Changeset 1482

Timestamp:

Feb 2, 2011, 4:40:22 PM (12 years ago)

Author:

robert@…

Message:

Implemented saving of queries

Location:

trunk

Files:

• grails-app/controllers/RestController.groovy (modified) (1 diff)
• grails-app/controllers/dbnp/authentication/LogoutController.groovy (modified) (2 diffs)
• grails-app/controllers/dbnp/query/AdvancedQueryController.groovy (modified) (8 diffs)
• grails-app/domain/dbnp/studycapturing/Sample.groovy (modified) (1 diff)
• grails-app/domain/dbnp/studycapturing/Study.groovy (modified) (1 diff)
• grails-app/services/dbnp/modules/ModuleCommunicationService.groovy (modified) (2 diffs)
• grails-app/views/advancedQuery/_criteria.gsp (added)
• grails-app/views/advancedQuery/_resultbuttons.gsp (added)
• grails-app/views/advancedQuery/index.gsp (modified) (3 diffs)
• grails-app/views/advancedQuery/list.gsp (added)
• grails-app/views/advancedQuery/results.gsp (modified) (5 diffs)
• grails-app/views/advancedQuery/sampleresults.gsp (modified) (5 diffs)
• grails-app/views/advancedQuery/studyresults.gsp (modified) (5 diffs)
• src/groovy/dbnp/query/Criterion.groovy (modified) (8 diffs)
• src/groovy/dbnp/query/SampleSearch.groovy (modified) (6 diffs)
• src/groovy/dbnp/query/Search.groovy (modified) (14 diffs)
• src/groovy/dbnp/query/StudySearch.groovy (modified) (7 diffs)
• web-app/css/advancedQuery.css (modified) (2 diffs)
• web-app/css/default_style.css (modified) (1 diff)
• web-app/js/advancedQuery.js (added)

trunk/grails-app/controllers/RestController.groovy

@@ -525 +525 @@
 
                         def user = AuthenticationService.getRemotelyLoggedInUser( params.consumer, params.token );
-                        render( ['isOwner': study.isOwner(user), 'canRead': study.canRead(user), 'canWrite': study.canWrite(user)] as JSON )
+                        def auth = ['isOwner': study.isOwner(user), 'canRead': study.canRead(user), 'canWrite': study.canWrite(user)];
+                        log.trace "Authorization for study " + study.title + " and user " + user.username + ": " + auth
+                        render auth as JSON;
                 } else {
                         response.sendError(400)

trunk/grails-app/controllers/dbnp/authentication/LogoutController.groovy

@@ -16 +16 @@
                 }
                 // TODO  put any pre-logout code here
+                
+                // Remove all queries from session
+                session.queries = [];
         }
 
@@ -30 +33 @@
                         redirect uri: SpringSecurityUtils.securityConfig.logout.filterProcessesUrl // '/j_spring_security_logout'
                 }
+
+                // Remove all queries from session
+                session.queries = [];
         }
 }

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

@@ -12 +12 @@
 class AdvancedQueryController {
         def moduleCommunicationService;
+        def authenticationService
+
+        def entitiesToSearchFor = [ 'Study': 'Studies', 'Sample': 'Samples']
         
-        def entitiesToSearchFor = [ 'Study': 'Studies', 'Sample': 'Samples']
-    def index = {
-                [entitiesToSearchFor: entitiesToSearchFor, searchableFields: getSearchableFields()]
-    }
+        /**
+         * Shows search screen
+         */
+        def index = {
+                // Check whether criteria have been given before
+                def criteria = [];
+                if( params.criteria ) {
+                        criteria = parseCriteria( params.criteria, false )
+                }
+                [entitiesToSearchFor: entitiesToSearchFor, searchableFields: getSearchableFields(), criteria: criteria]
+        }
 
         /**
@@ -38 +48 @@
                 // Create a search object and let it do the searching
                 Search search;
-                String view;
+                String view = determineView( params.entity );
                 switch( params.entity ) {
-                        case "Study":   search = new StudySearch();             view = "studyresults";  break;
-                        case "Sample":  search = new SampleSearch();    view = "sampleresults"; break;
-                        
-                        // This exception will only be thrown if the entitiesToSearchFor contains more entities than 
+                        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 );    
-                }
-                
+                        default:                throw new Exception( "Can't search for entities of type " + params.entity );
+                }
                 search.execute( parseCriteria( params.criteria ) );
-                
-                render( view: view, model: [search: search] );
+
+                // Save search in session
+                def queryId = saveSearch( search );
+                render( view: view, model: [search: search, queryId: queryId] );
+        }
+
+        /**
+         * Removes a specified search from session
+         * @param       id      queryId of the search to discard
+         */
+        def discard = {
+                Integer queryId
+                try {
+                        queryId = params.id as Integer
+                } catch( Exception e ) {
+                        flash.error = "Incorrect search ID given to discard"
+                        redirect( action: "index" );
+                        return
+                }
+
+                discardSearch( queryId );
+                flash.message = "Search has been discarded"
+                redirect( action: "list" );
+        }
+
+        /**
+         * Shows a specified search from session
+         * @param       id      queryId of the search to show
+         */
+        def show = {
+                Integer queryId
+                try {
+                        queryId = params.id as Integer
+                } catch( Exception e ) {
+                        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: "index" );
+                        return;
+                }
+
+                // Determine which view to show
+                def view = determineView( s.entity );
+                render( view: view, model: [search: s, queryId: queryId] );
+        }
+
+        /**
+         * Shows a list of searches that have been saved in session
+         * @param       id      queryId of the search to show
+         */
+        def list = {
+                def searches = listSearches();
+
+                if( !searches || searches.size() == 0 ) {
+                        flash.message = "No previous searches found";
+                        redirect( action: "index" );
+                        return;
+                }
+                [searches: searches]
         }
         
