Re: [galaxy-dev] Connecting LDAP with Galaxy

2016-08-09 Thread Tiago Antao 

Hi,


I was reading a bit about this (I manage a LDAP server, but I am far
from a specialist) and the format is actually too flexible: Any UTF-8
encoding with up to 64 characters.

I suspect basic punctation marks would be enough. Though I could see a
Windows based SSO system (AD) accepting spaces and maybe even that 
being

a usual convention (just speculating here).

But _s and .s are probably very common across existing installations.


Let's start with that at first :)
Do you have time to work on this or can create a tracking issue?



I do not have time to work on this, but I created the issue some time 
ago:


https://github.com/galaxyproject/galaxy/issues/2593


Tiago
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[galaxy-dev] Doubled arguments from loc files in tests

2016-08-09 Thread Peter Cock 
Hello all,

Recently I've been debugging various problems with my Galaxy tool TravisCI
tests as part of moving to using "planemo test" rather than the fragile system
I first created which mimicked a pre-ToolShed manual install:

https://blastedbio.blogspot.co.uk/2013/09/using-travis-ci-for-testing-galaxy-tools.html

Progress:

https://travis-ci.org/peterjc/galaxy_mira - passing now :)
https://travis-ci.org/peterjc/pico_galaxy - probably a loc file problem
https://travis-ci.org/peterjc/galaxy_blast - different loc file problem

This email is about the problems testing the BLAST wrappers where I
am using a BLAST database defined in test-data/*.loc files.

(I wasted some time today trying moving/copying the loc files and
databases to different places before I noticed the issue below)

Problem lines quoted are from this run, galaxy master or dev branch:
https://travis-ci.org/peterjc/galaxy_blast/builds/150072050
as of this commit:
https://github.com/peterjc/galaxy_blast/commit/03f81e7fb1e0562b46b8b2a2079c94f04c1f3adf

Some of the command expect a single BLAST database from the
test-data/*.loc files, and the test should do that, but we get:

blastdbcmd ... -db path,path ...
rpsblast ... -db path,path ...
rpstblastn ... -db path,path ...

Here we should get ... -db path (once only), not repeated with a
comma, e.g.

galaxy.jobs.command_factory INFO 2016-08-05 14:55:08,543 Built script
[/tmp/tmp9NURC9/job_working_directory/000/58/tool_script.sh] for tool
command[blastdbcmd -version >
/tmp/tmp9NURC9/tmp/GALAXY_VERSION_STRING_58 2>&1; blastdbcmd -dbtype
prot -db 
"/home/travis/build/peterjc/galaxy_blast/test-data/four_human_proteins.fasta,/home/travis/build/peterjc/galaxy_blast/galaxy-dev/test-data/four_human_proteins.fasta"
-info -out "/tmp/tmp9NURC9/files/000/dataset_58.dat"]

For other tools you can select multiple databases as input, and
the blastn tests try that, e.g. a working test gave this (where the
space is deliberate as that's how the NCBI handle multiple DB
arguments):

blastn ... -db "path1 path2"

galaxy.jobs.command_factory INFO 2016-08-05 14:58:01,783 Built script
[/tmp/tmp9NURC9/job_working_directory/000/76/tool_script.sh] for tool
command[blastn -version > /tmp/tmp9NURC9/tmp/GALAXY_VERSION_STRING_76
2>&1; blastn -query "/tmp/tmp9NURC9/files/000/dataset_75.dat" -db
"/home/travis/build/peterjc/galaxy_blast/test-data/three_human_mRNA.fasta
/home/travis/build/peterjc/galaxy_blast/galaxy-dev/test-data/three_human_mRNA.fasta"
-task megablast -evalue 0.001 -out
"/tmp/tmp9NURC9/files/000/dataset_76.dat" -outfmt 6 -num_threads
"${GALAXY_SLOTS:-8}"]

But when a single database is given we get a repeated path:

blastn ... -db "path path"

galaxy.jobs.command_factory INFO 2016-08-05 14:58:22,901 Built script
[/tmp/tmp9NURC9/job_working_directory/000/78/tool_script.sh] for tool
command[blastn -version > /tmp/tmp9NURC9/tmp/GALAXY_VERSION_STRING_78
2>&1; blastn -query "/tmp/tmp9NURC9/files/000/dataset_77.dat" -db
"/home/travis/build/peterjc/galaxy_blast/test-data/rhodopsin_nucs.fasta
/home/travis/build/peterjc/galaxy_blast/galaxy-dev/test-data/rhodopsin_nucs.fasta"
-task megablast -evalue 0.001 -out
"/tmp/tmp9NURC9/files/000/dataset_78.dat" -outfmt 6 -num_threads
"${GALAXY_SLOTS:-8}"]

Any thoughts on where this is breaking? In planemo?

These tests are working locally via "planemo test" (older
version of planemo, older version of Galaxy, Python 2.6).

