1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/commits/53d3c967d373/ Changeset: 53d3c967d373 User: greg Date: 2013-05-16 02:15:11 Summary: Add the ability for a repository owner to check a "Skip automated testing of tools in this revision" checkbox on the Manage repository page. If checked, the tool shed automated test framework will skip testing the tools in that revision. Affected #: 2 files

diff -r f2e183a522d8b1d08ff293f23cce254cc4597721 -r 53d3c967d373c3b0589a31a4e400b01786cea091 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 @@ -341,7 +341,7 @@ message += '<ul>' message += '<li>you are authorized to update them</li>' message += '<li>the latest installable revision contains at least 1 tool</li>' - message += '<li>the latest installable revision has <b>Skip tool tests</b> checked</li>' + message += '<li>the latest installable revision has <b>Skip automated testing of tools in this revision</b> checked</li>' message += '</ul>' kwd[ 'message' ] = message kwd[ 'status' ] = 'warning' @@ -649,7 +649,7 @@ message = 'This list contains repositories that match the following criteria:<br>' message += '<ul>' message += '<li>the latest installable revision contains at least 1 tool</li>' - message += '<li>the latest installable revision has <b>Skip tool tests</b> checked</li>' + message += '<li>the latest installable revision has <b>Skip automated testing of tools in this revision</b> checked</li>' message += '</ul>' kwd[ 'message' ] = message kwd[ 'status' ] = 'warning' @@ -1976,29 +1976,31 @@ @web.expose @web.require_login( "manage repository" ) def manage_repository( self, trans, id, **kwd ): - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) + message = util.restore_text( kwd.get( 'message', '' ) ) + status = kwd.get( 'status', 'done' ) repository = suc.get_repository_in_tool_shed( trans, id ) repo_dir = repository.repo_path( trans.app ) repo = hg.repository( suc.get_configured_ui(), repo_dir ) - repo_name = util.restore_text( params.get( 'repo_name', repository.name ) ) - changeset_revision = util.restore_text( params.get( 'changeset_revision', repository.tip( trans.app ) ) ) - description = util.restore_text( params.get( 'description', repository.description ) ) - long_description = util.restore_text( params.get( 'long_description', repository.long_description ) ) + repo_name = util.restore_text( kwd.get( 'repo_name', repository.name ) ) + changeset_revision = util.restore_text( kwd.get( 'changeset_revision', repository.tip( trans.app ) ) ) + description = util.restore_text( kwd.get( 'description', repository.description ) ) + long_description = util.restore_text( kwd.get( 'long_description', repository.long_description ) ) avg_rating, num_ratings = self.get_ave_item_rating_data( trans.sa_session, repository, webapp_model=trans.model ) - display_reviews = util.string_as_bool( params.get( 'display_reviews', False ) ) - alerts = params.get( 'alerts', '' ) + display_reviews = util.string_as_bool( kwd.get( 'display_reviews', False ) ) + alerts = kwd.get( 'alerts', '' ) alerts_checked = CheckboxField.is_checked( alerts ) - category_ids = util.listify( params.get( 'category_id', '' ) ) + skip_tool_tests = kwd.get( 'skip_tool_tests', '' ) + skip_tool_tests_checked = CheckboxField.is_checked( skip_tool_tests ) + skip_tool_tests_comment = kwd.get( 'skip_tool_tests_comment', '' ) + category_ids = util.listify( kwd.get( 'category_id', '' ) ) if repository.email_alerts: email_alerts = json.from_json_string( repository.email_alerts ) else: email_alerts = [] - allow_push = params.get( 'allow_push', '' ) + allow_push = kwd.get( 'allow_push', '' ) error = False user = trans.user - if params.get( 'edit_repository_button', False ): + if kwd.get( 'edit_repository_button', False ): flush_needed = False # TODO: add a can_manage in the security agent. if not ( user.email == repository.user.email or trans.user_is_admin() ): @@ -2034,7 +2036,32 @@ trans.sa_session.add( repository ) trans.sa_session.flush() message += "The repository information has been updated." - elif params.get( 'manage_categories_button', False ): + elif kwd.get( 'skip_tool_tests_button', False ): + repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, id, changeset_revision ) + skip_tool_test = repository_metadata.skip_tool_tests + if skip_tool_test: + # Handle the mapper behavior. + skip_tool_test = skip_tool_test[ 0 ] + if skip_tool_tests_checked: + if skip_tool_test: + comment = skip_tool_test.comment + if comment != skip_tool_tests_comment: + skip_tool_test.comment = skip_tool_tests_comment + trans.sa_session.add( skip_tool_test ) + trans.sa_session.flush() + else: + skip_tool_test = trans.model.SkipToolTest( repository_metadata_id=repository_metadata.id, + initial_changeset_revision=changeset_revision, + comment=skip_tool_tests_comment ) + trans.sa_session.add( skip_tool_test ) + trans.sa_session.flush() + message = "Tools in this revision will be tested by the automated test framework." + else: + if skip_tool_test: + trans.sa_session.delete( skip_tool_test ) + trans.sa_session.flush() + message = "Tools in this revision will not be tested by the automated test framework." + elif kwd.get( 'manage_categories_button', False ): flush_needed = False # Delete all currently existing categories. for rca in repository.categories: @@ -2043,14 +2070,14 @@ if category_ids: # Create category associations for category_id in category_ids: - category = trans.sa_session.query(model.Category).get( trans.security.decode_id( category_id ) ) + category = trans.sa_session.query( trans.model.Category ).get( trans.security.decode_id( category_id ) ) rca = trans.app.model.RepositoryCategoryAssociation( repository, category ) trans.sa_session.add( rca ) trans.sa_session.flush() message = "The repository information has been updated." - elif params.get( 'user_access_button', False ): + elif kwd.get( 'user_access_button', False ): if allow_push not in [ 'none' ]: - remove_auth = params.get( 'remove_auth', '' ) + remove_auth = kwd.get( 'remove_auth', '' ) if remove_auth: usernames = '' else: @@ -2062,7 +2089,7 @@ usernames = ','.join( usernames ) repository.set_allow_push( trans.app, usernames, remove_auth=remove_auth ) message = "The repository information has been updated." - elif params.get( 'receive_email_alerts_button', False ): + elif kwd.get( 'receive_email_alerts_button', False ): flush_needed = False if alerts_checked: if user.email not in email_alerts: @@ -2097,6 +2124,7 @@ repository_metadata = None metadata = None is_malicious = False + skip_tool_test = None repository_dependencies = None if changeset_revision != suc.INITIAL_CHANGELOG_HASH: repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, id, changeset_revision ) @@ -2114,6 +2142,11 @@ metadata = repository_metadata.metadata is_malicious = repository_metadata.malicious if repository_metadata: + skip_tool_test = repository_metadata.skip_tool_tests + if skip_tool_test: + # Handle the mapper behavior. + skip_tool_test = skip_tool_test[ 0 ] + skip_tool_tests_checked = True metadata = repository_metadata.metadata # Get a dictionary of all repositories upon which the contents of the current repository_metadata record depend. repository_dependencies = \ @@ -2136,6 +2169,7 @@ message += malicious_error status = 'error' malicious_check_box = CheckboxField( 'malicious', checked=is_malicious ) + skip_tool_tests_check_box = CheckboxField( 'skip_tool_tests', checked=skip_tool_tests_checked ) categories = suc.get_categories( trans ) selected_categories = [ rca.category_id for rca in repository.categories ] containers_dict = container_util.build_repository_containers_for_tool_shed( trans, repository, changeset_revision, repository_dependencies, repository_metadata ) @@ -2159,6 +2193,8 @@ display_reviews=display_reviews, num_ratings=num_ratings, alerts_check_box=alerts_check_box, + skip_tool_tests_check_box=skip_tool_tests_check_box, + skip_tool_test=skip_tool_test, malicious_check_box=malicious_check_box, message=message, status=status )

