14752386992

Committed 30 Apr 2025 10:25AM UTC coverage: 64.96% (-0.1%) from 65.095%

Build # 14752386992

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web-flow

Commit Message

TRUNK-6316 Upgrade Hibernate Search to 6.2.4 (#5005)

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501 of 591 new or added lines in 24 files covered. (84.77%)

21 existing lines in 6 files now uncovered.

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91.46

/api/src/main/java/org/openmrs/api/db/hibernate/HibernatePatientDAO.java

/**
 * This Source Code Form is subject to the terms of the Mozilla Public License,
 * v. 2.0. If a copy of the MPL was not distributed with this file, You can
 * obtain one at http://mozilla.org/MPL/2.0/. OpenMRS is also distributed under
 * the terms of the Healthcare Disclaimer located at http://openmrs.org/license.
 *
 * Copyright (C) OpenMRS Inc. OpenMRS is a registered trademark and the OpenMRS
 * graphic logo is a trademark of OpenMRS Inc.
 */
package org.openmrs.api.db.hibernate;

import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import java.util.Comparator;
import java.util.Date;
import java.util.HashMap;
import java.util.LinkedList;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.regex.Pattern;

import org.apache.commons.collections.CollectionUtils;
import org.apache.commons.lang3.StringUtils;
import org.hibernate.Criteria;
import org.hibernate.Query;
import org.hibernate.SQLQuery;
import org.hibernate.SessionFactory;
import org.hibernate.criterion.Order;
import org.hibernate.criterion.Restrictions;
import org.hibernate.persister.entity.AbstractEntityPersister;
import org.hibernate.search.engine.search.predicate.SearchPredicate;
import org.hibernate.search.engine.search.predicate.dsl.SearchPredicateFactory;
import org.openmrs.Allergies;
import org.openmrs.Allergy;
import org.openmrs.Location;
import org.openmrs.Patient;
import org.openmrs.PatientIdentifier;
import org.openmrs.PatientIdentifierType;
import org.openmrs.PatientIdentifierType.UniquenessBehavior;
import org.openmrs.PatientProgram;
import org.openmrs.Person;
import org.openmrs.PersonAttribute;
import org.openmrs.PersonName;
import org.openmrs.api.context.Context;
import org.openmrs.api.db.DAOException;
import org.openmrs.api.db.PatientDAO;
import org.openmrs.api.db.hibernate.search.SearchQueryUnique;
import org.openmrs.api.db.hibernate.search.session.SearchSessionFactory;
import org.openmrs.util.OpenmrsConstants;
import org.openmrs.util.OpenmrsUtil;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

/**
 * Hibernate specific database methods for the PatientService
 *
 * @see org.openmrs.api.context.Context
 * @see org.openmrs.api.db.PatientDAO
 * @see org.openmrs.api.PatientService
 */
public class HibernatePatientDAO implements PatientDAO {
        
        private static final Logger log = LoggerFactory.getLogger(HibernatePatientDAO.class);
        
        /**
         * Hibernate session factory
         */
        private SessionFactory sessionFactory;
        
        private SearchSessionFactory searchSessionFactory;
        
        /**
         * Set session factory
         *
         * @param sessionFactory
         */
        public void setSessionFactory(SessionFactory sessionFactory) {
                this.sessionFactory = sessionFactory;
        }

        public void setSearchSessionFactory(SearchSessionFactory searchSessionFactory) {
                this.searchSessionFactory = searchSessionFactory;
        }

        /**
     * @param patientId  internal patient identifier
     * @return           patient with given internal identifier
         * @see org.openmrs.api.PatientService#getPatient(java.lang.Integer)
         */
        @Override
        public Patient getPatient(Integer patientId) {
                return (Patient) sessionFactory.getCurrentSession().get(Patient.class, patientId);
        }
        
        /**
     * @param patient  patient to be created or updated
     * @return         patient who was created or updated
         * @see org.openmrs.api.db.PatientDAO#savePatient(org.openmrs.Patient)
         */
        @Override
        public Patient savePatient(Patient patient) throws DAOException {
                if (patient.getPatientId() == null) {
                        // if we're saving a new patient, just do the normal thing
                        // and rows in the person and patient table will be created by
                        // hibernate
                        sessionFactory.getCurrentSession().saveOrUpdate(patient);
                        return patient;
                } else {
                        // if we're updating a patient, its possible that a person
                        // row exists but a patient row does not. hibernate does not deal
                        // with this correctly right now, so we must create a dummy row
                        // in the patient table before saving
                        
