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commit/galaxy-central: inithello: Remove debug filtering.
by commits-noreply＠bitbucket.org 04 May '13

04 May '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c823b1404fea/ Changeset: c823b1404fea User: inithello Date: 2013-05-04 15:07:50 Summary: Remove debug filtering. Affected #: 1 file diff -r d207aa915b9d89167858439df97bf385669b4a2d -r c823b1404fea2350d9c0b2d0ebc4965d7f9ffcb8 test/install_and_test_tool_shed_repositories/functional_tests.py --- a/test/install_and_test_tool_shed_repositories/functional_tests.py +++ b/test/install_and_test_tool_shed_repositories/functional_tests.py @@ -572,14 +572,7 @@ # it will record the result of the tests, and if any failed, the traceback and captured output of the tool that was run. # After all tests have completed, the repository is uninstalled, so that the previous test cases don't interfere with # the next repository's functional tests. - keep_skipping = True for repository_info_dict in detailed_repository_list: - if repository_info_dict[ 'name' ] == 'simsearch' and repository_info_dict[ 'changeset_revision' ] == '430f55978191': - keep_skipping = False - if keep_skipping: - continue - if repository_info_dict[ 'name' ] == 'sortmerna': - continue """ Each repository_info_dict looks something like: { Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: When deleting a history and marking associated jobs deleted, first check that there is a job to mark.
by commits-noreply＠bitbucket.org 03 May '13

03 May '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d207aa915b9d/ Changeset: d207aa915b9d User: jgoecks Date: 2013-05-04 00:02:57 Summary: When deleting a history and marking associated jobs deleted, first check that there is a job to mark. Affected #: 1 file diff -r e7feb8e93b6e862b8b450dc5a9636297cea28516 -r d207aa915b9d89167858439df97bf385669b4a2d lib/galaxy/webapps/galaxy/controllers/history.py --- a/lib/galaxy/webapps/galaxy/controllers/history.py +++ b/lib/galaxy/webapps/galaxy/controllers/history.py @@ -563,11 +563,14 @@ self.sa_session.add( history ) self.sa_session.flush() for hda in history.datasets: - job = hda.creating_job_associations[0].job - if job.history_id == history.id and job.state in [ trans.app.model.Job.states.QUEUED, trans.app.model.Job.states.RUNNING, trans.app.model.Job.states.NEW ]: - # No need to check other outputs since the job's parent history is this history - job.mark_deleted( trans.app.config.track_jobs_in_database ) - trans.app.job_manager.job_stop_queue.put( job.id ) + # Not all datasets have jobs associated with them (e.g., datasets imported from libraries). + if hda.creating_job_associations: + # HDA has associated job, so try marking it deleted. + job = hda.creating_job_associations[0].job + if job.history_id == history.id and job.state in [ trans.app.model.Job.states.QUEUED, trans.app.model.Job.states.RUNNING, trans.app.model.Job.states.NEW ]: + # No need to check other outputs since the job's parent history is this history + job.mark_deleted( trans.app.config.track_jobs_in_database ) + trans.app.job_manager.job_stop_queue.put( job.id ) # Regardless of whether it was previously deleted, we make a new history active trans.new_history() return trans.show_ok_message( "History deleted, a new history is active", refresh_frames=['history'] ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 03 May '13

03 May '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/45a70edb67ba/ Changeset: 45a70edb67ba User: dan Date: 2013-05-03 22:02:39 Summary: Provide user to tools as __user__. Affected #: 2 files diff -r b5ea0e100bdaf47d53d11fa2beb39f4218fa8136 -r 45a70edb67baae53fa97de95b4e39004687a0c23 lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -678,13 +678,16 @@ # These can be passed on the command line if wanted as $__user_*__ if job.history and job.history.user: + user = job.history.user user_id = '%d' % job.history.user.id user_email = str(job.history.user.email) user_name = str(job.history.user.username) else: + user = None user_id = 'Anonymous' user_email = 'Anonymous' user_name = 'Anonymous' + incoming['__user__'] = user incoming['__user_id__'] = incoming['userId'] = user_id incoming['__user_email__'] = incoming['userEmail'] = user_email incoming['__user_name__'] = user_name diff -r b5ea0e100bdaf47d53d11fa2beb39f4218fa8136 -r 45a70edb67baae53fa97de95b4e39004687a0c23 