Merge pull request #139 from thehyve/trait_v2

Merge The Hyve trait_v2 into PhenotypeFoundation master

grails-app/conf/Config.groovy

@@ -266,9 +266,9 @@ gscf.baseURL = grails.serverURL
 // Default configuration of manuals
 gscf {
     documents {
-        quickstart = "downloads/quickstart_study_capturing.pdf"
-        manual = "downloads/gscf_user_guide.pdf"
-        license = "downloads/license_terms.pdf"
-        sam_userguide = "downloads/SAM_User_Guide.pdf"
+        quickstart = "/downloads/quickstart_study_capturing.pdf"
+        manual = "/downloads/gscf_user_guide.pdf"
+        license = "/downloads/license_terms.pdf"
+        sam_userguide = "/downloads/SAM_User_Guide.pdf"
     }
 }

grails-app/conf/default.properties

@@ -1,6 +1,6 @@
 ## Server URL ##
 grails.serverURL=http://localhost:8080/gscf
-gscf.baseURL=http://localhost:8080/gscf/
+gscf.baseURL=http://localhost:8080/gscf
 
 ## In-Memory Database ##
 dataSource.driverClassName=org.h2.Driver
@@ -55,7 +55,7 @@ gscf.reCapitalizeSampleNames=true
 
 # Locations of issues and documents
 gscf.issueURL=https://github.com/PhenotypeFoundation/GSCF/issues
-gscf.documents.quickstart=downloads/quickstart_study_capturing.pdf
-gscf.documents.manual=downloads/gscf_user_guide.pdf
-gscf.documents.license=downloads/license_terms.pdf
-gscf.documents.sam_userguide=downloads/SAM_User_Guide.pdf
+gscf.documents.quickstart=/downloads/quickstart_study_capturing.pdf
+gscf.documents.manual=/downloads/gscf_user_guide.pdf
+gscf.documents.license=/downloads/license_terms.pdf
+gscf.documents.sam_userguide=/downloads/SAM_User_Guide.pdf

local-plugins/GDT/grails-app/controllers/org/dbnp/gdt/TemplateEditorController.groovy

@@ -291,13 +291,12 @@ class TemplateEditorController {
      * 				On error the method gives a HTTP response status 500 and the error
      */
     def updateTemplate = {
-        // set content type
-        response.setContentType("text/plain; charset=UTF-8")
 
         // Search for the template field
         def template = Template.get(params.id);
         if (!template) {
             response.status = 404;
+            response.setContentType("text/plain; charset=UTF-8")
             render 'Template not found';
             return;
         }
@@ -307,11 +306,21 @@ class TemplateEditorController {
             def version = params.version.toLong()
             if (template.version > version) {
                 response.status = 500;
+                response.setContentType("text/plain; charset=UTF-8")
                 render 'Template was updated while you were working on it. Please reload and try again.';
                 return
             }
         }
 
+        // Check if the name already exists
+        def dupeCandidate = Template.findByName(params.name)
+        if (dupeCandidate && dupeCandidate != template) {
+            response.status = 500
+            response.setContentType("text/plain; charset=UTF-8")
+            render 'A template with that name already exists. Please choose a different name.'
+            return
+        }
+
         template.properties = params
         if (!template.hasErrors() && template.save(flush: true)) {
             def html = g.render(plugin: 'gdt', template: 'elements/liTemplate', model: [template: template, templateadmin: authenticationService.getLoggedInUser().hasTemplateAdminRights()]);
@@ -320,6 +329,7 @@ class TemplateEditorController {
             render output as JSON;
         } else {
             response.status = 500;
+            response.setContentType("text/plain; charset=UTF-8")
             render 'Template was not updated because errors occurred.';
             return
         }
@@ -951,4 +961,4 @@ class TemplateEditorController {
 
         return true;
     }
-}
+}

local-plugins/GDT/grails-app/domain/org/dbnp/gdt/Template.groovy

@@ -105,7 +105,7 @@ class Template extends Identity {
 		this()
 
 		// copy base values
-		this.name			= otherTemplate.name + " (Copy)"
+		this.name			= createUniqueName(otherTemplate.name)
 		this.description	= otherTemplate.description
 		this.entity			= otherTemplate.entity
 
