EA-207: Implement an API for Fetching Visits with Notes and Diagnosis

api/src/main/java/org/openmrs/module/emrapi/db/EmrApiDAO.java

@@ -1,5 +1,8 @@
 package org.openmrs.module.emrapi.db;
 
+import org.openmrs.Patient;
+import org.openmrs.module.emrapi.visit.VisitWithDiagnoses;
+
 import java.util.List;
 import java.util.Map;
 
@@ -8,4 +11,15 @@ public interface EmrApiDAO {
     <T> List<T> executeHql(String queryString, Map<String, Object> parameters, Class<T> clazz);
 
     <T> List<T> executeHqlFromResource(String resource, Map<String, Object> parameters, Class<T> clazz);
+
+    /**
+     * Fetches visits with note encounters and diagnoses of a patient.
+     *
+     * @param patient the patient
+     * @param startIndex the start index of the number of visits to fetch
+     * @param limit the limit of the number of visits to fetch
+     *
+     * @return a list of visits that has note encounters and diagnoses
+     */
+    List<VisitWithDiagnoses> getVisitsWithNotesAndDiagnosesByPatient(Patient patient, int startIndex, int limit);
 }

api/src/main/java/org/openmrs/module/emrapi/db/EmrApiDAOImpl.java

@@ -1,29 +1,41 @@
 package org.openmrs.module.emrapi.db;
 
+import lombok.Setter;
 import org.apache.commons.io.IOUtils;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 import org.hibernate.Query;
+import org.openmrs.Diagnosis;
+import org.openmrs.EncounterType;
+import org.openmrs.Patient;
+import org.openmrs.Visit;
 import org.openmrs.api.db.hibernate.DbSessionFactory;
+import org.openmrs.module.emrapi.EmrApiProperties;
+import org.openmrs.module.emrapi.visit.VisitWithDiagnoses;
 
 import java.io.IOException;
 import java.io.InputStream;
 import java.nio.charset.StandardCharsets;
 import java.util.Collection;
+import java.util.Comparator;
+import java.util.HashMap;
+import java.util.HashSet;
 import java.util.List;
 import java.util.Map;
+import java.util.Set;
+import java.util.stream.Collectors;
 
 public class EmrApiDAOImpl implements EmrApiDAO {
 
    protected final Log log = LogFactory.getLog(getClass());
 
+   @Setter
    private DbSessionFactory sessionFactory;
-
-   public void setSessionFactory(DbSessionFactory sessionFactory) {
-      this.sessionFactory = sessionFactory;
-   }
-
-   @Override
+
+   @Setter
+   private EmrApiProperties emrApiProperties;
+
+	@Override
    @SuppressWarnings("unchecked")
    public <T> List<T> executeHql(String queryString, Map<String, Object> parameters, Class<T> clazz) {
       Query query = sessionFactory.getCurrentSession().createQuery(queryString);
@@ -55,4 +67,54 @@ public <T> List<T> executeHqlFromResource(String resource, Map<String, Object> p
       }
       return executeHql(hql, parameters, clazz);
    }
+
+   public List<VisitWithDiagnoses> getVisitsWithNotesAndDiagnosesByPatient(Patient patient, int startIndex, int limit) {
+
+      String visitNoteEncounterTypeUuid = emrApiProperties.getVisitNoteEncounterType().getUuid();
+
+      String hqlVisit="SELECT DISTINCT v FROM Visit v " +
+              "LEFT JOIN FETCH v.encounters enc " +
+              "LEFT JOIN enc.encounterType et " +
+              "WHERE v.patient.id = :patientId " +
+              "AND (et.uuid = :encounterTypeUuid OR enc IS NULL) " +
+              "ORDER BY v.startDatetime DESC";
+
+      Query visitQuery = sessionFactory.getCurrentSession().createQuery(hqlVisit);
+
+      visitQuery.setParameter("patientId", patient.getId());
+      visitQuery.setParameter("encounterTypeUuid", visitNoteEncounterTypeUuid);
+      visitQuery.setFirstResult(startIndex);
+      visitQuery.setMaxResults(limit);
+
+      List<Visit> visits = visitQuery.list();
+
+      String hqlDiagnosis = "SELECT DISTINCT diag FROM Diagnosis diag " +
+              "JOIN diag.encounter e " +
+              "WHERE e.visit.id IN :visitIds";
+
+      List<Integer> visitIds = visits.stream()
+              .map(Visit::getId)
+              .collect(Collectors.toList());
+
+      List<Diagnosis> diagnoses = sessionFactory.getCurrentSession()
+              .createQuery(hqlDiagnosis)
+              .setParameterList("visitIds", visitIds)
+              .list();
+
+      Map<Visit, Set<Diagnosis>> visitToDiagnosesMap = new HashMap<>();
+      for (Diagnosis diagnosis : diagnoses) {
+         Visit visit = diagnosis.getEncounter().getVisit();
+         visitToDiagnosesMap
+                 .computeIfAbsent(visit, v -> new HashSet<>())
+                 .add(diagnosis);
+      }
+
+      List<VisitWithDiagnoses> visitWithDiagnoses = visits.stream()
+              .sorted(Comparator.comparing(Visit::getStartDatetime).reversed())
+              .map(visit -> new VisitWithDiagnoses(visit, visitToDiagnosesMap.getOrDefault(visit, new HashSet<>())))
+              .collect(Collectors.toList());
+
+      return visitWithDiagnoses;
+   }
+
 }