                        // Check to make sure we have a row in the patient table already.
                        // If we don't have a row, create it so Hibernate doesn't bung
                        // things up
                        insertPatientStubIfNeeded(patient);
                        
                        // Note: A merge might be necessary here because hibernate thinks that Patients
                        // and Persons are the same objects.  So it sees a Person object in the
                        // cache and claims it is a duplicate of this Patient object.
                        sessionFactory.getCurrentSession().saveOrUpdate(patient);
                        
                        return patient;
                }
        }
        
        /**
         * Inserts a row into the patient table This avoids hibernate's bunging of our
         * person/patient/user inheritance
         *
         * @param patient
         */
        private void insertPatientStubIfNeeded(Patient patient) {
                
                boolean stubInsertNeeded = false;
                
                if (patient.getPatientId() != null) {
                        // check if there is a row with a matching patient.patient_id
                        String sql = "SELECT 1 FROM patient WHERE patient_id = :patientId";
                        Query query = sessionFactory.getCurrentSession().createSQLQuery(sql);
                        query.setInteger("patientId", patient.getPatientId());
                        
                        stubInsertNeeded = (query.uniqueResult() == null);
                }
                
                if (stubInsertNeeded) {
                        //If not yet persisted
                        if (patient.getCreator() == null) {
                                patient.setCreator(Context.getAuthenticatedUser());
                        }
                        //If not yet persisted
                        if (patient.getDateCreated() == null) {
                                patient.setDateCreated(new Date());
                        }
                        
                        String insert = "INSERT INTO patient (patient_id, creator, voided, date_created) VALUES (:patientId, :creator, :voided, :dateCreated)";
                        Query query = sessionFactory.getCurrentSession().createSQLQuery(insert);
                        query.setInteger("patientId", patient.getPatientId());
                        query.setInteger("creator", patient.getCreator().getUserId());
                        query.setBoolean("voided", false);
                        query.setDate("dateCreated", patient.getDateCreated());
                        
                        query.executeUpdate();
                        
                        //Without evicting person, you will get this error when promoting person to patient
                        //org.hibernate.NonUniqueObjectException: a different object with the same identifier
                        //value was already associated with the session: [org.openmrs.Patient#]
                        //see TRUNK-3728
                        Person person = (Person) sessionFactory.getCurrentSession().get(Person.class, patient.getPersonId());
                        sessionFactory.getCurrentSession().evict(person);
                }
                
        }
        
        public List<Patient> getPatients(String query, List<PatientIdentifierType> identifierTypes,
                boolean matchIdentifierExactly, Integer start, Integer length) throws DAOException{
                
                if (StringUtils.isBlank(query) || (length != null && length < 1) || identifierTypes == null || identifierTypes.isEmpty())  {
                        return Collections.emptyList();
                }
                
                Integer tmpStart = start;
                if (tmpStart == null || tmpStart < 0) {
                        tmpStart = 0;
                }
                
                Integer tmpLength = length;
                if (tmpLength == null) {
                        tmpLength = HibernatePersonDAO.getMaximumSearchResults();
                }
                
                return findPatients(query, identifierTypes, matchIdentifierExactly, tmpStart, tmpLength);
        }
        
        /**
         * @see org.openmrs.api.db.PatientDAO#getPatients(String, boolean, Integer, Integer)
         * <strong>Should</strong> return exact match first
         */
        @Override
        public List<Patient> getPatients(String query, boolean includeVoided, Integer start, Integer length) throws DAOException {
                if (StringUtils.isBlank(query) || (length != null && length < 1)) {
                        return Collections.emptyList();
                }

                Integer tmpStart = start;
                if (tmpStart == null || tmpStart < 0) {
                        tmpStart = 0;
                }

                Integer tmpLength = length;
                if (tmpLength == null) {
                        tmpLength = HibernatePersonDAO.getMaximumSearchResults();
                }

                List<Patient> patients = findPatients(query, includeVoided, tmpStart, tmpLength);

                return new ArrayList<>(patients);
        }
        
        /**
         * @see org.openmrs.api.db.PatientDAO#getPatients(String, Integer, Integer)
         */
        @Override
        public List<Patient> getPatients(String query, Integer start, Integer length) throws DAOException {
                return getPatients(query, false, start, length);
        }
        
        private void setFirstAndMaxResult(Criteria criteria, Integer start, Integer length) {
                if (start != null) {
                        criteria.setFirstResult(start);
                }
                
                int maximumSearchResults = HibernatePersonDAO.getMaximumSearchResults();
                if (length != null && length < maximumSearchResults) {
                        criteria.setMaxResults(length);
                } else {
                        log.debug("Limiting the size of the number of matching patients to {}", maximumSearchResults);
                        criteria.setMaxResults(maximumSearchResults);
                }
        }
        
