BIG 1.0 update. See 1.0 tag for large details. Moved namespace from e…

…du.gatech -> edu.gatech.chai
nightingaleproject · Nov 3, 2020 · ebede2f · ebede2f
1 parent be16e04
commit ebede2f
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Showing 76 changed files with 608 additions and 415 deletions.
diff --git a/pom.xml b/pom.xml
@@ -4,7 +4,7 @@
 
   <groupId>edu.gatech</groupId>
   <artifactId>VRDR</artifactId>
-  <version>v0.1.8-R4</version>
+  <version>v1.0.0-R4</version>
   <packaging>jar</packaging>
 
   <name>VRDR</name>

diff --git a/src/main/java/edu/gatech/VRDR/model/DecedentEducationLevel.java b/src/main/java/edu/gatech/VRDR/model/DecedentEducationLevel.java
diff --git a/src/main/java/edu/gatech/VRDR/model/InjuryIncident.java b/src/main/java/edu/gatech/VRDR/model/InjuryIncident.java
diff --git a/src/main/java/edu/gatech/VRDR/model/MannerOfDeath.java b/src/main/java/edu/gatech/VRDR/model/MannerOfDeath.java
diff --git a/src/main/java/edu/gatech/VRDR/model/util/DecedentEducationLevelUtil.java b/src/main/java/edu/gatech/VRDR/model/util/DecedentEducationLevelUtil.java
diff --git a/src/main/java/edu/gatech/VRDR/model/util/DecedentTransportationRoleUtil.java b/src/main/java/edu/gatech/VRDR/model/util/DecedentTransportationRoleUtil.java
diff --git a/src/main/java/edu/gatech/VRDR/model/util/FuneralHomeUtil.java b/src/main/java/edu/gatech/VRDR/model/util/FuneralHomeUtil.java
diff --git a/src/main/java/edu/gatech/VRDR/model/util/InjuryIncidentUtil.java b/src/main/java/edu/gatech/VRDR/model/util/InjuryIncidentUtil.java
diff --git a/src/main/java/edu/gatech/VRDR/model/util/MannerOfDeathUtil.java b/src/main/java/edu/gatech/VRDR/model/util/MannerOfDeathUtil.java
diff --git a/.../gatech/VRDR/context/VRDRFhirContext.java → ...ch/chai/VRDR/context/VRDRFhirContext.java b/.../gatech/VRDR/context/VRDRFhirContext.java → ...ch/chai/VRDR/context/VRDRFhirContext.java
@@ -1,39 +1,39 @@
-package edu.gatech.VRDR.context;
+package edu.gatech.chai.VRDR.context;
 
 import ca.uhn.fhir.context.FhirContext;
-import edu.gatech.VRDR.model.AutopsyPerformedIndicator;
-import edu.gatech.VRDR.model.BirthRecordIdentifier;
-import edu.gatech.VRDR.model.CauseOfDeathCondition;
-import edu.gatech.VRDR.model.CauseOfDeathPathway;
-import edu.gatech.VRDR.model.Certifier;
-import edu.gatech.VRDR.model.ConditionContributingToDeath;
-import edu.gatech.VRDR.model.DeathCertificate;
-import edu.gatech.VRDR.model.DeathCertificateDocument;
-import edu.gatech.VRDR.model.DeathCertificateReference;
-import edu.gatech.VRDR.model.DeathCertification;
-import edu.gatech.VRDR.model.DeathDate;
-import edu.gatech.VRDR.model.DeathLocation;
-import edu.gatech.VRDR.model.DeathPronouncementPerformer;
-import edu.gatech.VRDR.model.Decedent;
-import edu.gatech.VRDR.model.DecedentAge;
-import edu.gatech.VRDR.model.DecedentDispositionMethod;
-import edu.gatech.VRDR.model.DecedentEducationLevel;
-import edu.gatech.VRDR.model.DecedentUsualWork;
-import edu.gatech.VRDR.model.DecedentFather;
-import edu.gatech.VRDR.model.DecedentMother;
-import edu.gatech.VRDR.model.DecedentPregnancy;
-import edu.gatech.VRDR.model.DecedentSpouse;
-import edu.gatech.VRDR.model.DecedentTransportationRole;
-import edu.gatech.VRDR.model.DispositionLocation;
-import edu.gatech.VRDR.model.ExaminerContacted;
-import edu.gatech.VRDR.model.FuneralHome;
-import edu.gatech.VRDR.model.FuneralServiceLicensee;
-import edu.gatech.VRDR.model.InjuryIncident;
-import edu.gatech.VRDR.model.InjuryLocation;
-import edu.gatech.VRDR.model.InterestedParty;
-import edu.gatech.VRDR.model.MannerOfDeath;
-import edu.gatech.VRDR.model.Mortician;
-import edu.gatech.VRDR.model.TobaccoUseContributedToDeath;
+import edu.gatech.chai.VRDR.model.AutopsyPerformedIndicator;
+import edu.gatech.chai.VRDR.model.BirthRecordIdentifier;
+import edu.gatech.chai.VRDR.model.CauseOfDeathCondition;
+import edu.gatech.chai.VRDR.model.CauseOfDeathPathway;
+import edu.gatech.chai.VRDR.model.Certifier;
+import edu.gatech.chai.VRDR.model.ConditionContributingToDeath;
+import edu.gatech.chai.VRDR.model.DeathCertificate;
+import edu.gatech.chai.VRDR.model.DeathCertificateDocument;
+import edu.gatech.chai.VRDR.model.DeathCertificateReference;
+import edu.gatech.chai.VRDR.model.DeathCertification;
+import edu.gatech.chai.VRDR.model.DeathDate;
+import edu.gatech.chai.VRDR.model.DeathLocation;
+import edu.gatech.chai.VRDR.model.DeathPronouncementPerformer;
+import edu.gatech.chai.VRDR.model.Decedent;
+import edu.gatech.chai.VRDR.model.DecedentAge;
+import edu.gatech.chai.VRDR.model.DecedentDispositionMethod;
+import edu.gatech.chai.VRDR.model.DecedentEducationLevel;
+import edu.gatech.chai.VRDR.model.DecedentFather;
+import edu.gatech.chai.VRDR.model.DecedentMother;
+import edu.gatech.chai.VRDR.model.DecedentPregnancy;
+import edu.gatech.chai.VRDR.model.DecedentSpouse;
+import edu.gatech.chai.VRDR.model.DecedentTransportationRole;
+import edu.gatech.chai.VRDR.model.DecedentUsualWork;
+import edu.gatech.chai.VRDR.model.DispositionLocation;
+import edu.gatech.chai.VRDR.model.ExaminerContacted;
+import edu.gatech.chai.VRDR.model.FuneralHome;
+import edu.gatech.chai.VRDR.model.FuneralServiceLicensee;
+import edu.gatech.chai.VRDR.model.InjuryIncident;
+import edu.gatech.chai.VRDR.model.InjuryLocation;
+import edu.gatech.chai.VRDR.model.InterestedParty;
+import edu.gatech.chai.VRDR.model.MannerOfDeath;
+import edu.gatech.chai.VRDR.model.Mortician;
+import edu.gatech.chai.VRDR.model.TobaccoUseContributedToDeath;
 
