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Merged
labkey-martyp merged 6 commits into from
Feb 13, 2025
Merged

Clinical updates #477

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3832eeb
Clinical updates
labkey-martyp Feb 12, 2025
5165e37
animal history qcstates
labkey-martyp Feb 13, 2025
c7cba37
Update nirc_ehr/resources/web/nirc_ehr/buttons/treatmentSubmit.js
labkey-martyp Feb 13, 2025
498ca89
CR feedback
labkey-martyp Feb 13, 2025
3911a18
unit updates
labkey-martyp Feb 13, 2025
23fd8a2
test updates
labkey-martyp Feb 13, 2025
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5 changes: 5 additions & 0 deletions nirc_ehr/resources/data/amount_units.tsv
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Original file line number Diff line number Diff line change
@@ -1,9 +1,14 @@
Unit
g
gummy
IU
mcg
mEq
mg
mL
no units
ounces
scoop
tablet
ug
units
16 changes: 11 additions & 5 deletions nirc_ehr/resources/data/conc_units.tsv
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Original file line number Diff line number Diff line change
@@ -1,12 +1,18 @@
Unit Denominator Numerator
g/gummy gummy g
g/mL mL g
g/tablet tablet g
g/tsp tsp g
IU/ml mL IU
mEq/ml mL mEq
IU/mL mL IU
mcg/mL mL mcg
mEq/mL mL mEq
mg/capsule capsule(s) mg
mg/ml mL mg
mg/implant implant mg
mg/kg kg mg
mg/mL mL mg
mg/piece piece(s) mg
mg/tablet tablet(s) mg
mg/tsp tsp mg
ug/ml mL ug
units/ml mL units
mL/kg kg mL
ug/mL mL ug
units/mL mL units
5 changes: 4 additions & 1 deletion nirc_ehr/resources/data/dosage_units.tsv
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Original file line number Diff line number Diff line change
@@ -1,10 +1,13 @@
Unit Numerator Denominator
1/8 scoop/kg 1/8 scoop kg
g/kg g kg
IU/kg IU kg
mcg/kg mcg kg
mEq/kg mEq kg
mg
mg/animal mg animal
mg/kg mg kg
ml/kg ml kg
mL/kg ml kg
no units
ounces/kg ounces kg
ug/kg ug kg
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6 changes: 6 additions & 0 deletions nirc_ehr/resources/data/volume_units.tsv
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Original file line number Diff line number Diff line change
@@ -1,10 +1,16 @@
Unit
capsule
capsule(s)
cup
drop(s)
gummy
implant
mg
mL
no units
ounce(s)
piece(s)
scoop
tablet
tablet(s)
tsp
8 changes: 7 additions & 1 deletion nirc_ehr/resources/queries/study/cases.js
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Expand Up @@ -15,8 +15,14 @@ function onInit(event, helper) {

EHR.Server.TriggerManager.registerHandlerForQuery(EHR.Server.TriggerManager.Events.BEFORE_UPSERT, 'study', 'cases', function(helper, errors, row, oldRow){
if (!helper.isETL()) {
if (row.enddate && !triggerHelper.canCloseCase(row.category)) {
if (row.enddate) {
if (!row.closeRemark) {
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@ankurjuneja ankurjuneja Feb 12, 2025

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may be having this check before canCloseCase avoids the db query during canCloseCase?

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@labkey-martyp labkey-martyp Feb 13, 2025

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yeah that makes sense to speed up the normal use case

EHR.Server.Utils.addError(errors, 'closeRemark', 'Close remark required when closing a case.', 'ERROR');
}

if(!triggerHelper.canCloseCase(row.category)) {
EHR.Server.Utils.addError(errors, 'enddate', 'Veterinarian permission required to close a case.', 'ERROR');
}
}

