    M lib/galaxy/model/migrate/versions/0024_page_slug_unique_constraint.py
    M lib/galaxy/model/migrate/versions/0025_user_info.py
    M lib/galaxy/model/migrate/versions/0026_cloud_tables.py
    M lib/galaxy/model/migrate/versions/0027_request_events.py
    M lib/galaxy/model/migrate/versions/0028_external_metadata_file_override.py
    M lib/galaxy/model/migrate/versions/0029_user_actions.py
    M lib/galaxy/model/migrate/versions/0031_community_and_workflow_tags.py
    M lib/galaxy/model/migrate/versions/0033_published_cols_for_histories_and_workflows.py
    M lib/galaxy/model/migrate/versions/0034_page_user_share_association.py
    M lib/galaxy/model/migrate/versions/0035_item_annotations_and_workflow_step_tags.py
    M lib/galaxy/model/migrate/versions/0036_add_deleted_column_to_library_template_assoc_tables.py
    M lib/galaxy/model/migrate/versions/0037_samples_library.py
    M lib/galaxy/model/migrate/versions/0038_add_inheritable_column_to_library_template_assoc_tables.py
    M lib/galaxy/model/migrate/versions/0039_add_synopsis_column_to_library_table.py
    M lib/galaxy/model/migrate/versions/0040_page_annotations.py
    M lib/galaxy/model/migrate/versions/0041_workflow_invocation.py
    M lib/galaxy/model/migrate/versions/0043_visualization_sharing_tagging_annotating.py
    M lib/galaxy/model/migrate/versions/0044_add_notify_column_to_request_table.py
    M lib/galaxy/model/migrate/versions/0045_request_type_permissions_table.py
    M lib/galaxy/model/migrate/versions/0046_post_job_actions.py
    M lib/galaxy/model/migrate/versions/0047_job_table_user_id_column.py
    M lib/galaxy/model/migrate/versions/0048_dataset_instance_state_column.py
    M lib/galaxy/model/migrate/versions/0049_api_keys_table.py
    M lib/galaxy/model/migrate/versions/0050_drop_cloud_tables.py
    M lib/galaxy/model/migrate/versions/0051_imported_col_for_jobs_table.py
    M lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py
    M lib/galaxy/model/migrate/versions/0053_item_ratings.py
    M lib/galaxy/model/migrate/versions/0055_add_pja_assoc_for_jobs.py
    M lib/galaxy/model/migrate/versions/0057_request_notify.py
    M lib/galaxy/model/migrate/versions/0058_history_import_export.py
    M lib/galaxy/model/migrate/versions/0059_sample_dataset_file_path.py
    M lib/galaxy/model/migrate/versions/0060_history_archive_import.py
    M lib/galaxy/model/migrate/versions/0062_user_openid_table.py
    M lib/galaxy/model/migrate/versions/0063_sequencer_table.py
    M lib/galaxy/model/migrate/versions/0064_add_run_and_sample_run_association_tables.py
    M lib/galaxy/model/migrate/versions/0065_add_name_to_form_fields_and_values.py
    M lib/galaxy/model/migrate/versions/0066_deferred_job_and_transfer_job_tables.py
    M lib/galaxy/model/migrate/versions/0067_populate_sequencer_table.py
    M lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py
    M lib/galaxy/model/migrate/versions/0069_rename_sequencer_form_type.py
    M lib/galaxy/model/migrate/versions/0070_add_info_column_to_deferred_job_table.py
    M lib/galaxy/model/migrate/versions/0071_add_history_and_workflow_to_sample.py
    M lib/galaxy/model/migrate/versions/0072_add_pid_and_socket_columns_to_transfer_job_table.py
    M lib/galaxy/model/migrate/versions/0073_add_ldda_to_implicit_conversion_table.py
    M lib/galaxy/model/migrate/versions/0074_add_purged_column_to_library_dataset_table.py
    M lib/galaxy/model/migrate/versions/0075_add_subindex_column_to_run_table.py
    M lib/galaxy/model/migrate/versions/0077_create_tool_tag_association_table.py
    M lib/galaxy/model/migrate/versions/0078_add_columns_for_disk_usage_accounting.py
    M lib/galaxy/model/migrate/versions/0079_input_library_to_job_table.py
    M lib/galaxy/model/migrate/versions/0080_quota_tables.py
    M lib/galaxy/model/migrate/versions/0081_add_tool_version_to_hda_ldda.py
    M lib/galaxy/model/migrate/versions/0082_add_tool_shed_repository_table.py
    M lib/galaxy/model/migrate/versions/0083_add_prepare_files_to_task.py
