commit/galaxy-central: 2 new changesets
2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ac3195ac1025/ changeset: ac3195ac1025 branch: next-stable user: inithello date: 2013-02-04 20:00:31 summary: Updated BWA's tool_dependencies.xml to no longer rely on a network connection to correctly complete functional tests. affected #: 4 files diff -r 1ab19b93abbdf10d831dd2b9804a0081d7867fac -r ac3195ac1025f73bcabeeafa66e93b964fbac7b2 test/tool_shed/base/twilltestcase.py --- a/test/tool_shed/base/twilltestcase.py +++ b/test/tool_shed/base/twilltestcase.py @@ -483,7 +483,10 @@ # Save the generated xml to the specified location. file( xml_filename, 'w' ).write( repository_dependency_xml ) def generate_temp_path( self, test_script_path, additional_paths=[] ): - return os.path.join( self.tool_shed_test_tmp_dir, test_script_path, os.sep.join( additional_paths ) ) + temp_path = os.path.join( self.tool_shed_test_tmp_dir, test_script_path, os.sep.join( additional_paths ) ) + if not os.path.exists( temp_path ): + os.makedirs( temp_path ) + return temp_path def get_datatypes_count( self ): url = '/admin/view_datatypes_registry' self.visit_galaxy_url( url ) diff -r 1ab19b93abbdf10d831dd2b9804a0081d7867fac -r ac3195ac1025f73bcabeeafa66e93b964fbac7b2 test/tool_shed/functional/test_1100_install_repository_with_complex_dependencies.py --- a/test/tool_shed/functional/test_1100_install_repository_with_complex_dependencies.py +++ b/test/tool_shed/functional/test_1100_install_repository_with_complex_dependencies.py @@ -1,6 +1,7 @@ from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os import tool_shed.base.test_db_util as test_db_util - +import logging +log = logging.getLogger(__name__) bwa_base_repository_name = 'bwa_base_repository_0100' bwa_base_repository_description = "BWA Base" bwa_base_repository_long_description = "BWA tool that depends on bwa 0.5.9, with a complex repository dependency pointing at bwa_tool_repository_0100" @@ -41,8 +42,15 @@ strings_displayed=[] ) if self.repository_is_new( repository ): running_standalone = True + old_tool_dependency = self.get_filename( os.path.join( 'bwa', 'complex', 'tool_dependencies.xml' ) ) + new_tool_dependency_path = self.generate_temp_path( 'test_1100', additional_paths=[ 'tool_dependency' ] ) + xml_filename = os.path.abspath( os.path.join( new_tool_dependency_path, 'tool_dependencies.xml' ) ) + log.debug( xml_filename ) + file( xml_filename, 'w' ).write( file( old_tool_dependency, 'r' ) + .read().replace( '__PATH__', self.get_filename( 'bwa/complex' ) ) ) self.upload_file( repository, - 'bwa/complex/tool_dependencies.xml', + xml_filename, + filepath=new_tool_dependency_path, strings_displayed=[], commit_message='Uploaded tool_dependencies.xml.' ) self.display_manage_repository_page( repository, strings_displayed=[ 'Tool dependencies', 'may not be', 'in this repository' ] ) @@ -171,8 +179,15 @@ base_repository = test_db_util.get_repository_by_name_and_owner( bwa_base_repository_name, common.test_user_1_name ) tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_tool_repository_name, common.test_user_1_name ) previous_changeset = self.get_repository_tip( tool_repository ) + old_tool_dependency = self.get_filename( os.path.join( 'bwa', 'complex', 'readme', 'tool_dependencies.xml' ) ) + new_tool_dependency_path = self.generate_temp_path( 'test_1100', additional_paths=[ 'tool_dependency' ] ) + xml_filename = os.path.abspath( os.path.join( new_tool_dependency_path, 'tool_dependencies.xml' ) ) + log.debug( xml_filename ) + file( xml_filename, 'w' ).write( file( old_tool_dependency, 'r' ) + .read().replace( '__PATH__', self.get_filename( 'bwa/complex' ) ) ) self.upload_file( tool_repository, - 