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;
035import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
036
037public class CPTImporter {
038
039  public static void main(String[] args) throws FHIRException, FileNotFoundException, IOException, ClassNotFoundException, SQLException {
040    new CPTImporter().doImport(args[0], args[1], args[2]);
041
042  }
043
044
045  private void doImport(String src, String version, String dst) throws FHIRException, FileNotFoundException, IOException, ClassNotFoundException, SQLException {
046
047    CodeSystem cs = new CodeSystem();
048    cs.setId("cpt");
049    cs.setUrl("http://www.ama-assn.org/go/cpt");
050    cs.setVersion(version);
051    cs.setName("AmaCPT");
052    cs.setTitle("AMA CPT");
053    cs.setStatus(PublicationStatus.ACTIVE);
054    cs.setDate(new Date());
055    cs.setContent(CodeSystemContentMode.COMPLETE);
056    cs.setCompositional(true);
057    cs.setPublisher("AMA");
058    cs.setValueSet("http://hl7.org/fhir/ValueSet/cpt-all");
059    cs.setCopyright("CPT © Copyright 2019 American Medical Association. All rights reserved. AMA and CPT are registered trademarks of the American Medical Association.");
060    cs.addProperty().setCode("modifier").setDescription("Whether code is a modifier code").setType(PropertyType.BOOLEAN);
061    cs.addProperty().setCode("modified").setDescription("Whether code has been modified (all base codes are not modified)").setType(PropertyType.BOOLEAN);
062    cs.addProperty().setCode("orthopox").setDescription("Whether code is one of the Pathology and Laboratory and Immunization Code(s) for Orthopoxvirus").setType(PropertyType.BOOLEAN);
063    cs.addProperty().setCode("telemedicine").setDescription("Whether code is appropriate for use with telemedicine (and the telemedicine modifier)").setType(PropertyType.BOOLEAN);
064    cs.addProperty().setCode("kind").setDescription("Kind of Code (see metadata)").setType(PropertyType.CODE);
065
066    defineMetadata(cs);
067    
068    System.out.println("LONGULT: "+readCodes(cs, Utilities.path(src, "LONGULT.txt"), false, null, null, null));
069    System.out.println("LONGUT: "+readCodes(cs, Utilities.path(src, "LONGUT.txt"), false, "upper", null, null));
070    System.out.println("MEDU: "+readCodes(cs, Utilities.path(src, "MEDU.txt"), false, "med", null, null));
071    System.out.println("SHORTU: "+readCodes(cs, Utilities.path(src, "SHORTU.txt"), false, "short", null, null));
072    System.out.println("ConsumerDescriptor: "+readCodes(cs, Utilities.path(src, "ConsumerDescriptor.txt"), true, "consumer", null, null));
073    System.out.println("ClinicianDescriptor: "+readCodes(cs, Utilities.path(src, "ClinicianDescriptor.txt"), true, "clinician", null, null));
074    System.out.println("OrthopoxvirusCodes: "+readCodes(cs, Utilities.path(src, "OrthopoxvirusCodes.txt"), false, null, null, "orthopox"));
075  
076    System.out.println("modifiers: "+processModifiers(cs, Utilities.path(src, "modifiers.csv")));
077    System.out.println("appendix P: "+processAppendixP(cs));
078    
079    
080    System.out.println("-------------------");
081    System.out.println(cs.getConcept().size());
082    int c = 0;
083    int k = 0;
084    for (ConceptDefinitionComponent cc: cs.getConcept()) {
085      c = Integer.max(c, cc.getProperty().size());
086      if (cc.getProperty().size() > 3) {
087        k++;
088      }
089    }
090    System.out.println(c);
091    System.out.println(k);
092    
093    new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(dst), cs); 
094    produceDB(Utilities.changeFileExt(dst, ".db"), cs);
095    
096    cs.setContent(CodeSystemContentMode.FRAGMENT);
097    cs.getConcept().removeIf(cc -> !Utilities.existsInList(cc.getCode(), "metadata-kinds", "metadata-designations", "99202", "99203", "0001A", "99252", "25", "P1", "1P", "F1", "95"));