        /**
         * @see org.openmrs.api.db.PatientDAO#getAllPatients(boolean)
         */
        @SuppressWarnings("unchecked")
        @Override
        public List<Patient> getAllPatients(boolean includeVoided) throws DAOException {
                Criteria criteria = sessionFactory.getCurrentSession().createCriteria(Patient.class);
                
                if (!includeVoided) {
                        criteria.add(Restrictions.eq("voided", false));
                }
                
                return criteria.list();
        }
        
        /**
         * @see org.openmrs.api.PatientService#purgePatientIdentifierType(org.openmrs.PatientIdentifierType)
         * @see org.openmrs.api.db.PatientDAO#deletePatientIdentifierType(org.openmrs.PatientIdentifierType)
         */
        @Override
        public void deletePatientIdentifierType(PatientIdentifierType patientIdentifierType) throws DAOException {
                sessionFactory.getCurrentSession().delete(patientIdentifierType);
        }
        
        /**
         * @see org.openmrs.api.PatientService#getPatientIdentifiers(java.lang.String, java.util.List, java.util.List, java.util.List, java.lang.Boolean)
         */
        @SuppressWarnings("unchecked")
        @Override
        public List<PatientIdentifier> getPatientIdentifiers(String identifier,
                List<PatientIdentifierType> patientIdentifierTypes, List<Location> locations, List<Patient> patients,
                Boolean isPreferred) throws DAOException {
                Criteria criteria = sessionFactory.getCurrentSession().createCriteria(PatientIdentifier.class);
                
                // join with the patient table to prevent patient identifiers from patients
                // that already voided getting returned
                criteria.createAlias("patient", "patient");

                criteria.add(Restrictions.eq("patient.voided", false));
                
                criteria.add(Restrictions.eq("voided", false));
                
                if (identifier != null) {
                        criteria.add(Restrictions.eq("identifier", identifier));
                }
                
                if (!patientIdentifierTypes.isEmpty()) {
                        criteria.add(Restrictions.in("identifierType", patientIdentifierTypes));
                }
                
                if (!locations.isEmpty()) {
                        criteria.add(Restrictions.in("location", locations));
                }
                
                if (!patients.isEmpty()) {
                        criteria.add(Restrictions.in("patient", patients));
                }
                
                if (isPreferred != null) {
                        criteria.add(Restrictions.eq("preferred", isPreferred));
                }
                
                return criteria.list();
        }
        
        /**
         * @see org.openmrs.api.db.PatientDAO#savePatientIdentifierType(org.openmrs.PatientIdentifierType)
         */
        @Override
        public PatientIdentifierType savePatientIdentifierType(PatientIdentifierType patientIdentifierType) throws DAOException {
                sessionFactory.getCurrentSession().saveOrUpdate(patientIdentifierType);
                return patientIdentifierType;
        }
        
        /**
         * @see org.openmrs.api.PatientDAO#deletePatient(org.openmrs.Patient)
         */
        @Override
        public void deletePatient(Patient patient) throws DAOException {
                HibernatePersonDAO.deletePersonAndAttributes(sessionFactory, patient);
        }
        
        /**
         * @see org.openmrs.api.PatientService#getPatientIdentifierType(java.lang.Integer)
         */
        @Override
        public PatientIdentifierType getPatientIdentifierType(Integer patientIdentifierTypeId) throws DAOException {
                return (PatientIdentifierType) sessionFactory.getCurrentSession().get(PatientIdentifierType.class,
                    patientIdentifierTypeId);
        }
        
        /**
         * <strong>Should</strong> not return null when includeRetired is false
         * <strong>Should</strong> not return retired when includeRetired is false
         * <strong>Should</strong> not return null when includeRetired is true
         * <strong>Should</strong> return all when includeRetired is true
         * <strong>Should</strong> return ordered
         * @see org.openmrs.api.db.PatientDAO#getAllPatientIdentifierTypes(boolean)
         */
        @SuppressWarnings("unchecked")
        @Override
        public List<PatientIdentifierType> getAllPatientIdentifierTypes(boolean includeRetired) throws DAOException {
                Criteria criteria = sessionFactory.getCurrentSession().createCriteria(PatientIdentifierType.class);
                
                if (!includeRetired) {
                        criteria.add(Restrictions.eq("retired", false));
                } else {
                        //retired last
                        criteria.addOrder(Order.asc("retired"));
                }
                
