Link crawler test fixes

WNPRC_EHR/resources/referenceStudy/study/datasets/datasets_manifest.xml

@@ -229,5 +229,8 @@
     <dataset name="BehaviorAbstract" id="5015" category="ColonyManagement" type="Standard">
       <tags/>
     </dataset>
+    <dataset name="cases" id="6020" category="Clinical" type="Standard">
+      <tags/>
+    </dataset>
   </datasets>
 </datasets>

WNPRC_EHR/resources/referenceStudy/study/datasets/datasets_metadata.xml

@@ -1,5 +1,55 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <tables xmlns="http://labkey.org/data/xml">
+<!--  Case dataset added just to clear errors for common EHR components -->
+  <table tableName="cases" tableDbType="TABLE">
+    <columns>
+      <column columnName="Id">
+        <datatype>varchar</datatype>
+        <propertyURI>http://cpas.labkey.com/Study#ParticipantId</propertyURI>
+        <importAliases>
+          <importAlias>ptid</importAlias>
+        </importAliases>
+      </column>
+      <column columnName="date">
+        <datatype>timestamp</datatype>
+        <propertyURI>http://cpas.labkey.com/Study#VisitDate</propertyURI>
+        <conceptURI>http://cpas.labkey.com/Study#VisitDate</conceptURI>
+      </column>
+      <column columnName="enddate">
+        <datatype>timestamp</datatype>
+        <propertyURI>urn:ehr.labkey.org/#EndDate</propertyURI>
+      </column>
+      <column columnName="caseid">
+        <datatype>varchar</datatype>
+        <propertyURI>urn:ehr.labkey.org/#CaseId</propertyURI>
+      </column>
+      <column columnName="reviewdate">
+        <datatype>timestamp</datatype>
+      </column>
+      <column columnName="category">
+        <datatype>varchar</datatype>
+      </column>
+      <column columnName="problemCategory">
+        <datatype>varchar</datatype>
+      </column>
+      <column columnName="problemSubcategory">
+        <datatype>varchar</datatype>
+      </column>
+      <column columnName="plan">
+        <datatype>varchar</datatype>
+      </column>
+      <column columnName="vetreview">
+        <datatype>varchar</datatype>
+        <propertyURI>urn:ehr.labkey.org/#VetReview</propertyURI>
+      </column>
+      <column columnName="vetreviewdate">
+        <datatype>timestamp</datatype>
+        <propertyURI>urn:ehr.labkey.org/#VetReviewDate</propertyURI>
+      </column>
+    </columns>
+    <tableTitle>Cases</tableTitle>
+  </table>
+<!--  -->
   <table tableName="breeding_encounters" tableDbType="TABLE">
     <description>Contains one row for each breeding pairing/assignment for a dam at the center.</description>
     <columns>

WNPRC_EHR/resources/views/dataAdmin.html

@@ -104,7 +104,6 @@
                     {queryName: 'dental_teeth', schemaName: 'ehr_lookups', title: 'Dental Teeth Field'},
 
                     {queryName: 'encounter_types', schemaName: 'ehr_lookups', title: 'Encounter Types'},
-                    {queryName: 'error_types', schemaName: 'ehr_lookups', title: 'Error Report Error Types'},
                     {queryName: 'gender_codes', schemaName: 'ehr_lookups', title: 'Gender Codes'},
                     {queryName: 'geographic_origins', schemaName: 'ehr_lookups', title: 'Geographic Origin Codes'},
                     {queryName: 'hematology_method', schemaName: 'ehr_lookups', title: 'Hematology Method'},

