DB migration failed, from Apollo 2.4.1 to 2.6.0

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DB migration failed, from Apollo 2.4.1 to 2.6.0

Wim S
Hi,

Thank you for the Apollo 2.6.0 release.

I am trying to deploy Apollo 2.6.0.  The database backend was created and populated using Apollo 2.4.1.

Deployment on Tomcat results in an empty  white page. I don't have access to the tomcat log.

Run local gives the following truncated (DB migration?) error. Or is there something else going on?

Is there a way to get the new Apollo 2.6.0 version to work with our current DB backend?


Thank you.




| Server running. Browse to http://localhost:8085/apollo
Configuring Shiro ...
Shiro Configured
Starting Quartz Scheduler in QuartzFactoryBean
| Error 2020-05-13 15:52:38,623 [localhost-startStop-1] ERROR liquibase  - Change Set changelog-2_6_0.groovy::1459788030180-1::nathandunn failed.  Error: Error executing SQL ALTER TABLE `synonym` DROP COLUMN `type_id`: Error on rename of './apollo2_dev/#sql-138a_2906d' to './apollo2_dev/synonym' (errno: 150)
Message: Error executing SQL ALTER TABLE `synonym` DROP COLUMN `type_id`: Error on rename of './apollo2_dev/#sql-138a_2906d' to './apollo2_dev/synonym' (errno: 150)
   
Line | Method
->>   62 | execute           in liquibase.executor.jvm.JdbcExecutor
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
|    104 | execute           in     ''
|   1091 | execute . . . . . in liquibase.database.AbstractDatabase
|   1075 | executeStatements in     ''
|    317 | execute . . . . . in liquibase.changelog.ChangeSet
|     27 | visit             in liquibase.changelog.visitor.UpdateVisitor
|     58 | run . . . . . . . in liquibase.changelog.ChangeLogIterator
|    114 | update            in liquibase.Liquibase
|    128 | doCall . . . . .  in grails.plugin.databasemigration.MigrationRunner$_runMigrations_closure2
|    120 | runMigrations     in grails.plugin.databasemigration.MigrationRunner
|     87 | doCall . . . . .  in grails.plugin.databasemigration.MigrationRunner$_autoRun_closure1
|    137 | executeInSession  in grails.plugin.databasemigration.MigrationUtils
|     58 | autoRun . . . . . in grails.plugin.databasemigration.MigrationRunner
|     97 | doCall            in DatabaseMigrationGrailsPlugin$_closure2
|    266 | run . . . . . . . in java.util.concurrent.FutureTask
|   1149 | runWorker         in java.util.concurrent.ThreadPoolExecutor
|    624 | run . . . . . . . in java.util.concurrent.ThreadPoolExecutor$Worker
^    748 | run               in java.lang.Thread
Caused by SQLException: Error on rename of './apollo2_dev/#sql-138a_2906d' to './apollo2_dev/synonym' (errno: 150)
->> 1086 | createSQLException in com.mysql.jdbc.SQLError
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
| Error 2020-05-13 15:52:38,893 [localhost-startStop-1] ERROR context.GrailsContextLoaderListener  - Error initializing the application: Migration failed for change set changelog-2_6_0.groovy::1459788030180-1::nathandunn:
     
Reason: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE `synonym` DROP COLUMN `type_id`: Error on rename of './apollo2_dev/#sql-138a_2906d' to './apollo2_dev/synonym' (errno: 150):
         
Caused By: Error executing SQL ALTER TABLE `synonym` DROP COLUMN `type_id`: Error on rename of './apollo2_dev/#sql-138a_2906d' to './apollo2_dev/synonym' (errno: 150):
         
Caused By: Error on rename of './apollo2_dev/#sql-138a_2906d' to './apollo2_dev/synonym' (errno: 150)
Message: Migration failed for change set changelog-2_6_0.groovy::1459788030180-1::nathandunn:
     
Reason: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE `synonym` DROP COLUMN `type_id`: Error on rename of './apollo2_dev/#sql-138a_2906d' to './apollo2_dev/synonym' (errno: 150):
         
Caused By: Error executing SQL ALTER TABLE `synonym` DROP COLUMN `type_id`: Error on rename of './apollo2_dev/#sql-138a_2906d' to './apollo2_dev/synonym' (errno: 150):
         
Caused By: Error on rename of './apollo2_dev/#sql-138a_2906d' to './apollo2_dev/synonym' (errno: 150)
   
Line | Method
->>  347 | execute          in liquibase.changelog.ChangeSet
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -




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Re: DB migration failed, from Apollo 2.4.1 to 2.6.0

nathandunn

Wim,

If you remove this block of code:


From grails-app/migrations/changelog-2_6_0.groovy does it work? 

Sorry, this works for 2.5.0 to 2.6.1 on PostgreSQL, but apparently not MySQL. 

Thanks,

Nathan


On May 18, 2020, at 5:53 AM, Wim S <[hidden email]> wrote:

Hi,

Thank you for the Apollo 2.6.0 release.

I am trying to deploy Apollo 2.6.0.  The database backend was created and populated using Apollo 2.4.1.

Deployment on Tomcat results in an empty  white page. I don't have access to the tomcat log.

Run local gives the following truncated (DB migration?) error. Or is there something else going on?

Is there a way to get the new Apollo 2.6.0 version to work with our current DB backend?


