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Added missing jurisdiction ids. Switched value urls to loinc/snomed o…
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…nly. No more oids for values.
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@MikeRileyGTRI
MikeRileyGTRI committed Sep 20, 2021
1 parent 7a38853 commit f92f843
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Showing 9 changed files with 113 additions and 79 deletions.
12 changes: 12 additions & 0 deletions src/main/java/edu/gatech/chai/VRDR/model/DeathLocation.java
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Expand Up @@ -26,6 +26,18 @@ public DeathLocation(String name, String jurisdicitionId, String description, Co
setPhysicalType(physicalType);
}

public DeathLocation(String name, String jurisdicitionId, String description, String type, Address address,
CodeableConcept physicalType) {
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));
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2 changes: 1 addition & 1 deletion src/main/java/edu/gatech/chai/VRDR/model/InjuryIncident.java
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Expand Up @@ -59,7 +59,7 @@ public void addInjuredAtWorkComponent(String injuredAtWork) {
}

public void addTransportationEventIndicatorComponent(String transportationRelationship) {
CodeableConcept transportationEventIndicatorCode = CommonUtil.findConceptFromCollectionUsingSimpleString(transportationRelationship, CommonUtil.yesNoNASet);
CodeableConcept transportationEventIndicatorCode = CommonUtil.findConceptFromCollectionUsingSimpleString(transportationRelationship, CommonUtil.yesNoUnknownSet);
addTransportationEventIndicatorComponent(transportationEventIndicatorCode);
}

