/** @see Encounter#getAllObs(null) */
@Test
@Verifies(
value = "should get both parent and child with child directly on encounter",
method = "getAllObs(null)")
public void getAllObs_shouldGetBothParentAndChildWithChildDirectlyOnEncounter() throws Exception {
Encounter enc = new Encounter();
// create and add an Obs
Obs parentObs = new Obs();
enc.addObs(parentObs);
// add a child to the obs and make sure that now that the Obs is an ObsGroup with one child:
Obs childObs = new Obs();
parentObs.addGroupMember(childObs);
// add the child obs directly to the encounter as well
childObs.setEncounter(enc);
enc.addObs(childObs);
// do the check
assertEquals(2, enc.getAllObs(true).size());
// this should return one of each -- the obsGroup and the child (because encounter_id is
// populated in the child Obs):
int numberOfChildObs = 0;
int numberofParentObs = 0;
for (Obs oTmp : enc.getAllObs(false)) {
if (oTmp.isObsGrouping()) numberofParentObs++;
else numberOfChildObs++;
}
assertEquals(1, numberOfChildObs);
assertEquals(1, numberofParentObs);
}
/**
* Convenience method that returns related Obs If the Obs argument is not an ObsGroup: a Set<Obs>
* will be returned containing all of the children of this Obs' parent that are not ObsGroups
* themselves. This will include this Obs by default, unless getObsGroup() returns null, in which
* case an empty set is returned. If the Obs argument is an ObsGroup: a Set<Obs> will be returned
* containing 1. all of this Obs' group members, and 2. all ancestor Obs that are not themselves
* obsGroups.
*
* @return Set<Obs>
*/
public Set<Obs> getRelatedObservations() {
Set<Obs> ret = new HashSet<Obs>();
if (this.isObsGrouping()) {
ret.addAll(this.getGroupMembers());
Obs parentObs = this;
while (parentObs.getObsGroup() != null) {
for (Obs obsSibling : parentObs.getObsGroup().getGroupMembers()) {
if (!obsSibling.isObsGrouping()) ret.add(obsSibling);
}
parentObs = parentObs.getObsGroup();
}
} else if (this.getObsGroup() != null) {
for (Obs obsSibling : this.getObsGroup().getGroupMembers()) {
if (!obsSibling.isObsGrouping()) ret.add(obsSibling);
}
}
return ret;
}
/** @return the number of obs groups in encounterCreated (0 if no encounter was created) */
public int getObsGroupCreatedCount() {
if (encounterCreated == null) return 0;
Collection<Obs> temp = encounterCreated.getAllObs();
if (temp == null) return 0;
int count = 0;
for (Obs o : temp) {
if (o.isObsGrouping()) ++count;
}
return count;
}
/** @see Encounter#getObs() */
@Test
@Verifies(value = "should get obs with two levels of hierarchy", method = "getObs()")
public void getObs_shouldGetObsWithTwoLevelsOfHierarchy() throws Exception {
Encounter enc = new Encounter();
// create and add an Obs
Obs parentObs = new Obs();
enc.addObs(parentObs);
// add a child to the obs and make sure that now that the Obs is an ObsGroup with one child:
Obs childObs = new Obs();
parentObs.addGroupMember(childObs);
// add the child obs directly to the encounter as well
childObs.setEncounter(enc);
enc.addObs(childObs);
// make the obs two levels deep
Obs grandChildObsOne = new Obs();
Obs grandChildObsTwo = new Obs();
childObs.addGroupMember(grandChildObsOne);
childObs.addGroupMember(grandChildObsTwo);
/// now getObs() should return the two leaf obs 2 levels down:
assertEquals(2, enc.getObs().size());
assertTrue(enc.getObs().contains(grandChildObsOne));
assertTrue(enc.getObs().contains(grandChildObsTwo));
// now grandChildObsOne isn't a leaf, it holds greatGrandChildObsOne, but the size of the set
// returned shouldn't change:
Obs greatGrandChildObsOne = new Obs();
grandChildObsOne.addGroupMember(greatGrandChildObsOne);
assertEquals(2, enc.getObs().size());
assertTrue(enc.getObs().contains(greatGrandChildObsOne));
assertTrue(enc.getObs().contains(grandChildObsTwo));
