Re: [galaxy-dev] view details not working

[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)


 CGI Varia

Re: [galaxy-dev] Connecting LDAP with Galaxy

[Björn Grüning]

Great, thanks Nicola!

Am 08.08.2016 um 23:53 schrieb Nicola Soranzo:
> There is one already: https://github.com/galaxyproject/galaxy/issues/2593
> 
> I may take a stab at it in the next days. 
> 
> Cheers, 
> Nicola 
> 
>  Björn Grüning ha scritto 
> 
>>
>>
>> Am 08.08.2016 um 20:14 schrieb Tiago Antao:
>>> 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?
>>
>> Thanks!
>> Bjoern
>>
>>> On 2016-08-08 11:21, James Taylor wrote:
 I don't think there is any good reason. Public username's main purpose
 originally was to generate slugs for URLs so we left out "-".
 Shouldn't break anything to add it.

 On Mon, Aug 8, 2016 at 12:24 PM, Björn Grüning
  wrote:
> Does anyone know why we have this restriction? Can we change it?
>
> Am 08.08.2016 um 17:31 schrieb Tiago Antao:
>> Sorry, that was what I meant and explained myself poorly.
>>
>> This is actually a very serious problem if one wants to integrate
>> Galaxy
>> in an existing SSO environment based on LDAP.
>>
>> Tiago
>>
>> On 2016-08-08 09:28, Nicola Soranzo wrote:
>>> Actually it's Galaxy (not the LDAP integration) that doesn't allow
>>> underscores in usernames, in fact if you try to register a new user on
>>> e.g. usegalaxy.org and the username has an underscore, you'll get this
>>> error:
>>>
>>> Public name must contain only lowercase letters, numbers and "-". It
>>> also has to be shorter than 255 characters but longer than 2.
>>>
>>> Cheers,
>>> Nicola
>>>
>>> On 08/08/16 16:08, Tiago Antao wrote:
 Hi,

 A serious problem that I have found with Galaxy integration with LDAP
 is that it does not allow underscores in the user name, and that is
 very common with production LDAP servers.

 On 2016-08-08 09:01, Nicola Soranzo wrote:
> Hi Miuki,
> the file config/auth_conf.xml.sample contains examples and
> documentation of possible values that you have to put in your
> config/auth_conf.xml , unfortunately a lot depends on what
> LDAP/Active
> Directory server you are using and how it is configured. You may
> need
> to ask advice to the system administrators of your LDAP server.
> If you
> have specific questions/problems, feel free to ask here on the
> mailing
> list and/or on the IRC channel.
>
> Cheers,
> Nicola
>
> On 01/08/16 20:45, Yip, Miu ki wrote:
>> Hi,
>>
>> I’m trying to configure a new instance of Galaxy and I want to use
>> LDAP for user authentication. I have taken a look at this wiki
>> page: https://wiki.galaxyproject.org/Admin/Config/ExternalUserAuth
>>
>> I followed the instructions and when I looked into the
>> auth_conf.xml file, I was unsure of what exactly Galaxy is looking
>> for when trying to connect with LDAP. Are there specific options
>> that I must give it? May I ask how Galaxy uses LDAP to authenticate
>> users?
>>
>> Thank you,
>> Miuki Yip
>> ___
>> Please keep all replies on the list by using "reply all"
>> in your mail client.  To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>>https://lists.galaxyproject.org/
>>
>> To search Galaxy mailing lists use the unified search at:
>>http://galaxyproject.org/search/mailinglists/
>
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>  https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
>  http://galaxyproject.org/search/mailinglists/

>>
>> ___
>> Please keep all replies on the list by using "reply all"
>> in your mail client.  To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>>  https://lists.galaxyproject.org/
>>
>> To search Galaxy mailing lis

Re: [galaxy-dev] Connecting LDAP with Galaxy

[Nicola Soranzo]

There is one already: https://github.com/galaxyproject/galaxy/issues/2593

I may take a stab at it in the next days. 

Cheers, 
Nicola 

 Björn Grüning ha scritto 

>
>
>Am 08.08.2016 um 20:14 schrieb Tiago Antao:
>> 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?
>
>Thanks!
>Bjoern
>
>> On 2016-08-08 11:21, James Taylor wrote:
>>> I don't think there is any good reason. Public username's main purpose
>>> originally was to generate slugs for URLs so we left out "-".
>>> Shouldn't break anything to add it.
>>>
>>> On Mon, Aug 8, 2016 at 12:24 PM, Björn Grüning
>>>  wrote:
 Does anyone know why we have this restriction? Can we change it?

 Am 08.08.2016 um 17:31 schrieb Tiago Antao:
> Sorry, that was what I meant and explained myself poorly.
>
> This is actually a very serious problem if one wants to integrate
> Galaxy
> in an existing SSO environment based on LDAP.
>
> Tiago
>
> On 2016-08-08 09:28, Nicola Soranzo wrote:
>> Actually it's Galaxy (not the LDAP integration) that doesn't allow
>> underscores in usernames, in fact if you try to register a new user on
>> e.g. usegalaxy.org and the username has an underscore, you'll get this
>> error:
>>
>> Public name must contain only lowercase letters, numbers and "-". It
>> also has to be shorter than 255 characters but longer than 2.
>>
>> Cheers,
>> Nicola
>>
>> On 08/08/16 16:08, Tiago Antao wrote:
>>> Hi,
>>>
>>> A serious problem that I have found with Galaxy integration with LDAP
>>> is that it does not allow underscores in the user name, and that is
>>> very common with production LDAP servers.
>>>
>>> On 2016-08-08 09:01, Nicola Soranzo wrote:
 Hi Miuki,
 the file config/auth_conf.xml.sample contains examples and
 documentation of possible values that you have to put in your
 config/auth_conf.xml , unfortunately a lot depends on what
 LDAP/Active
 Directory server you are using and how it is configured. You may
 need
 to ask advice to the system administrators of your LDAP server.
 If you
 have specific questions/problems, feel free to ask here on the
 mailing
 list and/or on the IRC channel.

 Cheers,
 Nicola

 On 01/08/16 20:45, Yip, Miu ki wrote:
> Hi,
>
> I’m trying to configure a new instance of Galaxy and I want to use
> LDAP for user authentication. I have taken a look at this wiki
> page: https://wiki.galaxyproject.org/Admin/Config/ExternalUserAuth
>
> I followed the instructions and when I looked into the
> auth_conf.xml file, I was unsure of what exactly Galaxy is looking
> for when trying to connect with LDAP. Are there specific options
> that I must give it? May I ask how Galaxy uses LDAP to authenticate
> users?
>
> Thank you,
> Miuki Yip
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
>http://galaxyproject.org/search/mailinglists/

 ___
 Please keep all replies on the list by using "reply all"
 in your mail client.  To manage your subscriptions to this
 and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

 To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
>>>
>
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>  https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
>  http://galaxyproject.org/search/mailinglists/
 ___
 Please keep all replies on the list by using "reply 

Re: [galaxy-dev] Connecting LDAP with Galaxy

[Björn Grüning]

Am 08.08.2016 um 20:14 schrieb Tiago Antao:
> 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?

Thanks!
Bjoern

> On 2016-08-08 11:21, James Taylor wrote:
>> I don't think there is any good reason. Public username's main purpose
>> originally was to generate slugs for URLs so we left out "-".
>> Shouldn't break anything to add it.
>>
>> On Mon, Aug 8, 2016 at 12:24 PM, Björn Grüning
>>  wrote:
>>> Does anyone know why we have this restriction? Can we change it?
>>>
>>> Am 08.08.2016 um 17:31 schrieb Tiago Antao:
 Sorry, that was what I meant and explained myself poorly.

 This is actually a very serious problem if one wants to integrate
 Galaxy
 in an existing SSO environment based on LDAP.

 Tiago

 On 2016-08-08 09:28, Nicola Soranzo wrote:
> Actually it's Galaxy (not the LDAP integration) that doesn't allow
> underscores in usernames, in fact if you try to register a new user on
> e.g. usegalaxy.org and the username has an underscore, you'll get this
> error:
>
> Public name must contain only lowercase letters, numbers and "-". It
> also has to be shorter than 255 characters but longer than 2.
>
> Cheers,
> Nicola
>
> On 08/08/16 16:08, Tiago Antao wrote:
>> Hi,
>>
>> A serious problem that I have found with Galaxy integration with LDAP
>> is that it does not allow underscores in the user name, and that is
>> very common with production LDAP servers.
>>
>> On 2016-08-08 09:01, Nicola Soranzo wrote:
>>> Hi Miuki,
>>> the file config/auth_conf.xml.sample contains examples and
>>> documentation of possible values that you have to put in your
>>> config/auth_conf.xml , unfortunately a lot depends on what
>>> LDAP/Active
>>> Directory server you are using and how it is configured. You may
>>> need
>>> to ask advice to the system administrators of your LDAP server.
>>> If you
>>> have specific questions/problems, feel free to ask here on the
>>> mailing
>>> list and/or on the IRC channel.
>>>
>>> Cheers,
>>> Nicola
>>>
>>> On 01/08/16 20:45, Yip, Miu ki wrote:
 Hi,

 I’m trying to configure a new instance of Galaxy and I want to use
 LDAP for user authentication. I have taken a look at this wiki
 page: https://wiki.galaxyproject.org/Admin/Config/ExternalUserAuth

 I followed the instructions and when I looked into the
 auth_conf.xml file, I was unsure of what exactly Galaxy is looking
 for when trying to connect with LDAP. Are there specific options
 that I must give it? May I ask how Galaxy uses LDAP to authenticate
 users?

