Skip to content

Commit

Permalink
Merge pull request #3 from MortalityReporting/ig1.3
Browse files Browse the repository at this point in the history
STU2 Master Merge
  • Loading branch information
MikeRileyGTRI authored Jul 25, 2022
2 parents d1295a7 + d01c6ed commit 99fd172
Show file tree
Hide file tree
Showing 131 changed files with 3,114 additions and 8,207 deletions.
106 changes: 53 additions & 53 deletions pom.xml
Original file line number Diff line number Diff line change
@@ -1,53 +1,53 @@
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>

<groupId>edu.gatech</groupId>
<artifactId>VRDR</artifactId>
<version>v1.2.3-R4-STU1.2</version>
<packaging>jar</packaging>

<name>VRDR</name>
<url>http://maven.apache.org</url>

<properties>
<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>4.1.0</fhir.version>
</properties>

<dependencies>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>4.13.1</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-base</artifactId>
<version>${fhir.version}</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-client</artifactId>
<version>${fhir.version}</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-structures-r4</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-r4</artifactId>
<version>${fhir.version}</version>
</dependency>
</dependencies>
</project>
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>

<groupId>edu.gatech</groupId>
<artifactId>VRDR</artifactId>
<version>v1.3.5-STU2</version>
<packaging>jar</packaging>

<name>VRDR</name>
<url>http://maven.apache.org</url>

<properties>
<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>4.1.0</fhir.version>
</properties>

<dependencies>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>3.8.1</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-base</artifactId>
<version>${fhir.version}</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-client</artifactId>
<version>${fhir.version}</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-structures-r4</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-r4</artifactId>
<version>${fhir.version}</version>
</dependency>
</dependencies>
</project>
248 changes: 128 additions & 120 deletions src/main/java/edu/gatech/chai/VRDR/context/VRDRFhirContext.java
Original file line number Diff line number Diff line change
@@ -1,120 +1,128 @@
package edu.gatech.chai.VRDR.context;

import ca.uhn.fhir.context.FhirContext;
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;