098    new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(Utilities.changeFileExt(dst, "-fragment.json")), cs); 
099    produceDB(Utilities.changeFileExt(dst, "-fragment.db"), cs);
100  }
101
102  private String processAppendixP(CodeSystem cs) {
103    List<String> tcodes = new ArrayList<>();
104    tcodes.add("90785");
105    tcodes.add("90791");
106    tcodes.add("90792");
107    tcodes.add("90832");
108    tcodes.add("90833");
109    tcodes.add("90834");
110    tcodes.add("90836");
111    tcodes.add("90837");
112    tcodes.add("90838");
113    tcodes.add("90839");
114    tcodes.add("90840");
115    tcodes.add("90845");
116    tcodes.add("90846");
117    tcodes.add("90847");
118    tcodes.add("92507");
119    tcodes.add("92508");
120    tcodes.add("92521");
121    tcodes.add("92522");
122    tcodes.add("92523");
123    tcodes.add("92524");
124    tcodes.add("96040");
125    tcodes.add("96110");
126    tcodes.add("96116");
127    tcodes.add("96160");
128    tcodes.add("96161");
129    tcodes.add("97802");
130    tcodes.add("97803");
131    tcodes.add("97804");
132    tcodes.add("99406");
133    tcodes.add("99407");
134    tcodes.add("99408");
135    tcodes.add("99409");
136    tcodes.add("99497");
137    tcodes.add("99498");
138
139    for (String c : tcodes) { 
140      ConceptDefinitionComponent cc = CodeSystemUtilities.findCode(cs.getConcept(), c);
141      if (cc == null) {
142        throw new Error("unable to find tcode "+c);
143      }
144      cc.addProperty().setCode("telemedicine").setValue(new BooleanType(true));
145    }    
146    return String.valueOf(tcodes.size());
147  }
148
149
150  private void produceDB(String path, CodeSystem cs) throws ClassNotFoundException, SQLException, IOException {
151    Connection con = connect(path);
152
153    Statement stmt = con.createStatement();
154    stmt.execute("insert into Information (name, value) values ('version', "+cs.getVersion()+")");        
155    for (ConceptDefinitionComponent cc: cs.getConcept()) {
156      if (!cc.getCode().startsWith("metadata")) {
157        stmt.execute("insert into Concepts (code, modifier) values ('"+cc.getCode()+"', "+isModifier(cc)+")");
158        int i = 0;
159        if (cc.hasDisplay()) {
160          stmt.execute("insert into Designations (code, type, sequence, value) values ('"+cc.getCode()+"', 'display', 0, '"+Utilities.escapeSql(cc.getDisplay())+"')");
161          i++;
162        }
163        for (ConceptDefinitionDesignationComponent d : cc.getDesignation()) {
164          stmt.execute("insert into Designations (code, type, sequence, value) values ('"+cc.getCode()+"', '"+d.getUse().getCode()+"', "+i+", '"+Utilities.escapeSql(d.getValue())+"')");
165          i++;
166        }
167        i = 0;
168        for (ConceptPropertyComponent p : cc.getProperty()) {
169          if (!Utilities.existsInList(p.getCode(), "modified", "modifier")) {
170            stmt.execute("insert into Properties (code, name, sequence, value) values ('"+cc.getCode()+"', '"+p.getCode()+"', "+i+", '"+p.getValue().primitiveValue()+"')");
171            i++;
172          }
173        }    
174      }
175    }
176
177  }
178
179  private String isModifier(ConceptDefinitionComponent cc) {
180    for (ConceptPropertyComponent p : cc.getProperty()) {
181      if (p.getCode().equals("modifier")) {
182        return p.getValue().primitiveValue().equals("true") ? "1" : "0";
183      }
184    }
185    return "0";
186  }
187
188
189  private Connection connect(String dest) throws SQLException, ClassNotFoundException, IOException {
190    //    Class.forName("com.mysql.jdbc.Driver");  
191    //    con = DriverManager.getConnection("jdbc:mysql://localhost:3306/omop?useSSL=false","root",{pwd}); 
