Sanjana | BDSHR - 874 | Cleaning up of computed patient age related c…

…olumns from encounter and patient death details.Queries to comput age dynamically from patient.since dob can be updated.
SharedHealth · Aug 17, 2015 · 21262ac · 21262ac
1 parent fcffd63
commit 21262ac
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Showing 12 changed files with 36 additions and 113 deletions.
diff --git a/src/main/java/org/sharedhealth/datasense/handler/DeathNoteHandler.java b/src/main/java/org/sharedhealth/datasense/handler/DeathNoteHandler.java
@@ -17,7 +17,6 @@
 import java.util.Date;
 import java.util.List;
 
-import static org.sharedhealth.datasense.util.DateUtil.*;
 import static org.sharedhealth.datasense.util.TrUrl.isConceptUrl;
 import static org.sharedhealth.datasense.util.TrUrl.isReferenceTermUrl;
 
@@ -95,9 +94,6 @@ private void mapDateOfDeathAndPatientAge(PatientDeathDetails patientDeathDetails
         Observation dateOfDeathObs = findObservation(composition, deathNoteObservation, datasenseProperties.getDateOfDeathUuid());
         Date dateOfDeath = getDateValue(encounter, dateOfDeathObs);
         patientDeathDetails.setDateOfDeath(dateOfDeath);
-        patientDeathDetails.setPatientAgeInYears(getYears(patientDeathDetails.getPatient().getDateOfBirth(), dateOfDeath));
-        patientDeathDetails.setPatientAgeInMonths(getMonths(patientDeathDetails.getPatient().getDateOfBirth(), dateOfDeath));
-        patientDeathDetails.setPatientAgeInDays(getDays(patientDeathDetails.getPatient().getDateOfBirth(), dateOfDeath));
     }
 
     private Date getDateValue(Encounter encounter, Observation dateOfDeathObs) {

diff --git a/src/main/java/org/sharedhealth/datasense/model/Encounter.java b/src/main/java/org/sharedhealth/datasense/model/Encounter.java
@@ -12,9 +12,6 @@ public class Encounter {
     private Patient patient;
     private Date encounterDateTime;
     private String locationCode;
-    private int patientAgeInYears;
-    private int patientAgeInMonths;
-    private int patientAgeInDays;
 
     public void setEncounterType(String encounterType) {
         this.encounterType = encounterType;
@@ -69,30 +66,6 @@ public String getLocationCode() {
         return null;
     }
 
-    public int getPatientAgeInYears() {
-        return patientAgeInYears;
-    }
-
-    public void setPatientAgeInYears(int patientAgeInYears) {
-        this.patientAgeInYears = patientAgeInYears;
-    }
-
-    public int getPatientAgeInMonths() {
-        return patientAgeInMonths;
-    }
-
-    public void setPatientAgeInMonths(int patientAgeInMonths) {
-        this.patientAgeInMonths = patientAgeInMonths;
-    }
-
-    public int getPatientAgeInDays() {
-        return patientAgeInDays;
-    }
-
-    public void setPatientAgeInDays(int patientAgeInDays) {
-        this.patientAgeInDays = patientAgeInDays;
-    }
-
     public String getEncounterId() {
         return encounterId;
     }

diff --git a/src/main/java/org/sharedhealth/datasense/model/PatientDeathDetails.java b/src/main/java/org/sharedhealth/datasense/model/PatientDeathDetails.java
@@ -6,9 +6,6 @@ public class PatientDeathDetails extends BaseResource {
     private Patient patient;
     private Encounter encounter;
     private Date dateOfDeath;
-    private int patientAgeInYears;
-    private int patientAgeInMonths;
-    private int patientAgeInDays;
     private String circumstancesOfDeath;
     private String causeOfDeathCode;
     private String causeOfDeathConceptUuid;
@@ -38,30 +35,6 @@ public void setDateOfDeath(Date dateOfDeath) {
         this.dateOfDeath = dateOfDeath;
     }
 
