Merge pull request #127 from thehyve/trait_v2

Merge The Hyve trait_v2 into master
PhenotypeFoundation · Jul 28, 2015 · 08aabaf · 08aabaf
2 parents 3d7c485 + c73b80e
commit 08aabaf
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Showing 15 changed files with 127 additions and 37 deletions.
diff --git a/application.properties b/application.properties
@@ -2,4 +2,4 @@
 #Sat Jan 05 12:13:45 CET 2013
 app.grails.version=2.4.5
 app.name=gscf
-app.version=0.9.5.4
+app.version=0.9.5.5
diff --git a/grails-app/controllers/dbnp/studycapturing/StudyController.groovy b/grails-app/controllers/dbnp/studycapturing/StudyController.groovy
@@ -117,6 +117,36 @@ class StudyController {
         render datatableData as JSON
     }
 
+
+    /**
+     * Returns data for a templated datatable with samples.
+     * 
+     * Due to the formatting of the data, this is a separate method
+     * @return
+     */
+    def dataTableSamples() {
+        // As we add columns to the table, we should shift the sort column
+        def sortColumn = params.int( "iSortCol_0" )
+
+        if( sortColumn > 3 )
+            params.iSortCol_0 = sortColumn - 3
+
+        def datatableData = getTemplatedDatatablesData({ sample ->
+            def defaultData = datatablesService.defaultEntityFormatter(sample)
+
+            // Remove the IDs, as they are irrelevant for now
+            defaultData = defaultData.tail()
+
+            // Add additional columns
+            defaultData.add(1, sample.parentSubject?.name )
+            defaultData.add(2, sample.parentEvent?.event?.name )
+            defaultData.add(3, sample.parentEvent?.eventGroup?.name )
+
+            defaultData
+        })
+        render datatableData as JSON
+    }
+
     /**
      * Returns data for a templated datatable. The type of entities is based on the template given.
      * @return

diff --git a/grails-app/controllers/dbnp/studycapturing/StudyEditController.groovy b/grails-app/controllers/dbnp/studycapturing/StudyEditController.groovy
@@ -233,18 +233,23 @@ class StudyEditController {
          */
         def deleteAssays() {
                 if( !request.post ) {
-                        response.status = 400
-                        render "Bad Request"
-                        return
+                    response.status = 400
+                    render "Bad Request"
+                    return
                 }
 
+                def numIds = params.list( 'ids' )?.size()
                 def numDeleted = deleteEntities( Assay )
 
-                if( numDeleted )
-                flash.message = "" + numDeleted + " assay(s) were deleted"
-                else
-                flash.error= "No assays were selected"
-
+                if( numIds ) {
+                    if( numDeleted == numIds )
+                        flash.message = "All " + numDeleted + " selected assay(s) were deleted"
+                    else
+                        flash.error = "" + numDeleted + " of the " + numIds + " selected assay(s) were deleted. Most probably the other assays contain measurements in one of the modules and cannot be deleted."
+                } else {
+                    flash.error= "No assays were selected"
+                }
+
                 redirect action: "assays", id: params.id
         }
 
@@ -481,13 +486,17 @@ class StudyEditController {
                                                 def entity = entityType.get( id.toLong() )
 
                                                 switch( entityType ) {
-                                                case Subject:
+                                                    case Subject:
                                                         study.deleteSubject( entity )
                                                         break
-                                                case Sample:
+                                                    case Sample:
                                                         study.deleteSample( entity )
                                                         break
-                                                case Assay:
+                                                    case Assay:
+                                                        // Can't delete assays with measurements    
+                                                        if( entity.hasMeasurements() ) {
+                                                            return
+                                                        }
                                                         study.deleteAssay( entity )
                                                         break
                                                 }

diff --git a/grails-app/views/home/index.gsp b/grails-app/views/home/index.gsp
@@ -288,7 +288,7 @@
                     <li><a target="_blank" href="${resource(dir:'downloads', file: 'license_terms.pdf')}" title="">License Terms</a></li>
                 </ul>
             </div>
-            <p class="note">If you encounter a problem or have a suggestion for improvement feel free to submit an issue <a href="#" title="">here</a></p>
+            <p class="note">If you encounter a problem or have a suggestion for improvement feel free to submit an issue <a href="${issueUrl}" title="">here</a></p>
         </div>
     </div>
 	<h1>Usage Statistics</h1>

diff --git a/grails-app/views/study/samples.gsp b/grails-app/views/study/samples.gsp
@@ -24,11 +24,17 @@
 
