Changeset 536

Timestamp:

Jun 7, 2010, 9:20:00 AM (14 years ago)

Author:

roberth

Message:

Samples are now shown in the study overview page. Also some tests are added and the bootstrap is updated to show some sample fields with a template

Location:

trunk

Files:

• grails-app/conf/BootStrap.groovy (modified) (1 diff)
• grails-app/controllers/dbnp/studycapturing/StudyController.groovy (modified) (2 diffs)
• grails-app/domain/dbnp/studycapturing/Event.groovy (modified) (1 diff)
• grails-app/domain/dbnp/studycapturing/Study.groovy (modified) (1 diff)
• grails-app/domain/dbnp/studycapturing/TemplateEntity.groovy (modified) (1 diff)
• grails-app/views/study/show.gsp (modified) (12 diffs)
• test/unit/dbnp/studycapturing/EventGroupTests.groovy (added)
• test/unit/dbnp/studycapturing/EventTests.groovy (modified) (1 diff)
• test/unit/dbnp/studycapturing/StudyTests.groovy (modified) (2 diffs)
• test/unit/dbnp/studycapturing/TemplateEntityTests.groovy (added)
• web-app/css/studies.css (modified) (1 diff)

trunk/grails-app/conf/BootStrap.groovy

@@ -960 +960 @@
                                                 name: currentSubject.name + '_B',
                                                 material: bloodTerm,
+                                                template: humanBloodSampleTemplate,
                                                 parentSubject: currentSubject,
                                                 parentEvent: bloodSamplingEvent
                                         );
+                                        currentSample.setFieldValue( "Text on vial", "T" + (Math.random() * 100L) )
 
                                         humanStudy.addToSubjects(currentSubject).addToSamples(currentSample).with { if (!validate()) { errors.each { println it} } else save()}

trunk/grails-app/controllers/dbnp/studycapturing/StudyController.groovy

@@ -31 +31 @@
     }
 
-    /*def create = {
-        def studyInstance = new Study()
-        studyInstance.properties = params
-        return [studyInstance: studyInstance]
-    }
-
-    def save = {
-        def studyInstance = new Study(params)
-        if (studyInstance.save(flush: true)) {
-            flash.message = "${message(code: 'default.created.message', args: [message(code: 'study.label', default: 'Study'), studyInstance.id])}"
-            redirect(action: "show", id: studyInstance.id)
-        }
-        else {
-            render(view: "create", model: [studyInstance: studyInstance])
-        }
-    }*/
-
     /**
      * Shows one or more studies
@@ -72 +55 @@
      */
     def events = {
-        def eventGroup = EventGroup.get(params.id)
+        def eventGroupId = Integer.parseInt( params.id );
+        def studyId      = Integer.parseInt( params.study );
+        def eventGroup;
+
+        // eventGroupId == -1 means that the orphaned events should be given
+        if( eventGroupId == -1 ) {
+            def studyInstance = Study.get( studyId )
+            
+            if (studyInstance == null) {
+                flash.message = "${message(code: 'default.not.found.message', args: [message(code: 'study.label', default: 'Study'), studyId])}"
+                redirect(action: "list");
+                return;
+            }
+
+            events = studyInstance.getOrphanEvents();
+        } else {
+            eventGroup = EventGroup.get(params.id)
+
+            if (eventGroup == null) {
+                flash.message = "${message(code: 'default.not.found.message', args: [message(code: 'eventgroup.label', default: 'Eventgroup'), params.id])}"
+                redirect(action: "list");
+                return;
+            }
+            events = eventGroup?.events;
+        }
 
