Hello all,

I'm having this same issue with Functional Test being broken. I've switched 
between 'stable' and 'default' and it doesn't seem to fix the issue. Its 
possible that I'm not switching properly? This is my first local install of 
Galaxy so I'm new to the structure, detailed help would be very appreciated.

Cheers
Ian

$ sudo hg update default
0 files updated, 0 files merged, 0 files removed, 0 files unresolved

$ hg heads | more

changeset:   10421:a477486bf18e
branch:      stable
tag:         tip
user:        Nate Coraor <n...@bx.psu.edu>
date:        Thu Sep 26 11:02:58 2013 -0400
summary:     Bugfix for tool-to-destination mapping, tool ids are lowercased 
but the mapping id was not lowercased.

changeset:   10411:c42567f43aa7
user:        greg
date:        Mon Aug 19 13:19:56 2013 -0400
summary:     Filter invalid objects when generating the list of 
repository_dependencies objects that are associated with a tool shed repository 
installed into Galaxy.

$ sudo hg update stable
194 files updated, 0 files merged, 48 files removed, 0 files unresolved

$ hg heads | more

changeset:   10421:a477486bf18e
branch:      stable
tag:         tip
user:        Nate Coraor <n...@bx.psu.edu>
date:        Thu Sep 26 11:02:58 2013 -0400
summary:     Bugfix for tool-to-destination mapping, tool ids are lowercased 
but the mapping id was not lowercased.

changeset:   10411:c42567f43aa7
user:        greg
date:        Mon Aug 19 13:19:56 2013 -0400
summary:     Filter invalid objects when generating the list of 
repository_dependencies objects that are associated with a tool shed repository 
installed into Galaxy.

