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TRUNK-5837: Migrate Cohort Domain from Hibernate Mapping XML to JPA annotations. #4892

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TRUNK-5837: Migrate Cohort Domain from Hibernate Mapping XML to JPA annotations. #4892

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2ac6eab
Update the cohort.java file
dilankavishka Jan 20, 2025
7e782ca
Update the hibernate.cfg.xml file
dilankavishka Jan 20, 2025
a382fb6
Remove the Cohort.hbm.xml file
dilankavishka Jan 20, 2025
f984bdd
made the changes for test files
dilankavishka Jan 20, 2025
28e3962
update the Cohort.java file
dilankavishka Jan 20, 2025
797cb9f
update the CohortServiceTest.java file
dilankavishka Jan 20, 2025
4b477fd
Update the Cohort.java file
dilankavishka Jan 21, 2025
5209a9f
method changes reverted
dilankavishka Feb 9, 2025
f0acb37
reverted changes on comments
dilankavishka Feb 11, 2025
bd0d5ce
remove the Set import in CohortServiceTest.java file
dilankavishka Feb 12, 2025
3182742
Merge branch 'master' into issue-trunk-5837
dilankavishka May 26, 2025
8e4412c
Merge branch 'master' into issue-trunk-5837
dilankavishka May 26, 2025
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50 changes: 36 additions & 14 deletions api/src/main/java/org/openmrs/Cohort.java
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Original file line number Diff line number Diff line change
Expand Up @@ -10,10 +10,19 @@
package org.openmrs;

import org.apache.commons.lang3.StringUtils;
import org.hibernate.annotations.GenericGenerator;
import org.hibernate.annotations.Parameter;
import org.hibernate.envers.Audited;

import javax.persistence.CascadeType;
import javax.persistence.Column;
import javax.persistence.Entity;
import javax.persistence.GeneratedValue;
import javax.persistence.GenerationType;
import javax.persistence.Id;
import javax.persistence.OneToMany;
import javax.persistence.Table;
import java.util.Arrays;
import java.util.Collection;
import java.util.Date;
import java.util.Set;
import java.util.TreeSet;
Expand All @@ -22,18 +31,31 @@
/**
* This class represents a list of patientIds.
*/
@Entity
@Table(name = "cohort")
@Audited
public class Cohort extends BaseChangeableOpenmrsData {

public static final long serialVersionUID = 0L;

@Id
@GeneratedValue(strategy = GenerationType.IDENTITY, generator = "cohort_id_seq")
@GenericGenerator(
name = "cohort_id_seq",
strategy = "native",
parameters = @Parameter(name = "sequence", value = "cohort_cohort_id_seq")
)
@Column(name = "cohort_id", nullable = false)
private Integer cohortId;

@Column(name = "name", nullable = false)
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@dkayiwa dkayiwa May 27, 2025

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Did you just forget to specify the length as was in the xml mapping file?

private String name;

@Column(name = "description", nullable = false)
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@dkayiwa dkayiwa May 27, 2025

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How about the length?

private String description;

private Collection<CohortMembership> memberships;
@OneToMany(mappedBy = "cohort", cascade = CascadeType.ALL, orphanRemoval = true)
private Set<CohortMembership> memberships;

public Cohort() {
memberships = new TreeSet<>();
Expand Down Expand Up @@ -89,7 +111,7 @@ public Cohort(String name, String description, Patient[] patients) {
* @param patientsOrIds optional collection which may contain Patients, or patientIds which may
* be Integers, Strings, or anything whose toString() can be parsed to an Integer.
*/
public Cohort(Collection<?> patientsOrIds) {
public Cohort(Set<?> patientsOrIds) {
this(null, null, patientsOrIds);
}

Expand All @@ -102,7 +124,7 @@ public Cohort(Collection<?> patientsOrIds) {
* @param patientsOrIds optional collection which may contain Patients, or patientIds which may
* be Integers, Strings, or anything whose toString() can be parsed to an Integer.
*/
public Cohort(String name, String description, Collection<?> patientsOrIds) {
public Cohort(String name, String description, Set<?> patientsOrIds) {
this(name, description, (Integer[]) null);
if (patientsOrIds != null) {
for (Object o : patientsOrIds) {
Expand Down Expand Up @@ -181,17 +203,17 @@ public boolean removeMembership(CohortMembership cohortMembership) {
* @param includeVoided boolean true/false to include/exclude voided memberships
* @return Collection of cohort memberships
*/
public Collection<CohortMembership> getMemberships(boolean includeVoided) {
public Set<CohortMembership> getMemberships(boolean includeVoided) {
if (includeVoided) {
return getMemberships();
}
return getMemberships().stream().filter(m -> m.getVoided() == includeVoided).collect(Collectors.toList());
return getMemberships().stream().filter(m -> m.getVoided() == includeVoided).collect(Collectors.toSet());
}

