Error when upgrading the database to version 110
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
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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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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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
______________________________**_____________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
The problem is that, like you pointed out, mysql allows identifier lengths of 255 for everything except indexes, which are stuck at 64. Most of the index names in Galaxy are auto-generated by SqlAlchemy, the ORM layer we use, based on the names of the tables and columns, and quite a few of these currently stretch beyond 64 characters. The SqlAlchemy MySQL dialect handles this more cleanly in newer versions, which we're in the middle of updating to. While we definitely do recommend that if you have the option to choose, go with postgres, Galaxy should function both now and in the future with MySQL. In this case, your galaxy will function just fine without that index. -Dannon On Sun, Mar 3, 2013 at 6:26 PM, Derrick Lin <klin938@gmail.com> wrote:
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
______________________________**_____________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
Hi Derrick and Dannon @ Derrick
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.
We are talking about the same step (it is all part of our upgrade to the 2013.02.08 release which in my case involved changing the db from 107 to 110), see: ~/lib/galaxy/model/migrate/versions0109_add_repository_dependency_tables.py Nevertheless, thanks for identifying the actual cause of the problem ie:
There is identifier length limit in MySQL which is 64
So I am just puzzled, why I don't get this particular error message. I asked our sysadmin again, and he claims not to see this error in the logs (for our developments server upgraded last week and our production server upgraded today). @ Dannon
While we definitely do recommend that if you have the option to choose, go with postgres, Galaxy should function both now and in the future with MySQL. In this case, your galaxy will function just fine without that index.
I assume there are a lot of 'old' Galaxy servers using MySQL around, where the 'galaxy admin' (like me) would love to switch to postgres. Maybe we can do a community effort putting together a "MySQL-to-postgres" protocol for a defined Galaxy release? And after that release, only postgres is supported. I am sure this would make a lot of things easier.....something to discuss in Oslo? Regards, Hans-Rudolf
On Mon, Mar 4, 2013 at 7:59 AM, Hans-Rudolf Hotz <hrh@fmi.ch> wrote:
@ Dannon
While we definitely do recommend that if you have the option to choose, go with postgres, Galaxy should function both now and in the future with MySQL. In this case, your galaxy will function just fine without that index.
I assume there are a lot of 'old' Galaxy servers using MySQL around, where the 'galaxy admin' (like me) would love to switch to postgres. Maybe we can do a community effort putting together a "MySQL-to-postgres" protocol for a defined Galaxy release? And after that release, only postgres is supported. I am sure this would make a lot of things easier.....something to discuss in Oslo?
Sure, it's definitely something to discuss if we keep running into these issues, but my hope is really that upgrading SqlAlchemy will obviate the need to deal with this at all, and that everything will 'just work' going forward with whatever database folks want to use. That said, if there are others who want to just go ahead and migrate from MySQL to postgres a tested protocol for doing so would be a great thing to try and put together as a community and I'd be happy to help. -Dannon
participants (3)
-
Dannon Baker -
Derrick Lin -
Hans-Rudolf Hotz