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
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