Thank you.




| Server running. Browse to http://localhost:8085/apollo
Configuring Shiro ...
Shiro Configured
Starting Quartz Scheduler in QuartzFactoryBean
| Error 2020-05-13 15:52:38,623 [localhost-startStop-1] ERROR liquibase  - Change Set changelog-2_6_0.groovy::1459788030180-1::nathandunn failed.  Error: Error executing SQL ALTER TABLE `synonym` DROP COLUMN `type_id`: Error on rename of './apollo2_dev/#sql-138a_2906d' to './apollo2_dev/synonym' (errno: 150)
Message: Error executing SQL ALTER TABLE `synonym` DROP COLUMN `type_id`: Error on rename of './apollo2_dev/#sql-138a_2906d' to './apollo2_dev/synonym' (errno: 150)
   
Line | Method
->>   62 | execute           in liquibase.executor.jvm.JdbcExecutor
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
|    104 | execute           in     ''
|   1091 | execute . . . . . in liquibase.database.AbstractDatabase
|   1075 | executeStatements in     ''
|    317 | execute . . . . . in liquibase.changelog.ChangeSet
|     27 | visit             in liquibase.changelog.visitor.UpdateVisitor
|     58 | run . . . . . . . in liquibase.changelog.ChangeLogIterator
|    114 | update            in liquibase.Liquibase
|    128 | doCall . . . . .  in grails.plugin.databasemigration.MigrationRunner$_runMigrations_closure2
|    120 | runMigrations     in grails.plugin.databasemigration.MigrationRunner
|     87 | doCall . . . . .  in grails.plugin.databasemigration.MigrationRunner$_autoRun_closure1
|    137 | executeInSession  in grails.plugin.databasemigration.MigrationUtils
|     58 | autoRun . . . . . in grails.plugin.databasemigration.MigrationRunner
|     97 | doCall            in DatabaseMigrationGrailsPlugin$_closure2
|    266 | run . . . . . . . in java.util.concurrent.FutureTask
|   1149 | runWorker         in java.util.concurrent.ThreadPoolExecutor
|    624 | run . . . . . . . in java.util.concurrent.ThreadPoolExecutor$Worker
^    748 | run               in java.lang.Thread
Caused by SQLException: Error on rename of './apollo2_dev/#sql-138a_2906d' to './apollo2_dev/synonym' (errno: 150)
->> 1086 | createSQLException in com.mysql.jdbc.SQLError
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
| Error 2020-05-13 15:52:38,893 [localhost-startStop-1] ERROR context.GrailsContextLoaderListener  - Error initializing the application: Migration failed for change set changelog-2_6_0.groovy::1459788030180-1::nathandunn:
     
Reason: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE `synonym` DROP COLUMN `type_id`: Error on rename of './apollo2_dev/#sql-138a_2906d' to './apollo2_dev/synonym' (errno: 150):
         
Caused By: Error executing SQL ALTER TABLE `synonym` DROP COLUMN `type_id`: Error on rename of './apollo2_dev/#sql-138a_2906d' to './apollo2_dev/synonym' (errno: 150):
         
Caused By: Error on rename of './apollo2_dev/#sql-138a_2906d' to './apollo2_dev/synonym' (errno: 150)
Message: Migration failed for change set changelog-2_6_0.groovy::1459788030180-1::nathandunn:
     
Reason: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE `synonym` DROP COLUMN `type_id`: Error on rename of './apollo2_dev/#sql-138a_2906d' to './apollo2_dev/synonym' (errno: 150):
         
Caused By: Error executing SQL ALTER TABLE `synonym` DROP COLUMN `type_id`: Error on rename of './apollo2_dev/#sql-138a_2906d' to './apollo2_dev/synonym' (errno: 150):
         
Caused By: Error on rename of './apollo2_dev/#sql-138a_2906d' to './apollo2_dev/synonym' (errno: 150)
   
Line | Method
->>  347 | execute          in liquibase.changelog.ChangeSet
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -





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Re: DB migration failed, from Apollo 2.4.1 to 2.6.0

Wim S
Hi Nathan,

Yes removing those lines worked, I could now deploy 2.6.0.

I also tried to disable counting the annotations as described here.  (not commenting in the other ticket to prevent spamming of the unintended people)

https://genomearchitect.readthedocs.io/en/latest/Configure.html?#count-annotations

Should I nest these configuration lines under another configuration, or should this go top level in the config?
I did add these lines to the config file, but I don't see a difference yet. I there a way that I can tell (other than the intended faster switching of chromosomes) that these lines were used. (i.e. should a count be missing somewhere now in the web interface).

Thank you.



Op maandag 18 mei 2020 18:41:10 UTC+2 schreef Nathan Dunn:

Wim,

If you remove this block of code:

<a href="https://github.com/GMOD/Apollo/blob/develop/grails-app/migrations/changelog-2_6_0.groovy#L3-L10" target="_blank" rel="nofollow" onmousedown="this.href=&#39;https://www.google.com/url?q\x3dhttps%3A%2F%2Fgithub.com%2FGMOD%2FApollo%2Fblob%2Fdevelop%2Fgrails-app%2Fmigrations%2Fchangelog-2_6_0.groovy%23L3-L10\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNHbJGeDpkDXBGx5DIPPhWOuTOXcyA&#39;;return true;" onclick="this.href=&#39;https://www.google.com/url?q\x3dhttps%3A%2F%2Fgithub.com%2FGMOD%2FApollo%2Fblob%2Fdevelop%2Fgrails-app%2Fmigrations%2Fchangelog-2_6_0.groovy%23L3-L10\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNHbJGeDpkDXBGx5DIPPhWOuTOXcyA&#39;;return true;">https://github.com/GMOD/Apollo/blob/develop/grails-app/migrations/changelog-2_6_0.groovy#L3-L10

From grails-app/migrations/changelog-2_6_0.groovy does it work? 

Sorry, this works for 2.5.0 to 2.6.1 on PostgreSQL, but apparently not MySQL. 

Thanks,

Nathan


On May 18, 2020, at 5:53 AM, Wim S <<a href="javascript:" target="_blank" gdf-obfuscated-mailto="7UjRawm7BQAJ" rel="nofollow" onmousedown="this.href=&#39;javascript:&#39;;return true;" onclick="this.href=&#39;javascript:&#39;;return true;">wim...@...> wrote:

Hi,

Thank you for the Apollo 2.6.0 release.

I am trying to deploy Apollo 2.6.0.  The database backend was created and populated using Apollo 2.4.1.

Deployment on Tomcat results in an empty  white page. I don't have access to the tomcat log.

Run local gives the following truncated (DB migration?) error. Or is there something else going on?

Is there a way to get the new Apollo 2.6.0 version to work with our current DB backend?


