1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/55bbaa8f5017/ Changeset: 55bbaa8f5017 User: dannon Date: 2013-08-30 18:06:10 Summary: Re-apply changes that got reverted in 10492:8f6f926f912e Affected #: 2 files diff -r 8f6f926f912e2aea3f11905498fd5f04f857ec97 -r 55bbaa8f5017e32dbe7968514a4f87b941ed2a0d lib/galaxy/webapps/tool_shed/controllers/repository.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py @@ -2664,7 +2664,7 @@ if repository: repo_dir = repository.repo_path( trans.app ) repo = hg.repository( suc.get_configured_ui(), repo_dir ) - tool_shed_status_dict = {} + tool_shed_status_dict = {} # Handle repository deprecation. tool_shed_status_dict[ 'repository_deprecated' ] = str( repository.deprecated ) # Handle latest installable revision. @@ -2680,7 +2680,7 @@ if changeset_revision == repository.tip( trans.app ): tool_shed_status_dict[ 'revision_update' ] = 'False' else: - repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, + repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, trans.security.encode_id( repository.id ), changeset_revision ) if repository_metadata: diff -r 8f6f926f912e2aea3f11905498fd5f04f857ec97 -r 55bbaa8f5017e32dbe7968514a4f87b941ed2a0d lib/tool_shed/util/shed_util_common.py --- a/lib/tool_shed/util/shed_util_common.py +++ b/lib/tool_shed/util/shed_util_common.py @@ -31,7 +31,7 @@ eggs.require( 'markupsafe' ) import markupsafe - + log = logging.getLogger( __name__ ) CHUNK_SIZE = 2**20 # 1Mb @@ -209,7 +209,7 @@ return tool_shed_url.split( ':' )[ 0 ] return tool_shed_url.rstrip( '/' ) -def clone_repository( repository_clone_url, repository_file_dir, ctx_rev ): +def clone_repository( repository_clone_url, repository_file_dir, ctx_rev ): """Clone the repository up to the specified changeset_revision. No subsequent revisions will be present in the cloned repository.""" try: commands.clone( get_configured_ui(), @@ -263,7 +263,7 @@ # was later uninstalled, this value should be received as the value of that change set to which the repository had been updated just prior # to it being uninstalled. current_changeset_revision = installed_changeset_revision - sa_session = app.model.context.current + sa_session = app.model.context.current tool_shed = get_tool_shed_from_clone_url( repository_clone_url ) if not owner: owner = get_repository_owner_from_clone_url( repository_clone_url ) @@ -351,7 +351,7 @@ new_elem = XmlET.SubElement( elem, key ) new_elem.text = value return elem - + def generate_repository_info_elem_from_repository( tool_shed_repository, parent_elem=None, **kwd ): return generate_repository_info_elem( tool_shed_repository.tool_shed, tool_shed_repository.name, @@ -394,7 +394,7 @@ def generate_tool_guid( repository_clone_url, tool ): """ Generate a guid for the installed tool. It is critical that this guid matches the guid for - the tool in the Galaxy tool shed from which it is being installed. The form of the guid is + the tool in the Galaxy tool shed from which it is being installed. The form of the guid is <tool shed host>/repos/<repository owner>/<repository name>/<tool id>/<tool version> """ tmp_url = clean_repository_clone_url( repository_clone_url ) @@ -417,7 +417,7 @@ tool_config = tool_dict[ 'tool_config' ] file_name = strip_path( tool_config ) guids_and_configs[ guid ] = file_name - # Parse the shed_tool_conf file in which all of this repository's tools are defined and generate the tool_panel_dict. + # Parse the shed_tool_conf file in which all of this repository's tools are defined and generate the tool_panel_dict. tree, error_message = xml_util.parse_xml( shed_tool_conf ) if tree is None: return tool_panel_dict @@ -535,7 +535,7 @@ Send a request to the tool shed to retrieve the ctx_rev for a repository defined by the combination of a name, owner and changeset revision. """ - url = url_join( tool_shed_url, + url = url_join( tool_shed_url, 'repository/get_ctx_rev?name=%s&owner=%s&changeset_revision=%s' % ( name, owner, changeset_revision ) ) ctx_rev = common_util.tool_shed_get( app, tool_shed_url, url ) return ctx_rev @@ -1385,7 +1385,7 @@ def reset_previously_installed_repository( trans, repository ): """ - Reset the atrributes of a tool_shed_repository that was previsouly installed. The repository will be in some state other than with a + Reset the atrributes of a tool_shed_repository that was previsouly installed. The repository will be in some state other than with a status of INSTALLED, so all atributes will be set to the default (NEW( state. This will enable the repository to be freshly installed. """ repository.deleted = False 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.