 Thank you,
 Miuki Yip
 ___
 Please keep all replies on the list by using "reply all"
 in your mail client.  To manage your subscriptions to this
 and other Galaxy lists, please use the interface at:
https://lists.galaxyproject.org/

 To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
>>>
>>> ___
>>> Please keep all replies on the list by using "reply all"
>>> in your mail client.  To manage your subscriptions to this
>>> and other Galaxy lists, please use the interface at:
>>>  https://lists.galaxyproject.org/
>>>
>>> To search Galaxy mailing lists use the unified search at:
>>>  http://galaxyproject.org/search/mailinglists/
>>

 ___
 Please keep all replies on the list by using "reply all"
 in your mail client.  To manage your subscriptions to this
 and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

 To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
>>> ___
>>> Please keep all replies on the list by using "reply all"
>>> in your mail client.  To manage your subscriptions to this
>>> and other Galaxy lists, please use the interface at:
>>>   https://lists.galaxyproject.org/
>>>
>>> To search Galaxy mailing lists use the unified search at:
>>>   http://galaxyproject.org/search/mailinglists/
> 
_

Re: [galaxy-dev] External user auth and API

[Eric Rasche]

Hi Sarah,

On 08. aug. 2016 13:58, Sarah DIEHL wrote:
> Hi Eric,
>
> thanks for the hint regarding uWSGI. What doesn't work is importing
> files from the local disk (of the galaxy server) to the data library
> (see attached screenshot). Everything else seems to be fine, I haven't
> encountered any other issues. Maybe it's a bug just in that function?
> Here is the error:
>
> 10.184.132.10 - - [30/Jul/2016:18:09:27 +0200] "POST
> /api/libraries/datasets?encoded_folder_id=F7b46bd6d01de922f&source=userdir_file&path=160308_WTCHG_254732_201.bam&file_type=auto&dbkey=?
> HTTP/1.1" 500 - "https://galaxy-server.uni.lu/library/list";
> "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:45.0) Gecko/20100101
> Firefox/45.0"
> Error - : use_remote_user is set but
> HTTP_REMOTE_USER header was not provided
> URL:
> https://galaxy-server.uni.lu/api/libraries/datasets?encoded_folder_id=F7b46bd6d01de922f&source=userdir_file&path=160308_WTCHG_254732_201.bam&file_type=auto&dbkey=?
> File
> '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/error.py',
> line 151 in __call__
>   app_iter = self.application(environ, sr_checker)
> File
> '/mnt/gaiagpfs/projects/galaxy/internal/.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 76 in __call__
>   return self.app( environ, start_response )
> File
> '/mnt/gaiagpfs/projects/galaxy/internal/.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
> 131 in __call__
>   return self.handle_request( environ, start_response )
> File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line
> 158 in handle_request
>   trans = self.transaction_factory( environ )
> File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/webapp.py',
> line 68 in 
>   self.set_transaction_factory( lambda e: self.transaction_chooser( e,
> galaxy_app, session_cookie ) )
> File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/webapp.py',
> line 99 in transaction_chooser
>   return GalaxyWebTransaction( environ, galaxy_app, self, session_cookie )
> File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/webapp.py',
> line 198 in __init__
>   self.error_message = self._authenticate_api( session_cookie )
> File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/webapp.py',
> line 380 in _authenticate_api
>   self._ensure_valid_session( session_cookie )
> File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/webapp.py',
> line 432 in _ensure_valid_session
>   "use_remote_user is set but %s header was not provided" %
> self.app.config.remote_user_header
> AssertionError: use_remote_user is set but HTTP_REMOTE_USER header was
> not provided
I'm afraid I do not have any help for this. Hopefully another galaxy
person can chime in here and help debug this.

>
>
> Best regards,
> Sarah
>
> 
> Sarah Diehl
> HPC System Administrator
>  
> UNIVERSITÉ DU LUXEMBOURG
>  
> LUXEMBOURG CENTRE FOR SYSTEMS BIOMEDICINE
> Campus Belval | Biotech II
> 6, avenue du Swing
> L-4371 Belvaux
> T +352 46 66 44 5360
> sarah.di...@uni.lu  http://lcsb.uni.lu
> 
> -
> This message is confidential and may contain privileged information.
> It is intended for the named recipient only. If you receive it in
> error please notify me and permanently delete the original message and
> any copies.
> -
>
>
> From: Eric Rasche mailto:e...@tamu.edu>>
> Organization: TAMU
> Date: Monday 8 August 2016 15:43
> To: Sarah DIEHL mailto:sarah.di...@uni.lu>>,
> "galaxy-dev@lists.galaxyproject.org
> "
>  >
> Subject: Re: [galaxy-dev] External user auth and API
>
>
>
> On 08. aug. 2016 13:25, Sarah DIEHL wrote:
>> Hi Eric,
>>
>> thanks a lot for the info and help! I'm running version 16.04 and my
>> apache conf is a bit different because I balance over multiple galaxy
>> web servers:
> Just as an aside, if you are still using this configuration method,
> you might consider switching to uWSGI
> ,
> it will drastically simplify your configuration and should be just as
> performant (if not more).
>
>>
>>
>> # API requests get routed through balancer with no authentication
>> RewriteCond %{QUERY_STRING} key=
>> R

Re: [galaxy-dev] Connecting LDAP with Galaxy

[Tiago Antao]

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.

On 2016-08-08 11:21, James Taylor wrote:

I don't think there is any good reason. Public username's main purpose
originally was to generate slugs for URLs so we left out "-".
Shouldn't break anything to add it.

On Mon, Aug 8, 2016 at 12:24 PM, Björn Grüning
 wrote:

Does anyone know why we have this restriction? Can we change it?

Am 08.08.2016 um 17:31 schrieb Tiago Antao:

Sorry, that was what I meant and explained myself poorly.

This is actually a very serious problem if one wants to integrate 
Galaxy

in an existing SSO environment based on LDAP.

Tiago

On 2016-08-08 09:28, Nicola Soranzo wrote:

Actually it's Galaxy (not the LDAP integration) that doesn't allow
underscores in usernames, in fact if you try to register a new user 
on
e.g. usegalaxy.org and the username has an underscore, you'll get 
this

error:

Public name must contain only lowercase letters, numbers and "-". It
also has to be shorter than 255 characters but longer than 2.

Cheers,
Nicola

On 08/08/16 16:08, Tiago Antao wrote:

Hi,

A serious problem that I have found with Galaxy integration with 
LDAP

is that it does not allow underscores in the user name, and that is
very common with production LDAP servers.

On 2016-08-08 09:01, Nicola Soranzo wrote:

Hi Miuki,
the file config/auth_conf.xml.sample contains examples and
documentation of possible values that you have to put in your
config/auth_conf.xml , unfortunately a lot depends on what 
LDAP/Active
Directory server you are using and how it is configured. You may 
need
to ask advice to the system administrators of your LDAP server. If 
you
have specific questions/problems, feel free to ask here on the 
mailing

list and/or on the IRC channel.

Cheers,
Nicola

On 01/08/16 20:45, Yip, Miu ki wrote:

Hi,

I’m trying to configure a new instance of Galaxy and I want to 
use

LDAP for user authentication. I have taken a look at this wiki
page: 
https://wiki.galaxyproject.org/Admin/Config/ExternalUserAuth


I followed the instructions and when I looked into the
auth_conf.xml file, I was unsure of what exactly Galaxy is 
looking

for when trying to connect with LDAP. Are there specific options
that I must give it? May I ask how Galaxy uses LDAP to 
authenticate

users?

Thank you,
Miuki Yip
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Re: [galaxy-dev] Connecting LDAP with Galaxy

[James Taylor]

I don't think there is any good reason. Public username's main purpose
originally was to generate slugs for URLs so we left out "-".
Shouldn't break anything to add it.

On Mon, Aug 8, 2016 at 12:24 PM, Björn Grüning
 wrote:
> Does anyone know why we have this restriction? Can we change it?
>
> Am 08.08.2016 um 17:31 schrieb Tiago Antao:
>> Sorry, that was what I meant and explained myself poorly.
>>
>> This is actually a very serious problem if one wants to integrate Galaxy
>> in an existing SSO environment based on LDAP.
>>
>> Tiago
>>
>> On 2016-08-08 09:28, Nicola Soranzo wrote:
>>> Actually it's Galaxy (not the LDAP integration) that doesn't allow
>>> underscores in usernames, in fact if you try to register a new user on
>>> e.g. usegalaxy.org and the username has an underscore, you'll get this
>>> error:
>>>
>>> Public name must contain only lowercase letters, numbers and "-". It
>>> also has to be shorter than 255 characters but longer than 2.
>>>
>>> Cheers,
>>> Nicola
>>>
>>> On 08/08/16 16:08, Tiago Antao wrote:
 Hi,

 A serious problem that I have found with Galaxy integration with LDAP
 is that it does not allow underscores in the user name, and that is
 very common with production LDAP servers.

