I do have a test case that should exercise interesting UTF-8 stuff.

Perhaps it would help to narrow down whether this is a problem of the
test case being too weak or my system having some sort of
configuration that is different than yours. Can you try to run

python run_client_tests.py --url=http://localhost:8913

(replacing the URL with whatever it should actually be based on your
setup.) Does that pass or fail? It should cause some logging on the
LWR side but if the above call complete without throwing an error than
the test case passed.

Thanks for your continued patience and sorry I have not been able to
reproduce the problem.

-John


On Mon, Dec 8, 2014 at 3:48 AM, Misharl Monsoor <mmons...@sb-roscoff.fr> wrote:
> Hi John,
>
> Thanks again for you help. So i place "sys.setdefaultencoding('utf-8')" at
> the top of the "lwr/web/framework.py", and i still have this bug.
>
> I use Python version "2.7 64 bits" to executes LWR on the windows server,
> and i encounter a "common" problem with the "setdefaultencoding" function
> which can't be loaded when doing "import sys" and
> "sys.setdefaultencoding('utf-8')". The hack that i found was to do
> "reload(sys)" then "sys.setdefaultencoding('utf-8')". But i still get the
> "utf8' codec can't decode byte" bug. Can it come from my input data which
> contains utf8 characters?
>
> Thank you very much,
>
> Bests regards,
>
> Misharl Monsoor
>
>
>
> Le 04/12/2014 06:25, John Chilton a écrit :
>
>> I have had one other report of this error previously - but I have not
>> been able to reproduce it. I have tried so hard to understand these
>> unicode/utf-8/Python 2 v 3/etc... issues and I must admit I simply
>> don't :(.
>>
>> Reading through http://farmdev.com/talks/unicode/ I found a hack that
>> might work, if you place:
>>
>> import sys
>> sys.setdefaultencoding('utf-8')
>>
>> at the top of lwr/web/framework.py does that fix the problem?
>>
>> -John
>>
>> On Wed, Nov 26, 2014 at 2:53 AM, Misharl Monsoor <mmons...@sb-roscoff.fr>
>> wrote:
>>>
>>> Hi John,
>>>
>>> I can confirm you that your advice putting "LWR_CURL_TRANSPORT=1" works
>>> very
>>> fine, thanks a lot! Sorry, i haven't expressed myself correctly for my
>>> second question, thanks for answering, it helps me.
>>> I have another problem with LWR, when executing the jobs on the Windows
>>> Server, i have the following bug (it happens a lot of time, and i must
>>> restart the LWR server in order for it to works):
>>>
>>>   File
>>> "C:\Python2764\lib\site-packages\paste-1.7.5.1-py2.7.egg\paste\httpserver
>>> py", line 287, in wsgi_execute
>>>     self.wsgi_start_response)
>>>   File "C:\Desktop\lwr_master\lwr\web\framework.py", l
>>> ne 37, in __call__
>>>     return controller(environ, start_response, **request_args)
>>>   File "C:\Desktop\lwr_master\lwr\web\framework.py", l
>>> ne 141, in controller_replacement
>>>     resp = self.__build_response(result)
>>>   File "C:\Desktop\lwr_master\lwr\web\framework.py", l
>>> ne 129, in __build_response
>>>     resp = Response(body=self.body(result))
>>>   File "C:\Desktop\lwr_master\lwr\web\framework.py", l
>>> ne 155, in body
>>>     body = dumps(result)
>>>   File "C:\Python2764\lib\json\__init__.py", line 243, in dumps
>>>     return _default_encoder.encode(obj)
>>>   File "C:\Python2764\lib\json\encoder.py", line 207, in encode
>>>     chunks = self.iterencode(o, _one_shot=True)
>>>   File "C:\Python2764\lib\json\encoder.py", line 270, in iterencode
>>>     return _iterencode(o, 0)
>>> nicodeDecodeError: 'utf8' codec can't decode byte 0x92 in position 718:
>>> invalid
>>> start byte
>>>
>>>
>>> Bests regards and thank you very much for your help,
>>>
>>> Misharl Monsoor.
>>>
>>>
>>>
>>> Le 21/11/2014 17:44, John Chilton a écrit :
>>>
>>>> On Wed, Nov 19, 2014 at 12:58 PM, Misharl Monsoor
>>>> <mmons...@sb-roscoff.fr> wrote:
>>>>>
>>>>> Hi John ,
>>>>>
>>>>> First all, thank you very much for your quick reply. I will test your
>>>>> suggestion about pycurl,  and tell you if it has worked. For the second
>>>>> question, i was wondering if it is possible with LWR to define a path
>>>>> (where
>>>>> are located the inputs) as an input (string input in the wrapper xml).
>>>>
>>>> Still not certain I understand - but I do not believe this is possible
>>>> for datasets - this is something that must be configured for the LWR
>>>> itself. If you have inputs to the tool that are not datasets - such as
>>>> reference or index data - those could potentially be specified this
>>>> way as just <data type="text"... in your tool. Those parameters will
>>>> be passed through on the command-line just like any other parameter.
>>>>
>>>> Hope this helps.
>>>> -John
>>>>
>>>>> Thank you again for your help,
>>>>>
>>>>> Misharl Monsoor.
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> Le 19/11/2014 15:30, John Chilton a écrit :
>>>>>
>>>>>> If you install pycurl (globally or in a Galaxy's virtualenv) and set
>>>>>> LWR_CURL_TRANSPORT=1 in Galaxy's environment than the LWR will stream
>>>>>> large files with CURL instead of the mmap hack.
>>>>>>
>>>>>> I don't understand your second question - the LWR should stream
>>>>>> whatever data inputs are selected by the user. If you want the tool to
>>>>>> be able to take many inputs you can use multiple="true" on your data
>>>>>> parameter or use a repeat block.
>>>>>> (https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax).
>>>>>>
>>>>>> Hope this helps,
>>>>>> -John
>>>>>>
>>>>>>
>>>>>> On Mon, Nov 17, 2014 at 3:04 AM, Misharl Monsoor
>>>>>> <mmons...@sb-roscoff.fr>
>>>>>> wrote:
>>>>>>>
>>>>>>> Hi everybody,
>>>>>>>
>>>>>>> In our lab, we are trying to connect our Galaxy instance to a Windows
>>>>>>> 7
>>>>>>> 64
>>>>>>> bits server, in order to executes programs that need to be run within
>>>>>>> Windows. However we have a problem concerning the size of the input
>>>>>>> that
>>>>>>> is
>>>>>>> uploaded to the Windows server, it doesn't accept inputs with a size
>>>>>>> >
>>>>>>> 1.3
>>>>>>> Gb ? We have the following problem with mmap function:
>>>>>>>
>>>>>>>          data = mmap.mmap(input.fileno(), 0, access=mmap.ACCESS_READ)
>>>>>>> error: [Errno 12] Cannot allocate memory
>>>>>>>
>>>>>>>
>>>>>>> I have another question concerning the inputs, is there a way to use
>>>>>>> several
>>>>>>> inputs that be uploaded to a Windows Server?
>>>>>>>
>>>>>>> Thank you very much in advance,
>>>>>>>
>>>>>>> Bests regards,
>>>>>>>
>>>>>>> Cheers,
>>>>>>>
>>>>>>> Misharl Monsoor
>>>>>>> ___________________________________________________________
>>>>>>> Please keep all replies on the list by using "reply all"
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>>>>>
>>>>>
>
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