Thank you.




| Server running. Browse to http://localhost:8085/apollo
Configuring Shiro ...
Shiro Configured
Starting Quartz Scheduler in QuartzFactoryBean
| Error 2020-05-13 15:52:38,623 [localhost-startStop-1] ERROR liquibase  - Change Set changelog-2_6_0.groovy::1459788030180-1::nathandunn failed.  Error: Error executing SQL ALTER TABLE `synonym` DROP COLUMN `type_id`: Error on rename of './apollo2_dev/#sql-138a_2906d' to './apollo2_dev/synonym' (errno: 150)
Message: Error executing SQL ALTER TABLE `synonym` DROP COLUMN `type_id`: Error on rename of './apollo2_dev/#sql-138a_2906d' to './apollo2_dev/synonym' (errno: 150)
   
Line | Method
->>   62 | execute           in liquibase.executor.jvm.JdbcExecutor
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
|    104 | execute           in     ''
|   1091 | execute . . . . . in liquibase.database.AbstractDatabase
|   1075 | executeStatements in     ''
|    317 | execute . . . . . in liquibase.changelog.ChangeSet
|     27 | visit             in liquibase.changelog.visitor.UpdateVisitor
|     58 | run . . . . . . . in liquibase.changelog.ChangeLogIterator
|    114 | update            in liquibase.Liquibase
|    128 | doCall . . . . .  in grails.plugin.databasemigration.MigrationRunner$_runMigrations_closure2
|    120 | runMigrations     in grails.plugin.databasemigration.MigrationRunner
|     87 | doCall . . . . .  in grails.plugin.databasemigration.MigrationRunner$_autoRun_closure1
|    137 | executeInSession  in grails.plugin.databasemigration.MigrationUtils
|     58 | autoRun . . . . . in grails.plugin.databasemigration.MigrationRunner
|     97 | doCall            in DatabaseMigrationGrailsPlugin$_closure2
|    266 | run . . . . . . . in java.util.concurrent.FutureTask
|   1149 | runWorker         in java.util.concurrent.ThreadPoolExecutor
|    624 | run . . . . . . . in java.util.concurrent.ThreadPoolExecutor$Worker
^    748 | run               in java.lang.Thread
Caused by SQLException: Error on rename of './apollo2_dev/#sql-138a_2906d' to './apollo2_dev/synonym' (errno: 150)
->> 1086 | createSQLException in com.mysql.jdbc.SQLError
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
| Error 2020-05-13 15:52:38,893 [localhost-startStop-1] ERROR context.GrailsContextLoaderListener  - Error initializing the application: Migration failed for change set changelog-2_6_0.groovy::1459788030180-1::nathandunn:
     
Reason: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE `synonym` DROP COLUMN `type_id`: Error on rename of './apollo2_dev/#sql-138a_2906d' to './apollo2_dev/synonym' (errno: 150):
         
Caused By: Error executing SQL ALTER TABLE `synonym` DROP COLUMN `type_id`: Error on rename of './apollo2_dev/#sql-138a_2906d' to './apollo2_dev/synonym' (errno: 150):
         
Caused By: Error on rename of './apollo2_dev/#sql-138a_2906d' to './apollo2_dev/synonym' (errno: 150)
Message: Migration failed for change set changelog-2_6_0.groovy::1459788030180-1::nathandunn:
     
Reason: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE `synonym` DROP COLUMN `type_id`: Error on rename of './apollo2_dev/#sql-138a_2906d' to './apollo2_dev/synonym' (errno: 150):
         
Caused By: Error executing SQL ALTER TABLE `synonym` DROP COLUMN `type_id`: Error on rename of './apollo2_dev/#sql-138a_2906d' to './apollo2_dev/synonym' (errno: 150):
         
Caused By: Error on rename of './apollo2_dev/#sql-138a_2906d' to './apollo2_dev/synonym' (errno: 150)
   
Line | Method
->>  347 | execute          in liquibase.changelog.ChangeSet
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -





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Re: DB migration failed, from Apollo 2.4.1 to 2.6.0

nathandunn


On May 19, 2020, at 4:42 AM, Wim S <[hidden email]> wrote:

Hi Nathan,

Yes removing those lines worked, I could now deploy 2.6.0.

Excellent.  I’m disabling those for a future release.  Thanks for letting me know about that, though curious it was an issue. 


I also tried to disable counting the annotations as described here.  (not commenting in the other ticket to prevent spamming of the unintended people)


Should I nest these configuration lines under another configuration, or should this go top level in the config?
I did add these lines to the config file, but I don't see a difference yet. I there a way that I can tell (other than the intended faster switching of chromosomes) that these lines were used. (i.e. should a count be missing somewhere now in the web interface).

In the organism and reference sequences panel annotations should be “0”.   If you aren’t having any performance problems (i.e., no page takes more than 10 seconds to load), I wouldn’t do this.   

Nathan






Thank you.



Op maandag 18 mei 2020 18:41:10 UTC+2 schreef Nathan Dunn:

Wim,

If you remove this block of code:

<a href="https://github.com/GMOD/Apollo/blob/develop/grails-app/migrations/changelog-2_6_0.groovy#L3-L10" target="_blank" rel="nofollow" onmousedown="this.href='https://www.google.com/url?q\x3dhttps%3A%2F%2Fgithub.com%2FGMOD%2FApollo%2Fblob%2Fdevelop%2Fgrails-app%2Fmigrations%2Fchangelog-2_6_0.groovy%23L3-L10\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNHbJGeDpkDXBGx5DIPPhWOuTOXcyA';return true;" onclick="this.href='https://www.google.com/url?q\x3dhttps%3A%2F%2Fgithub.com%2FGMOD%2FApollo%2Fblob%2Fdevelop%2Fgrails-app%2Fmigrations%2Fchangelog-2_6_0.groovy%23L3-L10\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNHbJGeDpkDXBGx5DIPPhWOuTOXcyA';return true;" class="">https://github.com/GMOD/Apollo/blob/develop/grails-app/migrations/changelog-2_6_0.groovy#L3-L10

From grails-app/migrations/changelog-2_6_0.groovy does it work? 