+        /**
+         * Shows a search screen where the user can search within the results of another search
+         * @param       id      queryId of the search to search in
+         */
+        def searchIn = {
+                Integer queryId
+                try {
+                        queryId = params.id as Integer
+                } catch( Exception e ) {
+                        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: "index" );
+                        return;
+                }
+
+                redirect( action: "index", params: [ "criteria.0.entityfield": s.entity, "criteria.0.operator": "in", "criteria.0.value": queryId ])
+        }
+
+        protected String determineView( String entity ) {
+                switch( entity ) {
+                        case "Study":   return "studyresults";  break;
+                        case "Sample":  return "sampleresults"; break;
+                        default:                return "results"; break;
+                }
+        }
+
         /**
          * Returns a map of entities with the names of the fields the user can search on
@@ -59 +164 @@
         protected def getSearchableFields() {
                 def fields = [:];
-                
+
                 // Retrieve all local search fields
                 getEntities().each {
                         def entity = getEntity( 'dbnp.studycapturing.' + it );
-                        
+
                         if( entity ) {
                                 def domainFields = entity.giveDomainFields();
                                 def templateFields = TemplateField.findAllByEntity( entity )
-                                
+
                                 def fieldNames = ( domainFields + templateFields ).collect { it.name }.unique() + 'Template'
-                                
+
                                 fields[ it ] = fieldNames.sort { a, b -> a[0].toUpperCase() + a[1..-1] <=> b[0].toUpperCase() + b[1..-1] };
                         }
                 }
-                
+
                 // Loop through all modules and check which fields are searchable
                 // Right now, we just combine the results for different entities
@@ -81 +186 @@
                                 def json = moduleCommunicationService.callModuleRestMethodJSON( module.url, callUrl );
                                 def moduleFields = [];
-                                entitiesToSearchFor.each { entity ->                                    
+                                entitiesToSearchFor.each { entity ->
                                         if( json[ entity.key ] ) {
                                                 json[ entity.key ].each { field ->
@@ -88 +193 @@
                                         }
                                 }
-                                
+
                                 // Remove 'module' from module name
                                 def moduleName = module.name.replace( 'module', '' ).trim()
-                                
+
                                 fields[ moduleName ] = moduleFields.unique();
                         } catch( Exception e ) {
@@ -97 +202 @@
                         }
                 }
-                
+
                 return fields;
         }
-        
+
         /**
          * Parses the criteria from the query form given by the user
@@ -115 +220 @@
          *              1.field: d
          *      ]
-         *
-         * @return      List with Criterion objects
-         */
-        protected List parseCriteria( def c ) {
+         * @param parseSearchIds        Determines whether searches are returned instead of their ids
+         * @return                                      List with Criterion objects
+         */
+        protected List parseCriteria( def formCriteria, def parseSearchIds = true ) {
                 ArrayList list = [];
-                
+                flash.error = "";
                 // Loop through all keys of c and remove the non-numeric ones
-                c.each {
-                        if( it.key ==~ /[0-9]+/ ) {
-                                def formCriterion = it.value;
+                for( c in formCriteria ) {
+                        if( c.key ==~ /[0-9]+/ ) {
+                                def formCriterion = c.value;
+                                
                                 Criterion criterion = new Criterion();
-                                
+
                                 // Split entity and field
                                 def field = formCriterion.entityfield?.split( /\./ );
-                                
                                 if( field.size() > 1 ) {
                                         criterion.entity = field[0].toString();
                                         criterion.field = field[1].toString();
                                 } else {
-                                        criterion.entity = null;
-                                        criterion.field = field;
+                                        criterion.entity = field[0];
+                                        criterion.field = null;
+                                }
+
+                                // Convert operator string to Operator-enum field
+                                try {
+                                        criterion.operator = Criterion.parseOperator( formCriterion.operator );
+                                } catch( Exception e) {
+                                        println "Operator " + formCriterion.operator + " could not be parsed: " + e.getMessage();
+                                        flash.error += "Criterion could not be used: operator " + formCriterion.operator + " is not valid.<br />\n";
+                                        continue;
                                 }
                                 
-                                // Convert operator string to Operator-enum field
-                                switch( formCriterion.operator ) {
-                                        case ">=":                      criterion.operator = Operator.gte; break;
-                                        case ">":                       criterion.operator = Operator.gt;  break;
-                                        case "<":                       criterion.operator = Operator.lte; break;
-                                        case "<=":                      criterion.operator = Operator.lt;  break;
-                                        case "contains":        criterion.operator = Operator.contains; break;
-                                        case "equals":          criterion.operator = Operator.equals; break;
+                                // Special case of the 'in' operator
+                                if( criterion.operator == Operator.insearch ) {
+                                        Search s
+                                        try {
+                                                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
+                                        } else {
+                                                criterion.value = s.id
+                                        }
+                                } else {
+                                        // Copy value
+                                        criterion.value = formCriterion.value;
                                 }
                                 