'bwa/complex/readme/tool_dependencies.xml', + xml_filename, + filepath=new_tool_dependency_path, strings_displayed=[], commit_message='Uploaded new tool_dependencies.xml.' ) # Verify that the dependency display has been updated as a result of the new tool_dependencies.xml file. diff -r 1ab19b93abbdf10d831dd2b9804a0081d7867fac -r ac3195ac1025f73bcabeeafa66e93b964fbac7b2 test/tool_shed/test_data/bwa/complex/readme/tool_dependencies.xml --- a/test/tool_shed/test_data/bwa/complex/readme/tool_dependencies.xml +++ b/test/tool_shed/test_data/bwa/complex/readme/tool_dependencies.xml @@ -3,12 +3,7 @@ <package name="bwa" version="0.5.9"><install version="1.0"><actions> - <action type="download_by_url">http://downloads.sourceforge.net/project/bio-bwa/bwa-0.5.9.tar.bz2</action> - <action type="shell_command">make</action> - <action type="move_file"> - <source>bwa</source> - <destination>$INSTALL_DIR/bin</destination> - </action> + <action type="download_by_url">file://__PATH__/bwa_base.tar</action><action type="set_environment"><environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable></action> diff -r 1ab19b93abbdf10d831dd2b9804a0081d7867fac -r ac3195ac1025f73bcabeeafa66e93b964fbac7b2 test/tool_shed/test_data/bwa/complex/tool_dependencies.xml --- a/test/tool_shed/test_data/bwa/complex/tool_dependencies.xml +++ b/test/tool_shed/test_data/bwa/complex/tool_dependencies.xml @@ -3,12 +3,7 @@ <package name="bwa" version="0.5.9"><install version="1.0"><actions> - <action type="download_by_url">http://downloads.sourceforge.net/project/bio-bwa/bwa-0.5.9.tar.bz2</action> - <action type="shell_command">make</action> - <action type="move_file"> - <source>bwa</source> - <destination>$INSTALL_DIR/bin</destination> - </action> + <action type="download_by_url">file://__PATH__/bwa_base.tar</action><action type="set_environment"><environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable></action> https://bitbucket.org/galaxy/galaxy-central/commits/b6be9c3a2d2d/ changeset: b6be9c3a2d2d user: inithello date: 2013-02-04 20:01:50 summary: Merged in changes from next-stable. affected #: 4 files diff -r 2faf4a9871bb58da2b16d1a8929a53c68f951cc0 -r b6be9c3a2d2df94f4d5236184a4392ec00961743 test/tool_shed/base/twilltestcase.py --- a/test/tool_shed/base/twilltestcase.py +++ b/test/tool_shed/base/twilltestcase.py @@ -483,7 +483,10 @@ # Save the generated xml to the specified location. file( xml_filename, 'w' ).write( repository_dependency_xml ) def generate_temp_path( self, test_script_path, additional_paths=[] ): - return os.path.join( self.tool_shed_test_tmp_dir, test_script_path, os.sep.join( additional_paths ) ) + temp_path = os.path.join( self.tool_shed_test_tmp_dir, test_script_path, os.sep.join( additional_paths ) ) + if not os.path.exists( temp_path ): + os.makedirs( temp_path ) + return temp_path def get_datatypes_count( self ): url = '/admin/view_datatypes_registry' self.visit_galaxy_url( url ) diff -r 2faf4a9871bb58da2b16d1a8929a53c68f951cc0 -r b6be9c3a2d2df94f4d5236184a4392ec00961743 test/tool_shed/functional/test_1100_install_repository_with_complex_dependencies.py --- a/test/tool_shed/functional/test_1100_install_repository_with_complex_dependencies.py +++ b/test/tool_shed/functional/test_1100_install_repository_with_complex_dependencies.py @@ -1,6 +1,7 @@ from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os import tool_shed.base.test_db_util as test_db_util - +import logging +log = logging.getLogger(__name__) bwa_base_repository_name = 'bwa_base_repository_0100' bwa_base_repository_description = "BWA Base" bwa_base_repository_long_description = "BWA tool that depends on bwa 0.5.9, with a complex repository dependency pointing at bwa_tool_repository_0100" @@ -41,8 +42,15 @@ strings_displayed=[] ) if