TRUNK-5492 Replace Person and Patient hbm mapping file with annotatio…

…ns (#2900)

* TRUNK-5492 Replace Person hbm mapping file with annotations

TRUNK-5492 Replace Patient hbm mapping file with annotations

TRUNK-5492 Fixed failing tests

TRUNK-5492 Added special auditable fields to Patient table

TRUNK-5492 Updated Auditable interceptor to set patient auditable fields instead of PatientSaveHandler

TRUNK-5492 Renamed properties back to their original names

TRUNK-5492 Removed unused code

TRUNK-5492 Removed unused code

TRUNK-5492 Removed changes in BaseOpenmrsData

TRUNK-5492 Removed changes in PersonServiceTest

TRUNK-5492 Removed explicit lazy loading from JPA mappings

TRUNK-5492 Removed more explicit lazy loading from JPA mappings

TRUNK-5492 Replaced @sort with @SortNatural

TRUNK-5492 Removed more explicit lazy loading from JPA mappings

* TRUNK-5492 Removed unnecessary tests and updated comments on BaseContextSensitiveTest

* TRUNK-5492 Removed getter/setter overrides and changed access type to property

api/src/main/java/org/openmrs/Patient.java

@@ -11,30 +11,87 @@
 
 import java.util.ArrayList;
 import java.util.Collection;
+import java.util.Date;
 import java.util.LinkedList;
 import java.util.List;
 import java.util.Set;
 import java.util.TreeSet;
 
+import javax.persistence.Access;
+import javax.persistence.AccessType;
+import javax.persistence.CascadeType;
+import javax.persistence.Column;
+import javax.persistence.Entity;
+import javax.persistence.JoinColumn;
+import javax.persistence.ManyToOne;
+import javax.persistence.OneToMany;
+import javax.persistence.PrimaryKeyJoinColumn;
+import javax.persistence.Table;
+
+import org.hibernate.annotations.SortNatural;
 import org.hibernate.search.annotations.ContainedIn;
+import org.hibernate.search.annotations.Field;
 
 /**
  * Defines a Patient in the system. A patient is simply an extension of a person and all that that
  * implies.
  * 
  * @version 2.0
  */
+@Entity
+@Table(name = "patient")
+@PrimaryKeyJoinColumn(name = "patient_id")
 public class Patient extends Person {
 
 	public static final long serialVersionUID = 93123L;
 
+	@Column(name = "patient_id", nullable = false, updatable = false, insertable = false)
 	private Integer patientId;
 
+	@Column(name = "allergy_status", length = 50)
 	private String allergyStatus = Allergies.UNKNOWN;
 
+	@OneToMany(mappedBy = "patient", cascade = CascadeType.ALL, orphanRemoval = true)
+	@SortNatural
 	@ContainedIn
 	private Set<PatientIdentifier> identifiers;
 
+	@ManyToOne
+	@JoinColumn(name = "creator", updatable = false)
+	@Access(AccessType.PROPERTY)
+	private User creator;
+
+	@Column(name = "date_created", nullable = false, updatable = false, length = 19)
+	@Access(AccessType.PROPERTY)
+	private Date dateCreated;
+
+	@Column(name = "voided", nullable = false)
+	@Access(AccessType.PROPERTY)
+	@Field
+	private Boolean voided = Boolean.FALSE;
+
+	@Column(name = "date_voided", length = 19)
+	@Access(AccessType.PROPERTY)
+	private Date dateVoided;
+
+	@ManyToOne
+	@JoinColumn(name = "voided_by")
+	@Access(AccessType.PROPERTY)
+	private User voidedBy;
+
+	@Column(name = "void_reason")
+	@Access(AccessType.PROPERTY)
+	private String voidReason;
+
+	@ManyToOne
+	@JoinColumn(name = "changed_by")
+	@Access(AccessType.PROPERTY)
+	private User changedBy;
+
+	@Column(name = "date_changed", length = 19)
+	@Access(AccessType.PROPERTY)
+	private Date dateChanged;
+
 	// Constructors
 
 	/** default constructor */
@@ -99,6 +156,9 @@ public Patient(Patient patient) {
 	 * @return internal identifier for patient
 	 */
 	public Integer getPatientId() {
+		if (this.patientId == null) {
+			this.patientId = getPersonId();
+		}
 		return this.patientId;
 	}
 
@@ -400,4 +460,5 @@ public void setId(Integer id) {
 	public Person getPerson() {
 		return this;
 	}
+
 }

api/src/main/java/org/openmrs/Person.java

@@ -20,7 +20,32 @@
 import java.util.Set;
 import java.util.TreeSet;
 