public VRDRFhirContext() {
ctx = FhirContext.forR4();
ctx.setDefaultTypeForProfile("http://hl7.org/fhir/us/vrdr/StructureDefinition/VRDR-Autopsy-Performed-Indicator",
AutopsyPerformedIndicator.class);
ctx.setDefaultTypeForProfile("http://hl7.org/fhir/us/vrdr/StructureDefinition/VRDR-Birth-Record-Identifier",
BirthRecordIdentifier.class);
ctx.setDefaultTypeForProfile("http://hl7.org/fhir/us/vrdr/StructureDefinition/VRDR-Cause-Of-Death-Condition",
CauseOfDeathCondition.class);
ctx.setDefaultTypeForProfile("http://hl7.org/fhir/us/vrdr/StructureDefinition/VRDR-Cause-of-Death-Pathway",
CauseOfDeathPathway.class);
ctx.setDefaultTypeForProfile("http://hl7.org/fhir/us/vrdr/StructureDefinition/VRDR-Certifier",
Certifier.class);
ctx.setDefaultTypeForProfile("http://hl7.org/fhir/us/vrdr/StructureDefinition/VRDR-Condition-Contributing-To-Death",
ConditionContributingToDeath.class);
ctx.setDefaultTypeForProfile("http://hl7.org/fhir/us/vrdr/StructureDefinition/VRDR-Death-Certificate",
DeathCertificate.class);
ctx.setDefaultTypeForProfile(
"http://hl7.org/fhir/us/vrdr/StructureDefinition/VRDR-Death-Certificate-Document",
DeathCertificateDocument.class);
ctx.setDefaultTypeForProfile("http://hl7.org/fhir/us/vrdr/StructureDefinition/VRDR-Death-Certificate-Reference",
DeathCertificateReference.class);
ctx.setDefaultTypeForProfile("http://hl7.org/fhir/us/vrdr/StructureDefinition/VRDR-Death-Certification",
DeathCertification.class);
ctx.setDefaultTypeForProfile("http://hl7.org/fhir/us/vrdr/StructureDefinition/VRDR-Death-Date",
DeathDate.class);
ctx.setDefaultTypeForProfile("http://hl7.org/fhir/us/vrdr/StructureDefinition/VRDR-Death-Location",
DeathLocation.class);
ctx.setDefaultTypeForProfile("http://hl7.org/fhir/us/vrdr/StructureDefinition/VRDR-Death-Pronouncement-Performer",
DeathPronouncementPerformer.class);
ctx.setDefaultTypeForProfile("http://hl7.org/fhir/us/vrdr/StructureDefinition/VRDR-Decedent",
Decedent.class);
ctx.setDefaultTypeForProfile("http://hl7.org/fhir/us/vrdr/StructureDefinition/VRDR-Decedent-Age",
DecedentAge.class);
ctx.setDefaultTypeForProfile("http://hl7.org/fhir/us/vrdr/StructureDefinition/VRDR-Decedent-Disposition-Method",
DecedentDispositionMethod.class);
ctx.setDefaultTypeForProfile("http://hl7.org/fhir/us/vrdr/StructureDefinition/VRDR-Decedent-Education-Level",
DecedentEducationLevel.class);
ctx.setDefaultTypeForProfile("http://hl7.org/fhir/us/vrdr/StructureDefinition/VRDR-Decedent-Usual-Work",
DecedentUsualWork.class);
ctx.setDefaultTypeForProfile("http://hl7.org/fhir/us/vrdr/StructureDefinition/VRDR-Decedent-Father",
DecedentFather.class);
ctx.setDefaultTypeForProfile("http://hl7.org/fhir/us/vrdr/StructureDefinition/VRDR-Decedent-Mother",
DecedentMother.class);
ctx.setDefaultTypeForProfile("http://hl7.org/fhir/us/vrdr/StructureDefinition/VRDR-Decedent-Pregnancy",
DecedentPregnancy.class);
ctx.setDefaultTypeForProfile("http://hl7.org/fhir/us/vrdr/StructureDefinition/VRDR-Decedent-Spouse",
DecedentSpouse.class);
ctx.setDefaultTypeForProfile("http://hl7.org/fhir/us/vrdr/StructureDefinition/VRDR-Decedent-Transportation-Role",
DecedentTransportationRole.class);
ctx.setDefaultTypeForProfile("http://hl7.org/fhir/us/vrdr/StructureDefinition/VRDR-Disposition-Location",
DispositionLocation.class);
ctx.setDefaultTypeForProfile("http://hl7.org/fhir/us/vrdr/StructureDefinition/VRDR-Examiner-Contacted",
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_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",
InjuryLocation.class);
ctx.setDefaultTypeForProfile("http://hl7.org/fhir/us/vrdr/StructureDefinition/VRDR-Interested-Party",
InterestedParty.class);
ctx.setDefaultTypeForProfile("http://hl7.org/fhir/us/vrdr/StructureDefinition/VRDR-Manner-of-Death",
MannerOfDeath.class);
ctx.setDefaultTypeForProfile("http://hl7.org/fhir/us/vrdr/StructureDefinition/VRDR-Mortician",
Mortician.class);
ctx.setDefaultTypeForProfile("http://hl7.org/fhir/us/vrdr/StructureDefinition/VRDR-Tobacco-Use-Contributed-To-Death",
TobaccoUseContributedToDeath.class);
}

public FhirContext getCtx() {
return ctx;
}

public void setCtx(FhirContext ctx) {
this.ctx = ctx;
}

}
package edu.gatech.chai.VRDR.context;

import ca.uhn.fhir.context.FhirContext;
import edu.gatech.chai.VRDR.model.AutopsyPerformedIndicator;
import edu.gatech.chai.VRDR.model.BirthRecordIdentifier;
import edu.gatech.chai.VRDR.model.CauseOfDeathPart1;
import edu.gatech.chai.VRDR.model.CauseOfDeathPart2;
import edu.gatech.chai.VRDR.model.Certifier;
import edu.gatech.chai.VRDR.model.CodedRaceAndEthnicity;
import edu.gatech.chai.VRDR.model.CodingStatusValues;
import edu.gatech.chai.VRDR.model.DeathCertificate;
import edu.gatech.chai.VRDR.model.DeathCertificateDocument;
import edu.gatech.chai.VRDR.model.DeathCertificationProcedure;
import edu.gatech.chai.VRDR.model.DeathDate;
import edu.gatech.chai.VRDR.model.DeathLocation;
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.DecedentMilitaryService;
import edu.gatech.chai.VRDR.model.DecedentMother;
import edu.gatech.chai.VRDR.model.DecedentPregnancyStatus;
import edu.gatech.chai.VRDR.model.DecedentSpouse;
import edu.gatech.chai.VRDR.model.DecedentUsualWork;
import edu.gatech.chai.VRDR.model.DispositionLocation;
import edu.gatech.chai.VRDR.model.EntityAxisCauseOfDeath;
import edu.gatech.chai.VRDR.model.ExaminerContacted;
import edu.gatech.chai.VRDR.model.FuneralHome;
import edu.gatech.chai.VRDR.model.InjuryIncident;
import edu.gatech.chai.VRDR.model.InjuryLocation;
import edu.gatech.chai.VRDR.model.MannerOfDeath;
import edu.gatech.chai.VRDR.model.ManualUnderlyingCauseOfDeath;
import edu.gatech.chai.VRDR.model.Mortician;
import edu.gatech.chai.VRDR.model.PlaceOfInjury;
import edu.gatech.chai.VRDR.model.RecordAxisCauseOfDeath;
import edu.gatech.chai.VRDR.model.SurgeryDate;
import edu.gatech.chai.VRDR.model.TobaccoUseContributedToDeath;

