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

commit/galaxy-central: Dave Bouvier: Tool shed functional tests for the $ENV[] environment variable inheritance feature.
by commits-noreply＠bitbucket.org 24 Jul '13

24 Jul '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b42dfe74e237/ Changeset: b42dfe74e237 User: Dave Bouvier Date: 2013-07-24 19:39:47 Summary: Tool shed functional tests for the $ENV[] environment variable inheritance feature. Affected #: 14 files diff -r b9bd309b4b72cce4f5bd277cd628b3855934d1f1 -r b42dfe74e237ea7f9c77059e427db92d9859bc67 test/tool_shed/base/twilltestcase.py --- a/test/tool_shed/base/twilltestcase.py +++ b/test/tool_shed/base/twilltestcase.py @@ -578,12 +578,8 @@ return None def get_env_sh_path( self, tool_dependency_name, tool_dependency_version, repository ): - env_sh_path = os.path.join( self.galaxy_tool_dependency_dir, - tool_dependency_name, - tool_dependency_version, - repository.owner, - repository.name, - repository.installed_changeset_revision, + '''Return the absolute path to an installed repository's env.sh file.''' + env_sh_path = os.path.join( self.get_tool_dependency_path( tool_dependency_name, tool_dependency_version, repository ), 'env.sh' ) return env_sh_path @@ -604,6 +600,15 @@ else: last_review = None return last_review + + def get_tool_dependency_path( self, tool_dependency_name, tool_dependency_version, repository ): + '''Return the absolute path for an installed tool dependency.''' + return os.path.join( self.galaxy_tool_dependency_dir, + tool_dependency_name, + tool_dependency_version, + repository.owner, + repository.name, + repository.installed_changeset_revision ) def get_or_create_repository( self, owner=None, strings_displayed=[], strings_not_displayed=[], **kwd ): repository = test_db_util.get_repository_by_name_and_owner( kwd[ 'name' ], owner ) diff -r b9bd309b4b72cce4f5bd277cd628b3855934d1f1 -r b42dfe74e237ea7f9c77059e427db92d9859bc67 test/tool_shed/functional/test_1420_tool_dependency_environment_inheritance.py --- /dev/null +++ b/test/tool_shed/functional/test_1420_tool_dependency_environment_inheritance.py @@ -0,0 +1,320 @@ +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__ ) + +category_name = 'Test 1420 Tool dependency environment variable inheritance' +category_description = 'Test script 1420 for interpolation of inherited environment variables.' +package_atlas_repository_name = 'package_atlas_3_10_1420' +package_bzlib_repository_name = 'package_bzlib_1_0_1420' +package_boost_repository_name = 'package_boost_1_53_1420' +package_numpy_repository_name = 'package_numpy_1_7_1420' +package_rdkit_repository_name = 'package_rdkit_2012_12_1420' +package_lapack_repository_name = 'package_lapack_3_4_1420' +package_atlas_repository_description = 'Automatically Tuned Linear Algebra Software' +package_bzlib_repository_description = 'Contains a tool dependency definition that downloads and compiles version 1.0 of the bzlib library.' +package_boost_repository_description = 'Contains a tool dependency definition that downloads and compiles version 1.53 of the boost C++ libraries' +package_numpy_repository_description = 'Contains a tool dependency definition that downloads and compiles version 1.7 of the the python numpy package' +package_rdkit_repository_description = 'Contains a tool dependency definition that downloads and compiles version 2012-12 of the RDKit cheminformatics and machine-learning package.' +package_lapack_repository_description = 'Linear Algebra PACKage' +package_atlas_repository_long_description = '%s: %s' % ( package_atlas_repository_name, package_atlas_repository_description ) +package_bzlib_repository_long_description = '%s: %s' % ( package_bzlib_repository_name, package_bzlib_repository_description ) +package_boost_repository_long_description = '%s: %s' % ( package_boost_repository_name, package_boost_repository_description ) +package_numpy_repository_long_description = '%s: %s' % ( package_numpy_repository_name, package_numpy_repository_description ) +package_rdkit_repository_long_description = '%s: %s' % ( package_rdkit_repository_name, package_rdkit_repository_description ) +package_lapack_repository_long_description = '%s: %s' % ( package_lapack_repository_name, package_lapack_repository_description ) + +''' +1. Create repository package_lapack_3_4_1420 + +2. Create repository package_atlas_3_10_1420 + +3. Create repository package_bzlib_1_0_1420 + +4. Create repository package_boost_1_53_1420 + +5. Create repository package_numpy_1_7_1420 + +6. Create repository package_rdkit_2012_12_1420 + +Repository dependency structure should be as follows: + Repository package_rdkit_2012_12_1420 + Repository package_boost_1_53_1420 (prior install required) + Repository package_bzlib_1_0_1420 (prior install required) + Repository package_numpy_1_7_1420 (prior install required) + Repository package_lapack_3_4_1420 (prior install required) + Repository package_atlas_3_10_1420 (prior install required) + +8. Install package_rdkit_2012_12 into Galaxy. + +9. Verify that the env.sh file for package_rdkit_2012_12_1420 also defines the variables inherited from package_numpy_1_7_1420 and package_boost_1_53_1420. +''' + +class TestEnvironmentInheritance( ShedTwillTestCase ): + '''Test referencing environment variables that were defined in a separate tool dependency.''' + + def test_0000_initiate_users_and_category( self ): + """Create necessary user accounts and login as an admin user.""" + self.logout() + self.login( email=common.admin_email, username=common.admin_username ) + admin_user = test_db_util.get_user( common.admin_email ) + assert admin_user is not None, 'Problem retrieving user with email %s from the database' % common.admin_email + admin_user_private_role = test_db_util.get_private_role( admin_user ) + self.create_category( name=category_name, description=category_description ) + self.logout() + self.login( email=common.test_user_2_email, username=common.test_user_2_name ) + test_user_2 = test_db_util.get_user( common.test_user_2_email ) + assert test_user_2 is not None, 'Problem retrieving user with email %s from the database' % common.test_user_2_email + test_user_2_private_role = test_db_util.get_private_role( test_user_2 ) + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + test_user_1 = test_db_util.get_user( common.test_user_1_email ) + assert test_user_1 is not None, 'Problem retrieving user with email %s from the database' % common.test_user_1_email + test_user_1_private_role = test_db_util.get_private_role( test_user_1 ) + + def test_0005_create_lapack_repository( self ): + '''Create and populate package_lapack_3_4_1420.''' + ''' + This is step 1 - Create repository package_lapack_3_4_1420. + + All tool dependency definitions should download and extract a tarball containing precompiled binaries from the local + filesystem and install them into the path specified by $INSTALL_DIR. + ''' + category = test_db_util.get_category_by_name( category_name ) + repository = self.get_or_create_repository( name=package_lapack_repository_name, + description=package_lapack_repository_description, + long_description=package_lapack_repository_long_description, + owner=common.test_user_1_name, + category_id=self.security.encode_id( category.id ), + strings_displayed=[] ) + # Load the original tool dependency definition into memory, then fill in the __PATH__ placeholder with the + # actual system path where the binary tarball is found. + tool_dependency_path = self.generate_temp_path( '1420_tool_dependency', additional_paths=[ 'package_lapack_3_4_1420' ] ) + precompiled_binary_tarball = self.get_filename( '1420_files/binary_tarballs/lapack.tar' ) + edited_tool_dependency_filename = self.get_filename( filepath=tool_dependency_path, filename='tool_dependencies.xml' ) + original_tool_dependency = self.get_filename( '1420_files/package_lapack_3_4_1420/tool_dependencies.xml' ) + tool_dependency_definition = file( original_tool_dependency, 'r' ).read().replace( '__PATH__', precompiled_binary_tarball ) + file( edited_tool_dependency_filename, 'w' ).write( tool_dependency_definition ) + # Upload the edited tool dependency definition to the package_lapack_3_4_1420 repository. + self.upload_file( repository, + filename='tool_dependencies.xml', + filepath=tool_dependency_path, + valid_tools_only=True, + uncompress_file=False, + remove_repo_files_not_in_tar=False, + commit_message='Populate package_lapack_3_4_1420 with tool dependency definitions.', + strings_displayed=[], + strings_not_displayed=[] ) + + def test_0010_create_atlas_repository( self ): + '''Create and populate package_atlas_3_10_1420.''' + ''' + This is step 1 - Create repository package_atlas_3_10_1420. + + All tool dependency definitions should download and extract a tarball containing precompiled binaries from the local + filesystem and install them into the path specified by $INSTALL_DIR. + ''' + category = test_db_util.get_category_by_name( category_name ) + repository = self.get_or_create_repository( name=package_atlas_repository_name, + description=package_atlas_repository_description, + long_description=package_atlas_repository_long_description, + owner=common.test_user_1_name, + category_id=self.security.encode_id( category.id ), + strings_displayed=[] ) + # Load the original tool dependency definition into memory, then fill in the __PATH__ placeholder with the + # actual system path where the binary tarball is found. + tool_dependency_path = self.generate_temp_path( '1420_tool_dependency', additional_paths=[ 'package_atlas_3_10_1420' ] ) + precompiled_binary_tarball = self.get_filename( '1420_files/binary_tarballs/atlas.tar' ) + edited_tool_dependency_filename = self.get_filename( filepath=tool_dependency_path, filename='tool_dependencies.xml' ) + original_tool_dependency = self.get_filename( '1420_files/package_atlas_3_10_1420/tool_dependencies.xml' ) + tool_dependency_definition = file( original_tool_dependency, 'r' ).read().replace( '__PATH__', precompiled_binary_tarball ) + file( edited_tool_dependency_filename, 'w' ).write( tool_dependency_definition ) + # Upload the edited tool dependency definition to the package_atlas_3_10_1420 repository. + self.upload_file( repository, + filename='tool_dependencies.xml', + filepath=tool_dependency_path, + valid_tools_only=True, + uncompress_file=False, + remove_repo_files_not_in_tar=False, + commit_message='Populate package_atlas_3_10_1420 with tool dependency definitions.', + strings_displayed=[], + strings_not_displayed=[] ) + + def test_0015_create_bzlib_repository( self ): + '''Create and populate package_bzlib_1_0_1420.''' + ''' + This is step 1 - Create repository package_bzlib_1_0_1420. + + All tool dependency definitions should download and extract a tarball containing precompiled binaries from the local + filesystem and install them into the path specified by $INSTALL_DIR. + ''' + category = test_db_util.get_category_by_name( category_name ) + repository = self.get_or_create_repository( name=package_bzlib_repository_name, + description=package_bzlib_repository_description, + long_description=package_bzlib_repository_long_description, + owner=common.test_user_1_name, + category_id=self.security.encode_id( category.id ), + strings_displayed=[] ) + # Load the original tool dependency definition into memory, then fill in the __PATH__ placeholder with the + # actual system path where the binary tarball is found. + tool_dependency_path = self.generate_temp_path( '1420_tool_dependency', additional_paths=[ 'package_bzlib_1_0_1420' ] ) + precompiled_binary_tarball = self.get_filename( '1420_files/binary_tarballs/bzlib.tar' ) + edited_tool_dependency_filename = self.get_filename( filepath=tool_dependency_path, filename='tool_dependencies.xml' ) + original_tool_dependency = self.get_filename( '1420_files/package_bzlib_1_0_1420/tool_dependencies.xml' ) + tool_dependency_definition = file( original_tool_dependency, 'r' ).read().replace( '__PATH__', precompiled_binary_tarball ) + file( edited_tool_dependency_filename, 'w' ).write( tool_dependency_definition ) + # Upload the edited tool dependency definition to the package_bzlib_1_0_1420 repository. + self.upload_file( repository, + filename='tool_dependencies.xml', + filepath=tool_dependency_path, + valid_tools_only=True, + uncompress_file=False, + remove_repo_files_not_in_tar=False, + commit_message='Populate package_bzlib_1_0_1420 with tool dependency definitions.', + strings_displayed=[], + strings_not_displayed=[] ) + + def test_0020_create_boost_repository( self ): + '''Create and populate package_boost_1_53_1420.''' + ''' + This is step 1 - Create repository package_boost_1_53_1420. + + All tool dependency definitions should download and extract a tarball containing precompiled binaries from the local + filesystem and install them into the path specified by $INSTALL_DIR. + ''' + category = test_db_util.get_category_by_name( category_name ) + repository = self.get_or_create_repository( name=package_boost_repository_name, + description=package_boost_repository_description, + long_description=package_boost_repository_long_description, + owner=common.test_user_1_name, + category_id=self.security.encode_id( category.id ), + strings_displayed=[] ) + # Load the original tool dependency definition into memory, then fill in the __PATH__ placeholder with the + # actual system path where the binary tarball is found. + tool_dependency_path = self.generate_temp_path( '1420_tool_dependency', additional_paths=[ 'package_boost_1_53_1420' ] ) + precompiled_binary_tarball = self.get_filename( '1420_files/binary_tarballs/boost.tar' ) + edited_tool_dependency_filename = self.get_filename( filepath=tool_dependency_path, filename='tool_dependencies.xml' ) + original_tool_dependency = self.get_filename( '1420_files/package_boost_1_53_1420/tool_dependencies.xml' ) + tool_dependency_definition = file( original_tool_dependency, 'r' ).read().replace( '__PATH__', precompiled_binary_tarball ) + file( edited_tool_dependency_filename, 'w' ).write( tool_dependency_definition ) + # Upload the edited tool dependency definition to the package_boost_1_53_1420 repository. + self.upload_file( repository, + filename='tool_dependencies.xml', + filepath=tool_dependency_path, + valid_tools_only=True, + uncompress_file=False, + remove_repo_files_not_in_tar=False, + commit_message='Populate package_boost_1_53_1420 with tool dependency definitions.', + strings_displayed=[], + strings_not_displayed=[] ) + + def test_0025_create_numpy_repository( self ): + '''Create and populate package_numpy_1_7_1420.''' + ''' + This is step 1 - Create repository package_numpy_1_7_1420. + + All tool dependency definitions should download and extract a tarball containing precompiled binaries from the local + filesystem and install them into the path specified by $INSTALL_DIR. + ''' + category = test_db_util.get_category_by_name( category_name ) + repository = self.get_or_create_repository( name=package_numpy_repository_name, + description=package_numpy_repository_description, + long_description=package_numpy_repository_long_description, + owner=common.test_user_1_name, + category_id=self.security.encode_id( category.id ), + strings_displayed=[] ) + # Load the original tool dependency definition into memory, then fill in the __PATH__ placeholder with the + # actual system path where the binary tarball is found. + tool_dependency_path = self.generate_temp_path( '1420_tool_dependency', additional_paths=[ 'package_numpy_1_7_1420' ] ) + precompiled_binary_tarball = self.get_filename( '1420_files/binary_tarballs/numpy.tar' ) + edited_tool_dependency_filename = self.get_filename( filepath=tool_dependency_path, filename='tool_dependencies.xml' ) + original_tool_dependency = self.get_filename( '1420_files/package_numpy_1_7_1420/tool_dependencies.xml' ) + tool_dependency_definition = file( original_tool_dependency, 'r' ).read().replace( '__PATH__', precompiled_binary_tarball ) + file( edited_tool_dependency_filename, 'w' ).write( tool_dependency_definition ) + # Upload the edited tool dependency definition to the package_numpy_1_7_1420 repository. + self.upload_file( repository, + filename='tool_dependencies.xml', + filepath=tool_dependency_path, + valid_tools_only=True, + uncompress_file=False, + remove_repo_files_not_in_tar=False, + commit_message='Populate package_numpy_1_7_1420 with tool dependency definitions.', + strings_displayed=[], + strings_not_displayed=[] ) + + def test_0030_create_rdkit_repository( self ): + '''Create and populate package_rdkit_2012_12_1420.''' + ''' + This is step 1 - Create repository package_rdkit_2012_12_1420. + + All tool dependency definitions should download and extract a tarball containing precompiled binaries from the local + filesystem and install them into the path specified by $INSTALL_DIR. + ''' + category = test_db_util.get_category_by_name( category_name ) + repository = self.get_or_create_repository( name=package_rdkit_repository_name, + description=package_rdkit_repository_description, + long_description=package_rdkit_repository_long_description, + owner=common.test_user_1_name, + category_id=self.security.encode_id( category.id ), + strings_displayed=[] ) + # Load the original tool dependency definition into memory, then fill in the __PATH__ placeholder with the + # actual system path where the binary tarball is found. + tool_dependency_path = self.generate_temp_path( '1420_tool_dependency', additional_paths=[ 'package_rdkit_2012_12_1420' ] ) + precompiled_binary_tarball = self.get_filename( '1420_files/binary_tarballs/rdkit.tar' ) + edited_tool_dependency_filename = self.get_filename( filepath=tool_dependency_path, filename='tool_dependencies.xml' ) + original_tool_dependency = self.get_filename( '1420_files/package_rdkit_2012_12_1420/tool_dependencies.xml' ) + tool_dependency_definition = file( original_tool_dependency, 'r' ).read().replace( '__PATH__', precompiled_binary_tarball ) + file( edited_tool_dependency_filename, 'w' ).write( tool_dependency_definition ) + # Upload the edited tool dependency definition to the package_rdkit_2012_12_1420 repository. + self.upload_file( repository, + filename='tool_dependencies.xml', + filepath=tool_dependency_path, + valid_tools_only=True, + uncompress_file=False, + remove_repo_files_not_in_tar=False, + commit_message='Populate package_rdkit_2012_12_1420 with tool dependency definitions.', + strings_displayed=[], + strings_not_displayed=[] ) + + def test_0035_install_rdkit_2012_12_repository( self ): + '''Install the package_rdkit_2012_12_1420 repository into Galaxy.''' + ''' + This is step 4 - Install package_rdkit_2012_12_1420 into Galaxy. + + Install package_rdkit_2012_12_1420 with tool dependencies selected to be installed. The result of this should be + package_atlas_3_10_1420, package_bzlib_1_0_1420, package_boost_1_53_1420, package_numpy_1_7_1420, package_rdkit_2012_12_1420, + and package_lapack_3_4_1420 being installed, and an env.sh generated for package_rdkit_2012_12_1420 that + contains environment variables defined in package_boost_1_53_1420 and package_numpy_1_7_1420. + ''' + self.galaxy_logout() + self.galaxy_login( email=common.admin_email, username=common.admin_username ) + post_submit_strings_displayed = [ 'package_rdkit_2012_12_1420', 'package_atlas_3_10_1420', 'package_bzlib_1_0_1420', + 'package_numpy_1_7_1420', 'package_lapack_3_4_1420', 'package_boost_1_53_1420' ] + self.install_repository( 'package_rdkit_2012_12_1420', + common.test_user_1_name, + category_name, + install_tool_dependencies=True, + post_submit_strings_displayed=post_submit_strings_displayed ) + + def test_0040_verify_env_sh_contents( self ): + '''Check the env.sh file for the appropriate contents.''' + ''' + This is step 5 - Verify that the env.sh file for package_rdkit_2012_12_1420 also defines the variables inherited from package_numpy_1_7_1420 + and package_boost_1_53_1420. Test for the numpy and boost tool dependency paths. + ''' + package_rdkit_repository = test_db_util.get_installed_repository_by_name_owner( 'package_rdkit_2012_12_1420', common.test_user_1_name ) + package_numpy_repository = test_db_util.get_installed_repository_by_name_owner( 'package_numpy_1_7_1420', common.test_user_1_name ) + package_boost_repository = test_db_util.get_installed_repository_by_name_owner( 'package_boost_1_53_1420', common.test_user_1_name ) + rdkit_env_sh = self.get_env_sh_path( tool_dependency_name='rdkit', + tool_dependency_version='2012_12_1', + repository=package_rdkit_repository ) + numpy_tool_dependency_path = self.get_tool_dependency_path( tool_dependency_name='numpy', + tool_dependency_version='1.7.1', + repository=package_numpy_repository ) + boost_tool_dependency_path = self.get_tool_dependency_path( tool_dependency_name='boost', + tool_dependency_version='1.53.0', + repository=package_boost_repository ) + rdkit_env_file_contents = file( rdkit_env_sh, 'r' ).read() + assert numpy_tool_dependency_path in rdkit_env_file_contents, 'Environment file for package_rdkit_2012_12_1420 does not contain numpy path.' + assert boost_tool_dependency_path in rdkit_env_file_contents, 'Environment file for package_rdkit_2012_12_1420 does not contain boost path.' diff -r b9bd309b4b72cce4f5bd277cd628b3855934d1f1 -r b42dfe74e237ea7f9c77059e427db92d9859bc67 test/tool_shed/test_data/1420_files/binary_tarballs/atlas.tar Binary file test/tool_shed/test_data/1420_files/binary_tarballs/atlas.tar has changed diff -r b9bd309b4b72cce4f5bd277cd628b3855934d1f1 -r b42dfe74e237ea7f9c77059e427db92d9859bc67 test/tool_shed/test_data/1420_files/binary_tarballs/boost.tar Binary file test/tool_shed/test_data/1420_files/binary_tarballs/boost.tar has changed diff -r b9bd309b4b72cce4f5bd277cd628b3855934d1f1 -r b42dfe74e237ea7f9c77059e427db92d9859bc67 test/tool_shed/test_data/1420_files/binary_tarballs/bzlib.tar Binary file test/tool_shed/test_data/1420_files/binary_tarballs/bzlib.tar has changed diff -r b9bd309b4b72cce4f5bd277cd628b3855934d1f1 -r b42dfe74e237ea7f9c77059e427db92d9859bc67 test/tool_shed/test_data/1420_files/binary_tarballs/lapack.tar Binary file test/tool_shed/test_data/1420_files/binary_tarballs/lapack.tar has changed diff -r b9bd309b4b72cce4f5bd277cd628b3855934d1f1 -r b42dfe74e237ea7f9c77059e427db92d9859bc67 test/tool_shed/test_data/1420_files/binary_tarballs/numpy.tar Binary file test/tool_shed/test_data/1420_files/binary_tarballs/numpy.tar has changed diff -r b9bd309b4b72cce4f5bd277cd628b3855934d1f1 -r b42dfe74e237ea7f9c77059e427db92d9859bc67 test/tool_shed/test_data/1420_files/binary_tarballs/rdkit.tar Binary file test/tool_shed/test_data/1420_files/binary_tarballs/rdkit.tar has changed diff -r b9bd309b4b72cce4f5bd277cd628b3855934d1f1 -r b42dfe74e237ea7f9c77059e427db92d9859bc67 test/tool_shed/test_data/1420_files/package_atlas_3_10_1420/tool_dependencies.xml --- /dev/null +++ b/test/tool_shed/test_data/1420_files/package_atlas_3_10_1420/tool_dependencies.xml @@ -0,0 +1,22 @@ +<tool_dependency> + <package name="atlas" version="3.10.1"> + <install version="1.0"> + <actions> +  + <action type="download_file">file://__PATH__</action> + <action type="move_directory_files"> + <source_directory>.</source_directory> + <destination_directory>$INSTALL_DIR</destination_directory> + </action> + <action type="set_environment"> + <environment_variable name="ATLAS_LIB_DIR" action="set_to">$INSTALL_DIR/atlas/lib</environment_variable> + <environment_variable name="ATLAS_INCLUDE_DIR" action="set_to">$INSTALL_DIR/atlas/include</environment_variable> + </action> + </actions> + </install> + <readme>ATLAS_LIB_DIR and ATLAS_INCLUDE_DIR (including libatlas.a) will be exported for later use. + During ATLAS library compilation, ATLAS performs code efficiency checks. These checks can only provide optimal results, if "frequency scaling" is disabled on the CPU, and no other load-intense processes are running. + Ideally, you should compile on an empty cluster node with CPU frequency scaling disabled (see "cpufreq-selector" or "cpufreq-set"). + </readme> + </package> +</tool_dependency> diff -r b9bd309b4b72cce4f5bd277cd628b3855934d1f1 -r b42dfe74e237ea7f9c77059e427db92d9859bc67 test/tool_shed/test_data/1420_files/package_boost_1_53_1420/tool_dependencies.xml --- /dev/null +++ b/test/tool_shed/test_data/1420_files/package_boost_1_53_1420/tool_dependencies.xml @@ -0,0 +1,29 @@ +<?xml version='1.0' encoding='utf-8'?> +<tool_dependency> + <package name="bzlib" version="1.0.6"> + <repository name="package_bzlib_1_0_1420" owner="user1" prior_installation_required="True" /> + </package> + <package name="boost" version="1.53.0"> + <install version="1.0"> + <actions> + <action type="download_by_url">file://__PATH__</action> + +  + <action type="set_environment_for_install"> + <repository name="package_bzlib_1_0_1420" owner="user1"> + <package name="bzlib" version="1.0.6" /> + </repository> + </action> + <action type="move_directory_files"> + <source_directory>.</source_directory> + <destination_directory>$INSTALL_DIR</destination_directory> + </action> + <action type="set_environment"> + <environment_variable action="set_to" name="BOOST_ROOT_DIR">$INSTALL_DIR/boost</environment_variable> + <environment_variable action="append_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/boost/lib/</environment_variable> + </action> + </actions> + </install> + <readme>Compiling boost requires a C++ compiler (typically gcc). You can access the boost root directory through the $BOOST_ROOT_DIR system variable. All modules will be build.</readme> + </package> +</tool_dependency> diff -r b9bd309b4b72cce4f5bd277cd628b3855934d1f1 -r b42dfe74e237ea7f9c77059e427db92d9859bc67 test/tool_shed/test_data/1420_files/package_bzlib_1_0_1420/tool_dependencies.xml --- /dev/null +++ b/test/tool_shed/test_data/1420_files/package_bzlib_1_0_1420/tool_dependencies.xml @@ -0,0 +1,21 @@ + <tool_dependency> + <package name="bzlib" version="1.0.6"> + <install version="1.0"> + <actions> +  + <action type="download_by_url">file://__PATH__</action> + <action type="move_directory_files"> + <source_directory>.</source_directory> + <destination_directory>$INSTALL_DIR</destination_directory> + </action> + <action type="set_environment"> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bzlib/bin</environment_variable> + <environment_variable name="BZLIB_LIB_DIR" action="set_to">$INSTALL_DIR/bzlib/lib</environment_variable> + <environment_variable name="BZLIB_INCLUDE_DIR" action="set_to">$INSTALL_DIR/bzlib/include</environment_variable> + <environment_variable name="BZLIB_SOURCE_DIR" action="set_to">$INSTALL_DIR/bzlib/source</environment_variable> + </action> + </actions> + </install> + <readme>Compiling bzlib requires make and a C compiler. You can access bzlib with $BZLIB_LIB_DIR and $BZLIB_INCLUDE_DIR.</readme> + </package> +</tool_dependency> diff -r b9bd309b4b72cce4f5bd277cd628b3855934d1f1 -r b42dfe74e237ea7f9c77059e427db92d9859bc67 test/tool_shed/test_data/1420_files/package_lapack_3_4_1420/tool_dependencies.xml --- /dev/null +++ b/test/tool_shed/test_data/1420_files/package_lapack_3_4_1420/tool_dependencies.xml @@ -0,0 +1,18 @@ +<tool_dependency> + <package name="lapack" version="3.4.2"> + <install version="1.0"> + <actions> +  + <action type="download_by_url">file://__PATH__</action> + <action type="move_directory_files"> + <source_directory>.</source_directory> + <destination_directory>$INSTALL_DIR</destination_directory> + </action> + <action type="set_environment"> + <environment_variable name="LAPACK_LIB_DIR" action="set_to">$INSTALL_DIR/lapack/lib</environment_variable> + </action> + </actions> + </install> + <readme>LAPACK requires gcc and gfortran. LAPACK_LIB_DIR will be set (including liblapack.a and libblas.a). </readme> + </package> +</tool_dependency> diff -r b9bd309b4b72cce4f5bd277cd628b3855934d1f1 -r b42dfe74e237ea7f9c77059e427db92d9859bc67 test/tool_shed/test_data/1420_files/package_numpy_1_7_1420/tool_dependencies.xml --- /dev/null +++ b/test/tool_shed/test_data/1420_files/package_numpy_1_7_1420/tool_dependencies.xml @@ -0,0 +1,35 @@ +<?xml version='1.0' encoding='utf-8'?> +<tool_dependency> + <package name="lapack" version="3.4.2"> + <repository name="package_lapack_3_4_1420" owner="user1" prior_installation_required="True" /> + </package> + <package name="atlas" version="3.10.1"> + <repository name="package_atlas_3_10_1420" owner="user1" prior_installation_required="True" /> + </package> + <package name="numpy" version="1.7.1"> + <install version="1.0"> + <actions> + <action type="download_by_url">file://__PATH__</action> + <action type="set_environment_for_install"> + <repository name="package_atlas_3_10_1420" owner="user1"> + <package name="atlas" version="3.10.1" /> + </repository> + <repository name="package_lapack_3_4_1420" owner="user1"> + <package name="lapack" version="3.4.2" /> + </repository> + </action> + <action type="move_directory_files"> + <source_directory>.</source_directory> + <destination_directory>$INSTALL_DIR</destination_directory> + </action> + <action type="set_environment"> + <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable> + <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> + <environment_variable action="set_to" name="PYTHONPATH_NUMPY">$INSTALL_DIR/lib/python</environment_variable> + <environment_variable action="set_to" name="PATH_NUMPY">$INSTALL_DIR/bin</environment_variable> + </action> + </actions> + </install> + <readme>Compiling numpy requires a C and Fortran compiler (typically gcc and gfortran). The PYTHONPATH for numpy can be accessed through PYTHONPATH_NUMPY and the binaries with PATH_NUMPY.</readme> + </package> +</tool_dependency> diff -r b9bd309b4b72cce4f5bd277cd628b3855934d1f1 -r b42dfe74e237ea7f9c77059e427db92d9859bc67 test/tool_shed/test_data/1420_files/package_rdkit_2012_12_1420/tool_dependencies.xml --- /dev/null +++ b/test/tool_shed/test_data/1420_files/package_rdkit_2012_12_1420/tool_dependencies.xml @@ -0,0 +1,43 @@ +<?xml version='1.0' encoding='utf-8'?> +<tool_dependency> + <package name="numpy" version="1.7.1"> + <repository name="package_numpy_1_7_1420" owner="user1" prior_installation_required="True" /> + </package> + <package name="boost" version="1.53.0"> + <repository name="package_boost_1_53_1420" owner="user1" prior_installation_required="True" /> + </package> + + <package name="rdkit" version="2012_12_1"> + <install version="1.0"> + <actions> +  + <action type="download_by_url">file://__PATH__</action> + +  + <action type="set_environment_for_install"> + <repository name="package_numpy_1_7_1420" owner="user1"> + <package name="numpy" version="1.7.1" /> + </repository> + <repository name="package_boost_1_53_1420" owner="user1"> + <package name="boost" version="1.53.0" /> + </repository> + </action> + +  + <action type="move_directory_files"> + <source_directory>.</source_directory> + <destination_directory>$INSTALL_DIR</destination_directory> + </action> + <action type="set_environment"> + <environment_variable action="set_to" name="RDBASE">$INSTALL_DIR/rdkit</environment_variable> + <environment_variable action="append_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/rdkit/lib/</environment_variable> + <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/rdkit/bin</environment_variable> + <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/rdkit/lib/python2.7/site-packages/</environment_variable> + <environment_variable action="prepend_to" name="PYTHONPATH">$ENV[PYTHONPATH_NUMPY]</environment_variable> + <environment_variable action="append_to" name="LD_LIBRARY_PATH">$ENV[BOOST_ROOT_DIR]/lib/</environment_variable> + </action> + </actions> + </install> + <readme>Compiling rdkit requires cmake, python headers, sqlite3, flex and bison.</readme> + </package> +</tool_dependency> 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: remove profiling methods
by commits-noreply＠bitbucket.org 24 Jul '13