+import javax.persistence.Basic;
+import javax.persistence.CascadeType;
+import javax.persistence.Column;
+import javax.persistence.Entity;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.Inheritance;
+import javax.persistence.InheritanceType;
+import javax.persistence.JoinColumn;
+import javax.persistence.ManyToOne;
+import javax.persistence.OneToMany;
+import javax.persistence.OrderBy;
+import javax.persistence.Table;
+import javax.persistence.Temporal;
+import javax.persistence.TemporalType;
+import javax.persistence.Transient;
+
 import org.codehaus.jackson.annotate.JsonIgnore;
+import org.hibernate.annotations.BatchSize;
+import org.hibernate.annotations.Cache;
+import org.hibernate.annotations.CacheConcurrencyStrategy;
+import org.hibernate.annotations.Formula;
+import org.hibernate.annotations.LazyCollection;
+import org.hibernate.annotations.LazyCollectionOption;
+import org.hibernate.annotations.SortNatural;
 import org.hibernate.search.annotations.ContainedIn;
 import org.hibernate.search.annotations.DocumentId;
 import org.hibernate.search.annotations.Field;
@@ -37,60 +62,106 @@
  * 
  * @see org.openmrs.Patient
  */
+@Entity
+@Table(name = "person")
+@Inheritance(strategy = InheritanceType.JOINED)
 public class Person extends BaseChangeableOpenmrsData {
 
 	public static final long serialVersionUID = 2L;
 
 	private static final Logger log = LoggerFactory.getLogger(Person.class);
 
+	@Id
+	@GeneratedValue(strategy = GenerationType.AUTO)
+	@Column(name = "person_id")
 	@DocumentId
 	protected Integer personId;
 
+	@OneToMany(mappedBy = "person", cascade = CascadeType.ALL, orphanRemoval = true)
+	@LazyCollection(LazyCollectionOption.FALSE)
+	@SortNatural
+	@OrderBy("voided asc, preferred desc, date_created desc")
+	@Cache(usage = CacheConcurrencyStrategy.READ_WRITE)
+	@BatchSize(size = 1000)
 	private Set<PersonAddress> addresses = null;
 
+	@OneToMany(mappedBy = "person", cascade = CascadeType.ALL, orphanRemoval = true)
+	@LazyCollection(LazyCollectionOption.FALSE)
+	@SortNatural
+	@OrderBy("voided asc, preferred desc, date_created desc")
+	@Cache(usage = CacheConcurrencyStrategy.READ_WRITE)
+	@BatchSize(size = 1000)
 	@ContainedIn
 	private Set<PersonName> names = null;
 
+	@OneToMany(mappedBy = "person", cascade = CascadeType.ALL, orphanRemoval = true)
+	@LazyCollection(LazyCollectionOption.FALSE)
+	@SortNatural
+	@Cache(usage = CacheConcurrencyStrategy.READ_WRITE)
+	@BatchSize(size = 1000)
 	@ContainedIn
 	private Set<PersonAttribute> attributes = null;
 
 	@Field
+	@Column(length = 50)
 	private String gender;
 
+	@Column(name = "birthdate", length = 10)
 	private Date birthdate;
 
+	@Basic
+	@Temporal(TemporalType.TIME)
 	private Date birthtime;
 
+	@Column(name = "birthdate_estimated")
 	private Boolean birthdateEstimated = false;
 
+	@Column(name = "deathdate_estimated")
 	private Boolean deathdateEstimated = false;
 
 	@Field
+	@Column(nullable = false)
 	private Boolean dead = false;
 
+	@Column(name = "death_date", length = 19)
 	private Date deathDate;
 
+	@ManyToOne
+	@JoinColumn(name = "cause_of_death")
 	private Concept causeOfDeath;
 
+	@Column(name = "cause_of_death_non_coded")
 	private String causeOfDeathNonCoded;
 
+	@ManyToOne
+	@JoinColumn(name = "creator", updatable = false, insertable = false)
 	private User personCreator;
 
+	@Column(name = "date_created", updatable = false, insertable = false, nullable = false, length = 19)
 	private Date personDateCreated;
 
+	@ManyToOne
+	@JoinColumn(name = "changed_by", updatable = false, insertable = false)
 	private User personChangedBy;
 
+	@Column(name = "date_changed", updatable = false, insertable = false, length = 19)
 	private Date personDateChanged;
 
+	@Column(name = "voided", updatable = false, insertable = false, nullable = false)
 	private Boolean personVoided = false;
 
