1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/commits/944e6ae11d5e/ Changeset: 944e6ae11d5e User: davebgx Date: 2014-03-20 21:53:25 Summary: Functional test script for installing, updating, uninstalling, and reinstalling a repository. Affected #: 2 files

diff -r b95ae5f6d6f513760fa01f596ca52fbc1cff9d6e -r 944e6ae11d5e870ae17b2c928034b4b7cd3b3bb9 test/tool_shed/base/test_db_util.py --- a/test/tool_shed/base/test_db_util.py +++ b/test/tool_shed/base/test_db_util.py @@ -63,11 +63,13 @@ .filter( galaxy.model.tool_shed_install.ToolShedRepository.table.c.id == repository_id ) \ .first()

-def get_installed_repository_by_name_owner( repository_name, owner ): - return install_session.query( galaxy.model.tool_shed_install.ToolShedRepository ) \ - .filter( and_( galaxy.model.tool_shed_install.ToolShedRepository.table.c.name == repository_name, - galaxy.model.tool_shed_install.ToolShedRepository.table.c.owner == owner ) ) \ - .first() +def get_installed_repository_by_name_owner( repository_name, owner, return_multiple=False ): + query = install_session.query( galaxy.model.tool_shed_install.ToolShedRepository ) \ + .filter( and_( galaxy.model.tool_shed_install.ToolShedRepository.table.c.name == repository_name, + galaxy.model.tool_shed_install.ToolShedRepository.table.c.owner == owner ) ) + if return_multiple: + return query.all() + return query.first()

def get_private_role( user ): for role in user.all_roles(): @@ -181,7 +183,7 @@ .filter( galaxy.model.User.table.c.email==email ) \ .first()

-def get_repository_by_name_and_owner( name, owner_username ): +def get_repository_by_name_and_owner( name, owner_username, return_multiple=False ): owner = get_user_by_name( owner_username ) repository = sa_session.query( model.Repository ) \ .filter( and_( model.Repository.table.c.name == name,

diff -r b95ae5f6d6f513760fa01f596ca52fbc1cff9d6e -r 944e6ae11d5e870ae17b2c928034b4b7cd3b3bb9 test/tool_shed/functional/test_1470_updating_installed_repositories.py --- /dev/null +++ b/test/tool_shed/functional/test_1470_updating_installed_repositories.py @@ -0,0 +1,138 @@ +from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os +import logging + +log = logging.getLogger(__name__) + +repository_name = 'filtering_1470' +repository_description = "Galaxy's filtering tool" +repository_long_description = "Long description of Galaxy's filtering tool" + +category_name = 'Test 1470 - Updating Installed Repositories' +category_description = 'Functional test suite to ensure that updating installed repositories does not create white ghosts.' + +''' +1. Install a repository into Galaxy. +2. In the Tool Shed, update the repository from Step 1. +3. In Galaxy, get updates to the repository. +4. In Galaxy, uninstall the repository. +5. In Galaxy, reinstall the repository. +6. Make sure step 5 created no white ghosts. +''' + + +class TestUpdateInstalledRepository( ShedTwillTestCase ): + '''Verify that the code correctly handles updating an installed repository, then uninstalling and reinstalling.''' + + def test_0000_initiate_users( self ): + """Create necessary user accounts.""" + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + test_user_1 = self.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' % test_user_1_email + test_user_1_private_role = self.test_db_util.get_private_role( test_user_1 ) + self.logout() + self.login( email=common.admin_email, username=common.admin_username ) + admin_user = self.test_db_util.get_user( common.admin_email ) + assert admin_user is not None, 'Problem retrieving user with email %s from the database' % admin_email + admin_user_private_role = self.test_db_util.get_private_role( admin_user ) + + def test_0005_create_filtering_repository( self ): + """Create and populate the filtering_0530 repository.""" + category = self.create_category( name=category_name, description=category_description ) + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + repository = self.get_or_create_repository( name=repository_name, + description=repository_description, + long_description=repository_long_description, + owner=common.test_user_1_name, + category_id=self.security.encode_id( category.id ), + strings_displayed=[] ) + self.upload_file( repository, + filename='filtering/filtering_1.1.0.tar', + filepath=None, + valid_tools_only=True, + uncompress_file=True, + remove_repo_files_not_in_tar=False, + commit_message='Uploaded filtering 1.1.0 tarball.', + strings_displayed=[], + strings_not_displayed=[] ) + + def test_0010_install_filtering_to_galaxy( self ): + '''Install the filtering_1470 repository to galaxy.''' + ''' + This is step 1 - Install a repository into Galaxy. + ''' + self.galaxy_logout() + self.galaxy_login( email=common.admin_email, username=common.admin_username ) + self.install_repository( repository_name, + common.test_user_1_name, + category_name, + install_tool_dependencies=False, + install_repository_dependencies=False, + new_tool_panel_section_label='Filtering' ) + installed_repository = self.test_db_util.get_installed_repository_by_name_owner( repository_name, + common.test_user_1_name ) + strings_displayed = [ 'filtering_1470', + self.url.replace( 'http://', '' ), + installed_repository.installed_changeset_revision, + installed_repository.changeset_revision ] + self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed ) + self.display_installed_repository_manage_page( installed_repository, + strings_displayed=strings_displayed ) + + def test_0015_update_repository( self ): + '''Upload a readme file to the filtering_1470 repository.''' + ''' + This is step 2 - In the Tool Shed, update the repository from Step 1. + + Importantly, this update should *not* create a new installable changeset revision, because that would + eliminate the process we're testing in this script. So, we upload a readme file. + ''' + repository = self.test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) + self.upload_file( repository, + filename='filtering/readme.txt', + filepath=None, + valid_tools_only=True, + uncompress_file=False, + remove_repo_files_not_in_tar=False, + commit_message='Uploaded readme.', + strings_displayed=[], + strings_not_displayed=[] ) + + def test_0020_get_repository_updates( self ): + '''Get updates to the installed repository.''' + ''' + This is step 3 - In Galaxy, get updates to the repository. + ''' + installed_repository = self.test_db_util.get_installed_repository_by_name_owner( repository_name, + common.test_user_1_name ) + self.update_installed_repository( installed_repository ) + + def test_0025_uninstall_repository( self ): + '''Uninstall the filtering_1470 repository.''' + ''' + This is step 4 - In Galaxy, uninstall the repository. + ''' + installed_repository = self.test_db_util.get_installed_repository_by_name_owner( repository_name, + common.test_user_1_name ) + self.uninstall_repository( installed_repository ) + + def test_0030_reinstall_repository( self ): + '''Reinstall the filtering_1470 repository.''' + ''' + This is step 5 - In Galaxy, reinstall the repository. + ''' + installed_repository = self.test_db_util.get_installed_repository_by_name_owner( repository_name, + common.test_user_1_name ) + self.reinstall_repository( installed_repository ) + + def test_0035_verify_absence_of_ghosts( self ): + '''Check the count of repositories in the database named filtering_1470 and owned by user1.''' + ''' + This is step 6 - Make sure step 5 created no white ghosts. + ''' + installed_repository = self.test_db_util.get_installed_repository_by_name_owner( repository_name, + common.test_user_1_name, + return_multiple=True ) + assert len( installed_repository ) == 1, 'Multiple filtering repositories found in the Galaxy database, possibly indicating a "white ghost" scenario.' +

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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