-    public int getPatientAgeInYears() {
-        return patientAgeInYears;
-    }
-
-    public void setPatientAgeInYears(int patientAgeInYears) {
-        this.patientAgeInYears = patientAgeInYears;
-    }
-
-    public int getPatientAgeInMonths() {
-        return patientAgeInMonths;
-    }
-
-    public void setPatientAgeInMonths(int patientAgeInMonths) {
-        this.patientAgeInMonths = patientAgeInMonths;
-    }
-
-    public int getPatientAgeInDays() {
-        return patientAgeInDays;
-    }
-
-    public void setPatientAgeInDays(int patientAgeInDays) {
-        this.patientAgeInDays = patientAgeInDays;
-    }
-
     public String getCircumstancesOfDeath() {
         return circumstancesOfDeath;
     }

diff --git a/src/main/java/org/sharedhealth/datasense/processor/ClinicalEncounterProcessor.java b/src/main/java/org/sharedhealth/datasense/processor/ClinicalEncounterProcessor.java
@@ -13,8 +13,6 @@
 
 import java.util.Date;
 
-import static org.sharedhealth.datasense.util.DateUtil.*;
-
 @Component("clinicalEncounterProcessor")
 public class ClinicalEncounterProcessor implements ResourceProcessor {
     private EncounterDao encounterDao;
@@ -57,7 +55,6 @@ private Encounter mapEncounterFields(org.hl7.fhir.instance.model.Encounter fhirE
         String encounterDate = composition.getComposition().getDateSimple().toString();
         Date encounterDateTime = DateUtil.parseDate(encounterDate);
         encounter.setEncounterDateTime(encounterDateTime);
-        setPatientAge(patient.getDateOfBirth(), encounterDateTime, encounter);
         return encounter;
     }
 
@@ -66,9 +63,4 @@ public void setNext(ResourceProcessor nextProcessor) {
         this.nextProcessor = nextProcessor;
     }
 
-    public void setPatientAge(Date birthDate, Date encounterDate, Encounter encounter) {
-        encounter.setPatientAgeInYears(getYears(birthDate, encounterDate));
-        encounter.setPatientAgeInMonths(getMonths(birthDate, encounterDate));
-        encounter.setPatientAgeInDays(getDays(birthDate, encounterDate));
-    }
 }
diff --git a/src/main/java/org/sharedhealth/datasense/repository/EncounterDao.java b/src/main/java/org/sharedhealth/datasense/repository/EncounterDao.java
@@ -21,17 +21,12 @@ public void save(Encounter encounter) {
         map.put("encounter_type", encounter.getEncounterType());
         map.put("visit_type", encounter.getEncounterVisitType());
         map.put("patient_hid", encounter.getPatient().getHid());
-        map.put("patient_age_years", encounter.getPatientAgeInYears());
-        map.put("patient_age_months", encounter.getPatientAgeInMonths());
-        map.put("patient_age_days", encounter.getPatientAgeInDays());
         map.put("location_id", encounter.getLocationCode());
         map.put("facility_id", encounter.getFacility().getFacilityId());
         jdbcTemplate.update("insert into encounter (encounter_id, encounter_datetime, encounter_type, visit_type, " +
-                "patient_hid, " +
-                "patient_age_years, patient_age_months, patient_age_days, encounter_location_id, facility_id) " +
+                "patient_hid, encounter_location_id, facility_id) " +
                 "values(:encounter_id, :encounter_datetime, :encounter_type , :visit_type , :patient_hid, " +
-                ":patient_age_years, :patient_age_months," +
-                " :patient_age_days , :location_id, :facility_id)", map);
+                ":location_id, :facility_id)", map);
     }
 
     public void deleteExisting(String healthId, String encounterId){

diff --git a/src/main/java/org/sharedhealth/datasense/repository/PatientDeathDetailsDao.java b/src/main/java/org/sharedhealth/datasense/repository/PatientDeathDetailsDao.java
@@ -23,19 +23,16 @@ public void save(PatientDeathDetails patientDeathDetails) {
         map.put("patient_hid", patientDeathDetails.getPatient().getHid());
         map.put("encounter_id", patientDeathDetails.getEncounter().getEncounterId());
         map.put("date_of_death", patientDeathDetails.getDateOfDeath());
-        map.put("patient_age_years", patientDeathDetails.getPatientAgeInYears());
-        map.put("patient_age_months", patientDeathDetails.getPatientAgeInMonths());
-        map.put("patient_age_days", patientDeathDetails.getPatientAgeInDays());
         map.put("circumstances_of_death", patientDeathDetails.getCircumstancesOfDeath());
         map.put("cause_concept_uuid", patientDeathDetails.getCauseOfDeathConceptUuid());
         map.put("cause_code", patientDeathDetails.getCauseOfDeathCode());
         map.put("uuid", patientDeathDetails.getUuid());
 
