Created
June 25, 2018 23:26
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mysql database migration errors on fresh mysql database
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| galaxy.queue_worker INFO 2018-06-25 16:18:23,098 [p:48241,w:0,m:0] [MainThread] Initializing main Galaxy Queue Worker on sqlalchemy+mysql+mysqldb://mvandenb:********@localhost/galaxy | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:23,268 [p:48241,w:0,m:0] [MainThread] No database, initializing | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:23,309 [p:48241,w:0,m:0] [MainThread] Migrating 0 -> 1... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:24,589 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:24,589 [p:48241,w:0,m:0] [MainThread] Migrating 1 -> 2... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:24,745 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:24,745 [p:48241,w:0,m:0] [MainThread] Migrating 2 -> 3... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:27,040 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:27,040 [p:48241,w:0,m:0] [MainThread] Migrating 3 -> 4... | |
| /Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/default.py:507: Warning: Duplicate index 'ix_galaxy_user_deleted' defined on the table 'galaxy.galaxy_user'. This is deprecated and will be disallowed in a future release. | |
| cursor.execute(statement, parameters) | |
| /Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/default.py:507: Warning: Duplicate index 'ix_galaxy_user_purged' defined on the table 'galaxy.galaxy_user'. This is deprecated and will be disallowed in a future release. | |
| cursor.execute(statement, parameters) | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:27,208 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:27,209 [p:48241,w:0,m:0] [MainThread] Migrating 4 -> 5... | |
| 0005_cleanup_datasets_fix DEBUG 2018-06-25 16:18:27,256 [p:48241,w:0,m:0] [MainThread] Fixing a discrepancy concerning deleted shared history items. | |
| /Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/orm/relationships.py:2435: SAWarning: Non-simple column elements in primary join condition for property HistoryDatasetAssociation.visible_children - consider using remote() annotations to mark the remote side. | |
| % self.prop | |
| /Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/orm/relationships.py:2435: SAWarning: Non-simple column elements in primary join condition for property LibraryDatasetDatasetAssociation.visible_children - consider using remote() annotations to mark the remote side. | |
| % self.prop | |
| 0005_cleanup_datasets_fix DEBUG 2018-06-25 16:18:27,315 [p:48241,w:0,m:0] [MainThread] 0 items affected, and restored. | |
| 0005_cleanup_datasets_fix DEBUG 2018-06-25 16:18:27,316 [p:48241,w:0,m:0] [MainThread] Time elapsed: 0.0591819286346 | |
| 0005_cleanup_datasets_fix DEBUG 2018-06-25 16:18:27,316 [p:48241,w:0,m:0] [MainThread] Fixing a discrepancy concerning cleaning up deleted history items shared before HDAs. | |
| 0005_cleanup_datasets_fix DEBUG 2018-06-25 16:18:27,317 [p:48241,w:0,m:0] [MainThread] 0 items affected, and restored. | |
| 0005_cleanup_datasets_fix DEBUG 2018-06-25 16:18:27,317 [p:48241,w:0,m:0] [MainThread] Time elapsed: 0.00133013725281 | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:27,320 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:27,321 [p:48241,w:0,m:0] [MainThread] Migrating 5 -> 6... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:27,598 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:27,599 [p:48241,w:0,m:0] [MainThread] This migration script changes certain values in the history_dataset_association.extension | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:27,599 [p:48241,w:0,m:0] [MainThread] column, specifically 'qual' is changed to be 'qual454'. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:27,599 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:27,599 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:27,599 [p:48241,w:0,m:0] [MainThread] Migrating 6 -> 7... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:27,798 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:27,798 [p:48241,w:0,m:0] [MainThread] This migration script creates the new history_user_share_association table, and adds | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:27,798 [p:48241,w:0,m:0] [MainThread] a new boolean type column to the history table. This provides support for sharing | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:27,798 [p:48241,w:0,m:0] [MainThread] histories in the same way that workflows are shared. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:27,798 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:27,799 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:27,799 [p:48241,w:0,m:0] [MainThread] Migrating 7 -> 8... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:28,382 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:28,382 [p:48241,w:0,m:0] [MainThread] This migration script adds the following new tables for supporting Galaxy forms: | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:28,382 [p:48241,w:0,m:0] [MainThread] 1) form_definition_current | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:28,383 [p:48241,w:0,m:0] [MainThread] 2) form_definition | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:28,383 [p:48241,w:0,m:0] [MainThread] 3) form_values | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:28,383 [p:48241,w:0,m:0] [MainThread] 4) request_type | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:28,383 [p:48241,w:0,m:0] [MainThread] 5) request | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:28,383 [p:48241,w:0,m:0] [MainThread] 6) sample | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:28,383 [p:48241,w:0,m:0] [MainThread] 7) sample_state | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:28,383 [p:48241,w:0,m:0] [MainThread] 8) sample_event | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:28,383 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:28,383 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:28,383 [p:48241,w:0,m:0] [MainThread] Migrating 8 -> 9... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:28,568 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:28,568 [p:48241,w:0,m:0] [MainThread] This migration script adds a new column to 2 tables: | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:28,568 [p:48241,w:0,m:0] [MainThread] 1) a new boolean type column named 'submitted' to the 'request' table | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:28,569 [p:48241,w:0,m:0] [MainThread] 2) a new string type column named 'bar_code' to the 'sample' table | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:28,569 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:28,569 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:28,569 [p:48241,w:0,m:0] [MainThread] Migrating 9 -> 10... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:28,760 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:28,760 [p:48241,w:0,m:0] [MainThread] This migration script adds the history_dataset_association_display_at_authorization table, | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:28,760 [p:48241,w:0,m:0] [MainThread] which allows 'private' datasets to be displayed at external sites without making them public. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:28,760 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:28,761 [p:48241,w:0,m:0] [MainThread] If using mysql, this script will display the following error, which is corrected in the next | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:28,761 [p:48241,w:0,m:0] [MainThread] migration script: | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:28,761 [p:48241,w:0,m:0] [MainThread] history_dataset_association_display_at_authorization table failed: (OperationalError) | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:28,761 [p:48241,w:0,m:0] [MainThread] (1059, "Identifier name 'ix_history_dataset_association_display_at_authorization_update_time' | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:28,761 [p:48241,w:0,m:0] [MainThread] is too long | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:28,761 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:28,761 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:28,761 [p:48241,w:0,m:0] [MainThread] Migrating 10 -> 11... | |
| /Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/default.py:507: Warning: Duplicate index 'ix_hdadaa_history_dataset_association_id' defined on the table 'galaxy.history_dataset_association_display_at_authorization'. This is deprecated and will be disallowed in a future release. | |
| cursor.execute(statement, parameters) | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:28,922 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:28,922 [p:48241,w:0,m:0] [MainThread] This script fixes a problem introduced in the previous migration script | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:28,922 [p:48241,w:0,m:0] [MainThread] 0010_hda_display_at_atuhz_table.py . MySQL has a name length limit and | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:28,923 [p:48241,w:0,m:0] [MainThread] thus the index "ix_hdadaa_history_dataset_association_id" has to be | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:28,923 [p:48241,w:0,m:0] [MainThread] manually created. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:28,923 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:28,923 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:28,923 [p:48241,w:0,m:0] [MainThread] Migrating 11 -> 12... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:29,227 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:29,227 [p:48241,w:0,m:0] [MainThread] This script adds a new user_address table that is currently only used with sample requests, where | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:29,227 [p:48241,w:0,m:0] [MainThread] a user can select from a list of his addresses to associate with the request. This script also | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:29,227 [p:48241,w:0,m:0] [MainThread] drops the request.submitted column which was boolean and replaces it with a request.state column | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:29,227 [p:48241,w:0,m:0] [MainThread] which is a string, allowing for more flexibility with request states. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:29,227 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:29,227 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:29,227 [p:48241,w:0,m:0] [MainThread] Migrating 12 -> 13... | |
| /Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/default.py:507: Warning: Duplicate index 'ix_lddaia_ldda_id' defined on the table 'galaxy.library_dataset_dataset_info_association'. This is deprecated and will be disallowed in a future release. | |
| cursor.execute(statement, parameters) | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:29,613 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:29,613 [p:48241,w:0,m:0] [MainThread] This migration script eliminates all of the tables that were used for the 1st version of the | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:29,613 [p:48241,w:0,m:0] [MainThread] library templates where template fields and contents were each stored as a separate table row | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:29,614 [p:48241,w:0,m:0] [MainThread] in various library item tables. All of these tables are dropped in this script, eliminating all | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:29,614 [p:48241,w:0,m:0] [MainThread] existing template data. A total of 14 existing tables are dropped. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:29,614 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:29,614 [p:48241,w:0,m:0] [MainThread] We're now basing library templates on forms, so field contents are | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:29,614 [p:48241,w:0,m:0] [MainThread] stored as a jsonified list in the form_values table. This script introduces the following 3 | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:29,614 [p:48241,w:0,m:0] [MainThread] new association tables: | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:29,614 [p:48241,w:0,m:0] [MainThread] 1) library_info_association | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:29,614 [p:48241,w:0,m:0] [MainThread] 2) library_folder_info_association | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:29,614 [p:48241,w:0,m:0] [MainThread] 3) library_dataset_dataset_info_association | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:29,614 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:29,614 [p:48241,w:0,m:0] [MainThread] If using mysql, this script will throw an (OperationalError) exception due to a long index name on | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:29,614 [p:48241,w:0,m:0] [MainThread] the library_dataset_dataset_info_association table, which is OK because the script creates an index | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:29,614 [p:48241,w:0,m:0] [MainThread] with a shortened name. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:29,614 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:29,614 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:29,614 [p:48241,w:0,m:0] [MainThread] Migrating 13 -> 14... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:29,865 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:29,866 [p:48241,w:0,m:0] [MainThread] Migration script to add support for "Pages". | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:29,866 [p:48241,w:0,m:0] [MainThread] 1) Creates Page and PageRevision tables | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:29,866 [p:48241,w:0,m:0] [MainThread] 2) Adds username column to User table | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:29,866 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:29,866 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:29,866 [p:48241,w:0,m:0] [MainThread] Migrating 14 -> 15... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:30,461 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:30,461 [p:48241,w:0,m:0] [MainThread] This migration script adds the tables necessary to support tagging of histories, | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:30,461 [p:48241,w:0,m:0] [MainThread] datasets, and history-dataset associations (user views of datasets). | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:30,461 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:30,462 [p:48241,w:0,m:0] [MainThread] If using mysql, this script will display the following error, which is corrected in the next | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:30,462 [p:48241,w:0,m:0] [MainThread] migration script: | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:30,462 [p:48241,w:0,m:0] [MainThread] history_dataset_association_tag_association table failed: (OperationalError) | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:30,462 [p:48241,w:0,m:0] [MainThread] (1059, "Identifier name 'ix_history_dataset_association_tag_association_history_dataset_association_id' | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:30,462 [p:48241,w:0,m:0] [MainThread] is too long) | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:30,462 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:30,462 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:30,462 [p:48241,w:0,m:0] [MainThread] Migrating 15 -> 16... | |
| /Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/default.py:507: Warning: Duplicate index 'ix_hda_ta_history_dataset_association_id' defined on the table 'galaxy.history_dataset_association_tag_association'. This is deprecated and will be disallowed in a future release. | |
| cursor.execute(statement, parameters) | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:30,600 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:30,600 [p:48241,w:0,m:0] [MainThread] This script fixes a problem introduced in 0015_tagging.py. MySQL has a name length | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:30,600 [p:48241,w:0,m:0] [MainThread] limit and thus the index "ix_hda_ta_history_dataset_association_id" has to be | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:30,600 [p:48241,w:0,m:0] [MainThread] manually created. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:30,600 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:30,600 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:30,600 [p:48241,w:0,m:0] [MainThread] Migrating 16 -> 17... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:30,769 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:30,769 [p:48241,w:0,m:0] [MainThread] This script adds 3 indexes to table columns: library_folder.name, | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:30,769 [p:48241,w:0,m:0] [MainThread] library_dataset.name, library_dataset_dataset_association.name. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:30,769 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:30,769 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:30,769 [p:48241,w:0,m:0] [MainThread] Migrating 17 -> 18... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:31,284 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:31,284 [p:48241,w:0,m:0] [MainThread] This migration script provides support for (a) ordering tags by recency and | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:31,284 [p:48241,w:0,m:0] [MainThread] (b) tagging pages. This script deletes all existing tags. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:31,284 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:31,284 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:31,285 [p:48241,w:0,m:0] [MainThread] Migrating 18 -> 19... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:31,525 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:31,525 [p:48241,w:0,m:0] [MainThread] This script creates a request.folder_id column which is a foreign | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:31,525 [p:48241,w:0,m:0] [MainThread] key to the library_folder table. This also adds a 'type' and 'layout' column | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:31,526 [p:48241,w:0,m:0] [MainThread] to the form_definition table. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:31,526 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:31,526 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:31,526 [p:48241,w:0,m:0] [MainThread] Migrating 19 -> 20... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:31,781 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:31,781 [p:48241,w:0,m:0] [MainThread] This script creates a job_to_output_library_dataset table for allowing library | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:31,781 [p:48241,w:0,m:0] [MainThread] uploads to run as regular jobs. To support this, a library_folder_id column is | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:31,781 [p:48241,w:0,m:0] [MainThread] added to the job table, and library_folder/output_library_datasets relations | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:31,782 [p:48241,w:0,m:0] [MainThread] are added to the Job object. An index is also added to the dataset.state | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:31,782 [p:48241,w:0,m:0] [MainThread] column. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:31,782 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:31,782 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:31,782 [p:48241,w:0,m:0] [MainThread] Migrating 20 -> 21... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:31,962 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:31,962 [p:48241,w:0,m:0] [MainThread] This migration script adds a user preferences table to Galaxy. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:31,962 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:31,962 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:31,962 [p:48241,w:0,m:0] [MainThread] Migrating 21 -> 22... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:32,172 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:32,172 [p:48241,w:0,m:0] [MainThread] Migration script to add support for storing visualizations. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:32,172 [p:48241,w:0,m:0] [MainThread] 1) Creates Visualization and VisualizationRevision tables | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:32,172 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:32,172 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:32,173 [p:48241,w:0,m:0] [MainThread] Migrating 22 -> 23... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:32,377 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:32,377 [p:48241,w:0,m:0] [MainThread] Migration script to add columns for tracking whether pages are deleted and | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:32,377 [p:48241,w:0,m:0] [MainThread] publicly accessible. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:32,377 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:32,377 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:32,377 [p:48241,w:0,m:0] [MainThread] Migrating 23 -> 24... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:32,549 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:32,550 [p:48241,w:0,m:0] [MainThread] Remove unique constraint from page slugs to allow creating a page with | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:32,550 [p:48241,w:0,m:0] [MainThread] the same slug as a deleted page. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:32,550 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:32,550 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:32,550 [p:48241,w:0,m:0] [MainThread] Migrating 24 -> 25... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:32,902 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:32,903 [p:48241,w:0,m:0] [MainThread] This script adds a foreign key to the form_values table in the galaxy_user table | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:32,903 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:32,903 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:32,903 [p:48241,w:0,m:0] [MainThread] Migrating 25 -> 26... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:33,410 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:33,410 [p:48241,w:0,m:0] [MainThread] This script adds tables needed for Galaxy cloud functionality. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:33,410 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:33,410 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:33,410 [p:48241,w:0,m:0] [MainThread] Migrating 26 -> 27... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:33,634 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:33,634 [p:48241,w:0,m:0] [MainThread] This migration script adds the request_event table and | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:33,634 [p:48241,w:0,m:0] [MainThread] removes the state field in the request table | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:33,634 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:33,634 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:33,634 [p:48241,w:0,m:0] [MainThread] Migrating 27 -> 28... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:33,800 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:33,800 [p:48241,w:0,m:0] [MainThread] This script adds the filename_override_metadata column to the JobExternalOutputMetadata table, | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:33,800 [p:48241,w:0,m:0] [MainThread] allowing existing metadata files to be written when using external metadata and a cluster | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:33,800 [p:48241,w:0,m:0] [MainThread] set up with read-only access to database/files | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:33,800 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:33,800 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:33,800 [p:48241,w:0,m:0] [MainThread] Migrating 28 -> 29... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:33,998 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:33,998 [p:48241,w:0,m:0] [MainThread] This migration script adds a user actions table to Galaxy. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:33,998 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:33,998 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:33,999 [p:48241,w:0,m:0] [MainThread] Migrating 29 -> 30... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:34,180 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:34,180 [p:48241,w:0,m:0] [MainThread] Migration script to add column for a history slug. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:34,180 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:34,180 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:34,180 [p:48241,w:0,m:0] [MainThread] Migrating 30 -> 31... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:34,776 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:34,776 [p:48241,w:0,m:0] [MainThread] Migration script to (a) add and populate necessary columns for doing community tagging of histories, datasets, and pages and (b) add table for doing individual and community tagging of workflows. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:34,776 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:34,777 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:34,777 [p:48241,w:0,m:0] [MainThread] Migrating 31 -> 32... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:34,964 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:34,964 [p:48241,w:0,m:0] [MainThread] Migration script to add slug column for stored workflow. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:34,965 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:34,965 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:34,965 [p:48241,w:0,m:0] [MainThread] Migrating 32 -> 33... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:35,291 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:35,291 [p:48241,w:0,m:0] [MainThread] Migration script to add necessary columns for distinguishing between viewing/importing and publishing histories, workflows, and pages. Script adds published column to histories and workflows and importable column to pages. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:35,291 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:35,291 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:35,291 [p:48241,w:0,m:0] [MainThread] Migrating 33 -> 34... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:35,502 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:35,502 [p:48241,w:0,m:0] [MainThread] Migration script to create a table for page-user share association. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:35,502 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:35,502 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:35,502 [p:48241,w:0,m:0] [MainThread] Migrating 34 -> 35... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,296 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,296 [p:48241,w:0,m:0] [MainThread] Migration script to (a) create tables for annotating objects and (b) create tags for workflow steps. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,296 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,296 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,296 [p:48241,w:0,m:0] [MainThread] Migrating 35 -> 36... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,580 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,580 [p:48241,w:0,m:0] [MainThread] Migration script to add a deleted column to the following tables: | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,580 [p:48241,w:0,m:0] [MainThread] library_info_association, library_folder_info_association, library_dataset_dataset_info_association. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,580 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,581 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,581 [p:48241,w:0,m:0] [MainThread] Migrating 36 -> 37... | |
| 0037_samples_library ERROR 2018-06-25 16:18:36,777 [p:48241,w:0,m:0] [MainThread] Deleting column 'library_id' to request table failed. | |
| Traceback (most recent call last): | |
| File "lib/galaxy/model/migrate/versions/0037_samples_library.py", line 91, in upgrade | |
| Request_table.c.library_id.drop() | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/migrate/changeset/schema.py", line 598, in drop | |
| engine._run_visitor(visitorcallable, self, connection, **kwargs) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1940, in _run_visitor | |
| conn._run_visitor(visitorcallable, element, **kwargs) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1549, in _run_visitor | |
| **kwargs).traverse_single(element) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/migrate/changeset/ansisql.py", line 56, in traverse_single | |
| ret = super(AlterTableVisitor, self).traverse_single(elem) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/sql/visitors.py", line 121, in traverse_single | |
| return meth(obj, **kw) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/migrate/changeset/ansisql.py", line 141, in visit_column | |
| self.execute() | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/migrate/changeset/ansisql.py", line 44, in execute | |
| return self.connection.execute(self.buffer.getvalue()) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 942, in execute | |
| return self._execute_text(object, multiparams, params) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1104, in _execute_text | |
| statement, parameters | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1200, in _execute_context | |
| context) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1413, in _handle_dbapi_exception | |
| exc_info | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/util/compat.py", line 203, in raise_from_cause | |
| reraise(type(exception), exception, tb=exc_tb, cause=cause) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1193, in _execute_context | |
| context) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/default.py", line 507, in do_execute | |
| cursor.execute(statement, parameters) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/MySQLdb/cursors.py", line 205, in execute | |
| self.errorhandler(self, exc, value) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/MySQLdb/connections.py", line 36, in defaulterrorhandler | |
| raise errorclass, errorvalue | |
| OperationalError: (_mysql_exceptions.OperationalError) (1553, "Cannot drop index 'ix_request_library_id': needed in a foreign key constraint") [SQL: u'\nALTER TABLE request DROP COLUMN library_id'] (Background on this error at: http://sqlalche.me/e/e3q8) | |
| 0037_samples_library ERROR 2018-06-25 16:18:36,796 [p:48241,w:0,m:0] [MainThread] Deleting column 'folder_id' to request table failed. | |
| Traceback (most recent call last): | |
| File "lib/galaxy/model/migrate/versions/0037_samples_library.py", line 96, in upgrade | |
| Request_table.c.folder_id.drop() | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/migrate/changeset/schema.py", line 598, in drop | |
| engine._run_visitor(visitorcallable, self, connection, **kwargs) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1940, in _run_visitor | |
| conn._run_visitor(visitorcallable, element, **kwargs) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1549, in _run_visitor | |
| **kwargs).traverse_single(element) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/migrate/changeset/ansisql.py", line 56, in traverse_single | |
| ret = super(AlterTableVisitor, self).traverse_single(elem) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/sql/visitors.py", line 121, in traverse_single | |
| return meth(obj, **kw) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/migrate/changeset/ansisql.py", line 141, in visit_column | |
| self.execute() | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/migrate/changeset/ansisql.py", line 44, in execute | |
| return self.connection.execute(self.buffer.getvalue()) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 942, in execute | |
| return self._execute_text(object, multiparams, params) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1104, in _execute_text | |
| statement, parameters | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1200, in _execute_context | |
| context) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1413, in _handle_dbapi_exception | |
| exc_info | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/util/compat.py", line 203, in raise_from_cause | |
| reraise(type(exception), exception, tb=exc_tb, cause=cause) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1193, in _execute_context | |
| context) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/default.py", line 507, in do_execute | |
| cursor.execute(statement, parameters) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/MySQLdb/cursors.py", line 205, in execute | |
| self.errorhandler(self, exc, value) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/MySQLdb/connections.py", line 36, in defaulterrorhandler | |
| raise errorclass, errorvalue | |
| OperationalError: (_mysql_exceptions.OperationalError) (1553, "Cannot drop index 'ix_request_folder_id': needed in a foreign key constraint") [SQL: u'\nALTER TABLE request DROP COLUMN folder_id'] (Background on this error at: http://sqlalche.me/e/e3q8) | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,946 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,946 [p:48241,w:0,m:0] [MainThread] This migration script removes the library_id & folder_id fields in the 'request' table and | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,946 [p:48241,w:0,m:0] [MainThread] adds the same to the 'sample' table. This also adds a 'datatx' column to request_type table | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,946 [p:48241,w:0,m:0] [MainThread] to store the sequencer login information. Finally, this adds a 'dataset_files' column to | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,946 [p:48241,w:0,m:0] [MainThread] the sample table. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,946 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,946 [p:48241,w:0,m:0] [MainThread] 0037_samples_library ERROR 2018-06-25 16:18:36,777 Deleting column 'library_id' to request table failed. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,946 [p:48241,w:0,m:0] [MainThread] Traceback (most recent call last): | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,946 [p:48241,w:0,m:0] [MainThread] File "lib/galaxy/model/migrate/versions/0037_samples_library.py", line 91, in upgrade | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,946 [p:48241,w:0,m:0] [MainThread] Request_table.c.library_id.drop() | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,946 [p:48241,w:0,m:0] [MainThread] File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/migrate/changeset/schema.py", line 598, in drop | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,946 [p:48241,w:0,m:0] [MainThread] engine._run_visitor(visitorcallable, self, connection, **kwargs) | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,946 [p:48241,w:0,m:0] [MainThread] File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1940, in _run_visitor | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,946 [p:48241,w:0,m:0] [MainThread] conn._run_visitor(visitorcallable, element, **kwargs) | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,946 [p:48241,w:0,m:0] [MainThread] File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1549, in _run_visitor | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,946 [p:48241,w:0,m:0] [MainThread] **kwargs).traverse_single(element) | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,946 [p:48241,w:0,m:0] [MainThread] File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/migrate/changeset/ansisql.py", line 56, in traverse_single | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,947 [p:48241,w:0,m:0] [MainThread] ret = super(AlterTableVisitor, self).traverse_single(elem) | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,947 [p:48241,w:0,m:0] [MainThread] File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/sql/visitors.py", line 121, in traverse_single | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,947 [p:48241,w:0,m:0] [MainThread] return meth(obj, **kw) | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,947 [p:48241,w:0,m:0] [MainThread] File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/migrate/changeset/ansisql.py", line 141, in visit_column | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,947 [p:48241,w:0,m:0] [MainThread] self.execute() | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,947 [p:48241,w:0,m:0] [MainThread] File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/migrate/changeset/ansisql.py", line 44, in execute | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,947 [p:48241,w:0,m:0] [MainThread] return self.connection.execute(self.buffer.getvalue()) | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,947 [p:48241,w:0,m:0] [MainThread] File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 942, in execute | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,947 [p:48241,w:0,m:0] [MainThread] return self._execute_text(object, multiparams, params) | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,947 [p:48241,w:0,m:0] [MainThread] File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1104, in _execute_text | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,947 [p:48241,w:0,m:0] [MainThread] statement, parameters | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,947 [p:48241,w:0,m:0] [MainThread] File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1200, in _execute_context | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,947 [p:48241,w:0,m:0] [MainThread] context) | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,947 [p:48241,w:0,m:0] [MainThread] File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1413, in _handle_dbapi_exception | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,947 [p:48241,w:0,m:0] [MainThread] exc_info | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,947 [p:48241,w:0,m:0] [MainThread] File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/util/compat.py", line 203, in raise_from_cause | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,947 [p:48241,w:0,m:0] [MainThread] reraise(type(exception), exception, tb=exc_tb, cause=cause) | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,947 [p:48241,w:0,m:0] [MainThread] File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1193, in _execute_context | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,947 [p:48241,w:0,m:0] [MainThread] context) | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,947 [p:48241,w:0,m:0] [MainThread] File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/default.py", line 507, in do_execute | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,947 [p:48241,w:0,m:0] [MainThread] cursor.execute(statement, parameters) | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,947 [p:48241,w:0,m:0] [MainThread] File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/MySQLdb/cursors.py", line 205, in execute | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,947 [p:48241,w:0,m:0] [MainThread] self.errorhandler(self, exc, value) | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,947 [p:48241,w:0,m:0] [MainThread] File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/MySQLdb/connections.py", line 36, in defaulterrorhandler | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,947 [p:48241,w:0,m:0] [MainThread] raise errorclass, errorvalue | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,948 [p:48241,w:0,m:0] [MainThread] OperationalError: (_mysql_exceptions.OperationalError) (1553, "Cannot drop index 'ix_request_library_id': needed in a foreign key constraint") [SQL: u'\nALTER TABLE request DROP COLUMN library_id'] (Background on this error at: http://sqlalche.me/e/e3q8) | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,948 [p:48241,w:0,m:0] [MainThread] 0037_samples_library ERROR 2018-06-25 16:18:36,777 Deleting column 'library_id' to request table failed. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,948 [p:48241,w:0,m:0] [MainThread] Traceback (most recent call last): | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,948 [p:48241,w:0,m:0] [MainThread] File "lib/galaxy/model/migrate/versions/0037_samples_library.py", line 91, in upgrade | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,948 [p:48241,w:0,m:0] [MainThread] Request_table.c.library_id.drop() | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,948 [p:48241,w:0,m:0] [MainThread] File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/migrate/changeset/schema.py", line 598, in drop | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,948 [p:48241,w:0,m:0] [MainThread] engine._run_visitor(visitorcallable, self, connection, **kwargs) | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,948 [p:48241,w:0,m:0] [MainThread] File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1940, in _run_visitor | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,948 [p:48241,w:0,m:0] [MainThread] conn._run_visitor(visitorcallable, element, **kwargs) | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,948 [p:48241,w:0,m:0] [MainThread] File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1549, in _run_visitor | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,948 [p:48241,w:0,m:0] [MainThread] **kwargs).traverse_single(element) | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,948 [p:48241,w:0,m:0] [MainThread] File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/migrate/changeset/ansisql.py", line 56, in traverse_single | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,948 [p:48241,w:0,m:0] [MainThread] ret = super(AlterTableVisitor, self).traverse_single(elem) | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,948 [p:48241,w:0,m:0] [MainThread] File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/sql/visitors.py", line 121, in traverse_single | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,948 [p:48241,w:0,m:0] [MainThread] return meth(obj, **kw) | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,948 [p:48241,w:0,m:0] [MainThread] File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/migrate/changeset/ansisql.py", line 141, in visit_column | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,948 [p:48241,w:0,m:0] [MainThread] self.execute() | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,948 [p:48241,w:0,m:0] [MainThread] File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/migrate/changeset/ansisql.py", line 44, in execute | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,948 [p:48241,w:0,m:0] [MainThread] return self.connection.execute(self.buffer.getvalue()) | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,948 [p:48241,w:0,m:0] [MainThread] File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 942, in execute | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,948 [p:48241,w:0,m:0] [MainThread] return self._execute_text(object, multiparams, params) | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,948 [p:48241,w:0,m:0] [MainThread] File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1104, in _execute_text | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,948 [p:48241,w:0,m:0] [MainThread] statement, parameters | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,948 [p:48241,w:0,m:0] [MainThread] File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1200, in _execute_context | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,949 [p:48241,w:0,m:0] [MainThread] context) | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,949 [p:48241,w:0,m:0] [MainThread] File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1413, in _handle_dbapi_exception | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,949 [p:48241,w:0,m:0] [MainThread] exc_info | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,949 [p:48241,w:0,m:0] [MainThread] File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/util/compat.py", line 203, in raise_from_cause | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,949 [p:48241,w:0,m:0] [MainThread] reraise(type(exception), exception, tb=exc_tb, cause=cause) | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,949 [p:48241,w:0,m:0] [MainThread] File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1193, in _execute_context | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,949 [p:48241,w:0,m:0] [MainThread] context) | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,949 [p:48241,w:0,m:0] [MainThread] File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/default.py", line 507, in do_execute | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,949 [p:48241,w:0,m:0] [MainThread] cursor.execute(statement, parameters) | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,949 [p:48241,w:0,m:0] [MainThread] File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/MySQLdb/cursors.py", line 205, in execute | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,949 [p:48241,w:0,m:0] [MainThread] self.errorhandler(self, exc, value) | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,949 [p:48241,w:0,m:0] [MainThread] File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/MySQLdb/connections.py", line 36, in defaulterrorhandler | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,949 [p:48241,w:0,m:0] [MainThread] raise errorclass, errorvalue | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,950 [p:48241,w:0,m:0] [MainThread] OperationalError: (_mysql_exceptions.OperationalError) (1553, "Cannot drop index 'ix_request_library_id': needed in a foreign key constraint") [SQL: u'\nALTER TABLE request DROP COLUMN library_id'] (Background on this error at: http://sqlalche.me/e/e3q8) | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,962 [p:48241,w:0,m:0] [MainThread] 0037_samples_library ERROR 2018-06-25 16:18:36,796 Deleting column 'folder_id' to request table failed. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,962 [p:48241,w:0,m:0] [MainThread] Traceback (most recent call last): | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,962 [p:48241,w:0,m:0] [MainThread] File "lib/galaxy/model/migrate/versions/0037_samples_library.py", line 96, in upgrade | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,962 [p:48241,w:0,m:0] [MainThread] Request_table.c.folder_id.drop() | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,962 [p:48241,w:0,m:0] [MainThread] File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/migrate/changeset/schema.py", line 598, in drop | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,962 [p:48241,w:0,m:0] [MainThread] engine._run_visitor(visitorcallable, self, connection, **kwargs) | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,962 [p:48241,w:0,m:0] [MainThread] File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1940, in _run_visitor | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,962 [p:48241,w:0,m:0] [MainThread] conn._run_visitor(visitorcallable, element, **kwargs) | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,962 [p:48241,w:0,m:0] [MainThread] File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1549, in _run_visitor | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,962 [p:48241,w:0,m:0] [MainThread] **kwargs).traverse_single(element) | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,962 [p:48241,w:0,m:0] [MainThread] File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/migrate/changeset/ansisql.py", line 56, in traverse_single | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,963 [p:48241,w:0,m:0] [MainThread] ret = super(AlterTableVisitor, self).traverse_single(elem) | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,963 [p:48241,w:0,m:0] [MainThread] File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/sql/visitors.py", line 121, in traverse_single | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,963 [p:48241,w:0,m:0] [MainThread] return meth(obj, **kw) | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,963 [p:48241,w:0,m:0] [MainThread] File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/migrate/changeset/ansisql.py", line 141, in visit_column | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,963 [p:48241,w:0,m:0] [MainThread] self.execute() | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,963 [p:48241,w:0,m:0] [MainThread] File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/migrate/changeset/ansisql.py", line 44, in execute | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,963 [p:48241,w:0,m:0] [MainThread] return self.connection.execute(self.buffer.getvalue()) | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,963 [p:48241,w:0,m:0] [MainThread] File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 942, in execute | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,963 [p:48241,w:0,m:0] [MainThread] return self._execute_text(object, multiparams, params) | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,963 [p:48241,w:0,m:0] [MainThread] File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1104, in _execute_text | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,963 [p:48241,w:0,m:0] [MainThread] statement, parameters | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,963 [p:48241,w:0,m:0] [MainThread] File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1200, in _execute_context | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,963 [p:48241,w:0,m:0] [MainThread] context) | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,963 [p:48241,w:0,m:0] [MainThread] File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1413, in _handle_dbapi_exception | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,963 [p:48241,w:0,m:0] [MainThread] exc_info | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,963 [p:48241,w:0,m:0] [MainThread] File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/util/compat.py", line 203, in raise_from_cause | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,963 [p:48241,w:0,m:0] [MainThread] reraise(type(exception), exception, tb=exc_tb, cause=cause) | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,963 [p:48241,w:0,m:0] [MainThread] File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1193, in _execute_context | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,963 [p:48241,w:0,m:0] [MainThread] context) | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,963 [p:48241,w:0,m:0] [MainThread] File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/default.py", line 507, in do_execute | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,963 [p:48241,w:0,m:0] [MainThread] cursor.execute(statement, parameters) | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,963 [p:48241,w:0,m:0] [MainThread] File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/MySQLdb/cursors.py", line 205, in execute | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,963 [p:48241,w:0,m:0] [MainThread] self.errorhandler(self, exc, value) | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,963 [p:48241,w:0,m:0] [MainThread] File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/MySQLdb/connections.py", line 36, in defaulterrorhandler | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,963 [p:48241,w:0,m:0] [MainThread] raise errorclass, errorvalue | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,963 [p:48241,w:0,m:0] [MainThread] OperationalError: (_mysql_exceptions.OperationalError) (1553, "Cannot drop index 'ix_request_folder_id': needed in a foreign key constraint") [SQL: u'\nALTER TABLE request DROP COLUMN folder_id'] (Background on this error at: http://sqlalche.me/e/e3q8) | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,964 [p:48241,w:0,m:0] [MainThread] 0037_samples_library ERROR 2018-06-25 16:18:36,796 Deleting column 'folder_id' to request table failed. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,964 [p:48241,w:0,m:0] [MainThread] Traceback (most recent call last): | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,964 [p:48241,w:0,m:0] [MainThread] File "lib/galaxy/model/migrate/versions/0037_samples_library.py", line 96, in upgrade | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,964 [p:48241,w:0,m:0] [MainThread] Request_table.c.folder_id.drop() | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,964 [p:48241,w:0,m:0] [MainThread] File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/migrate/changeset/schema.py", line 598, in drop | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,964 [p:48241,w:0,m:0] [MainThread] engine._run_visitor(visitorcallable, self, connection, **kwargs) | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,964 [p:48241,w:0,m:0] [MainThread] File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1940, in _run_visitor | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,964 [p:48241,w:0,m:0] [MainThread] conn._run_visitor(visitorcallable, element, **kwargs) | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,964 [p:48241,w:0,m:0] [MainThread] File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1549, in _run_visitor | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,964 [p:48241,w:0,m:0] [MainThread] **kwargs).traverse_single(element) | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,964 [p:48241,w:0,m:0] [MainThread] File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/migrate/changeset/ansisql.py", line 56, in traverse_single | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,964 [p:48241,w:0,m:0] [MainThread] ret = super(AlterTableVisitor, self).traverse_single(elem) | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,964 [p:48241,w:0,m:0] [MainThread] File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/sql/visitors.py", line 121, in traverse_single | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,964 [p:48241,w:0,m:0] [MainThread] return meth(obj, **kw) | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,964 [p:48241,w:0,m:0] [MainThread] File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/migrate/changeset/ansisql.py", line 141, in visit_column | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,964 [p:48241,w:0,m:0] [MainThread] self.execute() | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,964 [p:48241,w:0,m:0] [MainThread] File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/migrate/changeset/ansisql.py", line 44, in execute | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,964 [p:48241,w:0,m:0] [MainThread] return self.connection.execute(self.buffer.getvalue()) | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,964 [p:48241,w:0,m:0] [MainThread] File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 942, in execute | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,964 [p:48241,w:0,m:0] [MainThread] return self._execute_text(object, multiparams, params) | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,964 [p:48241,w:0,m:0] [MainThread] File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1104, in _execute_text | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,964 [p:48241,w:0,m:0] [MainThread] statement, parameters | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,964 [p:48241,w:0,m:0] [MainThread] File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1200, in _execute_context | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,964 [p:48241,w:0,m:0] [MainThread] context) | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,964 [p:48241,w:0,m:0] [MainThread] File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1413, in _handle_dbapi_exception | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,964 [p:48241,w:0,m:0] [MainThread] exc_info | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,965 [p:48241,w:0,m:0] [MainThread] File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/util/compat.py", line 203, in raise_from_cause | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,965 [p:48241,w:0,m:0] [MainThread] reraise(type(exception), exception, tb=exc_tb, cause=cause) | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,965 [p:48241,w:0,m:0] [MainThread] File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1193, in _execute_context | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,965 [p:48241,w:0,m:0] [MainThread] context) | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,965 [p:48241,w:0,m:0] [MainThread] File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/default.py", line 507, in do_execute | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,965 [p:48241,w:0,m:0] [MainThread] cursor.execute(statement, parameters) | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,965 [p:48241,w:0,m:0] [MainThread] File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/MySQLdb/cursors.py", line 205, in execute | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,965 [p:48241,w:0,m:0] [MainThread] self.errorhandler(self, exc, value) | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,965 [p:48241,w:0,m:0] [MainThread] File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/MySQLdb/connections.py", line 36, in defaulterrorhandler | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,965 [p:48241,w:0,m:0] [MainThread] raise errorclass, errorvalue | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,965 [p:48241,w:0,m:0] [MainThread] OperationalError: (_mysql_exceptions.OperationalError) (1553, "Cannot drop index 'ix_request_folder_id': needed in a foreign key constraint") [SQL: u'\nALTER TABLE request DROP COLUMN folder_id'] (Background on this error at: http://sqlalche.me/e/e3q8) | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,965 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:36,965 [p:48241,w:0,m:0] [MainThread] Migrating 37 -> 38... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:37,211 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:37,211 [p:48241,w:0,m:0] [MainThread] Migration script to add an inheritable column to the following tables: | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:37,211 [p:48241,w:0,m:0] [MainThread] library_info_association, library_folder_info_association. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:37,211 [p:48241,w:0,m:0] [MainThread] Also, in case of sqlite check if the previous migration script deleted the | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:37,211 [p:48241,w:0,m:0] [MainThread] request table and if so, restore the table. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:37,211 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:37,211 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:37,212 [p:48241,w:0,m:0] [MainThread] Migrating 38 -> 39... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:37,398 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:37,398 [p:48241,w:0,m:0] [MainThread] Migration script to add a synopsis column to the library table. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:37,398 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:37,398 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:37,398 [p:48241,w:0,m:0] [MainThread] Migrating 39 -> 40... | |
