Merge pull request #2 from MortalityReporting/ig1.3

Ig1.3
nightingaleproject · Mar 15, 2022 · d1295a7 · d1295a7
2 parents a1f9101 + 3369c00
commit d1295a7
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Showing 26 changed files with 807 additions and 130 deletions.
diff --git a/.gitignore b/.gitignore
@@ -0,0 +1,2 @@
+
+target/*
diff --git a/pom.xml b/pom.xml
@@ -4,7 +4,7 @@
 
   <groupId>edu.gatech</groupId>
   <artifactId>VRDR</artifactId>
-  <version>v1.0.4-R4</version>
+  <version>v1.2.3-R4-STU1.2</version>
   <packaging>jar</packaging>
 
   <name>VRDR</name>

diff --git a/src/main/java/edu/gatech/chai/VRDR/model/BirthRecordIdentifier.java b/src/main/java/edu/gatech/chai/VRDR/model/BirthRecordIdentifier.java
@@ -3,6 +3,7 @@
 import org.hl7.fhir.r4.model.CodeableConcept;
 import org.hl7.fhir.r4.model.DateTimeType;
 import org.hl7.fhir.r4.model.Observation;
+import org.hl7.fhir.r4.model.Reference;
 import org.hl7.fhir.r4.model.StringType;
 
 import ca.uhn.fhir.model.api.annotation.ResourceDef;
@@ -17,17 +18,22 @@ public BirthRecordIdentifier() {
 		CommonUtil.initResource(this);
 	}
 
-	public BirthRecordIdentifier(String value, CodeableConcept birthState,
+	public BirthRecordIdentifier(String value, Decedent decedent, CodeableConcept birthJurisdiction,
 			DateTimeType birthYear) {
 		this();
 		setStatus(BirthRecordIdentifierUtil.status);
 		setCode(BirthRecordIdentifierUtil.code);
+		setDecedent(decedent);
 		setValue(new StringType(value));
-		addBirthState(birthState);
+		addBirthState(birthJurisdiction);
 		addBirthYear(birthYear);
 	}
 
-	public CodeableConcept getBirthState() {
+	public void setDecedent(Decedent decedent) {
+		Reference reference = new Reference(decedent);
+		this.setSubject(reference);
+	}
+	public CodeableConcept getBirthJurisdiction() {
 		for (ObservationComponentComponent component : getComponent()) {
 			if (component.getCode().equalsShallow(BirthRecordIdentifierUtil.componentBirthStateCode)) {
 				return component.getValueCodeableConcept();
@@ -36,7 +42,7 @@ public CodeableConcept getBirthState() {
 		return null;
 	}
 
-	public void setBirthState(CodeableConcept birthState) {
+	public void setBirthJurisdiction(CodeableConcept birthState) {
 		for (ObservationComponentComponent component : getComponent()) {
 			if (component.getCode().equalsShallow(BirthRecordIdentifierUtil.componentBirthStateCode)) {
 				component.setValue(birthState);
@@ -78,4 +84,9 @@ private void addBirthYear(DateTimeType birthYear) {
 		birthYearComponent.setValue(birthYear);
 		addComponent(birthYearComponent);
 	}
+
+	public BirthRecordIdentifier setDataAbsentReason(String dataAbsentReason) {
+		this.setDataAbsentReason(CommonUtil.findConceptFromCollectionUsingSimpleString(dataAbsentReason, CommonUtil.dataAbsentReasonConceptSet));
+		return this;
+	}
 }
diff --git a/src/main/java/edu/gatech/chai/VRDR/model/CauseOfDeathCondition.java b/src/main/java/edu/gatech/chai/VRDR/model/CauseOfDeathCondition.java
@@ -1,22 +1,45 @@
 package edu.gatech.chai.VRDR.model;
 
+import java.util.List;
+
+import org.hl7.fhir.r4.model.CodeableConcept;
 import org.hl7.fhir.r4.model.Condition;
+import org.hl7.fhir.r4.model.Observation;
+import org.hl7.fhir.r4.model.Quantity;
 import org.hl7.fhir.r4.model.Reference;
+import org.hl7.fhir.r4.model.StringType;
 
 import ca.uhn.fhir.model.api.annotation.ResourceDef;
+import edu.gatech.chai.VRDR.model.util.CauseOfDeathConditionUtil;
 import edu.gatech.chai.VRDR.model.util.CommonUtil;
 
