Hi Hans,

We have a very nice MySQL server with a lot of RAM and associated storage (as well as Oracle for some other applications)
So we would like to avoid a third system to maintain.
And mysql is working well for my current 17.09 galaxy instance.

Fred

-----Message d'origine-----
De : Hans-Rudolf Hotz [mailto:hrh@fmi.ch]
Envoyé : jeudi 14 juin 2018 08:25
À : SAPET, Frederic <frederic.sapet@biogemma.com>; Galaxy-dev <galaxy-dev@lists.galaxyproject.org>
Objet : Re: [galaxy-dev] MySQL errors and warnings with a fresh install of Galaxy 18-05

Hi Fred

Sorry, I don't have an answer.... I am just wondering: If you start from 'scratch', why don't you use PostgreSQL?

Regards, Hans-Rudolf



On 06/13/2018 05:41 PM, SAPET, Frederic wrote:
> 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_associa
> tion_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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