| 0040_page_annotations ERROR 2018-06-25 16:18:37,596 [p:48241,w:0,m:0] [MainThread] Creating page_annotation_association table failed. | |
| Traceback (most recent call last): | |
| File "lib/galaxy/model/migrate/versions/0040_page_annotations.py", line 27, in upgrade | |
| PageAnnotationAssociation_table.create() | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/sql/schema.py", line 778, in create | |
| checkfirst=checkfirst) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1940, in _run_visitor | |
| conn._run_visitor(visitorcallable, element, **kwargs) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1549, in _run_visitor | |
| **kwargs).traverse_single(element) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/sql/visitors.py", line 121, in traverse_single | |
| return meth(obj, **kw) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/sql/ddl.py", line 796, in visit_table | |
| self.traverse_single(index) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/sql/visitors.py", line 121, in traverse_single | |
| return meth(obj, **kw) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/sql/ddl.py", line 823, in visit_index | |
| self.connection.execute(CreateIndex(index)) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 948, in execute | |
| return meth(self, multiparams, params) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/sql/ddl.py", line 68, in _execute_on_connection | |
| return connection._execute_ddl(self, multiparams, params) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1009, in _execute_ddl | |
| compiled | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1200, in _execute_context | |
| context) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1413, in _handle_dbapi_exception | |
| exc_info | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/util/compat.py", line 203, in raise_from_cause | |
| reraise(type(exception), exception, tb=exc_tb, cause=cause) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1193, in _execute_context | |
| context) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/default.py", line 507, in do_execute | |
| cursor.execute(statement, parameters) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/MySQLdb/cursors.py", line 205, in execute | |
| self.errorhandler(self, exc, value) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/MySQLdb/connections.py", line 36, in defaulterrorhandler | |
| raise errorclass, errorvalue | |
| OperationalError: (_mysql_exceptions.OperationalError) (1170, "BLOB/TEXT column 'annotation' used in key specification without a key length") [SQL: u'CREATE INDEX ix_page_annotation_association_annotation ON page_annotation_association (annotation)'] (Background on this error at: http://sqlalche.me/e/e3q8) | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:37,610 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:37,610 [p:48241,w:0,m:0] [MainThread] Migration script to (a) create tables for annotating pages. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:37,610 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:37,610 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:37,610 [p:48241,w:0,m:0] [MainThread] Migrating 40 -> 41... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:37,888 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:37,888 [p:48241,w:0,m:0] [MainThread] Migration script to create tables for tracking workflow invocations. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:37,888 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:37,888 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:37,888 [p:48241,w:0,m:0] [MainThread] Migrating 41 -> 42... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:38,166 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:38,166 [p:48241,w:0,m:0] [MainThread] Drop and readd workflow invocation tables, allowing null jobs | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:38,166 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:38,166 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:38,167 [p:48241,w:0,m:0] [MainThread] Migrating 42 -> 43... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:38,736 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:38,736 [p:48241,w:0,m:0] [MainThread] Migration script to create tables and columns for sharing visualizations. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:38,736 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:38,736 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:38,736 [p:48241,w:0,m:0] [MainThread] Migrating 43 -> 44... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:38,931 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:38,931 [p:48241,w:0,m:0] [MainThread] Migration script to add a notify column to the request table. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:38,931 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:38,931 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:38,931 [p:48241,w:0,m:0] [MainThread] Migrating 44 -> 45... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:39,414 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:39,414 [p:48241,w:0,m:0] [MainThread] Migration script to add the request_type_permissions table. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:39,414 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:39,414 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:39,415 [p:48241,w:0,m:0] [MainThread] Migrating 45 -> 46... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:39,625 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:39,625 [p:48241,w:0,m:0] [MainThread] Migration script to create tables for handling post-job actions. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:39,625 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:39,625 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:39,625 [p:48241,w:0,m:0] [MainThread] Migrating 46 -> 47... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:39,871 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:39,871 [p:48241,w:0,m:0] [MainThread] Add a user_id column to the job table. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:39,871 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:39,871 [p:48241,w:0,m:0] [MainThread] Updating user_id column in job table for 0 rows... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:39,871 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:39,872 [p:48241,w:0,m:0] [MainThread] Updated the user_id column for 0 rows in the job table. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:39,872 [p:48241,w:0,m:0] [MainThread] 0 rows have no user_id since the value was NULL in the galaxy_session table. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:39,872 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:39,872 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:39,872 [p:48241,w:0,m:0] [MainThread] Migrating 47 -> 48... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:40,130 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:40,130 [p:48241,w:0,m:0] [MainThread] Add a state column to the history_dataset_association and library_dataset_dataset_association table. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:40,130 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:40,130 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:40,130 [p:48241,w:0,m:0] [MainThread] Migrating 48 -> 49... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:40,375 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:40,375 [p:48241,w:0,m:0] [MainThread] Migration script to add the api_keys table. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:40,375 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:40,375 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:40,375 [p:48241,w:0,m:0] [MainThread] Migrating 49 -> 50... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:40,587 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:40,588 [p:48241,w:0,m:0] [MainThread] This script drops tables that were associated with the old Galaxy Cloud functionality. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:40,588 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:40,588 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:40,588 [p:48241,w:0,m:0] [MainThread] Migrating 50 -> 51... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:40,825 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:40,825 [p:48241,w:0,m:0] [MainThread] Migration script to add imported column for jobs table. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:40,826 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:40,826 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:40,826 [p:48241,w:0,m:0] [MainThread] Migrating 51 -> 52... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:41,052 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:41,052 [p:48241,w:0,m:0] [MainThread] Migration script to add the sample_dataset table and remove the 'dataset_files' column | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:41,052 [p:48241,w:0,m:0] [MainThread] from the 'sample' table | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:41,053 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:41,053 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:41,053 [p:48241,w:0,m:0] [MainThread] Migrating 52 -> 53... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:41,591 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:41,591 [p:48241,w:0,m:0] [MainThread] Migration script to create tables for rating histories, datasets, workflows, pages, and visualizations. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:41,591 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:41,591 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:41,591 [p:48241,w:0,m:0] [MainThread] Migrating 53 -> 54... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:41,856 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:41,856 [p:48241,w:0,m:0] [MainThread] Migration script to add dbkey column for visualization. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:41,856 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:41,856 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:41,856 [p:48241,w:0,m:0] [MainThread] Migrating 54 -> 55... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:42,093 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:42,094 [p:48241,w:0,m:0] [MainThread] Migration script to add the post_job_action_association table. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:42,094 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:42,094 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:42,094 [p:48241,w:0,m:0] [MainThread] Migrating 55 -> 56... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:42,312 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:42,312 [p:48241,w:0,m:0] [MainThread] Migration script to create tables for adding explicit workflow outputs. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:42,312 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:42,312 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:42,313 [p:48241,w:0,m:0] [MainThread] Migrating 56 -> 57... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:42,857 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:42,857 [p:48241,w:0,m:0] [MainThread] Migration script to modify the 'notify' field in the 'request' table from a boolean | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:42,857 [p:48241,w:0,m:0] [MainThread] to a JSONType | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:42,857 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:42,857 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:42,857 [p:48241,w:0,m:0] [MainThread] Migrating 57 -> 58... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:43,135 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:43,136 [p:48241,w:0,m:0] [MainThread] Migration script to create table for exporting histories to archives. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:43,136 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:43,136 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:43,136 [p:48241,w:0,m:0] [MainThread] Migrating 58 -> 59... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:43,364 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:43,364 [p:48241,w:0,m:0] [MainThread] Migration script to modify the 'file_path' field type in 'sample_dataset' table | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:43,364 [p:48241,w:0,m:0] [MainThread] to 'TEXT' so that it can support large file paths exceeding 255 characters | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:43,364 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:43,365 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:43,365 [p:48241,w:0,m:0] [MainThread] Migrating 59 -> 60... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:43,639 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:43,639 [p:48241,w:0,m:0] [MainThread] Migration script to create column and table for importing histories from | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:43,640 [p:48241,w:0,m:0] [MainThread] file archives. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:43,640 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:43,640 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:43,640 [p:48241,w:0,m:0] [MainThread] Migrating 60 -> 61... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:43,878 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:43,878 [p:48241,w:0,m:0] [MainThread] Migration script to create tables task management. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:43,879 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:43,879 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:43,879 [p:48241,w:0,m:0] [MainThread] Migrating 61 -> 62... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:44,155 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:44,155 [p:48241,w:0,m:0] [MainThread] Migration script to create table for associating sessions and users with | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:44,155 [p:48241,w:0,m:0] [MainThread] OpenIDs. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:44,155 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:44,155 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:44,155 [p:48241,w:0,m:0] [MainThread] Migrating 62 -> 63... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:44,451 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:44,451 [p:48241,w:0,m:0] [MainThread] Migration script to create a new 'sequencer' table | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:44,451 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:44,451 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:44,451 [p:48241,w:0,m:0] [MainThread] Migrating 63 -> 64... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:44,810 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:44,810 [p:48241,w:0,m:0] [MainThread] Migration script to add the run and sample_run_association tables. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:44,810 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:44,810 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:44,810 [p:48241,w:0,m:0] [MainThread] Migrating 64 -> 65... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:45,011 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:45,011 [p:48241,w:0,m:0] [MainThread] Migration script to add 'name' attribute to the JSON dict which describes | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:45,011 [p:48241,w:0,m:0] [MainThread] a form definition field and the form values in the database. In the 'form_values' | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:45,011 [p:48241,w:0,m:0] [MainThread] table, the 'content' column is now a JSON dict instead of a list. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:45,011 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:45,011 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:45,011 [p:48241,w:0,m:0] [MainThread] Migrating 65 -> 66... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:45,288 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:45,288 [p:48241,w:0,m:0] [MainThread] Migration script to create table for storing deferred job and managed transfer | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:45,288 [p:48241,w:0,m:0] [MainThread] information. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:45,288 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:45,288 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:45,288 [p:48241,w:0,m:0] [MainThread] Migrating 66 -> 67... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:45,557 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:45,557 [p:48241,w:0,m:0] [MainThread] Migration script to populate the 'sequencer' table and it is populated using unique | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:45,557 [p:48241,w:0,m:0] [MainThread] entries in the 'datatx_info' column in the 'request_type' table. It also deletes the 'datatx_info' | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:45,557 [p:48241,w:0,m:0] [MainThread] column in the 'request_type' table and adds a foreign key to the 'sequencer' table. The | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:45,557 [p:48241,w:0,m:0] [MainThread] actual contents of the datatx_info column are stored as form_values. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:45,557 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:45,557 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:45,557 [p:48241,w:0,m:0] [MainThread] Migrating 67 -> 68... | |
