Major revision update to model to reflect correct system uris. Update…

…d BuildDCD test.
gt-health · Apr 2, 2020 · 7717241 · 7717241
1 parent 8e91cac
commit 7717241
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Showing 72 changed files with 6,523 additions and 320 deletions.
diff --git a/pom.xml b/pom.xml
@@ -4,7 +4,7 @@
 
   <groupId>edu.gatech</groupId>
   <artifactId>VRDR</artifactId>
-  <version>v0.1.0-STUBallot1-REVISED</version>
+  <version>v0.1.0-STUBallot1-REVISED.1</version>
   <packaging>jar</packaging>
 
   <name>VRDR</name>
@@ -14,7 +14,7 @@
     <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
     <maven.compiler.source>1.8</maven.compiler.source>
   	<maven.compiler.target>1.8</maven.compiler.target>
-    <fhir.version>3.8.0</fhir.version>
+    <fhir.version>4.1.0</fhir.version>
   </properties>
 
   <dependencies>
@@ -44,5 +44,15 @@
     	<artifactId>hapi-fhir-structures-dstu3</artifactId>
     	<version>${fhir.version}</version>
     </dependency>
+    <dependency>
+    	<groupId>ca.uhn.hapi.fhir</groupId>
+    	<artifactId>hapi-fhir-validation</artifactId>
+    	<version>${fhir.version}</version>
+    </dependency>
+    <dependency>
+    	<groupId>ca.uhn.hapi.fhir</groupId>
+    	<artifactId>hapi-fhir-validation-resources-dstu3</artifactId>
+    	<version>${fhir.version}</version>
+    </dependency>
   </dependencies>
 </project>
diff --git a/src/main/java/edu/gatech/VRDR/model/BirthRecordIdentifier.java b/src/main/java/edu/gatech/VRDR/model/BirthRecordIdentifier.java
@@ -3,7 +3,6 @@
 import org.hl7.fhir.dstu3.model.CodeableConcept;
 import org.hl7.fhir.dstu3.model.DateTimeType;
 import org.hl7.fhir.dstu3.model.Observation;
-import org.hl7.fhir.dstu3.model.Reference;
 import org.hl7.fhir.dstu3.model.StringType;
 
 import ca.uhn.fhir.model.api.annotation.ResourceDef;

diff --git a/src/main/java/edu/gatech/VRDR/model/Certifier.java b/src/main/java/edu/gatech/VRDR/model/Certifier.java
@@ -6,7 +6,6 @@
 import org.hl7.fhir.dstu3.model.Practitioner;
 
 import ca.uhn.fhir.model.api.annotation.ResourceDef;
-import edu.gatech.VRDR.model.util.CertifierUtil;
 import edu.gatech.VRDR.model.util.CommonUtil;
 
 @ResourceDef(name = "Practitioner", profile = "http://hl7.org/fhir/us/vrdr/StructureDefinition/VRDR-Certifier")
@@ -17,11 +16,12 @@ public Certifier() {
 		CommonUtil.initResource(this);
 	}
 
-	public PractitionerQualificationComponent addQualification(String identifier, String type) {
+	public PractitionerQualificationComponent addQualification(String identifier, String type,String title) {
 		CodeableConcept identifierTypeCodeableConcept = CommonUtil.findConceptFromCollectionUsingSimpleString(type, CommonUtil.deathReportingIdentifierTypeCodes);
 		PractitionerQualificationComponent component = new PractitionerQualificationComponent(identifierTypeCodeableConcept);
+		component.setCode(new CodeableConcept().addCoding(new Coding("http://www.hl7.org/fhir/v2/0360/2.7",title,"")));
 		component.addIdentifier(new Identifier().setValue(identifier));
 		addQualification(component);
 		return component;
 	}
-}
+}
diff --git a/src/main/java/edu/gatech/VRDR/model/Decedent.java b/src/main/java/edu/gatech/VRDR/model/Decedent.java
@@ -145,4 +145,5 @@ public Identifier addIdentifier(String value) {
 		addIdentifier(identifier);
 		return identifier;
 	}
+	//TODO: Add handler for informant mapping
 }
diff --git a/src/main/java/edu/gatech/VRDR/model/DecedentEmploymentHistory.java b/src/main/java/edu/gatech/VRDR/model/DecedentEmploymentHistory.java
@@ -2,7 +2,6 @@
 
