1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/05528b8aa8a1/ Changeset: 05528b8aa8a1 User: greg Date: 2013-06-25 12:57:32 Summary: Fix for browsing a tool dependency installed with a tol shed repository. Affected #: 2 files
diff -r 80dcf7e41b4aec1d5608c05c870a634651af2924 -r 05528b8aa8a1decc291f582b34265918c68f798e lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -155,7 +155,8 @@ def browse_tool_dependency( self, trans, **kwd ): message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) - tool_dependency = tool_dependency_util.get_tool_dependency( trans, kwd[ 'id' ] ) + tool_dependency_ids = tool_dependency_util.get_tool_dependency_ids( as_string=False, **kwd ) + tool_dependency = tool_dependency_util.get_tool_dependency( trans, tool_dependency_ids[ 0 ] ) if tool_dependency.in_error_state: message = "This tool dependency is not installed correctly (see the <b>Tool dependency installation error</b> below). " message += "Choose <b>Uninstall this tool dependency</b> from the <b>Repository Actions</b> menu, correct problems " @@ -1166,6 +1167,18 @@ initiate_repository_installation_ids=encoded_repository_ids, reinstalling=True )
+ @web.expose + @web.require_admin + def repair_repository( self, trans, **kwd ): + """ + Inspect the repository dependency hierarchy for a specified repository and attempt to make sure they are all properly installed as well as + each repository's tool dependencies. + """ + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) + repository_id = kwd[ 'id' ] + tool_shed_repository = suc.get_installed_tool_shed_repository( trans, repository_id ) + @web.json def repository_installation_status_updates( self, trans, ids=None, status_list=None ): # Avoid caching
diff -r 80dcf7e41b4aec1d5608c05c870a634651af2924 -r 05528b8aa8a1decc291f582b34265918c68f798e templates/webapps/tool_shed/repository/common.mako --- a/templates/webapps/tool_shed/repository/common.mako +++ b/templates/webapps/tool_shed/repository/common.mako @@ -863,7 +863,7 @@ ${tool_dependency.name | h} %elif trans.webapp.name == 'galaxy' and tool_dependency.tool_dependency_id: %if tool_dependency.repository_id and tool_dependency.installation_status in [ trans.model.ToolDependency.installation_status.INSTALLED ]: - <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='browse_tool_dependency', id=trans.security.encode_id( tool_dependency.tool_dependency_id ), repository_id=trans.security.encode_id( tool_dependency.repository_id ) )}"> + <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='browse_tool_dependency', id=trans.security.encode_id( tool_dependency.tool_dependency_id ) )}"> ${tool_dependency.name | h} </a> %elif tool_dependency.installation_status not in [ trans.model.ToolDependency.installation_status.UNINSTALLED ]:
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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