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -2546,6 +2546,7 @@ param_dict['__root_dir__'] = param_dict['GALAXY_ROOT_DIR'] = os.path.abspath( self.app.config.root ) param_dict['__datatypes_config__'] = param_dict['GALAXY_DATATYPES_CONF_FILE'] = self.app.datatypes_registry.integrated_datatypes_configs param_dict['__admin_users__'] = self.app.config.admin_users + param_dict['__user__'] = RawObjectWrapper( param_dict.get( '__user__', None ) ) # Return the dictionary of parameters return param_dict def build_param_file( self, param_dict, directory=None ): @@ -3243,6 +3244,8 @@ """ def __init__( self, obj ): self.obj = obj + def __nonzero__( self ): + return bool( self.obj ) #FIXME: would it be safe/backwards compatible to rename .obj to .value, so that we can just inherit this method? def __str__( self ): return "%s:%s" % (self.obj.__module__, self.obj.__class__.__name__) def __getattr__( self, key ): https://bitbucket.org/galaxy/galaxy-central/commits/e7feb8e93b6e/ Changeset: e7feb8e93b6e User: dan Date: 2013-05-03 22:02:40 Summary: Update GenomeSpace tools to use __user__ as needed. Affected #: 2 files diff -r 45a70edb67baae53fa97de95b4e39004687a0c23 -r e7feb8e93b6e862b8b450dc5a9636297cea28516 tools/genomespace/genomespace_exporter.xml --- a/tools/genomespace/genomespace_exporter.xml +++ b/tools/genomespace/genomespace_exporter.xml @@ -3,10 +3,9 @@ <description> - send data to GenomeSpace</description><command interpreter="python">genomespace_exporter.py --genomespace_site "prod" - #assert $__user_id__ != 'Anonymous', Exception( 'You must be logged in to use this tool.' ) - #set $user = $__app__.model.User.get( $__user_id__ ) - #set $username = $user.preferences.get( 'genomespace_username', None ) - #set $token = $user.preferences.get( 'genomespace_token', None ) + #assert $__user__, Exception( 'You must be logged in to use this tool.' ) + #set $username = $__user__.preferences.get( 'genomespace_username', None ) + #set $token = $__user__.preferences.get( 'genomespace_token', None ) #assert None not in ( $username, $token ), Exception( 'You must associate a GenomeSpace OpenID with your account and log in with it.' ) #import binascii --username "${username}" @@ -36,7 +35,7 @@ <inputs><param format="data" name="input1" type="data" label="Send this dataset to GenomeSpace" /><param name="base_url" type="baseurl" /> - <param name="subdirectory" type="drill_down" display="radio" hierarchy="exact" multiple="False" label="Choose Target Directory" dynamic_options="galaxy_code_get_genomespace_folders( genomespace_site = 'prod', trans=__trans__, value=__value__, input_dataset=input1 )" help="Leave blank to generate automatically"/> + <param name="subdirectory" type="drill_down" display="radio" hierarchy="exact" multiple="False" optional="True" label="Choose Target Directory" dynamic_options="galaxy_code_get_genomespace_folders( genomespace_site = 'prod', trans=__trans__, value=__value__, input_dataset=input1 )" help="Leave blank to generate automatically"/><param name="filename" type="text" size="80" help="Leave blank to generate automatically" /></inputs><outputs> diff -r 45a70edb67baae53fa97de95b4e39004687a0c23 -r e7feb8e93b6e862b8b450dc5a9636297cea28516 tools/genomespace/genomespace_importer.xml --- a/tools/genomespace/genomespace_importer.xml +++ b/tools/genomespace/genomespace_importer.xml @@ -3,10 +3,9 @@ <description> - receive data from GenomeSpace</description><command interpreter="python">genomespace_importer.py --genomespace_site "prod" - #assert $__user_id__ != 'Anonymous', Exception( 'You must be logged in to use this tool.' ) - #set $user = $__app__.model.User.get( $__user_id__ ) - #set $username = $user.preferences.get( 'genomespace_username', None ) - #set $token = $user.preferences.get( 'genomespace_token', None ) + #assert $__user__, Exception( 'You must be logged in to use this tool.' ) + #set $username = $__user__.preferences.get( 'genomespace_username', None ) + #set $token = $__user__.preferences.get( 'genomespace_token', None ) #assert None not in ( $username, $token ), Exception( 'You must associate a GenomeSpace OpenID with your account and log in with it.' ) --username "${username}" --token "${token}" Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: inithello: Rename install_repository_tools to install_tool_shed_repositories. Use shed_util_common.url_join to generate the API url.
