Source code

001package org.hl7.fhir.convertors.misc;
002
003
004import java.io.File;
005import java.io.FileInputStream;
006import java.io.FileNotFoundException;
007import java.io.FileOutputStream;
008import java.io.IOException;
009import java.sql.Connection;
010import java.sql.DriverManager;
011import java.sql.SQLException;
012import java.sql.Statement;
013import java.util.Date;
014import java.util.List;
015import java.util.ArrayList;
016import java.util.Scanner;
017
018import org.hl7.fhir.exceptions.FHIRException;
019import org.hl7.fhir.r5.formats.IParser.OutputStyle;
020import org.hl7.fhir.r5.formats.JsonParser;
021import org.hl7.fhir.r5.model.CodeSystem;
022import org.hl7.fhir.r5.model.BooleanType;
023import org.hl7.fhir.r5.model.StringType;
024import org.hl7.fhir.r5.model.CodeType;
025import org.hl7.fhir.r5.model.CodeSystem.ConceptDefinitionComponent;
026import org.hl7.fhir.r5.model.CodeSystem.ConceptDefinitionDesignationComponent;
027import org.hl7.fhir.r5.model.CodeSystem.ConceptPropertyComponent;
028import org.hl7.fhir.r5.model.CodeSystem.PropertyType;
029import org.hl7.fhir.r5.model.Coding;
030import org.hl7.fhir.r5.model.Enumerations.CodeSystemContentMode;
031import org.hl7.fhir.r5.model.Enumerations.PublicationStatus;
032import org.hl7.fhir.r5.terminologies.CodeSystemUtilities;
033import org.hl7.fhir.utilities.CSVReader;
034import org.hl7.fhir.utilities.Utilities;
035
036public class CPTImporter {
037
038  public static void main(String[] args) throws FHIRException, FileNotFoundException, IOException, ClassNotFoundException, SQLException {
039    new CPTImporter().doImport(args[0], args[1], args[2]);
040
041  }
042
043
044  private void doImport(String src, String version, String dst) throws FHIRException, FileNotFoundException, IOException, ClassNotFoundException, SQLException {
045
046    CodeSystem cs = new CodeSystem();
047    cs.setId("cpt");
048    cs.setUrl("http://www.ama-assn.org/go/cpt");
049    cs.setVersion(version);
050    cs.setName("AmaCPT");
051    cs.setTitle("AMA CPT");
052    cs.setStatus(PublicationStatus.ACTIVE);
053    cs.setDate(new Date());
054    cs.setContent(CodeSystemContentMode.COMPLETE);
055    cs.setCompositional(true);
056    cs.setPublisher("AMA");
057    cs.setValueSet("http://hl7.org/fhir/ValueSet/cpt-all");
058    cs.setCopyright("CPT © Copyright 2019 American Medical Association. All rights reserved. AMA and CPT are registered trademarks of the American Medical Association.");
059    cs.addProperty().setCode("modifier").setDescription("Whether code is a modifier code").setType(PropertyType.BOOLEAN);
060    cs.addProperty().setCode("modified").setDescription("Whether code has been modified (all base codes are not modified)").setType(PropertyType.BOOLEAN);
061    cs.addProperty().setCode("orthopox").setDescription("Whether code is one of the Pathology and Laboratory and Immunization Code(s) for Orthopoxvirus").setType(PropertyType.BOOLEAN);
062    cs.addProperty().setCode("telemedicine").setDescription("Whether code is appropriate for use with telemedicine (and the telemedicine modifier)").setType(PropertyType.BOOLEAN);
063    cs.addProperty().setCode("kind").setDescription("Kind of Code (see metadata)").setType(PropertyType.CODE);
064
065    defineMetadata(cs);
066    
067    System.out.println("LONGULT: "+readCodes(cs, Utilities.path(src, "LONGULT.txt"), false, null, null, null));
068    System.out.println("LONGUT: "+readCodes(cs, Utilities.path(src, "LONGUT.txt"), false, "upper", null, null));
069    System.out.println("MEDU: "+readCodes(cs, Utilities.path(src, "MEDU.txt"), false, "med", null, null));
070    System.out.println("SHORTU: "+readCodes(cs, Utilities.path(src, "SHORTU.txt"), false, "short", null, null));
071    System.out.println("ConsumerDescriptor: "+readCodes(cs, Utilities.path(src, "ConsumerDescriptor.txt"), true, "consumer", null, null));
072    System.out.println("ClinicianDescriptor: "+readCodes(cs, Utilities.path(src, "ClinicianDescriptor.txt"), true, "clinician", null, null));
073    System.out.println("OrthopoxvirusCodes: "+readCodes(cs, Utilities.path(src, "OrthopoxvirusCodes.txt"), false, null, null, "orthopox"));