-                                // Copy value
-                                criterion.value = formCriterion.value;
-                                 
                                 list << criterion;
                         }
                 }
-                
+
                 return list;
         }
-        
+
         /**
          * Returns all entities for which criteria can be entered
@@ -165 +288 @@
                 return [ 'Study', 'Subject', 'Sample', 'Event', 'SamplingEvent', 'Assay' ]
         }
-        
-        /**
-        * Creates an object of the given entity.
-        *
-        * @return False if the entity is not a subclass of TemplateEntity
-        */
-   protected def getEntity( entityName ) {
-           // Find the templates
-           def entity
-           try { 
-                   entity = Class.forName(entityName, true, this.getClass().getClassLoader())
-
-                   // succes, is entity an instance of TemplateEntity?
-                   if (entity.superclass =~ /TemplateEntity$/ || entity.superclass.superclass =~ /TemplateEntity$/) {
-                           return entity;
-                   } else {
-                           return false;
-                   }
-           } catch( ClassNotFoundException e ) {
-                        log.error "Class " + entityName + " not found: " + e.getMessage()
-                        return null;
-           }
-
-   }
-
+
+        /**
+         * Creates an object of the given entity.
+         *
+         * @return False if the entity is not a subclass of TemplateEntity
+         */
+        protected def getEntity( entityName ) {
+                // Find the templates
+                def entity
+                try {
+                        entity = Class.forName(entityName, true, this.getClass().getClassLoader())
+
+                        // succes, is entity an instance of TemplateEntity?
+                        if (entity.superclass =~ /TemplateEntity$/ || entity.superclass.superclass =~ /TemplateEntity$/) {
+                                return entity;
+                        } else {
+                                return false;
+                        }
+                } catch( ClassNotFoundException e ) {
+                        log.error "Class " + entityName + " not found: " + e.getMessage()
+                        return null;
+                }
+
+        }
+
+
+        /***************************************************************************
+         * 
+         * Methods for saving results in session
+         * 
+         ***************************************************************************/
+
+        /**
+         * Saves the given search in session. Any search with the same criteria will be overwritten
+         *  
+         * @param s             Search to save
+         * @return              Id of the search for later reference
+         */
+        protected int saveSearch( Search s ) {
+                if( !session.queries )
+                        session.queries = [:]
+
+                // First check whether a search with the same criteria is already present
+                def previousSearch = retrieveSearchByCriteria( s.getCriteria() );
+                
+                def id
+                if( previousSearch ) {
+                        id = previousSearch.id;
+                } else {
+                        // Determine unique id
+                        id = ( session.queries*.key.max() ?: 0 ) + 1;
+                }
+                
+                s.id = id;
+                session.queries[ id ] = s;
+
+                println "On saveSearch: " + session.queries;
+                return id;
+        }
+
+        /**
+         * Retrieves a search from session with the same criteria as given
+         * @param criteria      List of criteria to search for
+         * @return                      Search that has this criteria, or null if no such search is found.
+         */
+        protected Search retrieveSearchByCriteria( List criteria ) {
+                if( !session.queries )
+                        return null
+                
+                if( !criteria )
+                        return null
+                        
+                for( query in session.queries ) {
+                        def key = query.key;
+                        def value = query.value;
+
+                        if( value.criteria && value.criteria.containsAll( criteria ) && criteria.containsAll( value.criteria ) ) {
+                                return value;
+                        }
+                }
+
+                return null;
+        }
+
+
+        /**
+         * Retrieves a search from session
+         * @param id    Id of the search
+         * @return              Search that belongs to this ID or null if no search is found
+         */
+        protected Search retrieveSearch( int id ) {
+                if( !session.queries || !session.queries[ id ] )
+                        return null
+
+                if( !( session.queries[ id ] instanceof Search ) )
+                        return null;
+
+                println "On retrieveSearch: " + session.queries;
+                return (Search) session.queries[ id ]
+        }
+
+        /**
+         * Removes a search from session
+         * @param id    Id of the search
+         * @return      Search that belonged to this ID or null if no search is found
+         */
+        protected Search discardSearch( int id ) {
+                if( !session.queries || !session.queries[ id ] )
+                        return null
+
+                def sessionSearch = session.queries[ id ];
+
+                session.queries.remove( id );
+
+                println "On discardSearch: " + session.queries;
+                if( !( sessionSearch instanceof Search ) )
+                        return null;
+
+                return (Search) sessionSearch
+        }
+
+        /**
+         * Retrieves a list of searches from session
+         * @return      List of searches from session
+         */
+        protected List listSearches() {
+                if( !session.queries )
+                        return []
+
+                return session.queries*.value.toList()
+        }
 }

trunk/grails-app/domain/dbnp/studycapturing/Sample.groovy

@@ -129 +129 @@
                 return name
         }
+
+        /**
+        * Basic equals method to check whether objects are equals, by comparing the ids
+        * @param o              Object to compare with
+        * @return               True iff the id of the given Sample is equal to the id of this Sample
+        */
+   public boolean equals( Object o ) {
+           if( o == null )
+                   return false;
+                   
+           if( !( o instanceof Sample ) )
+                   return false
+           
+           Sample s = (Sample) o;
+           
+           return this.id == s.id
+   }
         
         /**

trunk/grails-app/domain/dbnp/studycapturing/Study.groovy

@@ -522 +522 @@
                 return this.studyUUID;
         }
+        
+        /**
+         * Basic equals method to check whether objects are equals, by comparing the ids
+         * @param o             Object to compare with
+         * @return              True iff the id of the given Study is equal to the id of this Study
+         */
+        public boolean equals( Object o ) {
+                if( o == null )
+                        return false;
+                        
+                if( !( o instanceof Study ) )
+                        return false
+                
+                Study s = (Study) o;
+                
+                return this.id == s.id
+        }
 
