Re: [galaxy-dev] Fatal Error while uploading a File with special Characters

2015-09-10 Thread Dannon Baker 
Thanks.  Can you specify exactly which release (or even the exact
changeset) of the galaxy revision you're running, and what encoding the
database is currently set to?  I've reproduced the error with the latest
galaxy release, mysql 5.6.26 (utf8 encoding) and will get a fix out
shortly, but I want to make sure I'm testing your situation as well.

On Thu, Sep 10, 2015 at 10:14 AM, Matthias Enders <
m.end...@german-seed-alliance.de> wrote:

> It was the name of the File:
>
>
>
> Blühzeitpunkt.txt
>
>
>
> (for example)
>
>
>
> *Von:* Dannon Baker [mailto:dannon.ba...@gmail.com]
> *Gesendet:* Thursday, September 10, 2015 4:12 PM
> *An:* Matthias Enders 
> *Cc:* galaxy-dev@lists.galaxyproject.org
> *Betreff:* Re: [galaxy-dev] Fatal Error while uploading a File with
> special Characters
>
>
>
> You should definitely not have to purge a user to fix this (not that it
> should happen in the first place).  Was it the file with special
> characters, or the name of the file?
>
>
>
>
>
>
>
> On Thu, Sep 10, 2015 at 2:28 AM, Matthias Enders <
> m.end...@german-seed-alliance.de> wrote:
>
> Dear Galaxy Community,
>
> a User of our Galaxy Platform has produced a fatal error by uploading a
> file containing a German special character  (ä / ü / ö / ß). This resulted
> in the following status (only for the given user):
>
> - Upload was canceled: Status was "Failed Internal Server Error (500)"
> - All Histories were corrupt stating: "An error was encountered while
> loading the contents."
> - Tools can´t be used an stating (in Traceback):
> " UnicodeDecodeError: 'utf8' codec can't decode byte 0xfc in position 5:
> invalid start byte"
> "Module weberror.evalexception.middleware:364 in respond"
>
>
> This totally destroyed to current user and we have had to purge him in
> order to get him back to work, even losing all his datasets & histories!
>
> We are using an MySQL database as a backend. Is the Encoding of this
> database the problem? If yes: Which encoding is used/supported by galaxy?
>
> Thanks in advance!
>
> Matthias
> ___
> Please keep all replies on the list by using "reply all"
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> and other Galaxy lists, please use the interface at:
>   https://lists.galaxyproject.org/
>
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>
>
>
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Re: [galaxy-dev] Opening Galaxy with a specified History Name

2015-09-10 Thread rbrown1422 
Good afternoon John,

We are running a self defined workflow in Galaxy and have a unique history for 
each dataset we are working on.  This workflow is run repeatedly to tackle an 
entire dataset, requiring the user the use Galaxy multiple times with other 
steps outside of Galaxy.

The user enters via a web app, and we would like to bring the user into their 
Galaxy account with the correct history loaded for the dataset they are trying 
to process.
Is there a way to specify the history when starting Galaxy, not just use the 
last one from the previous session?

Thanks,
Bob

- Original Message -From: John Chilton To: 
rbrown1422@comcast.netCc: galaxy-dev@lists.galaxyproject.orgSent: Wed, 09 Sep 
2015 15:32:39 - (UTC)Subject: Re: [galaxy-dev] Opening Galaxy with a 
specified History Name

Can you please elaborate on what will be driving this? You cancertainly create 
a history and run jobs with the API. It sounds likewhat you want though is an 
external web application or something thatwill have a link to create a new 
history for the current users'ssession. I'm not sure this is currently 
supported since this wouldn'tinvolve the API but it can probably be hacked 
together for yourapplication.

