As for the error I encountered, it complained identifier of the index is too long. There is identifier length limit in MySQL which is 64: http://dev.mysql.com/doc/refman/5.5/en/identifiers.html But the "ix_repository_repository_dependency_association_tool_shed_repository_id" is 71 char long. Any one can confirm if the Galaxy will be OK without these indexes? Or it effectively means no MySQL support in the new Galaxy release? Regards, Derrick On Mon, Mar 4, 2013 at 10:13 AM, Derrick Lin <klin938@gmail.com> wrote:
HI Hans,
Yours happened when upgrading from 108 - 109 (which didn't happen to me).
If you have a chance to upgrade to release_2013.02.08, your database will be upgrade from 109 - 110, I am very interested to see if the index creation error happens to you as well.
Cheers, Derrick
On Fri, Mar 1, 2013 at 7:46 PM, Hans-Rudolf Hotz <hrh@fmi.ch> wrote:
Hi Derrick
This is interesting. we are also using MySQL and I got an error at the same step. However in my case the error message was:
" (OperationalError) (1050, "Table 'repository_repository_**dependency_association' already exists") "
the same was also the case for the repository_dependency table (see below for full error)
I have encountered this already several times over then last few years and struggled to understand what was really going on (why is it trying to build the table a second and a third time). Our sysadmins always insisted that there were no other error messages in the MySQL logs. So I ignored it. Knowing your error message, could now explain our situation. (see also below for the index description)
So far we have no problems...but we also don't work much with the tool shed.
Regards, Hans-Rudolf
mysql> show index from repository_repository_**dependency_association\G *************************** 1. row *************************** Table: repository_repository_**dependency_association Non_unique: 0 Key_name: PRIMARY Seq_in_index: 1 Column_name: id Collation: A Cardinality: 0 Sub_part: NULL Packed: NULL Null: Index_type: BTREE Comment: *************************** 2. row *************************** Table: repository_repository_**dependency_association Non_unique: 1 Key_name: tool_shed_repository_id Seq_in_index: 1 Column_name: tool_shed_repository_id Collation: A Cardinality: NULL Sub_part: NULL Packed: NULL Null: YES Index_type: BTREE Comment: *************************** 3. row *************************** Table: repository_repository_**dependency_association Non_unique: 1 Key_name: repository_dependency_id Seq_in_index: 1 Column_name: repository_dependency_id Collation: A Cardinality: NULL Sub_part: NULL Packed: NULL Null: YES Index_type: BTREE Comment: 3 rows in set (0.00 sec)
mysql>
108 -> 109...
Migration script to add the repository_dependency and repository_repository_**dependency_association tables.
0109_add_repository_**dependency_tables DEBUG 2013-02-26 14:04:55,820 Creating repository_dependency table failed: (OperationalError) (1050, "Table 'repository_dependency' already exists") u'\nCREATE TABLE repository_dependency (\n\tid INTEGER NOT NULL AUTO_INCREMENT, \n\tcreate_time DATETIME, \n\tupdate_time DATETIME, \n\ttool_shed_repository_id INTEGER NOT NULL, \n\tPRIMARY KEY (id), \n\t FOREIGN KEY(tool_shed_repository_id) REFERENCES tool_shed_repository (id)\n)\n\n' () 0109_add_repository_**dependency_tables DEBUG 2013-02-26 14:04:55,820 Creating repository_dependency table failed: (OperationalError) (1050, "Table 'repository_dependency' already exists") u'\nCREATE TABLE repository_dependency (\n\tid INTEGER NOT NULL AUTO_INCREMENT, \n\tcreate_time DATETIME, \n\tupdate_time DATETIME, \n\ttool_shed_repository_id INTEGER NOT NULL, \n\tPRIMARY KEY (id), \n\t FOREIGN KEY(tool_shed_repository_id) REFERENCES tool_shed_repository (id)\n)\n\n' () 0109_add_repository_**dependency_tables DEBUG 2013-02-26 14:04:55,821 Creating repository_repository_**dependency_association table failed: (OperationalError) (1050, "Table 'repository_repository_**dependency_association' already exists") u'\nCREATE TABLE repository_repository_**dependency_association (\n\tid INTEGER NOT NULL AUTO_INCREMENT, \n\tcreate_time DATETIME, \n\tupdate_time DATETIME, \n\ttool_shed_repository_id INTEGER, \n\trepository_dependency_id INTEGER, \n\tPRIMARY KEY (id), \n\t FOREIGN KEY(tool_shed_repository_id) REFERENCES tool_shed_repository (id), \n\t FOREIGN KEY(repository_dependency_id) REFERENCES repository_dependency (id)\n)\n\n' () 0109_add_repository_**dependency_tables DEBUG 2013-02-26 14:04:55,821 Creating repository_repository_**dependency_association table failed: (OperationalError) (1050, "Table 'repository_repository_**dependency_association' already exists") u'\nCREATE TABLE repository_repository_**dependency_association (\n\tid INTEGER NOT NULL AUTO_INCREMENT, \n\tcreate_time DATETIME, \n\tupdate_time DATETIME, \n\ttool_shed_repository_id INTEGER, \n\trepository_dependency_id INTEGER, \n\tPRIMARY KEY (id), \n\t FOREIGN KEY(tool_shed_repository_id) REFERENCES tool_shed_repository (id), \n\t FOREIGN KEY(repository_dependency_id) REFERENCES repository_dependency (id)\n)\n\n' () done
On 03/01/2013 05:22 AM, Derrick Lin wrote:
Hi guys,
I was given the following error when upgrading the database from 109 to 110:
0109_add_repository_**dependency_tables DEBUG 2013-03-01 15:14:15,554 Creating repository_repository_**dependency_association table failed: (OperationalError) (1059, "Identifier name 'ix_repository_repository_**dependency_association_tool_**shed_repository_id' is too long") u'CREATE INDEX ix_repository_repository_**dependency_association_tool_** shed_repository_id ON repository_repository_**dependency_association (tool_shed_repository_id)' () 0109_add_repository_**dependency_tables DEBUG 2013-03-01 15:14:15,554 Creating repository_repository_**dependency_association table failed: (OperationalError) (1059, "Identifier name 'ix_repository_repository_**dependency_association_tool_**shed_repository_id' is too long") u'CREATE INDEX ix_repository_repository_**dependency_association_tool_** shed_repository_id ON repository_repository_**dependency_association (tool_shed_repository_id)' ()
So I guess the indexes weren't created. I am using MySQL, is it a big deal for Galaxy?
Cheers, Derrick
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