diff --git a/WNPRC_EHR/resources/referenceStudy/study/datasets/datasets_manifest.xml b/WNPRC_EHR/resources/referenceStudy/study/datasets/datasets_manifest.xml
index afd1f41f4..af54a8e9d 100644
--- a/WNPRC_EHR/resources/referenceStudy/study/datasets/datasets_manifest.xml
+++ b/WNPRC_EHR/resources/referenceStudy/study/datasets/datasets_manifest.xml
@@ -229,5 +229,8 @@
+
+
+
\ No newline at end of file
diff --git a/WNPRC_EHR/resources/referenceStudy/study/datasets/datasets_metadata.xml b/WNPRC_EHR/resources/referenceStudy/study/datasets/datasets_metadata.xml
index ecb768871..82b520229 100644
--- a/WNPRC_EHR/resources/referenceStudy/study/datasets/datasets_metadata.xml
+++ b/WNPRC_EHR/resources/referenceStudy/study/datasets/datasets_metadata.xml
@@ -1,5 +1,55 @@
+
+
+
+
+ varchar
+ http://cpas.labkey.com/Study#ParticipantId
+
+ ptid
+
+
+
+ timestamp
+ http://cpas.labkey.com/Study#VisitDate
+ http://cpas.labkey.com/Study#VisitDate
+
+
+ timestamp
+ urn:ehr.labkey.org/#EndDate
+
+
+ varchar
+ urn:ehr.labkey.org/#CaseId
+
+
+ timestamp
+
+
+ varchar
+
+
+ varchar
+
+
+ varchar
+
+
+ varchar
+
+
+ varchar
+ urn:ehr.labkey.org/#VetReview
+
+
+ timestamp
+ urn:ehr.labkey.org/#VetReviewDate
+
+
+ Cases
+
+
Contains one row for each breeding pairing/assignment for a dam at the center.
diff --git a/WNPRC_EHR/resources/views/dataAdmin.html b/WNPRC_EHR/resources/views/dataAdmin.html
index 6ed14e725..a2a1c0794 100644
--- a/WNPRC_EHR/resources/views/dataAdmin.html
+++ b/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'},
diff --git a/WNPRC_EHR/resources/views/ehrAdmin.html b/WNPRC_EHR/resources/views/ehrAdmin.html
index bdcc617e3..f2fd84d6a 100644
--- a/WNPRC_EHR/resources/views/ehrAdmin.html
+++ b/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',
diff --git a/WNPRC_EHR/resources/views/moreReports.html b/WNPRC_EHR/resources/views/moreReports.html
index 327a03cdf..579c6a938 100644
--- a/WNPRC_EHR/resources/views/moreReports.html
+++ b/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'},
diff --git a/WNPRC_EHR/src/org/labkey/wnprc_ehr/WNPRC_EHRModule.java b/WNPRC_EHR/src/org/labkey/wnprc_ehr/WNPRC_EHRModule.java
index 21f40c0d8..85a6d4ade 100644
--- a/WNPRC_EHR/src/org/labkey/wnprc_ehr/WNPRC_EHRModule.java
+++ b/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();
}
diff --git a/WNPRC_EHR/src/org/labkey/wnprc_ehr/data/ColonyCensus/ColonyCensus.java b/WNPRC_EHR/src/org/labkey/wnprc_ehr/data/ColonyCensus/ColonyCensus.java
index f778d1d0d..dfc9cc255 100644
--- a/WNPRC_EHR/src/org/labkey/wnprc_ehr/data/ColonyCensus/ColonyCensus.java
+++ b/WNPRC_EHR/src/org/labkey/wnprc_ehr/data/ColonyCensus/ColonyCensus.java
@@ -135,36 +135,46 @@ public TreeMap getPopulationOverTimeForSpecies(Pop
Map 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);
- }
+ }
}
}
diff --git a/WNPRC_EHR/src/org/labkey/wnprc_ehr/pages/dataentry/NecropsySchedule.jsp b/WNPRC_EHR/src/org/labkey/wnprc_ehr/pages/dataentry/NecropsySchedule.jsp
index aea88ea34..2ced886e9 100644
--- a/WNPRC_EHR/src/org/labkey/wnprc_ehr/pages/dataentry/NecropsySchedule.jsp
+++ b/WNPRC_EHR/src/org/labkey/wnprc_ehr/pages/dataentry/NecropsySchedule.jsp
@@ -22,14 +22,14 @@
dependencies.add("fullcalendar");
}
%>
-
+
<%----%>
-
+
<%----%>
-
-
-
-
+
+
+
+
<%
SimpleQueryFactory queryFactory = new SimpleQueryFactory(getUser(), getContainer());
diff --git a/WNPRC_EHR/src/org/labkey/wnprc_ehr/pages/husbandry/WaterCalendar.jsp b/WNPRC_EHR/src/org/labkey/wnprc_ehr/pages/husbandry/WaterCalendar.jsp
index f6fa4fd0e..e5bfcf69e 100644
--- a/WNPRC_EHR/src/org/labkey/wnprc_ehr/pages/husbandry/WaterCalendar.jsp
+++ b/WNPRC_EHR/src/org/labkey/wnprc_ehr/pages/husbandry/WaterCalendar.jsp
@@ -106,7 +106,7 @@
%>
-
+