 On 2016-08-08 09:01, Nicola Soranzo wrote:
> Hi Miuki,
> the file config/auth_conf.xml.sample contains examples and
> documentation of possible values that you have to put in your
> config/auth_conf.xml , unfortunately a lot depends on what LDAP/Active
> Directory server you are using and how it is configured. You may need
> to ask advice to the system administrators of your LDAP server. If you
> have specific questions/problems, feel free to ask here on the mailing
> list and/or on the IRC channel.
>
> Cheers,
> Nicola
>
> On 01/08/16 20:45, Yip, Miu ki wrote:
>> Hi,
>>
>> I’m trying to configure a new instance of Galaxy and I want to use
>> LDAP for user authentication. I have taken a look at this wiki
>> page: https://wiki.galaxyproject.org/Admin/Config/ExternalUserAuth
>>
>> I followed the instructions and when I looked into the
>> auth_conf.xml file, I was unsure of what exactly Galaxy is looking
>> for when trying to connect with LDAP. Are there specific options
>> that I must give it? May I ask how Galaxy uses LDAP to authenticate
>> users?
>>
>> Thank you,
>> Miuki Yip
>> ___
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>>
>> ___
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Re: [galaxy-dev] Connecting LDAP with Galaxy

[Björn Grüning]

Does anyone know why we have this restriction? Can we change it?

Am 08.08.2016 um 17:31 schrieb Tiago Antao:
> Sorry, that was what I meant and explained myself poorly.
> 
> This is actually a very serious problem if one wants to integrate Galaxy
> in an existing SSO environment based on LDAP.
> 
> Tiago
> 
> On 2016-08-08 09:28, Nicola Soranzo wrote:
>> Actually it's Galaxy (not the LDAP integration) that doesn't allow
>> underscores in usernames, in fact if you try to register a new user on
>> e.g. usegalaxy.org and the username has an underscore, you'll get this
>> error:
>>
>> Public name must contain only lowercase letters, numbers and "-". It
>> also has to be shorter than 255 characters but longer than 2.
>>
>> Cheers,
>> Nicola
>>
>> On 08/08/16 16:08, Tiago Antao wrote:
>>> Hi,
>>>
>>> A serious problem that I have found with Galaxy integration with LDAP
>>> is that it does not allow underscores in the user name, and that is
>>> very common with production LDAP servers.
>>>
>>> On 2016-08-08 09:01, Nicola Soranzo wrote:
 Hi Miuki,
 the file config/auth_conf.xml.sample contains examples and
 documentation of possible values that you have to put in your
 config/auth_conf.xml , unfortunately a lot depends on what LDAP/Active
 Directory server you are using and how it is configured. You may need
 to ask advice to the system administrators of your LDAP server. If you
 have specific questions/problems, feel free to ask here on the mailing
 list and/or on the IRC channel.

 Cheers,
 Nicola

 On 01/08/16 20:45, Yip, Miu ki wrote:
> Hi,
>
> I’m trying to configure a new instance of Galaxy and I want to use
> LDAP for user authentication. I have taken a look at this wiki
> page: https://wiki.galaxyproject.org/Admin/Config/ExternalUserAuth
>
> I followed the instructions and when I looked into the
> auth_conf.xml file, I was unsure of what exactly Galaxy is looking
> for when trying to connect with LDAP. Are there specific options
> that I must give it? May I ask how Galaxy uses LDAP to authenticate
> users?
>
> Thank you,
> Miuki Yip
> ___
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> and other Galaxy lists, please use the interface at:
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>
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 ___
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>>>
> 
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Re: [galaxy-dev] Connecting LDAP with Galaxy

[Tiago Antao]

Sorry, that was what I meant and explained myself poorly.

This is actually a very serious problem if one wants to integrate Galaxy 
in an existing SSO environment based on LDAP.


Tiago

On 2016-08-08 09:28, Nicola Soranzo wrote:

Actually it's Galaxy (not the LDAP integration) that doesn't allow
underscores in usernames, in fact if you try to register a new user on
e.g. usegalaxy.org and the username has an underscore, you'll get this
error:

Public name must contain only lowercase letters, numbers and "-". It
also has to be shorter than 255 characters but longer than 2.

Cheers,
Nicola

On 08/08/16 16:08, Tiago Antao wrote:

Hi,

A serious problem that I have found with Galaxy integration with LDAP 
is that it does not allow underscores in the user name, and that is 
very common with production LDAP servers.


On 2016-08-08 09:01, Nicola Soranzo wrote:

Hi Miuki,
the file config/auth_conf.xml.sample contains examples and
documentation of possible values that you have to put in your
config/auth_conf.xml , unfortunately a lot depends on what 
LDAP/Active

Directory server you are using and how it is configured. You may need
to ask advice to the system administrators of your LDAP server. If 
you
have specific questions/problems, feel free to ask here on the 
mailing

list and/or on the IRC channel.

Cheers,
Nicola

On 01/08/16 20:45, Yip, Miu ki wrote:

Hi,

I’m trying to configure a new instance of Galaxy and I want to use 
LDAP for user authentication. I have taken a look at this wiki page: 
https://wiki.galaxyproject.org/Admin/Config/ExternalUserAuth


I followed the instructions and when I looked into the auth_conf.xml 
file, I was unsure of what exactly Galaxy is looking for when trying 
to connect with LDAP. Are there specific options that I must give 
it? May I ask how Galaxy uses LDAP to authenticate users?


Thank you,
Miuki Yip
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Re: [galaxy-dev] Connecting LDAP with Galaxy

[Nicola Soranzo]

Actually it's Galaxy (not the LDAP integration) that doesn't allow 
underscores in usernames, in fact if you try to register a new user on 
e.g. usegalaxy.org and the username has an underscore, you'll get this 
error:


Public name must contain only lowercase letters, numbers and "-". It 
also has to be shorter than 255 characters but longer than 2.


Cheers,
Nicola

On 08/08/16 16:08, Tiago Antao wrote:

Hi,

A serious problem that I have found with Galaxy integration with LDAP 
is that it does not allow underscores in the user name, and that is 
very common with production LDAP servers.


On 2016-08-08 09:01, Nicola Soranzo wrote:

Hi Miuki,
the file config/auth_conf.xml.sample contains examples and
documentation of possible values that you have to put in your
config/auth_conf.xml , unfortunately a lot depends on what LDAP/Active
Directory server you are using and how it is configured. You may need
to ask advice to the system administrators of your LDAP server. If you
have specific questions/problems, feel free to ask here on the mailing
list and/or on the IRC channel.

Cheers,
Nicola

On 01/08/16 20:45, Yip, Miu ki wrote:

Hi,

I’m trying to configure a new instance of Galaxy and I want to use 
LDAP for user authentication. I have taken a look at this wiki page: 
https://wiki.galaxyproject.org/Admin/Config/ExternalUserAuth


I followed the instructions and when I looked into the auth_conf.xml 
file, I was unsure of what exactly Galaxy is looking for when trying 
to connect with LDAP. Are there specific options that I must give 
it? May I ask how Galaxy uses LDAP to authenticate users?


Thank you,
Miuki Yip
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Re: [galaxy-dev] Connecting LDAP with Galaxy

[Tiago Antao]

Hi,

A serious problem that I have found with Galaxy integration with LDAP is 
that it does not allow underscores in the user name, and that is very 
common with production LDAP servers.


On 2016-08-08 09:01, Nicola Soranzo wrote:

Hi Miuki,
the file config/auth_conf.xml.sample contains examples and
documentation of possible values that you have to put in your
config/auth_conf.xml , unfortunately a lot depends on what LDAP/Active
Directory server you are using and how it is configured. You may need
to ask advice to the system administrators of your LDAP server. If you
have specific questions/problems, feel free to ask here on the mailing
list and/or on the IRC channel.

Cheers,
Nicola

On 01/08/16 20:45, Yip, Miu ki wrote:

Hi,

I’m trying to configure a new instance of Galaxy and I want to use 
LDAP for user authentication. I have taken a look at this wiki page: 
https://wiki.galaxyproject.org/Admin/Config/ExternalUserAuth


I followed the instructions and when I looked into the auth_conf.xml 
file, I was unsure of what exactly Galaxy is looking for when trying 
to connect with LDAP. Are there specific options that I must give it? 
May I ask how Galaxy uses LDAP to authenticate users?


Thank you,
Miuki Yip
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Re: [galaxy-dev] Connecting LDAP with Galaxy

[Nicola Soranzo]

Hi Miuki,
the file config/auth_conf.xml.sample contains examples and documentation 
of possible values that you have to put in your config/auth_conf.xml , 
unfortunately a lot depends on what LDAP/Active Directory server you are 
using and how it is configured. You may need to ask advice to the system 
administrators of your LDAP server. If you have specific 
questions/problems, feel free to ask here on the mailing list and/or on 
the IRC channel.


Cheers,
Nicola

On 01/08/16 20:45, Yip, Miu ki wrote:

Hi,

I’m trying to configure a new instance of Galaxy and I want to use LDAP for 
user authentication. I have taken a look at this wiki page: 
https://wiki.galaxyproject.org/Admin/Config/ExternalUserAuth

I followed the instructions and when I looked into the auth_conf.xml file, I 
was unsure of what exactly Galaxy is looking for when trying to connect with 
LDAP. Are there specific options that I must give it? May I ask how Galaxy uses 
LDAP to authenticate users?