 import org.hl7.fhir.dstu3.model.CodeableConcept;
 import org.hl7.fhir.dstu3.model.Observation;
-import org.hl7.fhir.dstu3.model.Observation.ObservationComponentComponent;
 
 import ca.uhn.fhir.model.api.annotation.ResourceDef;
 import edu.gatech.VRDR.model.util.CommonUtil;

diff --git a/src/main/java/edu/gatech/VRDR/model/DecedentPregnancy.java b/src/main/java/edu/gatech/VRDR/model/DecedentPregnancy.java
@@ -7,7 +7,6 @@
 import ca.uhn.fhir.model.api.annotation.ResourceDef;
 import edu.gatech.VRDR.model.util.CommonUtil;
 import edu.gatech.VRDR.model.util.DecedentPregnancyUtil;
-import edu.gatech.VRDR.model.util.TobaccoUseContributedToDeathUtil;
 
 @ResourceDef(name = "Observation", profile = "http://hl7.org/fhir/us/StructureDefinition/VRDR-Decedent-Pregnancy")
 public class DecedentPregnancy extends Observation {

diff --git a/src/main/java/edu/gatech/VRDR/model/ExaminerContacted.java b/src/main/java/edu/gatech/VRDR/model/ExaminerContacted.java
@@ -11,12 +11,12 @@
 public class ExaminerContacted extends Observation {
 	public ExaminerContacted() {
 		super();
+		setStatus(ExaminerContactedUtil.status);
+		setCode(ExaminerContactedUtil.code);
 		CommonUtil.initResource(this);
 	}
 	public ExaminerContacted(boolean value) {
 		this();
-		setStatus(ExaminerContactedUtil.status);
-		setCode(ExaminerContactedUtil.code);
 		setValue(new BooleanType(value));
 	}
 }
diff --git a/src/main/java/edu/gatech/VRDR/model/FuneralServiceLicensee.java b/src/main/java/edu/gatech/VRDR/model/FuneralServiceLicensee.java
@@ -4,7 +4,6 @@
 import org.hl7.fhir.dstu3.model.PractitionerRole;
 
 import ca.uhn.fhir.model.api.annotation.ResourceDef;
-import edu.gatech.VRDR.model.util.CommonUtil;
 
 @ResourceDef(name = "PractitionerRole", profile = "http://hl7.org/fhir/us/vrdr/StructureDefinition/VRDR_FuneralServiceLicensee")
 public class FuneralServiceLicensee extends PractitionerRole {

diff --git a/src/main/java/edu/gatech/VRDR/model/TobaccoUseContributedToDeath.java b/src/main/java/edu/gatech/VRDR/model/TobaccoUseContributedToDeath.java
@@ -1,8 +1,6 @@
 package edu.gatech.VRDR.model;
 
-import org.hl7.fhir.dstu3.model.BooleanType;
 import org.hl7.fhir.dstu3.model.CodeableConcept;
-import org.hl7.fhir.dstu3.model.Coding;
 import org.hl7.fhir.dstu3.model.Observation;
 
 import ca.uhn.fhir.model.api.annotation.ResourceDef;

diff --git a/src/main/java/edu/gatech/VRDR/model/util/CommonUtil.java b/src/main/java/edu/gatech/VRDR/model/util/CommonUtil.java
@@ -8,18 +8,18 @@
 import org.hl7.fhir.dstu3.model.Bundle;
 import org.hl7.fhir.dstu3.model.CodeableConcept;
 import org.hl7.fhir.dstu3.model.Coding;
+import org.hl7.fhir.dstu3.model.Composition.SectionComponent;
 import org.hl7.fhir.dstu3.model.DomainResource;
 import org.hl7.fhir.dstu3.model.Extension;
 import org.hl7.fhir.dstu3.model.IdType;
 import org.hl7.fhir.dstu3.model.Reference;
 import org.hl7.fhir.dstu3.model.Resource;
-import org.hl7.fhir.dstu3.model.Composition.SectionComponent;
 
 import edu.gatech.VRDR.model.DeathCertificate;
 import edu.gatech.VRDR.model.DeathCertificateDocument;
 
 public class CommonUtil {
-	public static String basicBooleanHL7System = "http://terminology.www.hl7.org/CodeSystem/v2-0136";
+	public static String basicBooleanHL7System = "http://hl7.org/CodeSystem/v2-0136";
 	public static String nullFlavorHL7System = "http://hl7.org/fhir/v3/NullFlavor";
 	public static CodeableConcept noCode = new CodeableConcept().addCoding(new Coding(basicBooleanHL7System,"N","No"));
 	public static CodeableConcept yesCode = new CodeableConcept().addCoding(new Coding(basicBooleanHL7System,"Y","Yes"));

