Hi John,
Thank you again for your help. So i tested the "python
run_client_tests.py --url=http://localhost:8913"; command on the lwr
server, and i don't have any error message (i guess that the test has
passed).
Bests regards,
Misharl Monsoor.
Le 18/12/2014 22:50, John Chilton a écrit :
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
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