by commits-noreply＠bitbucket.org 03 May '13

03 May '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b5ea0e100bda/ Changeset: b5ea0e100bda User: inithello Date: 2013-05-03 21:55:56 Summary: Rename install_repository_tools to install_tool_shed_repositories. Use shed_util_common.url_join to generate the API url. Affected #: 1 file diff -r 75e7383c5c794e02503dc03e0d5daf3694323b7d -r b5ea0e100bdaf47d53d11fa2beb39f4218fa8136 scripts/api/install_tool_shed_repositories.py --- /dev/null +++ b/scripts/api/install_tool_shed_repositories.py @@ -0,0 +1,52 @@ +#!/usr/bin/env python +""" +Install a specified repository revision from a specified tool shed into Galaxy. This example demonstrates installation of a repository that contains +valid tools, loading them into a section of the Galaxy tool panel or creating a new tool panel section. +You can choose if tool dependencies or repository dependencies should be installed, use --repository-deps or --tool-deps. + +This example requires a tool panel config file (e.g., tool_conf.xml, shed_tool_conf.xml, etc) to contain a tool panel section like the following: + +<section id="from_test_tool_shed" name="From Test Tool Shed" version=""> +</section> + +Here is a working example of how to use this script to install a repository from the test tool shed. +./install_repository_tools.py --api <api key> --local <galaxy base url> --url http://testtoolshed.g2.bx.psu.edu --name gregs_filter --owner greg --revision f28d5018f9cb --tool-deps +""" + +import os +import sys +import argparse +sys.path.insert( 0, os.path.dirname( __file__ ) ) +from common import submit + +def main( options ): + """Collect all user data and install the tools via the Galaxy API.""" + data = {} + data[ 'tool_shed_url' ] = options.tool_shed_url + data[ 'name' ] = options.name + data[ 'owner' ] = options.owner + data[ 'changeset_revision' ] = options.changeset_revision + if options.tool_panel_section_id: + data[ 'tool_panel_section_id' ] = options.tool_panel_section_id + elif options.new_tool_panel_section_label: + data[ 'new_tool_panel_section_label' ] = options.new_tool_panel_section_label + if options.install_repository_dependencies: + data[ 'install_repository_dependencies' ] = options.install_repository_dependencies + if options.install_tool_dependencies: + data[ 'install_tool_dependencies' ] = options.install_tool_dependencies + submit( options.api, '%s%s' % ( options.local_url.strip('/'), '/api/tool_shed_repositories/new/install_repository_revision' ), data ) + +if __name__ == '__main__': + parser = argparse.ArgumentParser( description='Installation of tool shed repositories via the Galaxy API.' ) + parser.add_argument( "-u", "--url", dest="tool_shed_url", required=True, help="Tool Shed URL" ) + parser.add_argument( "-a", "--api", dest="api", required=True, help="API Key" ) + parser.add_argument( "-l", "--local", dest="local_url", required=True, help="URL of the galaxy instance." ) + parser.add_argument( "-n", "--name", required=True, help="Repository name." ) + parser.add_argument( "-o", "--owner", required=True, help="Repository owner." ) + parser.add_argument( "-r", "--revision", dest="changeset_revision", required=True, help="Repository owner." ) + parser.add_argument( "--panel-section-id", dest="tool_panel_section_id", help="Tool panel section id if you want to add your repository to an existing tool section." ) + parser.add_argument( "--panel-section-name", dest="new_tool_panel_section_label", help="New tool panel section label. If specified a new tool section will be created." ) + parser.add_argument( "--repository-deps", dest="install_repository_dependencies", action="store_true", default=False, help="Install repository dependencies. [False]") + parser.add_argument( "--tool-deps", dest="install_tool_dependencies", action="store_true", default=False, help="Install tool dependencies. [False]" ) + options = parser.parse_args() + main( options ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dannon: Fix install_repository_tools script to appropriately handle a trailing slash in the URL.
