commit/galaxy-central: 2 new changesets
2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d2b9f616e66c/ Changeset: d2b9f616e66c Branch: next-stable User: greg Date: 2013-10-31 03:43:02 Summary: Fix for sert_environment tag in tool dependencies definitions. Affected #: 5 files diff -r 232ef8122d540d9a232b4f29e0a9d907ffaeae13 -r d2b9f616e66c6fe6c93cc78ef2132a09b1103afb lib/tool_shed/galaxy_install/repository_util.py --- a/lib/tool_shed/galaxy_install/repository_util.py +++ b/lib/tool_shed/galaxy_install/repository_util.py @@ -94,22 +94,23 @@ def get_installed_repositories_from_repository_dependencies( trans, repository_dependencies_dict ): installed_repositories = [] - for rd_key, rd_vals in repository_dependencies_dict.items(): - if rd_key in [ 'root_key', 'description' ]: - continue - # rd_key is something like: 'http://localhost:9009__ESEP__package_rdkit_2012_12__ESEP__test__ESEP__d635ff...' - # rd_val is something like: [['http://localhost:9009', 'package_numpy_1_7', 'test', 'cddd64ecd985', 'True']] - repository_components_tuple = container_util.get_components_from_key( rd_key ) - components_list = suc.extract_components_from_tuple( repository_components_tuple ) - tool_shed, name, owner, changeset_revision = components_list[ 0:4 ] - installed_repository = suc.get_tool_shed_repository_by_shed_name_owner_changeset_revision( trans.app, tool_shed, name, owner, changeset_revision ) - if installed_repository not in installed_repositories: - installed_repositories.append( installed_repository ) - for rd_val in rd_vals: - tool_shed, name, owner, changeset_revision = rd_val[ 0:4 ] + if repository_dependencies_dict and isinstance( repository_dependencies_dict, dict ): + for rd_key, rd_vals in repository_dependencies_dict.items(): + if rd_key in [ 'root_key', 'description' ]: + continue + # rd_key is something like: 'http://localhost:9009__ESEP__package_rdkit_2012_12__ESEP__test__ESEP__d635ff...' + # rd_val is something like: [['http://localhost:9009', 'package_numpy_1_7', 'test', 'cddd64ecd985', 'True']] + repository_components_tuple = container_util.get_components_from_key( rd_key ) + components_list = suc.extract_components_from_tuple( repository_components_tuple ) + tool_shed, name, owner, changeset_revision = components_list[ 0:4 ] installed_repository = suc.get_tool_shed_repository_by_shed_name_owner_changeset_revision( trans.app, tool_shed, name, owner, changeset_revision ) if installed_repository not in installed_repositories: installed_repositories.append( installed_repository ) + for rd_val in rd_vals: + tool_shed, name, owner, changeset_revision = rd_val[ 0:4 ] + installed_repository = suc.get_tool_shed_repository_by_shed_name_owner_changeset_revision( trans.app, tool_shed, name, owner, changeset_revision ) + if installed_repository not in installed_repositories: + installed_repositories.append( installed_repository ) return installed_repositories def get_prior_install_required_dict( trans, tsr_ids, repo_info_dicts ): diff -r 232ef8122d540d9a232b4f29e0a9d907ffaeae13 -r d2b9f616e66c6fe6c93cc78ef2132a09b1103afb lib/tool_shed/galaxy_install/tool_dependencies/install_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py @@ -796,7 +796,7 @@ pass return returncode, message -def set_environment( app, elem, tool_shed_repository ): +def set_environment( app, elem, tool_shed_repository, attr_tups_of_dependencies_for_install ): """ Create a ToolDependency to set an environment variable. This is different from the process used to set an environment variable that is associated with a package. An example entry in a tool_dependencies.xml file is:: @@ -814,42 +814,47 @@ tool_dependency = None env_var_version = elem.get( 'version', '1.0' ) for env_var_elem in elem: + # Althoug we're in a loop here, this method will always return only a single ToolDependency or None. + env_var_name = env_var_elem.get( 'name', None ) # The value of env_var_name must match the text value of at least 1 <requirement> tag in the tool config's <requirements> tag set whose # "type" attribute is "set_environment" (e.g., <requirement