                //required first
                criteria.addOrder(Order.desc("required"));
                criteria.addOrder(Order.asc("name"));
                criteria.addOrder(Order.asc("patientIdentifierTypeId"));
                
                return criteria.list();
        }
        
        /**
         * @see org.openmrs.api.db.PatientDAO#getPatientIdentifierTypes(java.lang.String,
         *      java.lang.String, java.lang.Boolean, java.lang.Boolean)
         *
         * <strong>Should</strong> return non retired patient identifier types with given name
         * <strong>Should</strong> return non retired patient identifier types with given format
         * <strong>Should</strong> return non retired patient identifier types that are not required
         * <strong>Should</strong> return non retired patient identifier types that are required
         * <strong>Should</strong> return non retired patient identifier types that has checkDigit
         * <strong>Should</strong> return non retired patient identifier types that has not CheckDigit
         * <strong>Should</strong> return only non retired patient identifier types
         * <strong>Should</strong> return non retired patient identifier types ordered by required first
         * <strong>Should</strong> return non retired patient identifier types ordered by required and name
         * <strong>Should</strong> return non retired patient identifier types ordered by required name and type id
         *
         */
        @SuppressWarnings("unchecked")
        @Override
        public List<PatientIdentifierType> getPatientIdentifierTypes(String name, String format, Boolean required,
                Boolean hasCheckDigit) throws DAOException {
                
                Criteria criteria = sessionFactory.getCurrentSession().createCriteria(PatientIdentifierType.class);
                
                if (name != null) {
                        criteria.add(Restrictions.eq("name", name));
                }
                
                if (format != null) {
                        criteria.add(Restrictions.eq("format", format));
                }
                
                if (required != null) {
                        criteria.add(Restrictions.eq("required", required));
                }
                
                if (hasCheckDigit != null) {
                        criteria.add(Restrictions.eq("checkDigit", hasCheckDigit));
                }
                
                criteria.add(Restrictions.eq("retired", false));
                
                //required first
                criteria.addOrder(Order.desc("required"));
                criteria.addOrder(Order.asc("name"));
                criteria.addOrder(Order.asc("patientIdentifierTypeId"));
                
                return criteria.list();
        }
        
        /**
     * @param attributes attributes on a Person or Patient object. similar to: [gender, givenName,
     *                   middleName, familyName]
     * @return           list of patients that match other patients
         * @see org.openmrs.api.db.PatientDAO#getDuplicatePatientsByAttributes(java.util.List)
         */
        @SuppressWarnings("unchecked")
        @Override
        public List<Patient> getDuplicatePatientsByAttributes(List<String> attributes) {
                List<Patient> patients = new ArrayList<>();
                List<Integer> patientIds = new ArrayList<>();

                if (!attributes.isEmpty()) {

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

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

                sortDuplicatePatients(patients, patientIds);
                return patients;
        }

        private String getDuplicatePatientsSQLString(List<String> attributes) {
                StringBuilder outerSelect = new StringBuilder("select distinct t1.patient_id from patient t1 ");
                final String t5 = " = t5.";
                Set<String> patientFieldNames = OpenmrsUtil.getDeclaredFields(Patient.class);
                Set<String> personFieldNames = OpenmrsUtil.getDeclaredFields(Person.class);
                Set<String> personNameFieldNames = OpenmrsUtil.getDeclaredFields(PersonName.class);
                Set<String> identifierFieldNames = OpenmrsUtil.getDeclaredFields(PatientIdentifier.class);

                List<String> whereConditions = new ArrayList<>();


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

                for (String attribute : attributes) {
                        if (attribute != null) {
                                attribute = attribute.trim();
                        }
                        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)) {
                                // check if outerSelect contains 'person' word, surrounded by spaces.
                                // otherwise it will wrongly match for example: 'person_name' etc.
                                if (!Arrays.asList(outerSelect.toString().split("\\s+")).contains("person")) {
                                        outerSelect.append("inner join person t2 on t1.patient_id = t2.person_id ");
                                        innerSelect.append("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];
                                        }
                                }

                                whereConditions.add(" t2." + attribute + t5 + attribute);
                                innerFields.add("person1." + attribute);
                        } else if (personNameFieldNames.contains(attribute)) {
                                if (!outerSelect.toString().contains("person_name")) {
                                        outerSelect.append("inner join person_name t3 on t1.patient_id = t3.person_id ");
                                        innerSelect.append("inner join person_name pn1 on p1.patient_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];
                                        }
                                }