    M lib/galaxy/model/migrate/versions/0084_add_ldda_id_to_implicit_conversion_table.py
    M lib/galaxy/model/migrate/versions/0085_add_task_info.py
    M lib/galaxy/model/migrate/versions/0086_add_tool_shed_repository_table_columns.py
    M lib/galaxy/model/migrate/versions/0087_tool_id_guid_map_table.py
    M lib/galaxy/model/migrate/versions/0088_add_installed_changeset_revison_column.py
    M lib/galaxy/model/migrate/versions/0089_add_object_store_id_columns.py
    M lib/galaxy/model/migrate/versions/0090_add_tool_shed_repository_table_columns.py
    M lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py
    M lib/galaxy/model/migrate/versions/0092_add_migrate_tools_table.py
    M lib/galaxy/model/migrate/versions/0093_add_job_params_col.py
    M lib/galaxy/model/migrate/versions/0094_add_job_handler_col.py
    M lib/galaxy/model/migrate/versions/0095_hda_subsets.py
    M lib/galaxy/model/migrate/versions/0096_openid_provider.py
    M lib/galaxy/model/migrate/versions/0097_add_ctx_rev_column.py
    M lib/galaxy/model/migrate/versions/0098_genome_index_tool_data_table.py
    M lib/galaxy/model/migrate/versions/0099_add_tool_dependency_table.py
    M lib/galaxy/model/migrate/versions/0100_alter_tool_dependency_table_version_column.py
    M lib/galaxy/model/migrate/versions/0101_drop_installed_changeset_revision_column.py
    M lib/galaxy/model/migrate/versions/0102_add_tool_dependency_status_columns.py
    M lib/galaxy/model/migrate/versions/0103_add_tool_shed_repository_status_columns.py
    M lib/galaxy/model/migrate/versions/0104_update_genome_downloader_job_parameters.py
    M lib/galaxy/model/migrate/versions/0105_add_cleanup_event_table.py
    M lib/galaxy/model/migrate/versions/0106_add_missing_indexes.py
    M lib/galaxy/model/migrate/versions/0107_add_exit_code_to_job_and_task.py
    M lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py
    M lib/galaxy/model/migrate/versions/0109_add_repository_dependency_tables.py
    M lib/galaxy/model/migrate/versions/0110_add_dataset_uuid.py
    M lib/galaxy/model/migrate/versions/0111_add_job_destinations.py
    M lib/galaxy/model/migrate/versions/0112_add_data_manager_history_association_and_data_manager_job_association_tables.py
    M lib/galaxy/model/migrate/versions/0113_update_migrate_tools_table.py
    M lib/galaxy/model/migrate/versions/0114_update_migrate_tools_table_again.py
    M lib/galaxy/model/migrate/versions/0115_longer_user_password_field.py
    M lib/galaxy/model/migrate/versions/0116_drop_update_available_col_add_tool_shed_status_col.py
    M lib/galaxy/model/migrate/versions/0117_add_user_activation.py
    M lib/galaxy/model/migrate/versions/0118_add_hda_extended_metadata.py
    M lib/galaxy/model/migrate/versions/0119_job_metrics.py
    M lib/galaxy/model/migrate/versions/0120_dataset_collections.py
    M lib/galaxy/model/migrate/versions/0121_workflow_uuids.py
    M lib/galaxy/model/migrate/versions/0122_grow_mysql_blobs.py
    M lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py
    M lib/galaxy/model/migrate/versions/0124_job_state_history.py
    M lib/galaxy/model/migrate/versions/0125_workflow_step_tracking.py
    M lib/galaxy/model/migrate/versions/0126_password_reset.py
    M lib/galaxy/model/migrate/versions/0127_output_collection_adjustments.py
    M lib/galaxy/model/migrate/versions/0128_session_timeout.py
    M lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py
    M lib/galaxy/model/migrate/versions/0130_change_pref_datatype.py
    M lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py
    M lib/galaxy/model/migrate/versions/0132_add_lastpasswordchange_to_user.py
    M lib/galaxy/model/migrate/versions/0133_add_dependency_column_to_job.py

  Log Message:
  -----------
  Merge pull request #3570 from nsoranzo/database_migrations

Database migrations: improvements and fixes


Compare: https://github.com/galaxyproject/galaxy/compare/27d871f20edc...68752b7db0c6

[galaxy-commits] [galaxyproject/galaxy] 0d21f6: Consolidate exception logging in db migrations

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