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build: add script to sync value sets from IG #88

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build: add script to sync value sets from IG #88

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fbd0007
build: add script to sync valuesets from IG
whichwit Nov 15, 2024
ff9a72c
clean up; remove python-fire
whichwit Nov 15, 2024
2638a42
explicit import
whichwit Nov 15, 2024
f9e9abb
refactor: changes to use generated valuesets from IG
srinivasveesam Nov 18, 2024
080f1ca
refactor: removed unused references from util clases and corrected co…
srinivasveesam Nov 21, 2024
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49 changes: 28 additions & 21 deletions src/main/java/edu/gatech/chai/VRDR/model/CodingStatusValues.java
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Original file line number Diff line number Diff line change
@@ -1,6 +1,10 @@
package edu.gatech.chai.VRDR.model;

import org.hl7.fhir.r4.model.*;
import org.hl7.fhir.r4.model.CodeableConcept;
import org.hl7.fhir.r4.model.Extension;
import org.hl7.fhir.r4.model.IntegerType;
import org.hl7.fhir.r4.model.Parameters;
import org.hl7.fhir.r4.model.StringType;

import ca.uhn.fhir.model.api.annotation.ResourceDef;
import edu.gatech.chai.VRDR.model.util.CodingStatusValuesUtil;
Expand All @@ -13,42 +17,45 @@ public CodingStatusValues() {
super();
CommonUtil.initResource(this);
}

public Parameters addShipmentNumber(String value) {
return addParameter("shipmentNumber",value);
return addParameter("shipmentNumber", value);
}

public Parameters addReceiptDate(String value) {
return addParameter("receiptDate",value);
return addParameter("receiptDate", value);
}

public Parameters addCoderStatus(String value) {
return addParameter("coderStatus",value);
return addParameter("coderStatus", value);
}

public Parameters addIntentionalReject(String value) {
CodeableConcept ccValue = CommonUtil.findConceptFromCollectionUsingSimpleString(value, CodingStatusValuesUtil.intentionalRejectValueset);
return addParameter("intentionalReject",ccValue);
CodeableConcept ccValue = CommonUtil.findConceptFromCollectionUsingSimpleString(value,
CodingStatusValuesUtil.intentionalRejectValueset);
return addParameter("intentionalReject", ccValue);
}

public Parameters addAcmeSystemReject(String value) {
CodeableConcept ccValue = CommonUtil.findConceptFromCollectionUsingSimpleString(value, CodingStatusValuesUtil.intentionalRejectValueset);
return addParameter("acmeSystemReject",ccValue);
CodeableConcept ccValue = CommonUtil.findConceptFromCollectionUsingSimpleString(value,
CodingStatusValuesUtil.systemRejectValueset);
return addParameter("acmeSystemReject", ccValue);
}

public Parameters addTransaxConversion(String value) {
CodeableConcept ccValue = CommonUtil.findConceptFromCollectionUsingSimpleString(value, CodingStatusValuesUtil.intentionalRejectValueset);
return addParameter("transaxConversion",ccValue);
CodeableConcept ccValue = CommonUtil.findConceptFromCollectionUsingSimpleString(value,
CodingStatusValuesUtil.transaxConversionValueset);
return addParameter("transaxConversion", ccValue);
}

public Parameters addParameter(String name, String value) {
ParametersParameterComponent ppc = new ParametersParameterComponent();
ppc.setName(name);
ppc.setValue(new StringType(value));
this.addParameter(ppc);
return this;
}

public Parameters addParameter(String name, CodeableConcept value) {
ParametersParameterComponent ppc = new ParametersParameterComponent();
ppc.setName(name);
Expand All @@ -58,11 +65,11 @@ public Parameters addParameter(String name, CodeableConcept value) {
}

public Integer getCoderStatus() {
return getParameter("coderStatus") == null ? null : ((IntegerType)getParameter("coderStatus")).getValue();
return getParameter("coderStatus") == null ? null : ((IntegerType) getParameter("coderStatus")).getValue();
}

public String getShipmentNumber() {
return getParameter("shipmentNumber") == null ? null : ((StringType)getParameter("shipmentNumber")).getValue();
return getParameter("shipmentNumber") == null ? null : ((StringType) getParameter("shipmentNumber")).getValue();
}

public static final String PartialDateExtensionUrl = "http://hl7.org/fhir/us/vrdr/StructureDefinition/PartialDate";
Expand All @@ -82,7 +89,7 @@ public Integer getReceiptDatePart(String datePartExtensionUrl) {
if (datePart == null || datePart.getValue() == null) {
return null;
}
return ((IntegerType)datePart.getValue()).getValue();
return ((IntegerType) datePart.getValue()).getValue();
}

public Integer getReceiptYear() {
Expand Down
18 changes: 5 additions & 13 deletions src/main/java/edu/gatech/chai/VRDR/model/util/ActivityAtTimeOfDeathUtil.java
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Original file line number Diff line number Diff line change
@@ -1,23 +1,15 @@
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;

import edu.gatech.chai.VRDR.model.valueset.ActivityAtTimeOfDeathVS;

