GSoC 2019: Patient search criteria added in openmrs core

.travis.yml

@@ -1,9 +1,9 @@
 language: java
 jdk:
- - oraclejdk8
+ - openjdk8
 script: mvn clean install --batch-mode
 matrix:
-    - jdk: oraclejdk8
+    - jdk: openjdk8
 branches:
   only:
     - master

api/pom.xml

@@ -209,6 +209,11 @@
 			<groupId>org.hibernate</groupId>
 			<artifactId>hibernate-validator</artifactId>
 	   </dependency>
+	   <dependency>
+			<groupId>mysql</groupId>
+			<artifactId>mysql-connector-java</artifactId>
+			<scope>test</scope>
+		</dependency>
        <dependency>
            <groupId>org.codehaus.jackson</groupId>
            <artifactId>jackson-core-asl</artifactId>
@@ -239,6 +244,14 @@
 		   <groupId>net.sf.ehcache</groupId>
 		   <artifactId>ehcache</artifactId>
        </dependency>
+	   <dependency>
+		   <groupId>org.aspectj</groupId>
+		   <artifactId>aspectjrt</artifactId>
+	   </dependency>
+	   <dependency>
+		   <groupId>org.aspectj</groupId>
+		   <artifactId>aspectjweaver</artifactId>
+	   </dependency>
    </dependencies>
    <build>
      <resources>

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

@@ -43,6 +43,8 @@ public class Drug extends BaseChangeableOpenmrsMetadata {
 
 	private String strength;
 
+	private Concept doseLimitUnits;
+
 	@IndexedEmbedded(includeEmbeddedObjectId = true)
 	private Concept concept;
 
@@ -276,4 +278,26 @@ public void addDrugReferenceMap(DrugReferenceMap drugReferenceMap) {
 			getDrugReferenceMaps().add(drugReferenceMap);
 		}
 	}
+
+	/**
+	 * Gets the doseLimitUnits which represents the units of the existing maximumDailyDose and
+	 * minimumDailyDose
+	 * 
+	 * @param Returns the doseLimitUnits.
+	 * @since 2.3.0
+	 */
+	public Concept getDoseLimitUnits() {
+		return doseLimitUnits;
+	}
+
+	/**
+	 * Sets the doseLimitUnits which represents the units of the existing maximumDailyDose and
+	 * minimumDailyDose
+	 * 
+	 * @param doseLimitUnits The doseLimitUnits to set.
+	 * @since 2.3.0
+	 */
+	public void setDoseLimitUnits(Concept doseLimitUnits) {
+		this.doseLimitUnits = doseLimitUnits;
+	}
 }

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

@@ -0,0 +1,43 @@
+/**
+ * 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;
+
+import org.hibernate.Session;
+import org.hibernate.SessionFactory;
+import org.hibernate.search.FullTextSession;
+import org.hibernate.search.Search;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Component;
+
+/**
+ * An instance of this class provides a factory for obtaining {@link FullTextSession} instances.
+ * Having this factory as a spring bean provides a mechanism that allows external code and modules
+ * to advise the factory. It is highly recommended to use this factory to create instances of the
+ * {@link FullTextSession} rather than directly calling {@link Search#getFullTextSession(Session)}
+ * for proper functionality.
+ * 
+ * @since 2.2.1
+ */
+@Component("fullTextSessionFactory")
+public class FullTextSessionFactory {
+
+	@Autowired
+	private SessionFactory sessionFactory;
+
+	/**
+	 * Obtains a {@link FullTextSession} instance.
+	 * 
+	 * @return {@link FullTextSession} object
+	 */
+	public FullTextSession getFullTextSession() {
+		return Search.getFullTextSession(sessionFactory.getCurrentSession());
+	}
+
+}

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

@@ -20,7 +20,28 @@
 import java.util.Locale;
 import java.util.Set;
 