         // This parameter should give the startdate of the study in milliseconds
         // since 1-1-1970
         long startDate  = Long.parseLong( params.startDate )
-        
-        if (!eventGroup) {
-            flash.message = "${message(code: 'default.not.found.message', args: [message(code: 'eventgroup.label', default: 'Eventgroup'), params.id])}"
-            redirect(action: "list")
+
+        // Create JSON object
+        def json = [ 'dateTimeFormat': 'iso8601', events: [] ];
+
+        // Add all other events
+        for( event in events ) {
+            def parameters = []
+            for( templateField in event.giveTemplateFields() ) {
+                def value = event.getFieldValue( templateField.name );
+                if( value ) {
+                    parameters << templateField.name + " = " + value;
+                }
+            }
+
+             json.events << [
+                'start':    new Date( startDate + event.startTime * 1000 ),
+                'end':      new Date( startDate + event.endTime * 1000 ),
+                'durationEvent': !event.isSamplingEvent(),
+                'title': event.template.name + " (" + parameters.join( ', ' ) + ")",
+                'description': parameters
+            ]
         }
-        else {
-
-            // Create JSON object
-            def json = [ 'dateTimeFormat': 'iso8601', events: [] ];
-
-            // Add the start of the study as event
-            /*
-            json.events << [
-                'start':    startDate,
-                'durationEvent': false,
-                'title': "Start date study",
-                'color': 'red'
-            ]
-            */
-           
-            // Add all other events
-            for( event in eventGroup.events ) {
-                def parameters = []
-                for( templateField in event.giveTemplateFields() ) {
-                    def value = event.getFieldValue( templateField.name );
-                    if( value ) {
-                        parameters << templateField.name + " = " + value;
-                    }
-                }
-
-                 json.events << [
-                    'start':    new Date( startDate + event.startTime * 1000 ),
-                    'end':      new Date( startDate + event.endTime * 1000 ),
-                    'durationEvent': !event.isSamplingEvent(),
-                    'title': event.template.name + " (" + parameters.join( ', ' ) + ")",
-                    'description': parameters
-                ]
-            }
-            render json as JSON
-        }
+        render json as JSON
     }
 

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

@@ -84 +84 @@
         }
 
+        def belongsToGroup( Set<EventGroup> groups ){
+            def eventFound = false;
+            def that = this;
+            groups.each{ eventgroup ->
+                if( !eventFound ) {
+                    eventFound = ( that.id in eventgroup.events.id );
+                }
+            }
+
+            return eventFound;
+        }
+
         def String toString() {
                 return fieldExists('Description') ? getFieldValue('Description') : ""

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

@@ -66 +66 @@
         }
 
+        /**
+         * returns all events and sampling events that do not belong to a group
+         */
+        def Set<Event> getOrphanEvents() {
+            def orphans =
+                events.findAll{ event -> !event.belongsToGroup( eventGroups ) } +
+                samplingEvents.findAll { event -> !event.belongsToGroup( eventGroups ) };
+
+            return orphans;
+        }
+
         /**
          * Return the unique Subject templates that are used in this study

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

@@ -585 +585 @@
         /**
          * Convenience method. Returns all unique templates used within a collection of TemplateEntities.
+         *
+         * If the collection is empty, an empty set is returned. If none of the entities contains
+         * a template, also an empty set is returned.
          */
         static Set<Template> giveTemplates(Set<TemplateEntity> entityCollection) {
-                return entityCollection*.template.unique();
+            def set = entityCollection*.template.unique();
+
+            // If one or more entities does not have a template, the resulting
+            // set contains null. That is not what is meant.
+            return set.findAll { it != null };
         }
 

trunk/grails-app/views/study/show.gsp

@@ -1 +1 @@
 
 <%@ page import="dbnp.studycapturing.Study" %>
+<%@ page import="dbnp.studycapturing.EventGroup" %>
 <%@ page import="dbnp.studycapturing.RelTime" %>
 <html>
@@ -20 +21 @@
                 show: function(event, ui) {
                   // If the events tab is shown, the timeline should be redrawn
-                  if( ui.tab.hash == '#events' && !timelineloaded ) {
+                  if( ui.tab.hash == '#events-timeline' && !timelineloaded ) {
                     loadTimeline( 'eventstimeline', 'eventtitles', 0 );
                     timelineloaded = true;
@@ -86 +87 @@
 