 
-        String sql = "insert into patient_death_details (patient_hid, encounter_id, date_of_death, patient_age_years, patient_age_months, patient_age_days," +
+        String sql = "insert into patient_death_details (patient_hid, encounter_id, date_of_death, " +
                 "circumstances_of_death, cause_concept_uuid, cause_code, uuid) " +
-                "values(:patient_hid, :encounter_id, :date_of_death, :patient_age_years, :patient_age_months, :patient_age_days, " +
-                " :circumstances_of_death, :cause_concept_uuid, :cause_code, :uuid)";
+                "values(:patient_hid, :encounter_id, :date_of_death, " +
+                ":circumstances_of_death, :cause_concept_uuid, :cause_code, :uuid)";
 
         jdbcTemplate.update(sql, map);
     }

diff --git a/src/main/resources/db/changelog/db-changelog.xml b/src/main/resources/db/changelog/db-changelog.xml
@@ -668,4 +668,16 @@
             <column name="updated_at" type="datetime" defaultValueComputed="now()"/>
         </addColumn>
     </changeSet>
+    <changeSet id="sharedhealth-datasense-20150818-1513" author="sanjana" context="setup">
+        <comment>Dropping patient age columns in encounter table</comment>
+        <dropColumn columnName="patient_age_years" tableName="encounter"/>
+        <dropColumn columnName="patient_age_months" tableName="encounter"/>
+        <dropColumn columnName="patient_age_days" tableName="encounter"/>
+    </changeSet>
+    <changeSet id="sharedhealth-datasense-20150818-1520" author="sanjana" context="setup">
+        <comment>Dropping patient age columns in encounter table</comment>
+        <dropColumn columnName="patient_age_years" tableName="patient_death_details"/>
+        <dropColumn columnName="patient_age_months" tableName="patient_death_details"/>
+        <dropColumn columnName="patient_age_days" tableName="patient_death_details"/>
+    </changeSet>
 </databaseChangeLog>
diff --git a/src/test/java/org/sharedhealth/datasense/aqs/AqsExecutorIntegrationTest.java b/src/test/java/org/sharedhealth/datasense/aqs/AqsExecutorIntegrationTest.java
@@ -33,11 +33,11 @@ public class AqsExecutorIntegrationTest {
     public void shouldExecuteMultipleQueriesAndReturnResults() throws ExecutionException, InterruptedException {
         QueryDefinition admissionsMale = new QueryDefinition();
         admissionsMale.setQueryName("ipd_male_0_to_4");
-        admissionsMale.setQueryString("select count(distinct e.patient_hid) as v1 from encounter e, patient p where facility_id=':paramFacilityId:' and e.patient_hid=p.patient_hid and e.patient_age_years >= 0 and e.patient_age_years < 5 and p.gender='M' and LOWER(e.visit_type)='inpatient' and e.encounter_datetime =':paramStartDate:';");
+        admissionsMale.setQueryString("select count(distinct e.patient_hid) as v1 from encounter e, patient p where facility_id=':paramFacilityId:' and e.patient_hid=p.patient_hid and TIMESTAMPDIFF(YEAR, p.dob, e.encounter_datetime) between 0 and 5 and p.gender='M' and LOWER(e.visit_type)='inpatient' and e.encounter_datetime =':paramStartDate:';");
 
         QueryDefinition emergencyVisitsFemale = new QueryDefinition();
         emergencyVisitsFemale.setQueryName("emergency_female_15_to_24");
-        emergencyVisitsFemale.setQueryString("select count(distinct e.patient_hid) as v1 from encounter e, patient p where facility_id=':paramFacilityId:' and e.patient_hid=p.patient_hid and e.patient_age_years >= 15 and e.patient_age_years < 25 and p.gender='F' and LOWER(e.visit_type)='emergency' and e.encounter_datetime=':paramStartDate:';");
+        emergencyVisitsFemale.setQueryString("select count(distinct e.patient_hid) as v1 from encounter e, patient p where facility_id=':paramFacilityId:' and e.patient_hid=p.patient_hid and TIMESTAMPDIFF(YEAR, p.dob, e.encounter_datetime) between 15 and 25 and p.gender='F' and LOWER(e.visit_type)='emergency' and e.encounter_datetime=':paramStartDate:';");
 