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

                                whereConditions.add(" t4." + attribute + t5 + attribute);
                                innerFields.add("pi1." + attribute);
                        } else {
                                log.warn("Unidentified attribute: " + attribute);
                        }
                }
                if(CollectionUtils.isNotEmpty(innerFields) || CollectionUtils.isNotEmpty(whereConditions)) {
                        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<>();
                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);
                        }
                }
                patients.sort(new PatientIdComparator(patientIdOrder));
        }
        
        /**
         * @see org.openmrs.api.db.PatientDAO#getPatientByUuid(java.lang.String)
         */
        @Override
        public Patient getPatientByUuid(String uuid) {
                Patient p;
                
                p = (Patient) sessionFactory.getCurrentSession().createQuery("from Patient p where p.uuid = :uuid").setString(
                    "uuid", uuid).uniqueResult();
                
                return p;
        }
        
        @Override
        public PatientIdentifier getPatientIdentifierByUuid(String uuid) {
                return (PatientIdentifier) sessionFactory.getCurrentSession().createQuery(
                    "from PatientIdentifier p where p.uuid = :uuid").setString("uuid", uuid).uniqueResult();
        }
        
        /**
         * @see org.openmrs.api.db.PatientDAO#getPatientIdentifierTypeByUuid(java.lang.String)
         */
        @Override
        public PatientIdentifierType getPatientIdentifierTypeByUuid(String uuid) {
                return (PatientIdentifierType) sessionFactory.getCurrentSession().createQuery(
                    "from PatientIdentifierType pit where pit.uuid = :uuid").setString("uuid", uuid).uniqueResult();
        }
        
        /**
         * This method uses a SQL query and does not load anything into the hibernate session. It exists
         * because of ticket #1375.
         *
         * @see org.openmrs.api.db.PatientDAO#isIdentifierInUseByAnotherPatient(org.openmrs.PatientIdentifier)
         */
        @Override
        public boolean isIdentifierInUseByAnotherPatient(PatientIdentifier patientIdentifier) {
                boolean checkPatient = patientIdentifier.getPatient() != null
                        && patientIdentifier.getPatient().getPatientId() != null;
                boolean checkLocation = patientIdentifier.getLocation() != null
                        && patientIdentifier.getIdentifierType().getUniquenessBehavior() == UniquenessBehavior.LOCATION;
                
                // switched this to an hql query so the hibernate cache can be considered as well as the database
                String hql = "select count(*) from PatientIdentifier pi, Patient p where pi.patient.patientId = p.patientId "
                        + "and p.voided = false and pi.voided = false and pi.identifier = :identifier and pi.identifierType = :idType";
                
                if (checkPatient) {
                        hql += " and p.patientId != :ptId";
                }
                if (checkLocation) {
                        hql += " and pi.location = :locationId";
                }
                
                Query query = sessionFactory.getCurrentSession().createQuery(hql);
                query.setString("identifier", patientIdentifier.getIdentifier());
                query.setInteger("idType", patientIdentifier.getIdentifierType().getPatientIdentifierTypeId());
                if (checkPatient) {
                        query.setInteger("ptId", patientIdentifier.getPatient().getPatientId());
                }
                if (checkLocation) {
                        query.setInteger("locationId", patientIdentifier.getLocation().getLocationId());
                }
                return !"0".equals(query.uniqueResult().toString());
        }
        
        /**
     * @param patientIdentifierId  the patientIdentifier id
     * @return                     the patientIdentifier matching the Id
         * @see org.openmrs.api.db.PatientDAO#getPatientIdentifier(java.lang.Integer)
         */
        @Override
        public PatientIdentifier getPatientIdentifier(Integer patientIdentifierId) throws DAOException {
                
                return (PatientIdentifier) sessionFactory.getCurrentSession().get(PatientIdentifier.class, patientIdentifierId);
                
        }
        
        /**
     * @param patientIdentifier patientIndentifier to be created or updated
     * @return                  patientIndentifier that was created or updated
         * @see org.openmrs.api.db.PatientDAO#savePatientIdentifier(org.openmrs.PatientIdentifier)
         */
        @Override
        public PatientIdentifier savePatientIdentifier(PatientIdentifier patientIdentifier) {
                
                sessionFactory.getCurrentSession().saveOrUpdate(patientIdentifier);
                return patientIdentifier;
                
