Improved subject selection for subject groups

Subject selection can now be done using a datatable. This enables
the user to use the study design also for studies with large amounts
of subjects.

grails-app/controllers/dbnp/studycapturing/StudyEditDesignController.groovy

@@ -10,6 +10,7 @@ import dbnp.authentication.SecUser
 class StudyEditDesignController {
 	def authenticationService
 	def studyEditService
+        def datatablesService
 
 	def index() {
 		def study = getStudyFromRequest( params )
@@ -679,7 +680,7 @@ class StudyEditDesignController {
 	 */
 	def subjectGroupUpdate() {
 		def subjectGroup = SubjectGroup.get( params.long( "id" ) );
-
+                
 		if( !subjectGroup ) {
 			response.status = 404
 			render "Not found"
@@ -688,20 +689,20 @@ class StudyEditDesignController {
 
 		def name = params.get( "name" )
 		def result = [ "OK" ]
-
+		def subjectIds = params.subjects?.split(",")
 		if( name && name != subjectGroup.name ) {
 			subjectGroup.name = name
 
 			if( subjectGroup.save() ) {
-				handleSubjectsInSubjectGroup( params.list( "subjects[]" ), subjectGroup )
+				handleSubjectsInSubjectGroup( subjectIds, subjectGroup )
 				studyEditService.generateSamples( subjectGroup )
 			} else {
 				response.status = 500
 				result  = [ status: "Error" ]
 			}
 
 		} else {
-			handleSubjectsInSubjectGroup( params.list( "subjects[]" ), subjectGroup )
+			handleSubjectsInSubjectGroup( subjectIds, subjectGroup )
 			studyEditService.generateSamples( subjectGroup )
 		}
 
@@ -781,6 +782,48 @@ class StudyEditDesignController {
 		}
 
 	}
+
+        /**
+         * Returns data for the datatable to select subjects in a subjectgroup
+         * @return
+         */
+        def dataTableSubjectSelection() {
+                def study = Study.read( params.long( "id" ) )
+
+                if( !study ) {
+                    render dataTableError( "Invalid study given: " + study ) as JSON
+                    return
+                }
+
+                def searchParams = datatablesService.parseParams( params )
+                def data = studyEditService.getSubjectsForSubjectSelection( searchParams, study )
+
+                render datatablesService.createDatatablesOutput( data, params, { entry ->
+                        def output = entry as List
+                        def subject = entry[ 0 ]
+
+                        // Convert columns
+                        output[ 0 ] = subject.id
+
+                        // Generate output (the checkbox columns should be first
+                        output
+                }) as JSON
+        }
+
+        /**
+         * Returns an error response for the datatable
+         * @param error
+         * @return
+         */
+        protected def dataTableError( error ) {
+                return [
+                        sEcho:                                  params.sEcho,
+                        iTotalRecords:                  0,
+                        iTotalDisplayRecords:   0,
+                        aaData:                                 [],
+                        errorMessage:                   error
+                ]
+        }
 
 
 	/**

grails-app/services/dbnp/studycapturing/StudyEditService.groovy

@@ -61,6 +61,35 @@ class StudyEditService {
 
 		output 
 	}
+
+        /**
+         * Returns a proper list of subjects samples to generate a datatable for subject selection in a group
+         * @param params        Parameters to search
+                        int                     offset                  Display start point in the current data set.
+                        int                     max                             Number of records that the table can display in the current draw. It is expected that the number of records returned will be equal to this number, unless the server has fewer records to return.
+                        
+                        string          search                  Global search field
+                        
+                        int                     sortColumn              Column being sorted on (you will need to decode this number for your database)
+                        string          sortDirection   Direction to be sorted - "desc" or "asc".
+    
+                          Template      template                Template for the entities to read
+         * @return                      A map with all data. For example:
+                         List           entities                List with all entities
+                         int                    total                   Total number of records in the whole dataset (without taking search, offset and max into account)
+                         int                    totalFiltered   Total number of records in the search (without taking offset and max into account)
+                         int                    ids                             Total list of filtered ids
+         */
+        def getSubjectsForSubjectSelection( searchParams, study ) {
+            def query = generateHQLForSubjectSelection( searchParams, study )
+
+            // Also count the total number of results in the dataset
+            def output = generateOutput( query, searchParams, Subject )
+            output.total = Subject.countByParent( study )
+
+            output
+        }
+
 
 	/**
 	 * Returns a proper list of samples to generate a datatable with templated entities.
@@ -90,7 +119,6 @@ class StudyEditService {
 
