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Merged
labkey-martyp merged 12 commits into from
Aug 3, 2025
Merged

Link crawler test fixes #855

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58ebcf4
link crawler fixes
labkey-martyp Jul 20, 2025
ec426d0
Update skip lists
labkey-martyp Jul 27, 2025
f3fee71
Update WNPRC_EHR/src/org/labkey/wnprc_ehr/pages/dataentry/NecropsySch…
labkey-martyp Jul 30, 2025
27aa04d
Update WNPRC_EHR/src/org/labkey/wnprc_ehr/pages/dataentry/NecropsySch…
labkey-martyp Jul 30, 2025
09522bb
Update WNPRC_EHR/test/src/org/labkey/test/tests/wnprc_ehr/WNPRC_EHRTe…
labkey-martyp Jul 30, 2025
9fbbe80
Update WNPRC_EHR/test/src/org/labkey/test/tests/wnprc_ehr/WNPRC_EHRTe…
labkey-martyp Jul 30, 2025
b77a883
comments
labkey-martyp Jul 30, 2025
f74cff7
Merge branch '25.7_fb_ehr_link_crawler' of https://github.com/LabKey/…
labkey-martyp Jul 30, 2025
5621ce2
imports
labkey-martyp Jul 30, 2025
7f4211f
Another skip
labkey-martyp Jul 30, 2025
7909319
another module prop
labkey-martyp Jul 30, 2025
e43959e
skip another one
labkey-martyp Jul 31, 2025
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3 changes: 3 additions & 0 deletions WNPRC_EHR/resources/referenceStudy/study/datasets/datasets_manifest.xml
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Expand Up @@ -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>
50 changes: 50 additions & 0 deletions WNPRC_EHR/resources/referenceStudy/study/datasets/datasets_metadata.xml
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@@ -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>
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1 change: 0 additions & 1 deletion WNPRC_EHR/resources/views/dataAdmin.html
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Expand Up @@ -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'},
Expand Down
10 changes: 0 additions & 10 deletions WNPRC_EHR/resources/views/ehrAdmin.html
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Expand Up @@ -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'},
Expand Down Expand Up @@ -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',
Expand Down
1 change: 0 additions & 1 deletion WNPRC_EHR/resources/views/moreReports.html
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Expand Up @@ -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'},
Expand Down
5 changes: 5 additions & 0 deletions WNPRC_EHR/src/org/labkey/wnprc_ehr/WNPRC_EHRModule.java
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Expand Up @@ -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;
Expand Down Expand Up @@ -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();
}
Expand Down
62 changes: 36 additions & 26 deletions WNPRC_EHR/src/org/labkey/wnprc_ehr/data/ColonyCensus/ColonyCensus.java
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Expand Up @@ -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);
}

}
}
}

Expand Down
12 changes: 6 additions & 6 deletions WNPRC_EHR/src/org/labkey/wnprc_ehr/pages/dataentry/NecropsySchedule.jsp
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Expand Up @@ -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" nonce="<%=getScriptNonce()%>"></script>
Comment thread
github-advanced-security[bot] marked this conversation as resolved.
Fixed
<script src="https://cdnjs.cloudflare.com/ajax/libs/moment.js/2.12.0/moment.min.js" nonce="<%=getScriptNonce()%>"></script>
Comment thread
github-advanced-security[bot] marked this conversation as resolved.
Fixed

<%
SimpleQueryFactory queryFactory = new SimpleQueryFactory(getUser(), getContainer());
Expand Down
2 changes: 1 addition & 1 deletion WNPRC_EHR/src/org/labkey/wnprc_ehr/pages/husbandry/WaterCalendar.jsp
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Expand Up @@ -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 */
Expand Down
2 changes: 1 addition & 1 deletion WNPRC_EHR/src/org/labkey/wnprc_ehr/table/WNPRC_EHRCustomizer.java
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Expand Up @@ -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))
Expand Down
60 changes: 58 additions & 2 deletions WNPRC_EHR/test/src/org/labkey/test/tests/wnprc_ehr/WNPRC_EHRTest.java
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Expand Up @@ -248,6 +248,12 @@ public static void doSetup() throws Exception

initTest.updateEHRFormFrameworkTypes();

initTest.addWnprcEHRWebparts();
initTest._containerHelper.createSubfolder(EHR_FOLDER_PATH, "About The EHR", "Collaboration");
initTest._containerHelper.createSubfolder(EHR_FOLDER_PATH, "Backups", "Collaboration");
initTest._containerHelper.createSubfolder(EHR_FOLDER_PATH + "/Backups", "Gems Backups", "Collaboration");
initTest.addWNPRCGroups();

initTest.createEHRLinkedSchema("/" + EHR_FOLDER_PATH); // Needed for query validation
initTest._schemaHelper.createLinkedSchema("/" + EHR_FOLDER_PATH, "PublicSOPs", "/" + EHR_FOLDER_PATH, null, "lists", null, null);

