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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