        }
        
        /**
         * @see org.openmrs.api.PatientService#purgePatientIdentifier(org.openmrs.PatientIdentifier)
         * @see org.openmrs.api.db.PatientDAO#deletePatientIdentifier(org.openmrs.PatientIdentifier)
         */
        @Override
        public void deletePatientIdentifier(PatientIdentifier patientIdentifier) throws DAOException {
                
                sessionFactory.getCurrentSession().delete(patientIdentifier);
                
        }
        
        /**
         * @param query  the string to search on
         * @return       the number of patients matching the given search phrase
         * @see org.openmrs.api.db.PatientDAO#getCountOfPatients(String)
         */
        @Override
        public Long getCountOfPatients(String query) {
                return getCountOfPatients(query, false);
        }
        
        /**
         * @param query          the string to search on
         * @param includeVoided  true/false whether or not to included voided patients
         * @return               the number of patients matching the given search phrase
         * @see org.openmrs.api.db.PatientDAO#getCountOfPatients(String, boolean)
         */
        @Override
        public Long getCountOfPatients(String query, boolean includeVoided) {
                if (StringUtils.isBlank(query)) {
                        return 0L;
                }

                PersonQuery personQuery = new PersonQuery();

                return SearchQueryUnique.searchCount(searchSessionFactory,
                        SearchQueryUnique.newQuery(PatientIdentifier.class, f ->
                                        newPatientIdentifierSearchPredicate(f, query, includeVoided, false),
                                 "patient.personId", PatientIdentifier::getPatient).join(
                                         SearchQueryUnique.newQuery(PersonName.class, f ->
                                                personQuery.getPatientNameQuery(f, query, includeVoided),
                                         "person.personId", pN -> getPatient(pN.getPerson().getId())).join(
                                                 SearchQueryUnique.newQuery(PersonAttribute.class,
                                                f -> personQuery.getPatientAttributeQuery(f, query, includeVoided),
                                                 "person.personId", pA -> getPatient(pA.getPerson().getId())
                                        ))));
        }

    private List<Patient> findPatients(String query, boolean includeVoided) {
                return findPatients(query, includeVoided, null, null);
        }
        
        private List<Patient> findPatients(String query, List<PatientIdentifierType> identifierTypes, boolean matchExactly, 
                                                                           Integer start, Integer length) {
                Integer tmpStart = start;
                
                if (tmpStart == null) {
                        tmpStart = 0;
                }
                Integer maxLength = HibernatePersonDAO.getMaximumSearchResults();
                Integer tmpLength = length;
                if (tmpLength == null || tmpLength > maxLength) {
                        tmpLength = maxLength;
                }
                List<Patient> patients = new LinkedList<>();
                
                String minChars = Context.getAdministrationService().getGlobalProperty(OpenmrsConstants.GLOBAL_PROPERTY_MIN_SEARCH_CHARACTERS);
                
                if (!StringUtils.isNumeric(minChars)) {
                        minChars = "" + OpenmrsConstants.GLOBAL_PROPERTY_DEFAULT_MIN_SEARCH_CHARACTERS;
                }
                if (query.length() < Integer.parseInt(minChars)) {
                        return patients;
                }
                
                return SearchQueryUnique.search(searchSessionFactory, SearchQueryUnique.newQuery(PatientIdentifier.class, 
                        f -> f.bool().with(b -> {
                        b.must(getPatientIdentifierSearchPredicate(f, query, matchExactly));
                        List<Integer> identifierTypeIds = new ArrayList<Integer>();
                        for(PatientIdentifierType identifierType : identifierTypes) {
                                identifierTypeIds.add(identifierType.getId());
                        }
                        b.filter(f.terms().field("identifierType.patientIdentifierTypeId").matchingAny(identifierTypeIds));
                        b.filter(f.match().field("patient.isPatient").matching(true));
                }).toPredicate(), "patient.personId", PatientIdentifier::getPatient), tmpStart, tmpLength);
        }
        
        public List<Patient> findPatients(String query, boolean includeVoided, Integer start, Integer length) {
                Integer tmpStart = start;
                if (tmpStart == null) {
                        tmpStart = 0;
                }
                Integer maxLength = HibernatePersonDAO.getMaximumSearchResults();
                Integer tmpLength = length;
                if (tmpLength == null || tmpLength > maxLength) {
                        tmpLength = maxLength;
                }

                List<Patient> patients = new LinkedList<>();

