STU 1.3 Update

Changing packaging name from <packageversion>-<fhirversion>-<ig_version> to simpler: <packageversion>-<ig_version>. Updated resources to match VRDR_IG version 1.3. Updating examples in test/ folder
nightingaleproject · Mar 11, 2022 · 3369c00 · 3369c00
1 parent d939525
commit 3369c00
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Showing 15 changed files with 383 additions and 194 deletions.
diff --git a/.gitignore b/.gitignore
@@ -0,0 +1,2 @@
+
+target/*
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);

diff --git a/src/main/java/edu/gatech/chai/VRDR/model/CauseOfDeathCondition.java b/src/main/java/edu/gatech/chai/VRDR/model/CauseOfDeathCondition.java
@@ -1,26 +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.addCategory(CauseOfDeathConditionUtil.causeOfDeathConditionCategory);
+		this.setCode(CauseOfDeathConditionUtil.code);
 	}
 
-	public CauseOfDeathCondition(Decedent decedent) {
+	public CauseOfDeathCondition(Decedent decedent, Certifier certifier, String value, Quantity interval) {
 		super();
 		CommonUtil.initResource(this);
-		this.addCategory(CauseOfDeathConditionUtil.causeOfDeathConditionCategory);
+		this.setCode(CauseOfDeathConditionUtil.code);
 		setDecedent(decedent);
+		setPerformer(certifier);
+		setValue(value);
+		createInterval(interval);
+	}
+
+	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) {
@@ -38,32 +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 Reference getCertifier() {
-		return asserter;
+	public List<Reference> getCertifiers(int index) {
+		return performer;
 	}
 
-	public Condition setClinicalStatus(String clinicalStatus) {
-		CodeableConcept clinicalStatusCC = CommonUtil.findConceptFromCollectionUsingSimpleString(clinicalStatus, CauseOfDeathConditionUtil.conditionClinicalStatusSet);
-		this.setClinicalStatus(clinicalStatusCC);
-		return this;
+	public List<Reference> getAsserters(int index) {
+		return performer;
 	}
 
-	public Condition setVerificationStatus(String verificationStatus) {
-		CodeableConcept verificationStatusCC = CommonUtil.findConceptFromCollectionUsingSimpleString(verificationStatus, CauseOfDeathConditionUtil.verificationStatusSet);
-		this.setVerificationStatus(verificationStatusCC);
-		return this;
+	public List<Reference> getPerformers(int index) {
+		return performer;
 	}
 
-	/*public Condition setCategory(String category) {
-		CodeableConcept categoryCC = CommonUtil.findConceptFromCollectionUsingSimpleString(category, CauseOfDeathConditionUtil.categorySet);
-		this.setVerificationStatus(categoryCC);
-		return this;
-	}*/
+	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
@@ -1,41 +1,34 @@
 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.addCategory(ConditionContributingToDeathUtil.conditionContributingToDeathCategory);
-	}
-
-	public ConditionContributingToDeath(Decedent decedent) {
-		super();
-		CommonUtil.initResource(this);
-		this.addCategory(CauseOfDeathConditionUtil.causeOfDeathConditionCategory);
-		setDecedent(decedent);
-	}
-
-	public ConditionContributingToDeath(Certifier certifier) {
-		super();
-		CommonUtil.initResource(this);
-		this.addCategory(CauseOfDeathConditionUtil.causeOfDeathConditionCategory);
-		setCertifier(certifier);
+		this.setCode(ConditionContributingToDeathUtil.code);
 	}
 
-	public ConditionContributingToDeath(Decedent decedent,  Certifier certifier) {
+	public ConditionContributingToDeath(Decedent decedent, Certifier certifier, String value) {
 		super();
 		CommonUtil.initResource(this);
+		this.setCode(ConditionContributingToDeathUtil.code);
 		setDecedent(decedent);
-		this.addCategory(CauseOfDeathConditionUtil.causeOfDeathConditionCategory);
-		setCertifier(certifier);
+		setPerformer(certifier);
+		setValue(value);
 	}
 
 	public void setDecedent(Decedent decedent) {
@@ -53,13 +46,39 @@ 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 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/DeathLocation.java b/src/main/java/edu/gatech/chai/VRDR/model/DeathLocation.java
@@ -15,33 +15,21 @@ public DeathLocation() {
 		super();
 		CommonUtil.initResource(this);
 	}
-	public DeathLocation(String name, String jurisdicitionId, String description, CodeableConcept type, Address address,
-			CodeableConcept physicalType) {
+	public DeathLocation(String name, String description, CodeableConcept type, Address address) {
 		this();
 		setName(name);
-		addJurisdictionIdExtension(jurisdicitionId);
 		setDescription(description);
 		addType(type);
 		setAddress(address);
-		setPhysicalType(physicalType);
 	}
 
-	public DeathLocation(String name, String jurisdicitionId, String description, String type, Address address,
-			CodeableConcept physicalType) {
+	public DeathLocation(String name, String description, String type, Address address) {
 		this();
 		CodeableConcept typeCC = CommonUtil.findConceptFromCollectionUsingSimpleString(type, DeathLocationUtil.placeOfDeathTypeSet);
 		setName(name);
-		addJurisdictionIdExtension(jurisdicitionId);
 		setDescription(description);
 		addType(typeCC);
 		setAddress(address);
-		setPhysicalType(physicalType);
 	}
 
-	public DeathLocation addJurisdictionIdExtension(String jurisdicitionId) {
-		Extension extension = new Extension(DeathLocationUtil.locationJurisdictionIdExtension);
-		extension.setValue(CommonUtil.findConceptFromCollectionUsingSimpleString(jurisdicitionId, CommonUtil.locationJurisdictionalConceptSet));
-		this.addExtension(extension);
-		return this;
-	}
 }