// add a sibling to one of the leaves. Add leaf to grandChildObsOne:
Obs greatGrandChildObsTwo = new Obs();
grandChildObsOne.addGroupMember(greatGrandChildObsTwo);
// now getObs() should return a set of size 3:
assertEquals(3, enc.getObs().size());
// make sure none of them are grouping obs
for (Obs oTmp : enc.getObs()) {
assertFalse(oTmp.isObsGrouping());
}
assertTrue(enc.getObs().contains(greatGrandChildObsOne));
assertTrue(enc.getObs().contains(greatGrandChildObsTwo));
assertTrue(enc.getObs().contains(grandChildObsTwo));
}
public static Set<Obs> generateObsSinglesFromSearchResults() {
SearchAPI searchAPI = SearchAPI.getInstance();
Set<Obs> obsSingles = new HashSet<Obs>();
for (ChartListItem item : searchAPI.getResults()) {
if (item != null && item instanceof ObsItem && ((ObsItem) item).getObsId() != null) {
int itemObsId = ((ObsItem) item).getObsId();
Obs obs = Context.getObsService().getObs(itemObsId);
if (obs != null && obs.getObsGroup() == null && !obs.isObsGrouping()) {
obsSingles.add(Context.getObsService().getObs(itemObsId));
}
}
}
return obsSingles;
}
@Test
public void shouldAddDiagnosesAdObservation() throws Exception {
executeDataSet("baseMetaData.xml");
executeDataSet("diagnosisMetaData.xml");
executeDataSet("shouldAddDiagnosisAsObservation.xml");
String cancerDiagnosisUuid = "d102c80f-1yz9-4da3-bb88-8122ce8868dh";
String encounterDateTime = "2005-01-02T00:00:00.000+0000";
String diagnosisDateTime = "2005-01-02T01:00:00.000+0000";
String postData =
"{"
+ "\"patientUuid\" : \"a76e8d23-0c38-408c-b2a8-ea5540f01b51\", "
+ "\"visitTypeUuid\" : \"b45ca846-c79a-11e2-b0c0-8e397087571c\", "
+ "\"encounterTypeUuid\": \"2b377dba-62c3-4e53-91ef-b51c68899891\", "
+ "\"encounterDateTime\" : \""
+ encounterDateTime
+ "\", "
+ "\"diagnoses\":["
+ "{\"order\":\"PRIMARY\", \"certainty\": \"CONFIRMED\", \"codedAnswer\": { \"uuid\": \""
+ cancerDiagnosisUuid
+ "\"}, \"diagnosisDateTime\": \""
+ diagnosisDateTime
+ "\" }"
+ "]"
+ "}";
EncounterTransaction response =
deserialize(
handle(newPostRequest("/rest/emrapi/encounter", postData)), EncounterTransaction.class);
Visit visit = visitService.getVisitByUuid(response.getVisitUuid());
Encounter encounter = visit.getEncounters().iterator().next();
Set<Obs> obsAtTopLevel = encounter.getObsAtTopLevel(false);
assertEquals(1, obsAtTopLevel.size());
Obs parentObservation = obsAtTopLevel.iterator().next();
assertTrue(parentObservation.isObsGrouping());
assertEquals(
DateUtils.parseDate(diagnosisDateTime, dateTimeFormat), parentObservation.getObsDatetime());
Set<Obs> diagnosisObservationGroupMembers = parentObservation.getGroupMembers();
assertEquals(3, diagnosisObservationGroupMembers.size());
ArrayList<String> valueCodedNames = getValuCodedNames(diagnosisObservationGroupMembers);
assertTrue(valueCodedNames.contains("Confirmed"));
assertTrue(valueCodedNames.contains("Primary"));
assertTrue(valueCodedNames.contains("Cancer"));
}
/** @see Encounter#getObs() */
@Test
@Verifies(value = "should only get child obs", method = "getObs()")
public void getObs_shouldOnlyGetChildObs() throws Exception {
Encounter encounter = new Encounter();
// create and add an Obs
Obs parentObs = new Obs();
encounter.addObs(parentObs);
// add a child to the obs and make sure that the Obs is an ObsGroup with one child:
Obs childObs = new Obs();
parentObs.addGroupMember(childObs);
// obsGroup should recurse and ONLY the child obs should be picked up:
assertEquals(1, encounter.getObs().size());
// make sure that the obs is the oChild
Obs obsInEncounter = (Obs) encounter.getObs().toArray()[0];
assertTrue(childObs.equals(obsInEncounter));
assertFalse(obsInEncounter.isObsGrouping());
}
/** @see Encounter#getAllObs(null) */
@Test
@Verifies(value = "should get both parent and child obs", method = "getAllObs(null)")