                String minChars = Context.getAdministrationService().getGlobalProperty(
                        OpenmrsConstants.GLOBAL_PROPERTY_MIN_SEARCH_CHARACTERS);

                if (!StringUtils.isNumeric(minChars)) {
                        minChars = "" + OpenmrsConstants.GLOBAL_PROPERTY_DEFAULT_MIN_SEARCH_CHARACTERS;
                }
                if (query.length() < Integer.parseInt(minChars)) {
                        return patients;
                }

                PersonQuery personQuery = new PersonQuery();

                patients = SearchQueryUnique.search(searchSessionFactory,
                        SearchQueryUnique.newQuery(PatientIdentifier.class, f -> 
                                        newPatientIdentifierSearchPredicate(f, query, includeVoided, false), 
                                 "patient.personId", PatientIdentifier::getPatient).join(
                                         SearchQueryUnique.newQuery(PersonName.class, f -> 
                                        personQuery.getPatientNameQuery(f, query, includeVoided),
                                         "person.personId", pN -> getPatient(pN.getPerson().getId())).join(
                                                 SearchQueryUnique.newQuery(PersonAttribute.class,
                                                f -> personQuery.getPatientAttributeQuery(f, query, includeVoided), 
                                                "person.personId", pA -> getPatient(pA.getPerson().getId())
                                                ))), start, length);

                return patients;
        }
        
        private SearchPredicate getPatientIdentifierSearchPredicate(SearchPredicateFactory f, String paramQuery, boolean matchExactly) {
                List<String> tokens = tokenizeIdentifierQuery(removeIdentifierPadding(paramQuery));
                final String query = StringUtils.join(tokens, " | ");
                //TODO: hibernate search identifierType?
                //fields.add("identifierType");
                return f.bool().with(b -> {
                        b.minimumShouldMatchNumber(1);
                        b.should(f.simpleQueryString().field("identifierPhrase").matching(query).boost(8f));
                        String matchMode = Context.getAdministrationService()
                                .getGlobalProperty(OpenmrsConstants.GLOBAL_PROPERTY_PATIENT_IDENTIFIER_SEARCH_MATCH_MODE);
                        if (matchExactly) {
                                b.should(f.simpleQueryString().field("identifierExact").matching(query).boost(4f));
                        }
                        else if (OpenmrsConstants.GLOBAL_PROPERTY_PATIENT_SEARCH_MATCH_START.equals(matchMode)) {
                                b.should(f.simpleQueryString().field("identifierStart").matching(query).boost(2f));
                        }
                        else  {
                                b.should(f.simpleQueryString().field("identifierAnywhere").matching(query));
                        }
                }).toPredicate();
        
        }

        private SearchPredicate newPatientIdentifierSearchPredicate(SearchPredicateFactory predicateFactory, String query, boolean includeVoided, boolean matchExactly) {
                return predicateFactory.bool().with(b -> {
                        b.must(getPatientIdentifierSearchPredicate(predicateFactory, query, matchExactly));

                        if (!includeVoided) {
                                b.filter(predicateFactory.match().field("voided").matching(false));
                                b.filter(predicateFactory.match().field("patient.voided").matching(false));
                        }
                        b.filter(predicateFactory.match().field("patient.isPatient").matching(true));
                }).toPredicate();
        }

        private String removeIdentifierPadding(String query) {
                String regex = Context.getAdministrationService().getGlobalProperty(OpenmrsConstants.GLOBAL_PROPERTY_PATIENT_IDENTIFIER_REGEX, "");
                if (Pattern.matches("^\\^.{1}\\*.*$", regex)) {
                        String padding = regex.substring(regex.indexOf("^") + 1, regex.indexOf("*"));
                        Pattern pattern = Pattern.compile("^" + padding + "+");
                        query = pattern.matcher(query).replaceFirst("");
                }
                return query;
        }

        /**
         * Copied over from PatientSearchCriteria...
         *
         * I have no idea how it is supposed to work, but tests pass...
         *
         * @param query
         * @return
         * @see PatientSearchCriteria
         */
        private List<String> tokenizeIdentifierQuery(String query) {
                List<String> searchPatterns = new ArrayList<>();

                String patternSearch = Context.getAdministrationService().getGlobalProperty(
                                OpenmrsConstants.GLOBAL_PROPERTY_PATIENT_IDENTIFIER_SEARCH_PATTERN, "");

                if (StringUtils.isBlank(patternSearch)) {
                        searchPatterns.add(query);
                } else {
                        // split the pattern before replacing in case the user searched on a comma
                        // replace the @SEARCH@, etc in all elements
                        for (String pattern : patternSearch.split(",")) {
                                searchPatterns.add(replaceSearchString(pattern, query));
                        }
                }
                return searchPatterns;
        }