Sorry, this works for 2.5.0 to 2.6.1 on PostgreSQL, but apparently not MySQL. 

Thanks,

Nathan


On May 18, 2020, at 5:53 AM, Wim S <<a href="javascript:" target="_blank" gdf-obfuscated-mailto="7UjRawm7BQAJ" rel="nofollow" onmousedown="this.href='javascript:';return true;" onclick="this.href='javascript:';return true;" class="">wim...@...> wrote:

Hi,

Thank you for the Apollo 2.6.0 release.

I am trying to deploy Apollo 2.6.0.  The database backend was created and populated using Apollo 2.4.1.

Deployment on Tomcat results in an empty  white page. I don't have access to the tomcat log.

Run local gives the following truncated (DB migration?) error. Or is there something else going on?

Is there a way to get the new Apollo 2.6.0 version to work with our current DB backend?


Thank you.




| Server running. Browse to http://localhost:8085/apollo
Configuring Shiro ...
Shiro Configured
Starting Quartz Scheduler in QuartzFactoryBean
| Error 2020-05-13 15:52:38,623 [localhost-startStop-1] ERROR liquibase  - Change Set changelog-2_6_0.groovy::1459788030180-1::nathandunn failed.  Error: Error executing SQL ALTER TABLE `synonym` DROP COLUMN `type_id`: Error on rename of './apollo2_dev/#sql-138a_2906d' to './apollo2_dev/synonym' (errno: 150)
Message: Error executing SQL ALTER TABLE `synonym` DROP COLUMN `type_id`: Error on rename of './apollo2_dev/#sql-138a_2906d' to './apollo2_dev/synonym' (errno: 150)
   
Line | Method
->>   62 | execute           in liquibase.executor.jvm.JdbcExecutor
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
|    104 | execute           in     ''
|   1091 | execute . . . . . in liquibase.database.AbstractDatabase
|   1075 | executeStatements in     ''
|    317 | execute . . . . . in liquibase.changelog.ChangeSet
|     27 | visit             in liquibase.changelog.visitor.UpdateVisitor
|     58 | run . . . . . . . in liquibase.changelog.ChangeLogIterator
|    114 | update            in liquibase.Liquibase
|    128 | doCall . . . . .  in grails.plugin.databasemigration.MigrationRunner$_runMigrations_closure2
|    120 | runMigrations     in grails.plugin.databasemigration.MigrationRunner
|     87 | doCall . . . . .  in grails.plugin.databasemigration.MigrationRunner$_autoRun_closure1
|    137 | executeInSession  in grails.plugin.databasemigration.MigrationUtils
|     58 | autoRun . . . . . in grails.plugin.databasemigration.MigrationRunner
|     97 | doCall            in DatabaseMigrationGrailsPlugin$_closure2
|    266 | run . . . . . . . in java.util.concurrent.FutureTask
|   1149 | runWorker         in java.util.concurrent.ThreadPoolExecutor
|    624 | run . . . . . . . in java.util.concurrent.ThreadPoolExecutor$Worker
^    748 | run               in java.lang.Thread
Caused by SQLException: Error on rename of './apollo2_dev/#sql-138a_2906d' to './apollo2_dev/synonym' (errno: 150)
->> 1086 | createSQLException in com.mysql.jdbc.SQLError
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
| Error 2020-05-13 15:52:38,893 [localhost-startStop-1] ERROR context.GrailsContextLoaderListener  - Error initializing the application: Migration failed for change set changelog-2_6_0.groovy::1459788030180-1::nathandunn:
     
Reason: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE `synonym` DROP COLUMN `type_id`: Error on rename of './apollo2_dev/#sql-138a_2906d' to './apollo2_dev/synonym' (errno: 150):
         
Caused By: Error executing SQL ALTER TABLE `synonym` DROP COLUMN `type_id`: Error on rename of './apollo2_dev/#sql-138a_2906d' to './apollo2_dev/synonym' (errno: 150):
         
Caused By: Error on rename of './apollo2_dev/#sql-138a_2906d' to './apollo2_dev/synonym' (errno: 150)
Message: Migration failed for change set changelog-2_6_0.groovy::1459788030180-1::nathandunn:
     
Reason: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE `synonym` DROP COLUMN `type_id`: Error on rename of './apollo2_dev/#sql-138a_2906d' to './apollo2_dev/synonym' (errno: 150):
         
Caused By: Error executing SQL ALTER TABLE `synonym` DROP COLUMN `type_id`: Error on rename of './apollo2_dev/#sql-138a_2906d' to './apollo2_dev/synonym' (errno: 150):
         
Caused By: Error on rename of './apollo2_dev/#sql-138a_2906d' to './apollo2_dev/synonym' (errno: 150)
   
Line | Method
->>  347 | execute          in liquibase.changelog.ChangeSet
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -






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Re: DB migration failed, from Apollo 2.4.1 to 2.6.0

Wim S
In the organism panel, the gene counts are 0.
In the ref-sequence panel, the gene counts are still shown for the active organism.

Switching chromosomes still takes close to a minute.

Maybe the query is still triggered somehow from the ref-sequence panel?

Wim

Op dinsdag 19 mei 2020 17:04:41 UTC+2 schreef Nathan Dunn:


On May 19, 2020, at 4:42 AM, Wim S <<a href="javascript:" target="_blank" gdf-obfuscated-mailto="32xDBFoEBgAJ" rel="nofollow" onmousedown="this.href=&#39;javascript:&#39;;return true;" onclick="this.href=&#39;javascript:&#39;;return true;">wim...@...> wrote:

Hi Nathan,

Yes removing those lines worked, I could now deploy 2.6.0.

Excellent.  I’m disabling those for a future release.  Thanks for letting me know about that, though curious it was an issue. 