 		<g:each in="${templates}" var="template">
 			<h3>Template: ${template.name}</h3>
-			<table id="samplesTable_${template.id}" data-templateId="${template.id}" data-fieldPrefix="sample" data-formId="sampleForm" class="samplesTable" rel="${g.createLink(action:"dataTableEntities", id: study.id, params: [template: template.id])}">
+			<table id="samplesTable_${template.id}" data-templateId="${template.id}" data-fieldPrefix="sample" data-formId="sampleForm" class="samplesTable" rel="${g.createLink(action:"dataTableSamples", id: study.id, params: [template: template.id])}">
 				<thead>
 					<tr>
+						<th data-fieldname="name">Name</th>
+						<th data-fieldname="subject" class="nonsortable">Subject</th>
+						<th data-fieldname="event" class="nonsortable">Event</th>
+						<th data-fieldname="group" class="nonsortable">Group</th>
 						<g:each in="${domainFields + template.getFields()}" var="field">
-							<th data-fieldname="${field.escapedName()}">${field.name}</th>
+							<g:unless test="${field.name == 'name'}">
+								<th data-fieldname="${field.escapedName()}">${field.name}</th>
+							</g:unless>
 						</g:each>
 					</tr>
 				</thead>

diff --git a/grails-app/views/studyEdit/assaysamples.gsp b/grails-app/views/studyEdit/assaysamples.gsp
@@ -36,7 +36,7 @@
 						</g:each>
 						<th>Sample</th>
 						<th>Subject</th>
-						<th>Eventgroup</th>
+						<th>Group</th>
 						<th>Sampling event</th>
 						<th>Sample template</th>
 						<th>Starttime (combined)</th>

diff --git a/local-plugins/GDT/grails-app/controllers/org/dbnp/gdt/TemplateEditorController.groovy b/local-plugins/GDT/grails-app/controllers/org/dbnp/gdt/TemplateEditorController.groovy
@@ -15,6 +15,7 @@
 package org.dbnp.gdt
 
 import grails.converters.*
+import grails.util.Holders
 
 class TemplateEditorController {
     def entityName
@@ -167,7 +168,7 @@ class TemplateEditorController {
         // set content type
         response.setContentType("text/html; charset=UTF-8")
 
-        render('view': 'error');
+        render('view': 'error', model: [ issueUrl: Holders.config.gscf.issueURL ] );
     }
 
     /**

diff --git a/local-plugins/GDT/grails-app/views/templateEditor/error.gsp b/local-plugins/GDT/grails-app/views/templateEditor/error.gsp
@@ -25,7 +25,7 @@
 
  <p>
 	 You tried to access the template editor in an invalid way. If you feel you get this message
-	 in error, please file a bugreport <a href="https://trac.nbic.nl/gscf/newticket?summary=templateEditor%20invalid%20request&version=${meta(name: 'app.version')}" target="_new">here</a> with as many details as possible.
+	 in error, please file a bugreport <a href="${issueUrl}" target="_new">here</a> with as many details as possible.
  </p>
 
  <g:if test="${layout == 'main'}">

diff --git a/local-plugins/GDT/src/groovy/org/dbnp/gdt/TemplateEntity.groovy b/local-plugins/GDT/src/groovy/org/dbnp/gdt/TemplateEntity.groovy
@@ -242,13 +242,16 @@ abstract class TemplateEntity extends Identity {
      * Retrieve a the value of a single field for a set of entities
      */
     public getColumnForEntities( def entities, TemplateField field ) {
+        if( !entities ) 
+            return []
+
         def fieldType = field.type
         String store = "template${fieldType.casedName}Fields"
 
         def columnData = this.class.executeQuery( "SELECT e.id, store FROM " + this.class.simpleName + " e INNER JOIN e." + store + " store WHERE e in (:entities) AND index(store) = :fieldName", [entities: entities, fieldName: field.name ] )
         def columnMap = columnData.collectEntries { [ (it[0]): it[1] ] }
 