Thank you,
Miuki Yip
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Re: [galaxy-dev] view details not working

[Nicola Soranzo]

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)


CGI Variables
-
 CONTENT_LENGTH: '0'
 HTTP_ACCEPT:
'text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8'
 HTTP_ACCEPT_ENCODING: 'gzip, deflate'
 HTTP_ACCEPT_LANGUAGE: 'en-US,en;q=0.5'
 HTTP_AUTHORIZATION: 'Basic Y2FoYWlzdjpXMXNtM3JoMWxs'
 HTTP_CONNECTION: 'close'
 HTTP_COOKIE:
'galaxysession=09218edcc0a8a75b31582a2cb50d757dc5f67b9b7cae48d9fdb3bd88e9d143d956083945f07b4710;

galaxycommunitysession=aeaf4b69c51e3d6d293956655fa9014fb7b92937bf5c098a096ed54161b02239b63b34c44bba22ac;

toolshedgalaxyurl="http://galaxy/";;
PPA_ID=56sqtkiu7jrubvee6tk03a3ve6;
webfx-tree-cookie-persistence=wfxt-4+wfxt-6+wfxt-10+wfxt-16+wfxt-18+wfxt-20'

 HTTP_DNT: '1'
 HTTP_HOST: 'galaxy*'
 HTTP_REFERER: 'http://galaxy***/'
 HTTP_REMOTE

Re: [galaxy-dev] Adding packages to depot.galaxyproject.org

[Peter Cock]

On Mon, Aug 8, 2016 at 3:27 PM, Björn Grüning  wrote:
> Hi Peter,
>
> Am 08.08.2016 um 15:54 schrieb Peter Cock:
>> On Mon, Aug 8, 2016 at 2:41 PM, Eric Rasche  wrote:
>>> Hi Peter,
>>>
>>> The cargo port is the ideal place for this, however it does not support
>>> manual uploads of files.
>>>
>>
>> Thanks Eric,
>>
>> You mean https://github.com/galaxyproject/cargo-port
>>
>> Is that something which might be addressed in future? The use case
>> is when a previously public file stops working (either temporarily or
>> permanently), so you can't use the official URL to make the cached
>> copy?
>>
>> Would it be OK to use a short lived URL like a personal dropbox URL,
>> and then once cached, update urls.tsv with the original official
>> (but broken) URL?
>
>
> Yes this is totally fine. We just need to have a way to verify and check
> tarballs before upload and we thought github and PR are a nice fit for this.
>
> Thanks,
> Bjoern

Let's try this then:

https://github.com/galaxyproject/cargo-port/pull/82

(I can't find the Mac binaries for MIRA 4.9.5, hopefully I might have
that on my home machine but it's a long shot.)

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

[Vincent Cahais]

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)
>>
>>
>> CGI Variables
>> -
>> CONTENT_LENGTH: '0'
>> HTTP_ACCEPT:
>> 'text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8'
>> HTTP_ACCEPT_ENCODING: 'gzip, deflate'
>> HTTP_ACCEPT_LANGUAGE: 'en-US,en;q=0.5'
>> HTTP_AUTHORIZATION: 'Basic Y2FoYWlzdjpXMXNtM3JoMWxs'
>> HTTP_CONNECTION: 'close'
>> HTTP_COOKIE:
>> 'galaxysession=09218edcc0a8a75b31582a2cb50d757dc5f67b9b7cae48d9fdb3bd88e9d143d956083945f07b4710;
>>  
>>
>> galaxycommunitysession=aeaf4b69c51e3d6d293956655fa9014fb7b92937bf5c098a096ed54161b02239b63b34c44bba22ac;
>>  
>>
>> toolshedgalaxyurl="http://galaxy/";;
>> PPA_ID=56sqtkiu7jrubvee6tk03a3ve6;
>> webfx-tree-cookie-persistence=wfxt-4+wfxt-6+wfxt-10+wfxt-16+wfxt-18+wfxt-20' 
>>
>> HTTP_DNT: '1'
>> HTTP_HOST: 'galaxy*'
>> HTTP_REFERER: 'http://galaxy***/'
>> HTTP_REMOTE_USER: '*'
>> HTTP_UPGRADE_INSECURE_REQUESTS: '1'
>> HTTP_USER_AGENT: 'Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:48.0)
>> Geck

Re: [galaxy-dev] Adding packages to depot.galaxyproject.org

[Martin Čech]

Peter:

depot is something we plan on maintaining and providing as a service as
long as Galaxy. The cargo-port we will also expand in future (eg to provide
dynamic fallback at installation time. It is the right place to put your
mira backups (and any other packages you care about in recipes).

Cheers,
M.

On Mon, Aug 8, 2016 at 9:54 AM Peter Cock  wrote:

> On Mon, Aug 8, 2016 at 2:41 PM, Eric Rasche  wrote:
> > Hi Peter,
> >
> > The cargo port is the ideal place for this, however it does not support
> > manual uploads of files.
> >
>
> Thanks Eric,
>
> You mean https://github.com/galaxyproject/cargo-port
>
> Is that something which might be addressed in future? The use case
> is when a previously public file stops working (either temporarily or
> permanently), so you can't use the official URL to make the cached
> copy?
>
> Would it be OK to use a short lived URL like a personal dropbox URL,
> and then once cached, update urls.tsv with the original official
> (but broken) URL?
>
> Peter
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>   https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/
___
Please keep all replies on the list by using "reply all"
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Re: [galaxy-dev] Adding packages to depot.galaxyproject.org

[Björn Grüning]

Hi Peter,

Am 08.08.2016 um 15:54 schrieb Peter Cock:
> On Mon, Aug 8, 2016 at 2:41 PM, Eric Rasche  wrote:
>> Hi Peter,
>>
>> The cargo port is the ideal place for this, however it does not support
>> manual uploads of files.
>>
> 
> Thanks Eric,
> 
> You mean https://github.com/galaxyproject/cargo-port
> 
> Is that something which might be addressed in future? The use case
> is when a previously public file stops working (either temporarily or
> permanently), so you can't use the official URL to make the cached
> copy?
> 
> Would it be OK to use a short lived URL like a personal dropbox URL,
> and then once cached, update urls.tsv with the original official
> (but broken) URL?


Yes this is totally fine. We just need to have a way to verify and check
tarballs before upload and we thought github and PR are a nice fit for this.

Thanks,
Bjoern

> Peter
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>   https://lists.galaxyproject.org/
> 
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/
> 
___
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Re: [galaxy-dev] view details not working

[Nicola Soranzo]

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)


CGI Variables
-
CONTENT_LENGTH: '0'
HTTP_ACCEPT:
'text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8'
HTTP_ACCEPT_ENCODING: 'gzip, deflate'
HTTP_ACCEPT_LANGUAGE: 'en-US,en;q=0.5'
HTTP_AUTHORIZATION: 'Basic Y2FoYWlzdjpXMXNtM3JoMWxs'
HTTP_CONNECTION: 'close'
HTTP_COOKIE:
'galaxysession=09218edcc0a8a75b31582a2cb50d757dc5f67b9b7cae48d9fdb3bd88e9d143d956083945f07b4710;
galaxycommunitysession=aeaf4b69c51e3d6d293956655fa9014fb7b92937bf5c098a096ed54161b02239b63b34c44bba22ac;
toolshedgalaxyurl="http://galaxy/";;
PPA_ID=56sqtkiu7jrubvee6tk03a3ve6;
webfx-tree-cookie-persistence=wfxt-4+wfxt-6+wfxt-10+wfxt-16+wfxt-18+wfxt-20'
HTTP_DNT: '1'
HTTP_HOST: 'galaxy*'
HTTP_REFERER: 'http://galaxy***/'
HTTP_REMOTE_USER: '*'
HTTP_UPGRADE_INSECURE_REQUESTS: '1'
HTTP_USER_AGENT: 'Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:48.0)
Gecko/20100101 Firefox/48.0'
PATH_INFO: '/datasets/38ebe14f4d38806a/show_params'
REMOTE_ADDR: '10.10.13.120'
REQUEST_METHOD: 'GET'
SCRIPT_NAME: '/galaxy'
SERVER_NAME: '***'
SERVER_PORT: '8080'
SERVER_PROTOCOL: 'HTTP/1.1'

WSGI Variables
--
application: 
is_api_request: False
paste.cookies: (,
'galaxysession=09218edcc0a8a75b31582a2cb50d757dc5f67b9b7cae48d9fdb3bd88e9d143d956083945f07b4710;
galaxycommunitysession=aeaf4b69c51e3d6d293956655fa9014fb7b92937bf5c098a096ed54161b02239b63b34c44bba22ac;
toolshedgalaxyurl="http://galaxy/";;
PPA_ID=56sqtkiu7jrubvee6tk03a3ve6;
webfx-tree-cookie-persistence=wfxt-4+wfxt-6+wfxt-10+wfxt-16+wfxt-18+wfxt-20')
paste.