074  
075    System.out.println("modifiers: "+processModifiers(cs, Utilities.path(src, "modifiers.csv")));
076    System.out.println("appendix P: "+processAppendixP(cs));
077    
078    
079    System.out.println("-------------------");
080    System.out.println(cs.getConcept().size());
081    int c = 0;
082    int k = 0;
083    for (ConceptDefinitionComponent cc: cs.getConcept()) {
084      c = Integer.max(c, cc.getProperty().size());
085      if (cc.getProperty().size() > 3) {
086        k++;
087      }
088    }
089    System.out.println(c);
090    System.out.println(k);
091    
092    new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(dst), cs); 
093    produceDB(Utilities.changeFileExt(dst, ".db"), cs);
094    
095    cs.setContent(CodeSystemContentMode.FRAGMENT);
096    cs.getConcept().removeIf(cc -> !Utilities.existsInList(cc.getCode(), "metadata-kinds", "metadata-designations", "99202", "99203", "0001A", "99252", "25", "P1", "1P", "F1", "95"));
097    new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.changeFileExt(dst, "-fragment.json")), cs); 
098    produceDB(Utilities.changeFileExt(dst, "-fragment.db"), cs);
099  }
100
101  private String processAppendixP(CodeSystem cs) {
102    List<String> tcodes = new ArrayList<>();
103    tcodes.add("90785");
104    tcodes.add("90791");
105    tcodes.add("90792");
106    tcodes.add("90832");
107    tcodes.add("90833");
108    tcodes.add("90834");
109    tcodes.add("90836");
110    tcodes.add("90837");
111    tcodes.add("90838");
112    tcodes.add("90839");
113    tcodes.add("90840");
114    tcodes.add("90845");
115    tcodes.add("90846");
116    tcodes.add("90847");
117    tcodes.add("92507");
118    tcodes.add("92508");
119    tcodes.add("92521");
120    tcodes.add("92522");
121    tcodes.add("92523");
122    tcodes.add("92524");
123    tcodes.add("96040");
124    tcodes.add("96110");
125    tcodes.add("96116");
126    tcodes.add("96160");
127    tcodes.add("96161");
128    tcodes.add("97802");
129    tcodes.add("97803");
130    tcodes.add("97804");
131    tcodes.add("99406");
132    tcodes.add("99407");
133    tcodes.add("99408");
134    tcodes.add("99409");
135    tcodes.add("99497");
136    tcodes.add("99498");
137
138    for (String c : tcodes) { 
139      ConceptDefinitionComponent cc = CodeSystemUtilities.findCode(cs.getConcept(), c);
140      if (cc == null) {
141        throw new Error("unable to find tcode "+c);
142      }
143      cc.addProperty().setCode("telemedicine").setValue(new BooleanType(true));
144    }    
145    return String.valueOf(tcodes.size());
146  }
147
148
149  private void produceDB(String path, CodeSystem cs) throws ClassNotFoundException, SQLException {
150    Connection con = connect(path);
151
152    Statement stmt = con.createStatement();
153    stmt.execute("insert into Information (name, value) values ('version', "+cs.getVersion()+")");        
154    for (ConceptDefinitionComponent cc: cs.getConcept()) {
155      if (!cc.getCode().startsWith("metadata")) {
156        stmt.execute("insert into Concepts (code, modifier) values ('"+cc.getCode()+"', "+isModifier(cc)+")");
157        int i = 0;
158        if (cc.hasDisplay()) {
159          stmt.execute("insert into Designations (code, type, sequence, value) values ('"+cc.getCode()+"', 'display', 0, '"+Utilities.escapeSql(cc.getDisplay())+"')");
160          i++;
161        }
162        for (ConceptDefinitionDesignationComponent d : cc.getDesignation()) {
163          stmt.execute("insert into Designations (code, type, sequence, value) values ('"+cc.getCode()+"', '"+d.getUse().getCode()+"', "+i+", '"+Utilities.escapeSql(d.getValue())+"')");
164          i++;
165        }
166        i = 0;
167        for (ConceptPropertyComponent p : cc.getProperty()) {
168          if (!Utilities.existsInList(p.getCode(), "modified", "modifier")) {
169            stmt.execute("insert into Properties (code, name, sequence, value) values ('"+cc.getCode()+"', '"+p.getCode()+"', "+i+", '"+p.getValue().primitiveValue()+"')");
170            i++;
171          }