if (!helper.isValidateOnly() && row.caseid && row.enddate && (row.enddate != oldRow.enddate)) {
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1 change: 1 addition & 0 deletions nirc_ehr/resources/views/animalHistory.html
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Expand Up @@ -12,6 +12,7 @@
showFilterOptionsTitle: true,
showReportsOption:true,
caseInsensitiveSubjects: true,
reportQCStates: ['Completed', 'Review Required', 'Abnormal'],
filterTypes: [{
xtype: 'ldk-singlesubjectfiltertype',
inputValue: LDK.panel.SingleSubjectFilterType.filterName,
Expand Down
4 changes: 2 additions & 2 deletions nirc_ehr/resources/web/nirc_ehr/buttons/SelectCaseButton.js
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Expand Up @@ -36,8 +36,8 @@ Ext4.define('NIRC_EHR.form.field.SelectCaseButton', {
if (taskid) {
let record = EHR.DataEntryUtils.getBoundRecord(this.up('panel'));
if (!record || !record.get('Id')) {
let clinRemarksPanel = this.up('#upperPanel')?.query('ehr-formpanel')?.find(panel => panel.formConfig.name === 'clinremarks');
let caseid = clinRemarksPanel?.store?.data?.get(0)?.get('caseid');
let tasksPanel = this.up('#upperPanel')?.query('ehr-formpanel')?.find(panel => panel.formConfig.name === 'tasks');
let caseid = tasksPanel?.store?.data?.get(0)?.get('caseid');
if (caseid) {
this.handleCaseSelect(caseid, false);
}
Expand Down
82 changes: 77 additions & 5 deletions nirc_ehr/resources/web/nirc_ehr/buttons/treatmentSubmit.js
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Expand Up @@ -9,11 +9,83 @@ EHR.DataEntryUtils.registerDataEntryFormButton('NIRC_TREATMENT_SUBMIT', {
disabled: true,
itemId: 'submitBtn',
handler: function(btn){
var panel = btn.up('ehr-dataentrypanel');
Ext4.Msg.confirm('Finalize Form', 'You are about to finalize this form. Do you want to do this?', function(v){
if(v == 'yes')
this.onSubmit(btn);
}, this);

const panel = btn.up('ehr-dataentrypanel');
const casesStore = panel?.storeCollection?.getClientStoreByName('cases');
if (casesStore) {
const rec = casesStore.getAt(0);
const caseid = casesStore.getAt(0).get('caseid');
if (!caseid) { // only check for new cases
const id = rec.get('Id');
const problemCategory = rec.get('problemCategory');
const category = rec.get('category');
if (id && problemCategory && category) {
const filters = [
LABKEY.Filter.create('Id', id),
LABKEY.Filter.create('category', category),
LABKEY.Filter.create('problemCategory', problemCategory),
LABKEY.Filter.create('isActive', true),
LABKEY.Filter.create('QCState/Label', "Completed", LABKEY.Filter.Types.EQUAL)
]
const caseid = rec.get('caseid');
if (caseid) {
filters.push(LABKEY.Filter.create('caseid', caseid, LABKEY.Filter.Types.NEQ))
}
LABKEY.Query.selectRows({
schemaName: 'study',
queryName: 'cases',
filterArray: filters,
columns: 'problemSubcategory',
scope: this,
failure: LDK.Utils.getErrorCallback(),
success: function (results) {
if (results.rows.length > 0) {
const subcategories = [];
for (let i = 0; i < results.rows.length; i++) {
subcategories.push(results.rows[i].problemSubcategory);
}
let msg;
if (subcategories.length === 1) {
msg = 'This animal already has a case with the problem ' + problemCategory + '. The subcategory is ' + results.rows[0].problemSubcategory + '. Do you still want to submit this case?';
}
else {
msg = 'This animal already has ' + subcategories.length + ' cases with the problem ' + problemCategory + '. The subcategories are ' + subcategories.join(', ') + '. Do you still want to submit this case?';
}