         // Send messages to modules about changes in this study

trunk/grails-app/services/dbnp/modules/ModuleCommunicationService.groovy

@@ -48 +48 @@
          * @return
          */
-        def invalidateStudy( Study study ) {
+        def invalidateStudy( def study ) {
                 moduleNotificationService.invalidateStudy( study );
         }
@@ -113 +113 @@
                 try {
                         def textResponse = url.toURL().getText()
-                        println "GSCF call to " + consumer + " URL: " + url
-                        println "GSCF response: " + textResponse
+                        log.trace "GSCF call to " + consumer + " URL: " + url
+                        log.trace "GSCF response: " + textResponse
                         restResponse = JSON.parse( textResponse )
                 } catch (Exception e) {

trunk/grails-app/views/advancedQuery/index.gsp

@@ -6 +6 @@
         <link rel="stylesheet" href="<g:resource dir="css" file="advancedQuery.css" />" type="text/css"/>
         <g:javascript src="advancedQuery.js" />
+        <script type="text/javascript">
+                // Make a list of fields to search in
+                var queryableFields = [
+                        <g:set var="j" value="${0}" />
+                        <g:each in="${searchableFields}" var="entity">
+                                <g:each in="${entity.value}" var="field">
+                                        <g:if test="${j > 0}">,</g:if>
+                                        {
+                                                value: "${entity.key.toString().encodeAsJavaScript()}.${field.toString().encodeAsJavaScript()}",
+                                                show: "${(field[0].toUpperCase() + field[1..-1]).encodeAsJavaScript()}",
+                                                label: "${entity.key.toString().encodeAsJavaScript()}.${field.toString().encodeAsJavaScript()}",
+                                                entity: "${entity.key.toString().encodeAsJavaScript()}"
+                                        }
+                                        <g:set var="j" value="1" />
+                                </g:each>
+                        </g:each>
+                ];
+        
+                <g:if test="${criteria && criteria.size() > 0}">
+                        // Show given criteria
+                        $(function() {
+                                <g:each in="${criteria}" var="criterion">
+                                        showCriterium("${criterion.entityField().encodeAsJavaScript()}", "${criterion.value.toString().encodeAsJavaScript()}", "${criterion.operator.toString().encodeAsJavaScript()}");
+                                </g:each>
+                                showHideNoCriteriaItem();
+                        });
+                </g:if>
+        </script>
 </head>
 <body>
@@ -11 +39 @@
 <h1>Query database</h1>
 
+<g:if test="${flash.error}">
+        <div class="error">
+                ${flash.error.toString().encodeAsHTML()}
+        </div>
+</g:if>
+<g:if test="${flash.message}">
+        <div class="message">
+                ${flash.message.toString().encodeAsHTML()}
+        </div>
+</g:if>
+
+<a href="<g:createLink action="list" />">View previous queries</a>
+
 <form id="input_criteria">
         <h2>Add criterium</h2>
-        <p>
+        <p class="explanation">
                 N.B. Comparing numerical values is done without taking into
                 account the units. E.g. a weight of 1 kg equals 1 grams.
         </p>
         <label for="field">Field</label>
-                <select name="field">
+                <select name="field" id="queryFieldSelect">
                         <option value=""></option>
                         <g:each in="${searchableFields}" var="entity">
@@ -29 +70 @@
                                 </optgroup>
                         </g:each>
-                </select> 
+                </select>
                 
         <label for="value">Comparison</label>

trunk/grails-app/views/advancedQuery/results.gsp

@@ -5 +5 @@
         <title>Query results</title>
         <link rel="stylesheet" href="<g:resource dir="css" file="advancedQuery.css" />" type="text/css"/>
-        <g:javascript src="advancedQuery.js" />
 </head>
 <body>
@@ -17 +16 @@
         <g:each in="${search.getCriteria()}" var="criterion">
                 <li>
-                        <span class="entityfield">${criterion.entity}.${criterion.field}</span>
+                        <span class="entityfield">${criterion.entityField()}</span>
                         <span class="operator">${criterion.operator}</span>
                         <span class="value">${criterion.value}</span>
@@ -28 +27 @@
 
 <g:if test="${search.getNumResults() > 0}">
-
+        <% 
+                def resultFields = search.getShowableResultFields();
+                def extraFields = resultFields[ search.getResults()[ 0 ].id ]?.keySet();
+        %>
         <table id="searchresults">
                 <thead>
@@ -34 +36 @@
                                 <th>Type</th>
                                 <th>Id</th>
+                                <g:each in="${extraFields}" var="fieldName">
+                                        <th>${fieldName}</th>
+                                </g:each>
                         </tr>
                 </thead>
@@ -40 +45 @@
                                 <td>${search.entity}</td>
                                 <td>${result.id}</td>
+                                <g:each in="${extraFields}" var="fieldName">
+                                        <td>
+                                                <% 
+                                                        def fieldValue = resultFields[ result.id ]?.get( fieldName );
+                                                        if( fieldValue ) { 
+                                                                if( fieldValue instanceof Collection )
+                                                                        fieldValue = fieldValue.collect { it.toString() }.findAll { it }.join( ', ' );
+                                                                else
+                                                                        fieldValue = fieldValue.toString();
+                                                        }
+                                                %>
+                                                ${fieldValue}
+                                        </td>
+                                </g:each>
+
                         </tr>
                 </g:each>
         </table>
 </g:if>
-<p>
-        <g:link action="index">Search again</g:link>
-</p>
+<g:render template="resultbuttons" model="[queryId: queryId]" />
+
 </body>
 </html>

trunk/grails-app/views/advancedQuery/sampleresults.gsp

@@ -5 +5 @@
         <title>Query results</title>
         <link rel="stylesheet" href="<g:resource dir="css" file="advancedQuery.css" />" type="text/css"/>
-        <g:javascript src="advancedQuery.js" />
 </head>
 <body>
@@ -12 +11 @@
 
 <p>
-        Your search for studies with:
+        Your search for samples with:
 </p>
-<ul id="criteria">
-        <g:each in="${search.getCriteria()}" var="criterion">
-                <li>
-                        <span class="entityfield">${criterion.entity}.${criterion.field}</span>
-                        <span class="operator">${criterion.operator}</span>
-                        <span class="value">${criterion.value}</span>
-                </li>
-        </g:each>
-</ul>
+<g:render template="criteria" model="[criteria: search.getCriteria()]" />
 <p> 
         resulted in ${search.getNumResults()} <g:if test="${search.getNumResults() == 1}">sample</g:if><g:else>samples</g:else>.
 </p>
 
