Functional tests broken, NameError: global name 'db_path' is not defined
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
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 ___________________________________________________________ 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/
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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
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
participants (2)
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Dave Bouvier -
Peter Cock