[galaxy-dev] view details not working

[Vincent Cahais]

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)


CGI Variables
-
   CONTENT_LENGTH: '0'
   HTTP_ACCEPT: 
'text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8'
   HTTP_ACCEPT_ENCODING: 'gzip, deflate'
   HTTP_ACCEPT_LANGUAGE: 'en-US,en;q=0.5'
   HTTP_AUTHORIZATION: 'Basic Y2FoYWlzdjpXMXNtM3JoMWxs'
   HTTP_CONNECTION: 'close'
   HTTP_COOKIE: 
'galaxysession=09218edcc0a8a75b31582a2cb50d757dc5f67b9b7cae48d9fdb3bd88e9d143d956083945f07b4710;
 
galaxycommunitysession=aeaf4b69c51e3d6d293956655fa9014fb7b92937bf5c098a096ed54161b02239b63b34c44bba22ac;
 
toolshedgalaxyurl="http://galaxy/";; 
PPA_ID=56sqtkiu7jrubvee6tk03a3ve6; 
webfx-tree-cookie-persistence=wfxt-4+wfxt-6+wfxt-10+wfxt-16+wfxt-18+wfxt-20'
   HTTP_DNT: '1'
   HTTP_HOST: 'galaxy*'
   HTTP_REFERER: 'http://galaxy***/'
   HTTP_REMOTE_USER: '*'
   HTTP_UPGRADE_INSECURE_REQUESTS: '1'
   HTTP_USER_AGENT: 'Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:48.0) 
Gecko/20100101 Firefox/48.0'
   PATH_INFO: '/datasets/38ebe14f4d38806a/show_params'
   REMOTE_ADDR: '10.10.13.120'
   REQUEST_METHOD: 'GET'
   SCRIPT_NAME: '/galaxy'
   SERVER_NAME: '***'
   SERVER_PORT: '8080'
   SERVER_PROTOCOL: 'HTTP/1.1'

WSGI Variables
--
   application: 
   is_api_request: False
   paste.cookies: (, 
'galaxysession=09218edcc0a8a75b31582a2cb50d757dc5f67b9b7cae48d9fdb3bd88e9d143d956083945f07b4710;
 
galaxycommunitysession=aeaf4b69c51e3d6d293956655fa9014fb7b92937bf5c098a096ed54161b02239b63b34c44bba22ac;
 
toolshedgalaxyurl="http://galaxy/";; 
PPA_ID=56sqtkiu7jrubvee6tk03a3ve6; 
webfx-tree-cookie-persistence=wfxt-4+wfxt-6+wfxt-10+wfxt-16+wfxt-18+wfxt-20')
   paste.expected_exceptions: []
   paste.httpexceptions: 
   paste.httpserver.proxy.host: 'dummy'
   paste.httpserver.proxy.scheme: 'http'
   paste.httpserver.thread_pool: 
   paste.recursive.forward: 
   paste.recursive.include: 
   pa

Re: [galaxy-dev] Adding packages to depot.galaxyproject.org

[Peter Cock]

On Mon, Aug 8, 2016 at 2:41 PM, Eric Rasche  wrote:
> Hi Peter,
>
> The cargo port is the ideal place for this, however it does not support
> manual uploads of files.
>

Thanks Eric,

You mean https://github.com/galaxyproject/cargo-port

Is that something which might be addressed in future? The use case
is when a previously public file stops working (either temporarily or
permanently), so you can't use the official URL to make the cached
copy?

Would it be OK to use a short lived URL like a personal dropbox URL,
and then once cached, update urls.tsv with the original official
(but broken) URL?

Peter
___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] External user auth and API

[Eric Rasche]

On 08. aug. 2016 13:25, Sarah DIEHL wrote:
> Hi Eric,
>
> thanks a lot for the info and help! I'm running version 16.04 and my
> apache conf is a bit different because I balance over multiple galaxy
> web servers:
Just as an aside, if you are still using this configuration method, you
might consider switching to uWSGI
, it
will drastically simplify your configuration and should be just as
performant (if not more).

>
>
> # API requests get routed through balancer with no authentication
> RewriteCond %{QUERY_STRING} key=
> RewriteRule ^/api/(.*) balancer://galaxy-noauth/api/$1 [P]
>
> # Regular requests get routed through balancer with LDAP
> authentication
> RewriteRule ^(.*) balancer://galaxy$1 [P]
>
> 
> BalancerMember  http://localhost:8080
> BalancerMember  http://localhost:8081
> BalancerMember  http://localhost:8082
> BalancerMember  http://localhost:8083
>
> RequestHeader set X-URL-SCHEME https
>
> AuthType Basic
> AuthBasicProvider ldap
> AuthName   "UL HPC Platform Authorized Users Only"
> AuthLDAPBindAuthoritative off
> AuthLDAPURL "ldap://…";
> Require valid-user
> RequestHeader set REMOTE_USER %{AUTHENTICATE_uid}e
>
> XSendFile on
> XSendFilePath /
>
> SetOutputFilter DEFLATE
> SetEnvIfNoCase Request_URI \.(?:gif|jpe?g|png)$ no-gzip dont-vary
> SetEnvIfNoCase Request_URI \.(?:t?gz|zip|bz2)$ no-gzip dont-vary
> SetEnvIfNoCase Request_URI /history/export_archive no-gzip
> dont-vary
> 
>
> 
> BalancerMember  http://localhost:8080
> BalancerMember  http://localhost:8081
> BalancerMember  http://localhost:8082
> BalancerMember  http://localhost:8083
>
> RequestHeader set X-URL-SCHEME https
>
> Satisfy any
>
> XSendFile on
> XSendFilePath /
>
> SetOutputFilter DEFLATE
> SetEnvIfNoCase Request_URI \.(?:gif|jpe?g|png)$ no-gzip dont-vary
> SetEnvIfNoCase Request_URI \.(?:t?gz|zip|bz2)$ no-gzip dont-vary
> SetEnvIfNoCase Request_URI /history/export_archive no-gzip
> dont-vary
> 
>
> What doesn't work when configured this way is data libraries' import
> from user directory function. Can you tell if my apache configuration
> is equivalent to yours?
Your configuration /looks/ equivalent, yes, but I may have overlooked
something, I have since forgotten some of the semantics of proxy balancers.
> Does the import functionality in the data libraries work for you?
Import datasets from data libraries to history? Yes, this does for me.
In what way does it break for you? Unauthenticated /api requests? It
seems odd that data libraries would be the only affected thing here,
since other things like the tool panel also make /api requests.
>
> This configuration worked fine with release 15.10, but doesn't anymore
> since I upgraded. Between those two version the default data libraries
> interface changed. What used to be "beta" before is now the default
> and only available option.
Old data libraries were deprecated

in favour of the new ones and removed in 16.01.
>
> Best regards,
> Sarah
>
>
> 
> Sarah Diehl
> HPC System Administrator
>  
> UNIVERSITÉ DU LUXEMBOURG
>  
> LUXEMBOURG CENTRE FOR SYSTEMS BIOMEDICINE
> Campus Belval | Biotech II
> 6, avenue du Swing
> L-4371 Belvaux
> T +352 46 66 44 5360
> sarah.di...@uni.lu  http://lcsb.uni.lu
> 
> -
> This message is confidential and may contain privileged information.
> It is intended for the named recipient only. If you receive it in
> error please notify me and permanently delete the original message and
> any copies.
> -
>
>
> From: Eric Rasche mailto:e...@tamu.edu>>
> Organization: TAMU
> Date: Monday 8 August 2016 15:09
> To: Sarah DIEHL mailto:sarah.di...@uni.lu>>,
> "galaxy-dev@lists.galaxyproject.org
> "
>  >
> Subject: Re: [galaxy-dev] External user auth and API
>
> Hi Sarah,
>
>
> On 08. aug. 2016 07:44, Sarah DIEHL wrote:
>> Dear all,
>>
>> since no one replied so far to the main problem I had and it might
>> have gotten lost in the conversation, I ask again: Does somebody know
>> how to configure external user auth with apache such that API (from
>> external, e.g. bioblend) and dataset import in the data libraries
>> work? When I configure apache to require auth for everything, the API
>> does not work. If I except the API from the apache auth, the dataset
>> import does not work.
>
> Our conf

Re: [galaxy-dev] Adding packages to depot.galaxyproject.org

[Eric Rasche]

Hi Peter,

The cargo port is the ideal place for this, however it does not support
manual uploads of files.

On 08. aug. 2016 13:37, Peter Cock wrote:
> Hello all,
>
> How do tool wrapper developers/packagers go about adding entries
> to the Galaxy depot? There isn't a GitHub repository for this is there?
>
> Specifically I want to upload some older MIRA releases, e.g. these
> URLs have broken, but I have the original files and checksums:
>
> http://downloads.sourceforge.net/project/mira-assembler/MIRA/development/mira_4.9.5_2_darwin14.3.0_x86_64_static.tar.bz2
> http://downloads.sourceforge.net/project/mira-assembler/MIRA/development/mira_4.9.5_2_linux-gnu_x86_64_static.tar.bz2
I would recommend the following though others who work on the cargo port
might chime in:

  * Upload those tarballs somewhere accessible
  * Add cargo port entries with your URLs

Then cargo port would at least have a copy you can reference in your tools.