-
 <g:if test="${search.getNumResults() > 0}">
-
+        <% 
+                def resultFields = search.getShowableResultFields();
+                def extraFields = resultFields[ search.getResults()[ 0 ].id ]?.keySet();
+        %>
         <table id="searchresults" class="paginate">
                 <thead>
@@ -35 +28 @@
                         <th>Study</th>
                         <th>Name</th>
+                        <g:each in="${extraFields}" var="fieldName">
+                                <th>${fieldName}</th>
+                        </g:each>
                 </tr>
                 </thead>
@@ -40 +36 @@
                 <g:each in="${search.getResults()}" var="sampleInstance" status="i">
                         <tr class="${(i % 2) == 0 ? 'odd' : 'even'}">
-
                                 <td><g:link controller="study" action="show" id="${sampleInstance?.parent?.id}">${sampleInstance?.parent?.title}</g:link></td>
                                 <td>${fieldValue(bean: sampleInstance, field: "name")}</td>
+                                <g:each in="${extraFields}" var="fieldName">
+                                        <td>
+                                                <% 
+                                                        def fieldValue = resultFields[ sampleInstance.id ]?.get( fieldName );
+                                                        if( fieldValue ) { 
+                                                                if( fieldValue instanceof Collection )
+                                                                        fieldValue = fieldValue.collect { it.toString() }.findAll { it }.join( ', ' );
+                                                                else
+                                                                        fieldValue = fieldValue.toString();
+                                                        }
+                                                %>
+                                                ${fieldValue}
+                                        </td>
+                                </g:each>
                         </tr>
                 </g:each>
@@ -49 +58 @@
 
 </g:if>
-<p>
-        <g:link action="index">Search again</g:link>
-</p>
+<g:render template="resultbuttons" model="[queryId: queryId]" />
 </body>
 </html>

trunk/grails-app/views/advancedQuery/studyresults.gsp

@@ -5 +5 @@
         <title>Query results</title>
         <link rel="stylesheet" href="<g:resource dir="css" file="advancedQuery.css" />" type="text/css"/>
-        <g:javascript src="advancedQuery.js" />
 </head>
 <body>
@@ -14 +13 @@
         Your search for studies with:
 </p>
-<ul id="criteria">
-        <g:each in="${search.getCriteria()}" var="criterion">
-                <li>
-                        <span class="entityfield">${criterion.entity}.${criterion.field}</span>
-                        <span class="operator">${criterion.operator}</span>
-                        <span class="value">${criterion.value}</span>
-                </li>
-        </g:each>
-</ul>
+<g:render template="criteria" model="[criteria: search.getCriteria()]" />
 <p> 
         resulted in ${search.getNumResults()} <g:if test="${search.getNumResults() == 1}">study</g:if><g:else>studies</g:else>.
 </p>
 <g:if test="${search.getNumResults() > 0}">
+        <% 
+                def resultFields = search.getShowableResultFields();
+                def extraFields = resultFields[ search.getResults()[ 0 ].id ]?.keySet();
+        %>
 
         <table id="searchresults" class="paginate">
@@ -37 +32 @@
                         <th>Events</th>
                         <th>Assays</th>
+                        <g:each in="${extraFields}" var="fieldName">
+                                <th>${fieldName}</th>
+                        </g:each>                       
                 </tr>
                 </thead>
@@ -79 +77 @@
                                         </g:else>
                                 </td>
-
+                                <g:each in="${extraFields}" var="fieldName">
+                                        <td>
+                                                <% 
+                                                        def fieldValue = resultFields[ studyInstance.id ]?.get( fieldName );
+                                                        if( fieldValue ) { 
+                                                                if( fieldValue instanceof Collection )
+                                                                        fieldValue = fieldValue.collect { it.toString() }.findAll { it }.join( ', ' );
+                                                                else
+                                                                        fieldValue = fieldValue.toString();
+                                                        }
+                                                %>
+                                                ${fieldValue}
+                                        </td>
+                                </g:each>
                         </tr>
                 </g:each>
@@ -86 +97 @@
 
 </g:if>
-<p>
-        <g:link action="index">Search again</g:link>
-</p>
+<g:render template="resultbuttons" model="[queryId: queryId]" />
 </body>
 </html>

trunk/src/groovy/dbnp/query/Criterion.groovy

@@ -3 +3 @@
 import java.text.SimpleDateFormat
 import org.dbnp.gdt.*
+import org.apache.commons.logging.LogFactory;
 
 /**
@@ -10 +11 @@
  */
 enum Operator {
-        equals, contains, gte, gt, lte, lt
+        equals( "=" ), contains( "contains" ), gte( ">="), gt( ">" ), lte( "<=" ), lt( "<" ), insearch( "in" )
+        Operator(String name) { this.name = name }
+        private final String name;
+        public String toString() { return name }
 }
 
@@ -19 +23 @@
  */
 class Criterion {
+        private static final log = LogFactory.getLog(this);
         public String entity
         public String field
@@ -25 +30 @@
 