type="set_environment">R_SCRIPT_PATH</requirement>). - env_var_name = env_var_elem.get( 'name', None ) env_var_action = env_var_elem.get( 'action', None ) if env_var_name and env_var_action: - install_dir = get_tool_dependency_install_dir( app=app, - repository_name=tool_shed_repository.name, - repository_owner=tool_shed_repository.owner, - repository_changeset_revision=tool_shed_repository.installed_changeset_revision, - tool_dependency_type='set_environment', - tool_dependency_name=env_var_name, - tool_dependency_version=None ) - tool_shed_repository_install_dir = get_tool_shed_repository_install_dir( app, tool_shed_repository ) - env_var_dict = td_common_util.create_env_var_dict( env_var_elem, tool_shed_repository_install_dir=tool_shed_repository_install_dir ) - if env_var_dict: - if not os.path.exists( install_dir ): - os.makedirs( install_dir ) - tool_dependency = tool_dependency_util.create_or_update_tool_dependency( app=app, - tool_shed_repository=tool_shed_repository, - name=env_var_name, - version=None, - type='set_environment', - status=app.model.ToolDependency.installation_status.INSTALLING, - set_status=True ) - env_entry, env_file = td_common_util.create_or_update_env_shell_file( install_dir, env_var_dict ) - if env_var_version == '1.0': - # Handle setting environment variables using a fabric method. - fabric_util.file_append( env_entry, env_file, skip_if_contained=True, make_executable=True ) - sa_session.refresh( tool_dependency ) - if tool_dependency.status != app.model.ToolDependency.installation_status.ERROR: - tool_dependency.status = app.model.ToolDependency.installation_status.INSTALLED - sa_session.add( tool_dependency ) - sa_session.flush() - print 'Environment variable ', env_var_name, 'set in', install_dir - else: - raise NotImplementedError( 'Only set_environment version 1.0 is currently supported (i.e., change your tag to be <set_environment version="1.0">).' ) + # Tool dependencies of type "set_environmnet" always have the version attribute set to None. + attr_tup = ( env_var_name, None, 'set_environment' ) + if attr_tup in attr_tups_of_dependencies_for_install: + install_dir = get_tool_dependency_install_dir( app=app, + repository_name=tool_shed_repository.name, + repository_owner=tool_shed_repository.owner, + repository_changeset_revision=tool_shed_repository.installed_changeset_revision, + tool_dependency_type='set_environment', + tool_dependency_name=env_var_name, + tool_dependency_version=None ) + tool_shed_repository_install_dir = get_tool_shed_repository_install_dir( app, tool_shed_repository ) + env_var_dict = td_common_util.create_env_var_dict( env_var_elem, tool_shed_repository_install_dir=tool_shed_repository_install_dir ) + if env_var_dict: + if not os.path.exists( install_dir ): + os.makedirs( install_dir ) + tool_dependency = tool_dependency_util.create_or_update_tool_dependency( app=app, + tool_shed_repository=tool_shed_repository, + name=env_var_name, + version=None, + type='set_environment', + status=app.model.ToolDependency.installation_status.INSTALLING, + set_status=True ) + env_entry, env_file = td_common_util.create_or_update_env_shell_file( install_dir, env_var_dict ) + if env_var_version == '1.0': + # Handle setting environment variables using a fabric method. + fabric_util.file_append( env_entry, env_file, skip_if_contained=True, make_executable=True ) + sa_session.refresh( tool_dependency ) + if tool_dependency.status != app.model.ToolDependency.installation_status.ERROR: + tool_dependency.status = app.model.ToolDependency.installation_status.INSTALLED + sa_session.add( tool_dependency ) + sa_session.flush() + print 'Environment variable ', env_var_name, 'set in', install_dir + else: + raise NotImplementedError( 'Only set_environment version 1.0 is currently supported (i.e., change your tag to be <set_environment version="1.0">).' ) + return tool_dependency def strip_path( fpath ): if not fpath: diff -r 232ef8122d540d9a232b4f29e0a9d907ffaeae13 -r d2b9f616e66c6fe6c93cc78ef2132a09b1103afb lib/tool_shed/util/common_install_util.py --- a/lib/tool_shed/util/common_install_util.py +++ b/lib/tool_shed/util/common_install_util.py @@ -483,24 +483,22 @@ app.model.ToolDependency.installation_status.ERROR ]: installed_tool_dependencies.append( tool_dependency ) elif elem.tag == 'set_environment': - env_var_name = elem.get( 'name', None ) - if env_var_name: - # Tool dependencies of type "set_environmnet" always have the version attribute set to None. - attr_tup = ( env_var_name, None, 'set_environment' ) - if attr_tup in attr_tups_of_dependencies_for_install: - try: - tool_dependency = set_environment( app, elem, tool_shed_repository ) - except Exception, e: - error_message = "Error setting environment for tool dependency: %s" % str( e ) - log.debug( error_message ) - if tool_dependency: - tool_dependency.status = app.model.ToolDependency.installation_status.ERROR - tool_dependency.error_message = error_message - sa_session.add( tool_dependency ) - sa_session.flush() - if tool_dependency and tool_dependency.status in [ app.model.ToolDependency.installation_status.INSTALLED, - app.model.ToolDependency.installation_status.ERROR ]: - installed_tool_dependencies.append( tool_dependency ) + # <set_environment version="1.0"> + # <environment_variable name="R_SCRIPT_PATH"action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable> + # </set_environment> + try: + tool_dependency = set_environment( app, elem, tool_shed_repository, attr_tups_of_dependencies_for_install ) + except Exception, e: + error_message = "Error setting environment for tool dependency: %s" % str( e ) + log.debug( error_message ) + if tool_dependency: + tool_dependency.status = app.model.ToolDependency.installation_status.ERROR + tool_dependency.error_message = error_message + sa_session.add( tool_dependency ) + sa_session.flush() + if tool_dependency and tool_dependency.status in [ app.model.ToolDependency.installation_status.INSTALLED, + app.model.ToolDependency.installation_status.ERROR ]: + installed_tool_dependencies.append( tool_dependency ) return installed_tool_dependencies def repository_dependency_needed_only_for_compiling_tool_dependency( repository, repository_dependency ): diff -r 232ef8122d540d9a232b4f29e0a9d907ffaeae13 -r d2b9f616e66c6fe6c93cc78ef2132a09b1103afb 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 @@ -58,7 +58,7 @@ commit_message='Uploaded tool_dependencies.xml.', 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' ] ) + self.display_manage_repository_page( repository, strings_displayed=[ 'Tool dependencies', 'type should be set to' ] ) def test_0010_create_bwa_base_repository( self ): '''Create and populate bwa_base_0100.''' diff -r 232ef8122d540d9a232b4f29e0a9d907ffaeae13 -r d2b9f616e66c6fe6c93cc78ef2132a09b1103afb test/tool_shed/functional/test_1230_uninstall_reinstall_repository_with_dependency_revisions.py --- a/test/tool_shed/functional/test_1230_uninstall_reinstall_repository_with_dependency_revisions.py +++ b/test/tool_shed/functional/test_1230_uninstall_reinstall_repository_with_dependency_revisions.py @@ -136,9 +136,13 @@ # repository, and this should add datatypes to the datatypes registry. If that is the case, verify that datatypes # have been added, otherwise verify that the count is unchanged. if running_standalone: - assert current_datatypes == base_datatypes_count + repository_datatypes_count, 'Installing emboss did not add new datatypes.' + assert current_datatypes == base_datatypes_count + repository_datatypes_count, \ + 'Installing emboss resulted in unexpected count in datatypes registry, expected: %s, actual: %s, original: %s, added from repo: %s' % \ + ( str( base_datatypes_count + repository_datatypes_count ), str( current_datatypes ), str( base_datatypes_count ), str( repository_datatypes_count ) ) else: - assert current_datatypes == base_datatypes_count, 'Installing emboss added new datatypes.' + assert current_datatypes == base_datatypes_count, \ + 'Installing emboss added new datatypes, current datatypes: %s, original datatypes: %s' % \ + ( str( current_datatypes ), str( base_datatypes_count ) ) def test_0015_uninstall_emboss_repository( self ): '''Uninstall