@@ -116,6 +116,16 @@ class Template extends Identity {
 		}
 	}
 
+	private static createUniqueName(name) {
+		def originalName = name
+		def i = 2
+		while (Template.findByName(name)) {
+			name = "${originalName} - ${i}"
+			i++
+		}
+		return name
+	}
+
 	/**
 	 * clone template
 	 * @param otherTemplate

local-plugins/GDT/src/groovy/org/dbnp/gdt/TemplateEntity.groovy

@@ -241,17 +241,23 @@ 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 ) 
+    public getColumnForEntities( def ids, TemplateField field ) {
+        if( !ids ) 
             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 columnData
+        if( isDomainField(field) ) {
+            columnData = this.class.executeQuery( "SELECT e.id, e." + field.name + " FROM " + this.class.simpleName + " e WHERE e.id in (:ids)", [ids: ids] )
+        } else {
+            columnData = this.class.executeQuery( "SELECT e.id, store FROM " + this.class.simpleName + " e INNER JOIN e." + store + " store WHERE e.id in (:ids) AND index(store) = :fieldName", [ids: ids, fieldName: field.name ] )
+        }
+
         def columnMap = columnData.collectEntries { [ (it[0]): it[1] ] }
 
-        entities.collect { it ? columnMap[ it.id ] : null }
+        ids.collect { it ? columnMap[ it ] : null }
     }
 
     /**

local-plugins/GDT/web-app/js/templateEditor.js

@@ -191,8 +191,14 @@ function updateTemplate( id ) {
             updateTemplateListItem( id, data.html );
 			userMessage( 'Your template was updated.', "okay" );
         },
-        error:      function( request ) {
-        	userMessage( "Could not update template", "errormessage" );
+        error:      function( request, textStatus, error ) {
+          var contentType = request.getResponseHeader('content-type')
+          if (contentType.indexOf('text/plain') > -1) {
+            userMessage( "Could not update template: " + request.responseText, "errormessage" );
+          }
+          else {
+            userMessage( "Could not update template: " + error, "errormessage" );
+          }
         },
 		complete: function( request, textStatus ) {
 			hideWaiting();
@@ -883,4 +889,4 @@ function updateOntologyLists( newObject) {
 function deleteOntology( id ) {
     $("#ontologies_" + id).children().remove(":selected");
     return false;
-}
+}

local-plugins/SAM/grails-app/conf/SamResources.groovy

@@ -7,7 +7,6 @@ modules = {
         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']
-        resource url: [dir: 'css', file: 'tooltip.css', plugin: 'dbxp-sam']
         resource url: [dir: 'images', file: 'subjectlayout.png', plugin: 'dbxp-sam'], attrs:[alt:''], disposition:'inline'
         resource url: [dir: 'images', file: 'samplelayout.png', plugin: 'dbxp-sam'], attrs:[alt:''], disposition:'inline'
         resource url: [dir: 'images', file: 'spinner.gif', plugin: 'dbxp-sam'], attrs:[alt:''], disposition:'inline'

local-plugins/SAM/grails-app/controllers/org/dbxp/sam/MeasurementController.groovy

@@ -162,8 +162,13 @@ class MeasurementController {
 		ids.each { id ->
 			def measurementInstance = Measurement.get(id)
 	        if (measurementInstance) {
+                def samSample = SAMSample.get(measurementInstance.sampleId)
                 try {
 					measurementInstance.delete(flush: true)
+                    // If this was the last measurement in the SAMSample, delete it also
+                    if (samSample.measurements.size() == 0) {
+                        samSample.delete(flush: true)
+                    }
 					numDeleted++;
 	            } catch (org.springframework.dao.DataIntegrityViolationException e) {
 	                log.error(e)

local-plugins/SAM/grails-app/domain/org/dbxp/sam/Measurement.groovy

@@ -43,6 +43,7 @@ class Measurement {
 	public static deleteByAssay( Assay a ) {
 		try {
 			Measurement.executeUpdate( "delete Measurement m WHERE m.sample IN( FROM SAMSample s where s.parentAssay = :assay )", [ assay: a ] );
+			SAMSample.executeUpdate("delete SAMSample s where s.parentAssay = :assay", [ assay: a ] )
 			return true;
 		} catch( Exception e ) {
 			e.printStackTrace();