         /**
+         * Retrieves a combination of the entity and field
+         * @return
+         */
+        public String entityField() {
+                return entity.toString() + ( field ? "." + field.toString() : "" );
+        }
+        
+        /**
          * Retrieves the correct value for this criterion in the given object (with template)
          *
          * @param entity                Entity to check for value. Should be a child of template entity
-         * @param criterion     Criterion to match on
-         * @return                      Value of the given field or null if the field doesn't exist
+         * @param criterion             Criterion to match on
+         * @return                              Value of the given field or null if the field doesn't exist
          */
         public def getFieldValue( TemplateEntity entity ) {
@@ -37 +50 @@
                 try {
                         def fieldValue
-                        if( field == "Template" ) {
+                        if( !field ) {
+                                fieldValue = entity
+                        } else if( field == "Template" ) {
                                 fieldValue = entity.template?.name
                         } else {
@@ -138 +153 @@
                 if( fieldValue == null )
                         return false;
-
+                
+                // in-search criteria have to be handled separately
+                if( this.operator == Operator.insearch ) {
+                        return this.value?.getResults()?.contains( fieldValue );
+                }       
+                
+                // Other criteria are handled based on the class of the value given.
                 def classname = fieldValue.class.getName();
                 classname = classname[classname.lastIndexOf( '.' ) + 1..-1].toLowerCase();
-
-                println "Match " + fieldValue + " of class " + classname + " with " + this
 
                 try {
@@ -185 +204 @@
                                 return fieldValue <= criterionValue;
                         case Operator.contains:
-                                return fieldValue.contains( criterionValue );
+                                // Contains operator can only be used on string values
+                                return fieldValue.toString().contains( criterionValue.toString() );
                         case Operator.equals:
                         default:
@@ -295 +315 @@
                 }
         }
+        
+        public static Operator parseOperator( String name ) throws Exception {
+                switch( name.trim() ) {
+                        case "=":  
+                        case "equals":          return Operator.equals; 
+                        case "contains":        return Operator.contains; 
+                        case ">=": 
+                        case "gte":                     return Operator.gte; 
+                        case ">": 
+                        case "gt":                      return Operator.gt; 
+                        case "<=": 
+                        case "lte":                     return Operator.lte; 
+                        case "<": 
+                        case "lt":                      return Operator.lt; 
+                        case "in":                      return Operator.insearch;
+                        default:
+                                throw new Exception( "Operator not found" ); 
+                }
+        }
 
         public String toString() {
-                return "[Criterion " + entity + "." + field + " " + operator + " " + value + "]";
+                return "[Criterion " + entityField() + " " + operator + " " + value + "]";
+        }
+        
+        public boolean equals( Object o ) {
+                if( o == null )
+                        return false;
+                
+                if( !( o instanceof Criterion ) ) 
+                        return false;
+                        
+                Criterion otherCriterion = (Criterion) o;
+                return  this.entity == otherCriterion.entity &&
+                                this.field == otherCriterion.field && 
+                                this.operator == otherCriterion.operator &&
+                                this.value == otherCriterion.value;
         }
 }

trunk/src/groovy/dbnp/query/SampleSearch.groovy

@@ -15 +15 @@
 package dbnp.query
 
+import java.util.Map;
+
 import dbnp.studycapturing.*
 import org.dbnp.gdt.*
+import org.apache.commons.logging.LogFactory;
 
 class SampleSearch extends Search {
+        private static final log = LogFactory.getLog(this);
         
         public SampleSearch() {
+                super();
+                                
                 this.entity = "Sample";
         }
@@ -57 +63 @@
         @Override
         void execute() {
-                // TODO: check for authorization for these studies?
+                super.execute();
 
                 // If no criteria are found, return all samples
                 if( !criteria || criteria.size() == 0 ) {
-                        results = Sample.list();
+                        results = Sample.list().findAll { it.parent?.canRead( this.user ) };
                         return;
                 }
@@ -72 +78 @@
                 def samples = []
                 if( getEntityCriteria( 'Study' ).size() > 0 ) {
-                        def studies = Study.findAll();
-                        
+                        def studies = Study.findAll().findAll { it.canRead( this.user ) };
+
                         studies = filterOnStudyCriteria( studies );
-                        
+
                         if( studies.size() == 0 ) {
                                 results = [];
                                 return;
                         }
-                        
+
                         def c = Sample.createCriteria()
                         samples = c.list {
                                 'in'( 'parent', studies )
                         }
+
+                        // Save data about the resulting studies in the
+                        // result fields array. The data that is now in the array
+                        // is saved based on the study id, not based on the sample id
+                        clearResultFields();
+                        saveResultFields( samples, getEntityCriteria( "Study" ), { sample, criterion ->
+                                return criterion.getFieldValue( sample.parent );
+                        });
                 } else {
-                        samples = Sample.findAll()
+                        samples = Sample.findAll().findAll { it.parent?.canRead( this.user ) }
                 }
 
@@ -94 +108 @@
                 samples = filterOnSamplingEventCriteria( samples );
                 samples = filterOnAssayCriteria( samples );
-                
+
                 samples = filterOnModuleCriteria( samples );
-                
+
                 // Save matches
                 results = samples;
@@ -168 +182 @@
                 if( getEntityCriteria( 'Assay' ).size() == 0 )
                         return samples
-                        
+
                 // There is no sample.assays property, so we have to look for assays another way: just find
                 // all assays that match the criteria
@@ -178 +192 @@
                         return criterion.matchOne( assay );
                 });
-                
+
                 // If no assays match these criteria, then no samples will match either
                 if( assays.size() == 0 )
                         return [];
-                
+
                 // Save sample data for later use
-                saveResultFields( samples, criteria, { sample, criterion -> 
-                         def sampleAssays = Assay.findByStudy( sample.parent ).findAll { it.samples?.contains( sample ) };
-                         if( sampleAssays && sampleAssays.size() > 0 ) 
-                                return sampleAssays.collect( criterion.getFieldValue( it ) )
-                        else 
+                saveResultFields( samples, criteria, { sample, criterion ->
+                        def sampleAssays = Assay.findByStudy( sample.parent ).findAll { it.samples?.contains( sample ) };
+                        if( sampleAssays && sampleAssays.size() > 0 )
+                                return sampleAssays.collect( criterion.getFieldValue( it ) )
+                        else
                                 return null
                 });
-                        
+
                 // Now filter the samples on whether they are attached to the filtered assays
                 return samples.findAll { sample ->
                         if( !sample.parent )
                                 return false;
-                        
+
                         def studyAssays = assays.findAll { it.parent.equals( sample.parent ); }
-                        
-                        // See if this sample is present in any of the matching assays. If so, 
+
+                        // See if this sample is present in any of the matching assays. If so,
                         // this sample matches the criteria
                         for( def assay in studyAssays ) {
-                                if( assay.samples?.contains( sample ) ) 
+                                if( assay.samples?.contains( sample ) )
                                         return true;
                         }
-                        
+
                         return false;
                 }
         }
+
+        /**
+         * Returns the saved field data that could be shown on screen. This means, the data 
+         * is filtered to show only data of the query results. Also, the study title and sample
+         * name are filtered out, in order to be able to show all data on the screen without
+         * checking further
+         *
+         * @return      Map with the entity id as a key, and a field-value map as value
+         */
+        public Map getShowableResultFields() {
+                Map showableFields = super.getShowableResultFields()
+                showableFields.each { sampleElement ->
+                        sampleElement.value = sampleElement.value.findAll { fieldElement ->
+                                fieldElement.key != "Study title" && fieldElement.key != "Sample name"
+                        }
+                }
+        }
 }