the emboss repository.''' https://bitbucket.org/galaxy/galaxy-central/commits/d656aa5dde98/ Changeset: d656aa5dde98 User: greg Date: 2013-10-31 03:43:47 Summary: Merged from next-stable Affected #: 6 files diff -r 51dc1b78858287d5fd376bccd9a88ba4b91b1cc2 -r d656aa5dde983ba8fce0cc6d2e4346943e582168 lib/tool_shed/galaxy_install/repository_util.py --- a/lib/tool_shed/galaxy_install/repository_util.py +++ b/lib/tool_shed/galaxy_install/repository_util.py @@ -94,22 +94,23 @@ def get_installed_repositories_from_repository_dependencies( trans, repository_dependencies_dict ): installed_repositories = [] - for rd_key, rd_vals in repository_dependencies_dict.items(): - if rd_key in [ 'root_key', 'description' ]: - continue - # rd_key is something like: 'http://localhost:9009__ESEP__package_rdkit_2012_12__ESEP__test__ESEP__d635ff...' - # rd_val is something like: [['http://localhost:9009', 'package_numpy_1_7', 'test', 'cddd64ecd985', 'True']] - repository_components_tuple = container_util.get_components_from_key( rd_key ) - components_list = suc.extract_components_from_tuple( repository_components_tuple ) - tool_shed, name, owner, changeset_revision = components_list[ 0:4 ] - installed_repository = suc.get_tool_shed_repository_by_shed_name_owner_changeset_revision( trans.app, tool_shed, name, owner, changeset_revision ) - if installed_repository not in installed_repositories: - installed_repositories.append( installed_repository ) - for rd_val in rd_vals: - tool_shed, name, owner, changeset_revision = rd_val[ 0:4 ] + if repository_dependencies_dict and isinstance( repository_dependencies_dict, dict ): + for rd_key, rd_vals in repository_dependencies_dict.items(): + if rd_key in [ 'root_key', 'description' ]: + continue + # rd_key is something like: 'http://localhost:9009__ESEP__package_rdkit_2012_12__ESEP__test__ESEP__d635ff...' + # rd_val is something like: [['http://localhost:9009', 'package_numpy_1_7', 'test', 'cddd64ecd985', 'True']] + repository_components_tuple = container_util.get_components_from_key( rd_key ) + components_list = suc.extract_components_from_tuple( repository_components_tuple ) + tool_shed, name, owner, changeset_revision = components_list[ 0:4 ] installed_repository = suc.get_tool_shed_repository_by_shed_name_owner_changeset_revision( trans.app, tool_shed, name, owner, changeset_revision ) if installed_repository not in installed_repositories: installed_repositories.append( installed_repository ) + for rd_val in rd_vals: + tool_shed, name, owner, changeset_revision = rd_val[ 0:4 ] + installed_repository = suc.get_tool_shed_repository_by_shed_name_owner_changeset_revision( trans.app, tool_shed, name, owner, changeset_revision ) + if installed_repository not in installed_repositories: + installed_repositories.append( installed_repository ) return installed_repositories def get_prior_install_required_dict( trans, tsr_ids, repo_info_dicts ): diff -r 51dc1b78858287d5fd376bccd9a88ba4b91b1cc2 -r d656aa5dde983ba8fce0cc6d2e4346943e582168 lib/tool_shed/galaxy_install/tool_dependencies/install_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py @@ -836,7 +836,7 @@ pass return returncode, message -def set_environment( app, elem, tool_shed_repository ): +def set_environment( app, elem, tool_shed_repository, attr_tups_of_dependencies_for_install ): """ Create a ToolDependency to set an environment variable. This is different from the process used to set an environment variable that is associated with a package. An example entry in a tool_dependencies.xml file is:: @@ -854,42 +854,47 @@ tool_dependency = None env_var_version = elem.get( 'version', '1.0' ) for env_var_elem in elem: + # Althoug we're in a loop here, this method will always return only a single ToolDependency or None. + env_var_name = env_var_elem.get( 'name', None ) # The value of env_var_name must match the text value of at least 1 <requirement> tag in the tool config's <requirements> tag set whose # "type" attribute is "set_environment" (e.g., <requirement type="set_environment">R_SCRIPT_PATH</requirement>). - env_var_name = env_var_elem.get( 