I also tried to disable counting the annotations as described here.  (not commenting in the other ticket to prevent spamming of the unintended people)

<a href="https://genomearchitect.readthedocs.io/en/latest/Configure.html?#count-annotations" target="_blank" rel="nofollow" onmousedown="this.href=&#39;https://www.google.com/url?q\x3dhttps%3A%2F%2Fgenomearchitect.readthedocs.io%2Fen%2Flatest%2FConfigure.html%3F%23count-annotations\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNF3m-1Flh3JipWFT5qQkF1M5ymwzg&#39;;return true;" onclick="this.href=&#39;https://www.google.com/url?q\x3dhttps%3A%2F%2Fgenomearchitect.readthedocs.io%2Fen%2Flatest%2FConfigure.html%3F%23count-annotations\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNF3m-1Flh3JipWFT5qQkF1M5ymwzg&#39;;return true;">https://genomearchitect.readthedocs.io/en/latest/Configure.html?#count-annotations

Should I nest these configuration lines under another configuration, or should this go top level in the config?
I did add these lines to the config file, but I don't see a difference yet. I there a way that I can tell (other than the intended faster switching of chromosomes) that these lines were used. (i.e. should a count be missing somewhere now in the web interface).

In the organism and reference sequences panel annotations should be “0”.   If you aren’t having any performance problems (i.e., no page takes more than 10 seconds to load), I wouldn’t do this.   

Nathan






Thank you.



Op maandag 18 mei 2020 18:41:10 UTC+2 schreef Nathan Dunn:

Wim,

If you remove this block of code:

<a href="https://github.com/GMOD/Apollo/blob/develop/grails-app/migrations/changelog-2_6_0.groovy#L3-L10" rel="nofollow" target="_blank" onmousedown="this.href=&#39;https://www.google.com/url?q\x3dhttps%3A%2F%2Fgithub.com%2FGMOD%2FApollo%2Fblob%2Fdevelop%2Fgrails-app%2Fmigrations%2Fchangelog-2_6_0.groovy%23L3-L10\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNHbJGeDpkDXBGx5DIPPhWOuTOXcyA&#39;;return true;" onclick="this.href=&#39;https://www.google.com/url?q\x3dhttps%3A%2F%2Fgithub.com%2FGMOD%2FApollo%2Fblob%2Fdevelop%2Fgrails-app%2Fmigrations%2Fchangelog-2_6_0.groovy%23L3-L10\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNHbJGeDpkDXBGx5DIPPhWOuTOXcyA&#39;;return true;">https://github.com/GMOD/Apollo/blob/develop/grails-app/migrations/changelog-2_6_0.groovy#L3-L10

From grails-app/migrations/changelog-2_6_0.groovy does it work? 

Sorry, this works for 2.5.0 to 2.6.1 on PostgreSQL, but apparently not MySQL. 

Thanks,

Nathan


On May 18, 2020, at 5:53 AM, Wim S <[hidden email]> wrote:

Hi,

Thank you for the Apollo 2.6.0 release.

I am trying to deploy Apollo 2.6.0.  The database backend was created and populated using Apollo 2.4.1.

Deployment on Tomcat results in an empty  white page. I don't have access to the tomcat log.

Run local gives the following truncated (DB migration?) error. Or is there something else going on?

Is there a way to get the new Apollo 2.6.0 version to work with our current DB backend?


Thank you.




| Server running. Browse to http://localhost:8085/apollo
Configuring Shiro ...
Shiro Configured
Starting Quartz Scheduler in QuartzFactoryBean
| Error 2020-05-13 15:52:38,623 [localhost-startStop-1] ERROR liquibase  - Change Set changelog-2_6_0.groovy::1459788030180-1::nathandunn failed.  Error: Error executing SQL ALTER TABLE `synonym` DROP COLUMN `type_id`: Error on rename of './apollo2_dev/#sql-138a_2906d' to './apollo2_dev/synonym' (errno: 150)
Message: Error executing SQL ALTER TABLE `synonym` DROP COLUMN `type_id`: Error on rename of './apollo2_dev/#sql-138a_2906d' to './apollo2_dev/synonym' (errno: 150)
   
Line | Method
->>   62 | execute           in liquibase.executor.jvm.JdbcExecutor
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
|    104 | execute           in     ''
|   1091 | execute . . . . . in liquibase.database.AbstractDatabase
|   1075 | executeStatements in     ''
|    317 | execute . . . . . in liquibase.changelog.ChangeSet
|     27 | visit             in liquibase.changelog.visitor.UpdateVisitor
|     58 | run . . . . . . . in liquibase.changelog.ChangeLogIterator
|    114 | update            in liquibase.Liquibase
|    128 | doCall . . . . .  in grails.plugin.databasemigration.MigrationRunner$_runMigrations_closure2
|    120 | runMigrations     in grails.plugin.databasemigration.MigrationRunner
|     87 | doCall . . . . .  in grails.plugin.databasemigration.MigrationRunner$_autoRun_closure1
|    137 | executeInSession  in grails.plugin.databasemigration.MigrationUtils
|     58 | autoRun . . . . . in grails.plugin.databasemigration.MigrationRunner
|     97 | doCall            in DatabaseMigrationGrailsPlugin$_closure2
|    266 | run . . . . . . . in java.util.concurrent.FutureTask
|   1149 | runWorker         in java.util.concurrent.ThreadPoolExecutor
|    624 | run . . . . . . . in java.util.concurrent.ThreadPoolExecutor$Worker
^    748 | run               in java.lang.Thread
Caused by SQLException: Error on rename of './apollo2_dev/#sql-138a_2906d' to './apollo2_dev/synonym' (errno: 150)
->> 1086 | createSQLException in com.mysql.jdbc.SQLError
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
| Error 2020-05-13 15:52:38,893 [localhost-startStop-1] ERROR context.GrailsContextLoaderListener  - Error initializing the application: Migration failed for change set changelog-2_6_0.groovy::1459788030180-1::nathandunn:
     
Reason: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE `synonym` DROP COLUMN `type_id`: Error on rename of './apollo2_dev/#sql-138a_2906d' to './apollo2_dev/synonym' (errno: 150):
         
Caused By: Error executing SQL ALTER TABLE `synonym` DROP COLUMN `type_id`: Error on rename of './apollo2_dev/#sql-138a_2906d' to './apollo2_dev/synonym' (errno: 150):
         