by commits-noreply＠bitbucket.org 03 May '13

03 May '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/75e7383c5c79/ Changeset: 75e7383c5c79 User: dannon Date: 2013-05-03 21:46:53 Summary: Fix install_repository_tools script to appropriately handle a trailing slash in the URL. Affected #: 1 file diff -r 324d023bbf59aafb4be03cbb9842456aab0a1965 -r 75e7383c5c794e02503dc03e0d5daf3694323b7d scripts/api/install_repository_tools.py --- a/scripts/api/install_repository_tools.py +++ b/scripts/api/install_repository_tools.py @@ -34,7 +34,7 @@ data[ 'install_repository_dependencies' ] = options.install_repository_dependencies if options.install_tool_dependencies: data[ 'install_tool_dependencies' ] = options.install_tool_dependencies - submit( options.api, '%s%s' % ( options.local_url, '/api/tool_shed_repositories/new/install_repository_revision' ), data ) + submit( options.api, '%s%s' % ( options.local_url.strip('/'), '/api/tool_shed_repositories/new/install_repository_revision' ), data ) if __name__ == '__main__': parser = argparse.ArgumentParser( description='Installation of tool shed repositories via the Galaxy API.' ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: inithello: Explicitly uninstall all installed repositories after each set of tests has finished running. This prevents certain edge cases from interfering with subsequent tests.
by commits-noreply＠bitbucket.org 03 May '13

03 May '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/324d023bbf59/ Changeset: 324d023bbf59 User: inithello Date: 2013-05-03 21:25:20 Summary: Explicitly uninstall all installed repositories after each set of tests has finished running. This prevents certain edge cases from interfering with subsequent tests. Affected #: 2 files diff -r e5577cd833abbd0ad072d55f4b56d1458105991b -r 324d023bbf59aafb4be03cbb9842456aab0a1965 test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py --- a/test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py +++ b/test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py @@ -3,8 +3,10 @@ from install_and_test_tool_shed_repositories.base.twilltestcase import InstallTestRepository log = logging.getLogger(__name__) + class InstallTestRepositories( InstallTestRepository ): """Abstract test case that installs and uninstalls a predefined list of repositories.""" + def do_installation( self, repository_info_dict ): self.logout() self.login( email='test(a)bx.psu.edu', username='test' ) @@ -73,7 +75,7 @@ return test_install_repository test_method = make_uninstall_method( repository_dict ) test_method.__doc__ = "Uninstall the repository %s." % repository_dict[ 'name' ] - namespace[ 'install_repository_%s' % repository_dict[ 'name' ] ] = test_method + namespace[ 'uninstall_repository_%s' % repository_dict[ 'name' ] ] = test_method # The new.classobj function returns a new class object, with name name, derived # from baseclasses (which should be a tuple of classes) and with namespace dict. new_class_obj = new.classobj( name, baseclasses, namespace ) diff -r e5577cd833abbd0ad072d55f4b56d1458105991b -r 324d023bbf59aafb4be03cbb9842456aab0a1965 test/install_and_test_tool_shed_repositories/functional_tests.py --- a/test/install_and_test_tool_shed_repositories/functional_tests.py +++ b/test/install_and_test_tool_shed_repositories/functional_tests.py @@ -179,19 +179,26 @@ return passed_tests return [] -def execute_uninstall_method( repository_dict ): - # Delete any configured tool functional tests from the test_toolbox.__dict__, otherwise nose will find them - # and try to re-run the tests after uninstalling the repository, which will cause false failure reports, - # since the test data has been deleted from disk by now. - tests_to_delete = [] - for key in test_toolbox.__dict__: - if key.startswith( 'TestForTool_' ): - log.info( 'Tool test found in test_toolbox, deleting: %s' % key ) - tests_to_delete.append( key ) - for key in tests_to_delete: - del test_toolbox.