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124 changes: 63 additions & 61 deletions src/main/java/edu/gatech/chai/VRDR/model/util/CommonUtil.java
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Expand Up @@ -30,7 +30,7 @@ public class CommonUtil {
public static String snomedSystemUrl = "http://snomed.info/sct";
public static String loincSystemUrl = "http://loinc.org";
public static String withinCityLimitsIndicatorUrl = "http://hl7.org/fhir/us/vrdr/StructureDefinition/Within-City-Limits-Indicator";
public static String locationJurisdictionUrl = "2.16.840.1.113883.6.92";
public static String locationJurisdictionOID = "urn:oid:2.16.840.1.113883.6.92";
public static String dataAbsentReasonUrl = "http://terminology.hl7.org/CodeSystem/data-absent-reason";
public static final String partialDatePartAbsentReasonURL = "http://hl7.org/fhir/us/vrdr/StructureDefinition/VRDR-Partial-date-part-absent-reason";
public static final String partialDateDateYearURL = "date-year";
Expand All @@ -57,7 +57,9 @@ public class CommonUtil {
public static final HashSet<CodeableConcept> certifierTypeSet = new HashSet<>(Arrays.asList(
new CodeableConcept().addCoding(new Coding(CommonUtil.snomedSystemUrl,"455381000124109","Medical Examiner/Coroner")),
new CodeableConcept().addCoding(new Coding(CommonUtil.snomedSystemUrl,"434641000124105","Physician certifed and pronounced death certificate")),
new CodeableConcept().addCoding(new Coding(CommonUtil.snomedSystemUrl,"434651000124107","Physician certified death certificate"))));
new CodeableConcept().addCoding(new Coding(CommonUtil.snomedSystemUrl,"434651000124107","Physician certified death certificate")),
new CodeableConcept().addCoding(new Coding(CommonUtil.nullFlavorHL7System,"OTH","Other"))
));
public static final HashSet<CodeableConcept> yesNoUnknownSet = new HashSet<>(Arrays.asList(yesCode,noCode,unknownCode));
public static final HashSet<CodeableConcept> yesNoNASet = new HashSet<>(Arrays.asList(yesCode,noCode,notApplicableCode));
public static final HashSet<CodeType> dataAbsentReasonCodeSet = new HashSet<>(Arrays.asList(
Expand Down Expand Up @@ -91,66 +93,66 @@ public class CommonUtil {
new CodeableConcept().addCoding(new Coding(CommonUtil.dataAbsentReasonUrl,"not-performed", "Not Performed")),
new CodeableConcept().addCoding(new Coding(CommonUtil.dataAbsentReasonUrl,"not-permitted", "Not Permitted"))));
public static final HashSet<CodeableConcept> locationJurisdictionalConceptSet = new HashSet<>(Arrays.asList(
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionUrl,"01","Alabama")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionUrl,"02","Alaska")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionUrl,"05", "Arkansas")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionUrl,"60", "American Samoa")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionUrl, "04", "Arizona")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionUrl,"06", "California")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionUrl,"08", "Colorado")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionUrl,"09", "Connecticut")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionUrl,"10", "Delaware")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionUrl,"11", "District of Columbia")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionUrl,"64", "Federated States of Micronesia")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionUrl,"12", "Florida")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionUrl,"13", "Georgia")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionUrl,"66", "Guam")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionUrl,"15", "Hawaii")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionUrl,"84", "Howland Island")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionUrl,"16", "Idaho")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionUrl,"17", "Illinois")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionUrl,"18", "Indiana")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionUrl,"19", "Iowa")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionUrl,"20", "Kansas")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionUrl,"21", "Kentucky")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionUrl,"22", "Louisiana")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionUrl,"23", "Maine")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionUrl,"24", "Maryland")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionUrl,"25", "Massachusetts")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionUrl,"26", "Michigan")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionUrl,"27", "Minnesota")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionUrl,"28", "Mississippi")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionUrl,"29", "Missouri")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionUrl,"MP", "Northern Mariana Islands")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionUrl,"30", "Montana")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionUrl,"31", "Nebraska")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionUrl,"32", "Nevada")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionUrl,"33", "New Hampshire")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionUrl,"34", "New Jersey")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionUrl,"35", "New Mexico")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionOID,"01","Alabama")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionOID,"02","Alaska")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionOID,"05", "Arkansas")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionOID,"60", "American Samoa")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionOID, "04", "Arizona")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionOID,"06", "California")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionOID,"08", "Colorado")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionOID,"09", "Connecticut")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionOID,"10", "Delaware")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionOID,"11", "District of Columbia")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionOID,"64", "Federated States of Micronesia")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionOID,"12", "Florida")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionOID,"13", "Georgia")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionOID,"66", "Guam")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionOID,"15", "Hawaii")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionOID,"84", "Howland Island")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionOID,"16", "Idaho")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionOID,"17", "Illinois")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionOID,"18", "Indiana")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionOID,"19", "Iowa")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionOID,"20", "Kansas")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionOID,"21", "Kentucky")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionOID,"22", "Louisiana")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionOID,"23", "Maine")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionOID,"24", "Maryland")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionOID,"25", "Massachusetts")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionOID,"26", "Michigan")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionOID,"27", "Minnesota")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionOID,"28", "Mississippi")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionOID,"29", "Missouri")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionOID,"MP", "Northern Mariana Islands")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionOID,"30", "Montana")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionOID,"31", "Nebraska")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionOID,"32", "Nevada")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionOID,"33", "New Hampshire")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionOID,"34", "New Jersey")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionOID,"35", "New Mexico")),
new CodeableConcept().addCoding(new Coding("urn:oid:2.16.840.1.113883.6.245","9755772", "New York City")), //Unique codesystem just for New York City
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionUrl,"36", "New York")), //Unique codesystem just for New York City
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionUrl,"37", "North Carolina")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionUrl,"38", "North Dekota")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionUrl,"69", "Northern Mariana Islands")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionUrl,"39", "Ohio")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionUrl,"40", "Oklahoma")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionUrl,"41", "Oregon")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionUrl,"42", "Pennsylvania")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionUrl,"72", "Puerto Rico")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionUrl,"44", "Rhode Island")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionUrl,"45", "South Carolina")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionUrl,"46", "South Dakota")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionUrl,"47", "Tennessee")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionUrl,"48", "Texas")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionUrl,"78", "U.S. Virgin Islands")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionUrl,"49", "Utah")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionUrl,"50", "Vermont")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionUrl,"51", "Virginia")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionUrl,"53", "Washington")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionUrl,"54", "West Virginia")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionUrl,"55", "Wisconsin")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionUrl,"56", "Wyoming"))));
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionOID,"36", "New York")), //Unique codesystem just for New York City
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionOID,"37", "North Carolina")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionOID,"38", "North Dekota")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionOID,"69", "Northern Mariana Islands")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionOID,"39", "Ohio")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionOID,"40", "Oklahoma")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionOID,"41", "Oregon")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionOID,"42", "Pennsylvania")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionOID,"72", "Puerto Rico")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionOID,"44", "Rhode Island")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionOID,"45", "South Carolina")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionOID,"46", "South Dakota")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionOID,"47", "Tennessee")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionOID,"48", "Texas")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionOID,"78", "U.S. Virgin Islands")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionOID,"49", "Utah")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionOID,"50", "Vermont")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionOID,"51", "Virginia")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionOID,"53", "Washington")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionOID,"54", "West Virginia")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionOID,"55", "Wisconsin")),
new CodeableConcept().addCoding(new Coding(CommonUtil.locationJurisdictionOID,"56", "Wyoming"))));
public static Extension getExtension(DomainResource resource, String url) {
for (Extension extension : resource.getExtension()) {
if (extension.getUrl().equals(url)) {
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4 changes: 4 additions & 0 deletions src/main/java/edu/gatech/chai/VRDR/model/util/DeathCertificationUtil.java
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Original file line number Diff line number Diff line change
@@ -1,5 +1,8 @@
package edu.gatech.chai.VRDR.model.util;

