December 2013 - galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: inithello: Add script to check the filesystem for empty tool dependency installation paths and optionally delete them.
by commits-noreply＠bitbucket.org 11 Dec '13

11 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/df88d6121d48/ Changeset: df88d6121d48 User: inithello Date: 2013-12-11 15:53:11 Summary: Add script to check the filesystem for empty tool dependency installation paths and optionally delete them. Affected #: 1 file diff -r 575625b28b035bb38e30c3ef994f0918844923e4 -r df88d6121d48b0b193d34445ce49916adf17a2d2 lib/tool_shed/scripts/check_filesystem_for_empty_tool_dependency_installation_paths.py --- /dev/null +++ b/lib/tool_shed/scripts/check_filesystem_for_empty_tool_dependency_installation_paths.py @@ -0,0 +1,70 @@ +import argparse +import os +import sys +import shutil + +new_path = [ os.path.join( os.getcwd(), "lib" ) ] +new_path.extend( sys.path[1:] ) +sys.path = new_path + +from tool_shed.galaxy_install.tool_dependencies.fabric_util import INSTALLATION_LOG + +def main( args ): + empty_installation_paths = [] + if not os.path.exists( args.basepath ): + print 'Tool dependency path %s does not exist.' % str( args.basepath ) + return 1 + print 'Checking path %s for empty tool dependency installation directories.' % args.basepath + for root, dirs, files in os.walk( args.basepath ): + path_parts = root.replace( args.basepath, '' ).lstrip( '/' ).split( os.sep ) + # Skip certain special directories. + if '__virtualenv_src' in dirs: + dirs.remove( '__virtualenv_src' ) + if 'environment_settings' in dirs: + dirs.remove( 'environment_settings' ) + # Do not process the current path if it does not match the pattern + # <name>/<version>/<owner>/<repository>/<changeset>. + if len( path_parts ) != 5: + continue + # We have a tool dependency installation path. + no_dirs = False + no_files = False + if len( dirs ) == 0: + no_dirs = True + if len( files ) == 0 or len( files ) == 1 and INSTALLATION_LOG in files: + no_files = True + if no_files and no_dirs and root not in empty_installation_paths: + empty_installation_paths.append( root ) + if len( empty_installation_paths ) > 0: + print 'The following %d tool dependency installation directories were found to be empty or contain only the file %s.' % \ + ( len( empty_installation_paths ), INSTALLATION_LOG ) + if args.delete: + for path in empty_installation_paths: + if os.path.exists( path ): + shutil.rmtree( path ) + print 'Deleted %s.' % path + else: + for empty_installation_path in empty_installation_paths: + print empty_installation_path + else: + print 'No empty tool dependency installation directories found.' + return 0 + +if __name__ == '__main__': + description = 'Determine if there are any tool dependency installation paths that should be removed. Remove them if ' + description += 'the --delete command line argument is provided.' + parser = argparse.ArgumentParser( description=description ) + parser.add_argument( '--delete', + dest='delete', + required=False, + action='store_true', + default=False, + help='Whether to delete empty folders or list them on exit.' ) + parser.add_argument( '--basepath', + dest='basepath', + required=True, + action='store', + metavar='name', + help='The base path where tool dependencies are installed.' ) + args = parser.parse_args() + sys.exit( main( args ) ) 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: dan: Fix for exception logging in Datatypes registry.
by commits-noreply＠bitbucket.org 11 Dec '13

11 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/575625b28b03/ Changeset: 575625b28b03 User: dan Date: 2013-12-11 15:48:47 Summary: Fix for exception logging in Datatypes registry. Affected #: 1 file diff -r 9e30fa92a4ab5531a834a1e9015a4e6d19ef8861 -r 575625b28b035bb38e30c3ef994f0918844923e4 lib/galaxy/datatypes/registry.py --- a/lib/galaxy/datatypes/registry.py +++ b/lib/galaxy/datatypes/registry.py @@ -348,7 +348,7 @@ try: aclass = getattr( module, datatype_class_name )() except Exception, e: - self.log.exception( 'Error calling method %s from class %s: %s' ( str( datatype_class_name ), str( module ), str( e ) ) ) + self.log.exception( 'Error calling method %s from class %s: %s', str( datatype_class_name ), str( module ), str( e ) ) ok = False if ok: if deactivate: 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: dan: Rename functions to prevent encapsulation / name mangling in test_toolbox.py and test_data_managers.py
by commits-noreply＠bitbucket.org 11 Dec '13

11 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/9e30fa92a4ab/ Changeset: 9e30fa92a4ab User: dan Date: 2013-12-11 15:00:01 Summary: Rename functions to prevent encapsulation / name mangling in test_toolbox.py and test_data_managers.py Affected #: 2 files diff -r 4541fabfeacf4d166d33eb8da6ba7fd638721850 -r 9e30fa92a4ab5531a834a1e9015a4e6d19ef8861 test/functional/test_data_managers.py --- a/test/functional/test_data_managers.py +++ b/test/functional/test_data_managers.py @@ -19,9 +19,9 @@ """ shed_tool_id = self.shed_tool_id - self.__handle_test_def_errors( testdef ) + self._handle_test_def_errors( testdef ) - galaxy_interactor = self.__galaxy_interactor( testdef ) + galaxy_interactor = self._galaxy_interactor( testdef ) test_history = galaxy_interactor.new_history() #history where inputs will be put, if any @@ -41,50 +41,11 @@ self.assertTrue( data_list ) - self.