trunk/src/groovy/dbnp/query/Search.groovy

@@ -16 +16 @@
 package dbnp.query
 
+import dbnp.authentication.SecUser
 import groovy.lang.Closure;
 
@@ -22 +23 @@
 
 import org.springframework.context.ApplicationContext
+import org.springframework.web.context.request.RequestContextHolder;
 import org.codehaus.groovy.grails.commons.ApplicationHolder;
 
@@ -28 +30 @@
 class Search {
         public String entity;
+        public SecUser user;
+        public Date executionDate;
+        public int id;  // Is only used when this query is saved in session
 
         protected List criteria;
@@ -42 +47 @@
         public void setResultFields( Map r ) { resultFields = r; }
 
+<<<<<<< .mine
+        public Search() {
+                ApplicationContext ctx = (ApplicationContext)ApplicationHolder.getApplication().getMainContext();
+                def authenticationService = ctx.getBean("authenticationService");
+                def sessionUser = authenticationService.getLoggedInUser();
+                
+                if( sessionUser )
+                        this.user = sessionUser;
+                else
+                        this.user = null
+        }
+        
+=======
+>>>>>>> .r1481
         /**
          * Returns the number of results found by this search
@@ -68 +87 @@
          * subclasses searching for a specific entity
          */
-        public void execute() {}
+        public void execute() {
+                this.executionDate = new Date();
+        }
 
         /**
@@ -146 +167 @@
                                         return Boolean.valueOf( value )
                                 } catch( Exception e ) {
-                                        println e.getMessage();
                                         return value.toString();
                                 }
@@ -178 +198 @@
         protected List filterOnTemplateEntityCriteria( List studies, String entityName, Closure valueCallback ) {
                 def criteria = getEntityCriteria( entityName );
+                
                 def checkCallback = { study, criterion ->
                         def value = valueCallback( study, criterion );
@@ -192 +213 @@
                 // Save the value of this entity for later use
                 saveResultFields( studies, criteria, valueCallback );
-
+                
                 return filterEntityList( studies, criteria, checkCallback);
         }
@@ -207 +228 @@
                         
                 // Determine the moduleCommunicationService
-                def ctx = ApplicationHolder.getApplication().getMainContext();
+                def ctx = (ApplicationContext)ApplicationHolder.getApplication().getMainContext();
                 def moduleCommunicationService = ctx.getBean("moduleCommunicationService");
                         
@@ -218 +239 @@
                         
                         if( moduleCriteria && moduleCriteria.size() > 0 ) {
-                                println "Filter " + entities.size() + " entities on " + module.name + " criteria: " + moduleCriteria.size();
-
                                 // Retrieve the data from the module
                                 def tokens = entities.collect { it.giveUUID() }.unique();
@@ -243 +262 @@
                                                 
                                                 // Save the value of this entity for later use
-                                                saveResultField( entity.id, criterion.field, value )
+                                                saveResultField( entity.id, criterion.entity + " " + criterion.field, value )
 
                                                 if( !( value instanceof Collection ) ) {
@@ -267 +286 @@
                                                                                 
                                 } catch( Exception e ) {
-                                        println( "Error while retrieving data from " + module.name + ": " + e.getMessage() )
+                                        log.error( "Error while retrieving data from " + module.name + ": " + e.getMessage() )
                                 }
                         }
@@ -285 +304 @@
                 for( criterion in criteria ) {
                         for( entity in entities ) {
-                                saveResultField( entity.id, criterion.field, valueCallback( entity, criterion ) )
+                                if( criterion.field )
+                                        saveResultField( entity.id, criterion.entity + ' ' + criterion.field, valueCallback( entity, criterion ) )
                         }
                 }
@@ -303 +323 @@
                 resultFields[ id ][ fieldName ] = value;
         }
+        
+        /** 
+         * Removes all data from the result field map
+         */
+        protected void clearResultFields() {
+                resultFields = [:]
+        }
+        
+        /**
+         * Returns the saved field data that could be shown on screen. This means, the data is filtered to show only data of the query results.
+         * 
+         * Subclasses could filter out the fields they don't want to show on the result screen (e.g. because they are shown regardless of the 
+         * query.)
+         * @return      Map with the entity id as a key, and a field-value map as value
+         */
+        public Map getShowableResultFields() {
+                def resultIds = getResults()*.id;
+                return getResultFields().findAll {
+                        resultIds.contains( it.key )
+                }
+        }
+        
+        public String toString() {
+                return ( this.entity ? this.entity + " search" : "Search" ) + " " + this.id
+        }
 }

trunk/src/groovy/dbnp/query/StudySearch.groovy

@@ -16 +16 @@
 
 import java.util.List;
+import java.util.Map;
 
 import dbnp.studycapturing.*
 import org.dbnp.gdt.*
+import org.apache.commons.logging.LogFactory;
 
 class StudySearch extends Search {
+        private static final log = LogFactory.getLog(this);
+        
         public StudySearch() {
+                super();
                 this.entity = "Study";
         }
@@ -59 +64 @@
         @Override
         void execute() {
-                // TODO: check for authorization for these studies?
-                def studies = Study.list();
+                super.execute();
 
