Changeset 1501 for trunk/grails-app/controllers/dbnp/query/AdvancedQueryController.groovy

Timestamp:

Feb 7, 2011, 4:07:54 PM (10 years ago)

Author:

robert@…

Message:

• Number of seconds for the rest controller to keep data in cache is now a configuration option
• After searching, it is possible to choose which action to perform on the search results.

File:

• trunk/grails-app/controllers/dbnp/query/AdvancedQueryController.groovy (modified) (22 diffs)

trunk/grails-app/controllers/dbnp/query/AdvancedQueryController.groovy

@@ -1 +1 @@
 package dbnp.query
+
 import dbnp.modules.*
 import org.dbnp.gdt.*
@@ -15 +16 @@
 
         def entitiesToSearchFor = [ 'Study': 'Studies', 'Sample': 'Samples']
-        
+
         /**
          * Shows search screen
@@ -25 +26 @@
                         criteria = parseCriteria( params.criteria, false )
                 }
-                [entitiesToSearchFor: entitiesToSearchFor, searchableFields: getSearchableFields(), criteria: criteria]
+                [searchModes: SearchMode.values(), entitiesToSearchFor: entitiesToSearchFor, searchableFields: getSearchableFields(), criteria: criteria]
         }
 
@@ -47 +48 @@
 
                 // Create a search object and let it do the searching
-                Search search;
+                Search search = determineSearch( params.entity );
                 String view = determineView( params.entity );
-                switch( params.entity ) {
-                        case "Study":   search = new StudySearch();     break;
-                        case "Sample":  search = new SampleSearch(); break;
-
-                        // This exception will only be thrown if the entitiesToSearchFor contains more entities than
-                        // mentioned in this switch structure.
-                        default:                throw new Exception( "Can't search for entities of type " + params.entity );
-                }
+
+                // Choose between AND and OR search. Default is given by the Search class itself.
+                switch( params.operator?.toString()?.toLowerCase() ) {
+                        case "or":
+                                search.searchMode = SearchMode.or;
+                                break;
+                        case "and":
+                                search.searchMode = SearchMode.and;
+                                break;
+                }
+
                 search.execute( parseCriteria( params.criteria ) );
 
                 // Save search in session
                 def queryId = saveSearch( search );
-                render( view: view, model: [search: search, queryId: queryId] );
+                render( view: view, model: [search: search, queryId: queryId, actions: determineActions(search)] );
         }
 
@@ -69 +73 @@
          */
         def discard = {
-                Integer queryId
-                try {
-                        queryId = params.id as Integer
-                } catch( Exception e ) {
+                def queryIds = params.list( 'id' );
+                queryIds = queryIds.findAll { it.isInteger() }.collect { Integer.valueOf( it ) }
+
+                if( queryIds.size() == 0 ) {
                         flash.error = "Incorrect search ID given to discard"
                         redirect( action: "index" );
@@ -78 +82 @@
                 }
 
-                discardSearch( queryId );
-                flash.message = "Search has been discarded"
+                queryIds.each { queryId ->
+                        discardSearch( queryId );
+                }
+
+                if( queryIds.size() > 1 ) {
+                        flash.message = "Searches have been discarded"
+                } else {
+                        flash.message = "Search has been discarded"
+                }
                 redirect( action: "list" );
         }
@@ -88 +99 @@
          */
         def show = {
-                Integer queryId
-                try {
-                        queryId = params.id as Integer
-                } catch( Exception e ) {
+                def queryId = params.int( 'id' );
+
+                if( !queryId ) {
                         flash.error = "Incorrect search ID given to show"
                         redirect( action: "index" );
@@ -107 +117 @@
                 // Determine which view to show
                 def view = determineView( s.entity );
-                render( view: view, model: [search: s, queryId: queryId] );
-        }
-
+                render( view: view, model: [search: s, queryId: queryId, actions: determineActions(s)] );
+        }
+
+        /**
+         * Performs an action on specific searchResults 
+         * @param       queryId         queryId of the search to show
+         * @param       id                      list with the ids of the results to perform the action on
+         * @param       actionName      Name of the action to perform
+         */
+        def performAction = {
+                def queryId = params.int( 'queryId' );
+                def selectedIds = params.list( 'id' ).findAll { it.isLong() }.collect { Long.parseLong(it) }
+                def actionName = params.actionName;
+                def moduleName = params.moduleName;
+
+                if( !queryId ) {
+                        flash.error = "Incorrect search ID given to show"
+                        redirect( action: "index" );
+                        return
+                }
+                
+                // Retrieve the search from session
+                Search s = retrieveSearch( queryId );
+                if( !s ) {
+                        flash.message = "Specified search could not be found"
+                        redirect( action: "list" );
+                        return;
+                }
+
+                // Determine the possible actions
+                def actions = determineActions(s, selectedIds );
+
+                // Find the right action to perform
+                def redirectUrl;
+                for( action in actions ) {
+                        if( action.module == moduleName && action.name == actionName ) {
+                                redirectUrl = action.url;
+                                break;
+                        }
+                }
+                
+                if( !redirectUrl ) {
+                        flash.error = "No valid action is given to perform";
+                        redirect( action: "show", id: queryId );
+                        return;
+                }
+                
+                redirect( url: redirectUrl );
+        }
+        
         /**
          * Shows a list of searches that have been saved in session
@@ -124 +181 @@
                 [searches: searches]
         }
-        
+
         /**
          * Shows a search screen where the user can search within the results of another search
@@ -130 +187 @@
          */
         def searchIn = {
-                Integer queryId
-                try {
-                        queryId = params.id as Integer
-                } catch( Exception e ) {
+                def queryIds = params.list( 'id' );
+                queryIds = queryIds.findAll { it.isInteger() }.collect { Integer.valueOf( it ) }
+
+                if( queryIds.size() == 0 ) {
                         flash.error = "Incorrect search ID given to show"
                         redirect( action: "index" );
@@ -139 +196 @@
                 }
 