> Message: 16
> Date: Thu, 3 Oct 2013 12:06:16 +0100
> From: Peter Cock <p.j.a.c...@googlemail.com>
> To: Galaxy Dev <galaxy-...@bx.psu.edu>
> Subject: [galaxy-dev] Functional tests broken,        NameError: global name
>       'db_path' is not defined
> Message-ID:
>       <CAKVJ-_63+TJrLT1=CyxJeFpk1Z=6w9i=MkbaHdc-=dsffck...@mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
> 
> Hi all,
> 
> Something has broken on the functional test framework.
> 
> Attempting to run the tests fails, as does just listing the IDs:
> 
> $ ./run_functional_tests.sh --list
> /mnt/galaxy/galaxy-central/eggs/twill-0.9-py2.6.egg/twill/other_packages/_mechanize_dist/_auth.py:14:
> DeprecationWarning: the md5 module is deprecated; use hashlib instead
>  import re, base64, urlparse, posixpath, md5, sha, sys, copy
> /mnt/galaxy/galaxy-central/eggs/twill-0.9-py2.6.egg/twill/other_packages/_mechanize_dist/_auth.py:14:
> DeprecationWarning: the sha module is deprecated; use the hashlib
> module instead
>  import re, base64, urlparse, posixpath, md5, sha, sys, copy
> /mnt/galaxy/galaxy-central/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg/pysam/__init__.py:1:
> RuntimeWarning: __builtin__.file size changed, may indicate binary
> incompatibility
>  from csamtools import *
> Traceback (most recent call last):
>  File "./scripts/functional_tests.py", line 457, in <module>
>    sys.exit( main() )
>  File "./scripts/functional_tests.py", line 246, in main
>    database_connection = 'sqlite:///' + os.path.join( db_path,
> 'universe.sqlite' )
> NameError: global name 'db_path' is not defined
> 'run_functional_tests.sh help'                  for help
> 
> 
> $ hg branch
> stable
> [galaxy@ppserver galaxy-central]$ hg heads | more
> changeset:   11805:a3c018044538
> tag:         tip
> user:        greg
> date:        Wed Oct 02 16:44:48 2013 -0400
> summary:     Eliminate the problematic "Select one" option from select fields.
> 
> changeset:   11761:a477486bf18e
> branch:      stable
> parent:      11689:4b1c7ad464ea
> user:        Nate Coraor <n...@bx.psu.edu>
> date:        Thu Sep 26 11:02:58 2013 -0400
> summary:     Bugfix for tool-to-destination mapping, tool ids are
> lowercased but the mapping id was not lowercased.
> 
> ...
> 
> 
> Regards,
> 
> Peter
> 
> 
> ------------------------------
> 
> Message: 17
> Date: Thu, 03 Oct 2013 08:53:47 -0400
> From: Dave Bouvier <d...@bx.psu.edu>
> To: Peter Cock <p.j.a.c...@googlemail.com>, Galaxy Dev
>       <galaxy-...@bx.psu.edu>
> Subject: Re: [galaxy-dev] Functional tests broken, NameError: global
>       name 'db_path' is not defined
> Message-ID: <524d68db.5060...@bx.psu.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> 
> Peter,
> 
> This bug was fixed on the default branch in 10427:33092bc258d7, or 
> whichever changeset that corresponds to in your repository. The relevant 
> changelog entry, if you want to find and apply it to your repository, is 
> as follows:
> 
> changeset:   10427:33092bc258d7
> user:        Carl Eberhard <carlfeberh...@gmail.com>
> date:        Wed Aug 21 10:00:09 2013 -0700
> summary:     Functional tests: fix sqlite db_path var; fix api test for 
> hda update with nonsense key
> 
> 
>    --Dave B.
> 
> On 10/03/2013 07:06 AM, Peter Cock wrote:
>> Hi all,
>> 
>> Something has broken on the functional test framework.
>> 
>> Attempting to run the tests fails, as does just listing the IDs:
>> 
>> $ ./run_functional_tests.sh --list
>> /mnt/galaxy/galaxy-central/eggs/twill-0.9-py2.6.egg/twill/other_packages/_mechanize_dist/_auth.py:14:
>> DeprecationWarning: the md5 module is deprecated; use hashlib instead
>>   import re, base64, urlparse, posixpath, md5, sha, sys, copy
>> /mnt/galaxy/galaxy-central/eggs/twill-0.9-py2.6.egg/twill/other_packages/_mechanize_dist/_auth.py:14:
>> DeprecationWarning: the sha module is deprecated; use the hashlib
>> module instead
>>   import re, base64, urlparse, posixpath, md5, sha, sys, copy
>> /mnt/galaxy/galaxy-central/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg/pysam/__init__.py:1:
>> RuntimeWarning: __builtin__.file size changed, may indicate binary
>> incompatibility
>>   from csamtools import *
>> Traceback (most recent call last):
>>   File "./scripts/functional_tests.py", line 457, in <module>
>>     sys.exit( main() )
>>   File "./scripts/functional_tests.py", line 246, in main
>>     database_connection = 'sqlite:///' + os.path.join( db_path,
>> 'universe.sqlite' )
>> NameError: global name 'db_path' is not defined
>> 'run_functional_tests.sh help'                  for help
>> 
>> 
>> $ hg branch
>> stable
>> [galaxy@ppserver galaxy-central]$ hg heads | more
>> changeset:   11805:a3c018044538
>> tag:         tip
>> user:        greg
>> date:        Wed Oct 02 16:44:48 2013 -0400
>> summary:     Eliminate the problematic "Select one" option from select 
>> fields.
>> 
>> changeset:   11761:a477486bf18e
>> branch:      stable
>> parent:      11689:4b1c7ad464ea
>> user:        Nate Coraor <n...@bx.psu.edu>
>> date:        Thu Sep 26 11:02:58 2013 -0400
>> summary:     Bugfix for tool-to-destination mapping, tool ids are
>> lowercased but the mapping id was not lowercased.
>> 
>> ...
>> 
>> 
>> 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:
>>   http://lists.bx.psu.edu/
>> 
>> To search Galaxy mailing lists use the unified search at:
>>   http://galaxyproject.org/search/mailinglists/
>> 
> 
> 
> ------------------------------
> 
> Message: 18
> Date: Thu, 3 Oct 2013 14:41:17 +0100
> From: Peter Cock <p.j.a.c...@googlemail.com>
> To: Dave Bouvier <d...@bx.psu.edu>
> Cc: Galaxy Dev <galaxy-...@bx.psu.edu>
> Subject: Re: [galaxy-dev] Functional tests broken, NameError: global
>       name 'db_path' is not defined
> Message-ID:
>       <cakvj-_4rhbrlm_zk__cxwrjkwwchr3khq3mggrknsv06awg...@mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
> 
> On Thu, Oct 3, 2013 at 1:53 PM, Dave Bouvier <d...@bx.psu.edu> wrote:
>> Peter,
>> 
>> This bug was fixed on the default branch in 10427:33092bc258d7, or whichever
>> changeset that corresponds to in your repository. The relevant changelog
>> entry, if you want to find and apply it to your repository, is as follows:
>> 
>> changeset:   10427:33092bc258d7
>> user:        Carl Eberhard <carlfeberh...@gmail.com>
>> date:        Wed Aug 21 10:00:09 2013 -0700
>> summary:     Functional tests: fix sqlite db_path var; fix api test for hda
>> update with nonsense key
>> 
>> 
>>   --Dave B.
> 
> Thanks - from the date that ought to be on my development system
> already, but I can check more specifically now.
> 
> Peter
> 
> 
> 
> 
> Message: 21
> Date: Thu, 3 Oct 2013 15:33:30 +0100
> From: Peter Cock <p.j.a.c...@googlemail.com>
> To: Dave Bouvier <d...@bx.psu.edu>
> Cc: Galaxy Dev <galaxy-...@bx.psu.edu>
> Subject: Re: [galaxy-dev] Functional tests broken, NameError: global
>       name 'db_path' is not defined
> Message-ID:
>       <CAKVJ-_4-qw=kz+5hstt6fhvvuborbfx1dvsdpx3eiaotypg...@mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
> 
> On Thu, Oct 3, 2013 at 1:53 PM, Dave Bouvier <d...@bx.psu.edu> wrote:
>> Peter,
>> 
>> This bug was fixed on the default branch in 10427:33092bc258d7, or whichever
>> changeset that corresponds to in your repository. The relevant changelog
>> entry, if you want to find and apply it to your repository, is as follows:
>> 
>> changeset:   10427:33092bc258d7
>> user:        Carl Eberhard <carlfeberh...@gmail.com>
>> date:        Wed Aug 21 10:00:09 2013 -0700
>> summary:     Functional tests: fix sqlite db_path var; fix api test for hda
>> update with nonsense key
>> 
> 
> Switching to the default branch did indeed fix it - so this needs
> to be added to the stable branch (not there yet):
> https://bitbucket.org/galaxy/galaxy-central/src/a477486bf18eafdd14dd7ba1e91e17f1b05e8121/scripts/functional_tests.py?at=stable
> 
> Thanks,
> 
> Peter
> 
> 


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