Merging gt-health changes to mrp. REVISED release.

nightingaleproject · Nov 12, 2019 · 8e91cac · 8e91cac
1 parent d57104f
commit 8e91cac
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Showing 23 changed files with 302 additions and 92 deletions.
diff --git a/pom.xml b/pom.xml
@@ -4,7 +4,7 @@
 
   <groupId>edu.gatech</groupId>
   <artifactId>VRDR</artifactId>
-  <version>v0.1.0</version>
+  <version>v0.1.0-STUBallot1-REVISED</version>
   <packaging>jar</packaging>
 
   <name>VRDR</name>

diff --git a/src/main/java/edu/gatech/VRDR/context/VRDRFhirContext.java b/src/main/java/edu/gatech/VRDR/context/VRDRFhirContext.java
@@ -27,7 +27,7 @@
 import edu.gatech.VRDR.model.DispositionLocation;
 import edu.gatech.VRDR.model.ExaminerContacted;
 import edu.gatech.VRDR.model.FuneralHome;
-import edu.gatech.VRDR.model.FuneralHomeDirector;
+import edu.gatech.VRDR.model.FuneralServiceLicensee;
 import edu.gatech.VRDR.model.InjuryIncident;
 import edu.gatech.VRDR.model.InjuryLocation;
 import edu.gatech.VRDR.model.InterestedParty;
@@ -93,8 +93,8 @@ public VRDRFhirContext() {
 				ExaminerContacted.class);
 		ctx.setDefaultTypeForProfile("http://hl7.org/fhir/us/vrdr/StructureDefinition/VRDR-Funeral-Home",
 				FuneralHome.class);
-		ctx.setDefaultTypeForProfile("http://hl7.org/fhir/us/vrdr/StructureDefinition/VRDR-Funeral-Home-Director",
-				FuneralHomeDirector.class);
+		ctx.setDefaultTypeForProfile("http://hl7.org/fhir/us/vrdr/StructureDefinition/VRDR_FuneralServiceLicensee",
+				FuneralServiceLicensee.class);
 		ctx.setDefaultTypeForProfile("http://hl7.org/fhir/us/vrdr/StructureDefinition/VRDR-Injury-Incident",
 				InjuryIncident.class);
 		ctx.setDefaultTypeForProfile("http://hl7.org/fhir/us/vrdr/StructureDefinition/VRDR-Injury-Location",

diff --git a/src/main/java/edu/gatech/VRDR/model/AutopsyPerformedIndicator.java b/src/main/java/edu/gatech/VRDR/model/AutopsyPerformedIndicator.java
@@ -17,17 +17,26 @@ public AutopsyPerformedIndicator() {
 		setStatus(AutopsyPerformedIdentifierUtil.status);
 		setCode(AutopsyPerformedIdentifierUtil.code);
 	}
-
-	public AutopsyPerformedIndicator(boolean autopsyPerformed,boolean resultsAvailable) {
+	
+	public AutopsyPerformedIndicator(boolean autopsyPerformed) {
 		this();
 		CodeableConcept autopsyPerformedConcept = autopsyPerformed ? CommonUtil.yesCode : CommonUtil.noCode;
 		setValue(autopsyPerformedConcept);
+	}
+
+	public AutopsyPerformedIndicator(boolean autopsyPerformed,boolean resultsAvailable) {
+		this(autopsyPerformed);
 		CodeableConcept autopsyResultsAvailableConcept = resultsAvailable ? CommonUtil.yesCode : CommonUtil.noCode;
 		addAutopsyResultsAvailableComponent(autopsyResultsAvailableConcept);
 	}
 