__verify_outputs( testdef, data_manager_history, shed_tool_id, data_list, galaxy_interactor ) + self._verify_outputs( testdef, data_manager_history, shed_tool_id, data_list, galaxy_interactor ) self.switch_history( id=self.security.encode_id( test_history.id ) ) galaxy_interactor.delete_history( test_history ) - - - #Methods below are from test_toolbox.py:ToolTestCase, but are not inherited properly - - def __galaxy_interactor( self, testdef ): - return build_interactor( self, testdef.interactor ) - - def __handle_test_def_errors(self, testdef): - # If the test generation had an error, raise - if testdef.error: - if testdef.exception: - raise testdef.exception - else: - raise Exception( "Test parse failure" ) - - def __verify_outputs( self, testdef, history, shed_tool_id, data_list, galaxy_interactor ): - maxseconds = testdef.maxseconds - - for output_index, output_tuple in enumerate(testdef.outputs): - # Get the correct hid - name, outfile, attributes = output_tuple - try: - output_data = data_list[ name ] - except (TypeError, KeyError): - # Legacy - fall back on ordered data list access if data_list is - # just a list (case with twill variant or if output changes its - # name). - if hasattr(data_list, "values"): - output_data = data_list.values()[ output_index ] - else: - output_data = data_list[ len(data_list) - len(testdef.outputs) + output_index ] - self.assertTrue( output_data is not None ) - try: - galaxy_interactor.verify_output( history, output_data, outfile, attributes=attributes, shed_tool_id=shed_tool_id, maxseconds=maxseconds ) - except Exception: - for stream in ['stdout', 'stderr']: - stream_output = galaxy_interactor.get_job_stream( history, output_data, stream=stream ) - print >>sys.stderr, self._format_stream( stream_output, stream=stream, format=True ) - raise def build_tests( tmp_dir=None, testing_shed_tools=False, master_api_key=None, user_api_key=None ): """ diff -r 4541fabfeacf4d166d33eb8da6ba7fd638721850 -r 9e30fa92a4ab5531a834a1e9015a4e6d19ef8861 test/functional/test_toolbox.py --- a/test/functional/test_toolbox.py +++ b/test/functional/test_toolbox.py @@ -20,9 +20,9 @@ """ shed_tool_id = self.shed_tool_id - self.__handle_test_def_errors( testdef ) + self._handle_test_def_errors( testdef ) - galaxy_interactor = self.__galaxy_interactor( testdef ) + galaxy_interactor = self._galaxy_interactor( testdef ) test_history = galaxy_interactor.new_history() @@ -31,14 +31,14 @@ data_list = galaxy_interactor.run_tool( testdef, test_history ) self.assertTrue( data_list ) - self.__verify_outputs( testdef, test_history, shed_tool_id, data_list, galaxy_interactor ) + self._verify_outputs( testdef, test_history, shed_tool_id, data_list, galaxy_interactor ) galaxy_interactor.delete_history( test_history ) - def __galaxy_interactor( self, testdef ): + def _galaxy_interactor( self, testdef ): return build_interactor( self, testdef.interactor ) - def __handle_test_def_errors(self, testdef): + def _handle_test_def_errors(self, testdef): # If the test generation had an error, raise if testdef.error: if testdef.exception: @@ -46,7 +46,7 @@ else: raise Exception( "Test parse failure" ) - def __verify_outputs( self, testdef, history, shed_tool_id, data_list, galaxy_interactor ): + def _verify_outputs( self, testdef, history, shed_tool_id, data_list, galaxy_interactor ): maxseconds = testdef.maxseconds for output_index, output_tuple in enumerate(testdef.outputs): 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: carlfeberhard: History API, show: include user_id
by commits-noreply＠bitbucket.org 10 Dec '13

10 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/4541fabfeacf/ Changeset: 4541fabfeacf User: carlfeberhard Date: 2013-12-10 22:18:25 Summary: History API, show: include user_id Affected #: 1 file diff -r da82785d730737313cf9af7348791cb4b0afc937 -r 4541fabfeacf4d166d33eb8da6ba7fd638721850 lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -474,6 +474,9 @@ """Returns history data in the form of a dictionary. """ history_dict = history.to_dict( view='element', value_mapper={ 'id':trans.security.encode_id }) + history_dict[ 'user_id' ] = None + if history.user_id: + history_dict[ 'user_id' ] = trans.security.encode_id( history.user_id ) history_dict[ 'nice_size' ] = history.get_disk_size( nice_size=True ) history_dict[ 'annotation' ] = history.get_item_annotation_str( trans.sa_session, trans.user, 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: greg: Fix for defining an error message when installing a tool dependency along with a tool shed repository.
by commits-noreply＠bitbucket.org 10 Dec '13

10 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/da82785d7307/ Changeset: da82785d7307 User: greg Date: 2013-12-10 21:27:51 Summary: Fix for defining an error message when installing a tool dependency along with a tool shed repository. Affected #: 1 file diff -r 8bdb1113ad0425aab54f31b4c5a37fe456a675d2 -r da82785d730737313cf9af7348791cb4b0afc937 lib/tool_shed/galaxy_install/tool_dependencies/install_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py @@ -93,7 +93,7 @@ env_file_builder.append_line( action="source", value=required_tool_dependency_env_file_path ) return_code = env_file_builder.return_code if return_code: - error_message = 'Error defining env.sh file for package %s, return_code: %s' % ( str( package_name, str( return_code ) ) ) + error_message = 'Error defining env.sh file for package %s, return_code: %s' % ( str( package_name ), str( return_code ) ) tool_dependency = tool_dependency_util.handle_tool_dependency_installation_error( app, tool_dependency, error_message, 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: carlfeberhard: Scatterplot (framework): remove backbone-relational
by commits-noreply＠bitbucket.org 10 Dec '13

10 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/8bdb1113ad04/ Changeset: 8bdb1113ad04 User: carlfeberhard Date: 2013-12-10 20:11:37 Summary: Scatterplot (framework): remove backbone-relational Affected #: 1 file diff -r d5217f01960360a9d7298fa679b839c806cab893 -r 8bdb1113ad0425aab54f31b4c5a37fe456a675d2 config/plugins/visualizations/scatterplot/templates/scatterplot.mako --- a/config/plugins/visualizations/scatterplot/templates/scatterplot.mako +++ b/config/plugins/visualizations/scatterplot/templates/scatterplot.mako @@ -15,7 +15,6 @@ <script type="text/javascript" src="/static/scripts/libs/jquery/jquery.migrate.js"></script><script type="text/javascript" src="/static/scripts/libs/underscore.js"></script><script type="text/javascript" src="/static/scripts/libs/backbone/backbone.js"></script> -<script type="text/javascript" src="/static/scripts/libs/backbone/backbone-relational.js"></script><script type="text/javascript" src="/static/scripts/libs/handlebars.runtime.js"></script><script type="text/javascript" src="/static/scripts/libs/d3.js"></script><script type="text/javascript" src="/static/scripts/libs/bootstrap.js"></script> 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: dan: Add Functional Testing support for locally and ToolShed installed Data Managers.
