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CPT Importer

This commit is contained in:
Grahame Grieve 2023-08-05 20:58:16 +10:00
parent 006058a379
commit 1fd7efe28b
2 changed files with 313 additions and 0 deletions
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309
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/CPTImporter.java Normal file
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@ -0,0 +1,309 @@
package org.hl7.fhir.convertors.misc;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.IOException;
import java.sql.Connection;
import java.sql.DriverManager;
import java.sql.SQLException;
import java.sql.Statement;
import java.util.Date;
import java.util.Scanner;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r5.formats.IParser.OutputStyle;
import org.hl7.fhir.r5.formats.JsonParser;
import org.hl7.fhir.r5.model.CodeSystem;
import org.hl7.fhir.r5.model.BooleanType;
import org.hl7.fhir.r5.model.StringType;
import org.hl7.fhir.r5.model.CodeType;
import org.hl7.fhir.r5.model.CodeSystem.ConceptDefinitionComponent;
import org.hl7.fhir.r5.model.CodeSystem.ConceptDefinitionDesignationComponent;
import org.hl7.fhir.r5.model.CodeSystem.ConceptPropertyComponent;
import org.hl7.fhir.r5.model.CodeSystem.PropertyType;
import org.hl7.fhir.r5.model.Coding;
import org.hl7.fhir.r5.model.Enumerations.CodeSystemContentMode;
import org.hl7.fhir.r5.model.Enumerations.PublicationStatus;
import org.hl7.fhir.r5.terminologies.CodeSystemUtilities;
import org.hl7.fhir.utilities.CSVReader;
import org.hl7.fhir.utilities.Utilities;
public class CPTImporter {
public static void main(String[] args) throws FHIRException, FileNotFoundException, IOException, ClassNotFoundException, SQLException {
new CPTImporter().doImport(args[0], args[1], args[2]);
}
private Connection con;
private void doImport(String src, String version, String dst) throws FHIRException, FileNotFoundException, IOException, ClassNotFoundException, SQLException {
CodeSystem cs = new CodeSystem();
cs.setId("cpt");
cs.setUrl("http://www.ama-assn.org/go/cpt");
cs.setVersion(version);
cs.setName("AmaCPT");
cs.setTitle("AMA CPT");
cs.setStatus(PublicationStatus.ACTIVE);
cs.setDate(new Date());
cs.setContent(CodeSystemContentMode.COMPLETE);
cs.setCompositional(true);
cs.setPublisher("AMA");
cs.setValueSet("http://hl7.org/fhir/ValueSet/cpt-all");
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("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(processModifiers(cs, Utilities.path(src, "modifiers.csv")));
System.out.println("-------------------");
System.out.println(cs.getConcept().size());
int c = 0;
int k = 0;
for (ConceptDefinitionComponent cc: cs.getConcept()) {
c = Integer.max(c, cc.getProperty().size());
if (cc.getProperty().size() > 3) {
k++;
}
}
System.out.println(c);
System.out.println(k);
new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(dst), cs);
connect(Utilities.changeFileExt(dst, ".db"));
Statement stmt = con.createStatement();
stmt.execute("insert into Information (name, value) values ('version', "+cs.getVersion()+")");
for (ConceptDefinitionComponent cc: cs.getConcept()) {
if (!cc.getCode().startsWith("metadata")) {
stmt.execute("insert into Concepts (code, modifier) values ('"+cc.getCode()+"', "+isModifier(cc)+")");
int i = 0;
if (cc.hasDisplay()) {
stmt.execute("insert into Designations (code, type, sequence, value) values ('"+cc.getCode()+"', 0, 0, '"+Utilities.escapeSql(cc.getDisplay())+"')");