        /**
         * Copied over from PatientSearchCriteria...
         *
         * I have no idea how it is supposed to work, but tests pass...
         *
         * Puts @SEARCH@, @SEARCH-1@, and @CHECKDIGIT@ into the search string
         *
         * @param regex the admin-defined search string containing the @..@'s to be replaced
         * @param identifierSearched the user entered search string
         * @return substituted search strings.
         *
         * @see PatientSearchCriteria#replaceSearchString(String, String)
         */
        private String replaceSearchString(String regex, String identifierSearched) {
                String returnString = regex.replaceAll("@SEARCH@", identifierSearched);
                if (identifierSearched.length() > 1) {
                        // for 2 or more character searches, we allow regex to use last character as check digit
                        returnString = returnString.replaceAll("@SEARCH-1@", identifierSearched.substring(0,
                                        identifierSearched.length() - 1));
                        returnString = returnString.replaceAll("@CHECKDIGIT@", identifierSearched
                                        .substring(identifierSearched.length() - 1));
                } else {
                        returnString = returnString.replaceAll("@SEARCH-1@", "");
                        returnString = returnString.replaceAll("@CHECKDIGIT@", "");
                }
                return returnString;
        }

    /**
         * @see org.openmrs..api.db.PatientDAO#getAllergies(org.openmrs.Patient)
         */
        //@Override
        @Override
        public List<Allergy> getAllergies(Patient patient) {
                Criteria criteria = sessionFactory.getCurrentSession().createCriteria(Allergy.class);
                criteria.add(Restrictions.eq("patient", patient));
                criteria.add(Restrictions.eq("voided", false));
                return criteria.list();
        }
        
        /**
         * @see org.openmrs.api.db.PatientDAO#getAllergyStatus(org.openmrs.Patient)
         */
        //@Override
        @Override
        public String getAllergyStatus(Patient patient) {

                return (String) sessionFactory.getCurrentSession().createSQLQuery(
                            "select allergy_status from patient where patient_id = :patientId").setInteger("patientId", patient.getPatientId()).uniqueResult();
        }
        
        /**
         * @see org.openmrs.api.db.PatientDAO#saveAllergies(org.openmrs.Patient,
         *      org.openmrsallergyapi.Allergies)
         */
        @Override
        public Allergies saveAllergies(Patient patient, Allergies allergies) {

                sessionFactory.getCurrentSession().createSQLQuery(
                            "update patient set allergy_status = :allergyStatus where patient_id = :patientId")
                            .setInteger("patientId", patient.getPatientId())
                            .setString("allergyStatus", allergies.getAllergyStatus())
                            .executeUpdate();
                
                for (Allergy allergy : allergies) {
                        sessionFactory.getCurrentSession().save(allergy);
                }
                        
                return allergies;
        }
        
        /**
         * @see org.openmrs.PatientDAO#getAllergy(Integer)
         */
        @Override
        public Allergy getAllergy(Integer allergyId) {
                return (Allergy) sessionFactory.getCurrentSession().createQuery("from Allergy a where a.allergyId = :allergyId")
                                .setInteger("allergyId", allergyId).uniqueResult();
        }
        
        /**
         * @see org.openmrs.PatientDAO#getAllergyByUuid(String)
         */
        @Override
        public Allergy getAllergyByUuid(String uuid) {
                return (Allergy) sessionFactory.getCurrentSession().createQuery("from Allergy a where a.uuid = :uuid")
                                .setString("uuid", uuid).uniqueResult();
        }

        /**
     * @see org.openmrs.api.db.PatientDAO#saveAllergy(org.openmrs.Allergy)
     */
    @Override
    public Allergy saveAllergy(Allergy allergy) {
            sessionFactory.getCurrentSession().save(allergy);
            return allergy;
    }


    /**
     * @see org.openmrs.api.db.PatientDAO#getPatientIdentifierByProgram(org.openmrs.PatientProgram)
     */
    public List<PatientIdentifier> getPatientIdentifierByProgram(PatientProgram patientProgram) {

        Criteria criteria = sessionFactory.getCurrentSession().createCriteria(PatientIdentifier.class);
        criteria.add(Restrictions.eq("patientProgram", patientProgram));
        return criteria.list();
    }
}

openmrs / openmrs-core / 14752386992

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