by commits-noreply＠bitbucket.org 10 Dec '13

10 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d5217f019603/ Changeset: d5217f019603 User: dan Date: 2013-12-10 18:59:29 Summary: Add Functional Testing support for locally and ToolShed installed Data Managers. Affected #: 7 files diff -r e76d57c33b48638268f9f4428165d1041298fc4b -r d5217f01960360a9d7298fa679b839c806cab893 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -394,6 +394,10 @@ return tool #No tool matches by version, simply return the first available tool found return rval[0] + #We now likely have a Toolshed guid passed in, but no supporting database entries + #If the tool exists by exact id and is loaded then provide exact match within a list + if tool_id in self.tools_by_id: + return[ self.tools_by_id[ tool_id ] ] return None def get_loaded_tools_by_lineage( self, tool_id ): diff -r e76d57c33b48638268f9f4428165d1041298fc4b -r d5217f01960360a9d7298fa679b839c806cab893 lib/galaxy/tools/data_manager/manager.py --- a/lib/galaxy/tools/data_manager/manager.py +++ b/lib/galaxy/tools/data_manager/manager.py @@ -133,7 +133,16 @@ self.tool_shed_repository_info_dict = dict( tool_shed=tool_shed, name=repository_name, owner=repository_owner, installed_changeset_revision=installed_changeset_revision ) #get tool_shed repo id tool_shed_repository = suc.get_tool_shed_repository_by_shed_name_owner_installed_changeset_revision( self.data_managers.app, tool_shed, repository_name, repository_owner, installed_changeset_revision ) - tool_shed_repository_id = self.data_managers.app.security.encode_id( tool_shed_repository.id ) + if tool_shed_repository is None: + log.warning( 'Could not determine tool shed repository from database. This should only ever happen when running tests.' ) + #we'll set tool_path manually here from shed_conf_file + tool_shed_repository_id = None + try: + tool_path = util.parse_xml( elem.get( 'shed_conf_file' ) ).getroot().get( 'tool_path', tool_path ) + except Exception, e: + log.error( 'Error determining tool_path for Data Manager during testing: %s', e ) + else: + tool_shed_repository_id = self.data_managers.app.security.encode_id( tool_shed_repository.id ) #use shed_conf_file to determine tool_path shed_conf_file = elem.get( "shed_conf_file", None ) if shed_conf_file: diff -r e76d57c33b48638268f9f4428165d1041298fc4b -r d5217f01960360a9d7298fa679b839c806cab893 run_functional_tests.sh --- a/run_functional_tests.sh +++ b/run_functional_tests.sh @@ -16,6 +16,7 @@ echo "'run_functional_tests.sh -workflow test.xml' for running a workflow test case as defined by supplied workflow xml test file" echo "'run_functional_tests.sh -framework' for running through example tool tests testing framework features in test/functional/tools" echo "'run_functional_tests.sh -framework -id toolid' for testing one framework tool (in test/functional/tools/) with id 'toolid'" + echo "'run_functional_tests.sh -data_managers -id data_manager_id' for testing one Data Manager with id 'data_manager_id'" elif [ $1 = '-id' ]; then python ./scripts/functional_tests.py -v functional.test_toolbox:TestForTool_$2 --with-nosehtml --html-report-file run_functional_tests.html elif [ $1 = '-sid' ]; then @@ -51,6 +52,14 @@ fi elif [ $1 = '-workflow' ]; then python ./scripts/functional_tests.py -v functional.test_workflow:WorkflowTestCase --with-nosehtml --html-report-file ./test/tool_shed/run_functional_tests.html -workflow $2 +elif [ $1 = '-data_managers' ]; then + if [ ! $2 ]; then + python ./scripts/functional_tests.py -v functional.test_data_managers --with-nosehtml --html-report-file run_functional_tests.html -data_managers + elif [ $2 = '-id' ]; then + python ./scripts/functional_tests.py -v functional.test_data_managers:TestForDataManagerTool_$3 --with-nosehtml --html-report-file run_functional_tests.html -data_managers + else + python ./scripts/functional_tests.py -v functional.test_data_managers --with-nosehtml --html-report-file run_functional_tests.html -data_managers + fi elif [ $1 = '-framework' ]; then if [ ! $2 ]; then python ./scripts/functional_tests.py -v functional.test_toolbox --with-nosehtml --html-report-file run_functional_tests.html -framework diff -r e76d57c33b48638268f9f4428165d1041298fc4b -r d5217f01960360a9d7298fa679b839c806cab893 scripts/functional_tests.py --- a/scripts/functional_tests.py +++ b/scripts/functional_tests.py @@ -335,6 +335,11 @@ except OSError: pass + #Data Manager testing temp path + #For storing Data Manager outputs and .loc files so that real ones don't get clobbered + data_manager_test_tmp_path = tempfile.mkdtemp( prefix='data_manager_test_tmp', dir=galaxy_test_tmp_dir ) + galaxy_data_manager_data_path = tempfile.mkdtemp( prefix='data_manager_tool-data', dir=data_manager_test_tmp_path ) + # ---- Build Application -------------------------------------------------- master_api_key = os.environ.get( "GALAXY_TEST_MASTER_API_KEY", default_galaxy_master_key ) app = None @@ -360,6 +365,7 @@ tool_config_file=tool_config_file, tool_data_table_config_path=tool_data_table_config_path, tool_path=tool_path, + galaxy_data_manager_data_path=galaxy_data_manager_data_path, tool_parse_help=False, update_integrated_tool_panel=False, use_heartbeat=False, @@ -469,13 +475,24 @@ functional.test_workflow.WorkflowTestCase.workflow_test_file = workflow_test functional.test_workflow.WorkflowTestCase.master_api_key = master_api_key functional.test_workflow.WorkflowTestCase.user_api_key = os.environ.get( "GALAXY_TEST_USER_API_KEY", default_galaxy_user_key ) - import functional.test_toolbox - functional.test_toolbox.toolbox = app.toolbox - functional.test_toolbox.build_tests( - testing_shed_tools=testing_shed_tools, - master_api_key=master_api_key, - user_api_key=os.environ.get( "GALAXY_TEST_USER_API_KEY", default_galaxy_user_key ), - ) + data_manager_test = __check_arg( '-data_managers', param=False ) + if data_manager_test: + import functional.test_data_managers + functional.test_data_managers.data_managers = app.data_managers #seems like a hack... + functional.test_data_managers.build_tests( + tmp_dir=data_manager_test_tmp_path, + testing_shed_tools=testing_shed_tools, + master_api_key=master_api_key, + user_api_key=os.environ.get( "GALAXY_TEST_USER_API_KEY", default_galaxy_user_key ), + ) + else: #when testing data managers, do not test toolbox + import functional.test_toolbox + functional.test_toolbox.toolbox = app.toolbox + functional.test_toolbox.build_tests( + testing_shed_tools=testing_shed_tools, + master_api_key=master_api_key, + user_api_key=os.environ.get( "GALAXY_TEST_USER_API_KEY", default_galaxy_user_key ), + ) test_config = nose.config.Config( env=os.environ, ignoreFiles=ignore_files, plugins=nose.plugins.manager.DefaultPluginManager() ) test_config.configure( sys.argv ) result = run_tests( test_config ) diff -r e76d57c33b48638268f9f4428165d1041298fc4b -r d5217f01960360a9d7298fa679b839c806cab893 test/functional/test_data_managers.py --- /dev/null +++ b/test/functional/test_data_managers.py @@ -0,0 +1,149 @@ +import new +import sys +import tempfile +import os.path +import shutil +from test_toolbox import ToolTestCase +from base.interactor import build_interactor, stage_data_in_history +import logging +log = logging.getLogger( __name__ ) + +data_managers = None + +class DataManagerToolTestCase( ToolTestCase ): + """Test case that runs Data Manager tests based on a `galaxy.tools.test.ToolTest`""" + + def do_it( self, testdef ): + """ + Run through a tool test case. + """ + shed_tool_id = self.shed_tool_id + + self.__handle_test_def_errors( testdef ) + + galaxy_interactor = self.__galaxy_interactor( testdef ) + + test_history = galaxy_interactor.new_history() #history where inputs will be put, if any + + stage_data_in_history( galaxy_interactor, testdef.test_data(), test_history, shed_tool_id ) + + data_list = galaxy_interactor.run_tool( testdef, test_history ) #test_history will have inputs only, outputs are placed in the specialized data manager history + + #FIXME: Move history determination and switching into the interactor + data_manager_history = None + for assoc in reversed( test_history.user.data_manager_histories ): + if not assoc.history.deleted: + data_manager_history = assoc.history + break + self.switch_history( id=self.security.encode_id( data_manager_history.id ) ) + data_list = self.get_history_as_data_list() + #end + + self.assertTrue( data_list ) + + self.__verify_outputs( testdef, data_manager_history, shed_tool_id, data_list, galaxy_interactor ) + + self.switch_history( id=self.security.encode_id( test_history.id ) ) + + galaxy_interactor.delete_history( test_history ) + + + #Methods below are from test_toolbox.py:ToolTestCase, but are not inherited properly + + def __galaxy_interactor( self, testdef ): + return build_interactor( self, testdef.interactor ) + + def __handle_test_def_errors(self, testdef): + # If the test generation had an error, raise + if testdef.error: + if testdef.exception: + raise testdef.exception + else: + raise Exception( "Test parse failure" ) + + def __verify_outputs( self, testdef, history, shed_tool_id, data_list, galaxy_interactor ): + maxseconds = testdef.maxseconds + + for output_index, output_tuple in enumerate(testdef.outputs): + # Get the correct hid + name, outfile, attributes = output_tuple + try: + output_data = data_list[ name ] + except (TypeError, KeyError): + # Legacy - fall back on ordered data list access if data_list is + # just a list (case with twill variant or if output changes its + # name). + if hasattr(data_list, "values"): + output_data = data_list.values()[ output_index ] + else: + output_data = data_list[ len(data_list) - len(testdef.outputs) + output_index ] + self.assertTrue( output_data is not None ) + try: + galaxy_interactor.verify_output( history, output_data, outfile, attributes=attributes, shed_tool_id=shed_tool_id, maxseconds=maxseconds ) + except Exception: + for stream in ['stdout', 'stderr']: + stream_output = galaxy_interactor.get_job_stream( history, output_data, stream=stream ) + print >>sys.stderr, self._format_stream( stream_output, stream=stream, format=True ) + raise + +def build_tests( tmp_dir=None, testing_shed_tools=False, master_api_key=None, user_api_key=None ): + """ + If the module level variable `data_managers` is set, generate `DataManagerToolTestCase` + classes for all of its tests and put them into this modules globals() so + they can be discovered by nose. + """ + + if data_managers is None: + log.warning( 'data_managers was not set for Data Manager functional testing. Will not test.' ) + return + + # Push all the