Expand Down Expand Up @@ -281,7 +287,9 @@ public static void doSetup() throws Exception

initTest.checkUpdateProgramIncomeAccount();

initTest.notificationRevampSetup(); //TODO: to uncomment, fix issue mentioned here - https://www.labkey.org/WNPRC/support%20tickets/issues-details.view?issueId=51256
initTest.notificationRevampSetup();

initTest.populateAnimalRequestTableLookups();
}

private void billingSetup() throws Exception
Expand Down Expand Up @@ -389,6 +397,40 @@ private void addProcedureQueries() throws IOException, CommandException
log("Inserted " + numRows + " into ehr_billing.procedureQueryChargeIdAssoc table.");
}

@Override
protected List<String> skipLinksForCrawling()
{
List<String> links = new ArrayList<>(super.skipLinksForCrawling());
links.add("wnprc_ehr-PerDiems.view");
links.add("wnprc_ehr-WaterCalendar.view");
Comment on lines +406 to +407
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@labkey-tchad labkey-tchad Jul 29, 2025

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Please explain why these actions are skipped

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@labkey-martyp labkey-martyp Jul 30, 2025

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done

links.add("wnprc_ehr-NecropsySchedule.view");
return links;
}

@Override
protected List<String> skipLinksForValidation()
{
List<String> links = new ArrayList<>(super.skipLinksForValidation());
links.add("query-executeQuery.view?query.queryName=Current%20Colony%20Condition&schemaName=study");
links.add("query-executeQuery.view?schemaName=col_dump&query.queryName=mysql_check");
// links.add("ehr-dataEntryFormDetails.view?formtype=Enter%20Water%20Orders&taskid=");
links.add("wnprc_ehr-UnscheduleBCReports.view");
links.add("wnprc_ehr-ScheduleBCReports.view");
links.add("Documentation/Admin/project-begin.view");
links.add("Documentation/Data Management/project-begin.view");
links.add("Development Notes/project-begin.view");
links.add("/Logs/project-begin.view");
Comment on lines +413 to +429
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@labkey-tchad labkey-tchad Jul 29, 2025

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Please explain why these actions are skipped

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@labkey-martyp labkey-martyp Jul 30, 2025

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done

return links;
}

private void addWNPRCGroups()
{
_permissionsHelper.createGlobalPermissionsGroup("veterinarians (LDAP)");
_permissionsHelper.createGlobalPermissionsGroup("compliance (LDAP)");
_permissionsHelper.createGlobalPermissionsGroup("animalcare (LDAP)");
_permissionsHelper.createGlobalPermissionsGroup("pathology (LDAP)");
}

@LogMethod
@Override
protected void createTestSubjects() throws Exception
Expand Down Expand Up @@ -655,6 +697,18 @@ private void addFinanceRelatedWebParts(String container)
(new PortalHelper(this)).addWebPart("WNPRC Finance Admin");
}

private void addWnprcEHRWebparts()
{
log("Add WNPRC EHR Webparts.");

//enable Page Admin Mode
new SiteNavBar(getDriver()).enterPageAdminMode();

(new PortalHelper(this)).removeAllWebParts();
(new PortalHelper(this)).addWebPart("WNPRC Electronic Health Record ");
(new PortalHelper(this)).addWebPart("wnprcUnits");
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}

private void addBillingPublicWebParts()
{
log("Add WNPRC Billing PI Portal Section to PI Portal page.");
Expand Down Expand Up @@ -3185,6 +3239,7 @@ public void populateLookupValsDirect(String setName, String valName, String val)

public void populateAnimalRequestTableLookups() throws IOException, CommandException
{
goToEHRFolder();

populateLookupSet("animal_requests_sex");
populateLookupVals("animal_requests_sex", "value", "M");
Expand Down Expand Up @@ -3317,7 +3372,7 @@ public void testAnimalRequestFormSubmit() throws IOException, CommandException
DateTimeFormatter formatter = DateTimeFormatter.ofPattern("yyyy-MM-dd");
String formattedDate = currentDate.format(formatter);
goToEHRFolder();
populateAnimalRequestTableLookups();

navigateToAnimalRequestForm();
waitForText("Comments:");
//it's a timing issue. we have to wait until the form is loaded for it to be clickable.
Expand Down Expand Up @@ -3425,6 +3480,7 @@ public void updateProgramIncomeAccountWithValidPermissions() throws UnhandledAle
fillAnInputByName("newCreditToAccountField", "testString");
click(Locator.tagWithId("button","updateCreditToAccountButton"));

sleep(2000);
//Verifies the value has been changed, then continues. If value has not been changed, the test fails here.
assertEquals("Updated Program Income Account with invalid permissions.", "testString", Locator.id("ctaCell1").findElement(getDriver()).getText());
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Expand Down