WNPRC_EHR/resources/views/ehrAdmin.html

@@ -13,7 +13,6 @@
                 items: [
                     {name: 'Client Errors', url: '<%=contextPath%>' + '/shared/query-executeQuery.view?schemaName=auditlog&query.queryName=Client%20API%20Actions'},
                     {name: 'EHR Backups', url: '<%=contextPath%><%=containerPath%>/Backups/project-begin.view'},
-                    {name: 'ETL Admin', url: '<%=contextPath%><%=containerPath%>/onprc_ehr-etlAdmin.view'},
                     {name: 'Genetics Calculations', url: '<%=contextPath%><%=containerPath%>/ehr-geneticCalculationSettings.view'},
                     //{name: 'ETL Duration', url: '<%=contextPath%><%=containerPath%>/query-executeQuery.view?schemaName=core&query.queryName=Sync Duration'},
                     //{name: 'ETL History', url: '<%=contextPath%><%=containerPath%>/query-executeQuery.view?schemaName=core&query.queryName=Sync History'},
@@ -41,15 +40,6 @@
             {header: 'Logs',
                 items: [
                     {name: 'All Logs', url: '<%=contextPath%><%=containerPath%>/Logs/project-begin.view'},
-                    {name: 'Labkey.log', url: '<%=contextPath%>/files<%=containerPath%>/Logs/%40filesets/Tomcat%20Logs/labkey.log'},
-                    {name: 'Labkey-errors.log', url: '<%=contextPath%>/files<%=containerPath%>/Logs/%40filesets/Tomcat%20Logs/labkey-errors.log'},
-                    {name: 'ETL Log', url: '<%=contextPath%>/files<%=containerPath%>/Logs/%40filesets/Tomcat%20Logs/ehr-etl.log'},
-                    {name: 'ETL Errors Log', url: '<%=contextPath%>/files<%=containerPath%>/Logs/%40filesets/Tomcat%20Logs/ehr-etl-errors.log'},
-                    {name: 'ActiveMQ.log', url: '<%=contextPath%>/files<%=containerPath%>/Logs/%40filesets/ActiveMQ/activemq.log'},
-                    {name: 'Monit.log', url: '<%=contextPath%>/files<%=containerPath%>/Logs/%40filesets/Monit/monit.log'},
-                    {name: 'Munin.log', url: '<%=contextPath%>/files<%=containerPath%>/Logs/%40filesets/Munin/munin.log'},
-                    {name: 'Inbreeding Coefficients Reload Cron Job Log', url: '<%=contextPath%>/files<%=containerPath%>/Logs/%40filesets/Kinship/kinshipOut.txt'},
-                    {name: 'Kinship Reload Cron Job Log', url: '<%=contextPath%>/files<%=containerPath%>/Logs/%40filesets/Kinship/inbreedingOut.txt'}
                 ]
             },
             {header: 'Notifications',

WNPRC_EHR/resources/views/moreReports.html

@@ -12,7 +12,6 @@
             header: 'Reports',
             items: [
                 {name: 'Blood Needlesticks', url: '<%=contextPath%>' + ctx['EHRStudyContainer'] + '/query-executeQuery.view?schemaName=study&query.queryName=bloodNeedlesticks'},
-                {name: 'Housing By Room and Cage', url: '<%=contextPath%>' + ctx['EHRStudyContainer'] + '/query-executeQuery.view?schemaName=study&query.queryName=housingByRoomCage'},
                 {name: 'Per Diems (in testing)', url: '<%=contextPath%>' + ctx['EHRStudyContainer'] + '/query-executeQuery.view?schemaName=study&query.queryName=PerDiems'},
                 {name: 'Per Diems Raw Data (in testing)', url: '<%=contextPath%>' + ctx['EHRStudyContainer'] + '/query-executeQuery.view?schemaName=study&query.queryName=PerDiemsByDay'},
                 {name: 'Restraints Used', url: '<%=contextPath%>' + ctx['EHRStudyContainer'] + '/query-executeQuery.view?schemaName=study&query.queryName=restraintUsed'},

WNPRC_EHR/src/org/labkey/wnprc_ehr/WNPRC_EHRModule.java

@@ -45,10 +45,12 @@
 import org.labkey.api.query.DetailsURL;
 import org.labkey.api.query.QuerySchema;
 import org.labkey.api.resource.Resource;
+import org.labkey.api.security.Directive;
 import org.labkey.api.security.User;
 import org.labkey.api.security.roles.RoleManager;
 import org.labkey.api.view.WebPartFactory;
 import org.labkey.api.view.template.ClientDependency;
+import org.labkey.filters.ContentSecurityPolicyFilter;
 import org.labkey.wnprc_ehr.bc.BCReportRunner;
 import org.labkey.wnprc_ehr.buttons.ChangeBloodQCButton;
 import org.labkey.wnprc_ehr.buttons.CreateTaskButton;
@@ -193,6 +195,9 @@ protected void init() {
         addController(CONTROLLER_NAME, WNPRC_EHRController.class);
         addController(TEST_CONTROLLER_NAME, WNPRC_EHRTestController.class);
 