-@ResourceDef(name = "Condition", profile = "http://hl7.org/fhir/us/vrdr/StructureDefinition/VRDR-Cause-Of-Death-Condition")
-public class CauseOfDeathCondition extends Condition {
+//NOTE: While the resource name is "CauseOfDeathCondition", it actually derived from Observation
+@ResourceDef(name = "Observation", profile = "http://hl7.org/fhir/us/vrdr/StructureDefinition/VRDR-Cause-Of-Death-Condition")
+public class CauseOfDeathCondition extends Observation {
 	public CauseOfDeathCondition() {
 		super();
 		CommonUtil.initResource(this);
+		this.setCode(CauseOfDeathConditionUtil.code);
+	}
+
+	public CauseOfDeathCondition(Decedent decedent, Certifier certifier, String value, Quantity interval) {
+		super();
+		CommonUtil.initResource(this);
+		this.setCode(CauseOfDeathConditionUtil.code);
+		setDecedent(decedent);
+		setPerformer(certifier);
+		setValue(value);
+		createInterval(interval);
 	}
 
-	public CauseOfDeathCondition(Decedent decedent) {
+	public CauseOfDeathCondition(Decedent decedent, Certifier certifier, String value, String interval) {
 		super();
 		CommonUtil.initResource(this);
+		this.setCode(CauseOfDeathConditionUtil.code);
 		setDecedent(decedent);
+		setPerformer(certifier);
+		setValue(value);
+		createInterval(interval);
 	}
 
 	public void setDecedent(Decedent decedent) {
@@ -34,13 +57,54 @@ public Reference getDecedent() {
 
 	public void setCertifier(Certifier certifier) {
 		Reference reference = new Reference(certifier.getId());
-		this.asserter = reference;
+		this.performer.add(reference);
 	}
 	public void setAsserter(Certifier certifier) {
 		setCertifier(certifier);
 	}
+	public void setPerformer(Certifier certifier) {
+		setCertifier(certifier);
+	}
+
+	public List<Reference> getCertifiers(int index) {
+		return performer;
+	}
+
+	public List<Reference> getAsserters(int index) {
+		return performer;
+	}
 
-	public Reference getCertifier() {
-		return asserter;
+	public List<Reference> getPerformers(int index) {
+		return performer;
 	}
+
+	public Reference getCertifier(int index) {
+		return performer.get(index);
+	}
+
+	public void setValue(StringType value) {
+		if((value.getValue().length() > 120)) {
+			throw new IllegalArgumentException("CauseOfDeathCondition value "+value.getValue()+" is too long, must be 120 characters or less.");
+		}
+		this.setValue(value);
+	}
+
+	public void setValue(String value) {
+		setValue(new StringType(value));
+	}
+
+	public void createInterval(Quantity quantity) {
+		ObservationComponentComponent component = new ObservationComponentComponent();
+		component.setCode(CauseOfDeathConditionUtil.intervalComponentCode);
+		component.setValue(quantity);
+
+	}
+
+	public void createInterval(String string) {
+		ObservationComponentComponent component = new ObservationComponentComponent();
+		component.setCode(CauseOfDeathConditionUtil.intervalComponentCode);
+		component.setValue(new StringType(string));
+
+	}
+
 }
diff --git a/src/main/java/edu/gatech/chai/VRDR/model/ConditionContributingToDeath.java b/src/main/java/edu/gatech/chai/VRDR/model/ConditionContributingToDeath.java
@@ -1,27 +1,84 @@
 package edu.gatech.chai.VRDR.model;
 
+import java.util.List;
+
 import org.hl7.fhir.r4.model.Condition;
+import org.hl7.fhir.r4.model.Observation;
+import org.hl7.fhir.r4.model.Quantity;
 import org.hl7.fhir.r4.model.Reference;
+import org.hl7.fhir.r4.model.StringType;
+import org.hl7.fhir.r4.model.Observation.ObservationComponentComponent;
 
 import ca.uhn.fhir.model.api.annotation.ResourceDef;
+import edu.gatech.chai.VRDR.model.util.CauseOfDeathConditionUtil;
 import edu.gatech.chai.VRDR.model.util.CommonUtil;
+import edu.gatech.chai.VRDR.model.util.ConditionContributingToDeathUtil;
 