24 Jul '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b9bd309b4b72/ Changeset: b9bd309b4b72 User: carlfeberhard Date: 2013-07-24 17:06:51 Summary: History panel: remove profiling methods Affected #: 3 files diff -r 6fa490b703b062231da599fdd7f169d84eddc930 -r b9bd309b4b72cce4f5bd277cd628b3855934d1f1 lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -631,72 +631,6 @@ return trans.security.encode_dict_ids( hda_dict ) - def profile_get_hda_dict( self, trans, hda ): - """Profiles returning full details of this HDA in dictionary form. - """ - from galaxy.util.debugging import SimpleProfiler - profiler = SimpleProfiler() - profiler.start() - - hda_dict = hda.get_api_value( view='element' ) - profiler.report( '\t\t get_api_value' ) - history = hda.history - hda_dict[ 'api_type' ] = "file" - - # Add additional attributes that depend on trans can hence must be added here rather than at the model level. - can_access_hda = trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), hda.dataset ) - can_access_hda = ( trans.user_is_admin() or can_access_hda ) - hda_dict[ 'accessible' ] = can_access_hda - profiler.report( '\t\t accessible' ) - - # ---- return here if deleted AND purged OR can't access - purged = ( hda.purged or hda.dataset.purged ) - if ( hda.deleted and purged ) or not can_access_hda: - #TODO: get_api_value should really go AFTER this - only summary data - return ( profiler, trans.security.encode_dict_ids( hda_dict ) ) - - if trans.user_is_admin() or trans.app.config.expose_dataset_path: - hda_dict[ 'file_name' ] = hda.file_name - profiler.report( '\t\t file_name' ) - - hda_dict[ 'download_url' ] = url_for( 'history_contents_display', - history_id = trans.security.encode_id( history.id ), - history_content_id = trans.security.encode_id( hda.id ) ) - profiler.report( '\t\t download_url' ) - - # indeces, assoc. metadata files, etc. - meta_files = [] - for meta_type in hda.metadata.spec.keys(): - if isinstance( hda.metadata.spec[ meta_type ].param, FileParameter ): - meta_files.append( dict( file_type=meta_type ) ) - if meta_files: - hda_dict[ 'meta_files' ] = meta_files - profiler.report( '\t\t meta_files' ) - - # currently, the viz reg is optional - handle on/off - if trans.app.visualizations_registry: - hda_dict[ 'visualizations' ] = trans.app.visualizations_registry.get_visualizations( trans, hda ) - else: - hda_dict[ 'visualizations' ] = hda.get_visualizations() - profiler.report( '\t\t visualizations' ) - #TODO: it may also be wiser to remove from here and add as API call that loads the visualizations - # when the visualizations button is clicked (instead of preloading/pre-checking) - - # ---- return here if deleted - if hda.deleted and not purged: - return ( profiler, trans.security.encode_dict_ids( hda_dict ) ) - - # if a tool declares 'force_history_refresh' in its xml, when the hda -> ready, reload the history panel - # expensive - if( ( hda.state in [ 'running', 'queued' ] ) - and ( hda.creating_job and hda.creating_job.tool_id ) ): - tool_used = trans.app.toolbox.get_tool( hda.creating_job.tool_id ) - if tool_used and tool_used.force_history_refresh: - hda_dict[ 'force_history_refresh' ] = True - profiler.report( '\t\t force_history_refresh' ) - - return ( profiler, trans.security.encode_dict_ids( hda_dict ) ) - def get_hda_dict_with_error( self, trans, hda, error_msg='' ): return trans.security.encode_dict_ids({ 'id' : hda.id, diff -r 6fa490b703b062231da599fdd7f169d84eddc930 -r b9bd309b4b72cce4f5bd277cd628b3855934d1f1 lib/galaxy/webapps/galaxy/controllers/root.py --- a/lib/galaxy/webapps/galaxy/controllers/root.py +++ b/lib/galaxy/webapps/galaxy/controllers/root.py @@ -157,76 +157,6 @@ history_json = to_json_string( history_dictionary ), hda_json = to_json_string( hda_dictionaries ), show_deleted=show_deleted, show_hidden=show_hidden, hda_id=hda_id, log=log, message=message, status=status ) - @web.expose - def profile_history( self, trans, as_xml=False, show_deleted=None, show_hidden=None, hda_id=None, **kwd ): - """ - Same as above but adds SimpleProfiler to get some - profiling times for the operations done. - """ - if as_xml: - return self.history_as_xml( trans, - show_deleted=string_as_bool( show_deleted ), show_hidden=string_as_bool( show_hidden ) ) - - # get all datasets server-side, client-side will get flags and render appropriately - show_deleted = string_as_bool_or_none( show_deleted ) - show_purged = show_deleted - show_hidden = string_as_bool_or_none( show_hidden ) - params = Params( kwd ) - message = params.get( 'message', '' ) - #TODO: ugh... - message = message if message != 'None' else '' - status = params.get( 'status', 'done' ) - - if trans.app.config.require_login and not trans.user: - return trans.fill_template( '/no_access.mako', message = 'Please log in to access Galaxy histories.' ) - - def err_msg( where=None ): - where = where if where else 'getting the history data from the server' - err_msg = ( 'An error occurred %s. ' - + 'Please contact a Galaxy administrator if the problem persists.' ) %( where ) - return err_msg, 'error' - - profiler = SimpleProfiler() - profiler.start() - - history_dictionary = {} - hda_dictionaries = [] - import pprint - try: - history = trans.get_history( create=True ) - profiler.report( 'trans.get_history' ) - hdas = self.get_history_datasets( trans, history, - show_deleted=True, show_hidden=True, show_purged=True ) - profiler.report( 'get_history_datasets' ) - - for hda in hdas: - try: - ( hda_profiler, hda_dict ) = self.profile_get_hda_dict( trans, hda ) - profiler.reports.extend( hda_profiler.get_reports() ) - profiler.report( '\t hda -> dictionary (%s)' %( hda.name ) ) - hda_dictionaries.append( hda_dict ) - - except Exception, exc: - # don't fail entire list if hda err's, record and move on - log.error( 'Error bootstrapping hda %d: %s', hda.id, str( exc ), exc_info=True ) - hda_dictionaries.append( self.get_hda_dict_with_error( trans, hda, str( exc ) ) ) - profiler.report( 'hdas -> dictionaries' ) - - # re-use the hdas above to get the history data... - history_dictionary = self.get_history_dict( trans, history, hda_dictionaries=hda_dictionaries ) - profiler.report( 'history -> dictionary' ) - - except Exception, exc: - user_id = str( trans.user.id ) if trans.user else '(anonymous)' - log.error( 'Error bootstrapping history for user %s: %s', user_id, str( exc ), exc_info=True ) - message, status = err_msg() - history_dictionary[ 'error' ] = message - - return trans.stream_template_mako( "root/history.mako", - history_json = to_json_string( history_dictionary ), hda_json = to_json_string( hda_dictionaries ), - show_deleted=show_deleted, show_hidden=show_hidden, hda_id=hda_id, log=log, message=message, status=status, - profiling=profiler.get_reports() ) - ## ---- Dataset display / editing ---------------------------------------- @web.expose def display( self, trans, id=None, hid=None, tofile=None, toext=".txt", **kwd ): diff -r 6fa490b703b062231da599fdd7f169d84eddc930 -r b9bd309b4b72cce4f5bd277cd628b3855934d1f1 templates/webapps/galaxy/root/history.mako --- a/templates/webapps/galaxy/root/history.mako +++ b/templates/webapps/galaxy/root/history.mako @@ -213,10 +213,6 @@ galaxyPageSetUp(); // ostensibly, this is the App - %if 'profiling' in self.context.kwargs: - Galaxy.profiling = ${h.to_json_string( profiling )}.join( '\n' ); - %endif - //NOTE: for debugging on non-local instances (main/test) // 1. load history panel in own tab // 2. from console: new PersistantStorage( '__history_panel' ).set( 'debugging', true ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 24 Jul '13