public void getAllObs_shouldGetBothParentAndChildObs() throws Exception {
Encounter encounter = new Encounter();
// create and add an Obs
Obs parentObs = new Obs();
encounter.addObs(parentObs);
// add a child to the obs and make sure that the Obs is an ObsGroup with one child:
Obs childObs = new Obs();
parentObs.addGroupMember(childObs);
// assert that the parent obs is returned
assertNotNull(encounter.getAllObs(true));
assertEquals(1, encounter.getAllObs(true).size());
assertNotNull(encounter.getAllObs(false));
assertEquals(1, encounter.getAllObs(false).size());
Obs obsInEncounter = (Obs) encounter.getAllObs(false).toArray()[0];
assertTrue(obsInEncounter.isObsGrouping());
}
/**
* Column headers must be unique to avoid clobbering and to ensure it is clear which columns are
* grouped together by obsgroup. As such, duplicate concepts at the parent level or duplicate
* concepts in the same obs group are given a unique occurrence number. For instance, in an obs
* group Functional Review Of Symptoms, there might be two child obs with the concept Symptom
* Present. To distinguish them, one is given an occurrence number of 1 and the next an occurrence
* number of 2.
*
* @param fieldMap
* @param obs
* @return Map<Obs, Integer> the filled in fieldMap
*/
public static Map<Obs, Integer> addChildrenObsToFieldMap(Map<Obs, Integer> fieldMap, Obs obs) {
if (obs != null && obs.isObsGrouping()) {
Set<Obs> childSet = obs.getGroupMembers();
List<Obs> children = new ArrayList<Obs>(childSet);
Map<Concept, Integer> childMap = new HashMap<Concept, Integer>();
for (Obs o : children) {
// check for duplicate concepts among this batch of children
Integer occurrence =
(childMap.get(o.getConcept()) != null) ? childMap.get(o.getConcept()) : 0;
occurrence++;
childMap.put(o.getConcept(), occurrence);
fieldMap.put(o, occurrence);
addChildrenObsToFieldMap(fieldMap, o);
}
}
return fieldMap;
}
/** @see Encounter#getObs() */
@Test
@Verifies(value = "should not get child obs if child also on encounter", method = "getObs()")
public void getObs_shouldNotGetChildObsIfChildAlsoOnEncounter() throws Exception {
Encounter encounter = new Encounter();
// create and add an Obs
Obs parentObs = new Obs();
encounter.addObs(parentObs);
// add a child to the obs and make sure that now that the Obs is an ObsGroup with one child:
Obs childObs = new Obs();
parentObs.addGroupMember(childObs);
// add the child obs directly to the encounter as well
childObs.setEncounter(encounter);
encounter.addObs(childObs);
// do the check
assertEquals(1, encounter.getObs().size());
Obs obsInEncounter = (Obs) encounter.getObs().toArray()[0];
assertFalse(obsInEncounter.isObsGrouping());
}
/** @see Encounter#getObsAtTopLevel(null) */
@Test
@Verifies(value = "should only get parents obs", method = "getObsAtTopLevel(null)")
public void getObsAtTopLevel_shouldOnlyGetParentsObs() throws Exception {
Encounter encounter = new Encounter();
// create and add an Obs
Obs parentObs = new Obs();
encounter.addObs(parentObs);
// add a child to the obs and make sure that the Obs is an ObsGroup with one child:
Obs childObs = new Obs();
parentObs.addGroupMember(childObs);
// assert that the parent obs is returned by getObsAtTopLevel()
assertNotNull(encounter.getObsAtTopLevel(true));
assertEquals(1, encounter.getObsAtTopLevel(true).size());
assertNotNull(encounter.getObsAtTopLevel(false));
assertEquals(1, encounter.getObsAtTopLevel(false).size());
// make sure that the obs is the parent obs
Obs obsInEncounter = (Obs) encounter.getObsAtTopLevel(false).toArray()[0];
assertTrue(obsInEncounter.isObsGrouping());
}
/** @see Encounter#getObsAtTopLevel(null) */
@Test
@Verifies(
value = "should only return the grouped top level obs",
method = "getObsAtTopLevel(null)")
public void getObsAtTopLevel_shouldOnlyReturnTheGroupedTopLevelObs() throws Exception {