self.repository_is_new( repository ): running_standalone = True + old_tool_dependency = self.get_filename( os.path.join( 'bwa', 'complex', 'tool_dependencies.xml' ) ) + new_tool_dependency_path = self.generate_temp_path( 'test_1100', additional_paths=[ 'tool_dependency' ] ) + xml_filename = os.path.abspath( os.path.join( new_tool_dependency_path, 'tool_dependencies.xml' ) ) + log.debug( xml_filename ) + file( xml_filename, 'w' ).write( file( old_tool_dependency, 'r' ) + .read().replace( '__PATH__', self.get_filename( 'bwa/complex' ) ) ) self.upload_file( repository, - 'bwa/complex/tool_dependencies.xml', + xml_filename, + filepath=new_tool_dependency_path, strings_displayed=[], commit_message='Uploaded tool_dependencies.xml.' ) self.display_manage_repository_page( repository, strings_displayed=[ 'Tool dependencies', 'may not be', 'in this repository' ] ) @@ -171,8 +179,15 @@ base_repository = test_db_util.get_repository_by_name_and_owner( bwa_base_repository_name, common.test_user_1_name ) tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_tool_repository_name, common.test_user_1_name ) previous_changeset = self.get_repository_tip( tool_repository ) + old_tool_dependency = self.get_filename( os.path.join( 'bwa', 'complex', 'readme', 'tool_dependencies.xml' ) ) + new_tool_dependency_path = self.generate_temp_path( 'test_1100', additional_paths=[ 'tool_dependency' ] ) + xml_filename = os.path.abspath( os.path.join( new_tool_dependency_path, 'tool_dependencies.xml' ) ) + log.debug( xml_filename ) + file( xml_filename, 'w' ).write( file( old_tool_dependency, 'r' ) + .read().replace( '__PATH__', self.get_filename( 'bwa/complex' ) ) ) self.upload_file( tool_repository, - 'bwa/complex/readme/tool_dependencies.xml', + xml_filename, + filepath=new_tool_dependency_path, strings_displayed=[], commit_message='Uploaded new tool_dependencies.xml.' ) # Verify that the dependency display has been updated as a result of the new tool_dependencies.xml file. diff -r 2faf4a9871bb58da2b16d1a8929a53c68f951cc0 -r b6be9c3a2d2df94f4d5236184a4392ec00961743 test/tool_shed/test_data/bwa/complex/readme/tool_dependencies.xml --- a/test/tool_shed/test_data/bwa/complex/readme/tool_dependencies.xml +++ b/test/tool_shed/test_data/bwa/complex/readme/tool_dependencies.xml @@ -3,12 +3,7 @@ <package name="bwa" version="0.5.9"><install version="1.0"><actions> - <action type="download_by_url">http://downloads.sourceforge.net/project/bio-bwa/bwa-0.5.9.tar.bz2</action> - <action type="shell_command">make</action> - <action type="move_file"> - <source>bwa</source> - <destination>$INSTALL_DIR/bin</destination> - </action> + <action type="download_by_url">file://__PATH__/bwa_base.tar</action><action type="set_environment"><environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable></action> diff -r 2faf4a9871bb58da2b16d1a8929a53c68f951cc0 -r b6be9c3a2d2df94f4d5236184a4392ec00961743 test/tool_shed/test_data/bwa/complex/tool_dependencies.xml --- a/test/tool_shed/test_data/bwa/complex/tool_dependencies.xml +++ b/test/tool_shed/test_data/bwa/complex/tool_dependencies.xml @@ -3,12 +3,7 @@ <package name="bwa" version="0.5.9"><install version="1.0"><actions> - <action type="download_by_url">http://downloads.sourceforge.net/project/bio-bwa/bwa-0.5.9.tar.bz2</action> - <action type="shell_command">make</action> - <action type="move_file"> - <source>bwa</source> - <destination>$INSTALL_DIR/bin</destination> - </action> + <action type="download_by_url">file://__PATH__/bwa_base.tar</action><action type="set_environment"><environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable></action> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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