+import javax.persistence.Access;
+import javax.persistence.AccessType;
+import javax.persistence.AssociationOverride;
+import javax.persistence.AttributeOverride;
+import javax.persistence.Column;
+import javax.persistence.Entity;
+import javax.persistence.EnumType;
+import javax.persistence.Enumerated;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.JoinColumn;
+import javax.persistence.ManyToOne;
+import javax.persistence.OneToMany;
+import javax.persistence.OrderBy;
+import javax.persistence.SecondaryTable;
+import javax.persistence.Table;
+
 import org.apache.commons.lang3.StringUtils;
+import org.hibernate.annotations.BatchSize;
+import org.hibernate.annotations.Cascade;
+import org.hibernate.annotations.CascadeType;
 import org.openmrs.annotation.AllowDirectAccess;
 import org.openmrs.api.APIException;
 import org.openmrs.api.context.Context;
@@ -61,6 +82,12 @@
  * 
  * @see Encounter
  */
+@Entity
+@Table(name = "obs")
+@BatchSize(size = 25)
+@SecondaryTable(name = "obs_unused_fields")
+@AssociationOverride(name = "changedBy", joinColumns = @JoinColumn(table = "obs_unused_fields", name = "changed_by"))
+@AttributeOverride(name = "dateChanged", column = @Column(table = "obs_unused_fields", name = "date_changed"))
 public class Obs extends BaseChangeableOpenmrsData {
 
 	/**
@@ -91,12 +118,19 @@ public enum Status {
 
 	private static final int FORM_NAMESPACE_PATH_MAX_LENGTH = 255;
 
+	@Id
+	@GeneratedValue(strategy = GenerationType.AUTO)
+	@Column(name = "obs_id")
 	protected Integer obsId;
 
+	@JoinColumn(name = "concept_id")
+	@ManyToOne(optional = false)
 	protected Concept concept;
 
+	@Column(name = "obs_datetime", nullable = false, length = 19)
 	protected Date obsDatetime;
 
+	@Column(name = "accession_number")
 	protected String accessionNumber;
 
 	/**
@@ -106,55 +140,92 @@ public enum Status {
 	 * 
 	 * @see #isObsGrouping() (??)
 	 */
+	@JoinColumn(name = "obs_group_id")
+	@ManyToOne
 	protected Obs obsGroup;
 
 	/**
 	 * The list of obs grouped under this obs.
 	 */
 	@AllowDirectAccess
+	@OneToMany(mappedBy = "obsGroup")
+	@Cascade(CascadeType.DELETE)
+	@OrderBy("obs_id")
+	@BatchSize(size = 25)
+	@Access(AccessType.FIELD)
 	protected Set<Obs> groupMembers;
 
+	@JoinColumn(name = "value_coded")
+	@ManyToOne
 	protected Concept valueCoded;
 
+	@JoinColumn(name = "value_coded_name_id")
+	@ManyToOne
 	protected ConceptName valueCodedName;
 
+	@JoinColumn(name = "value_drug")
+	@ManyToOne
 	protected Drug valueDrug;
 
+	@Column(name = "value_group_id")
 	protected Integer valueGroupId;
 
+	@Column(name = "value_datetime", length = 19)
 	protected Date valueDatetime;
 
+	@Column(name = "value_numeric", length = 22)
 	protected Double valueNumeric;
 
+	@Column(name = "value_modifier", length = 2)
 	protected String valueModifier;
 
+	@Column(name = "value_text", length = 65535)
 	protected String valueText;
 
+	@Column(name = "value_complex")
 	protected String valueComplex;
 
 	// ComplexData is not persisted in the database.
 	protected transient ComplexData complexData;
 
+	@Column(name = "comments")
 	protected String comment;
 
-	protected transient Integer personId;
+	@Column(name = "person_id", nullable = false, insertable = false, updatable = false)
+	protected Integer personId;
 
+	@JoinColumn(name = "person_id")
+	@ManyToOne(optional = false)
 	protected Person person;
 
+	@JoinColumn(name = "order_id")
+	@ManyToOne
 	protected Order order;
 
+	@JoinColumn(name = "location_id")
+	@ManyToOne
 	protected Location location;
 
+	@JoinColumn(name = "encounter_id")
+	@ManyToOne
 	protected Encounter encounter;
 
+	@JoinColumn(name = "previous_version", unique = true)
+	@ManyToOne
 	private Obs previousVersion;
 
+	@Column(name = "form_namespace_and_path")
+	@Access(AccessType.FIELD)
 	private String formNamespaceAndPath;
 
-	private Boolean dirty = Boolean.FALSE;
+	private transient Boolean dirty = Boolean.FALSE;
 