public class VRDRFhirContext {
FhirContext ctx;

public VRDRFhirContext() {
ctx = FhirContext.forR4();
ctx.setDefaultTypeForProfile("http://hl7.org/fhir/us/vrdr/StructureDefinition/vrdr-activity-at-time-of-death",
AutopsyPerformedIndicator.class);
ctx.setDefaultTypeForProfile("http://hl7.org/fhir/us/vrdr/StructureDefinition/vrdr-autopsy-performed-indicator",
AutopsyPerformedIndicator.class);
ctx.setDefaultTypeForProfile("http://hl7.org/fhir/us/vrdr/StructureDefinition/vrdr-birth-record-identifier",
BirthRecordIdentifier.class);
ctx.setDefaultTypeForProfile("http://hl7.org/fhir/us/vrdr/StructureDefinition/vrdr-cause-of-death-part1",
CauseOfDeathPart1.class);
ctx.setDefaultTypeForProfile("http://hl7.org/fhir/us/vrdr/StructureDefinition/vrdr-cause-of-death-part2",
CauseOfDeathPart2.class);
ctx.setDefaultTypeForProfile("http://hl7.org/fhir/us/vrdr/StructureDefinition/vrdr-certifier",
Certifier.class);
ctx.setDefaultTypeForProfile("http://hl7.org/fhir/us/vrdr/StructureDefinition/vrdr-coded-race-and-ethnicity",
CodedRaceAndEthnicity.class);
ctx.setDefaultTypeForProfile("http://hl7.org/fhir/us/vrdr/StructureDefinition/vrdr-coding-status-values",
CodingStatusValues.class);
ctx.setDefaultTypeForProfile("http://hl7.org/fhir/us/vrdr/StructureDefinition/vrdr-death-certificate",
DeathCertificate.class);
ctx.setDefaultTypeForProfile(
"http://hl7.org/fhir/us/vrdr/StructureDefinition/vrdr-death-certificate-document",
DeathCertificateDocument.class);
ctx.setDefaultTypeForProfile("http://hl7.org/fhir/us/vrdr/StructureDefinition/vrdr-death-certification",
DeathCertificationProcedure.class);
ctx.setDefaultTypeForProfile("http://hl7.org/fhir/us/vrdr/StructureDefinition/vrdr-death-date",
DeathDate.class);
ctx.setDefaultTypeForProfile("http://hl7.org/fhir/us/vrdr/StructureDefinition/vrdr-death-location",
DeathLocation.class);
ctx.setDefaultTypeForProfile("http://hl7.org/fhir/us/vrdr/StructureDefinition/vrdr-decedent",
Decedent.class);
ctx.setDefaultTypeForProfile("http://hl7.org/fhir/us/vrdr/StructureDefinition/vrdr-decedent-age",
DecedentAge.class);
ctx.setDefaultTypeForProfile("http://hl7.org/fhir/us/vrdr/StructureDefinition/vrdr-decedent-disposition-method",
DecedentDispositionMethod.class);
ctx.setDefaultTypeForProfile("http://hl7.org/fhir/us/vrdr/StructureDefinition/vrdr-decedent-education-level",
DecedentEducationLevel.class);
ctx.setDefaultTypeForProfile("http://hl7.org/fhir/us/vrdr/StructureDefinition/vrdr-decedent-father",
DecedentFather.class);
ctx.setDefaultTypeForProfile("http://hl7.org/fhir/us/vrdr/StructureDefinition/vrdr-military-service",
DecedentMilitaryService.class);
ctx.setDefaultTypeForProfile("http://hl7.org/fhir/us/vrdr/StructureDefinition/vrdr-decedent-mother",
DecedentMother.class);
ctx.setDefaultTypeForProfile("http://hl7.org/fhir/us/vrdr/StructureDefinition/vrdr-decedent-pregnancy",
DecedentPregnancyStatus.class);
ctx.setDefaultTypeForProfile("http://hl7.org/fhir/us/vrdr/StructureDefinition/vrdr-decedent-spouse",
DecedentSpouse.class);
ctx.setDefaultTypeForProfile("http://hl7.org/fhir/us/vrdr/StructureDefinition/vrdr-decedent-usual-work",
DecedentUsualWork.class);
ctx.setDefaultTypeForProfile("http://hl7.org/fhir/us/vrdr/StructureDefinition/vrdr-disposition-location",
DispositionLocation.class);
ctx.setDefaultTypeForProfile("http://hl7.org/fhir/us/vrdr/StructureDefinition/entity-axis-cause-of-death",
EntityAxisCauseOfDeath.class);
ctx.setDefaultTypeForProfile("http://hl7.org/fhir/us/vrdr/StructureDefinition/vrdr-examiner-contacted",
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-injury-incident",
InjuryIncident.class);
ctx.setDefaultTypeForProfile("http://hl7.org/fhir/us/vrdr/StructureDefinition/vrdr-injury-location",
InjuryLocation.class);
ctx.setDefaultTypeForProfile("http://hl7.org/fhir/us/vrdr/StructureDefinition/vrdr-manner-of-death",
MannerOfDeath.class);
ctx.setDefaultTypeForProfile("http://hl7.org/fhir/us/vrdr/StructureDefinition/vrdr-manual-underlying-cause-of-death",
ManualUnderlyingCauseOfDeath.class);
ctx.setDefaultTypeForProfile("http://hl7.org/fhir/us/vrdr/StructureDefinition/vrdr-mortician",
Mortician.class);
ctx.setDefaultTypeForProfile("http://hl7.org/fhir/us/vrdr/StructureDefinition/vrdr-place-of-injury",
PlaceOfInjury.class);
ctx.setDefaultTypeForProfile("http://hl7.org/fhir/us/vrdr/StructureDefinition/vrdr-record-axis-cause-of-death",
RecordAxisCauseOfDeath.class);
ctx.setDefaultTypeForProfile("http://hl7.org/fhir/us/vrdr/StructureDefinition/vrdr-surgery-date",
SurgeryDate.class);
ctx.setDefaultTypeForProfile("http://hl7.org/fhir/us/vrdr/StructureDefinition/vrdr-Tobacco-Use-Contributed-To-Death",
TobaccoUseContributedToDeath.class);
}