-	public AutopsyPerformedIndicator(CodeableConcept autopsyPerformed,CodeableConcept resultsAvailable) {
+	public AutopsyPerformedIndicator(CodeableConcept autopsyPerformed) {
+		this();
 		setValue(autopsyPerformed);
+	}
+
+	public AutopsyPerformedIndicator(CodeableConcept autopsyPerformed,CodeableConcept resultsAvailable) {
+		this(autopsyPerformed);
 		addAutopsyResultsAvailableComponent(resultsAvailable);
 	}
 

diff --git a/src/main/java/edu/gatech/VRDR/model/CauseOfDeathCondition.java b/src/main/java/edu/gatech/VRDR/model/CauseOfDeathCondition.java
@@ -1,6 +1,7 @@
 package edu.gatech.VRDR.model;
 
 import org.hl7.fhir.dstu3.model.Condition;
+import org.hl7.fhir.dstu3.model.Reference;
 
 import ca.uhn.fhir.model.api.annotation.ResourceDef;
 import edu.gatech.VRDR.model.util.CommonUtil;
@@ -11,4 +12,29 @@ public CauseOfDeathCondition() {
 		super();
 		CommonUtil.initResource(this);
 	}
+
+	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;
+	}
+	public void setAsserter(Certifier certifier) {
+		setCertifier(certifier);
+	}
+
+	public Reference getCertifier() {
+		return asserter;
+	}
 }
diff --git a/src/main/java/edu/gatech/VRDR/model/Certifier.java b/src/main/java/edu/gatech/VRDR/model/Certifier.java
@@ -18,9 +18,8 @@ public Certifier() {
 	}
 
 	public PractitionerQualificationComponent addQualification(String identifier, String type) {
-		CodeableConcept typeCodeableConcept = new CodeableConcept()
-				.addCoding(new Coding().setCode(type).setSystem(CertifierUtil.qualificationSystemUrl));
-		PractitionerQualificationComponent component = new PractitionerQualificationComponent(typeCodeableConcept);
+		CodeableConcept identifierTypeCodeableConcept = CommonUtil.findConceptFromCollectionUsingSimpleString(type, CommonUtil.deathReportingIdentifierTypeCodes);
+		PractitionerQualificationComponent component = new PractitionerQualificationComponent(identifierTypeCodeableConcept);
 		component.addIdentifier(new Identifier().setValue(identifier));
 		addQualification(component);
 		return component;

diff --git a/src/main/java/edu/gatech/VRDR/model/ConditionContributingToDeath.java b/src/main/java/edu/gatech/VRDR/model/ConditionContributingToDeath.java
@@ -1,6 +1,7 @@
 package edu.gatech.VRDR.model;
 
 import org.hl7.fhir.dstu3.model.Condition;
+import org.hl7.fhir.dstu3.model.Reference;
 
 import ca.uhn.fhir.model.api.annotation.ResourceDef;
 import edu.gatech.VRDR.model.util.CommonUtil;
@@ -11,4 +12,16 @@ public ConditionContributingToDeath() {
 		super();
 		CommonUtil.initResource(this);
 	}
-}
+
+	public void setCertifier(Certifier certifier) {
+		Reference reference = new Reference(certifier.getId());
+		this.asserter = reference;
+	}
+	public void setAsserter(Certifier certifier) {
+		setCertifier(certifier);
+	}
+
+	public Reference getCertifier() {
+		return asserter;
+	}
+}
diff --git a/src/main/java/edu/gatech/VRDR/model/DeathCertificate.java b/src/main/java/edu/gatech/VRDR/model/DeathCertificate.java
@@ -22,6 +22,11 @@ public DeathCertificate() {
 		setStatus(DeathCertificateUtil.status);
 		setDate(new Date());
 	}
+
+	public DeathCertificate(DeathCertification resource) {
+		this();
+		addEvent(resource);
+	}
 
 	private CompositionAttesterComponent addAttesterCommon() {
 		CompositionAttesterComponent component = new CompositionAttesterComponent();

diff --git a/src/main/java/edu/gatech/VRDR/model/DeathCertificateReference.java b/src/main/java/edu/gatech/VRDR/model/DeathCertificateReference.java
@@ -1,5 +1,6 @@
 package edu.gatech.VRDR.model;
 
+import org.hl7.fhir.dstu3.model.Attachment;
 import org.hl7.fhir.dstu3.model.DocumentReference;
 import org.hl7.fhir.dstu3.model.Enumerations.DocumentReferenceStatus;
 