local-plugins/SAM/grails-app/views/SAMAssay/show.gsp

@@ -10,6 +10,7 @@
         	.delete_button { display: none; }
         	td:hover .delete_button { display: inline; }
         </style>
+        <r:require modules="tiptip" />
     </head>
     <body>
         <content tag="contextmenu">
@@ -101,10 +102,7 @@
                                             <g:if test="${isNumeric}">
                                                 <g:if test="${comments}">
                                                     <%-- numeric value and comments --%>
-                                                    <div class="tooltip">
-                                                    	${cellMeasurements[0].value}
-                                                    	<span>${comments}</span>
-                                                    </div>
+                                                    <span class="tooltip" title="${comments}"> ${cellMeasurements[0].value}</span>
                                                 </g:if>
                                                 <g:else>
                                                     <g:if test="${cellMeasurements[0].value==cellMeasurements[0].value.round(3)}">
@@ -113,16 +111,13 @@
                                                     </g:if>
                                                     <g:else>
                                                         <%-- long numeric value without comments; render short version and put entire number in tooltip --%>
-                                                        <span class="tooltip"> ${cellMeasurements[0].value.round(3).toString()}<span>${cellMeasurements[0].value}</span></span>
+                                                        <span class="tooltip" title="${cellMeasurements[0].value}"> ${cellMeasurements[0].value.round(3).toString()}</span>
                                                     </g:else>
                                                 </g:else>
                                             </g:if>
                                             <g:else>
                                                 <%-- measurement is not numeric, so use text value from comments --%>
-                                                <div class="tooltip">
-                                                	${comments}
-                                                	<span>${comments}</span>
-                                                </div>
+                                                <span class="tooltip" title="${comments}">${comments}</span>
 											</g:else>
 										</td>
 									</g:if>

local-plugins/dbxpBase/grails-app/controllers/dbnp/importer/ImporterController.groovy

@@ -222,7 +222,7 @@ class ImporterController {
             numLinesImported: numLinesImported,
 
             resultLink: importer.getLinkToResults(importInfo.parameter),
-
+            editLink: importer.getLinkToEdit(importInfo.parameter),
             importInfo: importInfo
         ])
     }

local-plugins/dbxpBase/grails-app/views/importer/finish.gsp

@@ -39,8 +39,11 @@
 		</g:else>
 		
 		<p>
-			You can review your data at the following page: <g:link url="${resultLink.url}">${resultLink.label}</g:link> or 
-			<g:link action="upload" params="${defaultParams + [importer:importInfo.importer]}">restart the importer</g:link>.  
+			You can choose to: <g:link url="${resultLink.url}">${resultLink.label}</g:link>,
+			<g:if test="${editLink}">
+				<g:link url="${editLink.url}">${editLink.label}</g:link>
+			</g:if>
+			or <g:link action="upload" params="${defaultParams + [importer:importInfo.importer]}">restart the importer</g:link>.
 		</p>
 					 
 

local-plugins/dbxpBase/src/groovy/dbnp/importer/AbstractImporter.groovy

@@ -48,4 +48,11 @@ public abstract class AbstractImporter implements Importer {
      * Returns whether the header options can only be selected for a single header.
      */
     public boolean headerMappingIsUnique() { true }
-}
+
+    /**
+     * Returns a link to the edit page
+     */
+    public Map getLinkToEdit(def parameters) {
+        return null
+    }
+}

local-plugins/dbxpBase/src/groovy/dbnp/importer/Importer.groovy

@@ -38,11 +38,17 @@ public interface Importer {
     public List<ImportValidationError> getValidationErrors()
 
     /**
-     * Returns a link to a page where results of the import can be seen. 
+     * Returns a link to a page where results of the import can be seen.
      * @return a map with two keys: url and label
      */
     public Map getLinkToResults(def parameters)
-
+
+    /**
+     * Returns a link to a page where results of the import can be edited.
+     * @return a map with two keys: url and label
+     */
+    public Map getLinkToEdit(def parameters)
+
     /**
      * Validates provided data.
      * @param   data            Matrix (List of lists) with the data that has been loaded from the excel/csv file
@@ -65,4 +71,4 @@ public interface Importer {
      *          false if the validation on any of the object has failed 
      */
     public boolean importData(def data, def mapping, def parameters)
-}
+}

scripts/_Events.groovy

@@ -25,3 +25,14 @@ eventCompileEnd = {
    ant.copy(file:"${basedir}/grails-app/conf/default.properties", todir:classesDirPath)
    ant.echo (message: "Default configuration file moved.")
 }
+
+eventConfigureTomcat = { tomcat ->
+        println "Configuring tomcat max post size"
+
+        try {
+            tomcat.connector.maxPostSize = 1073741824
+        }
+        catch (Throwable t) {
+            println t
+        }
+    }