+        ContentSecurityPolicyFilter.registerAllowedSources("bs_style", Directive.Style, "https://maxcdn.bootstrapcdn.com/bootstrap/3.3.6/css/bootstrap.min.css");
+        ContentSecurityPolicyFilter.registerAllowedSources("bs_font", Directive.Font, "https://maxcdn.bootstrapcdn.com/bootstrap/3.3.6/fonts/");
+
         registerRoles();
         registerPermissions();
     }

WNPRC_EHR/src/org/labkey/wnprc_ehr/data/ColonyCensus/ColonyCensus.java

@@ -135,36 +135,46 @@ public TreeMap<LocalDate, PopulationInstant> getPopulationOverTimeForSpecies(Pop
         Map<LocalDate, Integer> deltasPerDate = new HashMap<>();
         Integer animalsAtStart = 0;
 
-        for( String id : animalsBySpeciesId.get(species)) {
-            AnimalEventSet animalEventSet = animalEventSetsById.get(id);
-            for( StintAtPrimateCenter stint: animalEventSet.getStints() ) {
-                // Null startdate is okay...
-                LocalDate startDate = (stint.getStartDay() == null) ? null : new LocalDate(stint.getStartDay());
-                LocalDate endDate   = ( stint.getEndDay()  == null) ? null : new LocalDate(stint.getEndDay());
-
-
-                // Increment the counter for start of stints, if there was a start
-                if (startDate != null) {
-                    Integer currentStartDelta = deltasPerDate.get(startDate);
-                    if (currentStartDelta == null) {
-                        currentStartDelta = 0;
+        if (animalsBySpeciesId.get(species) != null)
+        {
+            for (String id : animalsBySpeciesId.get(species))
+            {
+                AnimalEventSet animalEventSet = animalEventSetsById.get(id);
+                for (StintAtPrimateCenter stint : animalEventSet.getStints())
+                {
+                    // Null startdate is okay...
+                    LocalDate startDate = (stint.getStartDay() == null) ? null : new LocalDate(stint.getStartDay());
+                    LocalDate endDate = (stint.getEndDay() == null) ? null : new LocalDate(stint.getEndDay());
+
+
+                    // Increment the counter for start of stints, if there was a start
+                    if (startDate != null)
+                    {
+                        Integer currentStartDelta = deltasPerDate.get(startDate);
+                        if (currentStartDelta == null)
+                        {
+                            currentStartDelta = 0;
+                        }
+                        deltasPerDate.put(startDate, currentStartDelta + 1);
+                    }
+                    else
+                    {
+                        // If there wasn't a start, assume the animal was always in the colony
+                        animalsAtStart++;
                     }
-                    deltasPerDate.put(startDate, currentStartDelta + 1);
-                }
-                else {
-                    // If there wasn't a start, assume the animal was always in the colony
-                    animalsAtStart++;
-                }
 
-                // Decrement the counter for end of stints, if there was an end
-                if ( endDate != null) {
-                    Integer currentEndDelta = deltasPerDate.get(endDate);
-                    if ( currentEndDelta == null ) {
-                        currentEndDelta = 0;
+                    // Decrement the counter for end of stints, if there was an end
+                    if (endDate != null)
+                    {
+                        Integer currentEndDelta = deltasPerDate.get(endDate);
+                        if (currentEndDelta == null)
+                        {
+                            currentEndDelta = 0;
+                        }
+                        deltasPerDate.put(endDate, currentEndDelta - 1);
                     }
-                    deltasPerDate.put(endDate, currentEndDelta - 1);
-                }
 