i++;
}
for (ConceptDefinitionDesignationComponent d : cc.getDesignation()) {
stmt.execute("insert into Designations (code, type, sequence, value) values ('"+cc.getCode()+"', '"+d.getUse().getCode()+"', "+i+", '"+Utilities.escapeSql(d.getValue())+"')");
i++;
}
i = 0;
for (ConceptPropertyComponent p : cc.getProperty()) {
if (!Utilities.existsInList(p.getCode(), "modified", "modifier")) {
stmt.execute("insert into Properties (code, name, sequence, value) values ('"+cc.getCode()+"', '"+p.getCode()+"', "+i+", '"+p.getValue().primitiveValue()+"')");
i++;
}
}
}
}
cs.getConcept().removeIf(cc -> !Utilities.existsInList(cc.getCode(), "metadata-kinds", "metadata-designations", "99202", "25"));
new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(dst+"-fragment"), cs);
}
private String isModifier(ConceptDefinitionComponent cc) {
for (ConceptPropertyComponent p : cc.getProperty()) {
if (p.getCode().equals("modifier")) {
return p.getValue().primitiveValue().equals("true") ? "1" : "0";
}
}
return "0";
}
private void connect(String dest) throws SQLException, ClassNotFoundException {
// Class.forName("com.mysql.jdbc.Driver");
// con = DriverManager.getConnection("jdbc:mysql://localhost:3306/omop?useSSL=false","root",{pwd});
new File(dest).delete();
con = DriverManager.getConnection("jdbc:sqlite:"+dest);
makeMetadataTable();
makeConceptsTable();
makeDesignationsTable();
makePropertiesTable();
}
private void makeDesignationsTable() throws SQLException {
Statement stmt = con.createStatement();
stmt.execute("CREATE TABLE Designations (\r\n"+
"`code` varchar(15) NOT NULL,\r\n"+
"`type` varchar(15) NOT NULL,\r\n"+
"`sequence` int NOT NULL,\r\n"+
"`value` text NOT NULL,\r\n"+
"PRIMARY KEY (`code`, `type`, `sequence`))\r\n");
}
private void makePropertiesTable() throws SQLException {
Statement stmt = con.createStatement();
stmt.execute("CREATE TABLE Properties (\r\n"+
"`code` varchar(15) NOT NULL,\r\n"+
"`name` varchar(15) NOT NULL,\r\n"+
"`sequence` int NOT NULL,\r\n"+
"`value` varchar(15) NOT NULL,\r\n"+
"PRIMARY KEY (`code`, `name`, `sequence`))\r\n");
}
private void makeConceptsTable() throws SQLException {
Statement stmt = con.createStatement();
stmt.execute("CREATE TABLE Concepts (\r\n"+
"`code` varchar(15) NOT NULL,\r\n"+
"`modifier` int DEFAULT NULL,\r\n"+
"PRIMARY KEY (`code`))\r\n");
}
private void makeMetadataTable() throws SQLException {
Statement stmt = con.createStatement();
stmt.execute("CREATE TABLE Information (\r\n"+
"`name` varchar(64) NOT NULL,\r\n"+
"`value` varchar(64) DEFAULT NULL,\r\n"+
"PRIMARY KEY (`name`))\r\n");
}
private void defineMetadata(CodeSystem cs) {
ConceptDefinitionComponent pc = mm(cs.addConcept().setCode("metadata-kinds"));
mm(pc.addConcept()).setCode("code").setDisplay("A normal CPT code");
mm(pc.addConcept()).setCode("cat-1").setDisplay("CPT Level I Modifiers");
mm(pc.addConcept()).setCode("cat-2").setDisplay("A Category II code or modifier");
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"));
mm(dc.addConcept()).setCode("upper").setDisplay("Uppercase variant of the display");
mm(dc.addConcept()).setCode("med").setDisplay("Medium length variant of the display (all uppercase)");
mm(dc.addConcept()).setCode("short").setDisplay("Short length variant of the display (all uppercase)");
mm(dc.addConcept()).setCode("consumer").setDisplay("Consumer Friendly representation for the concept");