+                def studies = Study.list().findAll { it.canRead( this.user ) };
+                
                 // If no criteria are found, return all studies
                 if( !criteria || criteria.size() == 0 ) {
@@ -75 +81 @@
                 studies = filterOnSamplingEventCriteria( studies );
                 studies = filterOnAssayCriteria( studies );
-
+                
                 studies = filterOnModuleCriteria( studies );
                 
@@ -81 +87 @@
                 results = studies;
         }
-        
+
         /**
          * Filters the given list of studies on the study criteria
@@ -97 +103 @@
          */
         protected List filterOnSubjectCriteria( List studies ) {
-                return filterOnTemplateEntityCriteria(studies, "Subject", { study, criterion -> 
+                return filterOnTemplateEntityCriteria(studies, "Subject", { study, criterion ->
                         return study.subjects?.collect { criterion.getFieldValue( it ); }
                 })
@@ -119 +125 @@
          */
         protected List filterOnEventCriteria( List studies ) {
-                return filterOnTemplateEntityCriteria(studies, "Event", { study, criterion -> 
+                return filterOnTemplateEntityCriteria(studies, "Event", { study, criterion ->
                         return study.events?.collect { criterion.getFieldValue( it ); }
                 })
         }
-        
+
         /**
-        * Filters the given list of studies on the sampling event criteria
-        * @param studies        Original list of studies
-        * @return                       List with all studies that match the event-criteria
-        */
-   protected List filterOnSamplingEventCriteria( List studies ) {
-                return filterOnTemplateEntityCriteria(studies, "SamplingEvent", { study, criterion -> 
+         * Filters the given list of studies on the sampling event criteria
+         * @param studies       Original list of studies
+         * @return                      List with all studies that match the event-criteria
+         */
+        protected List filterOnSamplingEventCriteria( List studies ) {
+                return filterOnTemplateEntityCriteria(studies, "SamplingEvent", { study, criterion ->
                         return study.samplingEvents?.collect { criterion.getFieldValue( it ); }
                 })
-   }
-        
+        }
+
         /**
          * Filters the given list of studies on the assay criteria
@@ -145 +151 @@
                 })
         }
+
+        /**
+         * Returns the saved field data that could be shown on screen. This means, the data
+         * is filtered to show only data of the query results. Also, the study title and sample
+         * name are filtered out, in order to be able to show all data on the screen without
+         * checking further
+         *
+         * @return      Map with the entity id as a key, and a field-value map as value
+         */
+        public Map getShowableResultFields() {
+                Map showableFields = super.getShowableResultFields()
+                showableFields.each { sampleElement ->
+                        sampleElement.value = sampleElement.value.findAll { fieldElement ->
+                                fieldElement.key != "Study title" && fieldElement.key != "Subject species"
+                        }
+                }
+                return showableFields
+        }
 }

trunk/web-app/css/advancedQuery.css

@@ -1 @@
-label { display: inline-block; zoom: 1; *display: inline; width: 110px; margin-top: 5px; }
+label { display: inline-block; zoom: 1; *display: inline; width: 110px; margin-top: 10px;  }
 
 #searchForm ul#criteria { margin-left: 110px; padding-left: 0px; margin-top: -19px; list-style-type: none;  }
 #searchForm ul#criteria li { margin: 2px 0; padding-left: 0; }
-#searchForm ul#criteria li span { display: inline-block; white-space: nowrap; overflow: hidden; text-overflow: ellipsis; margin-right: 5px; }
+#searchForm ul#criteria li span, 
+#searchForm ul#criteria li a { display: inline-block; white-space: nowrap; overflow: hidden; text-overflow: ellipsis; margin-right: 5px; }
 #searchForm ul#criteria li .entityfield { width: 200px; }
 #searchForm ul#criteria li .operator { width: 100px; }
 #searchForm ul#criteria li .value { width: 240px; }
 
+#searchForm ul#criteria li.emptyList { color: #666; }
 #searchForm ul#criteria li.emptyList:hover { cursor: default; }
 
@@ -14 +16 @@
 
 #input_criteria { display: block; float: right; width: 260px; border: 1px solid #666; padding: 10px; }
-#input_criteria h2 { margin-top: 2px; margin-bottom: 8px; }
+#input_criteria h2 { margin-top: 2px; margin-bottom: 8px; font-weight: bold; }
 #input_criteria label { width: 80px; margin-top: 8px; }
 #input_criteria input.text, #input_criteria select { width: 165px; }
 #input_criteria input.button {  margin-top: 8px; }
+#input_criteria .explanation { font-size: 10px; }
+
+.ui-menu-item .entity { color: #666; font-style: italic; }

trunk/web-app/css/default_style.css

@@ -196 +196 @@
 }
 
+#content .error {
+        border: 1px solid #f99; /* #006dba; */
+        margin-bottom: 10px;
+        margin-top: 10px;
+
+        background: #ffe0e0 url(../plugins/famfamfam-1.0.1/images/icons/error.png) 10px 10px no-repeat;
+        padding: 10px 10px 10px 33px;
+
+}
+
 /** END :: content **/
 /** START :: footer **/