Re: [galaxy-dev] Functional tests broken, NameError: global name 'db_path' is not defined
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 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 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 > To: Galaxy Dev > Subject: [galaxy-dev] Functional tests broken, NameError: global name > 'db_path' is not defined > Message-ID: > > 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 >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 > 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 > To: Peter Cock , Galaxy Dev > > 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 > 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 ke
Re: [galaxy-dev] Functional tests broken, NameError: global name 'db_path' is not defined
On Thu, Oct 3, 2013 at 1:53 PM, Dave Bouvier 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 > 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 ___ 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/
Re: [galaxy-dev] Functional tests broken, NameError: global name 'db_path' is not defined
On Thu, Oct 3, 2013 at 1:53 PM, Dave Bouvier 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 > 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 ___ 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/
Re: [galaxy-dev] Functional tests broken, NameError: global name 'db_path' is not defined
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 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 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 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/ ___ 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/
[galaxy-dev] 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 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 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/
