[galaxy-dev] Error in database after trying the innocently named, but devastatingly evil test in manage_db.sh

2013-02-08 Thread Thon de Boer 
Hi,

 

I had a small issue with the total usage of my galaxy system showing some 
negative random number so I figured my database was a little “off”.

 

I snooped around for some database management tools and found “manage_db.sh” 
which had an option innocently called “test”.

 

I ran it, without reading the little fine print that states: “Performs the 
upgrade and downgrade option on the given database. This is not a real test and 
may leave the database in a bad state. You should therefore better run the test 
on a copy of your database.”

 

Well…It surely did leave my database in a bad state since now I get this when I 
try to access the toolshed installed tools:

 


Error Traceback:


View as:http://srv151/admin_toolshed/browse_repositories Interactive  |   
http://srv151/admin_toolshed/browse_repositories Text  |   
http://srv151/admin_toolshed/browse_repositories XML  
http://srv151/admin_toolshed/browse_repositories (full)

⇝ ProgrammingError: (ProgrammingError) relation 
repository_repository_dependency_association does not exist LINE 2: FROM 
repository_repository_dependency_association ^ 'SELECT 
repository_repository_dependency_association.id AS 
repository_repository_dependency_association_id, 
repository_repository_dependency_association.create_time AS 
repository_repository_dependency_association_create_time, 
repository_repository_dependency_association.update_time AS 
repository_repository_dependency_association_update_time, 
repository_repository_dependency_association.tool_shed_repository_id AS 
repository_repository_dependency_association_tool_shed_re_1, 
repository_repository_dependency_association.repository_dependency_id AS 
repository_repository_dependency_association_repository_d_2 \nFROM 
repository_repository_dependency_association \nWHERE %(param_1)s = 
repository_repository_dependency_association.tool_shed_repository_id' 
{'param_1': 5}

URL:  http://srv151/admin_toolshed/browse_repositories 
http://srv151/admin_toolshed/browse_repositories

 

Is there ANY way I can rescue this fiasco? Suffice it to say I did not do it on 
a copy and did not do a backup (yes, I learned my lesson), but maybe some SQL 
skullduggery can help me?

 

Thanks


Thon

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Re: [galaxy-dev] Error in database after trying the innocently named, but devastatingly evil test in manage_db.sh

2013-02-08 Thread Daniel Blankenberg 
Hi Thon,

The test option runs the upgrade and downgrade of the latest migration script. 
I'm assuming that you had already run the latest migrations available and the 
server was up and running OK (other than the dataset size issue) before trying 
the test command.

On a COPY of your database, you can try this:

$ sh manage_db.sh version
XYZ
$ sh manage_db.sh downgrade [XYZ -1]
..
done
sh manage_db.sh upgrade XYZ

done

If it works, then you can try it on your real database. Of course, this will 
destroy whatever data existed in the table/columns of the latest migration (but 
it looks like you already lost them.)


Thanks for using Galaxy,

Dan


On Feb 8, 2013, at 2:32 PM, Thon de Boer wrote:

 Hi,
  
 I had a small issue with the total usage of my galaxy system showing some 
 negative random number so I figured my database was a little “off”.
  
 I snooped around for some database management tools and found “manage_db.sh” 
 which had an option innocently called “test”.
  
 I ran it, without reading the little fine print that states: “Performs the 
 upgrade and downgrade option on the given database. This is not a real test 
 and may leave the database in a bad state. You should therefore better run 
 the test on a copy of your database.”
  
 Well…It surely did leave my database in a bad state since now I get this when 
 I try to access the toolshed installed tools:
  
 Error Traceback:
 View as:   Interactive  |  Text  |  XML (full)
 ⇝ ProgrammingError: (ProgrammingError) relation 
 repository_repository_dependency_association does not exist LINE 2: FROM 
 repository_repository_dependency_association ^ 'SELECT 
 repository_repository_dependency_association.id AS 
 repository_repository_dependency_association_id, 
 repository_repository_dependency_association.create_time AS 
 repository_repository_dependency_association_create_time, 
 repository_repository_dependency_association.update_time AS 
 repository_repository_dependency_association_update_time, 
 repository_repository_dependency_association.tool_shed_repository_id AS 
 repository_repository_dependency_association_tool_shed_re_1, 
 repository_repository_dependency_association.repository_dependency_id AS 
 repository_repository_dependency_association_repository_d_2 \nFROM 
 repository_repository_dependency_association \nWHERE %(param_1)s = 
 repository_repository_dependency_association.tool_shed_repository_id' 
 {'param_1': 5}
 URL: http://srv151/admin_toolshed/browse_repositories
  
 Is there ANY way I can rescue this fiasco? Suffice it to say I did not do it 
 on a copy and did not do a backup (yes, I learned my lesson), but maybe some 
 SQL skullduggery can help me?
  