diff --git a/src/main/java/edu/gatech/VRDR/model/util/DeathCertificationUtil.java b/src/main/java/edu/gatech/VRDR/model/util/DeathCertificationUtil.java
@@ -5,7 +5,7 @@
 
 public class DeathCertificationUtil {
 	public static final CodeableConcept categoryFixedValue = new CodeableConcept()
-			.addCoding(new Coding().setCode("103693007"));
+			.addCoding(new Coding().setCode("103693007").setSystem("http://snomed.info/sct"));
 	public static final CodeableConcept codeFixedValue = new CodeableConcept()
 			.addCoding(new Coding().setCode("308646001"));
 }
diff --git a/src/main/java/edu/gatech/VRDR/model/util/DecedentUtil.java b/src/main/java/edu/gatech/VRDR/model/util/DecedentUtil.java
@@ -11,7 +11,7 @@ public class DecedentUtil {
 	public static final String birthSexExtensionURL = "http://hl7.org/fhir/us/core/StructureDefinition/us-core-birthsex";
 	public static final String birthSexValueSetURL = "http://hl7.org/fhir/us/core/ValueSet/us-core-birthsex";
 	public static final String birthPlaceExtensionURL = "http://hl7.org/fhir/StructureDefinition/birthPlace";
-	public static final String addressWithCityLimitsIndicatorExtensionURL = "http://hl7.org/fhir/us/vrdr/StructureDefinition/Within-City-Limits-Indicator";
+	public static final String addressWithinCityLimitsIndicatorExtensionURL = "http://hl7.org/fhir/us/vrdr/StructureDefinition/Within-City-Limits-Indicator";
 	public static final CodeableConcept identifierTypeFixedValue = new CodeableConcept()
 			.addCoding(new Coding().setCode("BR").setDisplay("Social Beneficiary Identifier"));
 	public static final String identifierSystem = "urn:oid:2.16.840.1.113883.4.1";

diff --git a/src/main/java/edu/gatech/VRDR/util/HumanNameParser.java b/src/main/java/edu/gatech/VRDR/util/HumanNameParser.java
@@ -0,0 +1,51 @@
+package edu.gatech.VRDR.util;
+
+import java.util.Arrays;
+import java.util.StringJoiner;
+
+import org.hl7.fhir.dstu3.model.HumanName;
+
+public class HumanNameParser {
+	private static final String[] prefixList = {"Mr.", "Mrs.", "Ms.", "Dr.", "Adm", "Capt", "Chief", "Gen", "Gov", "Hon", "Maj", "Prof", "Rabbi", "Rev", "Sister"};
+	private static final String[] suffixList = {"II", "III", "IV", "CPA", "DDS", "Esq", "Jr", "LLD", "MD", "PhD", "Ret", "Sr", "DO"};
+	public static HumanName createHumanName(String nameString) {
+		HumanName returnName = new HumanName();
+		String[] nameParts = nameString.split("\\s+");
+		if(nameParts.length == 1) {
+			returnName.addGiven(nameParts[0]);
+			return returnName;
+		}
+		if(nameParts.length == 2) {
+			returnName.addGiven(nameParts[0]);
+			returnName.setFamily(nameParts[1]);
+			return returnName;
+		}
+
+		boolean hasPrefix = false;
+		boolean hasSuffix = false;
+		int familyIndex = nameParts.length-1;
+		int givenStartIndex = 0;
+		if(Arrays.asList(prefixList).contains(nameParts[0])) {
+			returnName.addPrefix(nameParts[0]);
+			givenStartIndex = 1;
+		}
+		if(Arrays.asList(suffixList).contains(nameParts[nameParts.length-1])) {
+			returnName.addSuffix(nameParts[nameParts.length-1]);
+			familyIndex = nameParts.length-2;
+		}
+		String familyName = "";
+		String givenName = "";
+		if(hasSuffix) {
+			familyIndex = nameParts.length - 2;
+		}
+		StringJoiner joiner = new StringJoiner(" ");
+		for(int i = givenStartIndex; i < familyIndex; i++) {
+			joiner.add(nameParts[i]);
+		}
+		givenName = joiner.toString();
+		familyName = nameParts[familyIndex];
+		returnName.addGiven(givenName);
+		returnName.setFamily(familyName);
+		return returnName;
+	}
+}