Encounter encounter = new Encounter();
// create and add an Obs
Obs parentObs = new Obs();
encounter.addObs(parentObs);
// add a child to the obs and make sure that now that the Obs is an ObsGroup with one child:
Obs childObs = new Obs();
parentObs.addGroupMember(childObs);
// add the child obs directly to the encounter as well
childObs.setEncounter(encounter);
encounter.addObs(childObs);
// do the check
assertEquals(1, encounter.getObsAtTopLevel(false).size());
Obs obsInEncounter = (Obs) encounter.getObsAtTopLevel(false).toArray()[0];
assertTrue(obsInEncounter.isObsGrouping());
}
/**
*
* Returns the encounter with the obs that aren't used when populating form are removed.
* This *doesn't* save the encounter.
* TODO: handle Orders?
*
* @param e
* @param htmlform
* @return
* @throws Exception
*/
public static Encounter trimEncounterToMatchForm(Encounter e, HtmlForm htmlform) throws Exception {
//this should move existing obs from session to tag handlers.
FormEntrySession session = new FormEntrySession(e.getPatient(), e, FormEntryContext.Mode.VIEW, htmlform, null); // session gets a null HttpSession
session.getHtmlToDisplay();
if (log.isDebugEnabled()){
Map<Concept, List<Obs>> map = session.getContext().getExistingObs();
if (map != null){
for (Map.Entry<Concept, List<Obs>> existingObs : map.entrySet()){
List<Obs> oList = existingObs.getValue();
for (Obs oInner : oList)
log.debug("Obs in existingObs " + existingObs.getKey() + " " + oInner.getConcept());
}
}
Map<Obs, Set<Obs>> map2 = session.getContext().getExistingObsInGroups();
if (map2 != null){
for (Map.Entry<Obs, Set<Obs>> existingObsInGroups : map2.entrySet()){
Set<Obs> oList = existingObsInGroups.getValue();
for (Obs oInner : oList)
log.debug("Obs in existingObsInGroups " + existingObsInGroups.getKey().getConcept() + " " + oInner.getConcept());
}
}
}
Encounter ret = new Encounter();
ret.setCreator(e.getCreator());
ret.setEncounterDatetime(e.getEncounterDatetime());
EncounterCompatibility.setProvider(ret, EncounterCompatibility.getProvider(e));
ret.setLocation(e.getLocation());
ret.setDateCreated(e.getDateCreated());
ret.setPatient(e.getPatient());
//renders new encounter unsave-able:
ret.setEncounterId(e.getEncounterId());
for (Obs oTest : e.getAllObs()){
boolean found = false;
if (session.getContext().getExistingObs() != null && !oTest.isObsGrouping()){
List<Obs> obsList = session.getContext().getExistingObs().get(oTest.getConcept());
if (obsList != null && obsList.size() > 0){
for (Obs o : obsList){
if (o.getObsId().equals(oTest.getObsId())){
found = true;
continue;
}
}
}
}
if (!found && session.getContext().getExistingObsInGroups() != null){
for (Map.Entry<Obs, Set<Obs>> mapEntry : session.getContext().getExistingObsInGroups().entrySet()){
if (mapEntry.getKey().equals(oTest)){
found = true;
continue;
} else {
Set<Obs> oSet = mapEntry.getValue();
//note: oSet.contains fails for some reason
for (Obs o:oSet){
if (o.getObsId().equals(oTest.getObsId())){
found = true;
continue;
}
}
}
}
}
if (!found)
ret.addObs(oTest);
}
session = null;
return ret;
}
@Test
@Verifies(
value = "should return encounter with all child objects voided according to schema",
method = "voidEncounterByHtmlFormSchema")
public void testVoidEncounterByHtmlFormSchema_shouldReturnEncounterCorrectly() throws Exception {
executeDataSet(
XML_DATASET_PATH + new TestUtil().getTestDatasetFilename(XML_REGRESSION_TEST_DATASET));
Encounter e = new Encounter();
e.setPatient(Context.getPatientService().getPatient(2));
Date date = Context.getDateFormat().parse("01/02/2003");
e.setDateCreated(new Date());
e.setEncounterDatetime(date);
e.setLocation(Context.getLocationService().getLocation(2));
e.setProvider(Context.getPersonService().getPerson(502));
// add a bunch of obs...
