Hi Greg,

I tried to upgrade the GALAXY-CENTRAL version of my installation to fix the 90-91 upgrade bug, but I don't seem to see revision 271ccd09bc23 there...Is this issue fixed in galaxy central or only in the main installation?

Thanks

Thon

On Feb 07, 2012, at 08:11 AM, Greg Von Kuster <g...@bx.psu.edu> wrote:

Hi Thon,

The fix for this issue in now available in the central repo in change set  revision 271ccd09bc23.  Even though you have a working version of Galaxy, you should update your instance to at least this revision, and then do the following as soon as possible.

%sh manage_db.sh downgrade 90
91 -> 90... 
done

%sh manage_db.sh upgrade
90 -> 91... 

The problem was caused because you are running postgres version 9 and the original version of my migration script did not handle hex bytea for that version of postgres.

Thanks for finding this problem!

Greg

On Feb 6, 2012, at 10:08 PM, Anthonius deBoer wrote:

Oh, and whatever you did in the little patch, it worked...At least I have a working version of galaxy again and the database seems to be all intact..

Thanks!

Thon

On Feb 06, 2012, at 03:52 PM, Greg Von Kuster <g...@bx.psu.edu> wrote:

Can you replace lines 75 - 86 of the file ~/lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py with the following for loop and send me your paster log?

Thanks!

    for row in result:
        tool_shed_repository_id = row[0]
        try:
            repository_metadata = from_json_string( str( row[1] ) )
            # Create a new row in the tool table for each tool included in repository.  We will NOT
            # handle tool_version_associaions because we do not have the information we need to do so.
            tools = repository_metadata.get( 'tools', [] )
            for tool_dict in tools:
                cmd = "INSERT INTO tool_version VALUES (%s, %s, %s, '%s', %s)" % \
                    ( nextval( 'tool_version' ), localtimestamp(), localtimestamp(), tool_dict[ 'guid' ], tool_shed_repository_id )
                db_session.execute( cmd )
                count += 1
        except Exception, e:
            print "Repository metadata: ", str( row[1] )
            print "Exception setting tool versions for tools in tool_shed_repository with id: ", str( tool_shed_repository_id )
            print str( e )

The lines of code you are replacing look like this:

    for row in result:
        if row[1]:
            tool_shed_repository_id = row[0]
            repository_metadata = from_json_string( str( row[1] ) )
            # Create a new row in the tool table for each tool included in repository.  We will NOT
            # handle tool_version_associaions because we do not have the information we need to do so.
            tools = repository_metadata.get( 'tools', [] )
            for tool_dict in tools:
                cmd = "INSERT INTO tool_version VALUES (%s, %s, %s, '%s', %s)" % \
                    ( nextval( 'tool_version' ), localtimestamp(), localtimestamp(), tool_dict[ 'guid' ], tool_shed_repository_id )
                db_session.execute( cmd )
                count += 1


On Feb 6, 2012, at 5:23 PM, Anthonius deBoer wrote:

I manually dropped the tool_version and tool_association table in the database and I am left with the JSON error as shown below:

90 -> 91...

Migration script to create the tool_version and tool_version_association tables and drop the tool_id_guid_map table.

Traceback (most recent call last):
  File "./scripts/manage_db.py", line 63, in <module>
    main( repository=repo, url="" )
  File "/home/tdeboer/code/galaxy-central/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/shell.py", line 150, in main
    ret = command_func(**kwargs)
  File "/home/tdeboer/code/galaxy-central/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/api.py", line 221, in upgrade
    return _migrate(url, repository, version, upgrade=True, err=err, **opts)
  File "/home/tdeboer/code/galaxy-central/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/api.py", line 349, in _migrate
    schema.runchange(ver, change, changeset.step)
  File "/home/tdeboer/code/galaxy-central/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/schema.py", line 184, in runchange
    change.run(self.engine, step)
  File "/home/tdeboer/code/galaxy-central/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/script/py.py", line 101, in run
    func()
  File "lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py", line 78, in upgrade
    repository_metadata = from_json_string( str( row[1] ) )
  File "/home/tdeboer/code/galaxy-central/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs2.egg/simplejson/__init__.py", line 384, in loads
  File "/home/tdeboer/code/galaxy-central/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs2.egg/simplejson/decoder.py", line 402, in decode
  File "/home/tdeboer/code/galaxy-central/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs2.egg/simplejson/decoder.py", line 420, in raw_decode
simplejson.decoder.JSONDecodeError: No JSON object could be decoded: line 1 column 0 (char 0)


On Feb 06, 2012, at 02:08 PM, Anthonius deBoer <thondeb...@me.com> wrote:

Hi Greg,

I tried the downgrade/upgrade path and got the exact same message I sent before.
I am using a postgres database that is running on local host.
I did indeed install some toolshed repositories before I tried to upgrade.
I also tried to downgrade to 89 and then upgrade, with the exact same message.