/**
* @since 2.1.0
*/
public Collection<CohortMembership> getMemberships() {
public Set<CohortMembership> getMemberships() {
if (memberships == null) {
memberships = new TreeSet<>();
}
Expand All @@ -203,11 +225,11 @@ public Collection<CohortMembership> getMemberships() {
* @param asOfDate date used to return active memberships
* @return Collection of cohort memberships
*/
public Collection<CohortMembership> getActiveMemberships(Date asOfDate) {
return getMemberships().stream().filter(m -> m.isActive(asOfDate)).collect(Collectors.toList());
public Set<CohortMembership> getActiveMemberships(Date asOfDate) {
return getMemberships().stream().filter(m -> m.isActive(asOfDate)).collect(Collectors.toSet());
}

public Collection<CohortMembership> getActiveMemberships() {
public Set<CohortMembership> getActiveMemberships() {
return getActiveMemberships(new Date());
}

Expand All @@ -219,7 +241,7 @@ public CohortMembership getActiveMembership(Patient patient) {
}

public int size() {
return getMemberships().stream().filter(m -> !m.getVoided()).collect(Collectors.toList())
return getMemberships().stream().filter(m -> !m.getVoided()).collect(Collectors.toSet())
.size();
}

Expand Down Expand Up @@ -348,13 +370,13 @@ public void setMemberIds(Set<Integer> memberIds) {
}
}

public void setMemberships(Collection<CohortMembership> members) {
public void setMemberships(Set<CohortMembership> members) {
this.memberships = members;
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@wikumChamith wikumChamith May 27, 2025

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This is something minor. Do we need the space here :) ?

}

/**
* @since 1.5
* @see org.openmrs.OpenmrsObject#getId()
* @see OpenmrsObject#getId()
*/
@Override
public Integer getId() {
Expand All @@ -364,7 +386,7 @@ public Integer getId() {

/**
* @since 1.5
* @see org.openmrs.OpenmrsObject#setId(java.lang.Integer)
* @see OpenmrsObject#setId(Integer)
*/
@Override
public void setId(Integer id) {
Expand Down
1 change: 0 additions & 1 deletion api/src/main/resources/hibernate.cfg.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -82,7 +82,6 @@
<mapping resource="org/openmrs/api/db/hibernate/Program.hbm.xml" />
<mapping resource="org/openmrs/api/db/hibernate/ProgramWorkflow.hbm.xml" />
<mapping resource="org/openmrs/api/db/hibernate/ProgramWorkflowState.hbm.xml" />
<mapping resource="org/openmrs/api/db/hibernate/Cohort.hbm.xml" />
<mapping resource="org/openmrs/api/db/hibernate/CohortMembership.hbm.xml"/>
<mapping resource="org/openmrs/api/db/hibernate/OrderFrequency.hbm.xml" />

Expand Down
55 changes: 0 additions & 55 deletions api/src/main/resources/org/openmrs/api/db/hibernate/Cohort.hbm.xml
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This file was deleted.

13 changes: 5 additions & 8 deletions api/src/test/java/org/openmrs/CohortTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -14,14 +14,11 @@
import static org.junit.jupiter.api.Assertions.assertTrue;

import java.text.SimpleDateFormat;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Calendar;
import java.util.Collection;
import java.util.Date;
import java.util.GregorianCalendar;
import java.util.HashSet;
import java.util.List;
import java.util.Set;

import org.apache.commons.lang.ArrayUtils;
Expand All @@ -46,7 +43,7 @@ public void constructorWithIntegers_shouldAddMembersToCohort() {
@Test
public void constructorWithPatients_shouldAddMembersToCohort() {

List<Patient> patients = new ArrayList<>();
Set<Patient> patients = new HashSet<>();
Arrays.stream(ids).forEach(id -> patients.add(new Patient(id)));

Cohort cohort = new Cohort("name", "description", patients);
Expand All @@ -65,7 +62,7 @@ public void constructorWithCommaSeparatedIntegers_shouldAddMembersToCohort() {
@Test
public void getCommaSeparatedPatientIds_shouldReturnCommaSeparatedListOfPatients() {

List<Patient> patients = new ArrayList<>();
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@dkayiwa dkayiwa May 27, 2025

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Was this change required as part of the ticket?