Caused By: Error on rename of './apollo2_dev/#sql-138a_2906d' to './apollo2_dev/synonym' (errno: 150)
Message: Migration failed for change set changelog-2_6_0.groovy::1459788030180-1::nathandunn:
     
Reason: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE `synonym` DROP COLUMN `type_id`: Error on rename of './apollo2_dev/#sql-138a_2906d' to './apollo2_dev/synonym' (errno: 150):
         
Caused By: Error executing SQL ALTER TABLE `synonym` DROP COLUMN `type_id`: Error on rename of './apollo2_dev/#sql-138a_2906d' to './apollo2_dev/synonym' (errno: 150):
         
Caused By: Error on rename of './apollo2_dev/#sql-138a_2906d' to './apollo2_dev/synonym' (errno: 150)
   
Line | Method
->>  347 | execute          in liquibase.changelog.ChangeSet
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -






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Re: DB migration failed, from Apollo 2.4.1 to 2.6.0

nathandunn

If you have several thousand annotations on a reference sequence, it will likely take a minute or so.  

I **might** have a fix for this (it has been there for this last 5 years). 

For this version of Apollo, you really only want to annotate the differences if possible if you will have lots of annotated / more complex isoforms. 

Either way, we are aware of this, and are looking at updating the back end, but I’m not sure how long that will take. 

Nathan


On May 19, 2020, at 8:28 AM, Wim S <[hidden email]> wrote:

In the organism panel, the gene counts are 0.
In the ref-sequence panel, the gene counts are still shown for the active organism.

Switching chromosomes still takes close to a minute.

Maybe the query is still triggered somehow from the ref-sequence panel?

Wim

Op dinsdag 19 mei 2020 17:04:41 UTC+2 schreef Nathan Dunn:


On May 19, 2020, at 4:42 AM, Wim S <<a href="javascript:" target="_blank" gdf-obfuscated-mailto="32xDBFoEBgAJ" rel="nofollow" onmousedown="this.href='javascript:';return true;" onclick="this.href='javascript:';return true;" class="">wim...@...> wrote:

Hi Nathan,

Yes removing those lines worked, I could now deploy 2.6.0.

Excellent.  I’m disabling those for a future release.  Thanks for letting me know about that, though curious it was an issue. 


I also tried to disable counting the annotations as described here.  (not commenting in the other ticket to prevent spamming of the unintended people)

<a href="https://genomearchitect.readthedocs.io/en/latest/Configure.html?#count-annotations" target="_blank" rel="nofollow" onmousedown="this.href='https://www.google.com/url?q\x3dhttps%3A%2F%2Fgenomearchitect.readthedocs.io%2Fen%2Flatest%2FConfigure.html%3F%23count-annotations\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNF3m-1Flh3JipWFT5qQkF1M5ymwzg';return true;" onclick="this.href='https://www.google.com/url?q\x3dhttps%3A%2F%2Fgenomearchitect.readthedocs.io%2Fen%2Flatest%2FConfigure.html%3F%23count-annotations\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNF3m-1Flh3JipWFT5qQkF1M5ymwzg';return true;" class="">https://genomearchitect.readthedocs.io/en/latest/Configure.html?#count-annotations

Should I nest these configuration lines under another configuration, or should this go top level in the config?
I did add these lines to the config file, but I don't see a difference yet. I there a way that I can tell (other than the intended faster switching of chromosomes) that these lines were used. (i.e. should a count be missing somewhere now in the web interface).

In the organism and reference sequences panel annotations should be “0”.   If you aren’t having any performance problems (i.e., no page takes more than 10 seconds to load), I wouldn’t do this.   

Nathan






Thank you.



Op maandag 18 mei 2020 18:41:10 UTC+2 schreef Nathan Dunn:

Wim,

If you remove this block of code:

<a href="https://github.com/GMOD/Apollo/blob/develop/grails-app/migrations/changelog-2_6_0.groovy#L3-L10" rel="nofollow" target="_blank" onmousedown="this.href='https://www.google.com/url?q\x3dhttps%3A%2F%2Fgithub.com%2FGMOD%2FApollo%2Fblob%2Fdevelop%2Fgrails-app%2Fmigrations%2Fchangelog-2_6_0.groovy%23L3-L10\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNHbJGeDpkDXBGx5DIPPhWOuTOXcyA';return true;" onclick="this.href='https://www.google.com/url?q\x3dhttps%3A%2F%2Fgithub.com%2FGMOD%2FApollo%2Fblob%2Fdevelop%2Fgrails-app%2Fmigrations%2Fchangelog-2_6_0.groovy%23L3-L10\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNHbJGeDpkDXBGx5DIPPhWOuTOXcyA';return true;" class="">https://github.com/GMOD/Apollo/blob/develop/grails-app/migrations/changelog-2_6_0.groovy#L3-L10

From grails-app/migrations/changelog-2_6_0.groovy does it work? 

Sorry, this works for 2.5.0 to 2.6.1 on PostgreSQL, but apparently not MySQL. 

Thanks,

Nathan


On May 18, 2020, at 5:53 AM, Wim S <[hidden email]> wrote:

Hi,

Thank you for the Apollo 2.6.0 release.

I am trying to deploy Apollo 2.6.0.  The database backend was created and populated using Apollo 2.4.1.

Deployment on Tomcat results in an empty  white page. I don't have access to the tomcat log.

Run local gives the following truncated (DB migration?) error. Or is there something else going on?

Is there a way to get the new Apollo 2.6.0 version to work with our current DB backend?