data_managers tests to module level + G = globals() + + # Eliminate all previous tests from G. + for key, val in G.items(): + if key.startswith( 'TestForDataManagerTool_' ): + del G[ key ] + + #first we will loop through data table loc files and copy them to temporary location, then swap out filenames: + for data_table_name, data_table in data_managers.app.tool_data_tables.get_tables().iteritems(): + for filename, value in list( data_table.filenames.items() ): + new_filename = tempfile.NamedTemporaryFile( prefix=os.path.basename( filename ), dir=tmp_dir ).name + try: + shutil.copy( filename, new_filename ) + except IOError, e: + log.warning( "Failed to copy '%s' to '%s', will create empty file at '%s': %s", filename, new_filename, new_filename, e ) + open( new_filename, 'wb' ).close() + if 'filename' in value: + value[ 'filename' ] = new_filename + del data_table.filenames[ filename ] #remove filename:value pair + data_table.filenames[ new_filename ] = value #add new value by + + for i, ( data_manager_id, data_manager ) in enumerate( data_managers.data_managers.iteritems() ): + tool = data_manager.tool + if not tool: + log.warning( "No Tool has been specified for Data Manager: %s", data_manager_id ) + tool_data_tables = data_manager.data_managers.app.tool_data_tables + if tool.tests: + ##fixme data_manager.tool_shed_repository_info_dict should be filled when is toolshed based + shed_tool_id = None if not testing_shed_tools else tool.id + # Create a new subclass of ToolTestCase, dynamically adding methods + # named test_tool_XXX that run each test defined in the tool config. + name = "TestForDataManagerTool_" + data_manager_id.replace( ' ', '_' ) + baseclasses = ( DataManagerToolTestCase, ) + namespace = dict() + for j, testdef in enumerate( tool.tests ): + def make_test_method( td ): + def test_tool( self ): + self.do_it( td ) + return test_tool + test_method = make_test_method( testdef ) + test_method.__doc__ = "%s ( %s ) > %s" % ( tool.name, tool.id, testdef.name ) + namespace[ 'test_tool_%06d' % j ] = test_method + namespace[ 'shed_tool_id' ] = shed_tool_id + namespace[ 'master_api_key' ] = master_api_key + namespace[ 'user_api_key' ] = user_api_key + # 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 ) + G[ name ] = new_class_obj diff -r e76d57c33b48638268f9f4428165d1041298fc4b -r d5217f01960360a9d7298fa679b839c806cab893 test/functional/test_toolbox.py --- a/test/functional/test_toolbox.py +++ b/test/functional/test_toolbox.py @@ -2,11 +2,14 @@ import sys from base.twilltestcase import TwillTestCase from base.interactor import build_interactor, stage_data_in_history +from galaxy.tools import DataManagerTool import logging log = logging.getLogger( __name__ ) toolbox = None +#Do not test Data Managers as part of the standard Tool Test Framework. +TOOL_TYPES_NO_TEST = ( DataManagerTool, ) class ToolTestCase( TwillTestCase ): """Abstract test case that runs tests based on a `galaxy.tools.test.ToolTest`""" @@ -88,6 +91,9 @@ for i, tool_id in enumerate( toolbox.tools_by_id ): tool = toolbox.get_tool( tool_id ) + if isinstance( tool, TOOL_TYPES_NO_TEST ): + #We do not test certain types of tools (e.g. Data Manager tools) as part of ToolTestCase + continue if tool.tests: shed_tool_id = None if not testing_shed_tools else tool.id # Create a new subclass of ToolTestCase, dynamically adding methods diff -r e76d57c33b48638268f9f4428165d1041298fc4b -r d5217f01960360a9d7298fa679b839c806cab893 test/tool_shed/test_data/1460_files/data_manager_files/test_data_manager.tar Binary file test/tool_shed/test_data/1460_files/data_manager_files/test_data_manager.tar has changed Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: carlfeberhard: (pack scripts)
by commits-noreply＠bitbucket.org 10 Dec '13

10 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e76d57c33b48/ Changeset: e76d57c33b48 User: carlfeberhard Date: 2013-12-10 17:23:03 Summary: (pack scripts) Affected #: 1 file diff -r a06cdfe0a180c4c8aefaeb2bbc51d54ef7d64380 -r e76d57c33b48638268f9f4428165d1041298fc4b static/scripts/packed/mvc/dataset/hda-edit.js --- a/static/scripts/packed/mvc/dataset/hda-edit.js +++ b/static/scripts/packed/mvc/dataset/hda-edit.js @@ -1,1 +1,1 @@ -define(["mvc/dataset/hda-model","mvc/dataset/hda-base"],function(d,a){var f=a.HDABaseView.extend(LoggableMixin).extend({initialize:function(g){a.HDABaseView.prototype.initialize.call(this,g);this.hasUser=g.hasUser;this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton,this._render_rerunButton]},_render_titleButtons:function(){return a.HDABaseView.prototype._render_titleButtons.call(this).concat([this._render_editButton(),this._render_deleteButton()])},_render_editButton:function(){if((this.model.get("state")===d.HistoryDatasetAssociation.STATES.NEW)||(this.model.get("state")===d.HistoryDatasetAssociation.STATES.DISCARDED)||(this.model.get("state")===d.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){return null}var i=this.model.get("purged"),g=this.model.get("deleted"),h={title:_l("Edit Attributes"),href:this.urls.edit,target:this.linkTarget,classes:"dataset-edit"};if(g||i){h.disabled=true;if(i){h.title=_l("Cannot edit attributes of datasets removed from disk")}else{if(g){h.title=_l("Undelete dataset to edit attributes")}}}else{if(this.model.get("state")===d.HistoryDatasetAssociation.STATES.UPLOAD){h.disabled=true;h.title=_l("This dataset must finish uploading before it can be edited")}}h.faIcon="fa-pencil";return faIconButton(h)},_render_deleteButton:function(){if((this.model.get("state")===d.HistoryDatasetAssociation.STATES.NEW)||(this.model.get("state")===d.