24 Jul '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/881a16a71891/ Changeset: 881a16a71891 User: Dave Bouvier Date: 2013-07-24 16:54:37 Summary: Tool shed functional tests for the repository type feature. Affected #: 9 files diff -r 27b458743a117b5fb119915dc89bddc017625146 -r 881a16a718913fad393369059afe982ecb6b77bc test/tool_shed/base/twilltestcase.py --- a/test/tool_shed/base/twilltestcase.py +++ b/test/tool_shed/base/twilltestcase.py @@ -453,15 +453,15 @@ original_information = dict( repo_name=repository.name, description=repository.description, long_description=repository.long_description ) strings_displayed = [] strings_not_displayed = [] - for input_elem_name in [ 'repo_name', 'description', 'long_description' ]: + for input_elem_name in [ 'repo_name', 'description', 'long_description', 'repository_type' ]: if input_elem_name in kwd: - tc.fv( "1", input_elem_name, kwd[ input_elem_name ] ) + tc.fv( "edit_repository", input_elem_name, kwd[ input_elem_name ] ) strings_displayed.append( self.escape_html( kwd[ input_elem_name ] ) ) tc.submit( "edit_repository_button" ) self.check_for_strings( strings_displayed ) strings_displayed = [] for input_elem_name in [ 'repo_name', 'description', 'long_description' ]: - tc.fv( "1", input_elem_name, original_information[ input_elem_name ] ) + tc.fv( "edit_repository", input_elem_name, original_information[ input_elem_name ] ) strings_displayed.append( self.escape_html( original_information[ input_elem_name ] ) ) tc.submit( "edit_repository_button" ) self.check_for_strings( strings_displayed ) @@ -577,6 +577,16 @@ return datatypes_count.group( 1 ) return None + def get_env_sh_path( self, tool_dependency_name, tool_dependency_version, repository ): + env_sh_path = os.path.join( self.galaxy_tool_dependency_dir, + tool_dependency_name, + tool_dependency_version, + repository.owner, + repository.name, + repository.installed_changeset_revision, + 'env.sh' ) + return env_sh_path + def get_filename( self, filename, filepath=None ): if filepath is not None: return os.path.abspath( os.path.join( filepath, filename ) ) diff -r 27b458743a117b5fb119915dc89bddc017625146 -r 881a16a718913fad393369059afe982ecb6b77bc test/tool_shed/functional/test_0470_tool_dependency_repository_type.py --- /dev/null +++ b/test/tool_shed/functional/test_0470_tool_dependency_repository_type.py @@ -0,0 +1,253 @@ +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__ ) + +category_name = 'Test 0470 Tool dependency repository type' +category_description = 'Test script 0470 for changing repository types.' +package_libx11_repository_name = 'package_x11_client_1_5_proto_7_0_0470' +package_libx11_repository_description = "Contains a tool dependency definition that provides the X11 client libraries and core protocol header files." +package_libx11_repository_long_description = "Xlib is an X Window System protocol client library written in the C programming language." +package_emboss_repository_name = 'package_emboss_5_0_0_0470' +package_emboss_repository_description = "Contains a tool dependency definition that downloads and compiles version 5.0.0 of the EMBOSS tool suite." +package_emboss_repository_long_description = 'EMBOSS is "The European Molecular Biology Open Software Suite".' +datatypes_repository_name = 'emboss_datatypes_0470' +datatypes_repository_description = 'Galaxy applicable data formats used by Emboss tools.' +datatypes_repository_long_description = 'Galaxy applicable data formats used by Emboss tools. This repository contains no tools.' +emboss_repository_name = 'emboss_5_0470' +emboss_repository_description = "Galaxy wrappers for Emboss version 5.0.0 tools" +emboss_repository_long_description = "Galaxy wrappers for Emboss version 5.0.0 tools" + +''' +1. Create and populate a repository named package_x11_client_1_5_proto_7_0 that contains only a single file named tool_dependencies.xml. + Keep the repository type as the default "Unrestricted". + +2. Create a repository named package_emboss_5_0_0 of type "Unrestricted" that has a repository dependency definition that defines the + above package_x11_client_1_5_proto_7_0 repository. Upload the tool_dependencies.xml file such that it does not have a changeset_revision + defined so it will get automatically populated. + +3. Create a repository named emboss_5 of type "Unrestricted" that has a tool-dependencies.xml file defining a complex repository dependency + on the package_emboss_5_0_0 repository above. Upload the tool_dependencies.xml file such that it does not have a change set_revision defined + so it will get automatically populated. + +4. Add a comment to the tool_dependencies.xml file to be uploaded to the package_x11_client_1_5_prot_7_0 repository, creating a new installable + changeset revision at the repository tip. + +5. Add a comment to the tool_dependencies.xml file for the package_emboss_5_0_0 repository, eliminating the change set_revision attribute so + that it gets automatically populated when uploaded. After uploading the file, the package_emboss_5_0_0 repository should have 2 + installable changeset revisions. + +6. Add a comment to the tool_dependencies.xml file in the emboss_5 repository, eliminating the changeset_revision attribute so that it gets + automatically populated when uploaded. After uploading the file, the emboss5 repository should have 2 installable metadata revisions. + +7. Change the repository type of the package_x11_client_1_5_proto_7_0 repository to be tool_dependency_definition. + +8. Change the repository type of the package_emboss_5_0_0 repository to be tool_dependency_definition. + +9. Reset metadata on the package_emboss_5_0_0 repository. It should now have only it's tip as the installable revision. + +10. Reset metadata on the emboss_5 repository. It should now have only it's tip as the installable revision. +''' + +class TestEnvironmentInheritance( ShedTwillTestCase ): + '''Test referencing environment variables that were defined in a separate tool dependency.''' + + def test_0000_initiate_users_and_category( self ): + """Create necessary user accounts and login as an admin user.""" + self.logout() + self.login( email=common.admin_email, username=common.admin_username ) + admin_user = test_db_util.get_user( common.admin_email ) + assert admin_user is not None, 'Problem retrieving user with email %s from the database' % common.admin_email + admin_user_private_role = test_db_util.get_private_role( admin_user ) + self.create_category( name=category_name, description=category_description ) + self.logout() + self.login( email=common.test_user_2_email, username=common.test_user_2_name ) + test_user_2 = test_db_util.get_user( common.test_user_2_email ) + assert test_user_2 is not None, 'Problem retrieving user with email %s from the database' % common.test_user_2_email + test_user_2_private_role = test_db_util.get_private_role( test_user_2 ) + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + test_user_1 = test_db_util.get_user( common.test_user_1_email ) + assert test_user_1 is not None, 'Problem retrieving user with email %s from the database' % common.test_user_1_email + test_user_1_private_role = test_db_util.get_private_role( test_user_1 ) + + def test_0005_create_libx11_repository( self ): + '''Create and populate package_x11_client_1_5_proto_7_0_0470.''' + ''' + This is step 1 - Create and populate a repository named package_x11_client_1_5_proto_7_0. + + Create and populate a repository named package_x11_client_1_5_proto_7_0 that contains only a single file named tool_dependencies.xml. + Keep the repository type as the default "Unrestricted". + ''' + category = test_db_util.get_category_by_name( category_name ) + repository = self.get_or_create_repository( name=package_libx11_repository_name, + description=package_libx11_repository_description, + long_description=package_libx11_repository_long_description, + owner=common.test_user_1_name, + category_id=self.security.encode_id( category.id ), + strings_displayed=[] ) + # Upload the tool dependency definition to the package_x11_client_1_5_proto_7_0_0470 repository. + self.upload_file( repository, + filename='emboss/libx11_proto/first_tool_dependency/tool_dependencies.xml', + filepath=None, + valid_tools_only=True, + uncompress_file=False, + remove_repo_files_not_in_tar=False, + commit_message='Populate package_x11_client_1_5_proto_7_0_0470 with tool dependency definitions.', + strings_displayed=[], + strings_not_displayed=[] ) + + def test_0010_create_emboss_5_0_0_repository( self ): + '''Create and populate package_emboss_5_0_0_0470.''' + ''' + This is step 2 - Create a repository named package_emboss_5_0_0 of type "Unrestricted". + + Create a repository named package_emboss_5_0_0 of type "Unrestricted" that has a repository dependency definition that defines the + above package_x11_client_1_5_proto_7_0 repository. Upload the tool_dependencues.xml file such that it does not have a changeset_revision + defined so it will get automatically populated. + ''' + category = test_db_util.get_category_by_name( category_name ) + repository = self.get_or_create_repository( name=package_emboss_repository_name, + description=package_emboss_repository_description, + long_description=package_emboss_repository_long_description, + owner=common.test_user_1_name, + category_id=self.security.encode_id( category.id ), + strings_displayed=[] ) + # Upload the edited tool dependency definition to the package_emboss_5_0_0 repository. + self.upload_file( repository, + filename='emboss/emboss_5_0_0/first_tool_dependency/tool_dependencies.xml', + filepath=None, + valid_tools_only=True, + uncompress_file=False, + remove_repo_files_not_in_tar=False, + commit_message='Populate package_emboss_5_0_0_0470 with tool dependency definitions.', + strings_displayed=[], + strings_not_displayed=[] ) + + def test_0015_create_emboss_5_repository( self ): + '''Create and populate emboss_5_0470.''' + ''' + This is step 3 - Create a repository named emboss_5 of type "Unrestricted". + + Create a repository named emboss_5 of type "Unrestricted" that has a tool-dependencies.xml file defining a complex repository dependency + on the package_emboss_5_0_0 repository above. Upload the tool_dependencies.xml file such that it does not have a change set_revision defined + so it will get automatically populated. + ''' + category = test_db_util.get_category_by_name( category_name ) + repository = self.get_or_create_repository( name=emboss_repository_name, + description=emboss_repository_description, + long_description=emboss_repository_long_description, + owner=common.test_user_1_name, + category_id=self.security.encode_id( category.id ), + strings_displayed=[] ) + # Populate emboss_5 with tool and dependency definitions. + self.upload_file( repository, + filename='emboss/0470_files/emboss_complex_dependency.tar', + filepath=None, + valid_tools_only=True, + uncompress_file=True, + remove_repo_files_not_in_tar=False, + commit_message='Populate emboss_5 with tool and dependency definitions.', + strings_displayed=[], + strings_not_displayed=[] ) + + def test_0020_upload_updated_tool_dependency_to_package_x11( self ): + '''Upload a new tool_dependencies.xml to package_x11_client_1_5_proto_7_0_0470.''' + ''' + This is step 4 - Add a comment to the tool_dependencies.xml file to be uploaded to the package_x11_client_1_5_prot_7_0 repository, creating + a new installable changeset revision at the repository tip. + ''' + package_x11_repository = test_db_util.get_repository_by_name_and_owner( package_libx11_repository_name, common.test_user_1_name ) + # Upload the tool dependency definition to the package_x11_client_1_5_proto_7_0_0470 repository. + self.upload_file( package_x11_repository, + filename='emboss/libx11_proto/second_tool_dependency/tool_dependencies.xml', + filepath=None, + valid_tools_only=True, + uncompress_file=False, + remove_repo_files_not_in_tar=False, + commit_message='Populate package_x11_client_1_5_proto_7_0_0470 with tool dependency definitions.', + strings_displayed=[], + strings_not_displayed=[] ) + assert len( package_x11_repository.metadata_revisions ) == 1, 'package_x11_client_1_5_proto_7_0_0470 has incorrect number of metadata revisions' + + def test_0025_upload_updated_tool_dependency_to_package_emboss( self ): + '''Upload a new tool_dependencies.xml to package_emboss_5_0_0_0470.''' + ''' + This is step 5 - Add a comment to the tool_dependencies.xml file for the package_emboss_5_0_0 repository, eliminating + the change set_revision attribute so that it gets automatically populated when uploaded. After uploading the file, + the package_emboss_5_0_0 repository should have 2 installable changeset revisions. + ''' + package_emboss_repository = test_db_util.get_repository_by_name_and_owner( package_emboss_repository_name, common.test_user_1_name ) + # Populate package_emboss_5_0_0_0470 with updated tool dependency definition. + self.upload_file( package_emboss_repository, + filename='emboss/emboss_5_0_0/second_tool_dependency/tool_dependencies.xml', + filepath=None, + valid_tools_only=True, + uncompress_file=False, + remove_repo_files_not_in_tar=False, + commit_message='Populate package_emboss_5_0_0_0470 with tool dependency definitions.', + strings_displayed=[], + strings_not_displayed=[] ) + assert len( package_emboss_repository.metadata_revisions ) == 2, 'package_emboss_5_0_0_0470 has incorrect number of metadata revisions' + + def test_0030_upload_updated_tool_dependency_to_emboss_5_repository( self ): + '''Upload a new tool_dependencies.xml to emboss_5_0470.''' + ''' + This is step 6 - Add a comment to the tool_dependencies.xml file in the emboss_5 repository, eliminating the + changeset_revision attribute so that it gets automatically populated when uploaded. After uploading the file, + the emboss5 repository should have 2 installable metadata revisions. + ''' + emboss_repository = test_db_util.get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name ) + # Populate package_emboss_5_0_0_0470 with updated tool dependency definition. + self.upload_file( emboss_repository, + filename='emboss/0470_files/tool_dependencies.xml', + filepath=None, + valid_tools_only=True, + uncompress_file=False, + remove_repo_files_not_in_tar=False, + commit_message='Upload updated complex repository dependency definition to emboss_5_0470.', + strings_displayed=[], + strings_not_displayed=[] ) + assert len( emboss_repository.metadata_revisions ) == 2, 'package_emboss_5_0_0_0470 has incorrect number of metadata revisions' + + def test_0035_modify_package_x11_repository_type( self ): + '''Set package_x11_client_1_5_proto_7_0 type tool_dependency_definition.''' + ''' + This is step 7 - Change the repository type of the package_x11_client_1_5_proto_7_0 repository to be tool_dependency_definition. + ''' + package_x11_repository = test_db_util.get_repository_by_name_and_owner( package_libx11_repository_name, common.test_user_1_name ) + self.edit_repository_information( package_x11_repository, repository_type='tool_dependency_definition' ) + + def test_0040_modify_package_emboss_repository_type( self ): + '''Set package_emboss_5_0_0 to type tool_dependency_definition.''' + ''' + This is step 8 - Change the repository type of the package_emboss_5_0_0 repository to be tool_dependency_definition. + ''' + package_emboss_repository = test_db_util.get_repository_by_name_and_owner( package_emboss_repository_name, common.test_user_1_name ) + self.edit_repository_information( package_emboss_repository, repository_type='tool_dependency_definition' ) + + def test_0045_reset_repository_metadata( self ): + '''Reset metadata on package_emboss_5_0_0_0470 and package_x11_client_1_5_proto_7_0.''' + ''' + This is step 9 - Reset metadata on the package_emboss_5_0_0 and package_x11_client_1_5_proto_7_0 repositories. They should + now have only their tip as the installable revision. + ''' + package_emboss_repository = test_db_util.get_repository_by_name_and_owner( package_emboss_repository_name, common.test_user_1_name ) + package_x11_repository = test_db_util.get_repository_by_name_and_owner( package_libx11_repository_name, common.test_user_1_name ) + self.reset_repository_metadata( package_emboss_repository ) + self.reset_repository_metadata( package_x11_repository ) + assert len( package_emboss_repository.metadata_revisions ) == 1, 'Repository package_emboss_5_0_0 has %d installable revisions, expected 1.' % \ + len( package_emboss_repository.metadata_revisions ) + assert len( package_x11_repository.metadata_revisions ) == 1, 'Repository package_x11_client_1_5_proto_7_0 has %d installable revisions, expected 1.' % \ + len( package_x11_repository.metadata_revisions ) + + def test_0050_reset_emboss_5_metadata( self ): + '''Reset metadata on emboss_5.''' + ''' + This is step 10 - Reset metadata on the emboss_5 repository. It should now have only it's tip as the installable revision. + ''' + emboss_repository = test_db_util.get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name ) + self.reset_repository_metadata( emboss_repository ) + assert len( emboss_repository.metadata_revisions ) == 1, 'Repository emboss_5 has %d installable revisions, expected 1.' % \ + len( emboss_repository.metadata_revisions ) diff -r 27b458743a117b5fb119915dc89bddc017625146 -r 881a16a718913fad393369059afe982ecb6b77bc 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 @@ -56,7 +56,7 @@ uncompress_file=False, remove_repo_files_not_in_tar=False, commit_message='Uploaded tool_dependencies.xml.', - strings_displayed=[ 'The settings for <b>name</b>, <b>version</b> and <b>type</b> from a contained tool' ], + strings_displayed=[ 'This repository currently contains a single file named <b>tool_dependencies.xml</b>' ], strings_not_displayed=[] ) self.display_manage_repository_page( repository, strings_displayed=[ 'Tool dependencies', 'may not be', 'in this repository' ] ) @@ -262,13 +262,9 @@ '''Verify that the generated env.sh contains the right data.''' base_repository = test_db_util.get_installed_repository_by_name_owner( bwa_base_repository_name, common.test_user_1_name ) tool_repository = test_db_util.get_installed_repository_by_name_owner( bwa_package_repository_name, common.test_user_1_name ) - env_sh_path = os.path.join( self.galaxy_tool_dependency_dir, - 'bwa', - '0.5.9', - base_repository.owner, - base_repository.name, - base_repository.installed_changeset_revision, - 