 Thanks
 
 Thon
 ___
 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:
 
  http://lists.bx.psu.edu/

___
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:

  http://lists.bx.psu.edu/

Re: [galaxy-dev] Error in database after trying the innocently named, but devastatingly evil test in manage_db.sh

2013-02-08 Thread Thon de Boer 
Hi Dan,

 

I tried that but it failed ofcourse since the table it tries to drop from 109 
- 108 does not exisit.

 

sh manage_db.sh downgrade 108

109 - 108...

0109_add_repository_dependency_tables DEBUG 2013-02-08 13:04:33,464 Dropping 
repository_repository_dependency_association table failed: (ProgrammingError) 
table repository_repository_dependency_association does not exist

'\nDROP TABLE repository_repository_dependency_association' {}

0109_add_repository_dependency_tables DEBUG 2013-02-08 13:04:33,464 Dropping 
repository_repository_dependency_association table failed: (ProgrammingError) 
table repository_repository_dependency_association does not exist

'\nDROP TABLE repository_repository_dependency_association' {}

0109_add_repository_dependency_tables DEBUG 2013-02-08 13:04:33,467 Dropping 
repository_dependency table failed: (ProgrammingError) table 
repository_dependency does not exist

'\nDROP TABLE repository_dependency' {}

0109_add_repository_dependency_tables DEBUG 2013-02-08 13:04:33,467 Dropping 
repository_dependency table failed: (ProgrammingError) table 
repository_dependency does not exist

'\nDROP TABLE repository_dependency' {}

done

(galaxy_env)[svcgalaxy@srv151 g]$ sh manage_db.sh version

109

 

I just went into the database and create the two dummy tables and tried it 
again and it seem to work..

I downgraded and upgraded to 109…

 

Then I restarted Galaxy, reset the metatdata (which failed for 2 of my 13 
tools) and then I see this in the manage toolshed:

 


Error Traceback:


View as:http://srv151/admin_toolshed/browse_repositories Interactive  |   
http://srv151/admin_toolshed/browse_repositories Text  |   
http://srv151/admin_toolshed/browse_repositories XML  
http://srv151/admin_toolshed/browse_repositories (full)

⇝ ProgrammingError: (ProgrammingError) column 
repository_repository_dependency_association.id does not exist LINE 1: 
..._7f8dcc0e81d0_de8f CURSOR WITHOUT HOLD FOR SELECT repository... ^ 'SELECT 
repository_repository_dependency_association.id AS 
repository_repository_dependency_association_id, 
repository_repository_dependency_association.create_time AS 
repository_repository_dependency_association_create_time, 
repository_repository_dependency_association.update_time AS 
repository_repository_dependency_association_update_time, 
repository_repository_dependency_association.tool_shed_repository_id AS 
repository_repository_dependency_association_tool_shed_re_1, 
repository_repository_dependency_association.repository_dependency_id AS 
repository_repository_dependency_association_repository_d_2 \nFROM 
repository_repository_dependency_association \nWHERE %(param_1)s = 
repository_repository_dependency_association.tool_shed_repository_id' 
{'param_1': 5}

 

Slightly different error, but an error nonetheless…

 

Any more ideas?

I am (somewhat) OK with having to reload the toolshed tools but I can’t even 
install or manage any new toolsheds…

 

Thanks

 

Thon

From: Daniel Blankenberg [mailto:d...@bx.psu.edu] 
Sent: Friday, February 08, 2013 12:32 PM
To: Thon de Boer
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Error in database after trying the innocently named, 
but devastatingly evil test in manage_db.sh

 

Hi Thon,

 

The test option runs the upgrade and downgrade of the latest migration script. 
I'm assuming that you had already run the latest migrations available and the 
server was up and running OK (other than the dataset size issue) before trying 
the test command.

 

On a COPY of your database, you can try this:

 

$ sh manage_db.sh version

XYZ

$ sh manage_db.sh downgrade [XYZ -1]

..

done

sh manage_db.sh upgrade XYZ



done

 

If it works, then you can try it on your real database. Of course, this will 
destroy whatever data existed in the table/columns of the latest migration (but 
it looks like you already lost them.)

 

 

Thanks for using Galaxy,

 

Dan

 

 

On Feb 8, 2013, at 2:32 PM, Thon de Boer wrote:





Hi,

 

I had a small issue with the total usage of my galaxy system showing some 
negative random number so I figured my database was a little “off”.

 

I snooped around for some database management tools and found “manage_db.sh” 
which had an option innocently called “test”.

 

I ran it, without reading the little fine print that states: “Performs the 
upgrade and downgrade option on the given database. This is not a real test and 
may leave the database in a bad state. You should therefore better run the test 
on a copy of your database.”

 

Well…It surely did leave my database in a bad state since now I get this when I 
try to access the toolshed installed tools:

 


Error Traceback:


View as:http://srv151/admin_toolshed/browse_repositories Interactive  |   
http://srv151/admin_toolshed/browse_repositories Text  |   
http://srv151/admin_toolshed/browse_repositories XML  
http://srv151/admin_toolshed/browse_repositories (full)

⇝ ProgrammingError: (ProgrammingError) relation

Re: [galaxy-dev] Error in database after trying the innocently named, but devastatingly evil test in manage_db.sh

2013-02-08 Thread Thon de Boer 
OK..I tried it a few more times and this time with different results! HA! I 
knew I wasn’t insane…As long as you try anything often enough in the same 
manner, you WILL get a different outcome…Yea uncertainty principle!