Set<Patient> patients = new HashSet<>();
Arrays.stream(ids).forEach(id -> patients.add(new Patient(id)));

Cohort cohort = new Cohort("name", "description", patients);
Expand Down Expand Up @@ -94,7 +91,7 @@ public void union_shouldContainVoidedAndExpiredMemberships() throws Exception {
cohortTwo.addMembership(membershipTwo);

Cohort cohortUnion = Cohort.union(cohortOne, cohortTwo);
Collection<CohortMembership> unionOfMemberships = cohortUnion.getMemberships();
Set<CohortMembership> unionOfMemberships = cohortUnion.getMemberships();
unionOfMemberships.forEach(m -> {
assertTrue(m.getPatientId().equals(7) || m.getPatientId().equals(8));
assertTrue(m.getVoided() && m.getEndDate() != null);
Expand All @@ -120,7 +117,7 @@ public void subtract_shouldContainVoidedAndExpiredMemberships() throws Exception
cohortTwo.addMembership(membershipTwo);

Cohort cohortSubtract = Cohort.subtract(cohortOne, cohortTwo);
Collection<CohortMembership> subtractOfMemberships = cohortSubtract.getMemberships();
Set<CohortMembership> subtractOfMemberships = cohortSubtract.getMemberships();
subtractOfMemberships.forEach(m -> {
assertTrue(m.getPatientId().equals(7));
assertTrue(m.getVoided() && m.getEndDate() != null);
Expand All @@ -147,7 +144,7 @@ public void intersect_shouldContainVoidedAndExpiredMemberships() throws Exceptio
cohortTwo.addMembership(membershipTwo);

Cohort cohortIntersect = Cohort.intersect(cohortOne, cohortTwo);
Collection<CohortMembership> intersectOfMemberships = cohortIntersect.getMemberships();
Set<CohortMembership> intersectOfMemberships = cohortIntersect.getMemberships();
assertTrue(intersectOfMemberships.stream().anyMatch(m -> m.getVoided() || m.getEndDate() != null));
intersectOfMemberships.forEach(m -> {
assertTrue(m.getPatientId().equals(7));
Expand Down
11 changes: 6 additions & 5 deletions api/src/test/java/org/openmrs/api/CohortServiceTest.java
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Expand Up @@ -21,9 +21,10 @@

import java.text.ParseException;
import java.text.SimpleDateFormat;
import java.util.Collection;
//import java.util.Collection;
import java.util.Date;
import java.util.List;
import java.util.Set;

import org.apache.commons.lang3.time.DateUtils;
import org.junit.jupiter.api.BeforeEach;
Expand Down Expand Up @@ -677,7 +678,7 @@ public void getMemberships_shouldGetMembershipsAsOfADate() throws ParseException
cohort.addMembership(newMember);
service.saveCohort(cohort);

Collection<CohortMembership> membersAsOfDate = cohort.getActiveMemberships(dateToTest);
Set<CohortMembership> membersAsOfDate = cohort.getActiveMemberships(dateToTest);
assertFalse(membersAsOfDate.isEmpty());
assertTrue(membersAsOfDate.stream().anyMatch(m -> m.getStartDate().equals(dateToTest)));
}
Expand All @@ -700,7 +701,7 @@ public void getMemberships_shouldNotGetMatchingMembershipsAsOfADate() throws Exc
service.saveCohort(cohort);

Date dateToTest = dateFormat.parse("2016-11-01 00:00:00");
Collection<CohortMembership> membersAsOfDate = cohort.getActiveMemberships(dateToTest);
Set<CohortMembership> membersAsOfDate = cohort.getActiveMemberships(dateToTest);
assertFalse(membersAsOfDate.stream().anyMatch(m -> m.getStartDate().equals(dateToTest)));
}

Expand All @@ -724,7 +725,7 @@ public void getMemberships_shouldReturnVoidedMemberships() throws Exception {
cohort.addMembership(voidedMembership);

Context.getCohortService().saveCohort(cohort);
Collection<CohortMembership> allMemberships = cohort.getMemberships(true);
Set<CohortMembership> allMemberships = cohort.getMemberships(true);
assertEquals(3, allMemberships.size());
}

Expand All @@ -749,7 +750,7 @@ public void getMemberships_shouldReturnUnvoidedMemberships() throws Exception {
cohort.addMembership(voidedMembership);

Context.getCohortService().saveCohort(cohort);
Collection<CohortMembership> unvoidedMemberships = cohort.getMemberships(false);
Set<CohortMembership> unvoidedMemberships = cohort.getMemberships(false);
assertEquals(2, unvoidedMemberships.size());
}

Expand Down
2 changes: 2 additions & 0 deletions api/src/test/java/org/openmrs/api/OrderServiceTest.java
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Expand Up @@ -21,6 +21,7 @@

import org.openmrs.Allergy;
import org.openmrs.CareSetting;
import org.openmrs.Cohort;
import org.openmrs.Concept;
import org.openmrs.ConceptClass;
import org.openmrs.ConceptDatatype;
Expand Down Expand Up @@ -2740,6 +2741,7 @@ public void saveOrder_shouldFailIfTheJavaTypeOfThePreviousOrderDoesNotMatch() th
.addAnnotatedClass(ProgramAttributeType.class)
.addAnnotatedClass(HL7InError.class)
.addAnnotatedClass(OrderType.class)
.addAnnotatedClass(Cohort.class)
.getMetadataBuilder().build();


Expand Down