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){return null}var g=this,h={title:_l("Delete"),classes:"dataset-delete",onclick:function(){g.$el.find(".icon-btn.dataset-delete").trigger("mouseout");g.model["delete"]()}};if(this.model.get("deleted")||this.model.get("purged")){h={title:_l("Dataset is already deleted"),disabled:true}}h.faIcon="fa-times";return faIconButton(h)},_render_errButton:function(){if(this.model.get("state")!==d.HistoryDatasetAssociation.STATES.ERROR){return null}return faIconButton({title:_l("View or report this error"),href:this.urls.report_error,target:this.linkTarget,faIcon:"fa-bug"})},_render_rerunButton:function(){return faIconButton({title:_l("Run this job again"),href:this.urls.rerun,target:this.linkTarget,faIcon:"fa-refresh"})},_render_visualizationsButton:function(){var g=this.model.get("visualizations");if((!this.hasUser)||(!this.model.hasData())||(_.isEmpty(g))){return null}if(_.isObject(g[0])){return this._render_visualizationsFrameworkButton(g)}if(!this.urls.visualization){return null}var i=this.model.get("dbkey"),m=this.urls.visualization,j={},n={dataset_id:this.model.get("id"),hda_ldda:"hda"};if(i){n.dbkey=i}var h=faIconButton({title:_l("Visualize"),href:this.urls.visualization,faIcon:"fa-bar-chart-o"});var l=this;function k(o){switch(o){case"trackster":return b(m,n,i);case"scatterplot":return e(m,n,l.linkTarget);default:return function(){Galaxy.frame.add({title:"Visualization",type:"url",content:m+"/"+o+"?"+$.param(n)})}}}if(g.length===1){h.attr("data-original-title",g[0]);h.click(k(g[0]))}else{_.each(g,function(p){var o=p.charAt(0).toUpperCase()+p.slice(1);j[_l(o)]=k(p)});make_popupmenu(h,j)}return h},_render_visualizationsFrameworkButton:function(g){if(!(this.model.hasData())||!(g&&!_.isEmpty(g))){return null}var i=faIconButton({title:_l("Visualize"),faIcon:"fa-bar-chart-o"});i.addClass("visualize-icon");if(_.keys(g).length===1){i.attr("title",_.keys(g)[0]);i.attr("href",_.values(g)[0])}else{var j=[];_.each(g,function(k){j.push(k)});var h=new PopupMenu(i,j)}return i},_render_body_failed_metadata:function(){var h=$("<a/>").attr({href:this.urls.edit,target:this.linkTarget}).text(_l("set it manually or retry auto-detection")),g=$("<span/>").text(". "+_l("You may be able to")+" ").append(h),i=a.HDABaseView.prototype._render_body_failed_metadata.call(this);i.find(".warningmessagesmall strong").append(g);return i},_render_body_error:function(){var g=a.HDABaseView.prototype._render_body_error.call(this);g.find(".dataset-actions .left").prepend(this._render_errButton());return g},_render_body_ok:function(){var g=a.HDABaseView.prototype._render_body_ok.call(this);if(this.model.isDeletedOrPurged()){return g}this.makeDbkeyEditLink(g);if(this.hasUser){g.find(".dataset-actions .left").append(this._render_visualizationsButton());this._renderTags(g);this._renderAnnotation(g)}return g},_renderTags:function(g){this.tagsEditor=new TagsEditor({model:this.model,el:g.find(".tags-display"),onshowFirstTime:function(){this.render()},$activator:faIconButton({title:_l("Edit dataset tags"),classes:"dataset-tag-btn",faIcon:"fa-tags"}).appendTo(g.find(".dataset-actions .right"))})},_renderAnnotation:function(g){this.annotationEditor=new AnnotationEditor({model:this.model,el:g.find(".annotation-display"),onshowFirstTime:function(){this.render()},$activator:faIconButton({title:_l("Edit dataset annotation"),classes:"dataset-annotate-btn",faIcon:"fa-comment"}).appendTo(g.find(".dataset-actions .right"))})},makeDbkeyEditLink:function(g){if(this.model.get("metadata_dbkey")==="?"&&!this.model.isDeletedOrPurged()){g.find(".dataset-dbkey .value").replaceWith($('<a target="'+this.linkTarget+'">?</a>').attr("href",this.urls.edit))}},events:_.extend(_.clone(a.HDABaseView.prototype.events),{"click .dataset-undelete":function(g){this.model.undelete();return false},"click .dataset-unhide":function(g){this.model.unhide();return false},"click .dataset-purge":"confirmPurge"}),confirmPurge:function c(g){this.model.purge();return false},toString:function(){var g=(this.model)?(this.model+""):("(no model)");return"HDAView("+g+")"}});function e(g,i,h){action=function(){Galaxy.frame.add({title:"Scatterplot",type:"url",content:g+"/scatterplot?"+$.param(i),target:h,scratchbook:true});$("div.popmenu-wrapper").remove();return false};return action}function b(g,i,h){return function(){var j={};if(h){j["f-dbkey"]=h}$.ajax({url:g+"/list_tracks?"+$.param(j),dataType:"html",error:function(){alert(("Could not add this dataset to browser")+".")},success:function(k){var l=window.parent;l.Galaxy.modal.show({title:"View Data in a New or Saved Visualization",buttons:{Cancel:function(){l.Galaxy.modal.hide()},"View in saved visualization":function(){l.Galaxy.modal.show({title:"Add Data to Saved Visualization",body:k,buttons:{Cancel:function(){l.Galaxy.modal.hide()},"Add to visualization":function(){$(l.document).find("input[name=id]:checked").each(function(){l.Galaxy.modal.hide();var m=$(this).val();i.id=m;l.Galaxy.frame.add({title:"Trackster",type:"url",content:g+"/trackster?"