+	@Enumerated(EnumType.STRING)
+	@Column(length = 32)
 	private Interpretation interpretation;
 
+	@Enumerated(EnumType.STRING)
+	@Column(nullable = false, length = 16)
 	private Status status = Status.FINAL;
 
 	/** default constructor */

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

@@ -40,6 +40,8 @@ public enum Operator {
 
 	private List<OrderSetMember> orderSetMembers;
 
+	private Concept category;
+
 	/**
 	 * Gets the orderSetId
 	 *
@@ -96,7 +98,27 @@ public List<OrderSetMember> getOrderSetMembers() {
 	public void setOrderSetMembers(List<OrderSetMember> orderSetMembers) {
 		this.orderSetMembers = orderSetMembers;
 	}
-
+
+	/**
+	 * Gets the category
+	 *
+	 * @return the category
+	 * @since 2.3.0
+	 */
+	public Concept getCategory () {
+		return category;
+	}
+
+	/**
+	 * Sets the category
+	 *
+	 * @param category category to set
+	 * @since 2.3.0
+	 */
+	public void setCategory(Concept category) {
+		this.category = category;
+	}
+
 	/**
 	 * Adds an orderSetMember to the existing list of orderSetMembers
 	 * 

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

@@ -31,6 +31,7 @@
 import org.hibernate.annotations.SortNatural;
 import org.hibernate.search.annotations.ContainedIn;
 import org.hibernate.search.annotations.Field;
+import org.hibernate.search.annotations.Indexed;
 
 /**
  * Defines a Patient in the system. A patient is simply an extension of a person and all that that
@@ -41,6 +42,7 @@
 @Entity
 @Table(name = "patient")
 @PrimaryKeyJoinColumn(name = "patient_id")
+@Indexed
 public class Patient extends Person {
 
 	public static final long serialVersionUID = 93123L;

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

@@ -46,9 +46,14 @@
 import org.hibernate.annotations.LazyCollection;
 import org.hibernate.annotations.LazyCollectionOption;
 import org.hibernate.annotations.SortNatural;
+import org.hibernate.search.annotations.Analyze;
 import org.hibernate.search.annotations.ContainedIn;
+import org.hibernate.search.annotations.DateBridge;
 import org.hibernate.search.annotations.DocumentId;
 import org.hibernate.search.annotations.Field;
+import org.hibernate.search.annotations.Index;
+import org.hibernate.search.annotations.Indexed;
+import org.hibernate.search.annotations.Resolution;
 import org.openmrs.util.OpenmrsUtil;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -65,6 +70,7 @@
 @Entity
 @Table(name = "person")
 @Inheritance(strategy = InheritanceType.JOINED)
+@Indexed
 public class Person extends BaseChangeableOpenmrsData {
 
 	public static final long serialVersionUID = 2L;
@@ -102,10 +108,12 @@ public class Person extends BaseChangeableOpenmrsData {
 	@ContainedIn
 	private Set<PersonAttribute> attributes = null;
 
-	@Field
+	@Field(name="gender",index=Index.YES, analyze=Analyze.YES)
 	@Column(length = 50)
 	private String gender;
 
+	@Field(name="birthdate",index=Index.YES, analyze=Analyze.YES)
+	@DateBridge(resolution = Resolution.MILLISECOND)
 	@Column(name = "birthdate", length = 10)
 	private Date birthdate;
 

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

@@ -19,6 +19,7 @@
 import org.hibernate.EmptyInterceptor;
 import org.hibernate.type.Type;
 import org.openmrs.Auditable;
+import org.openmrs.Obs;
 import org.openmrs.OpenmrsObject;
 import org.openmrs.api.context.Context;
 import org.slf4j.Logger;
@@ -83,6 +84,10 @@ public boolean onFlushDirty(Object entity, Serializable id, Object[] currentStat
 			}
 
 			Map<String, Object> propertyValues = getPropertyValuesToUpdate();
+			if (entity instanceof Obs) {
+				propertyValues.remove("changedBy");
+				propertyValues.remove("dateChanged");
+			}
 			objectWasChanged = changeProperties(currentState, propertyNames, objectWasChanged, propertyValues, false);
 		}
 		return objectWasChanged;