-                // Retrieve the search from session
-                Search s = retrieveSearch( queryId );
-                if( !s ) {
-                        flash.message = "Specified search could not be found"
+                // Retrieve the searches from session
+                def params = [:]
+                queryIds.eachWithIndex { queryId, idx ->
+                        Search s = retrieveSearch( queryId );
+                        if( !s ) {
+                                flash.message = "Specified search " + queryId + " could not be found"
+                                return;
+                        } else {
+                                params[ "criteria." + idx + ".entityfield" ] = s.entity;
+                                params[ "criteria." + idx + ".operator" ] = "in";
+                                params[ "criteria." + idx + ".value" ] = queryId;
+                        }
+                }
+
+                redirect( action: "index", params: params)
+        }
+
+        /**
+         * Combines the results of multiple searches 
+         * @param       id      queryIds of the searches to combine 
+         */
+        def combine = {
+                def queryIds = params.list( 'id' );
+                queryIds = queryIds.findAll { it.isInteger() }.collect { Integer.valueOf( it ) }
+
+                if( queryIds.size() == 0 ) {
+                        flash.error = "Incorrect search ID given to combine"
                         redirect( action: "index" );
+                        return
+                }
+
+                // First determine whether the types match
+                def searches = [];
+                def type = "";
+                flash.error = "";
+                queryIds.eachWithIndex { queryId, idx ->
+                        Search s = retrieveSearch( queryId );
+                        if( !s ) {
+                                return;
+                        }
+
+                        if( type ) {
+                                if( type != s.entity ) {
+                                        flash.error = type + " and " + s.entity.toLowerCase() + " queries can't be combined. Selected queries of one type.";
+                                        return
+                                }
+                        } else {
+                                type = s.entity
+                        }
+                }
+
+                if( flash.error ) {
+                        redirect( action: "list" );
                         return;
                 }
 
-                redirect( action: "index", params: [ "criteria.0.entityfield": s.entity, "criteria.0.operator": "in", "criteria.0.value": queryId ])
+                if( !type ) {
+                        flash.error = "No correct query ids were given."
+                        redirect( action: "list" );
+                        return;
+                }
+
+                // Retrieve the searches from session
+                Search combined = determineSearch( type );
+                combined.searchMode = SearchMode.or;
+
+                queryIds.eachWithIndex { queryId, idx ->
+                        Search s = retrieveSearch( queryId );
+                        if( s ) {
+                                combined.addCriterion( new Criterion( entity: type, field: null, operator: Operator.insearch, value: s ) );
+                        }
+                }
+
+                // Execute search to combine the results
+                combined.execute();
+
+                def queryId = saveSearch( combined );
+                redirect( action: "show", id: queryId );
         }
 
@@ -155 +281 @@
                         case "Sample":  return "sampleresults"; break;
                         default:                return "results"; break;
+                }
+        }
+
+        /**
+         * Returns the search object used for searching
+         */
+        protected Search determineSearch( String entity ) {
+                switch( entity ) {
+                        case "Study":   return new StudySearch();
+                        case "Sample":  return new SampleSearch();
+
+                        // This exception will only be thrown if the entitiesToSearchFor contains more entities than
+                        // mentioned in this switch structure.
+                        default:                throw new Exception( "Can't search for entities of type " + entity );
                 }
         }
@@ -230 +370 @@
                         if( c.key ==~ /[0-9]+/ ) {
                                 def formCriterion = c.value;
-                                
+
                                 Criterion criterion = new Criterion();
 
