3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/fdd9dd36d6e6/ changeset: fdd9dd36d6e6 user: inithello date: 2013-01-30 20:54:41 summary: Enable specifying the location of the migrated tools' XML file. affected #: 1 file diff -r 43fa4cb72e0fdc207a07fc4c6402273ca4bd4fc6 -r fdd9dd36d6e6bdd17ecaa219c15a6afeb047748c lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -57,7 +57,7 @@ self.test_conf = resolve_path( kwargs.get( "test_conf", "" ), self.root ) # The value of migrated_tools_config is the file reserved for containing only those tools that have been eliminated from the distribution # and moved to the tool shed. - self.migrated_tools_config = resolve_path( "migrated_tools_conf.xml", self.root ) + self.migrated_tools_config = resolve_path( kwargs.get( 'migrated_tools_config', 'migrated_tools_conf.xml' ), self.root ) if 'tool_config_file' in kwargs: tcf = kwargs[ 'tool_config_file' ] elif 'tool_config_files' in kwargs: https://bitbucket.org/galaxy/galaxy-central/commits/8f56f551b194/ changeset: 8f56f551b194 user: inithello date: 2013-01-30 20:55:08 summary: Enable running tool shed functional tests with run_functional_tests.sh. affected #: 1 file diff -r fdd9dd36d6e6bdd17ecaa219c15a6afeb047748c -r 8f56f551b194ef92029b88c5a774bf3d13220af3 run_functional_tests.sh --- a/run_functional_tests.sh +++ b/run_functional_tests.sh @@ -6,11 +6,13 @@ if [ ! $1 ]; then python ./scripts/functional_tests.py -v --with-nosehtml --html-report-file run_functional_tests.html --exclude="^get" functional elif [ $1 = 'help' ]; then - echo "'run_functional_tests.sh' for testing all the tools in functional directory" - echo "'run_functional_tests.sh aaa' for testing one test case of 'aaa' ('aaa' is the file name with path)" - echo "'run_functional_tests.sh -id bbb' for testing one tool with id 'bbb' ('bbb' is the tool id)" - echo "'run_functional_tests.sh -sid ccc' for testing one section with sid 'ccc' ('ccc' is the string after 'section::')" - echo "'run_functional_tests.sh -list' for listing all the tool ids" + echo "'run_functional_tests.sh' for testing all the tools in functional directory" + echo "'run_functional_tests.sh aaa' for testing one test case of 'aaa' ('aaa' is the file name with path)" + echo "'run_functional_tests.sh -id bbb' for testing one tool with id 'bbb' ('bbb' is the tool id)" + echo "'run_functional_tests.sh -sid ccc' for testing one section with sid 'ccc' ('ccc' is the string after 'section::')" + echo "'run_functional_tests.sh -list' for listing all the tool ids" + echo "'run_functional_tests.sh -toolshed' for running all the test scripts in the ./test/tool_shed/functional directory" + echo "'run_functional_tests.sh -toolshed testscriptname' for running one test script named testscriptname in the .test/tool_shed/functional directory" 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 @@ -38,6 +40,12 @@ else python ./scripts/functional_tests.py -v functional.test_toolbox --with-nosehtml --html-report-file run_functional_tests.html -installed fi +elif [ $1 = '-toolshed' ]; then + if [ ! $2 ]; then + python ./test/tool_shed/functional_tests.py -v --with-nosehtml --html-report-file ./test/tool_shed/run_functional_tests.html ./test/tool_shed/functional + else + python ./test/tool_shed/functional_tests.py -v --with-nosehtml --html-report-file ./test/tool_shed/run_functional_tests.html $2 + fi else python ./scripts/functional_tests.py -v --with-nosehtml --html-report-file run_functional_tests.html $1 fi https://bitbucket.org/galaxy/galaxy-central/commits/2fcef8462899/ changeset: 2fcef8462899 user: inithello date: 2013-01-30 20:57:16 summary: Pass in a temporary file as migrated_tools_conf, so repositories without tools end up in the right location. affected #: 1 file diff -r 8f56f551b194ef92029b88c5a774bf3d13220af3 -r 2fcef846289917ccf394bb2fabba8f36d55d0039 test/tool_shed/functional_tests.py --- a/test/tool_shed/functional_tests.py +++ b/test/tool_shed/functional_tests.py @@ -124,6 +124,7 @@ galaxy_tool_data_table_conf_file = os.environ.get( 'GALAXY_TEST_TOOL_DATA_TABLE_CONF', os.path.join( tool_shed_test_tmp_dir, 'tool_data_table_conf.xml' ) ) galaxy_tool_conf_file = os.environ.get( 'GALAXY_TEST_TOOL_CONF', os.path.join( tool_shed_test_tmp_dir, 'test_tool_conf.xml' ) ) galaxy_shed_tool_conf_file = os.environ.get( 'GALAXY_TEST_SHED_TOOL_CONF', os.path.join( tool_shed_test_tmp_dir, 'test_shed_tool_conf.xml' ) ) + galaxy_migrated_tool_conf_file = os.environ.get( 'GALAXY_TEST_MIGRATED_TOOL_CONF', os.path.join( tool_shed_test_tmp_dir, 'test_migrated_tool_conf.xml' ) ) galaxy_tool_sheds_conf_file = os.environ.get( 'GALAXY_TEST_TOOL_SHEDS_CONF', os.path.join( tool_shed_test_tmp_dir, 'test_sheds_conf.xml' ) ) if 'GALAXY_TEST_TOOL_DATA_PATH' in os.environ: tool_data_path = os.environ.get( 'GALAXY_TEST_TOOL_DATA_PATH' ) @@ -141,6 +142,7 @@ new_repos_path = tempfile.mkdtemp( dir=tool_shed_test_tmp_dir ) galaxy_tempfiles = tempfile.mkdtemp( dir=tool_shed_test_tmp_dir ) galaxy_shed_tool_path = tempfile.mkdtemp( dir=tool_shed_test_tmp_dir ) + galaxy_migrated_tool_path = tempfile.mkdtemp( dir=tool_shed_test_tmp_dir ) galaxy_tool_dependency_dir = tempfile.mkdtemp( dir=tool_shed_test_tmp_dir ) os.environ[ 'GALAXY_TEST_TOOL_DEPENDENCY_DIR' ] = galaxy_tool_dependency_dir if 'TOOL_SHED_TEST_DBURI' in os.environ: @@ -258,6 +260,9 @@ shed_tool_conf_template_parser = string.Template( shed_tool_conf_xml_template ) shed_tool_conf_xml = shed_tool_conf_template_parser.safe_substitute( shed_tool_path=galaxy_shed_tool_path ) file( galaxy_shed_tool_conf_file, 'w' ).write( shed_tool_conf_xml ) + # Generate the migrated_tool_conf.xml file. + migrated_tool_conf_xml = shed_tool_conf_template_parser.safe_substitute( shed_tool_path=galaxy_migrated_tool_path ) + file( galaxy_migrated_tool_conf_file, 'w' ).write( migrated_tool_conf_xml ) os.environ[ 'GALAXY_TEST_SHED_TOOL_CONF' ] = galaxy_shed_tool_conf_file # ---- Build Galaxy Application -------------------------------------------------- @@ -275,6 +280,7 @@ tool_data_path = tool_data_path, shed_tool_path = galaxy_shed_tool_path, update_integrated_tool_panel = False, + migrated_tools_config = galaxy_migrated_tool_conf_file, tool_config_file = [ galaxy_tool_conf_file, galaxy_shed_tool_conf_file ], tool_sheds_config_file = galaxy_tool_sheds_conf_file, datatype_converters_config_file = "datatype_converters_conf.xml.sample", Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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