1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/41f724450789/ changeset: 41f724450789 user: greg date: 2012-06-06 19:26:15 summary: Fixes for getting updates to installed tool shed repositories. affected #: 2 files
diff -r 5343150e167ea8682f25849e7b01e1f40c4b440d -r 41f72445078999fd2a3f6471ee319a0be977097c lib/galaxy/web/controllers/admin_toolshed.py --- a/lib/galaxy/web/controllers/admin_toolshed.py +++ b/lib/galaxy/web/controllers/admin_toolshed.py @@ -174,6 +174,40 @@ return trans.response.send_redirect( url ) @web.expose @web.require_admin + def check_installed_tool_dependencies( self, trans, repository_id, relative_install_dir ): + """See if any tool dependencies need to be installed.""" + tool_dependencies_missing = False + repository = get_repository( trans, repository_id ) + if repository.includes_tool_dependencies: + # Get the tool_dependencies.xml file from the repository. + work_dir = make_tmp_directory() + tool_dependencies_config = get_config_from_repository( trans.app, + 'tool_dependencies.xml', + repository, + repository.changeset_revision, + work_dir, + install_dir=relative_install_dir ) + # Parse the tool_dependencies.xml config. + tree = ElementTree.parse( tool_dependencies_config ) + root = tree.getroot() + ElementInclude.include( root ) + fabric_version_checked = False + for elem in root: + if elem.tag == 'package': + package_name = elem.get( 'name', None ) + package_version = elem.get( 'version', None ) + if package_name and package_version: + install_dir = get_install_dir( trans.app, repository, repository.installed_changeset_revision, package_name, package_version ) + if not_installed( install_dir ): + tool_dependencies_missing = True + break + try: + shutil.rmtree( work_dir ) + except: + pass + return tool_dependencies_missing + @web.expose + @web.require_admin def deactivate_or_uninstall_repository( self, trans, **kwd ): params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) @@ -540,7 +574,8 @@ params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) - repository = get_repository( trans, kwd[ 'id' ] ) + repository_id = kwd[ 'id' ] + repository = get_repository( trans, repository_id ) description = util.restore_text( params.get( 'description', repository.description ) ) shed_tool_conf, tool_path, relative_install_dir = get_tool_panel_config_tool_path_install_dir( trans.app, repository ) repo_files_dir = os.path.abspath( os.path.join( relative_install_dir, repository.name ) ) @@ -558,34 +593,7 @@ trans.sa_session.add( repository ) trans.sa_session.flush() message = "Repository metadata has been reset." - tool_dependencies_missing = False - if repository.includes_tool_dependencies: - # See if any tool dependencies need to be installed, get the tool_dependencies.xml file from the repository. - work_dir = make_tmp_directory() - tool_dependencies_config = get_config_from_repository( trans.app, - 'tool_dependencies.xml', - repository, - repository.changeset_revision, - work_dir, - install_dir=relative_install_dir ) - # Parse the tool_dependencies.xml config. - tree = ElementTree.parse( tool_dependencies_config ) - root = tree.getroot() - ElementInclude.include( root ) - fabric_version_checked = False - for elem in root: - if elem.tag == 'package': - package_name = elem.get( 'name', None ) - package_version = elem.get( 'version', None ) - if package_name and package_version: - install_dir = get_install_dir( trans.app, repository, repository.installed_changeset_revision, package_name, package_version ) - if not_installed( install_dir ): - tool_dependencies_missing = True - break - try: - shutil.rmtree( work_dir ) - except: - pass + tool_dependencies_missing = self.check_installed_tool_dependencies( trans, repository_id, relative_install_dir ) return trans.fill_template( '/admin/tool_shed_repository/manage_repository.mako', repository=repository, description=description, @@ -782,7 +790,7 @@ repository = get_repository_by_shed_name_owner_changeset_revision( trans.app, tool_shed_url, name, owner, changeset_revision ) if changeset_revision and latest_changeset_revision and latest_ctx_rev: if changeset_revision == latest_changeset_revision: - message = "The cloned tool shed repository named '%s' is current (there are no updates available)." % name + message = "The installed repository named '%s' is current, there are no updates available. " % name else: shed_tool_conf, tool_path, relative_install_dir = get_tool_panel_config_tool_path_install_dir( trans.app, repository ) if relative_install_dir: @@ -801,13 +809,17 @@ repository.update_available = False trans.sa_session.add( repository ) trans.sa_session.flush() - message = "The cloned repository named '%s' has been updated to change set revision '%s'." % \ - ( name, latest_changeset_revision ) + message = "The installed repository named '%s' has been updated to change set revision '%s'. " % ( name, latest_changeset_revision ) + # See if any tool dependencies can be installed. + shed_tool_conf, tool_path, relative_install_dir = get_tool_panel_config_tool_path_install_dir( trans.app, repository ) + tool_dependencies_missing = self.check_installed_tool_dependencies( trans, trans.security.encode_id( repository.id ), relative_install_dir ) + if tool_dependencies_missing: + message += "Select <b>Install tool dependencies</b> from the repository's pop-up menu to install tool dependencies." else: - message = "The directory containing the cloned repository named '%s' cannot be found." % name + message = "The directory containing the installed repository named '%s' cannot be found. " % name status = 'error' else: - message = "The latest changeset revision could not be retrieved for the repository named '%s'." % name + message = "The latest changeset revision could not be retrieved for the installed repository named '%s'. " % name status = 'error' return trans.response.send_redirect( web.url_for( controller='admin_toolshed', action='manage_repository',
