Re: [galaxy-dev] Functional tests broken, NameError: global name 'db_path' is not defined

7 Oct 2013

      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 <nate@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 <nate@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.cock@googlemail.com>
To: Galaxy Dev <galaxy-dev@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+eg@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 <nate@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 <dave@bx.psu.edu>
To: Peter Cock <p.j.a.cock@googlemail.com>, Galaxy Dev
  <galaxy-dev@bx.psu.edu>
Subject: Re: [galaxy-dev] Functional tests broken, NameError: global
  name 'db_path' is not defined
Message-ID: <524D68DB.5060803@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 <carlfeberhard@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 <nate@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
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------------------------------
Message: 18
Date: Thu, 3 Oct 2013 14:41:17 +0100
From: Peter Cock <p.j.a.cock@googlemail.com>
To: Dave Bouvier <dave@bx.psu.edu>
Cc: Galaxy Dev <galaxy-dev@bx.psu.edu>
Subject: Re: [galaxy-dev] Functional tests broken, NameError: global
  name 'db_path' is not defined
Message-ID:
  <CAKVJ-_4rHBrLM_zK__cxWRJkwWChR3KhQ3mGgrkNsv06awG19w@mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
On Thu, Oct 3, 2013 at 1:53 PM, Dave Bouvier <dave@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 <carlfeberhard@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.cock@googlemail.com>
To: Dave Bouvier <dave@bx.psu.edu>
Cc: Galaxy Dev <galaxy-dev@bx.psu.edu>
Subject: Re: [galaxy-dev] Functional tests broken, NameError: global
  name 'db_path' is not defined
Message-ID:
  <CAKVJ-_4-qw=Kz+5HstT6fHvVUbORbfx1DvsDpX3eiAOTYPgGFA@mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
On Thu, Oct 3, 2013 at 1:53 PM, Dave Bouvier <dave@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 <carlfeberhard@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/a477486bf18eafdd14dd7ba1e91e...
Thanks,
Peter

UMD Bioinformatics

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