-John

On Sat, Sep 5, 2015 at 8:17 PM,  wrote:> To all,> I 
would like to open a Galaxy session programmatically (schedule Galaxy with> 
their user name and password) and have the Galaxy session open with a> history 
name I specify. So if there was work done previously under that> history name, 
those output files will appear in the history window --> without the user 
having to change the history name manually to see them.> Is this possible?> 
Thanks,> bob>> ___> 
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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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[galaxy-dev] Error when Installing package_galaxy_utils_1_0

2015-09-10 Thread Leslie Herrera 
Hello:

My lab is currently in the process of setting Galaxy up on our server.  I
have been installing the appropriate tools, but I am having difficulty
installing the package_galaxy_utils_1_0.  The error message is below.  If
this is something that is occuring on our end, would you please send
instuctions on how to fix it?  If I have sent this email to wrong address
or you need more information, please let me know.  Thank you very much for
your help.


Downloading
http://pypi.python.org/packages/source/d/distribute/distribute-0.6.38.tar.gz
Extracting in /tmp/tmp3dIIS_
Now working in /tmp/tmp3dIIS_/distribute-0.6.38
Building a Distribute egg in
/scratch/tmp-toolshed-mtdKjroZR/galaxy_sequence_utils-1.0.0
Traceback (most recent call last):
  File "setup.py", line 248, in 
scripts = scripts,
  File "/usr/lib/python2.7/distutils/core.py", line 111, in setup
_setup_distribution = dist = klass(attrs)
  File "/tmp/tmp3dIIS_/distribute-0.6.38/setuptools/dist.py", line
225, in __init__
_Distribution.__init__(self,attrs)
  File "/usr/lib/python2.7/distutils/dist.py", line 287, in __init__
self.finalize_options()
  File "/tmp/tmp3dIIS_/distribute-0.6.38/setuptools/dist.py", line
257, in finalize_options
ep.require(installer=self.fetch_build_egg)
  File "/tmp/tmp3dIIS_/distribute-0.6.38/pkg_resources.py", line 2027,
in require
working_set.resolve(self.dist.requires(self.extras),env,installer))
  File "/tmp/tmp3dIIS_/distribute-0.6.38/pkg_resources.py", line 2237,
in requires
dm = self._dep_map
  File "/tmp/tmp3dIIS_/distribute-0.6.38/pkg_resources.py", line 2466,
in _dep_map
self.__dep_map = self._compute_dependencies()
  File "/tmp/tmp3dIIS_/distribute-0.6.38/pkg_resources.py", line 2499,
in _compute_dependencies
common = frozenset(reqs_for_extra(None))
  File "/tmp/tmp3dIIS_/distribute-0.6.38/pkg_resources.py", line 2496,
in reqs_for_extra
if req.marker_fn(override={'extra':extra}):
  File "/tmp/tmp3dIIS_/distribute-0.6.38/_markerlib/markers.py", line
109, in marker_fn
return eval(compiled_marker, environment)
  File "", line 1, in 
NameError: name 'sys_platform' is not defined
/scratch/tmp-toolshed-mtdKjroZR/galaxy_sequence_utils-1.0.0/distribute-0.6.38-py2.7.egg
Traceback (most recent call last):
  File "setup.py", line 9, in 
use_setuptools()
  File 
"/scratch/tmp-toolshed-mtdKjroZR/galaxy_sequence_utils-1.0.0/distribute_setup.py",
line 152, in use_setuptools
return _do_download(version, download_base, to_dir, download_delay)
  File 
"/scratch/tmp-toolshed-mtdKjroZR/galaxy_sequence_utils-1.0.0/distribute_setup.py",
line 132, in _do_download
_build_egg(egg, tarball, to_dir)
  File 
"/scratch/tmp-toolshed-mtdKjroZR/galaxy_sequence_utils-1.0.0/distribute_setup.py",
line 123, in _build_egg
raise IOError('Could not build the egg.')
IOError: Could not build the egg.
-- 
Leslie A Herrera
Starr Lab Junior Specialist
MCB, 139 Briggs Hall
University of California, Davis
laherr...@ucdavis.edu
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Re: [galaxy-dev] Fatal Error while uploading a File with special Characters

2015-09-10 Thread Matthias Enders 
Hi,

MySQL:
Server version: 5.5.44-0ubuntu0.14.04.1 (Ubuntu)

MySQL-GalaxyDB Encoding: UTF8

Galaxy: Where can I find the current release und changeset of my Galaxy 
Instance?

