Thanks John -

Would it be more productive for us to port gsummary.py as a shed tool? 
best -
david


On Oct 2, 2014, at 6:46 AM, John Chilton <jmchil...@gmail.com> wrote:

> Thanks for the additional details - I am responding on list for people
> who may encounter similar problems in the future.
> 
> The job running code will provide both core tools and tool shed tools
> with the same PYTHONPATH - but some tools might setup a Python
> virtualenv for instance which would replace the PYTHONPATH completely
> I believe. Since gsummary is not in the tool shed - it will not be
> able to find any of the tool shed dependencies. These rpy issues are
> tough ones.
> 
> It should be possible to hack something together if you change the
> requirements in gsummary to be package requirements for R and Rpy and
> then find working env.sh files in tool_dependency_dir and copy them to
> tool_dependency_dir/R/2.11/env.sh and
> tool_dependency_dir/Rpy/1.0.3/env.sh respectively.
> 
> The tool shed is suppose to solve all of these pesky dependency
> problems - but not all the tools have been migrated and fixed yet.
> Thanks for your patience and for using Galaxy!
> 
> -John
> 
> On Wed, Oct 1, 2014 at 1:36 PM, David Bernick <dbern...@soe.ucsc.edu> wrote:
>> Hi John -
>> 
>> Yes, we are using MySQL. This event happened as a result of attempting to 
>> add/delete tools from our instance (Rpy_1_0_3 and R_2_11).
>> We ended up reloading the database from our nightly backup, and that got us 
>> going again.
>> 
>> The issue I was trying to solve when I "broke" the database was 
>> Summary_statistics not being able to find its Rpy module. I now have R and 
>> Rpy installed, such that tool-shed tools are happy with it, but gsummary.py 
>> is still unable to find Rpy.  We are attempting to solve this, but are as 
>> yet without a fix.  In the meantime, I have installed datamash, and that is 
>> working, It seems that tool-shed tools have a different PYTHONPATH than 
>> galaxy-dist tools?
>> 
>> As it happens, we also had a few cases with multiple instances of tool-shed 
>> tools being installed. Since this server is brand new, it was fine to delete 
>> them. I suppose that maybe we are now fitting in MySQL BLOBs now??
>> 
>> thanks again -
>> David
>> 
>> 
>> 
>> On Oct 1, 2014, at 9:44 AM, John Chilton <jmchil...@gmail.com> wrote:
>> 
>>> Hello David,
>>> 
>>> We don't have a workaround yet - but we (Dan did most of the
>>> investigating) understand the problem I think. You are using a MySQL
>>> database I assume? (Ignore the rest of this e-mail if not). I think
>>> MySQL has lower limits on the size of BLOBs that can be stored in the
>>> database than postgres - and we think the tool shed is tried to
>>> storing a really large blob of metadata in the database and it got
>>> truncated and now Galaxy is failing because it cannot load that entry
>>> as JSON.
>>> 
>>> The work around would be something like trying to find the truncated
>>> column in the tool_repositories table - deleting it and references -
>>> changing that column to a LONGBLOB and reinstalling that tool.
>>> 
>>> I have created a Trello card for this bug report.
>>> 
>>> https://trello.com/c/RbW6pOd2
>>> 
>>> It is said a lot but we strongly encourage not using MySQL.
>>> 
>>> It might be worth trying this patch
>>> (https://bitbucket.org/galaxy/galaxy-central/pull-request/511/allow-model-objects-to-be-loaded-when-they/diff#comment-3288189)
>>> from Dan as well. I am not sure what the tool shed would do if it
>>> cannot find the metadata though.
>>> 
>>> -John
>>> 
>>> On Mon, Sep 29, 2014 at 11:41 AM, David Bernick <dbern...@soe.ucsc.edu> 
>>> wrote:
>>>> Good morning -
>>>> 
>>>> I have acquired an Internal server error on our local galaxy install. It
>>>> seems to be an unterminated string.  How do I resolve this?
>>>> thanks in advance -
>>>> David Bernick
>>>> UCSC
>>>> 
>>>> Here is the relevant portion of the log (I hope).
>>>> 
>>>> Error - <type 'exceptions.ValueError'>: Unterminated string starting at:
>>>> line 1 column 65528 (char 65528)
>>>> URL: http://campusrocks.cse.ucsc.edu:8080/admin/index
>>>> File
>>>> '/projects/galaxy/bin/galaxy-dist/lib/galaxy/web/framework/middleware/error.py',
>>>> line 149 in __call__
>>>> app_iter = self.application(environ, sr_checker)
>>>> File
>>>> '/projects/galaxy/bin/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/recursive.py',
>>>> line 84 in __call__
>>>> return self.application(environ, start_response)