api/src/main/java/org/openmrs/module/emrapi/visit/EmrApiVisitService.java

@@ -0,0 +1,13 @@
+package org.openmrs.module.emrapi.visit;
+
+import java.util.List;
+
+public interface EmrApiVisitService {
+    /**
+     * Fetches visits with note encounters and diagnoses of a patient by patient ID.
+     *
+     * @param patientUuid the UUID of the patient
+     * @return a list of visits that has note encounters and diagnoses
+     */
+    List<VisitWithDiagnoses> getVisitsWithNotesAndDiagnosesByPatient(String patientUuid, int startIndex, int limit);
+}

api/src/main/java/org/openmrs/module/emrapi/visit/EmrApiVisitServiceImpl.java

@@ -0,0 +1,31 @@
+package org.openmrs.module.emrapi.visit;
+
+import lombok.Setter;
+import org.hibernate.ObjectNotFoundException;
+import org.openmrs.Patient;
+import org.openmrs.api.PatientService;
+import org.openmrs.api.impl.BaseOpenmrsService;
+import org.openmrs.module.emrapi.db.EmrApiDAO;
+import org.springframework.stereotype.Service;
+
+import java.util.List;
+
+@Setter
+@Service
+public class EmrApiVisitServiceImpl extends BaseOpenmrsService implements EmrApiVisitService {
+
+    PatientService patientService;
+    EmrApiDAO emrApiDAO;
+
+    @Override
+    public List<VisitWithDiagnoses> getVisitsWithNotesAndDiagnosesByPatient(String patientUuid, int startIndex, int limit) {
+
+        Patient patient = patientService.getPatientByUuid(patientUuid);
+
+        if (patient == null) {
+            throw new ObjectNotFoundException("No patient found with uuid " + patientUuid, Patient.class.getName());
+        }
+
+        return emrApiDAO.getVisitsWithNotesAndDiagnosesByPatient(patient, startIndex, limit);
+    }
+}

api/src/main/java/org/openmrs/module/emrapi/visit/VisitWithDiagnoses.java

@@ -0,0 +1,22 @@
+package org.openmrs.module.emrapi.visit;
+
+import lombok.Getter;
+import lombok.Setter;
+import org.openmrs.Diagnosis;
+import org.openmrs.Visit;
+
+import java.util.Set;
+
+@Setter
+@Getter
+public class VisitWithDiagnoses {
+
+    private Visit visit;
+    private Set<Diagnosis> diagnoses;
+
+    public VisitWithDiagnoses(Visit visit, Set<Diagnosis> diagnoses) {
+       this.visit = visit;
+       this.diagnoses = diagnoses;
+    }
+
+}

api/src/main/resources/moduleApplicationContext.xml

@@ -315,10 +315,19 @@
         <constructor-arg ref="encounterService"/>
     </bean>
 