| 0068_rename_sequencer_to_external_services ERROR 2018-06-25 16:18:45,931 [p:48241,w:0,m:0] [MainThread] Deleting column 'sequencer_id' from the 'request_type' table failed. | |
| Traceback (most recent call last): | |
| File "lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py", line 133, in upgrade | |
| RequestType_table.c.sequencer_id.drop() | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/migrate/changeset/schema.py", line 598, in drop | |
| engine._run_visitor(visitorcallable, self, connection, **kwargs) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1940, in _run_visitor | |
| conn._run_visitor(visitorcallable, element, **kwargs) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1549, in _run_visitor | |
| **kwargs).traverse_single(element) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/migrate/changeset/ansisql.py", line 56, in traverse_single | |
| ret = super(AlterTableVisitor, self).traverse_single(elem) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/sql/visitors.py", line 121, in traverse_single | |
| return meth(obj, **kw) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/migrate/changeset/ansisql.py", line 141, in visit_column | |
| self.execute() | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/migrate/changeset/ansisql.py", line 44, in execute | |
| return self.connection.execute(self.buffer.getvalue()) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 942, in execute | |
| return self._execute_text(object, multiparams, params) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1104, in _execute_text | |
| statement, parameters | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1200, in _execute_context | |
| context) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1413, in _handle_dbapi_exception | |
| exc_info | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/util/compat.py", line 203, in raise_from_cause | |
| reraise(type(exception), exception, tb=exc_tb, cause=cause) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1193, in _execute_context | |
| context) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/default.py", line 507, in do_execute | |
| cursor.execute(statement, parameters) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/MySQLdb/cursors.py", line 205, in execute | |
| self.errorhandler(self, exc, value) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/MySQLdb/connections.py", line 36, in defaulterrorhandler | |
| raise errorclass, errorvalue | |
| OperationalError: (_mysql_exceptions.OperationalError) (1553, "Cannot drop index 'sequencer_id': needed in a foreign key constraint") [SQL: u'\nALTER TABLE request_type DROP COLUMN sequencer_id'] (Background on this error at: http://sqlalche.me/e/e3q8) | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:45,935 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:45,936 [p:48241,w:0,m:0] [MainThread] This migration script renames the sequencer table to 'external_service' table and | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:45,936 [p:48241,w:0,m:0] [MainThread] creates a association table, 'request_type_external_service_association' and | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:45,936 [p:48241,w:0,m:0] [MainThread] populates it. The 'sequencer_id' foreign_key from the 'request_type' table is removed. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:45,936 [p:48241,w:0,m:0] [MainThread] The 'sequencer_type_id' column is renamed to 'external_service_type_id' in the renamed | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:45,936 [p:48241,w:0,m:0] [MainThread] table 'external_service'. Finally, adds a foreign key to the external_service table in the | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:45,936 [p:48241,w:0,m:0] [MainThread] sample_dataset table and populates it. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:45,936 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:45,936 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:45,936 [p:48241,w:0,m:0] [MainThread] Migrating 68 -> 69... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:46,138 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:46,138 [p:48241,w:0,m:0] [MainThread] Migration script to rename the sequencer information form type to external service information form | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:46,138 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:46,138 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:46,138 [p:48241,w:0,m:0] [MainThread] Migrating 69 -> 70... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:46,364 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:46,365 [p:48241,w:0,m:0] [MainThread] Migration script to add 'info' column to the transfer_job table. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:46,365 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:46,365 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:46,365 [p:48241,w:0,m:0] [MainThread] Migrating 70 -> 71... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:46,639 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:46,639 [p:48241,w:0,m:0] [MainThread] Migration script to add 'workflow' and 'history' columns for a sample. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:46,639 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:46,639 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:46,639 [p:48241,w:0,m:0] [MainThread] Migrating 71 -> 72... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:47,281 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:47,281 [p:48241,w:0,m:0] [MainThread] Migration script to add 'pid' and 'socket' columns to the transfer_job table. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:47,281 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:47,281 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:47,281 [p:48241,w:0,m:0] [MainThread] Migrating 72 -> 73... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:47,545 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:47,546 [p:48241,w:0,m:0] [MainThread] Migration script to add 'ldda_parent_id' column to the implicitly_converted_dataset_association table. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:47,546 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:47,546 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:47,546 [p:48241,w:0,m:0] [MainThread] Migrating 73 -> 74... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:47,799 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:47,799 [p:48241,w:0,m:0] [MainThread] Migration script to add 'purged' column to the library_dataset table. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:47,800 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:47,800 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:47,800 [p:48241,w:0,m:0] [MainThread] Migrating 74 -> 75... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:48,049 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:48,049 [p:48241,w:0,m:0] [MainThread] Migration script to add a 'subindex' column to the run table. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:48,049 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:48,049 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:48,049 [p:48241,w:0,m:0] [MainThread] Migrating 75 -> 76... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:48,248 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:48,248 [p:48241,w:0,m:0] [MainThread] This migration script fixes the data corruption caused in the form_values | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:48,248 [p:48241,w:0,m:0] [MainThread] table (content json field) by migrate script 65. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:48,248 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:48,248 [p:48241,w:0,m:0] [MainThread] No corrupted rows found. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:48,248 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:48,248 [p:48241,w:0,m:0] [MainThread] Migrating 76 -> 77... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:48,574 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:48,574 [p:48241,w:0,m:0] [MainThread] Migration script to create table for storing tool tag associations. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:48,574 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:48,574 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:48,574 [p:48241,w:0,m:0] [MainThread] Migrating 77 -> 78... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:48,928 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:48,928 [p:48241,w:0,m:0] [MainThread] Migration script to add 'total_size' column to the dataset table, 'purged' | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:48,928 [p:48241,w:0,m:0] [MainThread] column to the HDA table, and 'disk_usage' column to the User and GalaxySession | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:48,928 [p:48241,w:0,m:0] [MainThread] tables. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:48,929 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:48,929 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:48,929 [p:48241,w:0,m:0] [MainThread] Migrating 78 -> 79... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:49,193 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:49,193 [p:48241,w:0,m:0] [MainThread] Migration script to add the job_to_input_library_dataset table. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:49,193 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:49,193 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:49,193 [p:48241,w:0,m:0] [MainThread] Migrating 79 -> 80... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:49,628 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:49,628 [p:48241,w:0,m:0] [MainThread] Migration script to create tables for disk quotas. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:49,628 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:49,628 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:49,628 [p:48241,w:0,m:0] [MainThread] Migrating 80 -> 81... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:49,890 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:49,890 [p:48241,w:0,m:0] [MainThread] Migration script to add a 'tool_version' column to the hda/ldda tables. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:49,890 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:49,890 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:49,890 [p:48241,w:0,m:0] [MainThread] Migrating 81 -> 82... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:50,208 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:50,208 [p:48241,w:0,m:0] [MainThread] Migration script to add the tool_shed_repository table. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:50,208 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:50,208 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:50,208 [p:48241,w:0,m:0] [MainThread] Migrating 82 -> 83... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:50,483 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:50,484 [p:48241,w:0,m:0] [MainThread] Migration script to add 'prepare_input_files_cmd' column to the task table and to rename a column. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:50,484 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:50,484 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:50,484 [p:48241,w:0,m:0] [MainThread] Migrating 83 -> 84... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:50,758 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:50,758 [p:48241,w:0,m:0] [MainThread] Migration script to add 'ldda_id' column to the implicitly_converted_dataset_association table. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:50,758 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:50,758 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:50,759 [p:48241,w:0,m:0] [MainThread] Migrating 84 -> 85... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:50,994 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:50,994 [p:48241,w:0,m:0] [MainThread] Migration script to add 'info' column to the task table. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:50,994 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:50,994 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:50,994 [p:48241,w:0,m:0] [MainThread] Migrating 85 -> 86... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:51,302 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:51,303 [p:48241,w:0,m:0] [MainThread] Migration script to add the metadata, update_available and includes_datatypes columns to the tool_shed_repository table. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:51,303 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:51,303 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:51,303 [p:48241,w:0,m:0] [MainThread] Migrating 86 -> 87... | |
| 0087_tool_id_guid_map_table ERROR 2018-06-25 16:18:51,561 [p:48241,w:0,m:0] [MainThread] Creating tool_id_guid_map table failed. | |
| Traceback (most recent call last): | |
| File "lib/galaxy/model/migrate/versions/0087_tool_id_guid_map_table.py", line 43, in upgrade | |
| ToolIdGuidMap_table.create() | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/sql/schema.py", line 778, in create | |
| checkfirst=checkfirst) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1940, in _run_visitor | |
| conn._run_visitor(visitorcallable, element, **kwargs) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1549, in _run_visitor | |
| **kwargs).traverse_single(element) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/sql/visitors.py", line 121, in traverse_single | |
| return meth(obj, **kw) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/sql/ddl.py", line 796, in visit_table | |
| self.traverse_single(index) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/sql/visitors.py", line 121, in traverse_single | |
| return meth(obj, **kw) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/sql/ddl.py", line 823, in visit_index | |
| self.connection.execute(CreateIndex(index)) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 948, in execute | |
| return meth(self, multiparams, params) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/sql/ddl.py", line 68, in _execute_on_connection | |
| return connection._execute_ddl(self, multiparams, params) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1009, in _execute_ddl | |
| compiled | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1200, in _execute_context | |
| context) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1413, in _handle_dbapi_exception | |
| exc_info | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/util/compat.py", line 203, in raise_from_cause | |
| reraise(type(exception), exception, tb=exc_tb, cause=cause) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1193, in _execute_context | |
| context) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/default.py", line 507, in do_execute | |
| cursor.execute(statement, parameters) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/MySQLdb/cursors.py", line 205, in execute | |
| self.errorhandler(self, exc, value) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/MySQLdb/connections.py", line 36, in defaulterrorhandler | |
| raise errorclass, errorvalue | |
| OperationalError: (_mysql_exceptions.OperationalError) (1170, "BLOB/TEXT column 'guid' used in key specification without a key length") [SQL: u'CREATE UNIQUE INDEX ix_tool_id_guid_map_guid ON tool_id_guid_map (guid)'] (Background on this error at: http://sqlalche.me/e/e3q8) | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:51,565 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:51,565 [p:48241,w:0,m:0] [MainThread] Migration script to create the tool_id_guid_map table. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:51,565 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:51,565 [p:48241,w:0,m:0] [MainThread] 0087_tool_id_guid_map_table ERROR 2018-06-25 16:18:51,561 Creating tool_id_guid_map table failed. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:51,566 [p:48241,w:0,m:0] [MainThread] Traceback (most recent call last): | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:51,566 [p:48241,w:0,m:0] [MainThread] File "lib/galaxy/model/migrate/versions/0087_tool_id_guid_map_table.py", line 43, in upgrade | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:51,566 [p:48241,w:0,m:0] [MainThread] ToolIdGuidMap_table.create() | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:51,566 [p:48241,w:0,m:0] [MainThread] File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/sql/schema.py", line 778, in create | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:51,566 [p:48241,w:0,m:0] [MainThread] checkfirst=checkfirst) | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:51,566 [p:48241,w:0,m:0] [MainThread] File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1940, in _run_visitor | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:51,573 [p:48241,w:0,m:0] [MainThread] conn._run_visitor(visitorcallable, element, **kwargs) | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:51,573 [p:48241,w:0,m:0] [MainThread] File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1549, in _run_visitor | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:51,573 [p:48241,w:0,m:0] [MainThread] **kwargs).traverse_single(element) | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:51,574 [p:48241,w:0,m:0] [MainThread] File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/sql/visitors.py", line 121, in traverse_single | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:51,574 [p:48241,w:0,m:0] [MainThread] return meth(obj, **kw) | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:51,574 [p:48241,w:0,m:0] [MainThread] File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/sql/ddl.py", line 796, in visit_table | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:51,574 [p:48241,w:0,m:0] [MainThread] self.traverse_single(index) | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:51,574 [p:48241,w:0,m:0] [MainThread] File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/sql/visitors.py", line 121, in traverse_single | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:51,574 [p:48241,w:0,m:0] [MainThread] return meth(obj, **kw) | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:51,574 [p:48241,w:0,m:0] [MainThread] File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/sql/ddl.py", line 823, in visit_index | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:51,574 [p:48241,w:0,m:0] [MainThread] self.connection.execute(CreateIndex(index)) | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:51,574 [p:48241,w:0,m:0] [MainThread] File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 948, in execute | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:51,574 [p:48241,w:0,m:0] [MainThread] return meth(self, multiparams, params) | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:51,574 [p:48241,w:0,m:0] [MainThread] File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/sql/ddl.py", line 