+$.param(i),scratchbook:true})})}}})},"View in new visualization":function(){l.Galaxy.modal.hide();var m=g+"/trackster?"+$.param(i);l.Galaxy.frame.add({title:"Trackster",type:"url",content:m,scratchbook:true})}}})}});return false}}return{HDAEditView:f}}); \ No newline at end of file +define(["mvc/dataset/hda-model","mvc/dataset/hda-base"],function(d,a){var f=a.HDABaseView.extend(LoggableMixin).extend({initialize:function(g){a.HDABaseView.prototype.initialize.call(this,g);this.hasUser=g.hasUser;this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton,this._render_rerunButton]},_render_titleButtons:function(){return a.HDABaseView.prototype._render_titleButtons.call(this).concat([this._render_editButton(),this._render_deleteButton()])},_render_editButton:function(){if((this.model.get("state")===d.HistoryDatasetAssociation.STATES.NEW)||(this.model.get("state")===d.HistoryDatasetAssociation.STATES.DISCARDED)||(this.model.get("state")===d.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){return null}var i=this.model.get("purged"),g=this.model.get("deleted"),h={title:_l("Edit Attributes"),href:this.urls.edit,target:this.linkTarget,classes:"dataset-edit"};if(g||i){h.disabled=true;if(i){h.title=_l("Cannot edit attributes of datasets removed from disk")}else{if(g){h.title=_l("Undelete dataset to edit attributes")}}}else{if(this.model.get("state")===d.HistoryDatasetAssociation.STATES.UPLOAD){h.disabled=true;h.title=_l("This dataset must finish uploading before it can be edited")}}h.faIcon="fa-pencil";return faIconButton(h)},_render_deleteButton:function(){if((this.model.get("state")===d.HistoryDatasetAssociation.STATES.NEW)||(this.model.get("state")===d.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){return null}var g=this,h={title:_l("Delete"),classes:"dataset-delete",onclick:function(){g.$el.find(".icon-btn.dataset-delete").trigger("mouseout");g.model["delete"]()}};if(this.model.get("deleted")||this.model.get("purged")){h={title:_l("Dataset is already deleted"),disabled:true}}h.faIcon="fa-times";return faIconButton(h)},_render_errButton:function(){if(this.model.get("state")!==d.HistoryDatasetAssociation.STATES.ERROR){return null}return faIconButton({title:_l("View or report this error"),href:this.urls.report_error,target:this.linkTarget,faIcon:"fa-bug"})},_render_rerunButton:function(){return faIconButton({title:_l("Run this job again"),href:this.urls.rerun,target:this.linkTarget,faIcon:"fa-refresh"})},_render_visualizationsButton:function(){var n=this.model.get("visualizations");if((!this.hasUser)||(!this.model.hasData())||(_.isEmpty(n))){return null}if(_.isObject(n[0])){return this._render_visualizationsFrameworkButton(n)}if(!this.urls.visualization){return null}var k=this.model.get("dbkey"),g=this.urls.visualization,j={},h={dataset_id:this.model.get("id"),hda_ldda:"hda"};if(k){h.dbkey=k}var l=faIconButton({title:_l("Visualize"),faIcon:"fa-bar-chart-o"});var m=this;function i(p){switch(p){case"trackster":return b(g,h,k);case"scatterplot":return e(g,h,m.linkTarget);default:return function(){Galaxy.frame.add({title:"Visualization",type:"url",content:g+"/"+p+"?"+$.param(h)})}}}function o(p){return p.charAt(0).toUpperCase()+p.slice(1)}if(n.length===1){l.attr("data-original-title",_l("Visualize in ")+_l(o(n[0])));l.click(i(n[0]))}else{_.each(n,function(p){j[_l(o(p))]=i(p)});make_popupmenu(l,j)}return l},_render_visualizationsFrameworkButton:function(g){if(!(this.model.hasData())||!(g&&!_.isEmpty(g))){return null}var i=faIconButton({title:_l("Visualize"),faIcon:"fa-bar-chart-o"});i.addClass("visualize-icon");if(_.keys(g).length===1){i.attr("title",_.keys(g)[0]);i.attr("href",_.values(g)[0])}else{var j=[];_.each(g,function(k){j.push(k)});var h=new PopupMenu(i,j)}return i},_render_body_failed_metadata:function(){var h=$("<a/>").attr({href:this.urls.edit,target:this.linkTarget}).text(_l("set it manually or retry auto-detection")),g=$("<span/>").text(". "+_l("You may be able to")+" ").append(h),i=a.HDABaseView.prototype._render_body_failed_metadata.call(this);i.find(".warningmessagesmall strong").append(g);return i},_render_body_error:function(){var g=a.HDABaseView.prototype._render_body_error.call(this);g.find(".dataset-actions .left").prepend(this._render_errButton());return g},_render_body_ok:function(){var g=a.HDABaseView.prototype._render_body_ok.call(this);if(this.model.isDeletedOrPurged()){return g}this.makeDbkeyEditLink(g);if(this.hasUser){g.find(".dataset-actions .left").append(this._render_visualizationsButton());this._renderTags(g);this._renderAnnotation(g)}return g},_renderTags:function(g){this.tagsEditor=new TagsEditor({model:this.model,el:g.find(".tags-display"),onshowFirstTime:function(){this.render()},$activator:faIconButton({title:_l("Edit dataset tags"),classes:"dataset-tag-btn",faIcon:"fa-tags"}).appendTo(g.find(".dataset-actions .right"))})},_renderAnnotation:function(g){this.annotationEditor=new AnnotationEditor({model:this.model,el:g.find(".annotation-display"),onshowFirstTime:function(){this.render()},$activator:faIconButton({title:_l("Edit dataset annotation"),classes:"dataset-annotate-btn",faIcon:"fa-comment"}).appendTo(g.find(".dataset-actions .right"))})},makeDbkeyEditLink:function(g){if(this.model.get("metadata_dbkey")==="?"