@@ -251 +391 @@
                                         continue;
                                 }
-                                
+
                                 // Special case of the 'in' operator
                                 if( criterion.operator == Operator.insearch ) {
@@ -258 +398 @@
                                                 s = retrieveSearch( Integer.parseInt( formCriterion.value ) );
                                         } catch( Exception e ) {}
-                                        
+
                                         if( !s ) {
                                                 flash.error += "Can't search within previous query: query not found";
                                                 continue;
                                         }
-                                        
+
                                         if( parseSearchIds ) {
                                                 criterion.value = s
@@ -273 +413 @@
                                         criterion.value = formCriterion.value;
                                 }
-                                
+
                                 list << criterion;
                         }
@@ -332 +472 @@
                 // First check whether a search with the same criteria is already present
                 def previousSearch = retrieveSearchByCriteria( s.getCriteria() );
-                
+
                 def id
                 if( previousSearch ) {
@@ -340 +480 @@
                         id = ( session.queries*.key.max() ?: 0 ) + 1;
                 }
-                
+
                 s.id = id;
                 session.queries[ id ] = s;
 
-                println "On saveSearch: " + session.queries;
                 return id;
         }
@@ -356 +495 @@
                 if( !session.queries )
                         return null
-                
+
                 if( !criteria )
                         return null
-                        
+
                 for( query in session.queries ) {
                         def key = query.key;
@@ -385 +524 @@
                         return null;
 
-                println "On retrieveSearch: " + session.queries;
                 return (Search) session.queries[ id ]
         }
@@ -402 +540 @@
                 session.queries.remove( id );
 
-                println "On discardSearch: " + session.queries;
                 if( !( sessionSearch instanceof Search ) )
                         return null;
@@ -419 +556 @@
                 return session.queries*.value.toList()
         }
+
+        /**
+         * Determine a list of actions that can be performed on specific entities
+         * @param entity                Name of the entity that the actions could be performed on
+         * @param selectedIds   List with ids of the selected items to perform an action on
+         * @return
+         */
+        protected List determineActions( Search s, def selectedIds = null ) {
+                return gscfActions( s, selectedIds ) + moduleActions( s, selectedIds );
+        }
+
+        /**
+         * Determine a list of actions that can be performed on specific entities by GSCF
+         * @param entity        Name of the entity that the actions could be performed on
+         * @param selectedIds   List with ids of the selected items to perform an action on
+         */
+        protected List gscfActions(Search s, def selectedIds = null) {
+                switch(s.entity) {
+                        case "Study":
+                                def exportParams = [:]
+                                s.filterResults(selectedIds).each {
+                                        exportParams[ it.code ] = it.id;
+                                }
+                                return [[
+                                                module: "gscf",
+                                                name:"simpletox",
+                                                description: "Export as SimpleTox",
+                                                url: createLink( controller: "exporter", action: "export", params: exportParams )
+                                        ]]
+                        case "Sample":
+                                return []
+                        default:
+                                return [];
+                }
+        }
+
+        /**
+         * Determine a list of actions that can be performed on specific entities by other modules
+         * @param entity        Name of the entity that the actions could be performed on
+         */
+        protected List moduleActions(Search s, def selectedIds = null) {
+                def actions = []
+
+                if( !s.getResults() || s.getResults().size() == 0 )
+                        return []
+
+                // Loop through all modules and check which actions can be performed on the
+                AssayModule.list().each { module ->
+                        // Remove 'module' from module name
+                        def moduleName = module.name.replace( 'module', '' ).trim()
+                        try {
+                                def callUrl = module.url + "/rest/getPossibleActions?entity=" + s.entity
+                                def json = moduleCommunicationService.callModuleRestMethodJSON( module.url, callUrl );
+
+                                // Check whether the entity is present in the return value
+                                if( json[ s.entity ] ) {
+                                        json[ s.entity ].each { action ->
+                                                def url = module.url + "/action/" + action.name
+                                                url += "?entity=" + s.entity
+                                                url += "&" + s.filterResults(selectedIds).collect { "tokens=" + it.giveUUID() }.join( "&" )
+                                                actions << [
+                                                                        module: moduleName,
+                                                                        name: action.name,
+                                                                        description: action.description + " (" + moduleName + ")",
+                                                                        url: url
+                                                                ];
+                                        }
+                                }
+                        } catch( Exception e ) {
+                                // Exception is thrown when the call to the module fails. No problems though.
+                                log.error "Error while fetching possible actions from " + module.name + ": " + e.getMessage()
+                        }
+                }
+
+                return actions;
+        }
+
 }