-@ResourceDef(name = "Condition", profile = "http://hl7.org/fhir/us/vrdr/StructureDefinition/VRDR-Condition-Contributing-To-Death")
-public class ConditionContributingToDeath extends Condition {
+@ResourceDef(name = "Observation", profile = "http://hl7.org/fhir/us/vrdr/StructureDefinition/VRDR-Condition-Contributing-To-Death")
+public class ConditionContributingToDeath extends Observation {
 	public ConditionContributingToDeath() {
 		super();
 		CommonUtil.initResource(this);
+		this.setCode(ConditionContributingToDeathUtil.code);
+	}
+
+	public ConditionContributingToDeath(Decedent decedent, Certifier certifier, String value) {
+		super();
+		CommonUtil.initResource(this);
+		this.setCode(ConditionContributingToDeathUtil.code);
+		setDecedent(decedent);
+		setPerformer(certifier);
+		setValue(value);
+	}
+
+	public void setDecedent(Decedent decedent) {
+		Reference reference = new Reference(decedent.getId());
+		this.subject = reference;
+	}
+
+	public void setSubject(Decedent decedent) {
+		setDecedent(decedent);
+	}
+
+	public Reference getDecedent() {
+		return subject;
 	}
 
 	public void setCertifier(Certifier certifier) {
 		Reference reference = new Reference(certifier.getId());
-		this.asserter = reference;
+		this.performer.add(reference);
 	}
 	public void setAsserter(Certifier certifier) {
 		setCertifier(certifier);
 	}
+	public void setPerformer(Certifier certifier) {
+		setCertifier(certifier);
+	}
+
+	public List<Reference> getCertifiers(int index) {
+		return performer;
+	}
+
+	public List<Reference> getAsserters(int index) {
+		return performer;
+	}
+
+	public List<Reference> getPerformers(int index) {
+		return performer;
+	}
+
+	public Reference getCertifier(int index) {
+		return performer.get(index);
+	}
+
+	public void setValue(StringType value) {
+		if((value.getValue().length() > 240)) {
+			throw new IllegalArgumentException("CauseOfDeathCondition value "+value.getValue()+" is too long, must be 240 characters or less.");
+		}
+		this.setValue(value);
+	}
 
-	public Reference getCertifier() {
-		return asserter;
+	public void setValue(String value) {
+		setValue(new StringType(value));
 	}
 }
diff --git a/src/main/java/edu/gatech/chai/VRDR/model/DeathCertificateDocument.java b/src/main/java/edu/gatech/chai/VRDR/model/DeathCertificateDocument.java
@@ -5,10 +5,13 @@
 import java.util.stream.Collectors;
 
 import org.hl7.fhir.r4.model.Bundle;
+import org.hl7.fhir.r4.model.Extension;
 import org.hl7.fhir.r4.model.Resource;
+import org.hl7.fhir.r4.model.StringType;
 
 import ca.uhn.fhir.model.api.annotation.ResourceDef;
 import edu.gatech.chai.VRDR.model.util.CommonUtil;
+import edu.gatech.chai.VRDR.model.util.DeathCertificateDocumentUtil;
 
 @ResourceDef(name = "Bundle", profile = "http://hl7.org/fhir/us/vrdr/StructureDefinition/VRDR-Death-Certificate-Document")
 public class DeathCertificateDocument extends Bundle {
@@ -19,6 +22,13 @@ public DeathCertificateDocument() {
 		setType(BundleType.DOCUMENT);
 	}
 
+	public void addAuxillaryStateIdentifier(String auxillaryStateIdentifierValue) {
+		Extension extension = new Extension();
+		extension.setUrl(DeathCertificateDocumentUtil.auxillaryStateIndentifierUrl);
+		extension.setValue(new StringType(auxillaryStateIdentifierValue));
+		this.getIdentifier().addExtension(extension);
+	}
+
 	//Helper Accessor methods
 
 	private List<Resource> getRecords(Class<? extends Resource> type){

diff --git a/src/main/java/edu/gatech/chai/VRDR/model/DeathDate.java b/src/main/java/edu/gatech/chai/VRDR/model/DeathDate.java
@@ -4,9 +4,11 @@
 
 import org.hl7.fhir.r4.model.DateTimeType;
 import org.hl7.fhir.r4.model.Extension;
+import org.hl7.fhir.r4.model.IntegerType;
 import org.hl7.fhir.r4.model.Location;
 import org.hl7.fhir.r4.model.Observation;
 import org.hl7.fhir.r4.model.Reference;
+import org.hl7.fhir.r4.model.Type;
 