+
     <bean id="emrApiDAOImpl" class="org.openmrs.module.emrapi.db.EmrApiDAOImpl">
         <property name="sessionFactory">
             <ref bean="dbSessionFactory"/>
         </property>
+        <property name="emrApiProperties">
+            <ref bean="emrApiProperties"/>
+        </property>
+    </bean>
+
+    <bean id="emrApiVisitService" class="org.openmrs.module.emrapi.visit.EmrApiVisitServiceImpl">
+        <property name="emrApiDAO" ref="emrApiDAOImpl"/>
+        <property name="patientService" ref="patientService"/>
     </bean>
 
     <bean id="visitResponseMapper" class="org.openmrs.module.emrapi.visit.VisitResponseMapper">

api/src/test/java/org/openmrs/module/emrapi/db/EmrApiDaoTest.java

@@ -0,0 +1,90 @@
+package org.openmrs.module.emrapi.db;
+
+import org.junit.Before;
+import org.junit.Test;
+import org.openmrs.Diagnosis;
+import org.openmrs.Encounter;
+import org.openmrs.Patient;
+import org.openmrs.module.emrapi.EmrApiContextSensitiveTest;
+import org.openmrs.module.emrapi.visit.VisitWithDiagnoses;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import java.util.List;
+import java.util.Set;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+
+public class EmrApiDaoTest extends EmrApiContextSensitiveTest {
+
+    @Autowired
+    private EmrApiDAO emrApiDAO;
+
+    @Before
+    public void setup() {
+        executeDataSet("baseTestDataset.xml");
+        executeDataSet("pastVisitSetup.xml");
+    }
+
+    @Test
+    public void shouldFetchVisitsWithNotesAndDiagnosesByPatientId() {
+        String visitNoteEncounterTypeUuid = "d7151f82-c1f3-4152-a605-2f9ea7414a79";
+
+        Patient patient = new Patient();
+        patient.setPatientId(109);
+
+        List<VisitWithDiagnoses> visits = emrApiDAO.getVisitsWithNotesAndDiagnosesByPatient(patient,0,10);
+        assertNotNull(visits);
+        assert visits.size() == 3;
+
+        VisitWithDiagnoses firstVisit = visits.get(2);
+        Set<Encounter> firstVisitEncounters = firstVisit.getVisit().getEncounters();
+        Set<Diagnosis> firstVisitDiagnoses = firstVisit.getDiagnoses();
+
+        assert firstVisit.getVisit().getId() == 1014;
+        assert firstVisit.getVisit().getPatient().getPatientId() == 109;
+        assert firstVisitEncounters.size() == 2;
+        assert firstVisitDiagnoses.size() == 3;
+
+        for (Encounter encounter : firstVisitEncounters) {
+            assert encounter.getEncounterType().getUuid().equals(visitNoteEncounterTypeUuid);
+        }
+
+        VisitWithDiagnoses secondVisit = visits.get(1);
+        Set<Encounter> secondVisitEncounters = secondVisit.getVisit().getEncounters();
+        Set<Diagnosis> secondVisitDiagnoses = secondVisit.getDiagnoses();
+
+        assert secondVisit.getVisit().getId() == 1015;
+        assert secondVisit.getVisit().getPatient().getPatientId() == 109;
+        assert secondVisitEncounters.size() == 1;
+        assert secondVisitDiagnoses.size() == 2;
+
+        for (Encounter encounter : secondVisitEncounters) {
+            assert encounter.getEncounterType().getUuid().equals(visitNoteEncounterTypeUuid);
+        }
+
+        VisitWithDiagnoses thirdVisit = visits.get(0);
+        Set<Encounter> thirdVisitEncounters = thirdVisit.getVisit().getEncounters();
+        Set<Diagnosis> thirdVisitDiagnoses = thirdVisit.getDiagnoses();
+
+        assert thirdVisit.getVisit().getId() == 1017;
+        assert thirdVisit.getVisit().getPatient().getPatientId() == 109;
+        assert thirdVisitEncounters.isEmpty();
+        assert thirdVisitDiagnoses.isEmpty();
+
+    }
+
+    @Test
+    public void shouldFetchVisitsWithNotesAndDiagnosesWithPagination() {
+        Patient patient = new Patient();
+        patient.setPatientId(109);
+
+        List<VisitWithDiagnoses> visits = emrApiDAO.getVisitsWithNotesAndDiagnosesByPatient(patient,0,1);
+        assertNotNull(visits);
+        assert visits.size() == 1;
+
+        VisitWithDiagnoses mostRecentVisit = visits.get(0);
+        assert mostRecentVisit.getVisit().getId() == 1017;
+    }
+
+}