 public class VRDRFhirContext {
 	FhirContext ctx;

diff --git a/...VRDR/model/AutopsyPerformedIndicator.java → ...VRDR/model/AutopsyPerformedIndicator.java b/...VRDR/model/AutopsyPerformedIndicator.java → ...VRDR/model/AutopsyPerformedIndicator.java
@@ -1,12 +1,12 @@
-package edu.gatech.VRDR.model;
+package edu.gatech.chai.VRDR.model;
 
 import org.hl7.fhir.r4.model.CodeableConcept;
 import org.hl7.fhir.r4.model.Observation;
 import org.hl7.fhir.r4.model.Reference;
 
 import ca.uhn.fhir.model.api.annotation.ResourceDef;
-import edu.gatech.VRDR.model.util.AutopsyPerformedIndicatorUtil;
-import edu.gatech.VRDR.model.util.CommonUtil;
+import edu.gatech.chai.VRDR.model.util.AutopsyPerformedIndicatorUtil;
+import edu.gatech.chai.VRDR.model.util.CommonUtil;
 
 @ResourceDef(name = "Observation", profile = "http://hl7.org/fhir/us/vrdr/StructureDefinition/VRDR-Autopsy-Performed-Indicator")
 public class AutopsyPerformedIndicator extends Observation {
@@ -39,6 +39,13 @@ public AutopsyPerformedIndicator(CodeableConcept autopsyPerformed,CodeableConcep
 		this(autopsyPerformed);
 		addAutopsyResultsAvailableComponent(resultsAvailable);
 	}
+
+	public AutopsyPerformedIndicator(String autopsyPerformed,String resultsAvailable) {
+		CodeableConcept autopsyPerformedConcept = CommonUtil.findConceptFromCollectionUsingSimpleString(autopsyPerformed, AutopsyPerformedIndicatorUtil.booleanSet);
+		CodeableConcept autopsyResultsAvailableConcept = CommonUtil.findConceptFromCollectionUsingSimpleString(resultsAvailable, AutopsyPerformedIndicatorUtil.booleanSet);
+		setValue(autopsyPerformedConcept);
+		addAutopsyResultsAvailableComponent(autopsyResultsAvailableConcept);
+	}
 
 	public void setDecedent(Decedent decedent) {
 		Reference reference = new Reference(decedent.getId());

diff --git a/...ech/VRDR/model/BirthRecordIdentifier.java → ...hai/VRDR/model/BirthRecordIdentifier.java b/...ech/VRDR/model/BirthRecordIdentifier.java → ...hai/VRDR/model/BirthRecordIdentifier.java
@@ -1,13 +1,13 @@
-package edu.gatech.VRDR.model;
+package edu.gatech.chai.VRDR.model;
 
 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.StringType;
 
 import ca.uhn.fhir.model.api.annotation.ResourceDef;
-import edu.gatech.VRDR.model.util.BirthRecordIdentifierUtil;
-import edu.gatech.VRDR.model.util.CommonUtil;
+import edu.gatech.chai.VRDR.model.util.BirthRecordIdentifierUtil;
+import edu.gatech.chai.VRDR.model.util.CommonUtil;
 