>
> See also:
>
> https://www.freelists.org/post/mira_talk/Stable-download-URLs-on-sourceforge
> https://www.freelists.org/post/mira_talk/MIRA-495-now-missing-on-SourceForge
>
> I'm now running "planemo lint --urls ..." under TravisCI which flags
> the broken URLs immediately (rather than finding out when the
> installation fails later):
>
> https://github.com/peterjc/galaxy_mira/commit/4e26a4e3f3d69adaab657cb614e56ebcf9968592
> https://travis-ci.org/peterjc/galaxy_mira/jobs/150025836
>
> Regards,
>
> Peter
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>   https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/

-- 
Eric Rasche
Programmer II

Center for Phage Technology
Rm 312A, Biochemistry & Biophysics
Texas A&M University
College Station, TX 77843
e...@tamu.edu 
___
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[galaxy-dev] Adding packages to depot.galaxyproject.org

[Peter Cock]

Hello all,

How do tool wrapper developers/packagers go about adding entries
to the Galaxy depot? There isn't a GitHub repository for this is there?

Specifically I want to upload some older MIRA releases, e.g. these
URLs have broken, but I have the original files and checksums:

http://downloads.sourceforge.net/project/mira-assembler/MIRA/development/mira_4.9.5_2_darwin14.3.0_x86_64_static.tar.bz2
http://downloads.sourceforge.net/project/mira-assembler/MIRA/development/mira_4.9.5_2_linux-gnu_x86_64_static.tar.bz2

See also:

https://www.freelists.org/post/mira_talk/Stable-download-URLs-on-sourceforge
https://www.freelists.org/post/mira_talk/MIRA-495-now-missing-on-SourceForge

I'm now running "planemo lint --urls ..." under TravisCI which flags
the broken URLs immediately (rather than finding out when the
installation fails later):

https://github.com/peterjc/galaxy_mira/commit/4e26a4e3f3d69adaab657cb614e56ebcf9968592
https://travis-ci.org/peterjc/galaxy_mira/jobs/150025836

Regards,

Peter
___
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in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] External user auth and API

[Sarah DIEHL]

Hi Eric,

thanks a lot for the info and help! I'm running version 16.04 and my apache 
conf is a bit different because I balance over multiple galaxy web servers:


# API requests get routed through balancer with no authentication
RewriteCond %{QUERY_STRING} key=
RewriteRule ^/api/(.*) balancer://galaxy-noauth/api/$1 [P]

# Regular requests get routed through balancer with LDAP authentication
RewriteRule ^(.*) balancer://galaxy$1 [P]


BalancerMember  http://localhost:8080
BalancerMember  http://localhost:8081
BalancerMember  http://localhost:8082
BalancerMember  http://localhost:8083

RequestHeader set X-URL-SCHEME https

AuthType Basic
AuthBasicProvider ldap
AuthName   "UL HPC Platform Authorized Users Only"
AuthLDAPBindAuthoritative off
AuthLDAPURL "ldap://…";
Require valid-user
RequestHeader set REMOTE_USER %{AUTHENTICATE_uid}e

XSendFile on
XSendFilePath /

SetOutputFilter DEFLATE
SetEnvIfNoCase Request_URI \.(?:gif|jpe?g|png)$ no-gzip dont-vary
SetEnvIfNoCase Request_URI \.(?:t?gz|zip|bz2)$ no-gzip dont-vary
SetEnvIfNoCase Request_URI /history/export_archive no-gzip dont-vary



BalancerMember  http://localhost:8080
BalancerMember  http://localhost:8081
BalancerMember  http://localhost:8082
BalancerMember  http://localhost:8083

RequestHeader set X-URL-SCHEME https

Satisfy any

XSendFile on
XSendFilePath /

SetOutputFilter DEFLATE
SetEnvIfNoCase Request_URI \.(?:gif|jpe?g|png)$ no-gzip dont-vary
SetEnvIfNoCase Request_URI \.(?:t?gz|zip|bz2)$ no-gzip dont-vary
SetEnvIfNoCase Request_URI /history/export_archive no-gzip dont-vary


What doesn't work when configured this way is data libraries' import from user 
directory function. Can you tell if my apache configuration is equivalent to 
yours? Does the import functionality in the data libraries work for you?

This configuration worked fine with release 15.10, but doesn't anymore since I 
upgraded. Between those two version the default data libraries interface 
changed. What used to be "beta" before is now the default and only available 
option.

Best regards,
Sarah



Sarah Diehl
HPC System Administrator

UNIVERSITÉ DU LUXEMBOURG

LUXEMBOURG CENTRE FOR SYSTEMS BIOMEDICINE
Campus Belval | Biotech II
6, avenue du Swing
L-4371 Belvaux
T +352 46 66 44 5360
sarah.di...@uni.lu 
http://lcsb.uni.lu
-
This message is confidential and may contain privileged information. It is 
intended for the named recipient only. If you receive it in error please notify 
me and permanently delete the original message and any copies.
-


From: Eric Rasche mailto:e...@tamu.edu>>
Organization: TAMU
Date: Monday 8 August 2016 15:09
To: Sarah DIEHL mailto:sarah.di...@uni.lu>>, 
"galaxy-dev@lists.galaxyproject.org" 
mailto:galaxy-dev@lists.galaxyproject.org>>
Subject: Re: [galaxy-dev] External user auth and API

Hi Sarah,


On 08. aug. 2016 07:44, Sarah DIEHL wrote:
Dear all,

since no one replied so far to the main problem I had and it might have gotten 
lost in the conversation, I ask again: Does somebody know how to configure 
external user auth with apache such that API (from external, e.g. bioblend) and 
dataset import in the data libraries work? When I configure apache to require 
auth for everything, the API does not work. If I except the API from the apache 
auth, the dataset import does not work.

Our configuration looks like the following (just switching CAS for LDAP.)


Satisfy Any
Allow from all



AuthName "CAS"
AuthType CAS
Require valid-user
RequestHeader set X-URL-SCHEME https
XSendFile on
XSendFilePath /
RequestHeader set CAS-User 
"%{REMOTE_USER}s...@tamu.edu"

ProxyPass /galaxy uwsgi://127.0.0.1:4001/

I.e. we disable authentication on the /api route. On 16.01+ (I think it was 
patched then, but 16.04 is a safer bet) this will work correctly and your users 
will be able to use the API. On previous versions the /api route would fail for 
web users if exposed in this manner.

If I switch to the new galaxy-internal LDAP auth features, will that solve this 
problem?
Yes, this is an alternate solution.

Any hints are appreciated!

Best regards,
Sarah



Sarah Diehl
HPC System Administrator

UNIVERSITÉ DU LUXEMBOURG

LUXEMBOURG CENTRE FOR SYSTEMS BIOMEDICINE
Campus Belval | Biotech II
6, avenue du Swing
L-4371 Belvaux
T +352 46 66 44 5360
sarah.di...@uni.lu 

Re: [galaxy-dev] External user auth and API

[Eric Rasche]

Hi Sarah,


On 08. aug. 2016 07:44, Sarah DIEHL wrote:
> Dear all,
>
> since no one replied so far to the main problem I had and it might
> have gotten lost in the conversation, I ask again: Does somebody know
> how to configure external user auth with apache such that API (from
> external, e.g. bioblend) and dataset import in the data libraries
> work? When I configure apache to require auth for everything, the API
> does not work. If I except the API from the apache auth, the dataset
> import does not work.

Our configuration looks like the following (just switching CAS for LDAP.)


Satisfy Any
Allow from all



AuthName "CAS"
AuthType CAS
Require valid-user
RequestHeader set X-URL-SCHEME https
XSendFile on
XSendFilePath /
RequestHeader set CAS-User "%{REMOTE_USER}s...@tamu.edu"

ProxyPass /galaxy uwsgi://127.0.0.1:4001/

I.e. we disable authentication on the /api route. On 16.01+ (I think it
was patched then, but 16.04 is a safer bet) this will work correctly and
your users will be able to use the API. On previous versions the /api
route would fail for web users if exposed in this manner.
>
> If I switch to the new galaxy-internal LDAP auth features, will that
> solve this problem?
Yes, this is an alternate solution.
>
> Any hints are appreciated!
>
> Best regards,
> Sarah
>
>
> 
> Sarah Diehl
> HPC System Administrator
>  
> UNIVERSITÉ DU LUXEMBOURG
>  
> LUXEMBOURG CENTRE FOR SYSTEMS BIOMEDICINE
> Campus Belval | Biotech II
> 6, avenue du Swing
> L-4371 Belvaux
> T +352 46 66 44 5360
> sarah.di...@uni.lu  http://lcsb.uni.lu
> 
> -
> This message is confidential and may contain privileged information.
> It is intended for the named recipient only. If you receive it in
> error please notify me and permanently delete the original message and
> any copies.
> -
>
>
> From: galaxy-dev  > on behalf of
> Sarah DIEHL mailto:sarah.di...@uni.lu>>
> Date: Monday 1 August 2016 13:06
> To: Nicola Soranzo mailto:nsora...@tiscali.it>>,
> "galaxy-dev@lists.galaxyproject.org
> "
>  >
> Subject: Re: [galaxy-dev] Remote user auth and API
>
> Hi Nicola,
>
> thanks a lot for the help! Yes, it's a self-signed certificate, I
> didn't bother with letsencrypt yet ;-).
>
> So now the error turned to
> ConnectionError: GET: error 401: b' HTML 2.0//EN">\n\n401 Authorization
> Required\n\nAuthorization
> Required\nThis server could not verify that you\nare
> authorized to access the document\nrequested. Either you supplied the
> wrong\ncredentials (e.g., bad password), or your\nbrowser doesn\'t
> understand how to supply\nthe credentials
> required.\n\n', 0 attempts left: None
> which is what I expected, since apache now wants the authentication
> through LDAP.
>
> So anybody know what the right settings are to get both the dataset
> import and the API working with external user auth over apache and LDAP?
>
> Thanks,
> Sarah
>
> 
> Sarah Diehl
> HPC System Administrator
>  
> UNIVERSITÉ DU LUXEMBOURG
>  
> LUXEMBOURG CENTRE FOR SYSTEMS BIOMEDICINE
> Campus Belval | Biotech II
> 6, avenue du Swing
> L-4371 Belvaux
> T +352 46 66 44 5360
> sarah.di...@uni.lu  http://lcsb.uni.lu
> 
> -
> This message is confidential and may contain privileged information.
> It is intended for the named recipient only. If you receive it in
> error please notify me and permanently delete the original message and
> any copies.
> -
>
>
> From: Nicola Soranzo  > on behalf of Nicola Soranzo
> mailto:nsora...@tiscali.it>>
> Date: Monday 1 August 2016 12:58
> To: Sarah DIEHL mailto:sarah.di...@uni.lu>>,
> "galaxy-dev@lists.galaxyproject.org
> "
>  >
> Subject: Re: [galaxy-dev] Remote user auth and API
>
> Hi Sarah!
> I guess that your problem is with an untrusted certificate, you can
> get one for free at https://letsencrypt.org/
>
> You can disable certificate verification in bioblend as in the example
> below:
>
> import bioblend.galaxy
> gi = bioblend.galaxy.GalaxyInstance(url=my_server, key=my_key)
> gi.verify = False
>
> Cheers,
> Nicola
>
> On 01/08/16 09:08, Sarah DIEHL wrote:
>> Dear all,
>>
>> since the recent update to 16.04 I get the following error when
>> trying to import a file from a us