Peter
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Re: [galaxy-dev] view details not working

2016-08-09 Thread Vincent Cahais 
Thank you Nicola, it works.


Le 08/08/2016 à 16:52, Nicola Soranzo a écrit :
> Hi Vincent,
> you have to update to have the latest commits in the release_16.04 
> branch. Please try this:
> 1) run
>
> git status
>
> to check on which branch you are. You may have in the output either:
> "On branch master"
> or
> "On branch release_16.04"
>
> 2.1) If you are on the master branch, run:
>
> git fetch
> git checkout release_16.04
> git pull  --ff-only
>
> 2.2) If you are already on the release_16.04 branch, just run:
>
> git pull --ff-only
>
> Hope than helps!
>
> Cheers,
> Nicola
>
> On 08/08/16 15:37, Vincent Cahais wrote:
>> Hi Nicola,
>>
>> It's suppose to be the 16.04.
>>
>> commit b79474083b08860923f7f28fc1e7442b53f925db
>> Merge: 7c94ac8 5aefe1b
>> Author: Martin Cech 
>> Date:   Wed Apr 20 15:22:20 2016 -0400
>>
>>   Merge pull request #2206 from dannon/master
>>
>>   Sanity check of master update.
>>
>> Le 08/08/2016 à 16:14, Nicola Soranzo a écrit :
>>> Hi Vincent,
>>> what release of Galaxy are you using? It should be fixed by
>>> https://github.com/galaxyproject/galaxy/pull/2312 , which is available
>>> in latest release_16.01 and following.
>>>
>>> Cheers,
>>> Nicola
>>>
>>> On 08/08/16 14:58, Vincent Cahais wrote:
 Dear all,

 I have a very strange bug on my galaxy server.

 The view details button is not working anymore for the new datasets. I
 get an Internal server Error.

 It's still working for older datasets, it's only an issue for the new
 one, independently of the tool.

 Best regards

 Vincent


 **.**.***.*** - - [08/août/2016:15:32:31 +0200] "GET
 /galaxy/datasets/38ebe14f4d38806a/show_params HTTP/1.1" 500 -
 "http://galaxy***/; "Mozilla/5.0 (X11; Ubuntu; Linux x86_64;
 rv:48.0) Gecko/20100101 Firefox/48.0"
 Error - : 'ascii' codec can't
 decode byte 0xc3 in position 10: ordinal not in range(128)
 URL: 
 http://galaxy.iarc.fr/galaxy/datasets/38ebe14f4d38806a/show_params
 File
 '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/error.py', 

 line 151 in __call__
  app_iter = self.application(environ, sr_checker)
 File
 '/home/galaxy/galaxy-dist/.venv/local/lib/python2.7/site-packages/paste/recursive.py',
  


 line 85 in __call__
  return self.application(environ, start_response)
 File
 '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/remoteuser.py',
  


 line 179 in __call__
  return self.app( environ, start_response )
 File
 '/home/galaxy/galaxy-dist/.venv/local/lib/python2.7/site-packages/paste/httpexceptions.py',
  


 line 640 in __call__
  return self.application(environ, start_response)
 File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line
 126 in __call__
  return self.handle_request( environ, start_response )
 File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line
 184 in handle_request
  body = method( trans, **kwargs )
 File
 '/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/dataset.py',
  


 line 1030 in show_params
  has_parameter_errors=has_parameter_errors )
 File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/webapp.py', 
 line
 809 in fill_template
  return self.fill_template_mako( filename, **kwargs )
 File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/webapp.py', 
 line
 823 in fill_template_mako
  return template.render( **data )
 File
 '/home/galaxy/galaxy-dist/.venv/local/lib/python2.7/site-packages/mako/template.py',
  


 line 445 in render
  return runtime._render(self, self.callable_, args, data)
 File
 '/home/galaxy/galaxy-dist/.venv/local/lib/python2.7/site-packages/mako/runtime.py',
  


 line 829 in _render
  **_kwargs_for_callable(callable_, data))

 File
 '/home/galaxy/galaxy-dist/.venv/local/lib/python2.7/site-packages/mako/runtime.py',
  


 line 864 in _render_context
  _exec_template(inherit, lclcontext, args=args, kwargs=kwargs)
 File
 '/home/galaxy/galaxy-dist/.venv/local/lib/python2.7/site-packages/mako/runtime.py',
  


 line 890 in _exec_template
  callable_(context, *args, **kwargs)
 File
 '/home/galaxy/galaxy-dist/database/compiled_templates/base.mako.py',
 line 61 in render_body
  __M_writer(unicode(next.body()))
 File
 '/home/galaxy/galaxy-dist/database/compiled_templates/show_params.mako.py',
  


 line 74 in render_body
 __M_writer(unicode(hda.create_time.strftime(trans.app.config.pretty_datetime_format)))
  


 UnicodeDecodeError: 'ascii' codec can't decode byte 0xc3 in 
 position 10:
 ordinal not in range(128)