Mit freundlichen Grüßen
Matthias Enders
---
[cid:image001.png@01D03960.8254BEE0]

GERMAN SEED ALLIANCE GmbH
c/o Norddeutsche Pflanzenzucht
Hans-Georg Lembke KG
Hohenlieth, 24363 Holtsee
Tel.: +49 (0)4351/ 736-189
Fax: + 49 (0)4351/ 736-271
Mobil: +49 (0)151/ 14247360

Email: m.end...@german-seed-alliance.de

Firmensitz Köln
Amtsgericht Köln, HRB 73844

Von: Dannon Baker [mailto:dannon.ba...@gmail.com]
Gesendet: Thursday, September 10, 2015 4:53 PM
An: Matthias Enders 
Cc: galaxy-dev@lists.galaxyproject.org
Betreff: Re: [galaxy-dev] Fatal Error while uploading a File with special 
Characters

Thanks.  Can you specify exactly which release (or even the exact changeset) of 
the galaxy revision you're running, and what encoding the database is currently 
set to?  I've reproduced the error with the latest galaxy release, mysql 5.6.26 
(utf8 encoding) and will get a fix out shortly, but I want to make sure I'm 
testing your situation as well.

On Thu, Sep 10, 2015 at 10:14 AM, Matthias Enders 
> 
wrote:
It was the name of the File:

Blühzeitpunkt.txt

(for example)

Von: Dannon Baker [mailto:dannon.ba...@gmail.com]
Gesendet: Thursday, September 10, 2015 4:12 PM
An: Matthias Enders 
>
Cc: 
galaxy-dev@lists.galaxyproject.org
Betreff: Re: [galaxy-dev] Fatal Error while uploading a File with special 
Characters

You should definitely not have to purge a user to fix this (not that it should 
happen in the first place).  Was it the file with special characters, or the 
name of the file?



On Thu, Sep 10, 2015 at 2:28 AM, Matthias Enders 
> 
wrote:
Dear Galaxy Community,

a User of our Galaxy Platform has produced a fatal error by uploading a file 
containing a German special character  (ä / ü / ö / ß). This resulted in the 
following status (only for the given user):

- Upload was canceled: Status was "Failed Internal Server Error (500)"
- All Histories were corrupt stating: "An error was encountered while loading 
the contents."
- Tools can´t be used an stating (in Traceback):
" UnicodeDecodeError: 'utf8' codec can't decode byte 0xfc in position 5: 
invalid start byte"
"Module weberror.evalexception.middleware:364 in respond"


This totally destroyed to current user and we have had to purge him in order to 
get him back to work, even losing all his datasets & histories!

We are using an MySQL database as a backend. Is the Encoding of this database 
the problem? If yes: Which encoding is used/supported by galaxy?

Thanks in advance!

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


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[galaxy-dev] Fatal Error while uploading a File with special Characters

2015-09-10 Thread Matthias Enders 
Dear Galaxy Community,

a User of our Galaxy Platform has produced a fatal error by uploading a file 
containing a German special character  (ä / ü / ö / ß). This resulted in the 
following status (only for the given user):

- Upload was canceled: Status was "Failed Internal Server Error (500)"
- All Histories were corrupt stating: "An error was encountered while loading 
the contents."
- Tools can´t be used an stating (in Traceback):
" UnicodeDecodeError: 'utf8' codec can't decode byte 0xfc in position 5: 
invalid start byte"
"Module weberror.evalexception.middleware:364 in respond"


This totally destroyed to current user and we have had to purge him in order to 
get him back to work, even losing all his datasets & histories!

We are using an MySQL database as a backend. Is the Encoding of this database 
the problem? If yes: Which encoding is used/supported by galaxy?

Thanks in advance!

Matthias
___
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/