'env.sh' ) + env_sh_path = self.get_env_sh_path( tool_dependency_name='bwa', + tool_dependency_version='0.5.9', + repository=base_repository ) assert os.path.exists( env_sh_path ), 'env.sh was not generated in %s for this dependency.' % env_sh_path contents = file( env_sh_path, 'r' ).read() if tool_repository.installed_changeset_revision not in contents: diff -r 27b458743a117b5fb119915dc89bddc017625146 -r 881a16a718913fad393369059afe982ecb6b77bc test/tool_shed/test_data/emboss/0470_files/emboss_complex_dependency.tar Binary file test/tool_shed/test_data/emboss/0470_files/emboss_complex_dependency.tar has changed diff -r 27b458743a117b5fb119915dc89bddc017625146 -r 881a16a718913fad393369059afe982ecb6b77bc test/tool_shed/test_data/emboss/0470_files/tool_dependencies.xml --- /dev/null +++ b/test/tool_shed/test_data/emboss/0470_files/tool_dependencies.xml @@ -0,0 +1,7 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="emboss" version="5.0.0"> +  + <repository name="package_emboss_5_0_0_0470" owner="user1" /> + </package> +</tool_dependency> diff -r 27b458743a117b5fb119915dc89bddc017625146 -r 881a16a718913fad393369059afe982ecb6b77bc test/tool_shed/test_data/emboss/emboss_5_0_0/first_tool_dependency/tool_dependencies.xml --- /dev/null +++ b/test/tool_shed/test_data/emboss/emboss_5_0_0/first_tool_dependency/tool_dependencies.xml @@ -0,0 +1,48 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="libx11" version="1.5.0"> + <repository name="package_x11_client_1_5_proto_7_0_0470" owner="user1" prior_installation_required="True" /> + </package> + <package name="emboss" version="5.0.0"> + <install version="1.0"> + <actions> + <action type="download_by_url">ftp://emboss.open-bio.org/pub/EMBOSS/old/5.0.0/EMBOSS-5.0.0.tar.gz</action> + <action type="set_environment_for_install"> + <repository name="package_x11_client_1_5_proto_7_0_0470" owner="user1" prior_installation_required="True"> + <package name="libx11" version="1.5.0" /> + </repository> + </action> + <action type="template_command"> + #if env.get('X11_LIB_DIR', False) and env.get('X11_INCLUDE_DIR', False): + ./configure --prefix=$env.INSTALL_DIR --x-includes=$env.X11_INCLUDE_DIR --x-libraries=$env.X11_LIB_DIR + #else: + ./configure --prefix=$env.INSTALL_DIR + #end if + </action> + <action type="shell_command">make && make install</action> + <action extract="true" type="download_file">ftp://emboss.open-bio.org/pub/EMBOSS/old/5.0.0/PHYLIP-3.6b.tar.gz</action> + <action type="change_directory">PHYLIP-3.6b</action> + <action type="template_command"> + #if env.get('X11_LIB_DIR', False) and env.get('X11_INCLUDE_DIR', False): + ./configure --prefix=$env.INSTALL_DIR --x-includes=$env.X11_INCLUDE_DIR --x-libraries=$env.X11_LIB_DIR CFLAGS='-I$env.INSTALL_DIR/include' + #else: + ./configure --prefix=$env.INSTALL_DIR + #end if + </action> + <action type="shell_command">make && make install</action> + <action type="set_environment"> + <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> + </action> + </actions> + </install> + <readme> +These links provide information for building the Emboss package in most environments. + +System requirements +http://emboss.sourceforge.net/download/#Requirements + +Platform-dependent notes +http://emboss.sourceforge.net/download/#Platforms + </readme> + </package> +</tool_dependency> \ No newline at end of file diff -r 27b458743a117b5fb119915dc89bddc017625146 -r 881a16a718913fad393369059afe982ecb6b77bc test/tool_shed/test_data/emboss/emboss_5_0_0/second_tool_dependency/tool_dependencies.xml --- /dev/null +++ b/test/tool_shed/test_data/emboss/emboss_5_0_0/second_tool_dependency/tool_dependencies.xml @@ -0,0 +1,49 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="libx11" version="1.5.0"> + <repository name="package_x11_client_1_5_proto_7_0_0470" owner="user1" prior_installation_required="True" /> + </package> + <package name="emboss" version="5.0.0"> + <install version="1.0"> + <actions> +  + <action type="download_by_url">ftp://emboss.open-bio.org/pub/EMBOSS/old/5.0.0/EMBOSS-5.0.0.tar.gz</action> + <action type="set_environment_for_install"> + <repository name="package_x11_client_1_5_proto_7_0_0470" owner="user1" prior_installation_required="True"> + <package name="libx11" version="1.5.0" /> + </repository> + </action> + <action type="template_command"> + #if env.get('X11_LIB_DIR', False) and env.get('X11_INCLUDE_DIR', False): + ./configure --prefix=$env.INSTALL_DIR --x-includes=$env.X11_INCLUDE_DIR --x-libraries=$env.X11_LIB_DIR + #else: + ./configure --prefix=$env.INSTALL_DIR + #end if + </action> + <action type="shell_command">make && make install</action> + <action extract="true" type="download_file">ftp://emboss.open-bio.org/pub/EMBOSS/old/5.0.0/PHYLIP-3.6b.tar.gz</action> + <action type="change_directory">PHYLIP-3.6b</action> + <action type="template_command"> + #if env.get('X11_LIB_DIR', False) and env.get('X11_INCLUDE_DIR', False): + ./configure --prefix=$env.INSTALL_DIR --x-includes=$env.X11_INCLUDE_DIR --x-libraries=$env.X11_LIB_DIR CFLAGS='-I$env.INSTALL_DIR/include' + #else: + ./configure --prefix=$env.INSTALL_DIR + #end if + </action> + <action type="shell_command">make && make install</action> + <action type="set_environment"> + <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> + </action> + </actions> + </install> + <readme> +These links provide information for building the Emboss package in most environments. + +System requirements +http://emboss.sourceforge.net/download/#Requirements + +Platform-dependent notes +http://emboss.sourceforge.net/download/#Platforms + </readme> + </package> +</tool_dependency> \ No newline at end of file diff -r 27b458743a117b5fb119915dc89bddc017625146 -r 881a16a718913fad393369059afe982ecb6b77bc test/tool_shed/test_data/emboss/libx11_proto/first_tool_dependency/tool_dependencies.xml --- /dev/null +++ b/test/tool_shed/test_data/emboss/libx11_proto/first_tool_dependency/tool_dependencies.xml @@ -0,0 +1,22 @@ +<tool_dependency> + <package name="libx11" version="1.5.0"> + <install version="1.0"> + <actions> + <action type="download_by_url">ftp://ftp.x.org/pub/X11R7.7/src/proto/xproto-7.0.23.tar.bz2</action> + <action type="shell_command">./configure --prefix=$INSTALL_DIR</action> + <action type="shell_command">make && make install</action> + <action type="set_environment"> + <environment_variable name="X11_INCLUDE_DIR" action="set_to">$INSTALL_DIR/include</environment_variable> + </action> + <action type="download_file" extract="true">ftp://ftp.x.org/pub/X11R7.7/src/lib/libX11-1.5.0.tar.bz2</action> + <action type="change_directory">libX11-1.5.0</action> + <action type="shell_command">./configure --prefix=$INSTALL_DIR CFLAGS='-I$INSTALL_DIR/include'</action> + <action type="shell_command">make && make install</action> + <action type="set_environment"> + <environment_variable name="X11_LIB_DIR" action="set_to">$INSTALL_DIR/lib</environment_variable> + </action> + </actions> + </install> + <readme>Xlib is an X Window System protocol client library written in the C programming language. It contains functions for interacting with an X server. These functions allow programmers to write programs without knowing the details of the protocol. Few applications use Xlib directly; rather, they employ other libraries that use Xlib functions to provide widget toolkits.</readme> + </package> +</tool_dependency> \ No newline at end of file diff -r 27b458743a117b5fb119915dc89bddc017625146 -r 881a16a718913fad393369059afe982ecb6b77bc test/tool_shed/test_data/emboss/libx11_proto/second_tool_dependency/tool_dependencies.xml --- /dev/null +++ b/test/tool_shed/test_data/emboss/libx11_proto/second_tool_dependency/tool_dependencies.xml @@ -0,0 +1,23 @@ +<tool_dependency> + <package name="libx11" version="1.5.0"> + <install version="1.0"> + <actions> +  + <action type="download_by_url">ftp://ftp.x.org/pub/X11R7.7/src/proto/xproto-7.0.23.tar.bz2</action> + <action type="shell_command">./configure --prefix=$INSTALL_DIR</action> + <action type="shell_command">make && make install</action> + <action type="set_environment"> + <environment_variable name="X11_INCLUDE_DIR" action="set_to">$INSTALL_DIR/include</environment_variable> + </action> + <action type="download_file" extract="true">ftp://ftp.x.org/pub/X11R7.7/src/lib/libX11-1.5.0.tar.bz2</action> + <action type="change_directory">libX11-1.5.0</action> + <action type="shell_command">./configure --prefix=$INSTALL_DIR CFLAGS='-I$INSTALL_DIR/include'</action> + <action type="shell_command">make && make install</action> + <action type="set_environment"> + <environment_variable name="X11_LIB_DIR" action="set_to">$INSTALL_DIR/lib</environment_variable> + </action> + </actions> + </install> + <readme>Xlib is an X Window System protocol client library written in the C programming language. It contains functions for interacting with an X server. These functions allow programmers to write programs without knowing the details of the protocol. Few applications use Xlib directly; rather, they employ other libraries that use Xlib functions to provide widget toolkits.</readme> + </package> +</tool_dependency> \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/commits/6fa490b703b0/ Changeset: 6fa490b703b0 User: Dave Bouvier Date: 2013-07-24 16:58:05 Summary: Merged in changes. Affected #: 9 files diff -r 528bee4dd14addc5db2b59a0a229e3aa441f8fda -r 6fa490b703b062231da599fdd7f169d84eddc930 test/tool_shed/base/twilltestcase.py --- a/test/tool_shed/base/twilltestcase.py +++ b/test/tool_shed/base/twilltestcase.py @@ -453,15 +453,15 @@ original_information = dict( repo_name=repository.name, description=repository.description, long_description=repository.long_description ) strings_displayed = [] strings_not_displayed = [] - for input_elem_name in [ 'repo_name', 'description', 'long_description' ]: + for input_elem_name in [ 'repo_name', 'description', 'long_description', 'repository_type' ]: if input_elem_name in kwd: - tc.fv( "1", input_elem_name, kwd[ input_elem_name ] ) + tc.fv( "edit_repository", input_elem_name, kwd[ input_elem_name ] ) strings_displayed.append( self.escape_html( kwd[ input_elem_name ] ) ) tc.submit( "edit_repository_button" ) self.check_for_strings( strings_displayed ) strings_displayed = [] for input_elem_name in [ 'repo_name', 'description', 'long_description' ]: - tc.fv( "1", input_elem_name, original_information[ input_elem_name ] ) + tc.fv( "edit_repository", input_elem_name, original_information[ input_elem_name ] ) strings_displayed.append( self.escape_html( original_information[ input_elem_name ] ) ) tc.submit( "edit_repository_button" ) self.check_for_strings( strings_displayed ) @@ -577,6 +577,16 @@ return datatypes_count.group( 1 ) return None + def get_env_sh_path( self, tool_dependency_name, tool_dependency_version, repository ): + env_sh_path = os.path.join( self.galaxy_tool_dependency_dir, + tool_dependency_name, + tool_dependency_version, + repository.owner, + repository.name, + repository.installed_changeset_revision, + 'env.sh' ) + return env_sh_path + def get_filename( self, filename, filepath=None ): if filepath is not None: return os.path.abspath( os.path.join( filepath, filename ) ) diff -r 528bee4dd14addc5db2b59a0a229e3aa441f8fda -r 6fa490b703b062231da599fdd7f169d84eddc930 test/tool_shed/functional/test_0470_tool_dependency_repository_type.py --- /dev/null +++ b/test/tool_shed/functional/test_0470_tool_dependency_repository_type.py @@ -0,0 +1,253 @@ +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__ ) + +category_name = 'Test 0470 Tool dependency repository type' +category_description = 'Test script 0470 for changing repository types.' +package_libx11_repository_name = 'package_x11_client_1_5_proto_7_0_0470' +package_libx11_repository_description = "Contains a tool dependency definition that provides the X11 client libraries and core protocol header files." +package_libx11_repository_long_description = "Xlib is an X Window System protocol client library written in the C programming language." +package_emboss_repository_name = 'package_emboss_5_0_0_0470' +package_emboss_repository_description = "Contains a tool dependency definition that downloads and compiles version 5.0.0 of the EMBOSS tool suite." +package_emboss_repository_long_description = 'EMBOSS is "The European Molecular Biology Open Software Suite".' +datatypes_repository_name = 'emboss_datatypes_0470' +datatypes_repository_description = 'Galaxy applicable data formats used by Emboss tools.' +datatypes_repository_long_description = 'Galaxy applicable data formats used by Emboss tools. This repository contains no tools.' +emboss_repository_name = 'emboss_5_0470' +emboss_repository_description = "Galaxy wrappers for Emboss version 5.0.0 tools" +emboss_repository_long_description = "Galaxy wrappers for Emboss version 5.0.0 tools" + +''' +1. Create and populate a repository named package_x11_client_1_5_proto_7_0 that contains only a single file named tool_dependencies.xml. + Keep the repository type as the default "Unrestricted". + +2. Create a repository named package_emboss_5_0_0 of type "Unrestricted" that has a repository dependency definition that defines the + above package_x11_client_1_5_proto_7_0 repository. Upload the tool_dependencies.xml file such that it does not have a changeset_revision + defined so it will get automatically populated. + +3. Create a repository named emboss_5 of type "Unrestricted" that has a tool-dependencies.xml file defining a complex repository dependency + on the package_emboss_5_0_0 repository above. Upload the tool_dependencies.xml file such that it does not have a change set_revision defined + so it will get automatically populated. + +4. Add a comment to the tool_dependencies.xml file to be uploaded to the package_x11_client_1_5_prot_7_0 repository, creating a new installable + changeset revision at the repository tip. + +5. Add a comment to the tool_dependencies.xml file for the package_emboss_5_0_0 repository, eliminating the change set_revision attribute so + that it gets automatically populated when uploaded. After uploading the file, the package_emboss_5_0_0 repository should have 2 + installable changeset revisions. + +6. Add a comment to the tool_dependencies.xml file in the emboss_5 repository, eliminating the changeset_revision attribute so that it gets + automatically populated when uploaded. After uploading the file, the emboss5 repository should have 2 installable metadata revisions. + +7. Change the repository type of the package_x11_client_1_5_proto_7_0 repository to be tool_dependency_definition. + +8. Change the repository type of the package_emboss_5_0_0 repository to be tool_dependency_definition. + +9. Reset metadata on the package_emboss_5_0_0 repository. It should now have only it's tip as the installable revision. + +10. Reset metadata on the emboss_5 repository. It should now have only it's tip as the installable revision. +''' + +class TestEnvironmentInheritance( ShedTwillTestCase ): + '''Test referencing environment variables that were defined in a separate tool dependency.''' + + def test_0000_initiate_users_and_category( self ): + """Create necessary user accounts and login as an admin user.""" + self.logout() + self.login( email=common.admin_email, username=common.admin_username ) + admin_user = test_db_util.get_user( common.admin_email ) + assert admin_user is not None, 'Problem retrieving user with email %s from the database' % common.admin_email + admin_user_private_role = test_db_util.get_private_role( admin_user ) + self.create_category( name=category_name, description=category_description ) + self.logout() + self.login( email=common.test_user_2_email, username=common.test_user_2_name ) + test_user_2 = test_db_util.get_user( common.test_user_2_email ) + assert test_user_2 is not None, 'Problem retrieving user with email %s from the database' % common.test_user_2_email + test_user_2_private_role = test_db_util.get_private_role( test_user_2 ) + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + test_user_1 = test_db_util.get_user( common.test_user_1_email ) + assert test_user_1 is not None, 'Problem retrieving user with email %s from the database' % common.test_user_1_email + test_user_1_private_role = test_db_util.get_private_role( test_user_1 ) + + def test_0005_create_libx11_repository( self ): + '''Create and populate package_x11_client_1_5_proto_7_0_0470.''' + ''' + This is step 1 - Create and populate a repository named package_x11_client_1_5_proto_7_0. + + Create and populate a repository named package_x11_client_1_5_proto_7_0 that contains only a single file named tool_dependencies.xml. + Keep the repository type as the default "Unrestricted". + ''' + category = test_db_util.get_category_by_name( category_name ) + repository = self.get_or_create_repository( name=package_libx11_repository_name, + description=package_libx11_repository_description, + long_description=package_libx11_repository_long_description, + owner=common.test_user_1_name, + category_id=self.security.encode_id( category.id ), + strings_displayed=[] ) + # Upload the tool dependency definition to the package_x11_client_1_5_proto_7_0_0470 repository. + self.upload_file( repository, + filename='emboss/libx11_proto/first_tool_dependency/tool_dependencies.xml', + filepath=None, + valid_tools_only=True, + uncompress_file=False, + remove_repo_files_not_in_tar=False, + commit_message='Populate package_x11_client_1_5_proto_7_0_0470 with tool dependency definitions.', + strings_displayed=[], + strings_not_displayed=[] ) + + def test_0010_create_emboss_5_0_0_repository( self ): + '''Create and populate package_emboss_5_0_0_0470.''' + ''' + This is step 2 - Create a repository named package_emboss_5_0_0 of type "Unrestricted". + + Create a repository named package_emboss_5_0_0 of type "Unrestricted" that has a repository dependency definition that defines the + above package_x11_client_1_5_proto_7_0 repository. Upload the tool_dependencues.xml file such that it does not have a changeset_revision + defined so it will get automatically populated. + ''' + category = test_db_util.get_category_by_name( category_name ) + repository = self.get_or_create_repository( name=package_emboss_repository_name, + description=package_emboss_repository_description, + long_description=package_emboss_repository_long_description, + owner=common.test_user_1_name, + category_id=self.security.encode_id( category.id ), + strings_displayed=[] ) + # Upload the edited tool dependency definition to the package_emboss_5_0_0 repository. + self.upload_file( repository, + filename='emboss/emboss_5_0_0/first_tool_dependency/tool_dependencies.xml', + filepath=None, + valid_tools_only=True, + uncompress_file=False, + remove_repo_files_not_in_tar=False, + commit_message='Populate package_emboss_5_0_0_0470 with tool dependency definitions.', + strings_displayed=[], + strings_not_displayed=[] ) + + def test_0015_create_emboss_5_repository( self ): + '''Create and populate emboss_5_0470.''' + ''' + This is step 3 - Create a repository named emboss_5 of type "Unrestricted". + + Create a repository named emboss_5 of type "Unrestricted" that has a tool-dependencies.xml file defining a complex repository dependency + on the package_emboss_5_0_0 repository above. Upload the tool_dependencies.xml file such that it does not have a change set_revision defined + so it will get automatically populated. + ''' + category = test_db_util.get_category_by_name( category_name ) + repository = self.get_or_create_repository( name=emboss_repository_name, + description=emboss_repository_description, + long_description=emboss_repository_long_description, + owner=common.test_user_1_name, + category_id=self.security.encode_id( category.id ), + strings_displayed=[] ) + # Populate emboss_5 with tool and dependency definitions. + self.upload_file( repository, + filename='emboss/0470_files/emboss_complex_dependency.tar', + filepath=None, + valid_tools_only=True, + uncompress_file=True, + remove_repo_files_not_in_tar=False, + commit_message='Populate emboss_5 with tool and dependency definitions.', + strings_displayed=[], + strings_not_displayed=[] ) + + def test_0020_upload_updated_tool_dependency_to_package_x11( self ): + '''Upload a new tool_dependencies.xml to package_x11_client_1_5_proto_7_0_0470.''' + ''' + This is step 4 - Add a comment to the tool_dependencies.xml file to be uploaded to the package_x11_client_1_5_prot_7_0 repository, creating + a new installable changeset revision at the repository tip. + ''' + package_x11_repository = test_db_util.get_repository_by_name_and_owner( package_libx11_repository_name, common.test_user_1_name ) + # Upload the tool dependency definition to the package_x11_client_1_5_proto_7_0_0470 repository. + self.upload_file( package_x11_repository, + filename='emboss/libx11_proto/second_tool_dependency/tool_dependencies.xml', + filepath=None, + valid_tools_only=True, + uncompress_file=False, + remove_repo_files_not_in_tar=False, + commit_message='Populate package_x11_client_1_5_proto_7_0_0470 with tool dependency definitions.', + strings_displayed=[], + strings_not_displayed=[] ) + assert len( package_x11_repository.metadata_revisions ) == 1, 'package_x11_client_1_5_proto_7_0_0470 has incorrect number of metadata revisions' + + def test_0025_upload_updated_tool_dependency_to_package_emboss( self ): + '''Upload a new tool_dependencies.xml to package_emboss_5_0_0_0470.''' + ''' + This is step 5 - Add a comment to the tool_dependencies.xml file for the package_emboss_5_0_0 repository, eliminating + the change set_revision attribute so that it gets automatically populated when uploaded. After uploading the file, + the package_emboss_5_0_0 repository should have 2 installable changeset revisions. + ''' + package_emboss_repository = test_db_util.get_repository_by_name_and_owner( package_emboss_repository_name, common.test_user_1_name ) + # Populate package_emboss_5_0_0_0470 with updated tool dependency definition. + self.upload_file( package_emboss_repository, + filename='emboss/emboss_5_0_0/second_tool_dependency/tool_dependencies.xml', + filepath=None, + valid_tools_only=True, + uncompress_file=False, + remove_repo_files_not_in_tar=False, + commit_message='Populate package_emboss_5_0_0_0470 with tool dependency definitions.', + strings_displayed=[], + strings_not_displayed=[] ) + assert len( package_emboss_repository.metadata_revisions ) == 2, 'package_emboss_5_0_0_0470 has incorrect number of metadata revisions' + + def test_0030_upload_updated_tool_dependency_to_emboss_5_repository( self ): + '''Upload a new tool_dependencies.xml to emboss_5_0470.''' + ''' + This is step 6 - Add a comment to the tool_dependencies.xml file in the emboss_5 repository, eliminating the + changeset_revision attribute so that it gets automatically populated when uploaded. After uploading the file, + the emboss5 repository should have 2 installable metadata revisions. + ''' + emboss_repository = test_db_util.get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name ) + # Populate package_emboss_5_0_0_0470 with updated tool dependency definition. + self.upload_file( emboss_repository, + filename='emboss/0470_files/tool_dependencies.xml', + filepath=None, + valid_tools_only=True, + uncompress_file=False, + remove_repo_files_not_in_tar=False, + commit_message='Upload updated complex repository dependency definition to emboss_5_0470.', + strings_displayed=[], + strings_not_displayed=[] ) + assert len( emboss_repository.metadata_revisions ) == 2, 'package_emboss_5_0_0_0470 has incorrect number of metadata revisions' + + def test_0035_modify_package_x11_repository_type( self ): + '''Set package_x11_client_1_5_proto_7_0 type tool_dependency_definition.''' + ''' + This is step 7 - Change the repository type of the package_x11_client_1_5_proto_7_0 repository to be tool_dependency_definition. + ''' + package_x11_repository = test_db_util.get_repository_by_name_and_owner( package_libx11_repository_name, common.test_user_1_name ) + self.edit_repository_information( package_x11_repository, repository_type='tool_dependency_definition' ) + + def test_0040_modify_package_emboss_repository_type( self ): + '''Set package_emboss_5_0_0 to type tool_dependency_definition.''' + ''' + This is step 8 - Change the repository type of the package_emboss_5_0_0 repository to be tool_dependency_definition. + ''' + package_emboss_repository = test_db_util.get_repository_by_name_and_owner( package_emboss_repository_name, common.test_user_1_name ) + self.edit_repository_information( package_emboss_repository, repository_type='tool_dependency_definition' ) + + def test_0045_reset_repository_metadata( self ): + '''Reset metadata on package_emboss_5_0_0_0470 and package_x11_client_1_5_proto_7_0.''' + ''' + This is step 9 - Reset metadata on the package_emboss_5_0_0 and package_x11_client_1_5_proto_7_0 repositories. They should + now have only their tip as the installable revision. + ''' + package_emboss_repository = test_db_util.get_repository_by_name_and_owner( package_emboss_repository_name, common.test_user_1_name ) + package_x11_repository = test_db_util.get_repository_by_name_and_owner( package_libx11_repository_name, common.test_user_1_name ) + self.reset_repository_metadata( package_emboss_repository ) + self.reset_repository_metadata( package_x11_repository ) + assert len( package_emboss_repository.metadata_revisions ) == 1, 'Repository package_emboss_5_0_0 has %d installable revisions, expected 1.' % \ + len( package_emboss_repository.metadata_revisions ) + assert len( package_x11_repository.metadata_revisions ) == 1, 'Repository package_x11_client_1_5_proto_7_0 has %d installable revisions, expected 1.' % \ + len( package_x11_repository.metadata_revisions ) + + def test_0050_reset_emboss_5_metadata( self ): + '''Reset metadata on emboss_5.''' + ''' + This is step 10 - Reset metadata on the emboss_5 repository. It should now have only it's tip as the installable revision. + ''' + emboss_repository = test_db_util.get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name ) + self.reset_repository_metadata( emboss_repository ) + assert len( emboss_repository.metadata_revisions ) == 1, 'Repository emboss_5 has %d installable revisions, expected 1.' % \ + len( emboss_repository.metadata_revisions ) diff -r 528bee4dd14addc5db2b59a0a229e3aa441f8fda -r 6fa490b703b062231da599fdd7f169d84eddc930 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 @@ -56,7 +56,7 @@ uncompress_file=False, remove_repo_files_not_in_tar=False, commit_message='Uploaded tool_dependencies.xml.', - strings_displayed=[ 'The settings for <b>name</b>, <b>version</b> and <b>type</b> from a contained tool' ], + strings_displayed=[ 'This repository currently contains a single file named <b>tool_dependencies.xml</b>' ], strings_not_displayed=[] ) self.display_manage_repository_page( repository, strings_displayed=[ 'Tool dependencies', 'may not be', 'in this repository' ] ) @@ -262,13 +262,9 @@ '''Verify that the generated env.sh contains the right data.''' base_repository = test_db_util.get_installed_repository_by_name_owner( bwa_base_repository_name, common.test_user_1_name ) tool_repository = test_db_util.get_installed_repository_by_name_owner( bwa_package_repository_name, common.test_user_1_name ) - env_sh_path = os.path.join( self.galaxy_tool_dependency_dir, - 'bwa', - '0.5.9', - base_repository.owner, - base_repository.name, - base_repository.installed_changeset_revision, - 'env.sh' ) + env_sh_path = self.get_env_sh_path( tool_dependency_name='bwa', + tool_dependency_version='0.5.9', + repository=base_repository ) assert os.path.exists( env_sh_path ), 'env.sh was not generated in %s for this dependency.' % env_sh_path contents = file( env_sh_path, 'r' ).read() if tool_repository.installed_changeset_revision not in contents: diff -r 528bee4dd14addc5db2b59a0a229e3aa441f8fda -r 6fa490b703b062231da599fdd7f169d84eddc930 test/tool_shed/test_data/emboss/0470_files/emboss_complex_dependency.tar Binary file test/tool_shed/test_data/emboss/0470_files/emboss_complex_dependency.tar has changed diff -r 528bee4dd14addc5db2b59a0a229e3aa441f8fda -r 6fa490b703b062231da599fdd7f169d84eddc930 test/tool_shed/test_data/emboss/0470_files/tool_dependencies.xml --- /dev/null +++ b/test/tool_shed/test_data/emboss/0470_files/tool_dependencies.xml @@ -0,0 +1,7 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="emboss" version="5.0.0"> +  + <repository name="package_emboss_5_0_0_0470" owner="user1" /> + </package> +</tool_dependency> diff -r 528bee4dd14addc5db2b59a0a229e3aa441f8fda -r 6fa490b703b062231da599fdd7f169d84eddc930 test/tool_shed/test_data/emboss/emboss_5_0_0/first_tool_dependency/tool_dependencies.xml --- /dev/null +++ b/test/tool_shed/test_data/emboss/emboss_5_0_0/first_tool_dependency/tool_dependencies.xml @@ -0,0 +1,48 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="libx11" version="1.5.0"> + <repository name="package_x11_client_1_5_proto_7_0_0470" owner="user1" prior_installation_required="True" /> + </package> + <package name="emboss" version="5.0.0"> + <install version="1.0"> + <actions> + <action type="download_by_url">ftp://emboss.open-bio.org/pub/EMBOSS/old/5.0.0/EMBOSS-5.0.0.tar.gz</action> + <action type="set_environment_for_install"> + <repository name="package_x11_client_1_5_proto_7_0_0470" owner="user1" prior_installation_required="True"> + <package name="libx11" version="1.5.0" /> + </repository> + </action> + <action type="template_command"> + #if env.get('X11_LIB_DIR', False) and env.get('X11_INCLUDE_DIR', False): + ./configure --prefix=$env.INSTALL_DIR --x-includes=$env.X11_INCLUDE_DIR --x-libraries=$env.X11_LIB_DIR + #else: + ./configure --prefix=$env.INSTALL_DIR + #end if + </action> + <action type="shell_command">make && make install</action> + <action extract="true" type="download_file">ftp://emboss.open-bio.org/pub/EMBOSS/old/5.0.0/PHYLIP-3.6b.tar.gz</action> + <action type="change_directory">PHYLIP-3.6b</action> + <action type="template_command"> + #if env.get('X11_LIB_DIR', False) and env.get('X11_INCLUDE_DIR', False): + ./configure --prefix=$env.INSTALL_DIR --x-includes=$env.X11_INCLUDE_DIR --x-libraries=$env.X11_LIB_DIR CFLAGS='-I$env.INSTALL_DIR/include' + #else: + ./configure --prefix=$env.INSTALL_DIR + #end if + </action> + <action type="shell_command">make && make install</action> + <action type="set_environment"> + <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> + </action> + </actions> + </install> + <readme> +These links provide information for building the Emboss package in most environments. + +System requirements +http://emboss.sourceforge.net/download/#Requirements + +Platform-dependent notes +http://emboss.sourceforge.net/download/#Platforms + </readme> + </package> +</tool_dependency> \ No newline at end of file diff -r 528bee4dd14addc5db2b59a0a229e3aa441f8fda -r 6fa490b703b062231da599fdd7f169d84eddc930 test/tool_shed/test_data/emboss/emboss_5_0_0/second_tool_dependency/tool_dependencies.xml --- /dev/null +++ b/test/tool_shed/test_data/emboss/emboss_5_0_0/second_tool_dependency/tool_dependencies.xml @@ -0,0 +1,49 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="libx11" version="1.5.0"> + <repository name="package_x11_client_1_5_proto_7_0_0470" owner="user1" prior_installation_required="True" /> + </package> + <package name="emboss" version="5.0.0"> + <install version="1.0"> + <actions> +  + <action type="download_by_url">ftp://emboss.open-bio.org/pub/EMBOSS/old/5.0.0/EMBOSS-5.0.0.tar.gz</action> + <action type="set_environment_for_install"> + <repository name="package_x11_client_1_5_proto_7_0_0470" owner="user1" prior_installation_required="True"> + <package name="libx11" version="1.5.0" /> + </repository> + </action> + <action type="template_command"> + #if env.get('X11_LIB_DIR', False) and env.get('X11_INCLUDE_DIR', False): + ./configure --prefix=$env.INSTALL_DIR --x-includes=$env.X11_INCLUDE_DIR --x-libraries=$env.X11_LIB_DIR + #else: + ./configure --prefix=$env.INSTALL_DIR + #end if + </action> + <action type="shell_command">make && make install</action> + <action extract="true" type="download_file">ftp://emboss.open-bio.org/pub/EMBOSS/old/5.0.0/PHYLIP-3.6b.tar.gz</action> + <action type="change_directory">PHYLIP-3.6b</action> + <action type="template_command"> + #if env.get('X11_LIB_DIR', False) and env.get('X11_INCLUDE_DIR', False): + ./configure --prefix=$env.INSTALL_DIR --x-includes=$env.X11_INCLUDE_DIR --x-libraries=$env.X11_LIB_DIR CFLAGS='-I$env.INSTALL_DIR/include' + #else: + ./configure --prefix=$env.INSTALL_DIR + #end if + </action> + <action type="shell_command">make && make install</action> + <action type="set_environment"> + <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> + </action> + </actions> + </install> + <readme> +These links provide information for building the Emboss package in most environments. + +System requirements +http://emboss.sourceforge.net/download/#Requirements + +Platform-dependent notes +http://emboss.sourceforge.net/download/#Platforms + </readme> + </package> +</tool_dependency> \ No newline at end of file diff -r 528bee4dd14addc5db2b59a0a229e3aa441f8fda -r 6fa490b703b062231da599fdd7f169d84eddc930 test/tool_shed/test_data/emboss/libx11_proto/first_tool_dependency/tool_dependencies.xml --- /dev/null +++ b/test/tool_shed/test_data/emboss/libx11_proto/first_tool_dependency/tool_dependencies.xml @@ -0,0 +1,22 @@ +<tool_dependency> + <package name="libx11" version="1.5.0"> + <install version="1.0"> + <actions> + <action type="download_by_url">ftp://ftp.x.org/pub/X11R7.7/src/proto/xproto-7.0.23.tar.bz2</action> + <action type="shell_command">./configure --prefix=$INSTALL_DIR</action> + <action type="shell_command">make && make install</action> + <action type="set_environment"> + <environment_variable name="X11_INCLUDE_DIR" action="set_to">$INSTALL_DIR/include</environment_variable> + </action> + <action type="download_file" extract="true">ftp://ftp.x.org/pub/X11R7.7/src/lib/libX11-1.5.0.tar.bz2</action> + <action type="change_directory">libX11-1.5.0</action> + <action type="shell_command">./configure --prefix=$INSTALL_DIR CFLAGS='-I$INSTALL_DIR/include'</action> + <action type="shell_command">make && make install</action> + <action type="set_environment"> + <environment_variable name="X11_LIB_DIR" action="set_to">$INSTALL_DIR/lib</environment_variable> + </action> + </actions> + </install> + <readme>Xlib is an X Window System protocol client library written in the C programming language. It contains functions for interacting with an X server. These functions allow programmers to write programs without knowing the details of the protocol. Few applications use Xlib directly; rather, they employ other libraries that use Xlib functions to provide widget toolkits.</readme> + </package> +</tool_dependency> \ No newline at end of file diff -r 528bee4dd14addc5db2b59a0a229e3aa441f8fda -r 6fa490b703b062231da599fdd7f169d84eddc930 test/tool_shed/test_data/emboss/libx11_proto/second_tool_dependency/tool_dependencies.xml --- /dev/null +++ b/test/tool_shed/test_data/emboss/libx11_proto/second_tool_dependency/tool_dependencies.xml @@ -0,0 +1,23 @@ +<tool_dependency> + <package name="libx11" version="1.5.0"> + <install version="1.0"> + <actions> +  + <action type="download_by_url">ftp://ftp.x.org/pub/X11R7.7/src/proto/xproto-7.0.23.tar.bz2</action> + <action type="shell_command">./configure --prefix=$INSTALL_DIR</action> + <action type="shell_command">make && make install</action> + <action type="set_environment"> + <environment_variable name="X11_INCLUDE_DIR" action="set_to">$INSTALL_DIR/include</environment_variable> + </action> + <action type="download_file" extract="true">ftp://ftp.x.org/pub/X11R7.7/src/lib/libX11-1.5.0.tar.bz2</action> + <action type="change_directory">libX11-1.5.0</action> + <action type="shell_command">./configure --prefix=$INSTALL_DIR CFLAGS='-I$INSTALL_DIR/include'</action> + <action type="shell_command">make && make install</action> + <action type="set_environment"> + <environment_variable name="X11_LIB_DIR" action="set_to">$INSTALL_DIR/lib</environment_variable> + </action> + </actions> + </install> + <readme>Xlib is an X Window System protocol client library written in the C programming language. It contains functions for interacting with an X server. These functions allow programmers to write programs without knowing the details of the protocol. Few applications use Xlib directly; rather, they employ other libraries that use Xlib functions to provide widget toolkits.</readme> + </package> +</tool_dependency> \ No newline at end of file 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.

