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Link crawler test fixes (#855)
* Add cases dataset to avoid errors in core EHR components on test server * Remove invalid lookup (error_types) from list of editable lookups * Remove invalid links from EHR admin page * Remove invalid housing report link from more reports * Register bootstrap 3.3.6 style and fonts as allowed CSP sources * Fix various NPEs found using sporadic test data * Add nonces to necropsy schedule * Update WNPRC test to do more WNPRC set up to mimic the production server --------- Co-authored-by: Trey Chadick <tchad@labkey.com>
1 parent 7897fd1 commit b405a2f

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

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

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

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

‎WNPRC_EHR/resources/views/dataAdmin.html‎

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

‎WNPRC_EHR/resources/views/ehrAdmin.html‎

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

‎WNPRC_EHR/resources/views/moreReports.html‎

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

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

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

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

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dependencies.add("fullcalendar");
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}
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%>
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<script src="https://code.jquery.com/jquery-1.12.4.min.js" integrity="sha256-ZosEbRLbNQzLpnKIkEdrPv7lOy9C27hHQ+Xp8a4MxAQ=" crossorigin="anonymous"></script>
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<script src="https://code.jquery.com/jquery-1.12.4.min.js" nonce="<%=getScriptNonce()%>" integrity="sha256-ZosEbRLbNQzLpnKIkEdrPv7lOy9C27hHQ+Xp8a4MxAQ=" crossorigin="anonymous"></script>
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<%--<script src='https://cdnjs.cloudflare.com/ajax/libs/fullcalendar/2.6.0/fullcalendar.js'></script>--%>
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<link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.6/css/bootstrap.min.css">
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<link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.6/css/bootstrap.min.css" nonce="<%=getScriptNonce()%>">
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<%--<link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.6/css/bootstrap.css">--%>
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<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>
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<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>
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<script src="https://cdnjs.cloudflare.com/ajax/libs/bootstrap-datetimepicker/4.17.37/js/bootstrap-datetimepicker.min.js"></script>
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<script src="https://cdnjs.cloudflare.com/ajax/libs/moment.js/2.12.0/moment.min.js"></script>
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<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>
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<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>
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<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>
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<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>
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<%
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SimpleQueryFactory queryFactory = new SimpleQueryFactory(getUser(), getContainer());

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

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

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

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String formType = (String) ctx.get(new FieldKey(getBoundColumn().getFieldKey().getParent(), "formtype"));
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String qcState = (String) ctx.get(new FieldKey(getBoundColumn().getFieldKey().getParent(), "QCState$Label"));
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if (isExt4Form("form", formType))
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if (formType != null && isExt4Form("form", formType))
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{
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ActionURL url = new ActionURL("ehr", "dataEntryForm.view", us.getContainer());
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if ("Research Ultrasounds".equalsIgnoreCase(formType))

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