 	}
 
-
 	/**
 	 * Generates the HQL to search
 	 * @return Map	
@@ -308,7 +336,78 @@ class StudyEditService {
 			params: hqlParams
 		]
 	}
-
+
+    /**
+     * Generates the HQL to search assay samples
+     * @return Map
+     *              select
+     *              from
+     *              where
+     *              order
+     *              params
+     */
+    def generateHQLForSubjectSelection( searchParams, study ) {
+            def entity = Subject
+
+            // Search in
+            //      subject name
+            //      subject template name
+            //      subject speciies
+
+            // Create an HQL query as it gives us the most flexibility in searching and ordering
+            def from = " Subject s "
+            def joins = []
+            def whereClause = []
+            def hqlParams = [ study: study ]
+            def orderBy = ""
+
+            // Add joins for related information
+            joins << "s.template as template"
+
+            // First add searching
+            if( searchParams.search ) {
+                    // With searching, retrieving the data requires joining all text and term fields
+                    def searchTerm = searchParams.search.toLowerCase()
+                    hqlParams[ "search" ] = "%" + searchTerm + "%"
+
+                    whereClause << "lower(s.name) LIKE :search"
+                    whereClause << "lower(template.name) LIKE :search"
+                    whereClause << "lower(s.species.name) LIKE :search"
+            }
+
+            // Add ordering; to determine the column to sort on
+            def sortColumnIndex = searchParams.sortColumn ?: 0
+            def sortOrder = searchParams.sortDirection ?: "ASC"
+
+            def fields = [
+                    "s.name",
+                    "template.name",
+                    "s.species.name",
+            ]
+
+            if( sortColumnIndex != null || sortColumnIndex < fields.size() ) {
+                    orderBy = fields[ sortColumnIndex ] + " " + sortOrder
+            }
+
+            // Now build up the query, except for the SELECT part.
+            if( joins )
+                    from += " LEFT JOIN " + joins.join( " LEFT JOIN " )
+
+            def where =  "s.parent = :study"
+
+            if( whereClause )
+                    where += " AND (" + whereClause.join( " OR " ) + ") "
+
+            [
+                    select: "s, " + fields.join( ", " ),
+                    from: from,
+                    where: where,
+                    order: orderBy,
+                    params: hqlParams
+            ]
+    }
+
+
 	def putParentIntoEntity( entity, params ) {
 		// Was a parentID given
 		if( params.parentId ) {

grails-app/views/studyEditDesign/index.gsp

@@ -4,7 +4,7 @@
 	<meta name="layout" content="main" />
 	<title>Study edit wizard</title>
 
-	<r:require modules="studyEdit" />
+	<r:require modules="studyEdit,gscf-datatables" />
 </head>
 <body>
 	<div class="basicTabLayout studyEdit studyProperties">
@@ -98,20 +98,25 @@
 			<label>Name: </label><input type="text" name="subjectgroup-name" id="subjectgroup-name" /><br />
 
 			<div id="design-subjects">
-				<span class="subjects">
-					<g:set var="subjectCount" value="${study.subjects?.size()}" />
-					<g:set var="numRows" value="${Math.max( (int)subjectCount / 3, 1 )}" />
-					<g:each in="${study.subjects}" var="subject" status="i">
-						<span class="subject">
-							<input type="checkbox" name="subjectgroup_subjects" id="subjectgroup_subjects_${subject.id}" value="${subject.id}" /> ${subject.name}
-						</span>
-
-						<g:if test="${( i + 1 ) % numRows == 0}">
-							</span>
-							<span class="subjects">
-						</g:if>
-					</g:each>
-				</span>
+				<table id="selectSubjectsTable" data-fieldPrefix="subject" class="subjectsTable selectMulti" rel="${g.createLink(action:"dataTableSubjectSelection", id: study.id)}">
+					<thead>
+						<tr>
+							<th>Name</th>
+							<th>Template</th>
+							<th>Species</th>
+						</tr>
+					</thead>
+					<tfoot>
+						<tr><td>
+							<div class="messagebar loadingSelection">
+								Loading selection of subjects. Please be patient. 
+							</div>						
+							<div class="messagebar selectAll">
+								You selected all items on this page. Would you <a href="#">select all items on other pages</a> as well? 
+							</div>						
+						</td></tr>
+					</tfoot>
+				</table>	
 			</div>				
 		</div>
 

web-app/css/default.css

@@ -1504,3 +1504,26 @@ img.icon {
 /** END :: Message Boxes **/
 
 div.usermanagement { font-size: 0.8em; }
+
+.overlay { 
+  position: fixed;
+  top: 0;
+  left: 0;
+  width: 100%;
+  height: 100%;
+  z-index: 10000;
+  background-color: white;
+  opacity: 0.8;	
+}
+
+.overlay .message {
+	display: block;
+	position: fixed;
+
+	top: 50%;
+    width: 100%;
+    margin-top: -0.5em;
+
+    text-align: center;
+    font-weight: bold;
+}

web-app/css/studyEdit.css

@@ -69,6 +69,7 @@ div .contacts_dialog {
 
 /** Study design styles **/
 
+#subjectGroupDialog table { width: 100%; }
 .subjectsTable th { white-space: nowrap;}
 table.dataTable td.dataTables_empty { text-align: left; }