1 0

commit/galaxy-central: greg: Apply Peter Cock's patch for appending a .rst extension to readme file names in tool shed repositories.
by commits-noreply＠bitbucket.org 24 Jul '13

24 Jul '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/528bee4dd14a/ Changeset: 528bee4dd14a User: greg Date: 2013-07-24 16:51:30 Summary: Apply Peter Cock's patch for appending a .rst extension to readme file names in tool shed repositories. Affected #: 1 file diff -r e22f360cda1363d0c93a86d64c17032e7507b296 -r 528bee4dd14addc5db2b59a0a229e3aa441f8fda lib/tool_shed/util/metadata_util.py --- a/lib/tool_shed/util/metadata_util.py +++ b/lib/tool_shed/util/metadata_util.py @@ -990,6 +990,7 @@ valid_filenames.extend( map( lambda f: '%s.rst' % f, readme_files ) ) valid_filenames.extend( readme_files ) valid_filenames.append( '%s.txt' % repository_name ) + valid_filenames.append( '%s.rst' % repository_name ) return valid_filenames def get_relative_path_to_repository_file( root, name, relative_install_dir, work_dir, shed_config_dict, resetting_all_metadata_on_repository ): 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.

1 0

commit/galaxy-central: greg: Render tool shed repository readme files as rst only if the file name ends with .rst.
by commits-noreply＠bitbucket.org 24 Jul '13

24 Jul '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e22f360cda13/ Changeset: e22f360cda13 User: greg Date: 2013-07-24 16:34:21 Summary: Render tool shed repository readme files as rst only if the file name ends with .rst. Affected #: 1 file diff -r 27b458743a117b5fb119915dc89bddc017625146 -r e22f360cda1363d0c93a86d64c17032e7507b296 templates/webapps/tool_shed/repository/common.mako --- a/templates/webapps/tool_shed/repository/common.mako +++ b/templates/webapps/tool_shed/repository/common.mako @@ -600,8 +600,10 @@ <%def name="render_readme( readme, pad, parent, row_counter )"><% + from tool_shed.util.shed_util_common import to_safe_string from galaxy.util import rst_to_html encoded_id = trans.security.encode_id( readme.id ) + render_rst = readme.name.endswith( '.rst' ) %><style type="text/css"> #readme_table{ table-layout:fixed; @@ -620,7 +622,11 @@ id="libraryItem-${encoded_id}"><td style="padding-left: ${pad+20}px;"><table id="readme_table"> - <tr><td>${ rst_to_html( readme.text ) }</td></tr> + %if render_rst: + <tr><td>${ rst_to_html( readme.text ) }</td></tr> + %else: + <tr><td>${readme.name}<br/>${ to_safe_string( readme.text, to_html=True ) }</td></tr> + %endif </table></td></tr> 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.

1 0

commit/galaxy-central: Dave Bouvier: Fix to correctly handle comments in repository dependency definitions.
by commits-noreply＠bitbucket.org 24 Jul '13

24 Jul '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/27b458743a11/ Changeset: 27b458743a11 User: Dave Bouvier Date: 2013-07-24 16:17:03 Summary: Fix to correctly handle comments in repository dependency definitions. Affected #: 1 file diff -r fdcd30ffdafd0a11ba7c90d5c01d1a3b5cb1f60c -r 27b458743a117b5fb119915dc89bddc017625146 lib/tool_shed/util/commit_util.py --- a/lib/tool_shed/util/commit_util.py +++ b/lib/tool_shed/util/commit_util.py @@ -236,15 +236,16 @@ root = tree.getroot() if root.tag == 'repositories': for index, elem in enumerate( root ): - # <repository name="molecule_datatypes" owner="test" changeset_revision="1a070566e9c6" /> - populated, elem, error_message = handle_repository_dependency_elem( trans, elem ) - if error_message: - exception_message = 'The repository_dependencies.xml file contains an invalid <repository> tag. %s' % error_message - raise Exception( exception_message ) - if populated: - root[ index ] = elem - if not altered: - altered = True + if elem.tag == 'repository': + # <repository name="molecule_datatypes" owner="test" changeset_revision="1a070566e9c6" /> + populated, elem, error_message = handle_repository_dependency_elem( trans, elem ) + if error_message: + exception_message = 'The repository_dependencies.xml file contains an invalid <repository> tag. %s' % error_message + raise Exception( exception_message ) + if populated: + root[ index ] = elem + if not altered: + altered = True return altered, root return False, None 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.