Thank you.




| Server running. Browse to http://localhost:8085/apollo
Configuring Shiro ...
Shiro Configured
Starting Quartz Scheduler in QuartzFactoryBean
| Error 2020-05-13 15:52:38,623 [localhost-startStop-1] ERROR liquibase  - Change Set changelog-2_6_0.groovy::1459788030180-1::nathandunn failed.  Error: Error executing SQL ALTER TABLE `synonym` DROP COLUMN `type_id`: Error on rename of './apollo2_dev/#sql-138a_2906d' to './apollo2_dev/synonym' (errno: 150)
Message: Error executing SQL ALTER TABLE `synonym` DROP COLUMN `type_id`: Error on rename of './apollo2_dev/#sql-138a_2906d' to './apollo2_dev/synonym' (errno: 150)
   
Line | Method
->>   62 | execute           in liquibase.executor.jvm.JdbcExecutor
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
|    104 | execute           in     ''
|   1091 | execute . . . . . in liquibase.database.AbstractDatabase
|   1075 | executeStatements in     ''
|    317 | execute . . . . . in liquibase.changelog.ChangeSet
|     27 | visit             in liquibase.changelog.visitor.UpdateVisitor
|     58 | run . . . . . . . in liquibase.changelog.ChangeLogIterator
|    114 | update            in liquibase.Liquibase
|    128 | doCall . . . . .  in grails.plugin.databasemigration.MigrationRunner$_runMigrations_closure2
|    120 | runMigrations     in grails.plugin.databasemigration.MigrationRunner
|     87 | doCall . . . . .  in grails.plugin.databasemigration.MigrationRunner$_autoRun_closure1
|    137 | executeInSession  in grails.plugin.databasemigration.MigrationUtils
|     58 | autoRun . . . . . in grails.plugin.databasemigration.MigrationRunner
|     97 | doCall            in DatabaseMigrationGrailsPlugin$_closure2
|    266 | run . . . . . . . in java.util.concurrent.FutureTask
|   1149 | runWorker         in java.util.concurrent.ThreadPoolExecutor
|    624 | run . . . . . . . in java.util.concurrent.ThreadPoolExecutor$Worker
^    748 | run               in java.lang.Thread
Caused by SQLException: Error on rename of './apollo2_dev/#sql-138a_2906d' to './apollo2_dev/synonym' (errno: 150)
->> 1086 | createSQLException in com.mysql.jdbc.SQLError
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
| Error 2020-05-13 15:52:38,893 [localhost-startStop-1] ERROR context.GrailsContextLoaderListener  - Error initializing the application: Migration failed for change set changelog-2_6_0.groovy::1459788030180-1::nathandunn:
     
Reason: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE `synonym` DROP COLUMN `type_id`: Error on rename of './apollo2_dev/#sql-138a_2906d' to './apollo2_dev/synonym' (errno: 150):
         
Caused By: Error executing SQL ALTER TABLE `synonym` DROP COLUMN `type_id`: Error on rename of './apollo2_dev/#sql-138a_2906d' to './apollo2_dev/synonym' (errno: 150):
         
Caused By: Error on rename of './apollo2_dev/#sql-138a_2906d' to './apollo2_dev/synonym' (errno: 150)
Message: Migration failed for change set changelog-2_6_0.groovy::1459788030180-1::nathandunn:
     
Reason: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE `synonym` DROP COLUMN `type_id`: Error on rename of './apollo2_dev/#sql-138a_2906d' to './apollo2_dev/synonym' (errno: 150):
         
Caused By: Error executing SQL ALTER TABLE `synonym` DROP COLUMN `type_id`: Error on rename of './apollo2_dev/#sql-138a_2906d' to './apollo2_dev/synonym' (errno: 150):
         
Caused By: Error on rename of './apollo2_dev/#sql-138a_2906d' to './apollo2_dev/synonym' (errno: 150)
   
Line | Method
->>  347 | execute          in liquibase.changelog.ChangeSet
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -







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Re: DB migration failed, from Apollo 2.4.1 to 2.6.0

Wim S
Ok thank you for the information.

Op dinsdag 19 mei 2020 18:09:54 UTC+2 schreef Nathan Dunn:

If you have several thousand annotations on a reference sequence, it will likely take a minute or so.  

I **might** have a fix for this (it has been there for this last 5 years). 

For this version of Apollo, you really only want to annotate the differences if possible if you will have lots of annotated / more complex isoforms. 

Either way, we are aware of this, and are looking at updating the back end, but I’m not sure how long that will take. 

Nathan


On May 19, 2020, at 8:28 AM, Wim S <<a href="javascript:" target="_blank" gdf-obfuscated-mailto="fRi1-ugHBgAJ" rel="nofollow" onmousedown="this.href=&#39;javascript:&#39;;return true;" onclick="this.href=&#39;javascript:&#39;;return true;">wim...@...> wrote:

In the organism panel, the gene counts are 0.
In the ref-sequence panel, the gene counts are still shown for the active organism.

Switching chromosomes still takes close to a minute.

Maybe the query is still triggered somehow from the ref-sequence panel?

Wim

Op dinsdag 19 mei 2020 17:04:41 UTC+2 schreef Nathan Dunn:


On May 19, 2020, at 4:42 AM, Wim S <[hidden email]> wrote:

Hi Nathan,

Yes removing those lines worked, I could now deploy 2.6.0.

Excellent.  I’m disabling those for a future release.  Thanks for letting me know about that, though curious it was an issue. 


I also tried to disable counting the annotations as described here.  (not commenting in the other ticket to prevent spamming of the unintended people)

<a href="https://genomearchitect.readthedocs.io/en/latest/Configure.html?#count-annotations" rel="nofollow" target="_blank" onmousedown="this.href=&#39;https://www.google.com/url?q\x3dhttps%3A%2F%2Fgenomearchitect.readthedocs.io%2Fen%2Flatest%2FConfigure.html%3F%23count-annotations\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNF3m-1Flh3JipWFT5qQkF1M5ymwzg&#39;;return true;" onclick="this.href=&#39;https://www.google.com/url?q\x3dhttps%3A%2F%2Fgenomearchitect.readthedocs.io%2Fen%2Flatest%2FConfigure.html%3F%23count-annotations\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNF3m-1Flh3JipWFT5qQkF1M5ymwzg&#39;;return true;">https://genomearchitect.readthedocs.io/en/latest/Configure.html?#count-annotations

Should I nest these configuration lines under another configuration, or should this go top level in the config?
I did add these lines to the config file, but I don't see a difference yet. I there a way that I can tell (other than the intended faster switching of chromosomes) that these lines were used. (i.e. should a count be missing somewhere now in the web interface).