__dict__[ key ] - # Generate a test method to uninstall this repository through the embedded Galaxy application's web interface. - test_install_repositories.generate_uninstall_method( repository_dict ) +def execute_uninstall_method( app ): + # Clean out any generated tests. + remove_generated_tests( app ) + sa_session = app.model.context.current + repositories_to_uninstall = sa_session.query( app.model.ToolShedRepository ).all() + for repository in repositories_to_uninstall: + if repository.status == app.model.ToolShedRepository.states.UNINSTALLED: + continue + if repository.status not in [ app.model.ToolShedRepository.installation_status.UNINSTALLED, + app.model.ToolShedRepository.installation_status.ERROR, + app.model.ToolShedRepository.installation_status.INSTALLED ]: + repository.status = app.model.ToolShedRepository.installation_status.ERROR + sa_session.add( repository ) + sa_session.flush() + name = str( repository.name ) + owner = str( repository.owner ) + changeset_revision = str( repository.installed_changeset_revision ) + repository_dict = dict( name=name, owner=owner, changeset_revision=changeset_revision ) + # Generate a test method to uninstall this repository through the embedded Galaxy application's web interface. + test_install_repositories.generate_uninstall_method( repository_dict ) # Set up nose to run the generated uninstall method as a functional test. test_config = nose.config.Config( env=os.environ, plugins=nose.plugins.manager.DefaultPluginManager() ) test_config.configure( sys.argv ) @@ -309,6 +316,25 @@ else: return update( tool_shed_api_key, '%s' % ( url_join( galaxy_tool_shed_url, 'api', 'repository_revisions', metadata_id ) ), params, return_formatted=False ) +def remove_generated_tests( app ): + # Delete any configured tool functional tests from the test_toolbox.__dict__, otherwise nose will find them + # and try to re-run the tests after uninstalling the repository, which will cause false failure reports, + # since the test data has been deleted from disk by now. + tests_to_delete = [] + global test_toolbox + for key in test_toolbox.__dict__: + if key.startswith( 'TestForTool_' ): + log.info( 'Tool test found in test_toolbox, deleting: %s' % key ) + # We can't delete this test just yet, we're still iterating over __dict__. + tests_to_delete.append( key ) + tool_id = key.replace( 'TestForTool_', '' ) + if tool_id in app.toolbox.tools_by_id: + # But we can remove the relevant tool from app.toolbox.tools_by_id. + del app.toolbox.tools_by_id[ tool_id ] + for key in tests_to_delete: + # Now delete the tests found in the previous loop. + del test_toolbox.__dict__[ key ] + def run_tests( test_config ): loader = nose.loader.TestLoader( config=test_config ) test_config.plugins.addPlugin( ReportResults() ) @@ -417,12 +443,12 @@ global_conf = { '__file__' : 'universe_wsgi.ini.sample' } if not database_connection.startswith( 'sqlite://' ): kwargs[ 'database_engine_option_max_overflow' ] = '20' + kwargs[ 'database_engine_option_pool_size' ] = '10' app = UniverseApplication( admin_users = 'test(a)bx.psu.edu', allow_user_creation = True, allow_user_deletion = True, allow_library_path_paste = True, database_connection = database_connection, - database_engine_option_pool_size = '10', datatype_converters_config_file = "datatype_converters_conf.xml.sample", file_path = galaxy_file_path, global_conf = global_conf, @@ -546,7 +572,14 @@ # it will record the result of the tests, and if any failed, the traceback and captured output of the tool that was run. # After all tests have completed, the repository is uninstalled, so that the previous test cases don't interfere with # the next repository's functional tests. + keep_skipping = True for repository_info_dict in detailed_repository_list: + if repository_info_dict[ 'name' ] == 'simsearch' and repository_info_dict[ 'changeset_revision' ] == '430f55978191': + keep_skipping = False + if keep_skipping: + continue + if repository_info_dict[ 'name' ] == 'sortmerna': + continue """ Each repository_info_dict looks something like: { @@ -575,10 +608,13 @@ metadata_revision_id = repository_info_dict.get( 'id', None ) # Add the URL for the tool shed we're installing from, so the automated installation methods go to the right place. repository_info_dict[ 'tool_shed_url' ] = galaxy_tool_shed_url - log.info( "Installing and testing revision %s of repository id %s..." % ( str( changeset_revision ), str( repository_id ) ) ) # Get the name and owner out of the repository info dict. - name = repository_info_dict[ 'name' ] - owner = repository_info_dict[ 'owner' ] + name = str( repository_info_dict[ 'name' ] ) + owner = str( repository_info_dict[ 'owner' ] ) + log.info( "Installing and testing revision %s of repository id %s (%s/%s)..." % \ + ( str( changeset_revision ), str( repository_id ), owner, name ) ) + # Explicitly clear tests from twill's test environment. + remove_generated_tests( app ) # Use the repository information dict to generate an install method that will install the repository into the embedded # Galaxy application, with tool dependencies and repository dependencies, if any. test_install_repositories.generate_install_method( repository_info_dict ) @@ -661,7 +697,7 @@ register_test_result( galaxy_tool_shed_url, metadata_revision_id, repository_status, passed_tests=False ) # Run the cleanup method. This removes tool functional test methods from the test_toolbox module and uninstalls the # repository using Twill. - execute_uninstall_method( repository_info_dict ) + execute_uninstall_method( app ) # Set the test_toolbox.toolbox module-level variable to the new app.toolbox. test_toolbox.toolbox = app.toolbox repositories_failed.append( dict( name=name, owner=owner, changeset_revision=changeset_revision ) ) @@ -675,6 +711,8 @@ os.environ[ 'GALAXY_TOOL_SHED_TEST_FILE' ] = galaxy_shed_tools_dict os.environ[ 'GALAXY_TEST_HOST' ] = galaxy_test_host os.environ[ 'GALAXY_TEST_PORT' ] = galaxy_test_port + # Explicitly clear tests from twill's test environment. + remove_generated_tests( app ) # Set the module-level variable 'toolbox', so that test.functional.test_toolbox will generate the appropriate test methods. test_toolbox.toolbox = app.toolbox # Generate the test methods for this installed repository. We need to pass in True here, or it will look @@ -751,14 +789,23 @@ register_test_result( galaxy_tool_shed_url, metadata_revision_id, repository_status, passed_tests=False ) log.debug( 'Revision %s of repository %s installed successfully, but did not pass functional tests.' % \ ( changeset_revision, name ) ) - # Run the cleanup method. This removes tool functional test methods from the test_toolbox module and uninstalls the + # Run the uninstall method. This removes tool functional test methods from the test_toolbox module and uninstalls the # repository using Twill. - success = execute_uninstall_method( repository_info_dict ) + log.debug( 'Uninstalling changeset revision %s of repository %s' % \ + ( repository_info_dict[ 'changeset_revision' ], repository_info_dict[ 'name' ] ) ) + success = execute_uninstall_method( app ) + if not success: + log.error( 'Repository %s failed to uninstall.' ) # Set the test_toolbox.toolbox module-level variable to the new app.toolbox. test_toolbox.toolbox = app.toolbox else: + # Even if the repository failed to install, execute the uninstall method, in case a dependency did succeed. + log.debug( 'Uninstalling repository %s' % repository_info_dict[ 'name' ] ) + success = execute_uninstall_method( app ) + if not success: + log.error( 'Repository %s failed to uninstall.' ) repositories_failed_install.append( dict( name=name, owner=owner, changeset_revision=changeset_revision ) ) - log.debug( 'Repository %s failed to install correctly.' % name ) + log.debug( 'Repository %s failed to install correctly.' % repository_info_dict[ 'name' ] ) except: log.exception( "Failure running tests" ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dannon: Make sure dependent eggs are loaded for sqlalchemy-migrate, regardless of entry point. This is a hack, and dependency management should/will eventually handle it.