 import ca.uhn.fhir.model.api.annotation.ResourceDef;
 import edu.gatech.chai.VRDR.model.util.CommonUtil;
@@ -49,4 +51,52 @@ public void addDatePronouncedDead(DateTimeType dtType) {
 		component.setValue(dtType);
 		addComponent(component);
 	}
+
+	public DeathDate addPartialDateExtension(IntegerType year,String yearDataAbsentReason, IntegerType month,String monthDataAbsentReason,
+			IntegerType day,String dayDataAbsentReason) {
+		if(this.value == null) {
+			this.value = new DateTimeType(); //Assuming a datetime value if uninitiated
+		}
+		Extension baseExtension = addPartialDateBaseExtension();
+		addPartialDateYear(baseExtension,year,yearDataAbsentReason);
+		addPartialDateMonth(baseExtension,month,monthDataAbsentReason);
+		addPartialDateDay(baseExtension,day,dayDataAbsentReason);
+		this.value.addExtension(baseExtension);
+		return this;
+	}
+
+	private Extension addPartialDateBaseExtension() {
+		Extension baseExtension = new Extension(CommonUtil.partialDatePartAbsentReasonURL);
+		return baseExtension;
+	}
+
+	private DeathDate addPartialDateYear(Extension baseExtension, IntegerType year,String dataAbsentReason) {
+		if(dataAbsentReason != null && !dataAbsentReason.isEmpty()) {
+			baseExtension.addExtension(new Extension(CommonUtil.partialDateDateYearAbsentReasonURL,CommonUtil.findCodeFromCollectionUsingSimpleString(dataAbsentReason, CommonUtil.dataAbsentReasonCodeSet)));
+		}
+		else if(year != null && !year.isEmpty()){
+			baseExtension.addExtension(new Extension(CommonUtil.partialDateDateYearURL,year));
+		}
+		return this;
+	}
+
+	private DeathDate addPartialDateMonth(Extension baseExtension, IntegerType month,String dataAbsentReason) {
+		if(dataAbsentReason != null && !dataAbsentReason.isEmpty()) {
+			baseExtension.addExtension(new Extension(CommonUtil.partialDateDateMonthAbsentReasonURL,CommonUtil.findCodeFromCollectionUsingSimpleString(dataAbsentReason, CommonUtil.dataAbsentReasonCodeSet)));
+		}
+		else if(month != null && !month.isEmpty()){
+			baseExtension.addExtension(new Extension(CommonUtil.partialDateDateMonthURL,month));
+		}
+		return this;
+	}
+
+	private DeathDate addPartialDateDay(Extension baseExtension, IntegerType day,String dataAbsentReason) {
+		if(dataAbsentReason != null || !dataAbsentReason.isEmpty()) {
+			baseExtension.addExtension(new Extension(CommonUtil.partialDateDateDayAbsentReasonURL,CommonUtil.findCodeFromCollectionUsingSimpleString(dataAbsentReason, CommonUtil.dataAbsentReasonCodeSet)));
+		}
+		else if(day != null && !day.isEmpty()){
+			baseExtension.addExtension(new Extension(CommonUtil.partialDateDateDayURL,day));
+		}
+		return this;
+	}
 }
diff --git a/src/main/java/edu/gatech/chai/VRDR/model/DeathLocation.java b/src/main/java/edu/gatech/chai/VRDR/model/DeathLocation.java
@@ -2,24 +2,34 @@
 
 import org.hl7.fhir.r4.model.Address;
 import org.hl7.fhir.r4.model.CodeableConcept;
+import org.hl7.fhir.r4.model.Extension;
 import org.hl7.fhir.r4.model.Location;
 
 import ca.uhn.fhir.model.api.annotation.ResourceDef;
 import edu.gatech.chai.VRDR.model.util.CommonUtil;
+import edu.gatech.chai.VRDR.model.util.DeathLocationUtil;
 
 @ResourceDef(name = "Location", profile = "http://hl7.org/fhir/us/vrdr/StructureDefinition/VRDR-Death-Location")
 public class DeathLocation extends Location {
 	public DeathLocation() {
 		super();
 		CommonUtil.initResource(this);
 	}
-	public DeathLocation(String name, String description, CodeableConcept type, Address address,
-			CodeableConcept physicalType) {
+	public DeathLocation(String name, String description, CodeableConcept type, Address address) {
 		this();
 		setName(name);
 		setDescription(description);
 		addType(type);
 		setAddress(address);
-		setPhysicalType(physicalType);
 	}
+
+	public DeathLocation(String name, String description, String type, Address address) {
+		this();
+		CodeableConcept typeCC = CommonUtil.findConceptFromCollectionUsingSimpleString(type, DeathLocationUtil.placeOfDeathTypeSet);
+		setName(name);
+		setDescription(description);
+		addType(typeCC);
+		setAddress(address);
+	}
+
 }