2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/0bb5714cb801/ Changeset: 0bb5714cb801 User: lepsiobec Date: 2013-12-18 19:59:20 Summary: aiding security flaw with downloading datasets in archives Affected #: 1 file diff -r cbd1387437ceba5be9b47dcbf9eb951086e410a1 -r 0bb5714cb8012515824fd3e435b683afd554cdd2 lib/galaxy/webapps/galaxy/controllers/library_common.py --- a/lib/galaxy/webapps/galaxy/controllers/library_common.py +++ b/lib/galaxy/webapps/galaxy/controllers/library_common.py @@ -18,7 +18,7 @@ from galaxy.util import inflector from galaxy.util.json import to_json_string, from_json_string from galaxy.util.streamball import StreamBall -from galaxy.web.base.controller import BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMetadataMixin +from galaxy.web.base.controller import BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMetadataMixin, UsesLibraryMixinItems from galaxy.web.form_builder import AddressField, CheckboxField, SelectField, build_select_field from galaxy.model.orm import and_, eagerload_all @@ -65,7 +65,7 @@ except: pass -class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMetadataMixin ): +class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMetadataMixin, UsesLibraryMixinItems ): @web.json def library_item_updates( self, trans, ids=None, states=None ): # Avoid caching @@ -1750,7 +1750,8 @@ ldda_ids = util.listify( ldda_ids ) for ldda_id in ldda_ids: try: - ldda = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( trans.security.decode_id( ldda_id ) ) + # Load the ldda requested and check whether the user has access to them + ldda = self.get_library_dataset_dataset_association( trans, ldda_id ) assert not ldda.dataset.purged lddas.append( ldda ) except: https://bitbucket.org/galaxy/galaxy-central/commits/0b2676366a82/ Changeset: 0b2676366a82 User: lepsiobec Date: 2013-12-18 20:08:19 Summary: Merge Affected #: 1 file diff -r 0bb5714cb8012515824fd3e435b683afd554cdd2 -r 0b2676366a82d61b5e46f4cae6a235e643548f78 install_and_test_tool_shed_repositories.sh --- a/install_and_test_tool_shed_repositories.sh +++ b/install_and_test_tool_shed_repositories.sh @@ -13,6 +13,10 @@ # If the tool shed url is not specified in tool_sheds_conf.xml, GALAXY_INSTALL_TEST_TOOL_SHEDS_CONF must be set to # a tool sheds configuration file that does specify that url or repository installation will fail. +# This script accepts the command line option -w to select which set of tests to run. The default behavior is to test +# first tool_dependency_definition repositories and then repositories with tools. Provide the value 'dependencies' +# to test only tool_dependency_definition repositories or 'tools' to test only repositories with tools. + if [ -z $GALAXY_INSTALL_TEST_TOOL_SHED_API_KEY ] ; then echo "This script requires the GALAXY_INSTALL_TEST_TOOL_SHED_API_KEY environment variable to be set and non-empty." exit 1 @@ -39,14 +43,41 @@ fi fi -# Test installation of repositories of type tool_dependency_definition. -python test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py $* -v --with-nosehtml --html-report-file \ - test/install_and_test_tool_shed_repositories/tool_dependency_definitions/run_functional_tests.html \ - test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py \ - test/functional/test_toolbox.py +test_tool_dependency_definitions () { + # Test installation of repositories of type tool_dependency_definition. + python test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py $* -v --with-nosehtml --html-report-file \ + test/install_and_test_tool_shed_repositories/tool_dependency_definitions/run_functional_tests.html \ + test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py \ + test/functional/test_toolbox.py +} -# Test installation of repositories that contain valid tools with defined functional tests and a test-data directory containing test files. -#python test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py $* -v --with-nosehtml --html-report-file \ -# test/install_and_test_tool_shed_repositories/repositories_with_tools/run_functional_tests.html \ -# test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py \ -# test/functional/test_toolbox.py +test_repositories_with_tools () { + # Test installation of repositories that contain valid tools with defined functional tests and a test-data directory containing test files. + python test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py $* -v --with-nosehtml --html-report-file \ + test/install_and_test_tool_shed_repositories/repositories_with_tools/run_functional_tests.html \ + test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py \ + test/functional/test_toolbox.py +} + +which='both' + +while getopts "w:" arg; do + case $arg in + w) + which=$OPTARG + ;; + esac +done + +case $which in + dependencies) + test_tool_dependency_definitions + ;; + tools) + test_repositories_with_tools + ;; + *) + test_tool_dependency_definitions + test_repositories_with_tools + ;; +esac Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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