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update CPT model per changes to doco

This commit is contained in:
Grahame Grieve 2023-08-18 13:48:24 +10:00
parent fa54f7748e
commit 5078a95016
1 changed files with 67 additions and 11 deletions
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78
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/CPTImporter.java
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@ -11,6 +11,8 @@ import java.sql.DriverManager;
import java.sql.SQLException;
import java.sql.Statement;
import java.util.Date;
import java.util.List;
import java.util.ArrayList;
import java.util.Scanner;
import org.hl7.fhir.exceptions.FHIRException;
@ -56,19 +58,23 @@ public class CPTImporter {
cs.setCopyright("CPT © Copyright 2019 American Medical Association. All rights reserved. AMA and CPT are registered trademarks of the American Medical Association.");
cs.addProperty().setCode("modifier").setDescription("Whether code is a modifier code").setType(PropertyType.BOOLEAN);
cs.addProperty().setCode("modified").setDescription("Whether code has been modified (all base codes are not modified)").setType(PropertyType.BOOLEAN);
cs.addProperty().setCode("orthopox").setDescription("Whether code is one of the Pathology and Laboratory and Immunization Code(s) for Orthopoxvirus").setType(PropertyType.BOOLEAN);
cs.addProperty().setCode("telemedicine").setDescription("Whether code is appropriate for use with telemedicine (and the telemedicine modifier)").setType(PropertyType.BOOLEAN);
cs.addProperty().setCode("kind").setDescription("Kind of Code (see metadata)").setType(PropertyType.CODE);
defineMetadata(cs);
System.out.println(readCodes(cs, Utilities.path(src, "LONGULT.txt"), false, null, null));
System.out.println(readCodes(cs, Utilities.path(src, "LONGUT.txt"), false, "upper", null));
System.out.println(readCodes(cs, Utilities.path(src, "MEDU.txt"), false, "med", null));
System.out.println(readCodes(cs, Utilities.path(src, "SHORTU.txt"), false, "short", null));
System.out.println(readCodes(cs, Utilities.path(src, "ConsumerDescriptor.txt"), true, "consumer", null));
System.out.println(readCodes(cs, Utilities.path(src, "ClinicianDescriptor.txt"), true, "clinician", null));
System.out.println(readCodes(cs, Utilities.path(src, "OrthopoxvirusCodes.txt"), false, null, "orthopod"));
System.out.println("LONGULT: "+readCodes(cs, Utilities.path(src, "LONGULT.txt"), false, null, null, null));
System.out.println("LONGUT: "+readCodes(cs, Utilities.path(src, "LONGUT.txt"), false, "upper", null, null));
System.out.println("MEDU: "+readCodes(cs, Utilities.path(src, "MEDU.txt"), false, "med", null, null));
System.out.println("SHORTU: "+readCodes(cs, Utilities.path(src, "SHORTU.txt"), false, "short", null, null));
System.out.println("ConsumerDescriptor: "+readCodes(cs, Utilities.path(src, "ConsumerDescriptor.txt"), true, "consumer", null, null));
System.out.println("ClinicianDescriptor: "+readCodes(cs, Utilities.path(src, "ClinicianDescriptor.txt"), true, "clinician", null, null));
System.out.println("OrthopoxvirusCodes: "+readCodes(cs, Utilities.path(src, "OrthopoxvirusCodes.txt"), false, null, null, "orthopox"));
System.out.println(processModifiers(cs, Utilities.path(src, "modifiers.csv")));
System.out.println("modifiers: "+processModifiers(cs, Utilities.path(src, "modifiers.csv")));
System.out.println("appendix P: "+processAppendixP(cs));
System.out.println("-------------------");
System.out.println(cs.getConcept().size());
@ -87,11 +93,59 @@ public class CPTImporter {
produceDB(Utilities.changeFileExt(dst, ".db"), cs);
cs.setContent(CodeSystemContentMode.FRAGMENT);
cs.getConcept().removeIf(cc -> !Utilities.existsInList(cc.getCode(), "metadata-kinds", "metadata-designations", "99202", "99203", "0001A", "25", "P1", "1P", "F1"));
cs.getConcept().removeIf(cc -> !Utilities.existsInList(cc.getCode(), "metadata-kinds", "metadata-designations", "99202", "99203", "0001A", "99252", "25", "P1", "1P", "F1", "95"));
new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.changeFileExt(dst, "-fragment.json")), cs);
produceDB(Utilities.changeFileExt(dst, "-fragment.db"), cs);
}
private String processAppendixP(CodeSystem cs) {
List<String> tcodes = new ArrayList<>();
tcodes.add("90785");
tcodes.add("90791");
tcodes.add("90792");
tcodes.add("90832");
tcodes.add("90833");
tcodes.add("90834");
tcodes.add("90836");
tcodes.add("90837");
tcodes.add("90838");
tcodes.add("90839");
tcodes.add("90840");
tcodes.add("90845");
tcodes.add("90846");
tcodes.add("90847");
tcodes.add("92507");
tcodes.add("92508");
tcodes.add("92521");
tcodes.add("92522");
tcodes.add("92523");
tcodes.add("92524");
tcodes.add("96040");
tcodes.add("96110");
tcodes.add("96116");
tcodes.add("96160");
tcodes.add("96161");
tcodes.add("97802");
tcodes.add("97803");
tcodes.add("97804");
tcodes.add("99406");
tcodes.add("99407");
tcodes.add("99408");
tcodes.add("99409");
tcodes.add("99497");
tcodes.add("99498");
for (String c : tcodes) {
ConceptDefinitionComponent cc = CodeSystemUtilities.findCode(cs.getConcept(), c);
if (cc == null) {
throw new Error("unable to find tcode "+c);
}
cc.addProperty().setCode("telemedicine").setValue(new BooleanType(true));
}
return String.valueOf(tcodes.size());
}
private void produceDB(String path, CodeSystem cs) throws ClassNotFoundException, SQLException {
Connection con = connect(path);
@ -197,7 +251,6 @@ public class CPTImporter {
mm(pc.addConcept()).setCode("physical-status").setDisplay("Anesthesia Physical Status Modifiers");
mm(pc.addConcept()).setCode("general").setDisplay("A general modifier");
mm(pc.addConcept()).setCode("hcpcs").setDisplay("Level II (HCPCS/National) Modifiers");
mm(pc.addConcept()).setCode("orthopox").setDisplay("");
mm(pc.addConcept()).setCode("metadata").setDisplay("A kind of code or designation");
ConceptDefinitionComponent dc = mm(cs.addConcept().setCode("metadata-designations"));
@ -251,7 +304,7 @@ public class CPTImporter {
return res;
}
private int readCodes(CodeSystem cs, String path, boolean hasConceptId, String use, String type) throws IOException {
private int readCodes(CodeSystem cs, String path, boolean hasConceptId, String use, String type, String boolProp) throws IOException {
int res = 0;
FileInputStream inputStream = null;
Scanner sc = null;
@ -286,6 +339,9 @@ public class CPTImporter {
} else if (type != null) {
cc.addProperty().setCode("kind").setValue(new CodeType(type));
}
if (boolProp != null) {
cc.addProperty().setCode(boolProp).setValue(new BooleanType(true));
}
if (use == null) {
if (cc.hasDisplay()) {
System.err.println("?");