192    ManagedFileAccess.file(dest).delete();
193    Connection con = DriverManager.getConnection("jdbc:sqlite:"+dest); 
194    makeMetadataTable(con);
195    makeConceptsTable(con);
196    makeDesignationsTable(con);
197    makePropertiesTable(con);
198    return con;    
199  }
200  
201  private void makeDesignationsTable(Connection con) throws SQLException {
202    Statement stmt = con.createStatement();
203    stmt.execute("CREATE TABLE Designations (\r\n"+
204        "`code` varchar(15) NOT NULL,\r\n"+
205        "`type` varchar(15) NOT NULL,\r\n"+
206        "`sequence` int NOT NULL,\r\n"+
207        "`value` text NOT NULL,\r\n"+
208        "PRIMARY KEY (`code`, `type`, `sequence`))\r\n");
209  }
210
211
212  private void makePropertiesTable(Connection con) throws SQLException {
213
214    Statement stmt = con.createStatement();
215    stmt.execute("CREATE TABLE Properties (\r\n"+
216        "`code` varchar(15) NOT NULL,\r\n"+
217        "`name` varchar(15) NOT NULL,\r\n"+
218        "`sequence` int NOT NULL,\r\n"+
219        "`value` varchar(15) NOT NULL,\r\n"+
220        "PRIMARY KEY (`code`, `name`, `sequence`))\r\n");
221
222  }
223
224
225  private void makeConceptsTable(Connection con) throws SQLException {
226
227    Statement stmt = con.createStatement();
228    stmt.execute("CREATE TABLE Concepts (\r\n"+
229        "`code` varchar(15) NOT NULL,\r\n"+
230        "`modifier` int DEFAULT NULL,\r\n"+
231        "PRIMARY KEY (`code`))\r\n");
232
233  }
234
235
236  private void makeMetadataTable(Connection con) throws SQLException {
237
238    Statement stmt = con.createStatement();
239    stmt.execute("CREATE TABLE Information (\r\n"+
240        "`name` varchar(64) NOT NULL,\r\n"+
241        "`value` varchar(64) DEFAULT NULL,\r\n"+
242        "PRIMARY KEY (`name`))\r\n");
243
244  }
245
246
247  private void defineMetadata(CodeSystem cs) {
248    ConceptDefinitionComponent pc = mm(cs.addConcept().setCode("metadata-kinds"));
249    mm(pc.addConcept()).setCode("code").setDisplay("A normal CPT code");
250    mm(pc.addConcept()).setCode("cat-1").setDisplay("CPT Level I Modifiers");
251    mm(pc.addConcept()).setCode("cat-2").setDisplay("A Category II code or modifier");
252    mm(pc.addConcept()).setCode("physical-status").setDisplay("Anesthesia Physical Status Modifiers");
253    mm(pc.addConcept()).setCode("general").setDisplay("A general modifier");
254    mm(pc.addConcept()).setCode("hcpcs").setDisplay("Level II (HCPCS/National) Modifiers");
255    mm(pc.addConcept()).setCode("metadata").setDisplay("A kind of code or designation");
256
257    ConceptDefinitionComponent dc = mm(cs.addConcept().setCode("metadata-designations"));
258    mm(dc.addConcept()).setCode("upper").setDisplay("Uppercase variant of the display");
259    mm(dc.addConcept()).setCode("med").setDisplay("Medium length variant of the display (all uppercase)");
260    mm(dc.addConcept()).setCode("short").setDisplay("Short length variant of the display (all uppercase)");
261    mm(dc.addConcept()).setCode("consumer").setDisplay("Consumer Friendly representation for the concept");
262    mm(dc.addConcept()).setCode("clinician").setDisplay("Clinician Friendly representation for the concept (can be more than one per concept)");
263  }
264
265  private ConceptDefinitionComponent mm(ConceptDefinitionComponent cc) {
266    cc.addProperty().setCode("kind").setValue(new CodeType("metadata"));
267    return cc;
268  }
269
270  private int processModifiers(CodeSystem cs, String path) throws FHIRException, FileNotFoundException, IOException {
271    CSVReader csv = new CSVReader(ManagedFileAccess.inStream(path));
272    csv.readHeaders();
273
274    int res = 0;
275    while (csv.line()) {
276      String code = csv.cell("Code");
277      String general = csv.cell("General");