68, in _execute_on_connection | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:51,574 [p:48241,w:0,m:0] [MainThread] return connection._execute_ddl(self, multiparams, params) | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:51,574 [p:48241,w:0,m:0] [MainThread] File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1009, in _execute_ddl | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:51,574 [p:48241,w:0,m:0] [MainThread] compiled | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:51,574 [p:48241,w:0,m:0] [MainThread] File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1200, in _execute_context | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:51,574 [p:48241,w:0,m:0] [MainThread] context) | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:51,574 [p:48241,w:0,m:0] [MainThread] File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1413, in _handle_dbapi_exception | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:51,574 [p:48241,w:0,m:0] [MainThread] exc_info | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:51,574 [p:48241,w:0,m:0] [MainThread] File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/util/compat.py", line 203, in raise_from_cause | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:51,575 [p:48241,w:0,m:0] [MainThread] reraise(type(exception), exception, tb=exc_tb, cause=cause) | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:51,575 [p:48241,w:0,m:0] [MainThread] File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1193, in _execute_context | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:51,575 [p:48241,w:0,m:0] [MainThread] context) | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:51,575 [p:48241,w:0,m:0] [MainThread] File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/default.py", line 507, in do_execute | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:51,575 [p:48241,w:0,m:0] [MainThread] cursor.execute(statement, parameters) | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:51,575 [p:48241,w:0,m:0] [MainThread] File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/MySQLdb/cursors.py", line 205, in execute | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:51,575 [p:48241,w:0,m:0] [MainThread] self.errorhandler(self, exc, value) | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:51,575 [p:48241,w:0,m:0] [MainThread] File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/MySQLdb/connections.py", line 36, in defaulterrorhandler | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:51,575 [p:48241,w:0,m:0] [MainThread] raise errorclass, errorvalue | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:51,575 [p:48241,w:0,m:0] [MainThread] OperationalError: (_mysql_exceptions.OperationalError) (1170, "BLOB/TEXT column 'guid' used in key specification without a key length") [SQL: u'CREATE UNIQUE INDEX ix_tool_id_guid_map_guid ON tool_id_guid_map (guid)'] (Background on this error at: http://sqlalche.me/e/e3q8) | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:51,575 [p:48241,w:0,m:0] [MainThread] 0087_tool_id_guid_map_table ERROR 2018-06-25 16:18:51,561 Creating tool_id_guid_map table failed. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:51,575 [p:48241,w:0,m:0] [MainThread] Traceback (most recent call last): | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:51,575 [p:48241,w:0,m:0] [MainThread] File "lib/galaxy/model/migrate/versions/0087_tool_id_guid_map_table.py", line 43, in upgrade | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:51,575 [p:48241,w:0,m:0] [MainThread] ToolIdGuidMap_table.create() | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:51,575 [p:48241,w:0,m:0] [MainThread] File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/sql/schema.py", line 778, in create | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:51,575 [p:48241,w:0,m:0] [MainThread] checkfirst=checkfirst) | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:51,575 [p:48241,w:0,m:0] [MainThread] File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1940, in _run_visitor | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:51,575 [p:48241,w:0,m:0] [MainThread] conn._run_visitor(visitorcallable, element, **kwargs) | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:51,576 [p:48241,w:0,m:0] [MainThread] File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1549, in _run_visitor | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:51,576 [p:48241,w:0,m:0] [MainThread] **kwargs).traverse_single(element) | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:51,576 [p:48241,w:0,m:0] [MainThread] File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/sql/visitors.py", line 121, in traverse_single | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:51,576 [p:48241,w:0,m:0] [MainThread] return meth(obj, **kw) | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:51,576 [p:48241,w:0,m:0] [MainThread] File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/sql/ddl.py", line 796, in visit_table | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:51,576 [p:48241,w:0,m:0] [MainThread] self.traverse_single(index) | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:51,576 [p:48241,w:0,m:0] [MainThread] File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/sql/visitors.py", line 121, in traverse_single | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:51,576 [p:48241,w:0,m:0] [MainThread] return meth(obj, **kw) | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:51,576 [p:48241,w:0,m:0] [MainThread] File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/sql/ddl.py", line 823, in visit_index | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:51,576 [p:48241,w:0,m:0] [MainThread] self.connection.execute(CreateIndex(index)) | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:51,576 [p:48241,w:0,m:0] [MainThread] File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 948, in execute | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:51,576 [p:48241,w:0,m:0] [MainThread] return meth(self, multiparams, params) | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:51,576 [p:48241,w:0,m:0] [MainThread] File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/sql/ddl.py", line 68, in _execute_on_connection | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:51,576 [p:48241,w:0,m:0] [MainThread] return connection._execute_ddl(self, multiparams, params) | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:51,576 [p:48241,w:0,m:0] [MainThread] File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1009, in _execute_ddl | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:51,576 [p:48241,w:0,m:0] [MainThread] compiled | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:51,576 [p:48241,w:0,m:0] [MainThread] File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1200, in _execute_context | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:51,576 [p:48241,w:0,m:0] [MainThread] context) | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:51,576 [p:48241,w:0,m:0] [MainThread] File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1413, in _handle_dbapi_exception | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:51,576 [p:48241,w:0,m:0] [MainThread] exc_info | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:51,576 [p:48241,w:0,m:0] [MainThread] File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/util/compat.py", line 203, in raise_from_cause | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:51,576 [p:48241,w:0,m:0] [MainThread] reraise(type(exception), exception, tb=exc_tb, cause=cause) | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:51,576 [p:48241,w:0,m:0] [MainThread] File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1193, in _execute_context | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:51,576 [p:48241,w:0,m:0] [MainThread] context) | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:51,577 [p:48241,w:0,m:0] [MainThread] File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/default.py", line 507, in do_execute | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:51,577 [p:48241,w:0,m:0] [MainThread] cursor.execute(statement, parameters) | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:51,577 [p:48241,w:0,m:0] [MainThread] File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/MySQLdb/cursors.py", line 205, in execute | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:51,577 [p:48241,w:0,m:0] [MainThread] self.errorhandler(self, exc, value) | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:51,577 [p:48241,w:0,m:0] [MainThread] File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/MySQLdb/connections.py", line 36, in defaulterrorhandler | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:51,577 [p:48241,w:0,m:0] [MainThread] raise errorclass, errorvalue | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:51,577 [p:48241,w:0,m:0] [MainThread] OperationalError: (_mysql_exceptions.OperationalError) (1170, "BLOB/TEXT column 'guid' used in key specification without a key length") [SQL: u'CREATE UNIQUE INDEX ix_tool_id_guid_map_guid ON tool_id_guid_map (guid)'] (Background on this error at: http://sqlalche.me/e/e3q8) | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:51,577 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:51,577 [p:48241,w:0,m:0] [MainThread] Migrating 87 -> 88... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:52,374 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:52,374 [p:48241,w:0,m:0] [MainThread] Migration script to add the installed_changeset_revision column to the tool_shed_repository table. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:52,374 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:52,375 [p:48241,w:0,m:0] [MainThread] Updated the installed_changeset_revision column for 0 rows in the tool_shed_repository table. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:52,375 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:52,375 [p:48241,w:0,m:0] [MainThread] Migrating 88 -> 89... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:52,721 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:52,721 [p:48241,w:0,m:0] [MainThread] Migration script to add 'object_store_id' column to various tables | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:52,721 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:52,721 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:52,721 [p:48241,w:0,m:0] [MainThread] Migrating 89 -> 90... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:52,991 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:52,991 [p:48241,w:0,m:0] [MainThread] Migration script to add the uninstalled and dist_to_shed columns to the tool_shed_repository table. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:52,991 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:52,991 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:52,991 [p:48241,w:0,m:0] [MainThread] Migrating 90 -> 91... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:53,305 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:53,305 [p:48241,w:0,m:0] [MainThread] Migration script to create the tool_version and tool_version_association tables and drop the tool_id_guid_map table. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:53,305 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:53,305 [p:48241,w:0,m:0] [MainThread] Added 0 rows to the new tool_version table. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:53,305 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:53,305 [p:48241,w:0,m:0] [MainThread] Migrating 91 -> 92... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:53,545 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:53,545 [p:48241,w:0,m:0] [MainThread] Migration script to create the migrate_tools table. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:53,546 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:53,546 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:53,546 [p:48241,w:0,m:0] [MainThread] Migrating 92 -> 93... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:53,809 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:53,809 [p:48241,w:0,m:0] [MainThread] Migration script to add a 'params' column to the 'job' table. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:53,809 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:53,809 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:53,809 [p:48241,w:0,m:0] [MainThread] Migrating 93 -> 94... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:54,078 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:54,078 [p:48241,w:0,m:0] [MainThread] Migration script to add a 'handler' column to the 'job' table. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:54,078 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:54,078 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:54,078 [p:48241,w:0,m:0] [MainThread] Migrating 94 -> 95... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:54,395 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:54,395 [p:48241,w:0,m:0] [MainThread] Migration script to create table for tracking history_dataset_association subsets. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:54,395 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:54,395 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:54,395 [p:48241,w:0,m:0] [MainThread] Migrating 95 -> 96... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:54,657 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:54,657 [p:48241,w:0,m:0] [MainThread] Migration script to add column to openid table for provider. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:54,657 [p:48241,w:0,m:0] [MainThread] Remove any OpenID entries with nonunique GenomeSpace Identifier | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:54,657 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:54,657 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:54,657 [p:48241,w:0,m:0] [MainThread] Migrating 96 -> 97... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:54,902 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:54,902 [p:48241,w:0,m:0] [MainThread] Migration script to add the ctx_rev column to the tool_shed_repository table. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:54,902 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:54,902 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:54,902 [p:48241,w:0,m:0] [MainThread] Migrating 97 -> 98... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:55,253 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:55,253 [p:48241,w:0,m:0] [MainThread] Migration script to create the genome_index_tool_data table. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:55,253 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:55,253 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:55,253 [p:48241,w:0,m:0] [MainThread] Migrating 98 -> 99... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:55,516 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:55,516 [p:48241,w:0,m:0] [MainThread] Migration script to add the tool_dependency table. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:55,516 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:55,516 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:55,516 [p:48241,w:0,m:0] [MainThread] Migrating 99 -> 100... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:55,757 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:55,757 [p:48241,w:0,m:0] [MainThread] Migration script to alter the type of the tool_dependency.version column from TrimmedString(40) to Text. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:55,757 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:55,757 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:55,758 [p:48241,w:0,m:0] [MainThread] Migrating 100 -> 101... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:56,014 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:56,014 [p:48241,w:0,m:0] [MainThread] Migration script to drop the installed_changeset_revision column from the tool_dependency table. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:56,014 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:56,014 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:56,014 [p:48241,w:0,m:0] [MainThread] Migrating 101 -> 102... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:56,297 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:56,297 [p:48241,w:0,m:0] [MainThread] Migration script to add status and error_message columns to the tool_dependency table and drop the uninstalled column from the tool_dependency table. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:56,298 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:56,298 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:56,298 [p:48241,w:0,m:0] [MainThread] Migrating 102 -> 103... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:56,572 [p:48241,w:0,m:0] [MainThread] Migration script to add status and error_message columns to the tool_shed_repository table. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:56,572 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:56,572 [p:48241,w:0,m:0] [MainThread] Migrating 103 -> 104... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:56,591 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:56,591 [p:48241,w:0,m:0] [MainThread] Migrating 104 -> 105... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:57,347 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:57,347 [p:48241,w:0,m:0] [MainThread] Migration script to add the cleanup_event* tables. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:57,347 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:57,347 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:57,347 [p:48241,w:0,m:0] [MainThread] Migrating 105 -> 106... | |
| 0106_add_missing_indexes DEBUG 2018-06-25 16:18:57,582 [p:48241,w:0,m:0] [MainThread] Creating index 'ix_metadata_file_lda_id' on column 'lda_id' in table 'metadata_file' | |
| 0106_add_missing_indexes DEBUG 2018-06-25 16:18:57,583 [p:48241,w:0,m:0] [MainThread] Creating index 'ix_history_importable' on column 'importable' in table 'history' | |
| 0106_add_missing_indexes DEBUG 2018-06-25 16:18:57,584 [p:48241,w:0,m:0] [MainThread] Creating index 'ix_sample_bar_code' on column 'bar_code' in table 'sample' | |
| 0106_add_missing_indexes DEBUG 2018-06-25 16:18:57,585 [p:48241,w:0,m:0] [MainThread] Creating index 'ix_request_type_deleted' on column 'deleted' in table 'request_type' | |
| 0106_add_missing_indexes DEBUG 2018-06-25 16:18:57,586 [p:48241,w:0,m:0] [MainThread] Creating index 'ix_galaxy_user_username' on column 'username' in table 'galaxy_user' | |
| /Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/default.py:507: Warning: Duplicate index 'ix_galaxy_user_username' defined on the table 'galaxy.galaxy_user'. This is deprecated and will be disallowed in a future release. | |
| cursor.execute(statement, parameters) | |
| 0106_add_missing_indexes DEBUG 2018-06-25 16:18:57,605 [p:48241,w:0,m:0] [MainThread] Creating index 'ix_form_definition_type' on column 'type' in table 'form_definition' | |