Ext4.Msg.confirm('Similar Case Exists', msg, function (v) {
if (v == 'yes')
this.onSubmit(btn);
}, this);
}
else {
Ext4.Msg.confirm('Finalize Form', 'You are about to finalize this form. Do you want to do this?', function (v) {
if (v == 'yes')
this.onSubmit(btn);
}, this);
}
}
});
}
else {
Ext4.Msg.confirm('Finalize Form', 'You are about to finalize this form. Do you want to do this?', function (v) {
if (v == 'yes')
this.onSubmit(btn);
}, this);
}
}
else {
Ext4.Msg.confirm('Finalize Form', 'You are about to finalize this form. Do you want to do this?', function (v) {
if (v == 'yes')
this.onSubmit(btn);
}, this);
}
}
else {
Ext4.Msg.confirm('Finalize Form', 'You are about to finalize this form. Do you want to do this?', function (v) {
if (v == 'yes')
this.onSubmit(btn);
}, this);
}
},
listeners: {
afterRender: function(btn){
Expand Down
9 changes: 0 additions & 9 deletions nirc_ehr/resources/web/nirc_ehr/model/sources/BehaviorDefaults.js
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Expand Up @@ -73,15 +73,6 @@ EHR.model.DataModelManager.registerMetadata('BehaviorDefaults', {
category: {
defaultValue: 'Behavior',
hidden: true
},
scheduledDate: {
columnConfig: {
width: 130,
fixed: true
},
},
treatmentId: {
hidden: true
}
},
'study.treatment_order': {
Expand Down
1 change: 1 addition & 0 deletions nirc_ehr/resources/web/nirc_ehr/model/sources/BehavioralCase.js
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Expand Up @@ -57,6 +57,7 @@ EHR.model.DataModelManager.registerMetadata('BehavioralCase', {
}
},
problemCategory: {
nullable: false,
editorConfig: {
listeners: {
select: function (field, recs) {
Expand Down
1 change: 1 addition & 0 deletions nirc_ehr/resources/web/nirc_ehr/model/sources/ClinicalCase.js
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Expand Up @@ -57,6 +57,7 @@ EHR.model.DataModelManager.registerMetadata('ClinicalCase', {
}
},
problemCategory: {
nullable: false,
editorConfig: {
listeners: {
select: function (field, recs) {
Expand Down
15 changes: 6 additions & 9 deletions nirc_ehr/resources/web/nirc_ehr/model/sources/ClinicalDefaults.js
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Expand Up @@ -53,6 +53,9 @@ EHR.model.DataModelManager.registerMetadata('ClinicalDefaults', {
}
},
procedure: {
lookup: {
filterArray: [LABKEY.Filter.create('active', true, LABKEY.Filter.Types.EQUAL)]
},
columnConfig: {
width: 250
}
Expand All @@ -63,15 +66,6 @@ EHR.model.DataModelManager.registerMetadata('ClinicalDefaults', {
defaultValue: 'Clinical',
hidden: true
},
scheduledDate: {
columnConfig: {
width: 130,
fixed: true
},
},
treatmentId: {
hidden: true
},
date: {
header: 'Date/Time',
}
Expand All @@ -83,6 +77,9 @@ EHR.model.DataModelManager.registerMetadata('ClinicalDefaults', {
},
// procedure data is not categorized, so not using procedure_category based selection
procedure: {
lookup: {
filterArray: [LABKEY.Filter.create('active', true, LABKEY.Filter.Types.EQUAL)]
},
columnConfig: {
width: 250
}
Expand Down
6 changes: 1 addition & 5 deletions nirc_ehr/src/org/labkey/nirc_ehr/dataentry/form/NIRCBehaviorRoundsFormType.java
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Expand Up @@ -12,10 +12,8 @@
import org.labkey.nirc_ehr.dataentry.section.NIRCCaseTemplateFormSection;
import org.labkey.nirc_ehr.dataentry.section.NIRCCasesFormPanelSection;
import org.labkey.nirc_ehr.dataentry.section.NIRCClinicalObservationsFormSection;
import org.labkey.nirc_ehr.dataentry.section.NIRCObservationOrdersFormSection;
import org.labkey.nirc_ehr.dataentry.section.NIRCTaskFormSection;
import org.labkey.nirc_ehr.dataentry.section.NIRCTreatmentGivenFormSection;
import org.labkey.nirc_ehr.dataentry.section.NIRCTreatmentOrderFormSection;