&&!this.model.isDeletedOrPurged()){g.find(".dataset-dbkey .value").replaceWith($('<a target="'+this.linkTarget+'">?</a>').attr("href",this.urls.edit))}},events:_.extend(_.clone(a.HDABaseView.prototype.events),{"click .dataset-undelete":function(g){this.model.undelete();return false},"click .dataset-unhide":function(g){this.model.unhide();return false},"click .dataset-purge":"confirmPurge"}),confirmPurge:function c(g){this.model.purge();return false},toString:function(){var g=(this.model)?(this.model+""):("(no model)");return"HDAView("+g+")"}});function e(g,i,h){action=function(){Galaxy.frame.add({title:"Scatterplot",type:"url",content:g+"/scatterplot?"+$.param(i),target:h,scratchbook:true});$("div.popmenu-wrapper").remove();return false};return action}function b(g,i,h){return function(){var j={};if(h){j["f-dbkey"]=h}$.ajax({url:g+"/list_tracks?"+$.param(j),dataType:"html",error:function(){alert(("Could not add this dataset to browser")+".")},success:function(k){var l=window.parent;l.Galaxy.modal.show({title:"View Data in a New or Saved Visualization",buttons:{Cancel:function(){l.Galaxy.modal.hide()},"View in saved visualization":function(){l.Galaxy.modal.show({title:"Add Data to Saved Visualization",body:k,buttons:{Cancel:function(){l.Galaxy.modal.hide()},"Add to visualization":function(){$(l.document).find("input[name=id]:checked").each(function(){l.Galaxy.modal.hide();var m=$(this).val();i.id=m;l.Galaxy.frame.add({title:"Trackster",type:"url",content:g+"/trackster?"+$.param(i),scratchbook:true})})}}})},"View in new visualization":function(){l.Galaxy.modal.hide();var m=g+"/trackster?"+$.param(i);l.Galaxy.frame.add({title:"Trackster",type:"url",content:m,scratchbook:true})}}})}});return false}}return{HDAEditView:f}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: carlfeberhard: History panel: fix href/click fn collision in visualizations button
by commits-noreply＠bitbucket.org 10 Dec '13

10 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a06cdfe0a180/ Changeset: a06cdfe0a180 User: carlfeberhard Date: 2013-12-10 17:21:16 Summary: History panel: fix href/click fn collision in visualizations button Affected #: 1 file diff -r 9202b520908dd37a25fce0cf53b585df10b6b59e -r a06cdfe0a180c4c8aefaeb2bbc51d54ef7d64380 static/scripts/mvc/dataset/hda-edit.js --- a/static/scripts/mvc/dataset/hda-edit.js +++ b/static/scripts/mvc/dataset/hda-edit.js @@ -184,7 +184,6 @@ var $icon = faIconButton({ title : _l( 'Visualize' ), - href : this.urls.visualization, faIcon : 'fa-bar-chart-o' }); @@ -199,9 +198,8 @@ case 'scatterplot': return create_scatterplot_action_fn( visualization_url, params, hdaView.linkTarget ); default: - return function(){// add widget - Galaxy.frame.add( - { + return function(){ + Galaxy.frame.add({ title : "Visualization", type : "url", content : visualization_url + '/' + visualization + '?' + $.param( params ) @@ -210,16 +208,19 @@ } } + function titleCase( string ){ + return string.charAt( 0 ).toUpperCase() + string.slice( 1 ); + } + // No need for popup menu because there's a single visualization. if( visualizations.length === 1 ){ - $icon.attr( 'data-original-title', visualizations[0] ); + $icon.attr( 'data-original-title', _l( 'Visualize in ' ) + _l( titleCase( visualizations[0] ) ) ); $icon.click( create_viz_action( visualizations[0] ) ); // >1: Populate menu dict with visualization fns, make the popupmenu } else { _.each( visualizations, function( visualization ) { - var titleCaseVisualization = visualization.charAt( 0 ).toUpperCase() + visualization.slice( 1 ); - popup_menu_dict[ _l( titleCaseVisualization ) ] = create_viz_action( visualization ); + popup_menu_dict[ _l( titleCase( visualization ) ) ] = create_viz_action( visualization ); }); make_popupmenu( $icon, popup_menu_dict ); } 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: dan: Allow ftp for GALAXY_TEST_DB_TEMPLATE and stricter check for protocol URL prefixes.
by commits-noreply＠bitbucket.org 10 Dec '13

10 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/9202b520908d/ Changeset: 9202b520908d User: dan Date: 2013-12-10 17:08:13 Summary: Allow ftp for GALAXY_TEST_DB_TEMPLATE and stricter check for protocol URL prefixes. Affected #: 1 file diff -r 738839e77188c2f42d956998f38daea619f3c35e -r 9202b520908dd37a25fce0cf53b585df10b6b59e scripts/functional_tests.py --- a/scripts/functional_tests.py +++ b/scripts/functional_tests.py @@ -182,7 +182,7 @@ if os.path.exists( source ): shutil.copy( source, db_path ) assert os.path.exists( db_path ) - elif source.lower().startswith( "http" ): + elif source.lower().startswith( ( "http://", "https://", "ftp://" ) ): urllib.urlretrieve( source, db_path ) else: raise Exception( "Failed to copy database template from source %s" % source ) @@ -323,6 +323,7 @@ # GALAXY_TEST_DBURI. The former requires a lot of setup # time, the latter results in test failures in certain # cases (namely tool shed tests expecting clean database). + log.debug( "Copying database template from %s.", os.environ['GALAXY_TEST_DB_TEMPLATE'] ) __copy_database_template(os.environ['GALAXY_TEST_DB_TEMPLATE'], db_path) database_auto_migrate = True database_connection = 'sqlite:///%s' % db_path 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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