1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/04b8060562f8/ changeset: 04b8060562f8 user: inithello date: 2013-02-12 21:00:28 summary: Tool shed functional tests for malformed XML in tool_dependencies.xml. affected #: 3 files diff -r 01e73b11a46f87b03af29581603378b06187051d -r 04b8060562f865fa5b3ec6dac4ecfe590bd3ec07 test/tool_shed/functional/test_0010_repository_with_tool_dependencies.py --- a/test/tool_shed/functional/test_0010_repository_with_tool_dependencies.py +++ b/test/tool_shed/functional/test_0010_repository_with_tool_dependencies.py @@ -63,20 +63,28 @@ 'freebayes/sam_fa_indices.loc.sample', strings_displayed=[], commit_message='Uploaded tool data table .loc file.' ) - def test_0025_upload_invalid_tool_dependency_xml( self ): + def test_0025_upload_malformed_tool_dependency_xml( self ): + '''Upload tool_dependencies.xml with bad characters in the readme tag.''' + repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) + self.upload_file( repository, + os.path.join( 'freebayes', 'malformed_tool_dependencies', 'tool_dependencies.xml' ), + valid_tools_only=False, + strings_displayed=[ 'Exception attempting to parse tool_dependencies.xml', 'not well-formed' ], + commit_message='Uploaded malformed tool dependency XML.' ) + def test_0030_upload_invalid_tool_dependency_xml( self ): '''Upload tool_dependencies.xml defining version 0.9.5 of the freebayes package.''' repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) self.upload_file( repository, os.path.join( 'freebayes', 'invalid_tool_dependencies', 'tool_dependencies.xml' ), strings_displayed=[ 'Name, version and type from a tool requirement tag does not match' ], commit_message='Uploaded invalid tool dependency XML.' ) - def test_0030_upload_valid_tool_dependency_xml( self ): + def test_0035_upload_valid_tool_dependency_xml( self ): '''Upload tool_dependencies.xml defining version 0.9.4_9696d0ce8a962f7bb61c4791be5ce44312b81cf8 of the freebayes package.''' repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) self.upload_file( repository, os.path.join( 'freebayes', 'tool_dependencies.xml' ), commit_message='Uploaded valid tool dependency XML.' ) - def test_0035_verify_tool_dependencies( self ): + def test_0040_verify_tool_dependencies( self ): '''Verify that the uploaded tool_dependencies.xml specifies the correct package versions.''' repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) self.display_manage_repository_page( repository, diff -r 01e73b11a46f87b03af29581603378b06187051d -r 04b8060562f865fa5b3ec6dac4ecfe590bd3ec07 test/tool_shed/functional/test_1010_install_repository_with_tool_dependencies.py --- a/test/tool_shed/functional/test_1010_install_repository_with_tool_dependencies.py +++ b/test/tool_shed/functional/test_1010_install_repository_with_tool_dependencies.py @@ -57,6 +57,11 @@ commit_message="Uploaded invalid_tool_dependencies/tool_dependencies.xml.", remove_repo_files_not_in_tar='No' ) self.upload_file( repository, + os.path.join( 'freebayes', 'malformed_tool_dependencies', 'tool_dependencies.xml' ), + valid_tools_only=False, + strings_displayed=[ 'Exception attempting to parse tool_dependencies.xml', 'not well-formed' ], + commit_message='Uploaded malformed tool dependency XML.' ) + self.upload_file( repository, 'freebayes/tool_dependencies.xml', valid_tools_only=False, commit_message="Uploaded tool_dependencies.xml", diff -r 01e73b11a46f87b03af29581603378b06187051d -r 04b8060562f865fa5b3ec6dac4ecfe590bd3ec07 test/tool_shed/test_data/freebayes/malformed_tool_dependencies/tool_dependencies.xml --- /dev/null +++ b/test/tool_shed/test_data/freebayes/malformed_tool_dependencies/tool_dependencies.xml @@ -0,0 +1,46 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="freebayes" version="0.9.5"> + <install version="1.0"> + <actions> + <action type="shell_command">git clone --recursive git://github.com/ekg/freebayes.git</action> + <action type="shell_command">git reset --hard 9696d0ce8a962f7bb61c4791be5ce44312b81cf8</action> + <action type="shell_command">make</action> + <action type="move_directory_files"> + <source_directory>bin</source_directory> + <destination_directory>$INSTALL_DIR/bin</destination_directory> + </action> + <action type="set_environment"> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> + </action> + </actions> + </install> + <readme> +FreeBayes requires g++ and the standard C and C++ development libraries. +Additionally, cmake is required for building the BamTools API. + </readme> + </package> + <package name="samtools" version="0.2.15"> + <install version="1.0"> + <actions> + <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.18/samtools-0.1.18.tar.bz2</action> + <action type="shell_command">sed -i .bak -e 's/-lcurses/-lncurses/g' Makefile</action> + <action type="shell_command">make</action> + <action type="move_file"> + <source>samtools</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>misc/maq2sam-long</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="set_environment"> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> + </action> + </actions> + </install> + <readme> +This readme tag has invalid XML >< + </readme> + </package> +</tool_dependency> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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