278      String physicalStatus = csv.cell("PhysicalStatus");
279      String levelOne = csv.cell("LevelOne");
280      String levelTwo = csv.cell("LevelTwo");
281      String hcpcs = csv.cell("HCPCS");
282      String defn = csv.cell("Definition");
283
284      res = Integer.max(res, defn.length());
285      ConceptDefinitionComponent cc = cs.addConcept().setCode(code);
286      cc.setDisplay(defn);    
287      cc.addProperty().setCode("modified").setValue(new BooleanType(false));
288      cc.addProperty().setCode("modifier").setValue(new BooleanType(true));
289      if ("1".equals(general)) { 
290        cc.addProperty().setCode("kind").setValue(new CodeType("general"));
291      }
292      if ("1".equals(physicalStatus)) { 
293        cc.addProperty().setCode("kind").setValue(new CodeType("physical-status"));
294      }
295      if ("1".equals(levelOne)) { 
296        cc.addProperty().setCode("kind").setValue(new CodeType("cat-1"));
297      }
298      if ("1".equals(levelTwo)) { 
299        cc.addProperty().setCode("kind").setValue(new CodeType("cat-2"));
300      }
301      if ("1".equals(hcpcs)) { 
302        cc.addProperty().setCode("kind").setValue(new CodeType("hcpcs"));
303      }
304    }
305    return res;
306  }
307
308  private int readCodes(CodeSystem cs, String path, boolean hasConceptId, String use, String type, String boolProp) throws IOException {
309    int res = 0;
310    FileInputStream inputStream = null;
311    Scanner sc = null;
312    try {
313        inputStream = ManagedFileAccess.inStream(path);
314        sc = new Scanner(inputStream, "UTF-8");
315        while (sc.hasNextLine()) {
316          String line = sc.nextLine();
317          if (hasConceptId) {
318            line = line.substring(7).trim();
319          }
320          String code = line.substring(0, 5);
321          String desc = line.substring(6);
322          if (desc.contains("\t")) {
323            desc = desc.substring(desc.indexOf("\t")+1);
324          }
325          res = Integer.max(res, desc.length());
326          ConceptDefinitionComponent cc = CodeSystemUtilities.getCode(cs, code);
327          if (cc == null) {
328            cc = cs.addConcept().setCode(code);
329            cc.addProperty().setCode("modifier").setValue(new BooleanType(false));
330            cc.addProperty().setCode("modified").setValue(new BooleanType(false));
331            if (type == null) {
332              if (Utilities.isInteger(code)) {
333                cc.addProperty().setCode("kind").setValue(new CodeType("code"));              
334              } else {
335                cc.addProperty().setCode("kind").setValue(new CodeType("cat-2"));                            
336              }
337            } else { 
338              cc.addProperty().setCode("kind").setValue(new CodeType(type));
339            }
340          } else if (type != null) {
341            cc.addProperty().setCode("kind").setValue(new CodeType(type));
342          }
343          if (boolProp != null) {
344            cc.addProperty().setCode(boolProp).setValue(new BooleanType(true));
345          }
346          if (use == null) {
347            if (cc.hasDisplay()) {
348              System.err.println("?");
349            }
350            cc.setDisplay(desc);            
351          } else {
352            cc.addDesignation().setUse(new Coding("http://www.ama-assn.org/go/cpt", use, null)).setValue(desc);
353          }
354        }
355        // note that Scanner suppresses exceptions
356        if (sc.ioException() != null) {
357          throw sc.ioException();
358        }
359    } finally {
360        if (inputStream != null) {
361            inputStream.close();
362        }
363        if (sc != null) {
364            sc.close();
365        }
366    }
367    return res;
368  }
369
370
371}