@@ -18,4 +19,12 @@ public DeathCertificateReference(DocumentReferenceStatus status) {
 		setStatus(status);
 		setType(DeathCertificateReferenceUtil.type);
 	}
+
+	public void addDeathCertificateURL(String urlString) {
+		DocumentReferenceContentComponent drcc = new DocumentReferenceContentComponent();
+		Attachment attachment = new Attachment();
+		attachment.setUrl(urlString);
+		drcc.setAttachment(attachment);
+		this.addContent(drcc);
+	}
 }
diff --git a/src/main/java/edu/gatech/VRDR/model/DeathCertification.java b/src/main/java/edu/gatech/VRDR/model/DeathCertification.java
@@ -1,5 +1,8 @@
 package edu.gatech.VRDR.model;
 
+import java.util.Date;
+
+import org.hl7.fhir.dstu3.model.DateTimeType;
 import org.hl7.fhir.dstu3.model.Procedure;
 
 import ca.uhn.fhir.model.api.annotation.ResourceDef;
@@ -16,5 +19,10 @@ public DeathCertification() {
 		setCategory(DeathCertificationUtil.categoryFixedValue);
 		setCode(DeathCertificationUtil.codeFixedValue);
 	}
+
+	public DeathCertification(Date performed) {
+		this();
+		this.setPerformed(new DateTimeType(performed));
+	}
 
-}
+}
diff --git a/src/main/java/edu/gatech/VRDR/model/DeathLocation.java b/src/main/java/edu/gatech/VRDR/model/DeathLocation.java
@@ -7,7 +7,7 @@
 import ca.uhn.fhir.model.api.annotation.ResourceDef;
 import edu.gatech.VRDR.model.util.CommonUtil;
 
-@ResourceDef(name = "Location", profile = "http://hl7.org/fhir/us/vrdr/StructureDefinition/@ResourceDef(name=\"Death Certificate Reference\", profile=\"http://hl7.org/fhir/us/vrdr/StructureDefinition/VRDR-Death-Location")
+@ResourceDef(name = "Location", profile = "http://hl7.org/fhir/us/vrdr/StructureDefinition/VRDR-Death-Location")
 public class DeathLocation extends Location {
 	public DeathLocation() {
 		super();

diff --git a/src/main/java/edu/gatech/VRDR/model/DeathPronouncementPerformer.java b/src/main/java/edu/gatech/VRDR/model/DeathPronouncementPerformer.java
@@ -8,7 +8,7 @@
 import ca.uhn.fhir.model.api.annotation.ResourceDef;
 import edu.gatech.VRDR.model.util.CommonUtil;
 
-@ResourceDef(name = "Practitioner", profile = "http://hl7.org/fhir/us/vrdr/StructureDefinition/@ResourceDef(name=\"Death Certificate Reference\", profile=\"http://hl7.org/fhir/us/vrdr/StructureDefinition/VRDR-Death-Pronouncement-Performer")
+@ResourceDef(name = "Practitioner", profile = "http://hl7.org/fhir/us/vrdr/StructureDefinition/VRDR-Death-Pronouncement-Performer")
 public class DeathPronouncementPerformer extends Practitioner {
 	public DeathPronouncementPerformer() {
 		super();

diff --git a/src/main/java/edu/gatech/VRDR/model/DecedentDispositionMethod.java b/src/main/java/edu/gatech/VRDR/model/DecedentDispositionMethod.java
@@ -19,4 +19,31 @@ public DecedentDispositionMethod(CodeableConcept value) {
 		this();
 		setValue(value);
 	}
+
+	public DecedentDispositionMethod(String code) {
+		this();
+		setValue(code);
+	}
+
+	public DecedentDispositionMethod(String code, String display) {
+		this();
+		setValue(code,display);
+	}
+
+	public void setValue(String code) {
+		CodeableConcept concept = CommonUtil.findConceptFromCollectionUsingSimpleString(code, DecedentDispositionMethodUtil.valueCodesetList);
+		if(concept != null) {
+			setValue(concept);
+		}
+	}
+
+	public void setValue(String code, String display) {
+		CodeableConcept concept = CommonUtil.findConceptFromCollectionUsingSimpleString(code, DecedentDispositionMethodUtil.valueCodesetList);
+		if(concept == null) {
+			concept = CommonUtil.findConceptFromCollectionUsingSimpleString(display, DecedentDispositionMethodUtil.valueCodesetList);
+		}
+		if(concept != null) {
+			setValue(concept);
+		}
+	}
 }
diff --git a/src/main/java/edu/gatech/VRDR/model/DecedentPregnancy.java b/src/main/java/edu/gatech/VRDR/model/DecedentPregnancy.java
@@ -1,11 +1,13 @@
 package edu.gatech.VRDR.model;
 