import java.util.Arrays;
import java.util.List;
Expand All @@ -34,9 +32,7 @@ public NIRCBehaviorRoundsFormType(DataEntryFormContext ctx, Module owner)
new NIRCCaseTemplateFormSection("Case Template", "Case Template", "nirc_ehr-casetemplatepanel", Arrays.asList(ClientDependency.supplierFromPath("nirc_ehr/panel/CaseTemplatePanel.js"))),
new NIRCCasesFormPanelSection("Behavior Case", ctx, true),
new NIRCClinicalObservationsFormSection(true, "cases"),
new NIRCObservationOrdersFormSection(null, true, "cases"),
new NIRCTreatmentGivenFormSection(true, "cases"),
new NIRCTreatmentOrderFormSection(true, "cases")
new NIRCTreatmentGivenFormSection(true, "cases")
));

setTemplateMode(AbstractFormSection.TEMPLATE_MODE.NO_ID);
Expand Down
7 changes: 0 additions & 7 deletions nirc_ehr/src/org/labkey/nirc_ehr/dataentry/form/NIRCClinicalRoundsFormType.java
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Expand Up @@ -13,12 +13,9 @@
import org.labkey.nirc_ehr.dataentry.section.NIRCCasesFormPanelSection;
import org.labkey.nirc_ehr.dataentry.section.NIRCClinicalObservationsFormSection;
import org.labkey.nirc_ehr.dataentry.section.NIRCHousingFormSection;
import org.labkey.nirc_ehr.dataentry.section.NIRCObservationOrdersFormSection;
import org.labkey.nirc_ehr.dataentry.section.NIRCProcedureFormSection;
import org.labkey.nirc_ehr.dataentry.section.NIRCProcedureOrderFormSection;
import org.labkey.nirc_ehr.dataentry.section.NIRCTaskFormSection;
import org.labkey.nirc_ehr.dataentry.section.NIRCTreatmentGivenFormSection;
import org.labkey.nirc_ehr.dataentry.section.NIRCTreatmentOrderFormSection;
import org.labkey.nirc_ehr.dataentry.section.NIRCVitalsFormSection;
import org.labkey.nirc_ehr.dataentry.section.NIRCWeightFormSection;

Expand All @@ -39,12 +36,8 @@ public NIRCClinicalRoundsFormType(DataEntryFormContext ctx, Module owner)
new NIRCCasesFormPanelSection("Clinical Case", ctx, false),
new NIRCWeightFormSection(true, false, true, "cases"),
new NIRCClinicalObservationsFormSection(true, "cases"),
new NIRCObservationOrdersFormSection(null, true, "cases"),
new NIRCProcedureFormSection(true, "cases"),
new NIRCProcedureOrderFormSection(true, "cases"),
new NIRCTreatmentGivenFormSection(true, "cases"),
new NIRCTreatmentOrderFormSection(true,
"cases"),
new NIRCVitalsFormSection(true, "cases"),
new NIRCBloodDrawFormSection(true, "cases"),
new NIRCHousingFormSection(true, true, true, "cases")
Expand Down
2 changes: 2 additions & 0 deletions nirc_ehr/src/org/labkey/nirc_ehr/dataentry/section/NIRCCasesFormPanelSection.java
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Expand Up @@ -61,6 +61,8 @@ protected List<FieldKey> getFieldKeys(TableInfo ti)
keys.remove(FieldKey.fromString("closeRemark"));
}

keys.add(FieldKey.fromString("qcstate/label"));

return keys;
}
}
27 changes: 27 additions & 0 deletions nirc_ehr/test/src/org.labkey.test/tests.nirc_ehr/NIRC_EHRTest.java
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Expand Up @@ -456,6 +456,9 @@ public void testClinicalObservation()
waitAndClickAndWait(Locator.linkWithText("Clinical Cases"));

