This also took out my job handlers (exception below). So the introduction
of non-ascii characters into the table (via the job stdout/stderr capture)
can make a galaxy instance pretty useless.

I was able to find the offending records using "SELECT count(*) FROM job
WHERE stderr similar to '%\x8b%';"
Turns out it was the byproduct of doing a path paste of some gzipped fastq
files (so they where never decompressed, just passed along), and then
fastq_groomer.py complains about the file having an invalid header (line
22?) reports back an invalid header and prints it out, thus the non-ascii
characters in the stderr.

I 'cleaned' the database with 'update job set stderr =
regexp_replace(stderr, '\x8b', '\x5f');'. But there should probably be some
safe guards put in place to stop this from happening.

Kyle



galaxy.jobs.handler INFO 2013-07-06 12:35:32,033 job handler stop queue
started
Traceback (most recent call last):
  File "/inside/depot4/galaxy/lib/galaxy/webapps/galaxy/buildapp.py", line
35, in app_factory
    app = UniverseApplication( global_conf = global_conf, **kwargs )
  File "/inside/depot4/galaxy/lib/galaxy/app.py", line 164, in __init__
    self.job_manager = manager.JobManager( self )
  File "/inside/depot4/galaxy/lib/galaxy/jobs/manager.py", line 36, in
__init__
    self.job_handler.start()
  File "/inside/depot4/galaxy/lib/galaxy/jobs/handler.py", line 34, in start
    self.job_queue.start()
  File "/inside/depot4/galaxy/lib/galaxy/jobs/handler.py", line 77, in start
    self.__check_jobs_at_startup()
  File "/inside/depot4/galaxy/lib/galaxy/jobs/handler.py", line 92, in
__check_jobs_at_startup
    & ( model.Job.handler == self.app.config.server_name ) ):
  File
"/inside/depot4/galaxy/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/orm/query.py",
line 2341, in instances
    fetch = cursor.fetchall()
  File
"/inside/depot4/galaxy/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/engine/base.py",
line 3204, in fetchall
    l = self.process_rows(self._fetchall_impl())
  File
"/inside/depot4/galaxy/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/engine/base.py",
line 3171, in _fetchall_impl
    return self.cursor.fetchall()
UnicodeDecodeError: 'ascii' codec can't decode byte 0x8b in position 404:
ordinal not in range(128)



On Fri, Jul 5, 2013 at 11:43 PM, Kyle Ellrott <kellr...@soe.ucsc.edu> wrote:

> I'm getting an exception when trying to look at the admin job management
> screen. It looks like SQLAlchemy doesn't like non-ascii characters. Any
> ideas about what to do?
>
>
> Error - <type 'exceptions.UnicodeDecodeError'>: 'ascii' codec can't decode
> byte 0x8b in position 404: ordinal not in range(128)
> URL: http://pk.kilokluster.ucsc.edu:8079/admin/jobs
> File '/inside/depot4/galaxy/lib/galaxy/web/framework/middleware/error.py',
> line 149 in __call__
>   app_iter = self.application(environ, sr_checker)
> File
> '/inside/depot4/galaxy/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py',
> line 84 in __call__
>   return self.application(environ, start_response)
> File
> '/inside/depot4/galaxy/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py',
> line 633 in __call__
>   return self.application(environ, start_response)
> File '/inside/depot4/galaxy/lib/galaxy/web/framework/base.py', line 132 in
> __call__
>   return self.handle_request( environ, start_response )
> File '/inside/depot4/galaxy/lib/galaxy/web/framework/base.py', line 190 in
> handle_request
>   body = method( trans, **kwargs )
> File '/inside/depot4/galaxy/lib/galaxy/web/framework/__init__.py', line
> 221 in decorator
>   return func( self, trans, *args, **kwargs )
> File '/inside/depot4/galaxy/lib/galaxy/web/base/controllers/admin.py',
> line 1053 in jobs
>   for job in jobs:
> File
> '/inside/depot4/galaxy/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/orm/query.py',
> line 2341 in instances
> File
> '/inside/depot4/galaxy/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/engine/base.py',
> line 3204 in fetchall
> File
> '/inside/depot4/galaxy/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/engine/base.py',
> line 3171 in _fetchall_impl
> UnicodeDecodeError: 'ascii' codec can't decode byte 0x8b in position 404:
> ordinal not in range(128)
>
>
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