               <g:set var="bandNr" value="${bandNr+1}" />
-
-              <g:each in="${study.eventGroups}" var="eventGroup" status="i">
+              <% 
+                def sortedEventGroups = study.eventGroups.sort( { a, b ->
+                    return a.name <=> b.name;
+                }  as Comparator );
+
+                def orphans = study.getOrphanEvents();
+                if( orphans.size() > 0 ) {
+                  sortedEventGroups.add( new EventGroup(
+                    id: -1,
+                    name: 'No group',
+                    events: orphans,
+                    subjects: []
+                  ));
+                }
+
+              %>
+              <g:each in="${sortedEventGroups}" var="eventGroup" status="i">
 
                 //------------- Eventgroup ${bandNr} ---------------
@@ -95 +111 @@
 
                 // Load events for this eventsource (using jquery)
-                var event_url = '${createLink(controller:'study', action:'events', id:eventGroup.id, params: [startDate: study.startDate.getTime() ])}';
+                var event_url = '${createLink(controller:'study', action:'events', id:( eventGroup.id ? eventGroup.id : -1 ), params: [ startDate: study.startDate.getTime(), study: study.id ])}';
                 $.getJSON(event_url, $.callback( _loadJSONEvents, [0, ${bandNr}, eventSources[${bandNr}], overviewEventSource, event_url] ) );
 
@@ -156 +172 @@
                 bandTitleInfo[ timelineNr ][ ${bandNr} ] = {
                   title: "${eventGroup.name}",
+                  className: "<g:if test="${ eventGroup.id == -1 || !eventGroup.id  }">no_group</g:if>",
                   subjects: "${showSubjects}"
                 };
@@ -163 +180 @@
 
               // Synchronize all bands
-              <g:each in="${study.eventGroups}" var="eventGroup" status="i">
+              <g:each in="${sortedEventGroups}" var="eventGroup" status="i">
                 bandInfos[${i + datesBandNr +1}].syncWith = ${datesBandNr};
               </g:each>
@@ -185 +202 @@
           <li><a href="#study">Study Information</a></li>
           <li><a href="#subjects">Subjects</a></li>
-          <li><a href="#events">Events</a></li>
-          <li><a href="#event-group">Event Groups</a></li>
+          <li><a href="#events-timeline">Events timeline</a></li>
+          <li><a href="#events-table">Events table</a></li>
           <li><a href="#assays">Assays</a></li>
+          <li><a href="#samples">Samples</a></li>
           <li><a href="#persons">Persons</a></li>
           <li><a href="#publications">Publications</a></li>
@@ -313 +331 @@
                     // so the list is filtered for unique values
                     subjectTemplates = studyList*.giveSubjectTemplates().flatten().unique()
-                    subjectFields = subjectTemplates*.fields.flatten().unique()
-
-                    showSubjectFields = subjectFields
-
-                    /* 
+                    if( !subjectTemplates ) {
+                      subjectTemplates = [];
+                      subjectFields = [];
+                    } else {
+                      subjectFields = subjectTemplates*.fields.flatten().unique()
+                      if( !subjectFields ) {
+                        subjectFields = [];
+                      }
+                    }
+
+                    /*
                      * These lines are rewritten because
                      * performance sucked
@@ -393 +417 @@
         </div>
 
-        <div id="events">
+        <div id="events-timeline">
           <g:if test="${studyList*.events.flatten().size()==0 && studyInstance*.samplingEvents.flatten().size()==0 }">
             No events in these studies
@@ -472 +496 @@
         </div>
 
-        <div id="event-group">
+        <div id="events-table">
           <g:if test="${studyList*.eventGroups.flatten().size()==0}">
             No event groups in this study
@@ -510 +534 @@
 