-        entities.collect { columnMap[ it.id ] }
+        entities.collect { it ? columnMap[ it.id ] : null }
     }
 
     /**

diff --git a/local-plugins/SAM/grails-app/conf/SamResources.groovy b/local-plugins/SAM/grails-app/conf/SamResources.groovy
@@ -2,7 +2,8 @@ modules = {
     sam2 {
         dependsOn 'jquery'
         dependsOn 'datatables'  // from dbxpModuleBase
-
+        dependsOn 'infoboxes'
+
         resource url: [dir: 'js', file: 'selectAddMore.js', plugin: 'dbxp-sam']
         resource url: [dir: 'js', file: 'removeWebFlowExecutionKey.js', plugin: 'dbxp-sam']
         resource url: [dir: 'css', file: 'sam.css', plugin: 'dbxp-sam']

diff --git a/local-plugins/SAM/grails-app/views/SAMAssay/show.gsp b/local-plugins/SAM/grails-app/views/SAMAssay/show.gsp
@@ -17,6 +17,11 @@
         </content>    
 		<h1>${module} ${assayInstance.name} / ${assayInstance.parent.title}</h1>
 
+		<span class="message info"> 
+			<span class="title">List of measurements</span> 
+			You can select measurements by clicking on them. Comments to the measurements are denoted with an icon.
+		</span>
+
 		<g:if test="${measurements.size() > 0}">
             <ul class="data_nav buttons ontop">
            		<li><g:link class="delete" controller="measurement" action="deleteByAssay" id="${assayInstance.id}" params="${[module: module]}" onClick="return confirm('Are you sure?');">Delete all measurements</g:link></li>
@@ -26,7 +31,7 @@
 			<form id="deleteform" action="<g:createLink controller="measurement" action="delete" />" method="post">
 				<input type="hidden" name="assayId" value="${assayInstance.id}" />
                 <input type="hidden" name="module" value="${module}" />
-				<table>
+				<table class="measurements"> 
 					<thead>
 						<tr>
 							<th></th>
@@ -39,7 +44,7 @@
 						<g:set var="measurementIndex" value="${0}" />
 						<g:each var="sample" in="${samples}">
 							<tr>
-								<td>${sample.name}</td>
+								<th>${sample.name}</th>
 
 								<g:each var="feature" in="${features}">
 									<%--
@@ -96,7 +101,10 @@
                                             <g:if test="${isNumeric}">
                                                 <g:if test="${comments}">
                                                     <%-- numeric value and comments --%>
-                                                    <span class="tooltip"> ${cellMeasurements[0].value}<span>${comments}</span></span>
+                                                    <div class="tooltip">
+                                                    	${cellMeasurements[0].value}
+                                                    	<span>${comments}</span>
+                                                    </div>
                                                 </g:if>
                                                 <g:else>
                                                     <g:if test="${cellMeasurements[0].value==cellMeasurements[0].value.round(3)}">
@@ -111,16 +119,12 @@
                                             </g:if>
                                             <g:else>
                                                 <%-- measurement is not numeric, so use text value from comments --%>
-                                                <span>${comments}</span>
+                                                <div class="tooltip">
+                                                	${comments}
+                                                	<span>${comments}</span>
+                                                </div>
 											</g:else>
 										</td>
-										<script>
-											$('#td${cellMeasurements[0].id}').on('click', function() {
-												var checkbox = $('#check${cellMeasurements[0].id}');
-												checkbox.prop('checked', !checkbox.prop('checked'));
-												$(this).toggleClass('selected', checkbox.prop('checked'));
-											});
-										</script>
 									</g:if>
 									<g:else>
 										<td></td>
@@ -159,5 +163,18 @@
 				to import your data	or add your measurements <g:link controller="measurement" action="create" params="${[module: module]}">manually</g:link>.
 			</p>
 		</g:else>
+
+		<r:script>
+			$('.measurements td').on('click', function() {
+				// Update checkbox on click
+				var checkbox = $(this).find( "input[type=checkbox]" );
+				checkbox.prop('checked', !checkbox.prop('checked'));
+				$(this).toggleClass('selected', checkbox.prop('checked'));
+			}).each(function(idx,el) {
+				// Initialize styling based on checkboxes
+				var checkbox = $(this).find( "input[type=checkbox]" );
+				$(this).toggleClass('selected', checkbox.prop('checked'));
+			});;
+		</r:script>
     </body>
 </html>
diff --git a/local-plugins/SAM/web-app/css/sam.css b/local-plugins/SAM/web-app/css/sam.css
@@ -141,9 +141,6 @@ td {
     text-overflow: clip;
 }
 