mm(dc.addConcept()).setCode("clinician").setDisplay("Clinician Friendly representation for the concept (can be more than one per concept)");
}
private ConceptDefinitionComponent mm(ConceptDefinitionComponent cc) {
cc.addProperty().setCode("kind").setValue(new CodeType("metadata"));
return cc;
}
private int processModifiers(CodeSystem cs, String path) throws FHIRException, FileNotFoundException, IOException {
CSVReader csv = new CSVReader(new FileInputStream(path));
csv.readHeaders();
int res = 0;
while (csv.line()) {
String code = csv.cell("Code");
String general = csv.cell("General");
String physicalStatus = csv.cell("PhysicalStatus");
String levelOne = csv.cell("LevelOne");
String levelTwo = csv.cell("LevelTwo");
String hcpcs = csv.cell("HCPCS");
String defn = csv.cell("Definition");
res = Integer.max(res, defn.length());
ConceptDefinitionComponent cc = cs.addConcept().setCode(code);
cc.setDisplay(defn);
cc.addProperty().setCode("modified").setValue(new BooleanType(false));
cc.addProperty().setCode("modifier").setValue(new BooleanType(true));
if ("1".equals(general)) {
cc.addProperty().setCode("kind").setValue(new CodeType("general"));
}
if ("1".equals(physicalStatus)) {
cc.addProperty().setCode("kind").setValue(new CodeType("physical-status"));
}
if ("1".equals(levelOne)) {
cc.addProperty().setCode("kind").setValue(new CodeType("cat-1"));
}
if ("1".equals(levelTwo)) {
cc.addProperty().setCode("kind").setValue(new CodeType("cat-2"));
}
if ("1".equals(hcpcs)) {
cc.addProperty().setCode("kind").setValue(new CodeType("hcpcs"));
}
}
return res;
}
private int readCodes(CodeSystem cs, String path, boolean hasConceptId, String use, String type) throws IOException {
int res = 0;
FileInputStream inputStream = null;
Scanner sc = null;
try {
inputStream = new FileInputStream(path);
sc = new Scanner(inputStream, "UTF-8");
while (sc.hasNextLine()) {
String line = sc.nextLine();
if (hasConceptId) {
line = line.substring(7).trim();
}
String code = line.substring(0, 5);
String desc = line.substring(6);
if (desc.contains("\t")) {
desc = desc.substring(desc.indexOf("\t")+1);
}
res = Integer.max(res, desc.length());
ConceptDefinitionComponent cc = CodeSystemUtilities.getCode(cs, code);
if (cc == null) {
cc = cs.addConcept().setCode(code);
cc.addProperty().setCode("modifier").setValue(new BooleanType(false));
cc.addProperty().setCode("modified").setValue(new BooleanType(false));
if (type == null) {
if (Utilities.isInteger(code)) {
cc.addProperty().setCode("kind").setValue(new CodeType("code"));
} else {
cc.addProperty().setCode("kind").setValue(new CodeType("cat-2"));
}
} else {
cc.addProperty().setCode("kind").setValue(new CodeType(type));
}
} else if (type != null) {
cc.addProperty().setCode("kind").setValue(new CodeType(type));
}
if (use == null) {
if (cc.hasDisplay()) {
System.err.println("?");
}
cc.setDisplay(desc);
} else {
cc.addDesignation().setUse(new Coding("http://www.ama-assn.org/go/cpt", use, null)).setValue(desc);
}
}
// note that Scanner suppresses exceptions
if (sc.ioException() != null) {
throw sc.ioException();
}
} finally {
if (inputStream != null) {
inputStream.close();
}
if (sc != null) {
sc.close();
}
}
return res;
}
}

4
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/Utilities.java
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@ -2127,4 +2127,8 @@ public class Utilities {
return url.contains("/") ? url.substring(url.lastIndexOf("/")+1) : url;
}
public static String escapeSql(String s) {
return s.replace("'", "''");
}
}