               <g:each in="${studyList}" var="studyInstance">
-
-                <g:each in="${studyInstance.eventGroups}" var="eventGroup" status="j">
+                <%
+                  def sortedEventGroups = studyInstance.eventGroups.sort( { a, b ->
+                      return a.name <=> b.name;
+                  }  as Comparator );
+
+                  def orphans = studyInstance.getOrphanEvents();
+                  if( orphans.size() > 0 ) {
+                    sortedEventGroups.add( new EventGroup(
+                      id: -1,
+                      name: 'No group',
+                      events: orphans,
+                      subjects: []
+                    ));
+                  }
+
+                %>
+                <g:each in="${sortedEventGroups}" var="eventGroup" status="j">
                   <tr class="${(i % 2) == 0 ? 'odd' : 'even'}">
                     <g:if test="${multipleStudies && j==0}">
-                      <td class="studytitle" rowspan="${studyInstance.eventGroups.size()}">
+                      <td class="studytitle" rowspan="${sortedEventGroups.size()}">
                         ${studyInstance.title}
                       </td>
@@ -595 +634 @@
                 </g:each>
               </g:each>
+            </table>
+          </g:else>
+        </div>
+
+        <div id="samples">
+
+          <g:if test="${studyList*.samples.flatten().size()==0}">
+            No samples in the selected studies
+          </g:if>
+          <g:else>
+            <table>
+              <thead>
+                <tr>
+                  <g:if test="${multipleStudies}">
+                    <th></th>
+                  </g:if>
+                  <g:each in="${new dbnp.studycapturing.Sample().giveDomainFields()}" var="field">
+                    <th>${field}</th>
+                  </g:each>
+
+                  <%
+                    // Determine a union of the fields for all different
+                    // samples in all studies. In order to show a proper list.
+                    // We want every field to appear just once,
+                    // so the list is filtered for unique values
+                    sampleTemplates = studyList*.giveSampleTemplates().flatten().unique()
+
+                    if( !sampleTemplates ) {
+                      sampleTemplates = [];
+                      sampleFields = [];
+                      showSampleFields = [];
+                    } else {
+                      sampleFields = sampleTemplates*.fields.flatten().unique()
+                      if( !sampleFields ) {
+                        sampleFields = [];
+                        showSampleFields = [];
+                      } else {
+                        // Filter out all fields that are left blank for all samples
+                        allSamples = studyList*.samples.flatten()
+
+                        showSampleFields = [];
+                        sampleFields.each { sampleField ->
+                          for( sample in allSamples )
+                          {
+                            // If the field is filled for this subject, we have to
+                            // show the field and should not check any other
+                            // samples (hence the break)
+                            if( sample.fieldExists( sampleField.name ) && sample.getFieldValue( sampleField.name ) ) {
+                              showSampleFields << sampleField;
+                              break;
+                            }
+                          }
+                        }
+                      }
+                    }
+                  %>
+
+                  <g:each in="${showSampleFields}" var="field">
+                    <th>${field}</th>
+                  </g:each>
+
+                </tr>
+              </thead>
+
+              <g:set var="i" value="${1}" />
+
+              <g:each in="${studyList}" var="studyInstance">
+                <%
+                  // Sort samples by name
+                  samples = studyInstance.samples;
+                  sortedSamples = samples.sort( { a, b -> a.name <=> b.name } as Comparator )
+                %>
+
+                <g:each in="${sortedSamples}" var="sample" status="j">
+                  <tr class="${(i % 2) == 0 ? 'odd' : 'even'}">
+                    <g:if test="${multipleStudies && j==0}">
+                      <td class="studytitle" rowspan="${sortedSamples.size()}">
+                        ${studyInstance.title}
+                      </td>
+                    </g:if>
+                    <g:each in="${sample.giveDomainFields()}" var="field">
+                      <td>${sample.getFieldValue(field.name)}</td>
+                    </g:each>
+
+                    <g:each in="${showSampleFields}" var="field">
+                      <td>
+                        <g:if test="${sample.fieldExists(field.name)}">
+                          ${sample.getFieldValue(field.name)}
+                        </g:if>
+                        <g:else>
+                          N/A
+                        </g:else>
+                      </td>
+                    </g:each>
+
+                  </tr>
+                  <g:set var="i" value="${i + 1}" />
+                </g:each>
+              </g:each>
+
             </table>
           </g:else>