import java.util.Arrays;
import java.util.HashSet;

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

Expand All @@ -8,4 +11,5 @@ public class DeathCertificationUtil {
.addCoding(new Coding(CommonUtil.snomedSystemUrl,"103693007","Diagnostic procedure"));
public static final CodeableConcept codeFixedValue = new CodeableConcept()
.addCoding(new Coding(CommonUtil.snomedSystemUrl,"308646001","Death certification"));

}
16 changes: 16 additions & 0 deletions src/main/java/edu/gatech/chai/VRDR/model/util/DeathLocationUtil.java
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@@ -1,5 +1,21 @@
package edu.gatech.chai.VRDR.model.util;

import java.util.Arrays;
import java.util.HashSet;

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

public class DeathLocationUtil {
public static String locationJurisdictionIdExtension = "http://hl7.org/fhir/us/vrdr/StructureDefinition/Location-Jurisdiction-Id";
public static final HashSet<CodeableConcept> placeOfDeathTypeSet = new HashSet<>(Arrays.asList(
new CodeableConcept().addCoding(new Coding(CommonUtil.snomedSystemUrl,"63238001","Dead on arrival at hospital")),
new CodeableConcept().addCoding(new Coding(CommonUtil.snomedSystemUrl,"440081000124100","Death in home")),
new CodeableConcept().addCoding(new Coding(CommonUtil.snomedSystemUrl,"440071000124103","Death in hospice")),
new CodeableConcept().addCoding(new Coding(CommonUtil.snomedSystemUrl,"16983000","Death in hospital")),
new CodeableConcept().addCoding(new Coding(CommonUtil.snomedSystemUrl,"450391000124102","Death in hospital-based emergency department or outpatient department (event)")),
new CodeableConcept().addCoding(new Coding(CommonUtil.snomedSystemUrl,"450381000124100","Death in nursing home or long term care facility (event)")),
new CodeableConcept().addCoding(new Coding(CommonUtil.nullFlavorHL7System,"OTH","Other")),
new CodeableConcept().addCoding(new Coding(CommonUtil.nullFlavorHL7System,"UNK","Unknown"))
));
}
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