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Merge pull request #1845 from karrtikiyer-tw/TRUNK-4949
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Trunk 4949
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@dkayiwa
dkayiwa committed Oct 19, 2016
2 parents c907036 + 79952f5 commit 9446f7c
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Showing 3 changed files with 312 additions and 73 deletions.
240 changes: 170 additions & 70 deletions api/src/main/java/org/openmrs/api/db/hibernate/HibernatePatientDAO.java
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Original file line number Diff line number Diff line change
Expand Up @@ -12,22 +12,28 @@
import java.lang.reflect.Field;
import java.util.ArrayList;
import java.util.Collections;
import java.util.Comparator;
import java.util.Date;
import java.util.HashMap;
import java.util.HashSet;
import java.util.LinkedHashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.Vector;

import org.apache.commons.lang.StringUtils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.hibernate.Criteria;
import org.hibernate.HibernateException;
import org.hibernate.Query;
import org.hibernate.SQLQuery;
import org.hibernate.SessionFactory;
import org.hibernate.criterion.Order;
import org.hibernate.criterion.Projections;
import org.hibernate.criterion.Restrictions;
import org.hibernate.persister.entity.AbstractEntityPersister;
import org.openmrs.Allergies;
import org.openmrs.Allergy;
import org.openmrs.Location;
Expand Down Expand Up @@ -425,85 +431,179 @@ public List<PatientIdentifierType> getPatientIdentifierTypes(String name, String
@SuppressWarnings("unchecked")
public List<Patient> getDuplicatePatientsByAttributes(List<String> attributes) {
List<Patient> patients = new Vector<Patient>();

List<Integer> patientIds = new Vector<Integer>();

if (attributes.size() > 0) {
String select = "select distinct p1 from Patient p1, Patient p2";
String where = " where p1 <> p2 ";
String orderBy = " order by ";

Class patient = Patient.class;
Set<String> patientFieldNames = new HashSet<String>(patient.getDeclaredFields().length);
for (Field f : patient.getDeclaredFields()) {
patientFieldNames.add(f.getName());
log.debug(f.getName());
}

Class person = Person.class;
Set<String> personFieldNames = new HashSet<String>(person.getDeclaredFields().length);
for (Field f : person.getDeclaredFields()) {
personFieldNames.add(f.getName());
log.debug(f.getName());
}

Class personName = PersonName.class;
Set<String> personNameFieldNames = new HashSet<String>(personName.getDeclaredFields().length);
for (Field f : personName.getDeclaredFields()) {
personNameFieldNames.add(f.getName());
log.debug(f.getName());
}

Class identifier = PatientIdentifier.class;
Set<String> identifierFieldNames = new HashSet<String>(identifier.getDeclaredFields().length);
for (Field f : identifier.getDeclaredFields()) {
identifierFieldNames.add(f.getName());
log.debug(f.getName());

String sqlString = getDuplicatePatientsSQLString(attributes);
if(sqlString != null) {

SQLQuery sqlquery = sessionFactory.getCurrentSession().createSQLQuery(sqlString);
patientIds = sqlquery.list();
if (patientIds.size() >= 1) {
Query query = sessionFactory.getCurrentSession().createQuery(
"from Patient p1 where p1.patientId in (:ids)");
query.setParameterList("ids", patientIds);
patients = query.list();
}
}

if (!attributes.contains("includeVoided")) {
where += "and p1.voided = false and p2.voided = false ";

}

sortDuplicatePatients(patients, patientIds);
return patients;
}

private String getDuplicatePatientsSQLString(List<String> attributes) {
String outerSelect = "select distinct t1.patient_id from patient t1 ";

Class patient = Patient.class;
Set<String> patientFieldNames = new HashSet<String>(patient.getDeclaredFields().length);
for (Field field : patient.getDeclaredFields()) {
patientFieldNames.add(field.getName());
log.debug(field.getName());
}

Class person = Person.class;
Set<String> personFieldNames = new HashSet<String>(person.getDeclaredFields().length);
for (Field field : person.getDeclaredFields()) {
personFieldNames.add(field.getName());
log.debug(field.getName());
}

Class personName = PersonName.class;

Set<String> personNameFieldNames = new HashSet<String>(personName.getDeclaredFields().length);
for (Field field : personName.getDeclaredFields()) {
personNameFieldNames.add(field.getName());
log.debug(field.getName());
}

Class identifier = PatientIdentifier.class;
Set<String> identifierFieldNames = new HashSet<String>(identifier.getDeclaredFields().length);
for (Field field : identifier.getDeclaredFields()) {
identifierFieldNames.add(field.getName());
log.debug(field.getName());
}
List<String> whereConditions = new ArrayList<String>();


List<String> innerFields = new ArrayList<String>();
String innerSelect = " from patient p1 ";

for (String attribute : attributes) {
if (attribute != null) {
attribute = attribute.trim();
}

for (String s : attributes) {
if (patientFieldNames.contains(s)) {
where += " and p1." + s + " = p2." + s;
orderBy += "p1." + s + ", ";
} else if (personFieldNames.contains(s)) {
if (!select.contains("Person ")) {
select += ", Person person1, Person person2";
where += " and p1.patientId = person1.personId and p2.patientId = person2.personId ";
if (patientFieldNames.contains(attribute)) {