1 0

commit/galaxy-central: carlfeberhard: base controller, get_history_dataset_association: remove deleted=False flag; api/histories, update: remove deleted flag; casperjs tests: update for previous and remove tool iframe code
by commits-noreply＠bitbucket.org 23 Jul '13

23 Jul '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/fdcd30ffdafd/ Changeset: fdcd30ffdafd User: carlfeberhard Date: 2013-07-23 19:55:39 Summary: base controller, get_history_dataset_association: remove deleted=False flag; api/histories, update: remove deleted flag; casperjs tests: update for previous and remove tool iframe code Affected #: 7 files diff -r 6187607058e66e1b8b31f2da905d603ae0c65f23 -r fdcd30ffdafd0a11ba7c90d5c01d1a3b5cb1f60c lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -512,7 +512,8 @@ """ #TODO: duplicate of above? alias to above (or vis-versa) self.security_check( trans, history, check_ownership=check_ownership, check_accessible=check_accessible ) - hda = self.get_object( trans, dataset_id, 'HistoryDatasetAssociation', check_ownership=False, check_accessible=False, deleted=False ) + hda = self.get_object( trans, dataset_id, 'HistoryDatasetAssociation', + check_ownership=False, check_accessible=False ) if check_accessible: if not trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), hda.dataset ): diff -r 6187607058e66e1b8b31f2da905d603ae0c65f23 -r fdcd30ffdafd0a11ba7c90d5c01d1a3b5cb1f60c lib/galaxy/webapps/galaxy/api/histories.py --- a/lib/galaxy/webapps/galaxy/api/histories.py +++ b/lib/galaxy/webapps/galaxy/api/histories.py @@ -193,7 +193,7 @@ """ #TODO: PUT /api/histories/{encoded_history_id} payload = { rating: rating } (w/ no security checks) try: - history = self.get_history( trans, id, check_ownership=True, check_accessible=True, deleted=True ) + history = self.get_history( trans, id, check_ownership=True, check_accessible=True ) # validation handled here and some parsing, processing, and conversion payload = self._validate_and_parse_update_payload( payload ) # additional checks here (security, etc.) diff -r 6187607058e66e1b8b31f2da905d603ae0c65f23 -r fdcd30ffdafd0a11ba7c90d5c01d1a3b5cb1f60c test/casperjs/api-hda-tests.js --- a/test/casperjs/api-hda-tests.js +++ b/test/casperjs/api-hda-tests.js @@ -217,7 +217,7 @@ deleted: true }); //this.debug( 'returned:\n' + this.jsonStr( returned ) ); - hdaShow = this.api.hdas.show( lastHistory.id, firstHda.id ); + hdaShow = this.api.hdas.show( lastHistory.id, firstHda.id, true ); this.test.assert( hdaShow.deleted === true, "Update set the deleted flag: " + hdaShow.deleted ); this.test.comment( 'update should allow changing the deleted flag back' ); diff -r 6187607058e66e1b8b31f2da905d603ae0c65f23 -r fdcd30ffdafd0a11ba7c90d5c01d1a3b5cb1f60c test/casperjs/api-history-tests.js --- a/test/casperjs/api-history-tests.js +++ b/test/casperjs/api-history-tests.js @@ -107,7 +107,7 @@ this.test.comment( 'A bad id to show should throw an error' ); this.assertRaises( function(){ this.api.histories.show( '1234123412341234' ); - }, 'Error in history API at showing history detail: 400 Bad Request', 'Raises an exception' ); + }, '400 Bad Request', 'Raises an exception' ); // ------------------------------------------------------------------------------------------- CREATE @@ -131,8 +131,10 @@ this.test.comment( 'calling delete should delete the given history and remove it from the standard index' ); var deletedHistory = this.api.histories.delete_( createdHistory.id ); //this.debug( 'returned from delete:\n' + this.jsonStr( deletedHistory ) ); - this.test.assert( deletedHistory === 'OK', - "Deletion returned 'OK' - even though that's not a great, informative response: " + deletedHistory ); + this.test.assert( deletedHistory.id === createdHistory.id, + "Deletion returned id matching created history: " + deletedHistory.id ); + this.test.assert( deletedHistory.deleted === true, + "Deletion return 'deleted: true': " + deletedHistory.deleted ); newFirstHistory = this.api.histories.index()[0]; //this.debug( 'newFirstHistory:\n' + this.jsonStr( newFirstHistory ) ); @@ -252,7 +254,7 @@ deleted: true }); //this.debug( 'returned:\n' + this.jsonStr( returned ) ); - historyShow = this.api.histories.show( newFirstHistory.id ); + historyShow = this.api.histories.show( newFirstHistory.id, true ); this.test.assert( historyShow.deleted === true, "Update set the deleted flag: " + historyShow.deleted ); this.test.comment( 'update should allow changing the deleted flag back' ); diff -r 6187607058e66e1b8b31f2da905d603ae0c65f23 -r fdcd30ffdafd0a11ba7c90d5c01d1a3b5cb1f60c test/casperjs/modules/api.js --- a/test/casperjs/modules/api.js +++ b/test/casperjs/modules/api.js @@ -261,7 +261,7 @@ }; HDAAPI.prototype.show = function show( historyId, id, deleted ){ - this.api.spaceghost.info( 'hdas.show: ' + [ historyId, id, (( deleted )?( 'w deleted' ):( '' )) ] ); + this.api.spaceghost.info( 'hdas.show: ' + [ historyId, id, (( deleted )?( 'w/deleted' ):( '' )) ] ); id = ( id === 'most_recently_used' )?( id ):( this.api.ensureId( id ) ); deleted = deleted || false; diff -r 6187607058e66e1b8b31f2da905d603ae0c65f23 -r fdcd30ffdafd0a11ba7c90d5c01d1a3b5cb1f60c test/casperjs/modules/tools.js --- a/test/casperjs/modules/tools.js +++ b/test/casperjs/modules/tools.js @@ -87,7 +87,7 @@ uploadInfo[ spaceghost.data.selectors.tools.upload.fileInput ] = filepath; // click the upload tool - spaceghost.thenOpen( spaceghost.baseUrl ).withToolPanel( function(){ + spaceghost.thenOpen( spaceghost.baseUrl, function(){ // we can apprently click a tool label without expanding the tool container for it this.clickLabel( spaceghost.data.labels.tools.upload.panelLabel ); this.jumpToMain( function(){ diff -r 6187607058e66e1b8b31f2da905d603ae0c65f23 -r fdcd30ffdafd0a11ba7c90d5c01d1a3b5cb1f60c test/casperjs/spaceghost.js --- a/test/casperjs/spaceghost.js +++ b/test/casperjs/spaceghost.js @@ -635,13 +635,6 @@ return this.withFrame( this.data.selectors.frames.history, then ); }; -/** Version of Casper#withFrame for the tool iframe. - * @param {Function} then function called when in the frame - */ -SpaceGhost.prototype.withToolPanel = function withToolPanel( then ){ - return this.withFrame( this.data.selectors.frames.tools, then ); -}; - /** Version of Casper#withFrame for the main iframe. * @param {Function} then function called when in the frame */ @@ -687,15 +680,6 @@ return this.jumpToFrame( this.data.selectors.frames.history, fn ); }; -/** Jumps into tools frame, exectutes fn, and jumps back to original frame. - * @param {Selector} frame the selector for the frame to jump to - * @param {Function} fn function called when in the frame - * @returns {Any} the return value of fn - */ -SpaceGhost.prototype.jumpToTools = function jumpToTools( fn ){ - return this.jumpToFrame( this.data.selectors.frames.tools, fn ); -}; - /** Jumps into main frame, exectutes fn, and jumps back to original frame. * @param {Selector} frame the selector for the frame to jump to * @param {Function} fn function called when in the frame @@ -1141,7 +1125,6 @@ frames : { main : 'galaxy_main', - tools : 'galaxy_tools', history : 'galaxy_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.

1 0

commit/galaxy-central: carlfeberhard: api/genomes, create: update docs
by commits-noreply＠bitbucket.org 23 Jul '13

23 Jul '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6187607058e6/ Changeset: 6187607058e6 User: carlfeberhard Date: 2013-07-23 16:12:59 Summary: api/genomes, create: update docs Affected #: 1 file diff -r 547bfb9b7bbe090f93dc4b0935522662bb9805b5 -r 6187607058e66e1b8b31f2da905d603ae0c65f23 lib/galaxy/webapps/galaxy/api/genomes.py --- a/lib/galaxy/webapps/galaxy/api/genomes.py +++ b/lib/galaxy/webapps/galaxy/api/genomes.py @@ -49,19 +49,14 @@ Download and/or index a genome. Parameters:: - - dbkey DB key of the build to download, ignored unless 'UCSC' is specified as the source - ncbi_name NCBI's genome identifier, ignored unless NCBI is specified as the source - ensembl_dbkey Ensembl's genome identifier, ignored unless Ensembl is specified as the source - url_dbkey DB key to use for this build, ignored unless URL is specified as the source - source Data source for this build. Can be: UCSC, Ensembl, NCBI, URL + liftover None or array of liftover url partial paths + dbkey DB key of the build to download indexers POST array of indexers to run after downloading (indexers[] = first, indexers[] = second, ...) + longname a more descriptive name for the genome func Allowed values: 'download' Download and index 'index' Index only - Returns:: - If no error: dict( status: 'ok', job: <job ID> ) @@ -69,6 +64,17 @@ dict( status: 'error', error: <error message> ) """ + #??: Planned? + #Parameters:: + # dbkey DB key of the build to download, ignored unless 'UCSC' is specified as the source + # ncbi_name NCBI's genome identifier, ignored unless NCBI is specified as the source + # ensembl_dbkey Ensembl's genome identifier, ignored unless Ensembl is specified as the source + # url_dbkey DB key to use for this build, ignored unless URL is specified as the source + # source Data source for this build. Can be: UCSC, Ensembl, NCBI, URL + # indexers POST array of indexers to run after downloading (indexers[] = first, indexers[] = second, ...) + # func Allowed values: + # 'download' Download and index + # 'index' Index only params = util.Params( payload ) from galaxy.web.controllers.data_admin import build_param_dict as massage paramdict = massage( params, trans ) 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 panel: disable (w/ message) display button for uploading files
by commits-noreply＠bitbucket.org 23 Jul '13