diff -r f2e183a522d8b1d08ff293f23cce254cc4597721 -r 53d3c967d373c3b0589a31a4e400b01786cea091 templates/webapps/tool_shed/repository/manage_repository.mako --- a/templates/webapps/tool_shed/repository/manage_repository.mako +++ b/templates/webapps/tool_shed/repository/manage_repository.mako @@ -58,6 +58,11 @@

can_view_change_log = not is_new

+ if repository_metadata and repository_metadata.includes_tools: + includes_tools = True + else: + includes_tools = False + if changeset_revision_is_repository_tip: tip_str = 'repository tip' sharable_link_label = 'Sharable link to this repository:' @@ -193,6 +198,36 @@ </div></div> ${render_repository_items( metadata, containers_dict, can_set_metadata=True )} +%if includes_tools: + <p/> + <div class="toolForm"> + <div class="toolFormTitle">Automated tool tests</div> + <div class="toolFormBody"> + <form name="skip_tool_tests" id="skip_tool_tests" action="${h.url_for( controller='repository', action='manage_repository', id=trans.security.encode_id( repository.id ), changeset_revision=repository_metadata.changeset_revision )}" method="post" > + <div class="form-row"> + <label>Skip automated testing of tools in this revision:</label> + ${skip_tool_tests_check_box.get_html()} + <div class="toolParamHelp" style="clear: both;"> + Check the box and click <b>Save</b> to skip automated testing of the tools in this revision. + </div> + </div> + <div style="clear: both"></div> + <div class="form-row"> + <label>Reason for skipping automated testing:</label> + %if skip_tool_test: + <pre><textarea name="skip_tool_tests_comment" rows="3" cols="80">${skip_tool_test.comment | h}</textarea></pre> + %else: + <textarea name="skip_tool_tests_comment" rows="3" cols="80"></textarea> + %endif + </div> + <div style="clear: both"></div> + <div class="form-row"> + <input type="submit" name="skip_tool_tests_button" value="Save"/> + </div> + </form> + </div> + </div> +%endif <p/><div class="toolForm"><div class="toolFormTitle">Manage categories</div>

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

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