| 0106_add_missing_indexes DEBUG 2018-06-25 16:18:57,606 [p:48241,w:0,m:0] [MainThread] Creating index 'ix_form_definition_layout' on column 'layout' in table 'form_definition' | |
| 0106_add_missing_indexes ERROR 2018-06-25 16:18:57,608 [p:48241,w:0,m:0] [MainThread] Unable to create index 'ix_form_definition_layout'. | |
| Traceback (most recent call last): | |
| File "lib/galaxy/model/migrate/versions/0106_add_missing_indexes.py", line 64, in upgrade | |
| Index(ix, t.c[col]).create() | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/sql/schema.py", line 3489, in create | |
| bind._run_visitor(ddl.SchemaGenerator, self) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1940, in _run_visitor | |
| conn._run_visitor(visitorcallable, element, **kwargs) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1549, in _run_visitor | |
| **kwargs).traverse_single(element) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/sql/visitors.py", line 121, in traverse_single | |
| return meth(obj, **kw) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/sql/ddl.py", line 823, in visit_index | |
| self.connection.execute(CreateIndex(index)) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 948, in execute | |
| return meth(self, multiparams, params) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/sql/ddl.py", line 68, in _execute_on_connection | |
| return connection._execute_ddl(self, multiparams, params) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1009, in _execute_ddl | |
| compiled | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1200, in _execute_context | |
| context) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1413, in _handle_dbapi_exception | |
| exc_info | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/util/compat.py", line 203, in raise_from_cause | |
| reraise(type(exception), exception, tb=exc_tb, cause=cause) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1193, in _execute_context | |
| context) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/default.py", line 507, in do_execute | |
| cursor.execute(statement, parameters) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/MySQLdb/cursors.py", line 205, in execute | |
| self.errorhandler(self, exc, value) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/MySQLdb/connections.py", line 36, in defaulterrorhandler | |
| raise errorclass, errorvalue | |
| OperationalError: (_mysql_exceptions.OperationalError) (1170, "BLOB/TEXT column 'layout' used in key specification without a key length") [SQL: u'CREATE INDEX ix_form_definition_layout ON form_definition (layout)'] (Background on this error at: http://sqlalche.me/e/e3q8) | |
| 0106_add_missing_indexes DEBUG 2018-06-25 16:18:57,609 [p:48241,w:0,m:0] [MainThread] Creating index 'ix_job_library_folder_id' on column 'library_folder_id' in table 'job' | |
| 0106_add_missing_indexes DEBUG 2018-06-25 16:18:57,616 [p:48241,w:0,m:0] [MainThread] Creating index 'ix_page_published' on column 'published' in table 'page' | |
| 0106_add_missing_indexes DEBUG 2018-06-25 16:18:57,617 [p:48241,w:0,m:0] [MainThread] Creating index 'ix_page_deleted' on column 'deleted' in table 'page' | |
| 0106_add_missing_indexes DEBUG 2018-06-25 16:18:57,617 [p:48241,w:0,m:0] [MainThread] Creating index 'ix_galaxy_user_form_values_id' on column 'form_values_id' in table 'galaxy_user' | |
| /Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/default.py:507: Warning: Duplicate index 'ix_galaxy_user_form_values_id' defined on the table 'galaxy.galaxy_user'. This is deprecated and will be disallowed in a future release. | |
| cursor.execute(statement, parameters) | |
| 0106_add_missing_indexes DEBUG 2018-06-25 16:18:57,644 [p:48241,w:0,m:0] [MainThread] Creating index 'ix_lia_deleted' on column 'deleted' in table 'library_info_association' | |
| /Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/default.py:507: Warning: Duplicate index 'ix_lia_deleted' defined on the table 'galaxy.library_info_association'. This is deprecated and will be disallowed in a future release. | |
| cursor.execute(statement, parameters) | |
| 0106_add_missing_indexes DEBUG 2018-06-25 16:18:57,663 [p:48241,w:0,m:0] [MainThread] Creating index 'ix_lfia_deleted' on column 'deleted' in table 'library_folder_info_association' | |
| /Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/default.py:507: Warning: Duplicate index 'ix_lfia_deleted' defined on the table 'galaxy.library_folder_info_association'. This is deprecated and will be disallowed in a future release. | |
| cursor.execute(statement, parameters) | |
| 0106_add_missing_indexes DEBUG 2018-06-25 16:18:57,682 [p:48241,w:0,m:0] [MainThread] Creating index 'ix_lddia_deleted' on column 'deleted' in table 'library_dataset_dataset_info_association' | |
| /Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/default.py:507: Warning: Duplicate index 'ix_lddia_deleted' defined on the table 'galaxy.library_dataset_dataset_info_association'. This is deprecated and will be disallowed in a future release. | |
| cursor.execute(statement, parameters) | |
| 0106_add_missing_indexes DEBUG 2018-06-25 16:18:57,697 [p:48241,w:0,m:0] [MainThread] Creating index 'ix_sample_library_id' on column 'library_id' in table 'sample' | |
| 0106_add_missing_indexes DEBUG 2018-06-25 16:18:57,697 [p:48241,w:0,m:0] [MainThread] Creating index 'ix_sample_folder_id' on column 'folder_id' in table 'sample' | |
| /Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/default.py:507: Warning: Duplicate index 'ix_sample_folder_id' defined on the table 'galaxy.sample'. This is deprecated and will be disallowed in a future release. | |
| cursor.execute(statement, parameters) | |
| 0106_add_missing_indexes DEBUG 2018-06-25 16:18:57,748 [p:48241,w:0,m:0] [MainThread] Creating index 'ix_lia_inheritable' on column 'inheritable' in table 'library_info_association' | |
| /Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/default.py:507: Warning: Duplicate index 'ix_lia_inheritable' defined on the table 'galaxy.library_info_association'. This is deprecated and will be disallowed in a future release. | |
| cursor.execute(statement, parameters) | |
| 0106_add_missing_indexes DEBUG 2018-06-25 16:18:57,764 [p:48241,w:0,m:0] [MainThread] Creating index 'ix_lfia_inheritable' on column 'inheritable' in table 'library_folder_info_association' | |
| /Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/default.py:507: Warning: Duplicate index 'ix_lfia_inheritable' defined on the table 'galaxy.library_folder_info_association'. This is deprecated and will be disallowed in a future release. | |
| cursor.execute(statement, parameters) | |
| 0106_add_missing_indexes DEBUG 2018-06-25 16:18:57,780 [p:48241,w:0,m:0] [MainThread] Creating index 'ix_job_imported' on column 'imported' in table 'job' | |
| 0106_add_missing_indexes DEBUG 2018-06-25 16:18:57,780 [p:48241,w:0,m:0] [MainThread] Creating index 'ix_request_notification' on column 'notification' in table 'request' | |
| 0106_add_missing_indexes ERROR 2018-06-25 16:18:57,782 [p:48241,w:0,m:0] [MainThread] Unable to create index 'ix_request_notification'. | |
| Traceback (most recent call last): | |
| File "lib/galaxy/model/migrate/versions/0106_add_missing_indexes.py", line 64, in upgrade | |
| Index(ix, t.c[col]).create() | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/sql/schema.py", line 3489, in create | |
| bind._run_visitor(ddl.SchemaGenerator, self) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1940, in _run_visitor | |
| conn._run_visitor(visitorcallable, element, **kwargs) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1549, in _run_visitor | |
| **kwargs).traverse_single(element) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/sql/visitors.py", line 121, in traverse_single | |
| return meth(obj, **kw) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/sql/ddl.py", line 823, in visit_index | |
| self.connection.execute(CreateIndex(index)) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 948, in execute | |
| return meth(self, multiparams, params) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/sql/ddl.py", line 68, in _execute_on_connection | |
| return connection._execute_ddl(self, multiparams, params) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1009, in _execute_ddl | |
| compiled | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1200, in _execute_context | |
| context) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1413, in _handle_dbapi_exception | |
| exc_info | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/util/compat.py", line 203, in raise_from_cause | |
| reraise(type(exception), exception, tb=exc_tb, cause=cause) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1193, in _execute_context | |
| context) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/default.py", line 507, in do_execute | |
| cursor.execute(statement, parameters) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/MySQLdb/cursors.py", line 205, in execute | |
| self.errorhandler(self, exc, value) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/MySQLdb/connections.py", line 36, in defaulterrorhandler | |
| raise errorclass, errorvalue | |
| OperationalError: (_mysql_exceptions.OperationalError) (1170, "BLOB/TEXT column 'notification' used in key specification without a key length") [SQL: u'CREATE INDEX ix_request_notification ON request (notification)'] (Background on this error at: http://sqlalche.me/e/e3q8) | |
| 0106_add_missing_indexes DEBUG 2018-06-25 16:18:57,783 [p:48241,w:0,m:0] [MainThread] Creating index 'ix_sd_external_service_id' on column 'external_service_id' in table 'sample_dataset' | |
| /Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/default.py:507: Warning: Duplicate index 'ix_sd_external_service_id' defined on the table 'galaxy.sample_dataset'. This is deprecated and will be disallowed in a future release. | |
| cursor.execute(statement, parameters) | |
| 0106_add_missing_indexes DEBUG 2018-06-25 16:18:57,812 [p:48241,w:0,m:0] [MainThread] Creating index 'ix_icda_ldda_parent_id' on column 'ldda_parent_id' in table 'implicitly_converted_dataset_association' | |
| /Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/default.py:507: Warning: Duplicate index 'ix_icda_ldda_parent_id' defined on the table 'galaxy.implicitly_converted_dataset_association'. This is deprecated and will be disallowed in a future release. | |
| cursor.execute(statement, parameters) | |
| 0106_add_missing_indexes DEBUG 2018-06-25 16:18:57,830 [p:48241,w:0,m:0] [MainThread] Creating index 'ix_library_dataset_purged' on column 'purged' in table 'library_dataset' | |
| 0106_add_missing_indexes DEBUG 2018-06-25 16:18:57,832 [p:48241,w:0,m:0] [MainThread] Creating index 'ix_run_subindex' on column 'subindex' in table 'run' | |
| 0106_add_missing_indexes DEBUG 2018-06-25 16:18:57,833 [p:48241,w:0,m:0] [MainThread] Creating index 'ix_history_dataset_association_purged' on column 'purged' in table 'history_dataset_association' | |
| 0106_add_missing_indexes DEBUG 2018-06-25 16:18:57,834 [p:48241,w:0,m:0] [MainThread] Creating index 'ix_galaxy_user_disk_usage' on column 'disk_usage' in table 'galaxy_user' | |
| 0106_add_missing_indexes DEBUG 2018-06-25 16:18:57,834 [p:48241,w:0,m:0] [MainThread] Creating index 'ix_galaxy_session_disk_usage' on column 'disk_usage' in table 'galaxy_session' | |
| 0106_add_missing_indexes DEBUG 2018-06-25 16:18:57,836 [p:48241,w:0,m:0] [MainThread] Creating index 'ix_icda_ldda_id' on column 'ldda_id' in table 'implicitly_converted_dataset_association' | |
| /Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/default.py:507: Warning: Duplicate index 'ix_icda_ldda_id' defined on the table 'galaxy.implicitly_converted_dataset_association'. This is deprecated and will be disallowed in a future release. | |
| cursor.execute(statement, parameters) | |
| 0106_add_missing_indexes DEBUG 2018-06-25 16:18:57,866 [p:48241,w:0,m:0] [MainThread] Creating index 'ix_tsr_includes_datatypes' on column 'includes_datatypes' in table 'tool_shed_repository' | |
| /Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/default.py:507: Warning: Duplicate index 'ix_tsr_includes_datatypes' defined on the table 'galaxy.tool_shed_repository'. This is deprecated and will be disallowed in a future release. | |
| cursor.execute(statement, parameters) | |
| 0106_add_missing_indexes DEBUG 2018-06-25 16:18:57,887 [p:48241,w:0,m:0] [MainThread] Creating index 'ix_dataset_object_store_id' on column 'object_store_id' in table 'dataset' | |
| 0106_add_missing_indexes DEBUG 2018-06-25 16:18:57,889 [p:48241,w:0,m:0] [MainThread] Creating index 'ix_job_object_store_id' on column 'object_store_id' in table 'job' | |
| 0106_add_missing_indexes DEBUG 2018-06-25 16:18:57,889 [p:48241,w:0,m:0] [MainThread] Creating index 'ix_metadata_file_object_store_id' on column 'object_store_id' in table 'metadata_file' | |
| 0106_add_missing_indexes DEBUG 2018-06-25 16:18:57,889 [p:48241,w:0,m:0] [MainThread] Creating index 'ix_job_handler' on column 'handler' in table 'job' | |
| 0106_add_missing_indexes DEBUG 2018-06-25 16:18:57,889 [p:48241,w:0,m:0] [MainThread] Creating index 'ix_galaxy_user_email' on column 'email' in table 'galaxy_user' | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:57,931 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:57,931 [p:48241,w:0,m:0] [MainThread] 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. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:57,931 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:57,931 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:57,931 [p:48241,w:0,m:0] [MainThread] Migrating 106 -> 107... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:58,220 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:58,220 [p:48241,w:0,m:0] [MainThread] Add the exit_code column to the Job and Task tables. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:58,220 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:58,220 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:58,220 [p:48241,w:0,m:0] [MainThread] Migrating 107 -> 108... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:59,158 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:59,158 [p:48241,w:0,m:0] [MainThread] Add the ExtendedMetadata and ExtendedMetadataIndex tables | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:59,158 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:59,158 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:59,158 [p:48241,w:0,m:0] [MainThread] Migrating 108 -> 109... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:59,512 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:59,512 [p:48241,w:0,m:0] [MainThread] Migration script to add the repository_dependency and repository_repository_dependency_association tables. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:59,512 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:59,513 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:59,513 [p:48241,w:0,m:0] [MainThread] Migrating 109 -> 110... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:59,819 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:59,820 [p:48241,w:0,m:0] [MainThread] Add UUID column to dataset table | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:59,820 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:59,820 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:18:59,820 [p:48241,w:0,m:0] [MainThread] Migrating 110 -> 111... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:00,129 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:00,129 [p:48241,w:0,m:0] [MainThread] Add support for job destinations to the job table | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:00,129 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:00,129 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:00,129 [p:48241,w:0,m:0] [MainThread] Migrating 111 -> 112... | |
| 0112_add_data_manager_history_association_and_data_manager_job_association_tables DEBUG 2018-06-25 16:19:00,463 [p:48241,w:0,m:0] [MainThread] Created data_manager_history_association table | |
| 0112_add_data_manager_history_association_and_data_manager_job_association_tables ERROR 2018-06-25 16:19:00,511 [p:48241,w:0,m:0] [MainThread] Creating data_manager_job_association table failed. | |
| Traceback (most recent call last): | |
| File "lib/galaxy/model/migrate/versions/0112_add_data_manager_history_association_and_data_manager_job_association_tables.py", line 41, in upgrade | |
| DataManagerJobAssociation_table.create() | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/sql/schema.py", line 778, in create | |
| checkfirst=checkfirst) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1940, in _run_visitor | |
| conn._run_visitor(visitorcallable, element, **kwargs) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1549, in _run_visitor | |
| **kwargs).traverse_single(element) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/sql/visitors.py", line 121, in traverse_single | |
| return meth(obj, **kw) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/sql/ddl.py", line 796, in visit_table | |
| self.traverse_single(index) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/sql/visitors.py", line 121, in traverse_single | |
| return meth(obj, **kw) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/sql/ddl.py", line 823, in visit_index | |
| self.connection.execute(CreateIndex(index)) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 948, in execute | |
| return meth(self, multiparams, params) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/sql/ddl.py", line 68, in _execute_on_connection | |
| return connection._execute_ddl(self, multiparams, params) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1009, in _execute_ddl | |
| compiled | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1200, in _execute_context | |
| context) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1413, in _handle_dbapi_exception | |
| exc_info | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/util/compat.py", line 203, in raise_from_cause | |
| reraise(type(exception), exception, tb=exc_tb, cause=cause) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1193, in _execute_context | |
| context) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/default.py", line 507, in do_execute | |
| cursor.execute(statement, parameters) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/MySQLdb/cursors.py", line 205, in execute | |
| self.errorhandler(self, exc, value) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/MySQLdb/connections.py", line 36, in defaulterrorhandler | |
| raise errorclass, errorvalue | |