172        }    
173      }
174    }
175
176  }
177
178  private String isModifier(ConceptDefinitionComponent cc) {
179    for (ConceptPropertyComponent p : cc.getProperty()) {
180      if (p.getCode().equals("modifier")) {
181        return p.getValue().primitiveValue().equals("true") ? "1" : "0";
182      }
183    }
184    return "0";
185  }
186
187
188  private Connection connect(String dest) throws SQLException, ClassNotFoundException {
189    //    Class.forName("com.mysql.jdbc.Driver");  
190    //    con = DriverManager.getConnection("jdbc:mysql://localhost:3306/omop?useSSL=false","root",{pwd}); 
191    new File(dest).delete();
192    Connection con = DriverManager.getConnection("jdbc:sqlite:"+dest); 
193    makeMetadataTable(con);
194    makeConceptsTable(con);
195    makeDesignationsTable(con);
196    makePropertiesTable(con);
197    return con;    
198  }
199  
200  private void makeDesignationsTable(Connection con) throws SQLException {
201    Statement stmt = con.createStatement();
202    stmt.execute("CREATE TABLE Designations (\r\n"+
203        "`code` varchar(15) NOT NULL,\r\n"+
204        "`type` varchar(15) NOT NULL,\r\n"+
205        "`sequence` int NOT NULL,\r\n"+
206        "`value` text NOT NULL,\r\n"+
207        "PRIMARY KEY (`code`, `type`, `sequence`))\r\n");
208  }
209
210
211  private void makePropertiesTable(Connection con) throws SQLException {
212
213    Statement stmt = con.createStatement();
214    stmt.execute("CREATE TABLE Properties (\r\n"+
215        "`code` varchar(15) NOT NULL,\r\n"+
216        "`name` varchar(15) NOT NULL,\r\n"+
217        "`sequence` int NOT NULL,\r\n"+
218        "`value` varchar(15) NOT NULL,\r\n"+
219        "PRIMARY KEY (`code`, `name`, `sequence`))\r\n");
220
221  }
222
223
224  private void makeConceptsTable(Connection con) throws SQLException {
225
226    Statement stmt = con.createStatement();
227    stmt.execute("CREATE TABLE Concepts (\r\n"+
228        "`code` varchar(15) NOT NULL,\r\n"+
229        "`modifier` int DEFAULT NULL,\r\n"+
230        "PRIMARY KEY (`code`))\r\n");
231
232  }
233
234
235  private void makeMetadataTable(Connection con) throws SQLException {
236
237    Statement stmt = con.createStatement();
238    stmt.execute("CREATE TABLE Information (\r\n"+
239        "`name` varchar(64) NOT NULL,\r\n"+
240        "`value` varchar(64) DEFAULT NULL,\r\n"+
241        "PRIMARY KEY (`name`))\r\n");
242
243  }
244
245
246  private void defineMetadata(CodeSystem cs) {
247    ConceptDefinitionComponent pc = mm(cs.addConcept().setCode("metadata-kinds"));
248    mm(pc.addConcept()).setCode("code").setDisplay("A normal CPT code");
249    mm(pc.addConcept()).setCode("cat-1").setDisplay("CPT Level I Modifiers");
250    mm(pc.addConcept()).setCode("cat-2").setDisplay("A Category II code or modifier");
251    mm(pc.addConcept()).setCode("physical-status").setDisplay("Anesthesia Physical Status Modifiers");
252    mm(pc.addConcept()).setCode("general").setDisplay("A general modifier");
253    mm(pc.addConcept()).setCode("hcpcs").setDisplay("Level II (HCPCS/National) Modifiers");
254    mm(pc.addConcept()).setCode("metadata").setDisplay("A kind of code or designation");
255
256    ConceptDefinitionComponent dc = mm(cs.addConcept().setCode("metadata-designations"));
257    mm(dc.addConcept()).setCode("upper").setDisplay("Uppercase variant of the display");
258    mm(dc.addConcept()).setCode("med").setDisplay("Medium length variant of the display (all uppercase)");
259    mm(dc.addConcept()).setCode("short").setDisplay("Short length variant of the display (all uppercase)");
260    mm(dc.addConcept()).setCode("consumer").setDisplay("Consumer Friendly representation for the concept");
261    mm(dc.addConcept()).setCode("clinician").setDisplay("Clinician Friendly representation for the concept (can be more than one per concept)");
262  }
263
264  private ConceptDefinitionComponent mm(ConceptDefinitionComponent cc) {
265    cc.addProperty().setCode("kind").setValue(new CodeType("metadata"));
266    return cc;
267  }
268