23 Jul '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/547bfb9b7bbe/ Changeset: 547bfb9b7bbe User: carlfeberhard Date: 2013-07-23 15:32:22 Summary: History panel: disable (w/ message) display button for uploading files Affected #: 2 files diff -r 72cf2a3a6a2a5d476022072b6646dfbc1d519b09 -r 547bfb9b7bbe090f93dc4b0935522662bb9805b5 static/scripts/mvc/dataset/hda-base.js --- a/static/scripts/mvc/dataset/hda-base.js +++ b/static/scripts/mvc/dataset/hda-base.js @@ -235,6 +235,11 @@ displayBtnData.enabled = false; displayBtnData.title = _l( 'Cannot display datasets removed from disk' ); + // disable if still uploading + } else if( this.model.get( 'state' ) === HistoryDatasetAssociation.STATES.UPLOAD ){ + displayBtnData.enabled = false; + displayBtnData.title = _l( 'This dataset must finish uploading before it can be viewed' ); + } else { displayBtnData.title = _l( 'View data' ); @@ -243,7 +248,14 @@ // add frame manager option onclick event var self = this; - displayBtnData.on_click = function() { parent.frame_manager.frame_new({title: "Data Viewer", type: "url", location: "center", content: self.urls.display }); }; + displayBtnData.on_click = function(){ + parent.frame_manager.frame_new({ + title : "Data Viewer", + type : "url", + location: "center", + content : self.urls.display + }); + }; } this.displayButton = new IconButtonView({ model : new IconButton( displayBtnData ) }); diff -r 72cf2a3a6a2a5d476022072b6646dfbc1d519b09 -r 547bfb9b7bbe090f93dc4b0935522662bb9805b5 static/scripts/packed/mvc/dataset/hda-base.js --- a/static/scripts/packed/mvc/dataset/hda-base.js +++ b/static/scripts/packed/mvc/dataset/hda-base.js @@ -1,1 +1,1 @@ -var HDABaseView=Backbone.View.extend(LoggableMixin).extend({tagName:"div",className:"historyItemContainer",initialize:function(a){if(a.logger){this.logger=this.model.logger=a.logger}this.log(this+".initialize:",a);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton];if(!a.urlTemplates){throw ("HDAView needs urlTemplates on initialize")}this.urlTemplates=a.urlTemplates;this.expanded=a.expanded||false;this.model.bind("change",function(c,d){var b=_.without(_.keys(d.changes),"display_apps","display_types");if(b.length){this.render()}else{if(this.expanded){this._render_displayApps()}}},this)},render:function(){var b=this,e=this.model.get("id"),c=this.model.get("state"),a=$("<div/>").attr("id","historyItem-"+e),d=(this.$el.children().size()===0);this.$el.attr("id","historyItemContainer-"+e);this.urls=this._renderUrls(this.urlTemplates,this.model.toJSON());a.addClass("historyItemWrapper").addClass("historyItem").addClass("historyItem-"+c);a.append(this._render_warnings());a.append(this._render_titleBar());this._setUpBehaviors(a);this.body=$(this._render_body());a.append(this.body);this.$el.fadeOut("fast",function(){b.$el.children().remove();b.$el.append(a).fadeIn("fast",function(){b.log(b+" rendered:",b.$el);var f="rendered";if(d){f+=":initial"}else{if(b.model.inReadyState()){f+=":ready"}}b.trigger(f)})});return this},_renderUrls:function(d,a){var b=this,c={};_.each(d,function(e,f){if(_.isObject(e)){c[f]=b._renderUrls(e,a)}else{if(f==="meta_download"){c[f]=b._renderMetaDownloadUrls(e,a)}else{try{c[f]=_.template(e,a)}catch(g){throw (b+"._renderUrls error: "+g+"\n rendering:"+e+"\n with "+JSON.stringify(a))}}}});return c},_renderMetaDownloadUrls:function(b,a){return _.map(a.meta_files,function(c){return{url:_.template(b,{id:a.id,file_type:c.file_type}),file_type:c.file_type}})},_setUpBehaviors:function(a){a=a||this.$el;make_popup_menus(a);a.find(".tooltip").tooltip({placement:"bottom"})},_render_warnings:function(){return $(jQuery.trim(HDABaseView.templates.messages(this.model.toJSON())))},_render_titleBar:function(){var a=$('<div class="historyItemTitleBar" style="overflow: hidden"></div>');a.append(this._render_titleButtons());a.append('<span class="state-icon"></span>');a.append(this._render_titleLink());return a},_render_titleButtons:function(){var a=$('<div class="historyItemButtons"></div>');a.append(this._render_displayButton());return a},_render_displayButton:function(){if((this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(this.model.get("state")===HistoryDatasetAssociation.STATES.NEW)||(!this.model.get("accessible"))){this.displayButton=null;return null}var a={icon_class:"display",target:"galaxy_main"};if(this.model.get("purged")){a.enabled=false;a.title=_l("Cannot display datasets removed from disk")}else{a.title=_l("View data");a.href="javascript:parent.frame_manager.frame_new({title: 'Data Viewer', type: 'url', location: 'center', content: '"+this.urls.display+"'});"}this.displayButton=new IconButtonView({model:new IconButton(a)});return this.displayButton.render().$el},_render_titleLink:function(){return $(jQuery.trim(HDABaseView.templates.titleLink(_.extend(this.model.toJSON(),{urls:this.urls}))))},_render_hdaSummary:function(){var a=_.extend(this.model.toJSON(),{urls:this.urls});return HDABaseView.templates.hdaSummary(a)},_render_primaryActionButtons:function(c){var a=this,b=$("<div/>").attr("id","primary-actions-"+this.model.get("id"));_.each(c,function(d){b.append(d.call(a))});return b},_render_downloadButton:function(){if(this.model.get("purged")||!this.model.hasData()){return null}var a=HDABaseView.templates.downloadLinks(_.extend(this.model.toJSON(),{urls:this.urls}));return $(a.trim())},_render_showParamsButton:function(){this.showParamsButton=new IconButtonView({model:new IconButton({title:_l("View details"),href:this.urls.show_params,target:"galaxy_main",icon_class:"information"})});return this.showParamsButton.render().$el},_render_displayAppArea:function(){return $("<div/>").addClass("display-apps")},_render_displayApps:function(c){c=c||this.$el;var d=c.find("div.display-apps"),a=this.model.get("display_types"),b=this.model.get("display_apps");if((!this.model.hasData())||(!c||!c.length)||(!d.length)){return}d.html(null);if(!_.isEmpty(a)){d.append(HDABaseView.templates.displayApps({displayApps:a}))}if(!_.isEmpty(b)){d.append(HDABaseView.templates.displayApps({displayApps:b}))}},_render_peek:function(){var a=this.model.get("peek");if(!a){return null}return $("<div/>").append($("<pre/>").attr("id","peek"+this.model.get("id")).addClass("peek").append(a))},_render_body:function(){var a=$("<div/>").attr("id","info-"+this.model.get("id")).addClass("historyItemBody").attr("style","display: none");if(this.expanded){this._render_body_html(a);a.css("display","block")}return a},_render_body_html:function(a){a.html("");switch(this.model.get("state")){case HistoryDatasetAssociation.STATES.NEW:this._render_body_new(a);break;case HistoryDatasetAssociation.STATES.NOT_VIEWABLE:this._render_body_not_viewable(a);break;case HistoryDatasetAssociation.STATES.UPLOAD:this._render_body_uploading(a);break;case HistoryDatasetAssociation.STATES.PAUSED:this._render_body_paused(a);break;case HistoryDatasetAssociation.STATES.QUEUED:this._render_body_queued(a);break;case HistoryDatasetAssociation.STATES.RUNNING:this._render_body_running(a);break;case HistoryDatasetAssociation.STATES.ERROR:this._render_body_error(a);break;case HistoryDatasetAssociation.STATES.DISCARDED:this._render_body_discarded(a);break;case HistoryDatasetAssociation.STATES.SETTING_METADATA:this._render_body_setting_metadata(a);break;case HistoryDatasetAssociation.STATES.EMPTY:this._render_body_empty(a);break;case HistoryDatasetAssociation.STATES.FAILED_METADATA:this._render_body_failed_metadata(a);break;case HistoryDatasetAssociation.STATES.OK:this._render_body_ok(a);break;default:a.append($('<div>Error: unknown dataset state "'+this.model.get("state")+'".</div>'))}a.append('<div style="clear: both"></div>');this._setUpBehaviors(a)},_render_body_new:function(b){var a=_l("This is a new dataset and not all of its data are available yet");b.append($("<div>"+_l(a)+"</div>"))},_render_body_not_viewable:function(a){a.append($("<div>"+_l("You do not have permission to view dataset")+"</div>"))},_render_body_uploading:function(a){a.append($("<div>"+_l("Dataset is uploading")+"</div>"))},_render_body_queued:function(a){a.append($("<div>"+_l("Job is waiting to run")+"</div>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_paused:function(a){a.append($("<div>"+_l("Job is paused. Use the history menu to resume")+"</div>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_running:function(a){a.append("<div>"+_l("Job is currently running")+"</div>");a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_error:function(a){if(!this.model.get("purged")){a.append($("<div>"+this.model.get("misc_blurb")+"</div>"))}a.append((_l("An error occurred with this dataset")+": <i>"+$.trim(this.model.get("misc_info"))+"</i>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers.concat([this._render_downloadButton])))},_render_body_discarded:function(a){a.append("<div>"+_l("The job creating this dataset was cancelled before completion")+".</div>");a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_setting_metadata:function(a){a.append($("<div>"+_l("Metadata is being auto-detected")+".</div>"))},_render_body_empty:function(a){a.append($("<div>"+_l("No data")+": <i>"+this.model.get("misc_blurb")+"</i></div>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_failed_metadata:function(a){a.append($(HDABaseView.templates.failedMetadata(_.extend(this.model.toJSON(),{urls:this.urls}))));this._render_body_ok(a)},_render_body_ok:function(a){a.append(this._render_hdaSummary());if(this.model.isDeletedOrPurged()){a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton]));return}a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton]));a.append('<div class="clear"/>');a.append(this._render_displayAppArea());this._render_displayApps(a);a.append(this._render_peek())},events:{"click .historyItemTitle":"toggleBodyVisibility"},toggleBodyVisibility:function(c,a){var b=this;this.expanded=(a===undefined)?(!this.body.is(":visible")):(a);if(this.expanded){b._render_body_html(b.body);this.body.slideDown("fast",function(){b.trigger("body-expanded",b.model.get("id"))})}else{this.body.slideUp("fast",function(){b.trigger("body-collapsed",b.model.get("id"))})}},remove:function(b){var a=this;this.$el.fadeOut("fast",function(){a.$el.remove();a.off();if(b){b()}})},toString:function(){var a=(this.model)?(this.model+""):("(no model)");return"HDABaseView("+a+")"}});HDABaseView.templates={warningMsg:Handlebars.templates["template-warningmessagesmall"],messages:Handlebars.templates["template-hda-warning-messages"],titleLink:Handlebars.templates["template-hda-titleLink"],hdaSummary:Handlebars.templates["template-hda-hdaSummary"],downloadLinks:Handlebars.templates["template-hda-downloadLinks"],failedMetadata:Handlebars.templates["template-hda-failedMetadata"],displayApps:Handlebars.templates["template-hda-displayApps"]}; \ No newline at end of file +var HDABaseView=Backbone.View.extend(LoggableMixin).extend({tagName:"div",className:"historyItemContainer",initialize:function(a){if(a.logger){this.logger=this.model.logger=a.logger}this.log(this+".initialize:",a);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton];if(!a.urlTemplates){throw ("HDAView needs urlTemplates on initialize")}this.urlTemplates=a.urlTemplates;this.expanded=a.expanded||false;this.model.bind("change",function(c,d){var b=_.without(_.keys(d.changes),"display_apps","display_types");if(b.length){this.render()}else{if(this.expanded){this._render_displayApps()}}},this)},render:function(){var b=this,e=this.model.get("id"),c=this.model.get("state"),a=$("<div/>").attr("id","historyItem-"+e),d=(this.$el.children().size()===0);this.$el.attr("id","historyItemContainer-"+e);this.urls=this._renderUrls(this.urlTemplates,this.model.toJSON());a.addClass("historyItemWrapper").addClass("historyItem").addClass("historyItem-"+c);a.append(this._render_warnings());a.append(this._render_titleBar());this._setUpBehaviors(a);this.body=$(this._render_body());a.append(this.body);this.$el.fadeOut("fast",function(){b.$el.children().remove();b.$el.append(a).fadeIn("fast",function(){b.log(b+" rendered:",b.$el);var f="rendered";if(d){f+=":initial"}else{if(b.model.inReadyState()){f+=":ready"}}b.trigger(f)})});return this},_renderUrls:function(d,a){var b=this,c={};_.each(d,function(e,f){if(_.isObject(e)){c[f]=b._renderUrls(e,a)}else{if(f==="meta_download"){c[f]=b._renderMetaDownloadUrls(e,a)}else{try{c[f]=_.template(e,a)}catch(g){throw (b+"._renderUrls error: "+g+"\n rendering:"+e+"\n with "+JSON.stringify(a))}}}});return c},_renderMetaDownloadUrls:function(b,a){return _.map(a.meta_files,function(c){return{url:_.template(b,{id:a.id,file_type:c.file_type}),file_type:c.file_type}})},_setUpBehaviors:function(a){a=a||this.$el;make_popup_menus(a);a.find(".tooltip").tooltip({placement:"bottom"})},_render_warnings:function(){return $(jQuery.trim(HDABaseView.templates.messages(this.model.toJSON())))},_render_titleBar:function(){var a=$('<div class="historyItemTitleBar" style="overflow: hidden"></div>');a.append(this._render_titleButtons());a.append('<span class="state-icon"></span>');a.append(this._render_titleLink());return a},_render_titleButtons:function(){var a=$('<div class="historyItemButtons"></div>');a.append(this._render_displayButton());return a},_render_displayButton:function(){if((this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(this.model.get("state")===HistoryDatasetAssociation.STATES.NEW)||(!this.model.get("accessible"))){this.displayButton=null;return null}var b={icon_class:"display",target:"galaxy_main"};if(this.model.get("purged")){b.enabled=false;b.title=_l("Cannot display datasets removed from disk")}else{if(this.model.get("state")===HistoryDatasetAssociation.STATES.UPLOAD){b.enabled=false;b.title=_l("This dataset must finish uploading before it can be viewed")}else{b.title=_l("View data");b.href=this.urls.display;var a=this;b.on_click=function(){parent.frame_manager.frame_new({title:"Data Viewer",type:"url",location:"center",content:a.urls.display})}}}this.displayButton=new IconButtonView({model:new IconButton(b)});return this.displayButton.render().$el},_render_titleLink:function(){return $(jQuery.trim(HDABaseView.templates.titleLink(_.extend(this.model.toJSON(),{urls:this.urls}))))},_render_hdaSummary:function(){var a=_.extend(this.model.toJSON(),{urls:this.urls});return HDABaseView.templates.hdaSummary(a)},_render_primaryActionButtons:function(c){var a=this,b=$("<div/>").attr("id","primary-actions-"+this.model.get("id"));_.each(c,function(d){b.append(d.call(a))});return b},_render_downloadButton:function(){if(this.model.get("purged")||!this.model.hasData()){return null}var a=HDABaseView.templates.downloadLinks(_.extend(this.model.toJSON(),{urls:this.urls}));return $(a.trim())},_render_showParamsButton:function(){this.showParamsButton=new IconButtonView({model:new IconButton({title:_l("View details"),href:this.urls.show_params,target:"galaxy_main",icon_class:"information"})});return this.showParamsButton.render().$el},_render_displayAppArea:function(){return $("<div/>").addClass("display-apps")},_render_displayApps:function(c){c=c||this.$el;var d=c.find("div.display-apps"),a=this.model.get("display_types"),b=this.model.get("display_apps");if((!this.model.hasData())||(!c||!c.length)||(!d.length)){return}d.html(null);if(!_.isEmpty(a)){d.append(HDABaseView.templates.displayApps({displayApps:a}))}if(!_.isEmpty(b)){d.append(HDABaseView.templates.displayApps({displayApps:b}))}},_render_peek:function(){var a=this.model.get("peek");if(!a){return null}return $("<div/>").append($("<pre/>").attr("id","peek"+this.model.get("id")).addClass("peek").append(a))},_render_body:function(){var a=$("<div/>").attr("id","info-"+this.model.get("id")).addClass("historyItemBody").attr("style","display: none");if(this.expanded){this._render_body_html(a);a.css("display","block")}return a},_render_body_html:function(a){a.html("");switch(this.model.get("state")){case HistoryDatasetAssociation.STATES.NEW:this._render_body_new(a);break;case HistoryDatasetAssociation.STATES.NOT_VIEWABLE:this._render_body_not_viewable(a);break;case HistoryDatasetAssociation.STATES.UPLOAD:this._render_body_uploading(a);break;case HistoryDatasetAssociation.STATES.PAUSED:this._render_body_paused(a);break;case HistoryDatasetAssociation.STATES.QUEUED:this._render_body_queued(a);break;case HistoryDatasetAssociation.STATES.RUNNING:this._render_body_running(a);break;case HistoryDatasetAssociation.STATES.ERROR:this._render_body_error(a);break;case HistoryDatasetAssociation.STATES.DISCARDED:this._render_body_discarded(a);break;case HistoryDatasetAssociation.STATES.SETTING_METADATA:this._render_body_setting_metadata(a);break;case HistoryDatasetAssociation.STATES.EMPTY:this._render_body_empty(a);break;case HistoryDatasetAssociation.STATES.FAILED_METADATA:this._render_body_failed_metadata(a);break;case HistoryDatasetAssociation.STATES.OK:this._render_body_ok(a);break;default:a.append($('<div>Error: unknown dataset state "'+this.model.get("state")+'".</div>'))}a.append('<div style="clear: both"></div>');this._setUpBehaviors(a)},_render_body_new:function(b){var a=_l("This is a new dataset and not all of its data are available yet");b.append($("<div>"+_l(a)+"</div>"))},_render_body_not_viewable:function(a){a.append($("<div>"+_l("You do not have permission to view dataset")+"</div>"))},_render_body_uploading:function(a){a.append($("<div>"+_l("Dataset is uploading")+"</div>"))},_render_body_queued:function(a){a.append($("<div>"+_l("Job is waiting to run")+"</div>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_paused:function(a){a.append($("<div>"+_l("Job is paused. Use the history menu to resume")+"</div>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_running:function(a){a.append("<div>"+_l("Job is currently running")+"</div>");a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_error:function(a){if(!this.model.get("purged")){a.append($("<div>"+this.model.get("misc_blurb")+"</div>"))}a.append((_l("An error occurred with this dataset")+": <i>"+$.trim(this.model.get("misc_info"))+"</i>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers.concat([this._render_downloadButton])))},_render_body_discarded:function(a){a.append("<div>"+_l("The job creating this dataset was cancelled before completion")+".</div>");a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_setting_metadata:function(a){a.append($("<div>"+_l("Metadata is being auto-detected")+".</div>"))},_render_body_empty:function(a){a.append($("<div>"+_l("No data")+": <i>"+this.model.get("misc_blurb")+"</i></div>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_failed_metadata:function(a){a.append($(HDABaseView.templates.failedMetadata(_.extend(this.model.toJSON(),{urls:this.urls}))));this._render_body_ok(a)},_render_body_ok:function(a){a.append(this._render_hdaSummary());if(this.model.isDeletedOrPurged()){a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton]));return}a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton]));a.append('<div class="clear"/>');a.append(this._render_displayAppArea());this._render_displayApps(a);a.append(this._render_peek())},events:{"click .historyItemTitle":"toggleBodyVisibility"},toggleBodyVisibility:function(c,a){var b=this;this.expanded=(a===undefined)?(!this.body.is(":visible")):(a);if(this.expanded){b._render_body_html(b.body);this.body.slideDown("fast",function(){b.trigger("body-expanded",b.model.get("id"))})}else{this.body.slideUp("fast",function(){b.trigger("body-collapsed",b.model.get("id"))})}},remove:function(b){var a=this;this.$el.fadeOut("fast",function(){a.$el.remove();a.off();if(b){b()}})},toString:function(){var a=(this.model)?(this.model+""):("(no model)");return"HDABaseView("+a+")"}});HDABaseView.templates={warningMsg:Handlebars.templates["template-warningmessagesmall"],messages:Handlebars.templates["template-hda-warning-messages"],titleLink:Handlebars.templates["template-hda-titleLink"],hdaSummary:Handlebars.templates["template-hda-hdaSummary"],downloadLinks:Handlebars.templates["template-hda-downloadLinks"],failedMetadata:Handlebars.templates["template-hda-failedMetadata"],displayApps:Handlebars.templates["template-hda-displayApps"]}; \ No newline at end of file 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: API histories, delete: ensure HTTPExceptions are raised, better return values; API workflows delete: add code 400 to not found clause, change to code 403 for not accessible clause
by commits-noreply＠bitbucket.org 22 Jul '13

22 Jul '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/72cf2a3a6a2a/ Changeset: 72cf2a3a6a2a User: carlfeberhard Date: 2013-07-22 23:04:52 Summary: API histories, delete: ensure HTTPExceptions are raised, better return values; API workflows delete: add code 400 to not found clause, change to code 403 for not accessible clause Affected #: 2 files diff -r 3a27539764348d4099669bc7fe94c9432e62aff0 -r 72cf2a3a6a2a5d476022072b6646dfbc1d519b09 lib/galaxy/webapps/galaxy/api/histories.py --- a/lib/galaxy/webapps/galaxy/api/histories.py +++ b/lib/galaxy/webapps/galaxy/api/histories.py @@ -4,7 +4,7 @@ import pkg_resources pkg_resources.require( "Paste" ) -from paste.httpexceptions import HTTPBadRequest, HTTPForbidden +from paste.httpexceptions import HTTPBadRequest, HTTPForbidden, HTTPInternalServerError, HTTPException from galaxy import web from galaxy.util import string_as_bool, restore_text @@ -124,6 +124,7 @@ if kwd.get( 'payload', None ): purge = string_as_bool( kwd['payload'].get( 'purge', False ) ) + rval = { 'id' : history_id } try: history = self.get_history( trans, history_id, check_ownership=True, check_accessible=False ) history.deleted = True @@ -152,14 +153,24 @@ # Now mark the history as purged history.purged = True self.sa_session.add( history ) + rval[ 'purged' ] = True trans.sa_session.flush() + rval[ 'deleted' ] = True - #TODO: better feedback than this... - except Exception, e: - return str( e ) + except HTTPInternalServerError, http_server_err: + log.exception( 'Histories API, delete: uncaught HTTPInternalServerError: %s, %s\n%s', + history_id, str( kwd ), str( http_server_err ) ) + raise + except HTTPException, http_exc: + raise + except Exception, exc: + log.exception( 'Histories API, delete: uncaught exception: %s, %s\n%s', + history_id, str( kwd ), str( exc ) ) + trans.response.status = 500 + rval.update({ 'error': str( exc ) }) - return 'OK' + return rval @web.expose_api def undelete( self, trans, id, **kwd ): diff -r 3a27539764348d4099669bc7fe94c9432e62aff0 -r 72cf2a3a6a2a5d476022072b6646dfbc1d519b09 lib/galaxy/webapps/galaxy/api/workflows.py --- a/lib/galaxy/webapps/galaxy/api/workflows.py +++ b/lib/galaxy/webapps/galaxy/api/workflows.py @@ -290,13 +290,14 @@ try: stored_workflow = trans.sa_session.query(self.app.model.StoredWorkflow).get(trans.security.decode_id(workflow_id)) - except Exception,e: + except Exception, e: + trans.response.status = 400 return ("Workflow with ID='%s' can not be found\n Exception: %s") % (workflow_id, str( e )) # check to see if user has permissions to selected workflow if stored_workflow.user != trans.user and not trans.user_is_admin(): if trans.sa_session.query(trans.app.model.StoredWorkflowUserShareAssociation).filter_by(user=trans.user, stored_workflow=stored_workflow).count() == 0: - trans.response.status = 400 + trans.response.status = 403 return("Workflow is not owned by or shared with current user") #Mark a workflow as deleted 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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