| OperationalError: (_mysql_exceptions.OperationalError) (1170, "BLOB/TEXT column 'data_manager_id' used in key specification without a key length") [SQL: u'CREATE INDEX ix_data_manager_job_association_data_manager_id ON data_manager_job_association (data_manager_id)'] (Background on this error at: http://sqlalche.me/e/e3q8) | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:00,515 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:00,515 [p:48241,w:0,m:0] [MainThread] Migration script to add the data_manager_history_association table and data_manager_job_association. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:00,515 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:00,515 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:00,515 [p:48241,w:0,m:0] [MainThread] Migrating 112 -> 113... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:00,532 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:00,532 [p:48241,w:0,m:0] [MainThread] Migration script to update the migrate_tools.repository_path column to point to the new location lib/tool_shed/galaxy_install/migrate. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:00,532 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:00,532 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:00,532 [p:48241,w:0,m:0] [MainThread] Migrating 113 -> 114... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:00,557 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:00,557 [p:48241,w:0,m:0] [MainThread] Migration script to update the migrate_tools.repository_path column to point to the new location lib/tool_shed/galaxy_install/migrate. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:00,557 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:00,557 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:00,557 [p:48241,w:0,m:0] [MainThread] Migrating 114 -> 115... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:00,600 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:00,600 [p:48241,w:0,m:0] [MainThread] Migrating 115 -> 116... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:00,906 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:00,906 [p:48241,w:0,m:0] [MainThread] Migration script to drop the update_available Boolean column and replace it with the tool_shed_status JSONType column in the tool_shed_repository table. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:00,906 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:00,906 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:00,906 [p:48241,w:0,m:0] [MainThread] Migrating 116 -> 117... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:01,215 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:01,216 [p:48241,w:0,m:0] [MainThread] Adds 'active' and 'activation_token' columns to the galaxy_user table. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:01,216 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:01,216 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:01,216 [p:48241,w:0,m:0] [MainThread] Migrating 117 -> 118... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:01,522 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:01,522 [p:48241,w:0,m:0] [MainThread] Add link from history_dataset_association to the extended_metadata table | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:01,522 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:01,522 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:01,522 [p:48241,w:0,m:0] [MainThread] Migrating 118 -> 119... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:01,917 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:01,917 [p:48241,w:0,m:0] [MainThread] Migration script for job metric plugins. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:01,918 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:01,918 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:01,918 [p:48241,w:0,m:0] [MainThread] Migrating 119 -> 120... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:03,124 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:03,124 [p:48241,w:0,m:0] [MainThread] Migration script for tables related to dataset collections. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:03,124 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:03,124 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:03,124 [p:48241,w:0,m:0] [MainThread] Migrating 120 -> 121... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:03,426 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:03,426 [p:48241,w:0,m:0] [MainThread] Add UUIDs to workflows | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:03,426 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:03,426 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:03,426 [p:48241,w:0,m:0] [MainThread] Migrating 121 -> 122... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:04,033 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:04,034 [p:48241,w:0,m:0] [MainThread] Migration script to grow MySQL blobs. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:04,034 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:04,034 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:04,034 [p:48241,w:0,m:0] [MainThread] Migrating 122 -> 123... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:04,731 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:04,731 [p:48241,w:0,m:0] [MainThread] Migration script for workflow request tables. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:04,731 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:04,731 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:04,731 [p:48241,w:0,m:0] [MainThread] Migrating 123 -> 124... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:05,080 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:05,080 [p:48241,w:0,m:0] [MainThread] Migration script for the job state history table | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:05,080 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:05,080 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:05,080 [p:48241,w:0,m:0] [MainThread] Migrating 124 -> 125... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:05,414 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:05,414 [p:48241,w:0,m:0] [MainThread] Migration script to enhance workflow step usability by adding labels and UUIDs. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:05,414 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:05,414 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:05,414 [p:48241,w:0,m:0] [MainThread] Migrating 125 -> 126... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:05,768 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:05,768 [p:48241,w:0,m:0] [MainThread] Migration script for the password reset table | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:05,768 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:05,768 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:05,769 [p:48241,w:0,m:0] [MainThread] Migrating 126 -> 127... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:06,163 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:06,163 [p:48241,w:0,m:0] [MainThread] Migration script updating collections tables for output collections. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:06,163 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:06,163 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:06,163 [p:48241,w:0,m:0] [MainThread] Migrating 127 -> 128... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:06,481 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:06,481 [p:48241,w:0,m:0] [MainThread] Migration script to add session update time (used for timeouts) | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:06,481 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:06,481 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:06,482 [p:48241,w:0,m:0] [MainThread] Migrating 128 -> 129... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:06,811 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:06,811 [p:48241,w:0,m:0] [MainThread] Migration script to allow invalidation of job external output metadata temp files | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:06,811 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:06,812 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:06,812 [p:48241,w:0,m:0] [MainThread] Migrating 129 -> 130... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:07,130 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:07,130 [p:48241,w:0,m:0] [MainThread] Migration script to change the 'value' column of 'user_preference' table from varchar to text. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:07,130 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:07,130 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:07,130 [p:48241,w:0,m:0] [MainThread] Migrating 130 -> 131... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:08,419 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:08,419 [p:48241,w:0,m:0] [MainThread] Migration script to support subworkflows and workflow request input parameters | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:08,419 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:08,419 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:08,419 [p:48241,w:0,m:0] [MainThread] Migrating 131 -> 132... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:08,460 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:08,461 [p:48241,w:0,m:0] [MainThread] Migrating 132 -> 133... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:08,789 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:08,789 [p:48241,w:0,m:0] [MainThread] Add dependencies column to jobs table | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:08,789 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:08,789 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:08,789 [p:48241,w:0,m:0] [MainThread] Migrating 133 -> 134... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:08,800 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:08,800 [p:48241,w:0,m:0] [MainThread] Migration script to set the 'deleted' column of the | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:08,800 [p:48241,w:0,m:0] [MainThread] 'history_dataset_association' table to True if 'purged' is True. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:08,800 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:08,800 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:08,800 [p:48241,w:0,m:0] [MainThread] Migrating 134 -> 135... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:09,231 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:09,232 [p:48241,w:0,m:0] [MainThread] This migration script adds support for storing tags in the context of a dataset in a library | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:09,232 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:09,232 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:09,232 [p:48241,w:0,m:0] [MainThread] Migrating 135 -> 136... | |
| 0136_collection_and_workflow_state ERROR 2018-06-25 16:19:09,677 [p:48241,w:0,m:0] [MainThread] Creating workflow_invocation_output_dataset_collection_association table failed. | |
| Traceback (most recent call last): | |
| File "lib/galaxy/model/migrate/versions/0136_collection_and_workflow_state.py", line 162, in __create | |
| table.create() | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/sql/schema.py", line 778, in create | |
| checkfirst=checkfirst) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1940, in _run_visitor | |
| conn._run_visitor(visitorcallable, element, **kwargs) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1549, in _run_visitor | |
| **kwargs).traverse_single(element) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/sql/visitors.py", line 121, in traverse_single | |
| return meth(obj, **kw) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/sql/ddl.py", line 791, in visit_table | |
| include_foreign_key_constraints=include_foreign_key_constraints | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 948, in execute | |
| return meth(self, multiparams, params) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/sql/ddl.py", line 68, in _execute_on_connection | |
| return connection._execute_ddl(self, multiparams, params) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1009, in _execute_ddl | |
| compiled | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1200, in _execute_context | |
| context) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1413, in _handle_dbapi_exception | |
| exc_info | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/util/compat.py", line 203, in raise_from_cause | |
| reraise(type(exception), exception, tb=exc_tb, cause=cause) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1193, in _execute_context | |
| context) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/default.py", line 507, in do_execute | |
| cursor.execute(statement, parameters) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/MySQLdb/cursors.py", line 205, in execute | |
| self.errorhandler(self, exc, value) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/MySQLdb/connections.py", line 36, in defaulterrorhandler | |
| raise errorclass, errorvalue | |
| OperationalError: (_mysql_exceptions.OperationalError) (1059, "Identifier name 'workflow_invocation_output_dataset_collection_association_ibfk_1' is too long") [SQL: u'\nCREATE TABLE workflow_invocation_output_dataset_collection_association (\n\tid INTEGER NOT NULL AUTO_INCREMENT, \n\tworkflow_invocation_id INTEGER, \n\tworkflow_step_id INTEGER, \n\tdataset_collection_id INTEGER, \n\tworkflow_output_id INTEGER, \n\tPRIMARY KEY (id), \n\tFOREIGN KEY(workflow_invocation_id) REFERENCES workflow_invocation (id), \n\tFOREIGN KEY(workflow_step_id) REFERENCES workflow_step (id), \n\tFOREIGN KEY(dataset_collection_id) REFERENCES history_dataset_collection_association (id), \n\tFOREIGN KEY(workflow_output_id) REFERENCES workflow_output (id)\n)\n\n'] (Background on this error at: http://sqlalche.me/e/e3q8) | |
| 0136_collection_and_workflow_state ERROR 2018-06-25 16:19:09,772 [p:48241,w:0,m:0] [MainThread] Creating workflow_invocation_step_output_dataset_collection_association table failed. | |
| Traceback (most recent call last): | |
| File "lib/galaxy/model/migrate/versions/0136_collection_and_workflow_state.py", line 162, in __create | |
| table.create() | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/sql/schema.py", line 778, in create | |
| checkfirst=checkfirst) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1940, in _run_visitor | |
| conn._run_visitor(visitorcallable, element, **kwargs) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1549, in _run_visitor | |
| **kwargs).traverse_single(element) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/sql/visitors.py", line 121, in traverse_single | |
| return meth(obj, **kw) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/sql/ddl.py", line 791, in visit_table | |
| include_foreign_key_constraints=include_foreign_key_constraints | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 948, in execute | |
| return meth(self, multiparams, params) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/sql/ddl.py", line 68, in _execute_on_connection | |
| return connection._execute_ddl(self, multiparams, params) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1009, in _execute_ddl | |
| compiled | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1200, in _execute_context | |
| context) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1413, in _handle_dbapi_exception | |
| exc_info | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/util/compat.py", line 203, in raise_from_cause | |
| reraise(type(exception), exception, tb=exc_tb, cause=cause) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1193, in _execute_context | |
| context) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/default.py", line 507, in do_execute | |
| cursor.execute(statement, parameters) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/MySQLdb/cursors.py", line 205, in execute | |
| self.errorhandler(self, exc, value) | |
| File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/MySQLdb/connections.py", line 36, in defaulterrorhandler | |
| raise errorclass, errorvalue | |
| OperationalError: (_mysql_exceptions.OperationalError) (1059, "Identifier name 'workflow_invocation_step_output_dataset_collection_association_ibfk_1' is too long") [SQL: u'\nCREATE TABLE workflow_invocation_step_output_dataset_collection_association (\n\tid INTEGER NOT NULL AUTO_INCREMENT, \n\tworkflow_invocation_step_id INTEGER, \n\tworkflow_step_id INTEGER, \n\tdataset_collection_id INTEGER, \n\toutput_name VARCHAR(255), \n\tPRIMARY KEY (id), \n\tFOREIGN KEY(workflow_invocation_step_id) REFERENCES workflow_invocation_step (id), \n\tFOREIGN KEY(workflow_step_id) REFERENCES workflow_step (id), \n\tFOREIGN KEY(dataset_collection_id) REFERENCES history_dataset_collection_association (id)\n)\n\n'] (Background on this error at: http://sqlalche.me/e/e3q8) | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:09,981 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:09,981 [p:48241,w:0,m:0] [MainThread] Migration script for collections and workflows connections. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:09,981 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:09,981 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:09,981 [p:48241,w:0,m:0] [MainThread] Migrating 136 -> 137... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:10,398 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:10,398 [p:48241,w:0,m:0] [MainThread] Add copied_from_job_id column to jobs table | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:10,398 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:10,398 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:10,398 [p:48241,w:0,m:0] [MainThread] Migrating 137 -> 138... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:10,778 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:10,778 [p:48241,w:0,m:0] [MainThread] Add version column to history_dataset_association table | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:10,778 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:10,778 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:10,779 [p:48241,w:0,m:0] [MainThread] Migrating 138 -> 139... | |
| 0139_add_history_dataset_association_history_table DEBUG 2018-06-25 16:19:11,222 [p:48241,w:0,m:0] [MainThread] Created history_dataset_association_history table | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:11,225 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:11,225 [p:48241,w:0,m:0] [MainThread] Migration script to add the history_dataset_association_history table. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:11,225 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:11,225 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:11,225 [p:48241,w:0,m:0] [MainThread] Migrating 139 -> 140... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:11,608 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:11,608 [p:48241,w:0,m:0] [MainThread] Add dataset_version column to job_to_input_dataset table | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:11,608 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:11,608 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:11,608 [p:48241,w:0,m:0] [MainThread] Migrating 140 -> 141... | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:12,071 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:12,072 [p:48241,w:0,m:0] [MainThread] Migration script to add a new tables for an OpenID Connect authentication and authorization. | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:12,072 [p:48241,w:0,m:0] [MainThread] | |
| galaxy.model.migrate.check INFO 2018-06-25 16:19:12,072 [p:48241,w:0,m:0] [MainThread] |
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