269  private int processModifiers(CodeSystem cs, String path) throws FHIRException, FileNotFoundException, IOException {
270    CSVReader csv = new CSVReader(new FileInputStream(path));
271    csv.readHeaders();
272
273    int res = 0;
274    while (csv.line()) {
275      String code = csv.cell("Code");
276      String general = csv.cell("General");
277      String physicalStatus = csv.cell("PhysicalStatus");
278      String levelOne = csv.cell("LevelOne");
279      String levelTwo = csv.cell("LevelTwo");
280      String hcpcs = csv.cell("HCPCS");
281      String defn = csv.cell("Definition");
282
283      res = Integer.max(res, defn.length());
284      ConceptDefinitionComponent cc = cs.addConcept().setCode(code);
285      cc.setDisplay(defn);    
286      cc.addProperty().setCode("modified").setValue(new BooleanType(false));
287      cc.addProperty().setCode("modifier").setValue(new BooleanType(true));
288      if ("1".equals(general)) { 
289        cc.addProperty().setCode("kind").setValue(new CodeType("general"));
290      }
291      if ("1".equals(physicalStatus)) { 
292        cc.addProperty().setCode("kind").setValue(new CodeType("physical-status"));
293      }
294      if ("1".equals(levelOne)) { 
295        cc.addProperty().setCode("kind").setValue(new CodeType("cat-1"));
296      }
297      if ("1".equals(levelTwo)) { 
298        cc.addProperty().setCode("kind").setValue(new CodeType("cat-2"));
299      }
300      if ("1".equals(hcpcs)) { 
301        cc.addProperty().setCode("kind").setValue(new CodeType("hcpcs"));
302      }
303    }
304    return res;
305  }
306
307  private int readCodes(CodeSystem cs, String path, boolean hasConceptId, String use, String type, String boolProp) throws IOException {
308    int res = 0;
309    FileInputStream inputStream = null;
310    Scanner sc = null;
311    try {
312        inputStream = new FileInputStream(path);
313        sc = new Scanner(inputStream, "UTF-8");
314        while (sc.hasNextLine()) {
315          String line = sc.nextLine();
316          if (hasConceptId) {
317            line = line.substring(7).trim();
318          }
319          String code = line.substring(0, 5);
320          String desc = line.substring(6);
321          if (desc.contains("\t")) {
322            desc = desc.substring(desc.indexOf("\t")+1);
323          }
324          res = Integer.max(res, desc.length());
325          ConceptDefinitionComponent cc = CodeSystemUtilities.getCode(cs, code);
326          if (cc == null) {
327            cc = cs.addConcept().setCode(code);
328            cc.addProperty().setCode("modifier").setValue(new BooleanType(false));
329            cc.addProperty().setCode("modified").setValue(new BooleanType(false));
330            if (type == null) {
331              if (Utilities.isInteger(code)) {
332                cc.addProperty().setCode("kind").setValue(new CodeType("code"));              
333              } else {
334                cc.addProperty().setCode("kind").setValue(new CodeType("cat-2"));                            
335              }
336            } else { 
337              cc.addProperty().setCode("kind").setValue(new CodeType(type));
338            }
339          } else if (type != null) {
340            cc.addProperty().setCode("kind").setValue(new CodeType(type));
341          }
342          if (boolProp != null) {
343            cc.addProperty().setCode(boolProp).setValue(new BooleanType(true));
344          }
345          if (use == null) {
346            if (cc.hasDisplay()) {
347              System.err.println("?");
348            }
349            cc.setDisplay(desc);            
350          } else {
351            cc.addDesignation().setUse(new Coding("http://www.ama-assn.org/go/cpt", use, null)).setValue(desc);
352          }
353        }
354        // note that Scanner suppresses exceptions
355        if (sc.ioException() != null) {
356          throw sc.ioException();
357        }
358    } finally {
359        if (inputStream != null) {
360            inputStream.close();
361        }
362        if (sc != null) {
363            sc.close();
364        }
365    }
366    return res;
367  }
368
369
370}