In the organism and reference sequences panel annotations should be “0”.   If you aren’t having any performance problems (i.e., no page takes more than 10 seconds to load), I wouldn’t do this.   

Nathan






Thank you.



Op maandag 18 mei 2020 18:41:10 UTC+2 schreef Nathan Dunn:

Wim,

If you remove this block of code:

<a href="https://github.com/GMOD/Apollo/blob/develop/grails-app/migrations/changelog-2_6_0.groovy#L3-L10" rel="nofollow" target="_blank" onmousedown="this.href=&#39;https://www.google.com/url?q\x3dhttps%3A%2F%2Fgithub.com%2FGMOD%2FApollo%2Fblob%2Fdevelop%2Fgrails-app%2Fmigrations%2Fchangelog-2_6_0.groovy%23L3-L10\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNHbJGeDpkDXBGx5DIPPhWOuTOXcyA&#39;;return true;" onclick="this.href=&#39;https://www.google.com/url?q\x3dhttps%3A%2F%2Fgithub.com%2FGMOD%2FApollo%2Fblob%2Fdevelop%2Fgrails-app%2Fmigrations%2Fchangelog-2_6_0.groovy%23L3-L10\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNHbJGeDpkDXBGx5DIPPhWOuTOXcyA&#39;;return true;">https://github.com/GMOD/Apollo/blob/develop/grails-app/migrations/changelog-2_6_0.groovy#L3-L10

From grails-app/migrations/changelog-2_6_0.groovy does it work? 

Sorry, this works for 2.5.0 to 2.6.1 on PostgreSQL, but apparently not MySQL. 

Thanks,

Nathan


On May 18, 2020, at 5:53 AM, Wim S <[hidden email]> wrote:

Hi,

Thank you for the Apollo 2.6.0 release.

I am trying to deploy Apollo 2.6.0.  The database backend was created and populated using Apollo 2.4.1.

Deployment on Tomcat results in an empty  white page. I don't have access to the tomcat log.

Run local gives the following truncated (DB migration?) error. Or is there something else going on?

Is there a way to get the new Apollo 2.6.0 version to work with our current DB backend?


Thank you.




| Server running. Browse to http://localhost:8085/apollo
Configuring Shiro ...
Shiro Configured
Starting Quartz Scheduler in QuartzFactoryBean
| Error 2020-05-13 15:52:38,623 [localhost-startStop-1] ERROR liquibase  - Change Set changelog-2_6_0.groovy::1459788030180-1::nathandunn failed.  Error: Error executing SQL ALTER TABLE `synonym` DROP COLUMN `type_id`: Error on rename of './apollo2_dev/#sql-138a_2906d' to './apollo2_dev/synonym' (errno: 150)
Message: Error executing SQL ALTER TABLE `synonym` DROP COLUMN `type_id`: Error on rename of './apollo2_dev/#sql-138a_2906d' to './apollo2_dev/synonym' (errno: 150)
   
Line | Method
->>   62 | execute           in liquibase.executor.jvm.JdbcExecutor
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
|    104 | execute           in     ''
|   1091 | execute . . . . . in liquibase.database.AbstractDatabase
|   1075 | executeStatements in     ''
|    317 | execute . . . . . in liquibase.changelog.ChangeSet
|     27 | visit             in liquibase.changelog.visitor.UpdateVisitor
|     58 | run . . . . . . . in liquibase.changelog.ChangeLogIterator
|    114 | update            in liquibase.Liquibase
|    128 | doCall . . . . .  in grails.plugin.databasemigration.MigrationRunner$_runMigrations_closure2
|    120 | runMigrations     in grails.plugin.databasemigration.MigrationRunner
|     87 | doCall . . . . .  in grails.plugin.databasemigration.MigrationRunner$_autoRun_closure1
|    137 | executeInSession  in grails.plugin.databasemigration.MigrationUtils
|     58 | autoRun . . . . . in grails.plugin.databasemigration.MigrationRunner
|     97 | doCall            in DatabaseMigrationGrailsPlugin$_closure2
|    266 | run . . . . . . . in java.util.concurrent.FutureTask
|   1149 | runWorker         in java.util.concurrent.ThreadPoolExecutor
|    624 | run . . . . . . . in java.util.concurrent.ThreadPoolExecutor$Worker
^    748 | run               in java.lang.Thread
Caused by SQLException: Error on rename of './apollo2_dev/#sql-138a_2906d' to './apollo2_dev/synonym' (errno: 150)
->> 1086 | createSQLException in com.mysql.jdbc.SQLError
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| Error 2020-05-13 15:52:38,893 [localhost-startStop-1] ERROR context.GrailsContextLoaderListener  - Error initializing the application: Migration failed for change set changelog-2_6_0.groovy::1459788030180-1::nathandunn:
     
Reason: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE `synonym` DROP COLUMN `type_id`: Error on rename of './apollo2_dev/#sql-138a_2906d' to './apollo2_dev/synonym' (errno: 150):
         
Caused By: Error executing SQL ALTER TABLE `synonym` DROP COLUMN `type_id`: Error on rename of './apollo2_dev/#sql-138a_2906d' to './apollo2_dev/synonym' (errno: 150):
         
Caused By: Error on rename of './apollo2_dev/#sql-138a_2906d' to './apollo2_dev/synonym' (errno: 150)
Message: Migration failed for change set changelog-2_6_0.groovy::1459788030180-1::nathandunn:
     
Reason: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE `synonym` DROP COLUMN `type_id`: Error on rename of './apollo2_dev/#sql-138a_2906d' to './apollo2_dev/synonym' (errno: 150):
         
Caused By: Error executing SQL ALTER TABLE `synonym` DROP COLUMN `type_id`: Error on rename of './apollo2_dev/#sql-138a_2906d' to './apollo2_dev/synonym' (errno: 150):
         
Caused By: Error on rename of './apollo2_dev/#sql-138a_2906d' to './apollo2_dev/synonym' (errno: 150)
   
Line | Method
->>  347 | execute          in liquibase.changelog.ChangeSet
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