 
         Map<String, Object> params = new HashMap<String, Object>() {{

diff --git a/src/test/java/org/sharedhealth/datasense/handler/DeathNoteHandlerIT.java b/src/test/java/org/sharedhealth/datasense/handler/DeathNoteHandlerIT.java
@@ -90,15 +90,6 @@ public void shouldSaveDateOfDeathFromDateOfDeathObservationResource() {
         assertEquals(DateUtil.parseDate("2014-12-28T00:00:00+05:30"), patientDeathDetails.getDateOfDeath());
     }
 
-    @Test
-    public void shouldSavePatientAgeFromDateOfDeathObservationResource() {
-        deathNoteHandler.process(deathNoteResource, composition);
-        PatientDeathDetails patientDeathDetails = findByEncounterId("shrEncounterId");
-        assertEquals(1, patientDeathDetails.getPatientAgeInYears());
-        assertEquals(12, patientDeathDetails.getPatientAgeInMonths());
-        assertEquals(365, patientDeathDetails.getPatientAgeInDays());
-    }
-
     @Test
     public void shouldSaveCircumstancesOfDeathObservationResource() {
         deathNoteHandler.process(deathNoteResource, composition);
@@ -115,7 +106,7 @@ public void shouldSaveCauseOfDeath() {
     }
 
     private PatientDeathDetails findByEncounterId(String shrEncounterId) {
-        String sql = "select patient_hid, encounter_id, date_of_death, patient_age_years, patient_age_months, patient_age_days, " +
+        String sql = "select patient_hid, encounter_id, date_of_death, " +
                 "circumstances_of_death, cause_concept_uuid, cause_code, uuid " +
                 "from patient_death_details where encounter_id= :encounter_id";
         HashMap<String, Object> map = new HashMap<>();
@@ -133,9 +124,6 @@ public PatientDeathDetails mapRow(ResultSet rs, int rowNum) throws SQLException
                 patientDeathDetails.setEncounter(encounter);
 
                 patientDeathDetails.setDateOfDeath(rs.getTimestamp("date_of_death"));
-                patientDeathDetails.setPatientAgeInYears(rs.getInt("patient_age_years"));
-                patientDeathDetails.setPatientAgeInMonths(rs.getInt("patient_age_months"));
-                patientDeathDetails.setPatientAgeInDays(rs.getInt("patient_age_days"));
                 patientDeathDetails.setCircumstancesOfDeath(rs.getString("circumstances_of_death"));
                 patientDeathDetails.setCauseOfDeathConceptUuid(rs.getString("cause_concept_uuid"));
                 patientDeathDetails.setCauseOfDeathCode(rs.getString("cause_code"));

diff --git a/src/test/java/org/sharedhealth/datasense/processor/ClinicalEncounterProcessorIT.java b/src/test/java/org/sharedhealth/datasense/processor/ClinicalEncounterProcessorIT.java
@@ -85,7 +85,7 @@ public void shouldSaveEncounter() throws Exception {
     private Encounter findEncounterById(String encounterId) {
         List<Encounter> encounters = jdbcTemplate.query(
                 "select encounter_id ,encounter_datetime, encounter_type, visit_type, patient_hid, " +
-                        "patient_age_years, patient_age_months, patient_age_days,encounter_location_id, facility_id " +
+                        "encounter_location_id, facility_id " +
                         "from encounter where encounter_id= :encounter_id", Collections.singletonMap("encounter_id",
                         encounterId),
                 new RowMapper<Encounter>() {
@@ -96,9 +96,6 @@ public Encounter mapRow(ResultSet rs, int rowNum) throws SQLException {
                         encounter.setEncounterDateTime(new Date(rs.getTimestamp("encounter_datetime").getTime()));
                         encounter.setEncounterType(rs.getString("encounter_type"));
                         encounter.setEncounterVisitType(rs.getString("visit_type"));
-                        encounter.setPatientAgeInYears(rs.getInt("patient_age_years"));
-                        encounter.setPatientAgeInMonths(rs.getInt("patient_age_months"));
-                        encounter.setPatientAgeInDays(rs.getInt("patient_age_days"));
                         encounter.setLocationCode(rs.getString("encounter_location_id"));
 