+                }
             }
         }
 

WNPRC_EHR/src/org/labkey/wnprc_ehr/pages/dataentry/NecropsySchedule.jsp

@@ -22,14 +22,14 @@
         dependencies.add("fullcalendar");
     }
 %>
-<script src="https://code.jquery.com/jquery-1.12.4.min.js" integrity="sha256-ZosEbRLbNQzLpnKIkEdrPv7lOy9C27hHQ+Xp8a4MxAQ=" crossorigin="anonymous"></script>
+<script src="https://code.jquery.com/jquery-1.12.4.min.js" nonce="<%=getScriptNonce()%>" integrity="sha256-ZosEbRLbNQzLpnKIkEdrPv7lOy9C27hHQ+Xp8a4MxAQ=" crossorigin="anonymous"></script>
 <%--<script src='https://cdnjs.cloudflare.com/ajax/libs/fullcalendar/2.6.0/fullcalendar.js'></script>--%>
-<link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.6/css/bootstrap.min.css">
+<link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.6/css/bootstrap.min.css" nonce="<%=getScriptNonce()%>">
 <%--<link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.6/css/bootstrap.css">--%>
-<script src="https://cdnjs.cloudflare.com/ajax/libs/bootstrap-3-typeahead/4.0.2/bootstrap3-typeahead.min.js" integrity="sha512-HWlJyU4ut5HkEj0QsK/IxBCY55n5ZpskyjVlAoV9Z7XQwwkqXoYdCIC93/htL3Gu5H3R4an/S0h2NXfbZk3g7w==" crossorigin="anonymous" referrerpolicy="no-referrer"></script>
-<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery.blockUI/2.70/jquery.blockUI.min.js" integrity="sha512-eYSzo+20ajZMRsjxB6L7eyqo5kuXuS2+wEbbOkpaur+sA2shQameiJiWEzCIDwJqaB0a4a6tCuEvCOBHUg3Skg==" crossorigin="anonymous" referrerpolicy="no-referrer"></script>
-<script src="https://cdnjs.cloudflare.com/ajax/libs/bootstrap-datetimepicker/4.17.37/js/bootstrap-datetimepicker.min.js"></script>
-<script src="https://cdnjs.cloudflare.com/ajax/libs/moment.js/2.12.0/moment.min.js"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/bootstrap-3-typeahead/4.0.2/bootstrap3-typeahead.min.js" nonce="<%=getScriptNonce()%>" integrity="sha512-HWlJyU4ut5HkEj0QsK/IxBCY55n5ZpskyjVlAoV9Z7XQwwkqXoYdCIC93/htL3Gu5H3R4an/S0h2NXfbZk3g7w==" crossorigin="anonymous" referrerpolicy="no-referrer"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery.blockUI/2.70/jquery.blockUI.min.js" nonce="<%=getScriptNonce()%>" integrity="sha512-eYSzo+20ajZMRsjxB6L7eyqo5kuXuS2+wEbbOkpaur+sA2shQameiJiWEzCIDwJqaB0a4a6tCuEvCOBHUg3Skg==" crossorigin="anonymous" referrerpolicy="no-referrer"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/bootstrap-datetimepicker/4.17.37/js/bootstrap-datetimepicker.min.js" integrity="sha512-Y+0b10RbVUTf3Mi0EgJue0FoheNzentTMMIE2OreNbqnUPNbQj8zmjK3fs5D2WhQeGWIem2G2UkKjAL/bJ/UXQ==" crossorigin="anonymous" referrerpolicy="no-referrer" nonce="<%=getScriptNonce()%>"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/moment.js/2.12.0/moment.min.js" integrity="sha512-vjqLmddiMORo2KKnzvlZ0fMnp7Z8+U+PIzG8h/TLVhZyXpbvdfiaPiZCVtzMIC91TeM5mNKIbTIMMlPAH70uoA==" crossorigin="anonymous" referrerpolicy="no-referrer" nonce="<%=getScriptNonce()%>"></script>
 
 <%
     SimpleQueryFactory queryFactory = new SimpleQueryFactory(getUser(), getContainer());

WNPRC_EHR/src/org/labkey/wnprc_ehr/pages/husbandry/WaterCalendar.jsp

@@ -106,7 +106,7 @@
 
 %>
 
-<link rel="stylesheet" href="https://stackpath.bootstrapcdn.com/bootstrap/3.3.6/css/bootstrap.min.css" />
+<link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.6/css/bootstrap.min.css" />
 
 <style type="text/css">
     /* Full Calendar heading */

WNPRC_EHR/src/org/labkey/wnprc_ehr/table/WNPRC_EHRCustomizer.java

@@ -197,7 +197,7 @@ public void renderGridCellContents(RenderContext ctx, HtmlWriter out)
                         String formType = (String) ctx.get(new FieldKey(getBoundColumn().getFieldKey().getParent(), "formtype"));
                         String qcState = (String) ctx.get(new FieldKey(getBoundColumn().getFieldKey().getParent(), "QCState$Label"));
 
-                        if (isExt4Form("form", formType))
+                        if (formType != null && isExt4Form("form", formType))
                         {
                             ActionURL url = new ActionURL("ehr", "dataEntryForm.view", us.getContainer());
                             if ("Research Ultrasounds".equalsIgnoreCase(formType))