'name', None ) env_var_action = env_var_elem.get( 'action', None ) if env_var_name and env_var_action: - install_dir = get_tool_dependency_install_dir( app=app, - repository_name=tool_shed_repository.name, - repository_owner=tool_shed_repository.owner, - repository_changeset_revision=tool_shed_repository.installed_changeset_revision, - tool_dependency_type='set_environment', - tool_dependency_name=env_var_name, - tool_dependency_version=None ) - tool_shed_repository_install_dir = get_tool_shed_repository_install_dir( app, tool_shed_repository ) - env_var_dict = td_common_util.create_env_var_dict( env_var_elem, tool_shed_repository_install_dir=tool_shed_repository_install_dir ) - if env_var_dict: - if not os.path.exists( install_dir ): - os.makedirs( install_dir ) - tool_dependency = tool_dependency_util.create_or_update_tool_dependency( app=app, - tool_shed_repository=tool_shed_repository, - name=env_var_name, - version=None, - type='set_environment', - status=app.model.ToolDependency.installation_status.INSTALLING, - set_status=True ) - env_entry, env_file = td_common_util.create_or_update_env_shell_file( install_dir, env_var_dict ) - if env_var_version == '1.0': - # Handle setting environment variables using a fabric method. - fabric_util.file_append( env_entry, env_file, skip_if_contained=True, make_executable=True ) - sa_session.refresh( tool_dependency ) - if tool_dependency.status != app.model.ToolDependency.installation_status.ERROR: - tool_dependency.status = app.model.ToolDependency.installation_status.INSTALLED - sa_session.add( tool_dependency ) - sa_session.flush() - print 'Environment variable ', env_var_name, 'set in', install_dir - else: - raise NotImplementedError( 'Only set_environment version 1.0 is currently supported (i.e., change your tag to be <set_environment version="1.0">).' ) + # Tool dependencies of type "set_environmnet" always have the version attribute set to None. + attr_tup = ( env_var_name, None, 'set_environment' ) + if attr_tup in attr_tups_of_dependencies_for_install: + install_dir = get_tool_dependency_install_dir( app=app, + repository_name=tool_shed_repository.name, + repository_owner=tool_shed_repository.owner, + repository_changeset_revision=tool_shed_repository.installed_changeset_revision, + tool_dependency_type='set_environment', + tool_dependency_name=env_var_name, + tool_dependency_version=None ) + tool_shed_repository_install_dir = get_tool_shed_repository_install_dir( app, tool_shed_repository ) + env_var_dict = td_common_util.create_env_var_dict( env_var_elem, tool_shed_repository_install_dir=tool_shed_repository_install_dir ) + if env_var_dict: + if not os.path.exists( install_dir ): + os.makedirs( install_dir ) + tool_dependency = tool_dependency_util.create_or_update_tool_dependency( app=app, + tool_shed_repository=tool_shed_repository, + name=env_var_name, + version=None, + type='set_environment', + status=app.model.ToolDependency.installation_status.INSTALLING, + set_status=True ) + env_entry, env_file = td_common_util.create_or_update_env_shell_file( install_dir, env_var_dict ) + if env_var_version == '1.0': + # Handle setting environment variables using a fabric method. + fabric_util.file_append( env_entry, env_file, skip_if_contained=True, make_executable=True ) + sa_session.refresh( tool_dependency ) + if tool_dependency.status != app.model.ToolDependency.installation_status.ERROR: + tool_dependency.status = app.model.ToolDependency.installation_status.INSTALLED + sa_session.add( tool_dependency ) + sa_session.flush() + print 'Environment variable ', env_var_name, 'set in', install_dir + else: + raise NotImplementedError( 'Only set_environment version 1.0 is currently supported (i.e., change your tag to be <set_environment version="1.0">).' ) + return tool_dependency def strip_path( fpath ): if not fpath: diff -r 51dc1b78858287d5fd376bccd9a88ba4b91b1cc2 -r d656aa5dde983ba8fce0cc6d2e4346943e582168 lib/tool_shed/util/common_install_util.py --- a/lib/tool_shed/util/common_install_util.py +++ b/lib/tool_shed/util/common_install_util.py @@ -483,24 +483,22 @@ app.model.ToolDependency.installation_status.ERROR ]: installed_tool_dependencies.append( tool_dependency ) elif elem.tag == 'set_environment': - env_var_name = elem.get( 'name', None ) - if env_var_name: - # Tool dependencies of type "set_environmnet" always have the version attribute set to None. - attr_tup = ( env_var_name, None, 'set_environment' ) - if attr_tup in attr_tups_of_dependencies_for_install: - try: - tool_dependency = set_environment( app, elem, tool_shed_repository ) - except Exception, e: - error_message = "Error setting environment for tool dependency: %s" % str( e ) - log.debug( error_message ) - if tool_dependency: - tool_dependency.status = app.model.ToolDependency.installation_status.ERROR - tool_dependency.error_message = error_message - sa_session.add( tool_dependency ) - sa_session.flush() - if tool_dependency and tool_dependency.status in [ app.model.ToolDependency.installation_status.INSTALLED, - app.model.ToolDependency.installation_status.ERROR ]: - installed_tool_dependencies.append( tool_dependency ) + # <set_environment version="1.0"> + # <environment_variable name="R_SCRIPT_PATH"action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable> + # </set_environment> + try: + tool_dependency = set_environment( app, elem, tool_shed_repository, attr_tups_of_dependencies_for_install ) + except Exception, e: + error_message = "Error setting environment for tool dependency: %s" % str( e ) + log.debug( error_message ) + if tool_dependency: + tool_dependency.status = app.model.ToolDependency.installation_status.ERROR + tool_dependency.error_message = error_message + sa_session.add( tool_dependency ) + sa_session.flush() + if tool_dependency and tool_dependency.status in [ app.model.ToolDependency.installation_status.INSTALLED, + app.model.ToolDependency.installation_status.ERROR ]: + installed_tool_dependencies.append( tool_dependency ) return installed_tool_dependencies def repository_dependency_needed_only_for_compiling_tool_dependency( repository, repository_dependency ): diff -r 51dc1b78858287d5fd376bccd9a88ba4b91b1cc2 -r d656aa5dde983ba8fce0cc6d2e4346943e582168 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 @@ -58,7 +58,7 @@ commit_message='Uploaded tool_dependencies.xml.', 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' ] ) + self.display_manage_repository_page( repository, strings_displayed=[ 'Tool dependencies', 'type should be set to' ] ) def test_0010_create_bwa_base_repository( self ): '''Create and populate bwa_base_0100.''' diff -r 51dc1b78858287d5fd376bccd9a88ba4b91b1cc2 -r d656aa5dde983ba8fce0cc6d2e4346943e582168 test/tool_shed/functional/test_1230_uninstall_reinstall_repository_with_dependency_revisions.py --- a/test/tool_shed/functional/test_1230_uninstall_reinstall_repository_with_dependency_revisions.py +++ b/test/tool_shed/functional/test_1230_uninstall_reinstall_repository_with_dependency_revisions.py @@ -136,9 +136,13 @@ # repository, and this should add datatypes to the datatypes registry. If that is the case, verify that datatypes # have been added, otherwise verify that the count is unchanged. if running_standalone: - assert current_datatypes == base_datatypes_count + repository_datatypes_count, 'Installing emboss did not add new datatypes.' + assert current_datatypes == base_datatypes_count + repository_datatypes_count, \ + 'Installing emboss resulted in unexpected count in datatypes registry, expected: %s, actual: %s, original: %s, added from repo: %s' % \ + ( str( base_datatypes_count + repository_datatypes_count ), str( current_datatypes ), str( base_datatypes_count ), str( repository_datatypes_count ) ) else: - assert current_datatypes == base_datatypes_count, 'Installing emboss added new datatypes.' + assert current_datatypes == base_datatypes_count, \ + 'Installing emboss added new datatypes, current datatypes: %s, original datatypes: %s' % \ + ( str( current_datatypes ), str( base_datatypes_count ) ) def test_0015_uninstall_emboss_repository( self ): '''Uninstall the emboss repository.''' 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