[galaxy-dev] pop up on click

[Mohamed Kassam]

Dear all,
I have  create a tool on javascript and html.
I tried to use the xml tool from ucsc and flymine.
I would like to know if it is possible to replace

http://www.flymine.org"; check_values="false" method="get">
go to Flymine server $GALAXY_URL



By something like onclick it will display a pop up windows instead of
opening the html adress on the same window.

Best regards,

Mohamed
___
Please keep all replies on the list by using "reply all"
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  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] External user auth and API

[Nicola Soranzo]

Hi Sarah,
I have no experience with the external user configuration (you may ask 
to Eric Rasche, maybe try to pop on the IRC channel on US day time), but 
if you use the embedded Galaxy LDAP (i.e. configuring it in 
config/auth_conf.xml ), that should work without any other change.


Cheers,
Nicola

On 08/08/16 08:44, Sarah DIEHL wrote:

Dear all,

since no one replied so far to the main problem I had and it might 
have gotten lost in the conversation, I ask again: Does somebody know 
how to configure external user auth with apache such that API (from 
external, e.g. bioblend) and dataset import in the data libraries 
work? When I configure apache to require auth for everything, the API 
does not work. If I except the API from the apache auth, the dataset 
import does not work.


If I switch to the new galaxy-internal LDAP auth features, will that 
solve this problem?


Any hints are appreciated!

Best regards,
Sarah



Sarah Diehl
HPC System Administrator
UNIVERSITÉ DU LUXEMBOURG
LUXEMBOURG CENTRE FOR SYSTEMS BIOMEDICINE
Campus Belval | Biotech II
6, avenue du Swing
L-4371 Belvaux
T +352 46 66 44 5360
sarah.di...@uni.lu http://lcsb.uni.lu 


-
This message is confidential and may contain privileged information. 
It is intended for the named recipient only. If you receive it in 
error please notify me and permanently delete the original message and 
any copies.

-


From: galaxy-dev > on behalf of 
Sarah DIEHL mailto:sarah.di...@uni.lu>>

Date: Monday 1 August 2016 13:06
To: Nicola Soranzo mailto:nsora...@tiscali.it>>, 
"galaxy-dev@lists.galaxyproject.org 
" 
>

Subject: Re: [galaxy-dev] Remote user auth and API

Hi Nicola,

thanks a lot for the help! Yes, it's a self-signed certificate, I 
didn't bother with letsencrypt yet ;-).


So now the error turned to
ConnectionError: GET: error 401: b'HTML 2.0//EN">\n\n401 Authorization 
Required\n\nAuthorization 
Required\nThis server could not verify that you\nare 
authorized to access the document\nrequested. Either you supplied the 
wrong\ncredentials (e.g., bad password), or your\nbrowser doesn\'t 
understand how to supply\nthe credentials 
required.\n\n', 0 attempts left: None
which is what I expected, since apache now wants the authentication 
through LDAP.


So anybody know what the right settings are to get both the dataset 
import and the API working with external user auth over apache and LDAP?


Thanks,
Sarah


Sarah Diehl
HPC System Administrator
UNIVERSITÉ DU LUXEMBOURG
LUXEMBOURG CENTRE FOR SYSTEMS BIOMEDICINE
Campus Belval | Biotech II
6, avenue du Swing
L-4371 Belvaux
T +352 46 66 44 5360
sarah.di...@uni.lu http://lcsb.uni.lu 


-
This message is confidential and may contain privileged information. 
It is intended for the named recipient only. If you receive it in 
error please notify me and permanently delete the original message and 
any copies.

-


From: Nicola Soranzo > on behalf of Nicola Soranzo 
mailto:nsora...@tiscali.it>>

Date: Monday 1 August 2016 12:58
To: Sarah DIEHL mailto:sarah.di...@uni.lu>>, 
"galaxy-dev@lists.galaxyproject.org 
" 
>

Subject: Re: [galaxy-dev] Remote user auth and API

Hi Sarah!
I guess that your problem is with an untrusted certificate, you can 
get one for free at https://letsencrypt.org/


You can disable certificate verification in bioblend as in the example 
below:


import bioblend.galaxy
gi = bioblend.galaxy.GalaxyInstance(url=my_server, key=my_key)
gi.verify = False

Cheers,
Nicola

On 01/08/16 09:08, Sarah DIEHL wrote:

Dear all,

since the recent update to 16.04 I get the following error when 
trying to import a file from a user directory to a data library:


AssertionError: use_remote_user is set but HTTP_REMOTE_USER header 
was not provided


I use apache as a proxy and use an LDAP server for authentication. In 
order to get the API to work previously the apache had to be set to 
not check authentication for the requests to /api. In the logs I can 
see that the dataset import is an request to the API, so since the 
auth is not checked then, there is also no REMOTE_USER header set.


What is the recommended way to solve this issue with the current 
Galaxy version? I disabled the special settings for /api and the 
dataset import works now.


I tried to check the API with an old test script based on bioblend, 
but I now get the following error:


ConnectionError: [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify 
failed (_ssl.c:645), 0 attempts left: None


Previously I could disable it with

import requests
requests.packages.urllib3.disable_warnings()

but that doesn't seem to work anymore (switched to Python 3 now). 
Since bioblen

Re: [galaxy-dev] conversion issue

[Rathert , Philipp , Dr .]

I tried to reinstall some tools, but I still get an error message:




Fatal error: Exit code 1 ()
bedtools: 
/galaxy-central/tool_deps/ucsc_tools/312/iuc/package_ucsc_tools_312/2d6bafd63401/lib/libstdc++.so.6:
 version `GLIBCXX_3.4.15' not found (required by bedtools)
needLargeMem: trying to allocate 0 bytes (limit: 1000)
Traceback (most recent call last):
  File 
"/shed_tools/toolshed.g2.bx.psu.edu/repos/brad-chapman/bam_to_bigwig/9163e1db4c16/bam_to_bigwig/bam_to_bigwig.py",
 line 122, in 
main(*args, **kwargs)
  File 
"/shed_tools/toolshed.g2.bx.psu.edu/repos/brad-chapman/bam_to_bigwig/9163e1db4c16/bam_to_bigwig/bam_to_bigwig.py",
 line 57, in main
convert_to_bigwig(temp_file, sizes, config, outfile)
  File 
"/shed_tools/toolshed.g2.bx.psu.edu/repos/brad-chapman/bam_to_bigwig/9163e1db4c16/bam_to_bigwig/bam_to_bigwig.py",
 line 104, in convert_to_bigwig
subprocess.check_call(cl)
  File 
"/galaxy-central/tool_deps/python/2.7.10/iuc/package_python_2_7_10/0339c4a9b87b/lib/python2.7/subprocess.py",
 line 540, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['bedGraphToBigWig', '/tmp/tmpkiKe2V', 
'/export/galaxy-central/database/files/003/dataset_3153-sizes.txt', 
'/export/galaxy-central/database/files/003/dataset_3153.dat']' returned 
non-zero exit status 255





It seems Bedrolls requires 


GLIBCXX_3.4.15

Since I am using Galaxy-docker I am not sure how to get this installed...





Always grateful for help.