//Fill out Clinical Case section with Id, Date, Open Remark
Ext4FieldRef problem = _helper.getExt4FieldForFormSection("Clinical Case", "Problem Area");
problem.clickTrigger();
problem.setValue("General abnormality");
_helper.setDataEntryField("openRemark", "Clinical Case WorkFlow - Test");
_helper.setDataEntryField("plan", "Case plan - Test");
_helper.getExt4FieldForFormSection("Clinical Case", "Open Date").setValue(LocalDateTime.now().minusDays(1).format(_dateFormat));
Expand Down Expand Up @@ -534,6 +537,8 @@ public void testClinicalObservation()
waitForTextToDisappear("Subjective: WARN: Must enter at least one comment");
waitAndClick(Ext4Helper.Locators.ext4Button("Edit"));
_helper.getExt4FieldForFormSection("Clinical Case", "Close Date").setValue(LocalDateTime.now().format(_dateFormat));
_helper.setDataEntryField("closeRemark", "Case closed.");

submitForm("Submit Final", "Finalize");

goToEHRFolder();
Expand Down Expand Up @@ -799,6 +804,9 @@ public void testClinicalCasesWorkflow()
waitAndClickAndWait(Locator.linkWithText("Clinical Cases"));

//Fill out Clinical Case section with Id, Date, Open Remark
Ext4FieldRef problem = _helper.getExt4FieldForFormSection("Clinical Case", "Problem Area");
problem.clickTrigger();
problem.setValue("Circulatory abnormality");
setFormElement(Locator.textarea("openRemark"), "Clinical Case WorkFlow - Test");
setFormElement(Locator.textarea("plan"), "Case plan");
setFormElement(Locator.name("Id"), animalId);
Expand Down Expand Up @@ -876,6 +884,10 @@ public void testClinicalCasesWorkflow()
Ext4Helper.Locators.ext4Button("Edit").findElement(getDriver()).click(); //click again
enddateField.setValue(LocalDateTime.now().minusDays(1).format(_dateFormat));

// Verify close remark required
waitForText("Close remark required when closing a case.");
_helper.setDataEntryField("closeRemark", "Case closed.");

//'Submit Final'
submitForm("Submit Final", "Finalize Form");

Expand Down Expand Up @@ -935,6 +947,10 @@ public void testBehavioralCases()
gotoEnterData();
waitAndClickAndWait(Locator.linkWithText("Behavioral Cases"));
waitForText("The field: Id is required");
Ext4FieldRef problem = _helper.getExt4FieldForFormSection("Behavior Case", "Problem Area");
problem.clickTrigger();
problem.setValue("Behavioral");
_helper.setDataEntryField("problemCategory", "Behavioral");
_helper.setDataEntryField("remark", "Behavioral case remarks");
_helper.getExt4FieldForFormSection("Behavior Case", "Open Date").setValue(LocalDateTime.now().minusDays(1).format(_dateFormat));
setFormElement(Locator.name("Id"), animalId1);
Expand Down Expand Up @@ -966,6 +982,12 @@ public void testBehavioralCases()
gotoEnterData();
waitAndClickAndWait(Locator.linkWithText("Behavioral Cases"));
waitForText("The field: Id is required");

// Set case problem
problem = _helper.getExt4FieldForFormSection("Behavior Case", "Problem Area");
problem.clickTrigger();
problem.setValue("Behavioral");

_helper.setDataEntryField("remark", "Behavioral case remarks ");
_helper.getExt4FieldForFormSection("Behavior Case", "Open Date").setValue(LocalDateTime.now().minusDays(31).format(_dateFormat));
setFormElement(Locator.name("Id"), animalId2);
Expand Down Expand Up @@ -1033,7 +1055,12 @@ public void testBehavioralCases()
_helper.setDataEntryField("remark", "Closing the case");
waitForTextToDisappear("Subjective: WARN: Must enter at least one comment");
waitAndClick(Ext4Helper.Locators.ext4Button("Edit"));

// Verify close remark required
_helper.getExt4FieldForFormSection("Behavior Case", "Close Date").setValue(LocalDateTime.now().format(_dateFormat));
waitForText("Close remark required when closing a case.");
_helper.setDataEntryField("closeRemark", "Case closed.");

submitForm("Submit Final", "Finalize");

goToEHRFolder();
Expand Down