AbstractEntityPersister aep = ((AbstractEntityPersister) sessionFactory.getClassMetadata(Patient.class));
String[] properties = aep.getPropertyColumnNames(attribute);
if (properties.length >= 1) {
attribute = properties[0];
}
whereConditions.add(" t1." + attribute + " = t5." + attribute);
innerFields.add("p1." + attribute);
} else if (personFieldNames.contains(attribute)) {
if (!outerSelect.contains("person")) {
outerSelect += "inner join person t2 on t1.patient_id = t2.person_id ";
innerSelect += "inner join person person1 on p1.patient_id = person1.person_id ";
}

AbstractEntityPersister aep = ((AbstractEntityPersister) sessionFactory.getClassMetadata(Person.class));
if (aep != null) {
String[] properties = aep.getPropertyColumnNames(attribute);
if (properties != null && properties.length >= 1) {
attribute = properties[0];
}
where += " and person1." + s + " = person2." + s;
orderBy += "person1." + s + ", ";
} else if (personNameFieldNames.contains(s)) {
if (!select.contains("PersonName")) {
select += ", PersonName pn1, PersonName pn2";
where += " and p1 = pn1.person and p2 = pn2.person ";
}

whereConditions.add(" t2." + attribute + " = t5." + attribute);
innerFields.add("person1." + attribute);
} else if (personNameFieldNames.contains(attribute)) {
if (!outerSelect.contains("person_name")) {
outerSelect += "inner join person_name t3 on t2.person_id = t3.person_id ";
innerSelect += "inner join person_name pn1 on person1.person_id = pn1.person_id ";
}

//Since we are firing a native query get the actual table column name from the field name of the entity
AbstractEntityPersister aep = ((AbstractEntityPersister) sessionFactory
.getClassMetadata(PersonName.class));
if (aep != null) {
String[] properties = aep.getPropertyColumnNames(attribute);

if (properties != null && properties.length >= 1) {
attribute = properties[0];
}
where += " and pn1." + s + " = pn2." + s;
orderBy += "pn1." + s + ", ";
} else if (identifierFieldNames.contains(s)) {
if (!select.contains("PatientIdentifier")) {
select += ", PatientIdentifier pi1, PatientIdentifier pi2";
where += " and p1 = pi1.patient and p2 = pi2.patient ";
}

whereConditions.add(" t3." + attribute + " = t5." + attribute);
innerFields.add("pn1." + attribute);
} else if (identifierFieldNames.contains(attribute)) {
if (!outerSelect.contains("patient_identifier")) {
outerSelect += "inner join patient_identifier t4 on t1.patient_id = t4.patient_id ";
innerSelect += "inner join patient_identifier pi1 on p1.patient_id = pi1.patient_id ";
}

AbstractEntityPersister aep = ((AbstractEntityPersister) sessionFactory
.getClassMetadata(PatientIdentifier.class));
if (aep != null) {

String[] properties = aep.getPropertyColumnNames(attribute);
if (properties != null && properties.length >= 1) {
attribute = properties[0];
}
where += " and pi1." + s + " = pi2." + s;
orderBy += "pi1." + s + ", ";
} else {
log.warn("Unidentified attribute: " + s);
}

whereConditions.add(" t4." + attribute + " = t5." + attribute);
innerFields.add("pi1." + attribute);
} else {
log.warn("Unidentified attribute: " + attribute);
}

int index = orderBy.lastIndexOf(", ");
orderBy = orderBy.substring(0, index);

select = select + where + orderBy;

Query query = sessionFactory.getCurrentSession().createQuery(select);

patients = query.list();
}

return patients;
if(innerFields.size() > 0 || whereConditions.size() > 0) {
String innerFieldsJoined = StringUtils.join(innerFields, ", ");
String whereFieldsJoined = StringUtils.join(whereConditions, " and ");
String innerWhereCondition = "";
if (!attributes.contains("includeVoided")) {
innerWhereCondition = " where p1.voided = false ";
}
String innerQuery = "(Select " + innerFieldsJoined + innerSelect + innerWhereCondition + " group by "
+ innerFieldsJoined + " having count(*) > 1" + " order by " + innerFieldsJoined + ") t5";
return outerSelect + ", " + innerQuery + " where " + whereFieldsJoined + ";";
}
return null;
}

private void sortDuplicatePatients(List<Patient> patients, List<Integer> patientIds) {

Map<Integer, Integer> patientIdOrder = new HashMap<Integer, Integer>();
int startPos = 0;
for (Integer id : patientIds) {
patientIdOrder.put(id, startPos++);
}
class PatientIdComparator implements Comparator<Patient> {

private Map<Integer, Integer> sortOrder;

public PatientIdComparator(Map<Integer, Integer> sortOrder) {
this.sortOrder = sortOrder;
}

@Override
public int compare(Patient patient1, Patient patient2) {
Integer patPos1 = sortOrder.get(patient1.getPatientId());
if (patPos1 == null) {
throw new IllegalArgumentException("Bad patient encountered: " + patient1.getPatientId());
}
Integer patPos2 = sortOrder.get(patient2.getPatientId());
if (patPos2 == null) {
throw new IllegalArgumentException("Bad patient encountered: " + patient2.getPatientId());
}
return patPos1.compareTo(patPos2);
}
}
Collections.sort(patients, new PatientIdComparator(patientIdOrder));
}

/**
Expand Down

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