public FhirContext getCtx() {
return ctx;
}

public void setCtx(FhirContext ctx) {
this.ctx = ctx;
}

}
Original file line number Diff line number Diff line change
@@ -0,0 +1,33 @@
package edu.gatech.chai.VRDR.model;

import org.hl7.fhir.r4.model.CodeableConcept;
import org.hl7.fhir.r4.model.Observation;

import ca.uhn.fhir.model.api.annotation.ResourceDef;
import edu.gatech.chai.VRDR.model.util.ActivityAtTimeOfDeathUtil;
import edu.gatech.chai.VRDR.model.util.CommonUtil;

@ResourceDef(name = "Observation", profile = "http://hl7.org/fhir/us/vrdr/StructureDefinition/vrdr-activity-at-time-of-death")
public class ActivityAtTimeOfDeath extends Observation{
/**
*
*/
private static final long serialVersionUID = 343890908919147936L;

public ActivityAtTimeOfDeath() {
super();
CommonUtil.initResource(this);
setCode(ActivityAtTimeOfDeathUtil.code);
}

public ActivityAtTimeOfDeath(CodeableConcept value) {
this();
setValue(value);
}

public ActivityAtTimeOfDeath(String value) {
this();
CodeableConcept valueCode = CommonUtil.findConceptFromCollectionUsingSimpleString(value, ActivityAtTimeOfDeathUtil.valueSet);
setValue(valueCode);
}
}
Loading

0 comments on commit 99fd172

Please sign in to comment.