by commits-noreply＠bitbucket.org 03 May '13

03 May '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e5577cd833ab/ Changeset: e5577cd833ab User: dannon Date: 2013-05-03 18:55:55 Summary: Make sure dependent eggs are loaded for sqlalchemy-migrate, regardless of entry point. This is a hack, and dependency management should/will eventually handle it. Affected #: 4 files diff -r 5aec1f220d4f1bccc9ac3f2b014d2727e0f0f907 -r e5577cd833abbd0ad072d55f4b56d1458105991b lib/galaxy/webapps/tool_shed/model/migrate/check.py --- a/lib/galaxy/webapps/tool_shed/model/migrate/check.py +++ b/lib/galaxy/webapps/tool_shed/model/migrate/check.py @@ -3,6 +3,7 @@ from galaxy import eggs import pkg_resources +pkg_resources.require( "SQLAlchemy" ) pkg_resources.require( "decorator" ) pkg_resources.require( "sqlalchemy-migrate" ) pkg_resources.require( "Tempita" ) diff -r 5aec1f220d4f1bccc9ac3f2b014d2727e0f0f907 -r e5577cd833abbd0ad072d55f4b56d1458105991b lib/tool_shed/galaxy_install/migrate/check.py --- a/lib/tool_shed/galaxy_install/migrate/check.py +++ b/lib/tool_shed/galaxy_install/migrate/check.py @@ -1,7 +1,9 @@ import sys, os, logging, subprocess from galaxy import eggs import pkg_resources +pkg_resources.require( "SQLAlchemy" ) pkg_resources.require( "decorator" ) +pkg_resources.require( "Tempita " ) pkg_resources.require( "sqlalchemy-migrate" ) from migrate.versioning import repository, schema diff -r 5aec1f220d4f1bccc9ac3f2b014d2727e0f0f907 -r e5577cd833abbd0ad072d55f4b56d1458105991b scripts/db_shell.py --- a/scripts/db_shell.py +++ b/scripts/db_shell.py @@ -20,6 +20,7 @@ import pkg_resources pkg_resources.require( "decorator" ) +pkg_resources.require( "Tempita" ) pkg_resources.require( "sqlalchemy-migrate" ) pkg_resources.require( "SQLAlchemy" ) diff -r 5aec1f220d4f1bccc9ac3f2b014d2727e0f0f907 -r e5577cd833abbd0ad072d55f4b56d1458105991b scripts/manage_tools.py --- a/scripts/manage_tools.py +++ b/scripts/manage_tools.py @@ -7,7 +7,9 @@ from galaxy import eggs import pkg_resources +pkg_resources.require( "SQLAlchemy" ) pkg_resources.require( "decorator" ) +pkg_resources.require( "Tempita " ) pkg_resources.require( "sqlalchemy-migrate" ) from migrate.versioning.shell import main Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dannon: Require decorator egg wherever we have sqlalchemy-migrate. Should be able to resolve dependencies and do this automatically
by commits-noreply＠bitbucket.org 03 May '13

03 May '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5aec1f220d4f/ Changeset: 5aec1f220d4f User: dannon Date: 2013-05-03 18:31:20 Summary: Require decorator egg wherever we have sqlalchemy-migrate. Should be able to resolve dependencies and do this automatically Affected #: 4 files diff -r b908c9fa3c46f1b625a6d32d991392380c79685a -r 5aec1f220d4f1bccc9ac3f2b014d2727e0f0f907 lib/galaxy/webapps/tool_shed/model/migrate/check.py --- a/lib/galaxy/webapps/tool_shed/model/migrate/check.py +++ b/lib/galaxy/webapps/tool_shed/model/migrate/check.py @@ -3,6 +3,7 @@ from galaxy import eggs import pkg_resources +pkg_resources.require( "decorator" ) pkg_resources.require( "sqlalchemy-migrate" ) pkg_resources.require( "Tempita" ) diff -r b908c9fa3c46f1b625a6d32d991392380c79685a -r 5aec1f220d4f1bccc9ac3f2b014d2727e0f0f907 lib/tool_shed/galaxy_install/migrate/check.py --- a/lib/tool_shed/galaxy_install/migrate/check.py +++ b/lib/tool_shed/galaxy_install/migrate/check.py @@ -1,6 +1,7 @@ import sys, os, logging, subprocess from galaxy import eggs import pkg_resources +pkg_resources.require( "decorator" ) pkg_resources.require( "sqlalchemy-migrate" ) from migrate.versioning import repository, schema diff -r b908c9fa3c46f1b625a6d32d991392380c79685a -r 5aec1f220d4f1bccc9ac3f2b014d2727e0f0f907 scripts/db_shell.py --- a/scripts/db_shell.py +++ b/scripts/db_shell.py @@ -19,6 +19,7 @@ from galaxy import eggs import pkg_resources +pkg_resources.require( "decorator" ) pkg_resources.require( "sqlalchemy-migrate" ) pkg_resources.require( "SQLAlchemy" ) diff -r b908c9fa3c46f1b625a6d32d991392380c79685a -r 5aec1f220d4f1bccc9ac3f2b014d2727e0f0f907 scripts/manage_tools.py --- a/scripts/manage_tools.py +++ b/scripts/manage_tools.py @@ -7,6 +7,7 @@ from galaxy import eggs import pkg_resources +pkg_resources.require( "decorator" ) pkg_resources.require( "sqlalchemy-migrate" ) from migrate.versioning.shell import main Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dannon: Require decorator egg in migrate/check to prevent sqlalchemy-migrate from dying in certain environments
by commits-noreply＠bitbucket.org 03 May '13

03 May '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b908c9fa3c46/ Changeset: b908c9fa3c46 User: dannon Date: 2013-05-03 18:26:40 Summary: Require decorator egg in migrate/check to prevent sqlalchemy-migrate from dying in certain environments Affected #: 1 file diff -r 4d4d8dd42491a81869642f1cfcb2f552e4af5a40 -r b908c9fa3c46f1b625a6d32d991392380c79685a lib/galaxy/model/migrate/check.py --- a/lib/galaxy/model/migrate/check.py +++ b/lib/galaxy/model/migrate/check.py @@ -4,6 +4,7 @@ from galaxy import eggs eggs.require( "SQLAlchemy" ) +eggs.require( "decorator" ) #Required by sqlalchemy-migrate eggs.require( "Tempita " ) #Required by sqlalchemy-migrate eggs.require( "sqlalchemy-migrate" ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Column cleanup in the repositories grid in the tool shed.
by commits-noreply＠bitbucket.org 03 May '13

03 May '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/4d4d8dd42491/ Changeset: 4d4d8dd42491 User: greg Date: 2013-05-03 17:26:12 Summary: Column cleanup in the repositories grid in the tool shed. Affected #: 2 files diff -r 4a1a2b6b4e8a14db4a7689ef09b8a2db965ddc8f -r 4d4d8dd42491a81869642f1cfcb2f552e4af5a40 lib/galaxy/webapps/tool_shed/controllers/repository.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py @@ -95,7 +95,9 @@ kwd[ 'id' ] = trans.security.encode_id( repository.id ) except: pass - return self.browse_repositories( trans, **kwd ) + return trans.response.send_redirect( web.url_for( controller='repository', + action='browse_repositories', + **kwd ) ) if 'operation' in kwd: operation = kwd[ 'operation' ].lower() if operation in [ "repositories_by_category", "repositories_by_user" ]: diff -r 4a1a2b6b4e8a14db4a7689ef09b8a2db965ddc8f -r 4d4d8dd42491a81869642f1cfcb2f552e4af5a40 lib/tool_shed/grids/repository_grids.py --- a/lib/tool_shed/grids/repository_grids.py +++ b/lib/tool_shed/grids/repository_grids.py @@ -211,11 +211,7 @@ key="description", attach_popup=False ), MetadataRevisionColumn( "Metadata Revisions" ), - TipRevisionColumn( "Tip Revision" ), - CategoryColumn( "Category", - model_class=model.Category, - key="Category.name", - attach_popup=False ), + ToolsFunctionallyCorrectColumn( "Tools Verified" ), UserColumn( "Owner", model_class=model.User, link=( lambda item: dict( operation="repositories_by_user", id=item.id ) ), Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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