+	@ManyToOne
+	@JoinColumn(name = "voided_by", updatable = false, insertable = false)
 	private User personVoidedBy;
 
+	@Column(name = "date_voided", updatable = false, insertable = false, length = 19)
 	private Date personDateVoided;
 
+	@Column(name = "void_reason", updatable = false, insertable = false)
 	private String personVoidReason;
 
 	@Field
+	@Formula("case when exists (select * from patient p where p.patient_id = person_id) then 1 else 0 end")
 	private boolean isPatient;
 
 	/**
@@ -99,8 +170,10 @@ public class Person extends BaseChangeableOpenmrsData {
 	 * This is "cached" for each user upon first load. When an attribute is changed, the cache is
 	 * cleared and rebuilt on next access.
 	 */
+	@Transient
 	Map<String, PersonAttribute> attributeMap = null;
 
+	@Transient
 	private Map<String, PersonAttribute> allAttributeMap = null;
 
 	/**

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

@@ -608,7 +608,7 @@ public boolean isIdentifierInUseByAnotherPatient(PatientIdentifier patientIdenti
 		        && 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.patient.patientId "
+		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) {

api/src/main/java/org/openmrs/api/handler/PatientSaveHandler.java

@@ -16,6 +16,7 @@
 import org.openmrs.User;
 import org.openmrs.annotation.Handler;
 import org.openmrs.aop.RequiredDataAdvice;
+import org.openmrs.api.context.Context;
 
 /**
  * This class deals with {@link Patient} objects when they are saved via a save* method in an
@@ -45,5 +46,10 @@ public void handle(Patient patient, User creator, Date dateCreated, String other
 				}
 			}
 		}
+
+		if(patient.getPatientId() == null){
+			patient.setCreator(Context.getAuthenticatedUser());
+			patient.setDateCreated(new Date());
+		}
 	}
 }

api/src/main/java/org/openmrs/api/handler/PersonSaveHandler.java

@@ -10,7 +10,10 @@
 package org.openmrs.api.handler;
 
 import java.util.Date;
+import java.util.HashSet;
+import java.util.Set;
 
+import org.openmrs.Address;
 import org.openmrs.Person;
 import org.openmrs.PersonAddress;
 import org.openmrs.PersonAttribute;
@@ -42,13 +45,16 @@ public void handle(Person person, User creator, Date dateCreated, String other)
 
 		// address collection
 		if (person.getAddresses() != null && !person.getAddresses().isEmpty()) {
+			Set<Address> blankAddresses = new HashSet<>();
 			for (PersonAddress pAddress : person.getAddresses()) {
-				if (pAddress.isBlank()){
-					person.removeAddress(pAddress);
+				if (pAddress.isBlank()) {
+					blankAddresses.add(pAddress);
 					continue;
 				}
 				pAddress.setPerson(person);
 			}
+
+			person.getAddresses().removeAll(blankAddresses);
 		}
 
 		// name collection

api/src/main/resources/hibernate.cfg.xml

@@ -52,7 +52,6 @@
         <mapping resource="org/openmrs/api/db/hibernate/FormResource.hbm.xml" />
 		<mapping resource="org/openmrs/api/db/hibernate/GlobalProperty.hbm.xml" />
 		<mapping resource="org/openmrs/api/db/hibernate/Obs.hbm.xml" />
-		<mapping resource="org/openmrs/api/db/hibernate/Person.hbm.xml" />
 		<mapping resource="org/openmrs/api/db/hibernate/PersonAttribute.hbm.xml" />
 		<mapping resource="org/openmrs/api/db/hibernate/PersonAttributeType.hbm.xml" />
 		<mapping resource="org/openmrs/api/db/hibernate/PersonAddress.hbm.xml" />
@@ -62,7 +61,6 @@
 		<mapping resource="org/openmrs/api/db/hibernate/LoginCredential.hbm.xml" />
 		<mapping resource="org/openmrs/api/db/hibernate/Privilege.hbm.xml" />
 		<mapping resource="org/openmrs/api/db/hibernate/Role.hbm.xml" />
-		<mapping resource="org/openmrs/api/db/hibernate/Patient.hbm.xml" />
 		<mapping resource="org/openmrs/api/db/hibernate/PatientIdentifier.hbm.xml" />
 		<mapping resource="org/openmrs/api/db/hibernate/PatientIdentifierType.hbm.xml" />
                 <mapping resource="org/openmrs/api/db/hibernate/PatientProgram.hbm.xml" />