Cheers,



Philipp



-Original message-
From: Rathert, Philipp, Dr. 
Sent: Friday 5th August 2016 16:26
To: Peter Cock 
Cc: Brad Chapman ; galaxy-dev@lists.galaxyproject.org
Subject: Re: [galaxy-dev] conversion issue

Hi Peter,



it looks like samtools is not functional





==> /home/galaxy/logs/uwsgi.log <==

galaxy.tools DEBUG 2016-08-05 14:25:25,686 Validated and populated state for 
tool request (52.679 ms)

galaxy.tools.actions INFO 2016-08-05 14:25:25,754 Handled output named out for 
tool 
toolshed.g2.bx.psu.edu/repos/brad-chapman/bam_to_bigwig/bam_to_bigwig/0.2.0 
(26.340 ms)

galaxy.tools.actions INFO 2016-08-05 14:25:25,767 Added output datasets to 
history (13.170 ms)

galaxy.tools.actions INFO 2016-08-05 14:25:25,793 Verified access to datasets 
for 
Job[unflushed,tool_id=toolshed.g2.bx.psu.edu/repos/brad-chapman/bam_to_bigwig/bam_to_bigwig/0.2.0]
 (11.785 ms)

galaxy.tools.actions INFO 2016-08-05 14:25:25,794 Setup for job 
Job[unflushed,tool_id=toolshed.g2.bx.psu.edu/repos/brad-chapman/bam_to_bigwig/bam_to_bigwig/0.2.0]
 complete, ready to flush (26.847 ms)

galaxy.tools.actions INFO 2016-08-05 14:25:25,841 Flushed transaction for job 
Job[id=2438,tool_id=toolshed.g2.bx.psu.edu/repos/brad-chapman/bam_to_bigwig/bam_to_bigwig/0.2.0]
 (47.380 ms)

galaxy.tools.execute DEBUG 2016-08-05 14:25:25,842 Tool 
[toolshed.g2.bx.psu.edu/repos/brad-chapman/bam_to_bigwig/bam_to_bigwig/0.2.0] 
created job [2438] (130.941 ms)

galaxy.tools.execute DEBUG 2016-08-05 14:25:25,851 Executed 1 job(s) for tool 
toolshed.g2.bx.psu.edu/repos/brad-chapman/bam_to_bigwig/bam_to_bigwig/0.2.0 
request: (164.591 ms)

172.17.0.1 - - [05/Aug/2016:14:25:25 +] "POST /api/tools HTTP/1.1" 200 - 
"http://129.69.102.30:8080/root  " "Mozilla/5.0 
(Macintosh; Intel Mac OS X 10_11_3) AppleWebKit/601.4.4 (KHTML, like Gecko) 
Version/9.0.3 Safari/601.4.4"

[pid: 381|app: 0|req: 53/85] 172.17.0.1 () {52 vars in 973 bytes} [Fri Aug  5 
14:25:25 2016] POST /api/tools => generated 983 bytes in 256 msecs (HTTP/1.1 
200) 3 headers in 124 bytes (1 switches on core 0)

172.17.0.1 - - [05/Aug/2016:14:25:25 +] "GET 
/api/histories/b701da857886499b/contents?v=dev HTTP/1.1" 200 - 
"http://129.69.102.30:8080/root  " "Mozilla/5.0 
(Macintosh; Intel Mac OS X 10_11_3) AppleWebKit/601.4.4 (KHTML, like Gecko) 
Version/9.0.3 Safari/601.4.4"

[pid: 382|app: 0|req: 33/86] 172.17.0.1 () {46 vars in 921 bytes} [Fri Aug  5 
14:25:25 2016] GET /api/histories/b701da857886499b/contents?v=dev => generated 
125847 bytes in 127 msecs (HTTP/1.1 200) 3 headers in 124 bytes (1 switches on 
core 2)



==> /home/galaxy/logs/handler0.log <==

galaxy.jobs DEBUG 2016-08-05 14:25:26,391 (2438) Working directory for job is: 
/export/galaxy-central/database/job_working_directory/002/2438

galaxy.jobs.handler DEBUG 2016-08-05 14:25:26,401 (2438) Dispatching to slurm 
runner

galaxy.jobs DEBUG 2016-08-05 14:25:26,436 (2438) Persisting job destination 
(destination id: slurm_cluster)

galaxy.jobs.runners DEBUG 2016-08-05 14:25:26,450 Job [2438] queued (48.081 ms)

galaxy.jobs.handler INFO 2016-08-05 14:25:26,457 (2438) Job dispatched

galaxy.tools.deps DEBUG 2016-08-05 14:25:26,693 Building dependency shell 
command for dependency 'pysam'

galaxy.tools.deps DEBUG 2016-08-05 14:25:26,693 Find dependency pysam version 
0.8.3

galaxy.tools.deps DEBUG 2016-08-05 14:25:26,700 Resolver tool_shed_packages 
returned  (isn

[galaxy-dev] External user auth and API

[Sarah DIEHL]

Dear all,

since no one replied so far to the main problem I had and it might have gotten 
lost in the conversation, I ask again: Does somebody know how to configure 
external user auth with apache such that API (from external, e.g. bioblend) and 
dataset import in the data libraries work? When I configure apache to require 
auth for everything, the API does not work. If I except the API from the apache 
auth, the dataset import does not work.

If I switch to the new galaxy-internal LDAP auth features, will that solve this 
problem?

Any hints are appreciated!

Best regards,
Sarah



Sarah Diehl
HPC System Administrator

UNIVERSITÉ DU LUXEMBOURG

LUXEMBOURG CENTRE FOR SYSTEMS BIOMEDICINE
Campus Belval | Biotech II
6, avenue du Swing
L-4371 Belvaux
T +352 46 66 44 5360
sarah.di...@uni.lu 
http://lcsb.uni.lu
-
This message is confidential and may contain privileged information. It is 
intended for the named recipient only. If you receive it in error please notify 
me and permanently delete the original message and any copies.
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From: galaxy-dev 
mailto:galaxy-dev-boun...@lists.galaxyproject.org>>
 on behalf of Sarah DIEHL mailto:sarah.di...@uni.lu>>
Date: Monday 1 August 2016 13:06
To: Nicola Soranzo mailto:nsora...@tiscali.it>>, 
"galaxy-dev@lists.galaxyproject.org" 
mailto:galaxy-dev@lists.galaxyproject.org>>
Subject: Re: [galaxy-dev] Remote user auth and API

Hi Nicola,

thanks a lot for the help! Yes, it's a self-signed certificate, I didn't bother 
with letsencrypt yet ;-).

So now the error turned to

ConnectionError: GET: error 401: b'\n\n401 Authorization 
Required\n\nAuthorization Required\nThis 
server could not verify that you\nare authorized to access the 
document\nrequested.  Either you supplied the wrong\ncredentials (e.g., bad 
password), or your\nbrowser doesn\'t understand how to supply\nthe credentials 
required.\n\n', 0 attempts left: None

which is what I expected, since apache now wants the authentication through 
LDAP.

So anybody know what the right settings are to get both the dataset import and 
the API working with external user auth over apache and LDAP?

Thanks,
Sarah


Sarah Diehl
HPC System Administrator

UNIVERSITÉ DU LUXEMBOURG

LUXEMBOURG CENTRE FOR SYSTEMS BIOMEDICINE
Campus Belval | Biotech II
6, avenue du Swing
L-4371 Belvaux
T +352 46 66 44 5360
sarah.di...@uni.lu 
http://lcsb.uni.lu
-
This message is confidential and may contain privileged information. It is 
intended for the named recipient only. If you receive it in error please notify 
me and permanently delete the original message and any copies.
-


From: Nicola Soranzo 
mailto:nicola.sora...@gmail.com>> on behalf of Nicola 
Soranzo mailto:nsora...@tiscali.it>>
Date: Monday 1 August 2016 12:58
To: Sarah DIEHL mailto:sarah.di...@uni.lu>>, 
"galaxy-dev@lists.galaxyproject.org" 
mailto:galaxy-dev@lists.galaxyproject.org>>
Subject: Re: [galaxy-dev] Remote user auth and API

Hi Sarah!
I guess that your problem is with an untrusted certificate, you can get one for 
free at https://letsencrypt.org/

You can disable certificate verification in bioblend as in the example below:

import bioblend.galaxy
gi = bioblend.galaxy.GalaxyInstance(url=my_server, key=my_key)
gi.verify = False

Cheers,
Nicola

On 01/08/16 09:08, Sarah DIEHL wrote:
Dear all,

since the recent update to 16.04 I get the following error when trying to 
import a file from a user directory to a data library:

AssertionError: use_remote_user is set but HTTP_REMOTE_USER header was not 
provided

I use apache as a proxy and use an LDAP server for authentication. In order to 
get the API to work previously the apache had to be set to not check 
authentication for the requests to /api. In the logs I can see that the dataset 
import is an request to the API, so since the auth is not checked then, there 
is also no REMOTE_USER header set.

What is the recommended way to solve this issue with the current Galaxy 
version? I disabled the special settings for /api and the dataset import works 
now.

I tried to check the API with an old test script based on bioblend, but I now 
get the following error:

ConnectionError: [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed 
(_ssl.c:645), 0 attempts left: None

Previously I could disable it with

import requests
requests.packages.urllib3.disable_warnings()

but that doesn't seem to work anymore (switched to Python 3 now). Since 
bioblend wraps all the requests methods, I cannot apply any of the common 
solutions I found online (e.g. set verify=False).

Any help to solve these issues is highly appreciated :-).

Best regards,
Sarah




Sarah Diehl
HPC System Administrator

UNIVERSITÉ DU LUXEMBOURG

LUXEMBOURG CENTRE FOR SYSTEMS BIOMEDICINE
Campus Belval | Biotech II
6, avenue du Swing
L-4371 Belvaux
T +