Hi,
I try to install galaxy 18-05. My database backend is MysqL (5.7.11-4
Percona Server)
I start from scratch (drop database, new directory with galaxy files
fetched with git)
So the database is first created when run.sh is used : :
Creating database for URI [mysql://….
I see warnings about duplicated indexes and OperationalError from
SQLAlchemy.
Some tables are then missing in my database
(workflow_invocation_output_dataset_collection_association and
workflow_invocation_output_dataset_collection_association).
And fields are still present (ie in request table : library_id and
folder_id)
Could you please help me ?
Thank you.
Fred
grep "^OperationalError:" FirstRun.log | cut -f 2- -d ","
"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)
"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)
"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)
"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)
"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)
"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)
"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)
"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)
"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)
"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)
grep "Warning" FirstRun.log | cut -f 3,4 -d ":"
Warning: Duplicate index 'ix_galaxy_user_deleted' defined on the table
'galaxydbBGAdev.galaxy_user'. This is deprecated and will be disallowed
in a future release.
Warning: Duplicate index 'ix_galaxy_user_purged' defined on the table
'galaxydbBGAdev.galaxy_user'. This is deprecated and will be disallowed
in a future release.
Warning: Duplicate index 'ix_hdadaa_history_dataset_association_id'
defined on the table
'galaxydbBGAdev.history_dataset_association_display_at_authorization'.
This is deprecated and will be disallowed in a future release.
Warning: Duplicate index 'ix_lddaia_ldda_id' defined on the table
'galaxydbBGAdev.library_dataset_dataset_info_association'. This is
deprecated and will be disallowed in a future release.
Warning: Duplicate index 'ix_hda_ta_history_dataset_association_id'
defined on the table
'galaxydbBGAdev.history_dataset_association_tag_association'. This is
deprecated and will be disallowed in a future release.
Warning: Duplicate index 'ix_galaxy_user_username' defined on the table
'galaxydbBGAdev.galaxy_user'. This is deprecated and will be disallowed
in a future release.
Warning: Duplicate index 'ix_galaxy_user_form_values_id' defined on the
table 'galaxydbBGAdev.galaxy_user'. This is deprecated and will be
disallowed in a future release.
Warning: Duplicate index 'ix_lia_deleted' defined on the table
'galaxydbBGAdev.library_info_association'. This is deprecated and will
be disallowed in a future release.
Warning: Duplicate index 'ix_lfia_deleted' defined on the table
'galaxydbBGAdev.library_folder_info_association'. This is deprecated and
will be disallowed in a future release.
Warning: Duplicate index 'ix_lddia_deleted' defined on the table
'galaxydbBGAdev.library_dataset_dataset_info_association'. This is
deprecated and will be disallowed in a future release.
Warning: Duplicate index 'ix_sample_folder_id' defined on the table
'galaxydbBGAdev.sample'. This is deprecated and will be disallowed in a
future release.
Warning: Duplicate index 'ix_lia_inheritable' defined on the table
'galaxydbBGAdev.library_info_association'. This is deprecated and will
be disallowed in a future release.
Warning: Duplicate index 'ix_lfia_inheritable' defined on the table
'galaxydbBGAdev.library_folder_info_association'. This is deprecated and
will be disallowed in a future release.
Warning: Duplicate index 'ix_sd_external_service_id' defined on the
table 'galaxydbBGAdev.sample_dataset'. This is deprecated and will be
disallowed in a future release.
Warning: Duplicate index 'ix_icda_ldda_parent_id' defined on the table
'galaxydbBGAdev.implicitly_converted_dataset_association'. This is
deprecated and will be disallowed in a future release.
Warning: Duplicate index 'ix_icda_ldda_id' defined on the table
'galaxydbBGAdev.implicitly_converted_dataset_association'. This is
deprecated and will be disallowed in a future release.
Warning: Duplicate index 'ix_tsr_includes_datatypes' defined on the
table 'galaxydbBGAdev.tool_shed_repository'. This is deprecated and will
be disallowed in a future release.
grep ERROR FirstRun.log | grep failed
0037_samples_library ERROR 2018-06-13 12:01:45,817 [p:17852,w:0,m:0]
[MainThread] Deleting column 'library_id' to request table failed.
0037_samples_library ERROR 2018-06-13 12:01:45,832 [p:17852,w:0,m:0]
[MainThread] Deleting column 'folder_id' to request table failed.
galaxy.model.migrate.check INFO 2018-06-13 12:01:47,129
[p:17852,w:0,m:0] [MainThread] 0037_samples_library ERROR 2018-06-13
12:01:45,817 Deleting column 'library_id' to request table failed.
galaxy.model.migrate.check INFO 2018-06-13 12:01:47,133
[p:17852,w:0,m:0] [MainThread] 0037_samples_library ERROR 2018-06-13
12:01:45,817 Deleting column 'library_id' to request table failed.
galaxy.model.migrate.check INFO 2018-06-13 12:01:47,137
[p:17852,w:0,m:0] [MainThread] 0037_samples_library ERROR 2018-06-13
12:01:45,832 Deleting column 'folder_id' to request table failed.
galaxy.model.migrate.check INFO 2018-06-13 12:01:47,142
[p:17852,w:0,m:0] [MainThread] 0037_samples_library ERROR 2018-06-13
12:01:45,832 Deleting column 'folder_id' to request table failed.
0040_page_annotations ERROR 2018-06-13 12:01:49,598 [p:17852,w:0,m:0]
[MainThread] Creating page_annotation_association table failed.
0068_rename_sequencer_to_external_services ERROR 2018-06-13 12:02:26,658
[p:17852,w:0,m:0] [MainThread] Deleting column 'sequencer_id' from the
'request_type' table failed.
0087_tool_id_guid_map_table ERROR 2018-06-13 12:02:48,300
[p:17852,w:0,m:0] [MainThread] Creating tool_id_guid_map table failed.
galaxy.model.migrate.check INFO 2018-06-13 12:02:48,309
[p:17852,w:0,m:0] [MainThread] 0087_tool_id_guid_map_table ERROR
2018-06-13 12:02:48,300 Creating tool_id_guid_map table failed.
galaxy.model.migrate.check INFO 2018-06-13 12:02:48,313
[p:17852,w:0,m:0] [MainThread] 0087_tool_id_guid_map_table ERROR
2018-06-13 12:02:48,300 Creating tool_id_guid_map table failed.
0112_add_data_manager_history_association_and_data_manager_job_association_tables
ERROR 2018-06-13 12:03:22,252 [p:17852,w:0,m:0] [MainThread] Creating
data_manager_job_association table failed.
0136_collection_and_workflow_state ERROR 2018-06-13 12:03:57,766
[p:17852,w:0,m:0] [MainThread] Creating
workflow_invocation_output_dataset_collection_association table failed.
0136_collection_and_workflow_state ERROR 2018-06-13 12:03:58,326
[p:17852,w:0,m:0] [MainThread] Creating
workflow_invocation_step_output_dataset_collection_association table failed.
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