TestUtil.addObs(e, 2474, Context.getConceptService().getConcept(656), date); // matches
TestUtil.addObs(e, 3017, Context.getConceptService().getConcept(767), date); // matches
TestUtil.addObs(e, 3032, new Date(), date); // matches
TestUtil.addObs(e, 1, 5000, date); // matches
TestUtil.addObs(e, 2, 5000, date); // not in form schema
TestUtil.addObs(e, 3, 5000, date); // not in form schema
TestUtil.addObs(e, 6, "blah blah", date); // matches
// 1004 is ANOTHER ALLERGY CONSTRUCT, 1005 is HYPER-ALLERGY CODED, 1001 is PENICILLIN
TestUtil.addObsGroup(
e,
1004,
new Date(),
1005,
Context.getConceptService().getConcept(1001),
new Date()); // matches
// 7 IS ALLERGY CONSTRUCT, 1000 IS ALLERGY CODED, 1003 IS OPENMRS
TestUtil.addObsGroup(
e,
7,
new Date(),
1000,
Context.getConceptService().getConcept(1003),
new Date()); // matches
TestUtil.addObsGroup(
e,
1000,
new Date(),
7,
Context.getConceptService().getConcept(1003),
new Date()); // does not match
Context.getEncounterService().saveEncounter(e);
Form form = new Form();
HtmlForm htmlform = new HtmlForm();
htmlform.setForm(form);
form.setEncounterType(new EncounterType());
htmlform.setDateChanged(new Date());
htmlform.setXmlData(
new TestUtil()
.loadXmlFromFile(
XML_DATASET_PATH + "returnSectionsAndConceptsInSectionsTestFormWithGroups.xml"));
HtmlFormEntryUtil.voidEncounterByHtmlFormSchema(e, htmlform, null);
// this is going to test out the voided state of the obs in the encounter after processing:
Assert.assertTrue(!e.isVoided());
for (Obs o : e.getAllObs(true)) {
if (o.getConcept().getConceptId().equals(2474)) Assert.assertTrue(o.isVoided());
if (o.getConcept().getConceptId().equals(3017)) Assert.assertTrue(o.isVoided());
if (o.getConcept().getConceptId().equals(3032)) Assert.assertTrue(o.isVoided());
if (o.getConcept().getConceptId().equals(1)) Assert.assertTrue(o.isVoided());
if (o.getConcept().getConceptId().equals(2)) Assert.assertTrue(!o.isVoided()); // not matched
if (o.getConcept().getConceptId().equals(3)) Assert.assertTrue(!o.isVoided()); // not matched
if (o.getConcept().getConceptId().equals(6)) Assert.assertTrue(o.isVoided());
if (o.getConcept().getConceptId().equals(1004)) Assert.assertTrue(o.isVoided());
if (o.getConcept().getConceptId().equals(1005)) Assert.assertTrue(o.isVoided());
// obsGroups
if (o.getConcept().getConceptId().equals(7) && o.isObsGrouping())
Assert.assertTrue(o.isVoided());
if (o.getConcept().getConceptId().equals(7) && !o.isObsGrouping())
Assert.assertTrue(!o.isVoided()); // not matched
if (o.getConcept().getConceptId().equals(1000) && o.isObsGrouping())
Assert.assertTrue(!o.isVoided()); // not matched
if (o.getConcept().getConceptId().equals(1000) && !o.isObsGrouping())
Assert.assertTrue(o.isVoided());
}
}