-/* Comments field in the assay overview */
-td.comments { background-color: pink; }
-
 /* Selected cells */
 td.selected { background-color: #CCFFCC; }
 
@@ -212,3 +209,17 @@ td.styleFeatureGroup {
     text-decoration: underline;
 }
 
+table.measurements td { 
+	vertical-align: middle; 
+	white-space: nowrap;
+	max-width: 60px;
+	overflow: hidden;
+	text-overflow: ellipsis; 
+}
+
+table.measurements td.comments { 
+	background-size: 12px 12px;
+	background-image: url(../../famfamfam-1.0.1/images/icons/page_edit.png);
+	background-position: center right;
+	background-repeat: no-repeat; 
+}
diff --git a/local-plugins/dbxpBase/grails-app/domain/dbnp/studycapturing/Assay.groovy b/local-plugins/dbxpBase/grails-app/domain/dbnp/studycapturing/Assay.groovy
@@ -2,6 +2,7 @@ package dbnp.studycapturing
 
 import org.dbnp.gdt.*
 import dbnp.authentication.*
+import org.dbxp.sam.Measurement
 
 /**
  * This class describes an Assay, which describes the application of a certain (omics) measurement to multiple samples.
@@ -124,4 +125,13 @@ class Assay extends TemplateEntity {
 			return 0
 		}
 	}
+
+    /**
+     * Checks whether the SAM module has measurements associated with this assay
+     */
+    public boolean hasMeasurements() {
+        def num = Measurement.executeQuery( "SELECT COUNT(*) FROM Measurement m WHERE m.sample.parentAssay = :assay", [ "assay": this ] )
+
+        return num[0] > 0
+    }
 }
diff --git a/web-app/js/studyEdit/studyEdit.design.eventGroupDialog.js b/web-app/js/studyEdit/studyEdit.design.eventGroupDialog.js
@@ -174,7 +174,7 @@ StudyEdit.design.eventGroups = {
 
 	edit: function( id, dataUrl ) {
 		var dialog = StudyEdit.design.eventGroups.dialog.get();
-		dialog.dialog( "option", "title", "Edit treatment & sample group" );
+		dialog.dialog( "option", "title", "Edit sample & treatment group" );
 		dialog.data( "eventgroup-id", id );
 
 		StudyEdit.design.eventGroups.dialog.open()
@@ -278,7 +278,8 @@ StudyEdit.design.eventGroups = {
 
 		if( confirm( "Deleting this treatment&sample group will also delete all samples that originated from it, and remove all instances of this group. Are you sure you want to delete the treatment&sample group?" ) ) {
 			$.post( url, data, function() {
-				console.log( "Eventgroup deleted" );
+				if( console && console.log )
+					console.log( "Eventgroup deleted" );
 			});
 
 			// Also delete the eventgroup from the timeline with subjectEventgroups

diff --git a/web-app/js/studyEdit/studyEdit.design.js b/web-app/js/studyEdit/studyEdit.design.js
@@ -168,7 +168,8 @@ StudyEdit.design.subjectEventGroups = {
 
 		if( !hasSamples || confirm( "Deleting this treatment&sample group will also delete all samples that originated from it. Are you sure you want to delete the group?" ) ) {
 			$.post( url, data, function() {
-				console.log( "SubjectEventgroup deleted" );
+				if( console && console.log )
+					console.log( "SubjectEventgroup deleted" );
 			});
 
 			return true;