 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;
 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 {
@@ -18,4 +20,25 @@ public DecedentPregnancy(CodeableConcept value) {
 		this();
 		setValue(value);
 	}
+
+	public DecedentPregnancy(String code) {
+		this();
+		setValue(code);
+	}
+
+	public DecedentPregnancy(String code, String display) {
+		this();
+		setValue(code,display);
+	}
+
+
+	public void setValue(String code) {
+		CodeableConcept concept = new CodeableConcept().addCoding(new Coding().setCode(code).setSystem(DecedentPregnancyUtil.codeValueSystem));
+		setValue(concept);
+	}
+
+	public void setValue(String code, String display) {
+		CodeableConcept concept = new CodeableConcept().addCoding(new Coding().setCode(code).setSystem(DecedentPregnancyUtil.codeValueSystem).setDisplay(display));
+		setValue(concept);
+	}
 }
diff --git a/src/main/java/edu/gatech/VRDR/model/FuneralHomeDirector.java b/src/main/java/edu/gatech/VRDR/model/FuneralHomeDirector.java
diff --git a/src/main/java/edu/gatech/VRDR/model/FuneralServiceLicensee.java b/src/main/java/edu/gatech/VRDR/model/FuneralServiceLicensee.java
@@ -0,0 +1,21 @@
+package edu.gatech.VRDR.model;
+
+import org.hl7.fhir.dstu3.model.CodeableConcept;
+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 {
+	public FuneralServiceLicensee() {
+		super();
+		//NOTE: Specifically not including id and meta tags from commonutil initresources
+		//Been exempted from the profile
+		//CommonUtil.initResource(this);
+	}
+	public FuneralServiceLicensee(CodeableConcept code) {
+		this();
+		addCode(code);
+	}
+}
diff --git a/src/main/java/edu/gatech/VRDR/model/TobaccoUseContributedToDeath.java b/src/main/java/edu/gatech/VRDR/model/TobaccoUseContributedToDeath.java
@@ -1,6 +1,8 @@
 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;
@@ -11,13 +13,35 @@
 public class TobaccoUseContributedToDeath extends Observation {
 	public TobaccoUseContributedToDeath() {
 		super();
+		setStatus(TobaccoUseContributedToDeathUtil.status);
+		setCode(TobaccoUseContributedToDeathUtil.code);
 		CommonUtil.initResource(this);
 	}
 
-	public TobaccoUseContributedToDeath(boolean value) {
+	public TobaccoUseContributedToDeath(String code) {
 		this();
-		setStatus(TobaccoUseContributedToDeathUtil.status);
-		setCode(TobaccoUseContributedToDeathUtil.code);
-		setValue(new BooleanType(value));
+		setValue(code);
+	}
+
+	public TobaccoUseContributedToDeath(String code, String display) {
+		this();
+		setValue(code,display);
+	}
+
+	public void setValue(String code) {
+		CodeableConcept concept = CommonUtil.findConceptFromCollectionUsingSimpleString(code, TobaccoUseContributedToDeathUtil.valueCodesetList);
+		if(concept != null) {
+			setValue(concept);
+		}
+	}
+
+	public void setValue(String code, String display) {
+		CodeableConcept concept = CommonUtil.findConceptFromCollectionUsingSimpleString(code, TobaccoUseContributedToDeathUtil.valueCodesetList);
+		if(concept == null) {
+			concept = CommonUtil.findConceptFromCollectionUsingSimpleString(display, TobaccoUseContributedToDeathUtil.valueCodesetList);
+		}
+		if(concept != null) {
+			setValue(concept);
+		}
 	}
 }