public class ActivityAtTimeOfDeathUtil {
public static final CodeableConcept code = new CodeableConcept()
.addCoding(new Coding(CommonUtil.loincSystemUrl, "80626-5", "Activity at time of death [CDC]"));
public static final String valueSetSystemUrl = "http://hl7.org/fhir/us/vrdr/CodeSystem/vrdr-activity-at-time-of-death-cs";
public static final HashSet<CodeableConcept> valueSet = new HashSet<>(Arrays.asList(
new CodeableConcept().addCoding(new Coding(valueSetSystemUrl,"0","While engaged in sports activity")),
new CodeableConcept().addCoding(new Coding(valueSetSystemUrl,"1","While engaged in leisure activities.")),
new CodeableConcept().addCoding(new Coding(valueSetSystemUrl,"2","While working for income")),
new CodeableConcept().addCoding(new Coding(valueSetSystemUrl,"3","While engaged in other types of work")),
new CodeableConcept().addCoding(new Coding(valueSetSystemUrl,"4","While resting, sleeping, eating, or engaging in other vital activities")),
new CodeableConcept().addCoding(new Coding(valueSetSystemUrl,"8","While engaged in other specified activities.")),
new CodeableConcept().addCoding(new Coding(valueSetSystemUrl,"9","During unspecified activity")),
CommonUtil.unknownCode
));
public static final String valueSetSystemUrl = ActivityAtTimeOfDeathVS.url;
public static final HashSet<CodeableConcept> valueSet = ActivityAtTimeOfDeathVS.valueSet;

}
5 changes: 3 additions & 2 deletions src/main/java/edu/gatech/chai/VRDR/model/util/AutopsyPerformedIndicatorUtil.java
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Original file line number Diff line number Diff line change
@@ -1,18 +1,19 @@
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;
import org.hl7.fhir.r4.model.Observation;
import org.hl7.fhir.r4.model.Observation.ObservationStatus;

import edu.gatech.chai.VRDR.model.valueset.YesNoUnknownNotApplicableVS;

public class AutopsyPerformedIndicatorUtil {
public static final CodeableConcept code = new CodeableConcept()
.addCoding(new Coding(CommonUtil.loincSystemUrl, "85699-7", "Autopsy was performed"));
public static final CodeableConcept componentAutopsyResultsAvailableCode = new CodeableConcept()
.addCoding(new Coding(CommonUtil.loincSystemUrl, "69436-4", "Autopsy results available"));
public static final ObservationStatus status = Observation.ObservationStatus.FINAL;
public static final HashSet<CodeableConcept> booleanSet = new HashSet<>(Arrays.asList(CommonUtil.yesCode, CommonUtil.noCode, CommonUtil.notApplicableCode));
public static final HashSet<CodeableConcept> booleanSet = YesNoUnknownNotApplicableVS.valueSet;
}
26 changes: 8 additions & 18 deletions src/main/java/edu/gatech/chai/VRDR/model/util/CodingStatusValuesUtil.java
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Original file line number Diff line number Diff line change
@@ -1,26 +1,16 @@
package edu.gatech.chai.VRDR.model.util;

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

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

import edu.gatech.chai.VRDR.model.valueset.IntentionalRejectVS;
import edu.gatech.chai.VRDR.model.valueset.SystemRejectVS;
import edu.gatech.chai.VRDR.model.valueset.TransaxConversionVS;

public class CodingStatusValuesUtil {
public static final String intentionalRejectSystemUrl = "http://hl7.org/fhir/us/vrdr/CodeSystem/vrdr-intentional-reject-cs";
public static final String systemRejectSystemUrl = "http://hl7.org/fhir/us/vrdr/CodeSystem/vrdr-system-reject-cs";
public static Set<CodeableConcept> intentionalRejectValueset = new HashSet<CodeableConcept>(Arrays.asList(
new CodeableConcept().addCoding(new Coding(intentionalRejectSystemUrl, "0", "Not Rejected")),
new CodeableConcept().addCoding(new Coding(intentionalRejectSystemUrl, "1", "MICAR Reject Dictionary Match")),
new CodeableConcept().addCoding(new Coding(intentionalRejectSystemUrl, "2", "ACME Reject")),
new CodeableConcept().addCoding(new Coding(intentionalRejectSystemUrl, "3", "MICAR Reject Rule Application")),
new CodeableConcept().addCoding(new Coding(intentionalRejectSystemUrl, "4", "Record Reviewed"))));
public static Set<CodeableConcept> systemRejectValueset = new HashSet<CodeableConcept>(Arrays.asList(
new CodeableConcept().addCoding(new Coding(systemRejectSystemUrl, "1", "Reject1")),
new CodeableConcept().addCoding(new Coding(systemRejectSystemUrl, "2", "Reject2")),
new CodeableConcept().addCoding(new Coding(systemRejectSystemUrl, "3", "Reject3")),
new CodeableConcept().addCoding(new Coding(systemRejectSystemUrl, "4", "Reject4")),
new CodeableConcept().addCoding(new Coding(systemRejectSystemUrl, "5", "Reject5")),
new CodeableConcept().addCoding(new Coding(systemRejectSystemUrl, "9", "Reject9"))));

public static Set<CodeableConcept> intentionalRejectValueset = IntentionalRejectVS.valueSet;
public static Set<CodeableConcept> systemRejectValueset = SystemRejectVS.valueSet;
public static Set<CodeableConcept> transaxConversionValueset = TransaxConversionVS.valueSet;
}
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