 @ResourceDef(name = "Observation", profile = "http://hl7.org/fhir/us/vrdr/StructureDefinition/VRDR-BirthRecordIdentifier")
 public class BirthRecordIdentifier extends Observation {

diff --git a/...ech/VRDR/model/CauseOfDeathCondition.java → ...hai/VRDR/model/CauseOfDeathCondition.java b/...ech/VRDR/model/CauseOfDeathCondition.java → ...hai/VRDR/model/CauseOfDeathCondition.java
@@ -1,11 +1,10 @@
-package edu.gatech.VRDR.model;
+package edu.gatech.chai.VRDR.model;
 
-import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.r4.model.Condition;
 import org.hl7.fhir.r4.model.Reference;
 
 import ca.uhn.fhir.model.api.annotation.ResourceDef;
-import edu.gatech.VRDR.model.util.CommonUtil;
+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 {
@@ -14,6 +13,12 @@ public CauseOfDeathCondition() {
 		CommonUtil.initResource(this);
 	}
 
+	public CauseOfDeathCondition(Decedent decedent) {
+		super();
+		CommonUtil.initResource(this);
+		setDecedent(decedent);
+	}
+
 	public void setDecedent(Decedent decedent) {
 		Reference reference = new Reference(decedent.getId());
 		this.subject = reference;

diff --git a/...atech/VRDR/model/CauseOfDeathPathway.java → .../chai/VRDR/model/CauseOfDeathPathway.java b/...atech/VRDR/model/CauseOfDeathPathway.java → .../chai/VRDR/model/CauseOfDeathPathway.java
@@ -1,10 +1,10 @@
-package edu.gatech.VRDR.model;
+package edu.gatech.chai.VRDR.model;
 
 import org.hl7.fhir.r4.model.ListResource;
 
 import ca.uhn.fhir.model.api.annotation.ResourceDef;
-import edu.gatech.VRDR.model.util.CauseOfDeathPathwayUtil;
-import edu.gatech.VRDR.model.util.CommonUtil;
+import edu.gatech.chai.VRDR.model.util.CauseOfDeathPathwayUtil;
+import edu.gatech.chai.VRDR.model.util.CommonUtil;
 
 @ResourceDef(name = "List", profile = "http://hl7.org/fhir/us/vrdr/StructureDefinition/VRDR-Cause-of-Death-Pathway")
 public class CauseOfDeathPathway extends ListResource {

diff --git a/...java/edu/gatech/VRDR/model/Certifier.java → ...edu/gatech/chai/VRDR/model/Certifier.java b/...java/edu/gatech/VRDR/model/Certifier.java → ...edu/gatech/chai/VRDR/model/Certifier.java
@@ -1,12 +1,11 @@
-package edu.gatech.VRDR.model;
+package edu.gatech.chai.VRDR.model;
 
 import org.hl7.fhir.r4.model.CodeableConcept;
-import org.hl7.fhir.r4.model.Coding;
 import org.hl7.fhir.r4.model.Identifier;
 import org.hl7.fhir.r4.model.Practitioner;
 
 import ca.uhn.fhir.model.api.annotation.ResourceDef;
-import edu.gatech.VRDR.model.util.CommonUtil;
+import edu.gatech.chai.VRDR.model.util.CommonUtil;
 
 @ResourceDef(name = "Practitioner", profile = "http://hl7.org/fhir/us/vrdr/StructureDefinition/VRDR-Certifier")
 public class Certifier extends Practitioner {
@@ -16,10 +15,9 @@ public Certifier() {
 		CommonUtil.initResource(this);
 	}
 
-	public PractitionerQualificationComponent addQualification(String identifier, String type,String title) {
-		CodeableConcept identifierTypeCodeableConcept = CommonUtil.findConceptFromCollectionUsingSimpleString(type, CommonUtil.deathReportingIdentifierTypeCodes);
+	public PractitionerQualificationComponent addQualification(String identifier, String type) {
+		CodeableConcept identifierTypeCodeableConcept = CommonUtil.findConceptFromCollectionUsingSimpleString(type, CommonUtil.certifierTypeSet);
 		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/...R/model/ConditionContributingToDeath.java → ...R/model/ConditionContributingToDeath.java b/...R/model/ConditionContributingToDeath.java → ...R/model/ConditionContributingToDeath.java
@@ -1,10 +1,10 @@
-package edu.gatech.VRDR.model;
+package edu.gatech.chai.VRDR.model;
 
 import org.hl7.fhir.r4.model.Condition;
 import org.hl7.fhir.r4.model.Reference;
 
 import ca.uhn.fhir.model.api.annotation.ResourceDef;
-import edu.gatech.VRDR.model.util.CommonUtil;
+import edu.gatech.chai.VRDR.model.util.CommonUtil;
 
 @ResourceDef(name = "Condition", profile = "http://hl7.org/fhir/us/vrdr/StructureDefinition/VRDR-Condition-Contributing-To-Death")
 public class ConditionContributingToDeath extends Condition {