diff -r 5343150e167ea8682f25849e7b01e1f40c4b440d -r 41f72445078999fd2a3f6471ee319a0be977097c lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -599,6 +599,9 @@ repository = get_repository_by_name_and_owner( trans, name, owner ) repo_dir = repository.repo_path repo = hg.repository( get_configured_ui(), repo_dir ) + # Default to the current changeset revision. + update_to_ctx = get_changectx_for_changeset( repo, changeset_revision ) + latest_changeset_revision = changeset_revision from_update_manager = webapp == 'update_manager' if from_update_manager: update = 'true' @@ -608,80 +611,45 @@ url = '%sadmin_toolshed/update_to_changeset_revision?tool_shed_url=%s' % ( galaxy_url, url_for( '/', qualified=True ) ) url += '&name=%s&owner=%s&changeset_revision=%s&latest_changeset_revision=' % ( repository.name, repository.user.username, changeset_revision ) if changeset_revision == repository.tip: - # If changeset_revision is the repository tip, we know there are no additional updates for the tools. + # If changeset_revision is the repository tip, there are no additional updates. if from_update_manager: return no_update # Return the same value for changeset_revision and latest_changeset_revision. - url += repository.tip + url += latest_changeset_revision else: repository_metadata = get_repository_metadata_by_changeset_revision( trans, trans.security.encode_id( repository.id ), changeset_revision ) if repository_metadata: - # If changeset_revision is in the repository_metadata table for this repository, then we know there are no additional updates - # for the tools. + # If changeset_revision is in the repository_metadata table for this repository, there are no additional updates. if from_update_manager: return no_update else: # Return the same value for changeset_revision and latest_changeset_revision. - url += changeset_revision + url += latest_changeset_revision else: - # TODO: Re-engineer this to define the change set for update to be the one just before the next change set in the repository_metadata - # table for this repository. # The changeset_revision column in the repository_metadata table has been updated with a new changeset_revision value since the - # repository was cloned. Load each tool in the repository's changeset_revision to generate a list of tool guids, since guids - # differentiate tools by id and version. - ctx = get_changectx_for_changeset( repo, changeset_revision ) - if ctx is not None: - work_dir = make_tmp_directory() - tool_guids = [] - for filename in ctx: - # Find all tool configs in this repository changeset_revision. - if filename not in NOT_TOOL_CONFIGS and filename.endswith( '.xml' ): - is_tool_config, valid, tool, error_message = load_tool_from_tmp_directory( trans, - repo, - repo_dir, - ctx, - filename, - work_dir ) - if valid and tool is not None: - tool_guids.append( generate_tool_guid( trans, repository, tool ) ) - tool_guids.sort() - if tool_guids: - # Compare our list of tool guids against those in each repository_metadata record for the repository to find the - # repository_metadata record with the changeset_revision value we want to pass back to the caller. - found = False - for repository_metadata in get_repository_metadata_by_repository_id( trans, trans.security.encode_id( repository.id ) ): - metadata = repository_metadata.metadata - metadata_tool_guids = [] - for tool_dict in metadata[ 'tools' ]: - metadata_tool_guids.append( tool_dict[ 'guid' ] ) - metadata_tool_guids.sort() - if tool_guids == metadata_tool_guids: - # We've found the repository_metadata record whose changeset_revision value has been updated. - if from_update_manager: - return update - url += repository_metadata.changeset_revision - # Get the ctx_rev for the discovered changeset_revision. - latest_ctx = get_changectx_for_changeset( repo, repository_metadata.changeset_revision ) - found = True - break - if not found: - # There must be a problem in the data, so we'll just send back the received changeset_revision. - log.debug( "Possible data corruption - updated repository_metadata cannot be found for repository id %d." % repository.id ) - if from_update_manager: - return no_update - url += changeset_revision - else: - # There are no tools in the changeset_revision, so no tool updates are possible. - if from_update_manager: - return no_update - url += changeset_revision - try: - shutil.rmtree( work_dir ) - except: - pass - url += '&latest_ctx_rev=%s' % str( latest_ctx.rev() ) + # repository was installed. We need to find the changeset_revision to which we need to update. + update_to_changeset_hash = None + for changeset in repo.changelog: + changeset_hash = str( repo.changectx( changeset ) ) + ctx = get_changectx_for_changeset( repo, changeset_hash ) + if update_to_changeset_hash: + if get_repository_metadata_by_changeset_revision( trans, trans.security.encode_id( repository.id ), changeset_hash ): + # We found a RepositoryMetadata record. + if changeset_hash == repository.tip: + # The current ctx is the repository tip, so use it. + update_to_ctx = get_changectx_for_changeset( repo, changeset_hash ) + latest_changeset_revision = changeset_hash + else: + update_to_ctx = get_changectx_for_changeset( repo, update_to_changeset_hash ) + latest_changeset_revision = update_to_changeset_hash + break + elif not update_to_changeset_hash and changeset_hash == changeset_revision: + # We've found the changeset in the changelog for which we need to get the next update. + update_to_changeset_hash = changeset_hash + url += str( latest_changeset_revision ) + url += '&latest_ctx_rev=%s' % str( update_to_ctx.rev() ) return trans.response.send_redirect( url ) @web.expose def contact_owner( self, trans, id, **kwd ):
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