 

I also had to resort to downloading the whole complete galaxy-dist from 11-Jan 
since the current development version of galaxy-dist is broken, but I’m back in 
business and first order is to create a backup plan

 

Thon

 

From: galaxy-dev-boun...@lists.bx.psu.edu 
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Thon de Boer
Sent: Friday, February 08, 2013 1:23 PM
To: 'Daniel Blankenberg'
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Error in database after trying the innocently named, 
but devastatingly evil test in manage_db.sh

 

Hi Dan,

 

I tried that but it failed ofcourse since the table it tries to drop from 109 
- 108 does not exisit.

 

sh manage_db.sh downgrade 108

109 - 108...

0109_add_repository_dependency_tables DEBUG 2013-02-08 13:04:33,464 Dropping 
repository_repository_dependency_association table failed: (ProgrammingError) 
table repository_repository_dependency_association does not exist

'\nDROP TABLE repository_repository_dependency_association' {}

0109_add_repository_dependency_tables DEBUG 2013-02-08 13:04:33,464 Dropping 
repository_repository_dependency_association table failed: (ProgrammingError) 
table repository_repository_dependency_association does not exist

'\nDROP TABLE repository_repository_dependency_association' {}

0109_add_repository_dependency_tables DEBUG 2013-02-08 13:04:33,467 Dropping 
repository_dependency table failed: (ProgrammingError) table 
repository_dependency does not exist

'\nDROP TABLE repository_dependency' {}

0109_add_repository_dependency_tables DEBUG 2013-02-08 13:04:33,467 Dropping 
repository_dependency table failed: (ProgrammingError) table 
repository_dependency does not exist

'\nDROP TABLE repository_dependency' {}

done

(galaxy_env)[svcgalaxy@srv151 g]$ sh manage_db.sh version

109

 

I just went into the database and create the two dummy tables and tried it 
again and it seem to work..

I downgraded and upgraded to 109…

 

Then I restarted Galaxy, reset the metatdata (which failed for 2 of my 13 
tools) and then I see this in the manage toolshed:

 


Error Traceback:


View as:http://srv151/admin_toolshed/browse_repositories Interactive  |   
http://srv151/admin_toolshed/browse_repositories Text  |   
http://srv151/admin_toolshed/browse_repositories XML  
http://srv151/admin_toolshed/browse_repositories (full)

⇝ ProgrammingError: (ProgrammingError) column 
repository_repository_dependency_association.id does not exist LINE 1: 
..._7f8dcc0e81d0_de8f CURSOR WITHOUT HOLD FOR SELECT repository... ^ 'SELECT 
repository_repository_dependency_association.id AS 
repository_repository_dependency_association_id, 
repository_repository_dependency_association.create_time AS 
repository_repository_dependency_association_create_time, 
repository_repository_dependency_association.update_time AS 
repository_repository_dependency_association_update_time, 
repository_repository_dependency_association.tool_shed_repository_id AS 
repository_repository_dependency_association_tool_shed_re_1, 
repository_repository_dependency_association.repository_dependency_id AS 
repository_repository_dependency_association_repository_d_2 \nFROM 
repository_repository_dependency_association \nWHERE %(param_1)s = 
repository_repository_dependency_association.tool_shed_repository_id' 
{'param_1': 5}

 

Slightly different error, but an error nonetheless…

 

Any more ideas?

I am (somewhat) OK with having to reload the toolshed tools but I can’t even 
install or manage any new toolsheds…

 

Thanks

 

Thon

From: Daniel Blankenberg [mailto:d...@bx.psu.edu] 
Sent: Friday, February 08, 2013 12:32 PM
To: Thon de Boer
Cc: galaxy-dev@lists.bx.psu.edu mailto:galaxy-dev@lists.bx.psu.edu 
Subject: Re: [galaxy-dev] Error in database after trying the innocently named, 
but devastatingly evil test in manage_db.sh

 

Hi Thon,

 

The test option runs the upgrade and downgrade of the latest migration script. 
I'm assuming that you had already run the latest migrations available and the 
server was up and running OK (other than the dataset size issue) before trying 
the test command.

 

On a COPY of your database, you can try this:

 

$ sh manage_db.sh version

XYZ

$ sh manage_db.sh downgrade [XYZ -1]

..

done

sh manage_db.sh upgrade XYZ



done

 

If it works, then you can try it on your real database. Of course, this will 
destroy whatever data existed in the table/columns of the latest migration (but 
it looks like you already lost them.)

 

 

Thanks for using Galaxy,

 

Dan

 

 

On Feb 8, 2013, at 2:32 PM, Thon de Boer wrote:

 

Hi,

 

I had a small issue with the total usage of my galaxy system showing some 
negative random number so I figured my database was a little “off”.

 

I snooped around for