>>>> File
>>>> '/projects/galaxy/bin/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpexceptions.py',
>>>> line 633 in __call__
>>>> return self.application(environ, start_response)
>>>> File '/projects/galaxy/bin/galaxy-dist/lib/galaxy/web/framework/base.py',
>>>> line 132 in __call__
>>>> return self.handle_request( environ, start_response )
>>>> File '/projects/galaxy/bin/galaxy-dist/lib/galaxy/web/framework/base.py',
>>>> line 190 in handle_request
>>>> body = method( trans, **kwargs )
>>>> File
>>>> '/projects/galaxy/bin/galaxy-dist/lib/galaxy/web/framework/__init__.py',
>>>> line 383 in decorator
>>>> return func( self, trans, *args, **kwargs )
>>>> File
>>>> '/projects/galaxy/bin/galaxy-dist/lib/galaxy/web/base/controllers/admin.py',
>>>> line 34 in index
>>>> installing_repository_ids =
>>>> suc.get_ids_of_tool_shed_repositories_being_installed( trans.app,
>>>> as_string=True )
>>>> File
>>>> '/projects/galaxy/bin/galaxy-dist/lib/tool_shed/util/shed_util_common.py',
>>>> line 277 in get_ids_of_tool_shed_repositories_being_installed
>>>> app.install_model.ToolShedRepository.status == loading_datatypes_status )
>>>> ):
>>>> File
>>>> '/projects/galaxy/bin/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py',
>>>> line 2348 in instances
>>>> File
>>>> '/projects/galaxy/bin/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/mapper.py',
>>>> line 2120 in _instance
>>>> File
>>>> '/projects/galaxy/bin/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/mapper.py',
>>>> line 1974 in populate_state
>>>> File
>>>> '/projects/galaxy/bin/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/strategies.py',
>>>> line 150 in fetch_col
>>>> File
>>>> '/projects/galaxy/bin/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/types.py',
>>>> line 658 in process
>>>> File '/projects/galaxy/bin/galaxy-dist/lib/galaxy/model/custom_types.py',
>>>> line 52 in process_result_value
>>>> return json_decoder.decode( str( _sniffnfix_pg9_hex(value) ) )
>>>> File '/usr/lib64/python2.6/json/decoder.py', line 319 in decode
>>>> obj, end = self.raw_decode(s, idx=_w(s, 0).end())
>>>> File '/usr/lib64/python2.6/json/decoder.py', line 336 in raw_decode
>>>> obj, end = self._scanner.iterscan(s, **kw).next()
>>>> File '/usr/lib64/python2.6/json/scanner.py', line 55 in iterscan
>>>> rval, next_pos = action(m, context)
>>>> File '/usr/lib64/python2.6/json/decoder.py', line 183 in JSONObject
>>>> value, end = iterscan(s, idx=end, context=context).next()
>>>> File '/usr/lib64/python2.6/json/scanner.py', line 55 in iterscan
>>>> rval, next_pos = action(m, context)
>>>> File '/usr/lib64/python2.6/json/decoder.py', line 217 in JSONArray
>>>> value, end = iterscan(s, idx=end, context=context).next()
>>>> File '/usr/lib64/python2.6/json/scanner.py', line 55 in iterscan
>>>> rval, next_pos = action(m, context)
>>>> File '/usr/lib64/python2.6/json/decoder.py', line 183 in JSONObject
>>>> value, end = iterscan(s, idx=end, context=context).next()
>>>> File '/usr/lib64/python2.6/json/scanner.py', line 55 in iterscan
>>>> rval, next_pos = action(m, context)
>>>> File '/usr/lib64/python2.6/json/decoder.py', line 217 in JSONArray
>>>> value, end = iterscan(s, idx=end, context=context).next()
>>>> File '/usr/lib64/python2.6/json/scanner.py', line 55 in iterscan
>>>> rval, next_pos = action(m, context)
>>>> File '/usr/lib64/python2.6/json/decoder.py', line 183 in JSONObject
>>>> value, end = iterscan(s, idx=end, context=context).next()
>>>> File '/usr/lib64/python2.6/json/scanner.py', line 55 in iterscan
>>>> rval, next_pos = action(m, context)
>>>> File '/usr/lib64/python2.6/json/decoder.py', line 217 in JSONArray
>>>> value, end = iterscan(s, idx=end, context=context).next()
>>>> File '/usr/lib64/python2.6/json/scanner.py', line 55 in iterscan
>>>> rval, next_pos = action(m, context)
>>>> File '/usr/lib64/python2.6/json/decoder.py', line 217 in JSONArray
>>>> value, end = iterscan(s, idx=end, context=context).next()
>>>> File '/usr/lib64/python2.6/json/scanner.py', line 55 in iterscan
>>>> rval, next_pos = action(m, context)
>>>> File '/usr/lib64/python2.6/json/decoder.py', line 155 in JSONString
>>>> return scanstring(match.string, match.end(), encoding, strict)
>>>> ValueError: Unterminated string starting at: line 1 column 65528 (char
>>>> 65528)
>>>> 
>>>> 
>>>> ___________________________________________________________
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>> 


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