                         Patient patient = new Patient();

diff --git a/src/test/resources/csv/encounters.csv b/src/test/resources/csv/encounters.csv
@@ -1,13 +1,13 @@
-encounter_id,encounter_datetime,encounter_type,visit_type,patient_hid,patient_age_years,patient_age_months,patient_age_days,encounter_location_id,facility_id,created_at
-100,2014-12-23,REG,outpatient,129,7,1,20,302618,1000
-103,2014-12-23,Consultation,outpatient,129,7,1,20,302618,1000
-110,2014-12-23,REG,outpatient,122,6,1,20,302618,1000
-111,2014-12-23,Consultation,outpatient,122,6,1,20,302618,1000
-101,2014-12-23,REG,inpatient,121,3,2,20,302618,1000
-102,2014-12-23,REG,outpatient,124,12,1,20,302618,1000
-104,2014-12-23,REG,outpatient,127,34,1,20,302618,1000
-105,2014-12-23,Consultation,outpatient,127,34,1,20,302618,1000
-106,2014-12-23,Consultation,inpatient,121,3,2,20,302618,1000
-107,2014-12-23,REG,inpatient,130,6,1,20,302618,1000
-108,2014-12-23,Consultation,inpatient,130,6,1,20,302618,1000
-109,2014-12-23,Consultation,inpatient,130,6,1,20,302618,1000
+encounter_id,encounter_datetime,encounter_type,visit_type,patient_hid,encounter_location_id,facility_id,created_at
+100,2014-12-23,REG,outpatient,129,302618,1000
+103,2014-12-23,Consultation,outpatient,129,302618,1000
+110,2014-12-23,REG,outpatient,122,302618,1000
+111,2014-12-23,Consultation,outpatient,122,302618,1000
+101,2014-12-23,REG,inpatient,121,302618,1000
+102,2014-12-23,REG,outpatient,124,302618,1000
+104,2014-12-23,REG,outpatient,127,302618,1000
+105,2014-12-23,Consultation,outpatient,127,302618,1000
+106,2014-12-23,Consultation,inpatient,121,302618,1000
+107,2014-12-23,REG,inpatient,130,302618,1000
+108,2014-12-23,Consultation,inpatient,130,302618,1000
+109,2014-12-23,Consultation,inpatient,130,302618,1000
diff --git a/src/test/resources/dhis/queries/query_list_1.json b/src/test/resources/dhis/queries/query_list_1.json
@@ -4,11 +4,11 @@
     "queries": [
       {
         "queryName": "Query_1",
-        "query": "select count(distinct e.patient_hid) as v1 from encounter e, patient p where facility_id=:FACILITY: and e.patient_hid=p.patient_hid and e.patient_age_years >= :MIN_YEAR: and e.patient_age_years < :MAX_YEAR: and p.gender=':GENDER:' and e.visit_type=':VISIT_TYPE:' and encounter_datetime=':ENC_DATE:';"
+        "query": "select count(distinct e.patient_hid) as v1 from encounter e, patient p where facility_id=:FACILITY: and e.patient_hid=p.patient_hid and TIMESTAMPDIFF(YEAR, p.dob, e.encounter_datetime) between :MIN_YEAR: and :MAX_YEAR: and p.gender=':GENDER:' and e.visit_type=':VISIT_TYPE:' and encounter_datetime=':ENC_DATE:';"
       },
       {
         "queryName": "Query_2",
-        "query": "select count(distinct e.patient_hid) as v2 from encounter e, patient p where facility_id=:FACILITY: and e.patient_hid=p.patient_hid and e.patient_age_years >= :MIN_YEAR: and e.patient_age_years < :MAX_YEAR: and p.gender=':GENDER2:' and e.visit_type=':VISIT_TYPE:' and encounter_datetime=':ENC_DATE:';"
+        "query": "select count(distinct e.patient_hid) as v2 from encounter e, patient p where facility_id=:FACILITY: and e.patient_hid=p.patient_hid and TIMESTAMPDIFF(YEAR, p.dob, e.encounter_datetime) between :MIN_YEAR: and :MAX_YEAR: and p.gender=':GENDER2:' and e.visit_type=':VISIT_TYPE:' and encounter_datetime=':ENC_DATE:';"
       }
     ]
   }