Thon

On Feb 06, 2012, at 10:51 AM, Greg Von Kuster <g...@bx.psu.edu> wrote:

Hello Thon,

Attempting to run the migration script twice to the same version always poses problems.  Can you downgrade successfully as follows?

sh manage_db.sh downgrade 90

If so, downgrade, then upgrade again and send the paster log from the clean upgrade if you see a problem.  Also:
What database are you using?  
Have you installed any tool shed repositories into your local Galaxy instance?

Thanks,

Greg


On Feb 6, 2012, at 1:32 PM, Thon Deboer wrote:

Hi,

I updated to the latest galaxy-central version but got this error when trying to upgrade...

Any ideas? It seems the table had already been created (this was the second time I run upgrade) but the JSON error was one that showed up the first time...)

Thanks

Thon

 sh manage_db.sh upgrade
90 -> 91...

Migration script to create the tool_version and tool_version_association tables and drop the tool_id_guid_map table.

0091_add_tool_version_tables DEBUG 2012-02-06 10:23:39,847 Creating tool_version table failed: (ProgrammingError) relation "tool_version" already exists
 '\nCREATE TABLE tool_version (\n\tid SERIAL NOT NULL, \n\tcreate_time TIMESTAMP WITHOUT TIME ZONE, \n\tupdate_time TIMESTAMP WITHOUT TIME ZONE, \n\ttool_id VARCHAR(255), \n\ttool_shed_repository_id INTEGER, \n\tPRIMARY KEY (id), \n\t FOREIGN KEY(tool_shed_repository_id) REFERENCES tool_shed_repository (id)\n)\n\n' {}
0091_add_tool_version_tables DEBUG 2012-02-06 10:23:39,847 Creating tool_version table failed: (ProgrammingError) relation "tool_version" already exists
 '\nCREATE TABLE tool_version (\n\tid SERIAL NOT NULL, \n\tcreate_time TIMESTAMP WITHOUT TIME ZONE, \n\tupdate_time TIMESTAMP WITHOUT TIME ZONE, \n\ttool_id VARCHAR(255), \n\ttool_shed_repository_id INTEGER, \n\tPRIMARY KEY (id), \n\t FOREIGN KEY(tool_shed_repository_id) REFERENCES tool_shed_repository (id)\n)\n\n' {}
0091_add_tool_version_tables DEBUG 2012-02-06 10:23:39,863 Creating tool_version_association table failed: (ProgrammingError) relation "tool_version_association" already exists
 '\nCREATE TABLE tool_version_association (\n\tid SERIAL NOT NULL, \n\ttool_id INTEGER NOT NULL, \n\tparent_id INTEGER NOT NULL, \n\tPRIMARY KEY (id), \n\t FOREIGN KEY(tool_id) REFERENCES tool_version (id), \n\t FOREIGN KEY(parent_id) REFERENCES tool_version (id)\n)\n\n' {}
0091_add_tool_version_tables DEBUG 2012-02-06 10:23:39,863 Creating tool_version_association table failed: (ProgrammingError) relation "tool_version_association" already exists
 '\nCREATE TABLE tool_version_association (\n\tid SERIAL NOT NULL, \n\ttool_id INTEGER NOT NULL, \n\tparent_id INTEGER NOT NULL, \n\tPRIMARY KEY (id), \n\t FOREIGN KEY(tool_id) REFERENCES tool_version (id), \n\t FOREIGN KEY(parent_id) REFERENCES tool_version (id)\n)\n\n' {}
Traceback (most recent call last):
  File "./scripts/manage_db.py", line 63, in <module>
    main( repository=repo, url="" )
  File "/home/tdeboer/code/galaxy-central/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/shell.py", line 150, in main
    ret = command_func(**kwargs)
  File "/home/tdeboer/code/galaxy-central/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/api.py", line 221, in upgrade
    return _migrate(url, repository, version, upgrade=True, err=err, **opts)
  File "/home/tdeboer/code/galaxy-central/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/api.py", line 349, in _migrate
    schema.runchange(ver, change, changeset.step)
  File "/home/tdeboer/code/galaxy-central/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/schema.py", line 184, in runchange
    change.run(self.engine, step)
  File "/home/tdeboer/code/galaxy-central/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/script/py.py", line 101, in run
    func()
  File "lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py", line 78, in upgrade
    repository_metadata = from_json_string( str( row[1] ) )
  File "/home/tdeboer/code/galaxy-central/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs2.egg/simplejson/__init__.py", line 384, in loads
  File "/home/tdeboer/code/galaxy-central/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs2.egg/simplejson/decoder.py", line 402, in decode
  File "/home/tdeboer/code/galaxy-central/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs2.egg/simplejson/decoder.py", line 420, in raw_decode
simplejson.decoder.JSONDecodeError: No JSON object could be decoded: line 1 column 0 (char 0)



Regards,

Thon de Boer, Ph.D.
Bioinformatics Guru
+1-650-799-6839




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Hi G
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