trunk/test/unit/dbnp/studycapturing/EventTests.groovy

@@ -12 +12 @@
     }
 
-    void testSomething() {
+    void testBelongsToGroup() {
+        def events = [];
+        10.times {
+            events[ it ] = new Event(
+                id: it,
+                startTime: 3600,
+                endTime: 3800
+            )
+            println( 'Created event ' + it );
+        }
+        def evGroup1 = new EventGroup(
+            name: 'group1',
+            events: events[0..4]
+        )
+        def evGroup2 = new EventGroup(
+            name: 'group2',
+            events: events[3..6]
+        )
+
+        Set<EventGroup> set1 = new HashSet<EventGroup>();
+        Set<EventGroup> set2 = new HashSet<EventGroup>();
+        Set<EventGroup> setBoth = new HashSet<EventGroup>();
+        Set<EventGroup> setEmpty = new HashSet<EventGroup>();
+        set1.add( evGroup1 );
+        set2.add( evGroup2 );
+        setBoth.add( evGroup1 );
+        setBoth.add( evGroup2 );
+
+        assert events[0].belongsToGroup( set1 );
+        assert events[3].belongsToGroup( set1 );
+        assert !events[6].belongsToGroup( set1 );
+
+        assert events[3].belongsToGroup( set2 );
+        assert events[6].belongsToGroup( set2 );
+
+        assert !events[0].belongsToGroup( setEmpty );
+        assert !events[8].belongsToGroup( setEmpty );
+
+        assert events[0].belongsToGroup( setBoth );
+        assert events[3].belongsToGroup( setBoth );
+        assert events[6].belongsToGroup( setBoth );
+
+        assert !events[7].belongsToGroup( setBoth );
 
     }

trunk/test/unit/dbnp/studycapturing/StudyTests.groovy

@@ -2 +2 @@
 
 import grails.test.*
-
+import groovy.util.GroovyTestCase
 class StudyTests extends GrailsUnitTestCase {
     protected void setUp() {
@@ -12 +12 @@
     }
 
-    void testSomething() {
+    protected void assertCollectionEquals( Collection set1, Collection set2 ) {
+        set1.each {
+            assert it in set2;
+        }
+        set2.each {
+            assert it in set1;
+        }
 
     }
+
+    void testGetOrphanEvents() {
+        def events = [];
+        10.times {
+            events[ it ] = new Event(
+                id: it,
+                startTime: 3600,
+                endTime: 3800
+            )
+            println( 'Created event ' + it );
+        }
+        def evGroup1 = new EventGroup(
+            name: 'group1',
+            events: events[0..4]
+        )
+        def evGroup2 = new EventGroup(
+            name: 'group2',
+            events: events[3..6]
+        )
+
+        // No events should give no orphan events
+        def study1 = new Study( title: 'Studytitle 1', events: [], eventGroups: [] );
+        assert study1.getOrphanEvents().size() == 0;
+
+        // Not even with a group
+        study1.eventGroups = [ evGroup1 ];
+        assert study1.getOrphanEvents().size() == 0;
+
+        // Events 0..4 are part of evGroup1
+        study1.events = events[0..8];
+        println(  study1.getOrphanEvents().id )
+        println(  events[ 5..8].id )
+        
+        assertCollectionEquals( study1.getOrphanEvents(), events[ 5..8 ] );
+
+        // Remove the evGroup
+        study1.eventGroups = [];
+        assertCollectionEquals( study1.getOrphanEvents(), events[ 0..8 ] );
+
+        // Add multiple groups
+        study1.eventGroups = [ evGroup1, evGroup2 ];
+        assertCollectionEquals( study1.getOrphanEvents(), events[ 7..8 ] );
+
+        // Remove events again
+        study1.events = [];
+        assert study1.getOrphanEvents().size() == 0;
+    }
 }

trunk/web-app/css/studies.css

@@ -84 +84 @@
 
 .eventtitles .studytitle { font-weight: bold; background-color: transparent; }
+.eventtitles .no_group { color: #990000; }