api/src/test/resources/metadata/pastVisitSetup.xml

@@ -0,0 +1,29 @@
+<?xml version='1.0' encoding='UTF-8'?>
+
+<dataset>
+
+  <encounter_type encounter_type_id="1003" name="Visit Note" description="Visit note" creator="1" date_created="2023-10-15 10:00:00.0" retired="false" uuid="d7151f82-c1f3-4152-a605-2f9ea7414a79"/>
+  <encounter_type encounter_type_id="1004" name="Vitals" description="For capturing vital signs" creator="1" date_created="2023-10-15 10:00:00.0" retired="false" uuid="d92ca5dc-7fd0-4fa2-b726-ab16fbc53fc1"/>
+
+  <!-- Person (Patient) Information -->
+  <person person_id="109" gender="M" dead="false" creator="1" birthdate_estimated="0"
+          date_created="2023-10-15 10:30:00.0" voided="false" void_reason=""
+          uuid="8604d42e-3ca8-11e3-bf2b-0d0c09861e97"/>
+  <person_name person_name_id="109" person_id="109" preferred="true" prefix="" given_name="Scott" middle_name=""
+               family_name="Clark" family_name_suffix="" creator="1" date_created="2023-10-15 10:31:00.0"
+               voided="false" void_reason="" uuid="8f9e3a7b-6482-487d-9abe-c07b123c4f08"/>
+
+  <!-- Patient Record -->
+  <patient patient_id="109" creator="1" date_created="2023-10-15 10:32:00.0" voided="false" />
+
+  <!-- Location Information -->
+  <location location_id="1901" name="Location tagged to visit" creator="1" date_created="2023-10-15 10:35:00.0" retired="false" uuid="f1771d8e-bf1f-4dc5-957f-9d40a5eebf08"/>
+
+  <!-- Visit Information -->
+  <visit visit_id="1014" patient_id="109" visit_type_id="1" date_started="2023-10-20 09:00:00.0" date_stopped="2023-10-20 09:30:00.0" location_id="1901" creator="1" date_created="2023-10-20 09:05:00.0" voided="0" uuid="1esd5218-6b78-11e0-93c3-18a905e044dc" />
+
+  <!-- Encounter Information (Visit Note) -->
+  <encounter encounter_id="2001" visit_id="1014" encounter_type="1003" patient_id="109" location_id="1901" form_id="1" encounter_datetime="2023-10-20 09:10:00.0" creator="1" date_created="2023-10-20 09:12:00.0" voided="false" uuid="a123d653-444b-4118-9c83-a3715b82d4ac"/>
+  <encounter encounter_id="2002" visit_id="1014" encounter_type="1004" patient_id="109" location_id="1901" form_id="1" encounter_datetime="2023-10-20 09:10:00.0" creator="1" date_created="2023-10-20 09:12:00.0" voided="false" uuid="a9a41017-2593-442a-bb88-c80358692d1e"/>
+
+</dataset>