001package org.hl7.fhir.r4.terminologies;
002
003/*
004  Copyright (c) 2011+, HL7, Inc.
005  All rights reserved.
006  
007  Redistribution and use in source and binary forms, with or without modification, 
008  are permitted provided that the following conditions are met:
009    
010   * Redistributions of source code must retain the above copyright notice, this 
011     list of conditions and the following disclaimer.
012   * Redistributions in binary form must reproduce the above copyright notice, 
013     this list of conditions and the following disclaimer in the documentation 
014     and/or other materials provided with the distribution.
015   * Neither the name of HL7 nor the names of its contributors may be used to 
016     endorse or promote products derived from this software without specific 
017     prior written permission.
018  
019  THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 
020  ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 
021  WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. 
022  IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, 
023  INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT 
024  NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR 
025  PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, 
026  WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) 
027  ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE 
028  POSSIBILITY OF SUCH DAMAGE.
029  
030 */
031
032import java.io.FileInputStream;
033import java.io.FileNotFoundException;
034import java.io.FileOutputStream;
035import java.io.IOException;
036
037import javax.xml.parsers.DocumentBuilder;
038import javax.xml.parsers.DocumentBuilderFactory;
039import javax.xml.parsers.ParserConfigurationException;
040
041import org.hl7.fhir.exceptions.FHIRFormatError;
042import org.hl7.fhir.r4.formats.XmlParser;
043import org.hl7.fhir.r4.model.Bundle;
044import org.hl7.fhir.r4.model.Bundle.BundleType;
045import org.hl7.fhir.r4.model.CodeableConcept;
046import org.hl7.fhir.r4.model.Coding;
047import org.hl7.fhir.r4.model.DateTimeType;
048import org.hl7.fhir.r4.model.InstantType;
049import org.hl7.fhir.r4.model.Meta;
050import org.hl7.fhir.utilities.Utilities;
051import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
052import org.hl7.fhir.utilities.xml.XMLUtil;
053import org.w3c.dom.Document;
054import org.w3c.dom.Element;
055import org.xml.sax.SAXException;
056import org.xmlpull.v1.XmlPullParserException;
057
058/**
059 * This class converts the LOINC XML representation that the FHIR build tool
060 * uses internally to a set of DataElements in an atom feed
061 * 
062 * @author Grahame
063 *
064 */
065@Deprecated
066public class LoincToDEConvertor {
067
068  public static void main(String[] args)
069      throws FHIRFormatError, IOException, XmlPullParserException, SAXException, ParserConfigurationException {
070    if (args.length == 0) {
071      System.out.println("FHIR LOINC to CDE convertor. ");
072      System.out.println("");
073      System.out.println("This tool converts from LOINC to A set of DataElement definitions.");
074      System.out.println("");
075      System.out.println("Usage: [jar(path?)] [dest] (-defn [definitions]) where: ");
076      System.out.println("* [dest] is a file name of the bundle to produce");
077      System.out.println(
078          "* [definitions] is the file name of a file produced by exporting the main LOINC table from the mdb to XML");
079      System.out.println("");
080    } else {
081      LoincToDEConvertor exe = new LoincToDEConvertor();
082      exe.setDest(args[0]);
083      for (int i = 1; i < args.length; i++) {
084        if (args[i].equals("-defn"))
085          exe.setDefinitions(args[i + 1]);
086      }
087      exe.process();
088    }
089
090  }
091
092  private String dest;
093  private String definitions;
094
095  public String getDest() {
096    return dest;
097  }
098
099  public void setDest(String dest) {
100    this.dest = dest;
101  }
102
103  public String getDefinitions() {
104    return definitions;
105  }
106
107  public void setDefinitions(String definitions) {
108    this.definitions = definitions;
109  }
110
111  private Document xml;
112  private Bundle bundle;
113  private DateTimeType now;
114
115  public Bundle process(String sourceFile)
116      throws FileNotFoundException, SAXException, IOException, ParserConfigurationException {
117    this.definitions = sourceFile;
118    log("Begin. Produce Loinc CDEs in " + dest + " from " + definitions);
119    loadLoinc();
120    log("LOINC loaded");
121
122    now = DateTimeType.now();
123
124    bundle = new Bundle();
125    bundle.setType(BundleType.COLLECTION);
126    bundle.setId("http://hl7.org/fhir/commondataelement/loinc");
127    bundle.setMeta(new Meta().setLastUpdatedElement(InstantType.now()));
128
129    processLoincCodes();
130    return bundle;
131  }
132
133  public void process()
134      throws FHIRFormatError, IOException, XmlPullParserException, SAXException, ParserConfigurationException {
135    log("Begin. Produce Loinc CDEs in " + dest + " from " + definitions);
136    loadLoinc();
137    log("LOINC loaded");
138
139    now = DateTimeType.now();
140
141    bundle = new Bundle();
142    bundle.setId("http://hl7.org/fhir/commondataelement/loinc");
143    bundle.setMeta(new Meta().setLastUpdatedElement(InstantType.now()));
144
145    processLoincCodes();
146    if (dest != null) {
147      log("Saving...");
148      saveBundle();
149    }
150    log("Done");
151
152  }
153
154  private void log(String string) {
155    System.out.println(string);
156
157  }
158
159  private void loadLoinc() throws FileNotFoundException, SAXException, IOException, ParserConfigurationException {
160    DocumentBuilderFactory factory = XMLUtil.newXXEProtectedDocumentBuilderFactory();
161    factory.setNamespaceAware(true);
162    DocumentBuilder builder = factory.newDocumentBuilder();
163
164    xml = builder.parse(ManagedFileAccess.inStream(definitions));
165  }
166
167  private void saveBundle() throws FHIRFormatError, IOException, XmlPullParserException {
168    XmlParser xml = new XmlParser();
169    FileOutputStream s = ManagedFileAccess.outStream(dest);
170    xml.compose(s, bundle, true);
171    s.close();
172  }
173
174  private String col(Element row, String name) {
175    Element e = XMLUtil.getNamedChild(row, name);
176    if (e == null)
177      return null;
178    String text = e.getTextContent();
179    return text;
180  }
181
182  private boolean hasCol(Element row, String name) {
183    return Utilities.noString(col(row, name));
184  }
185
186  private void processLoincCodes() {
187    Element row = XMLUtil.getFirstChild(xml.getDocumentElement());
188    int i = 0;
189    while (row != null) {
190      i++;
191      if (i % 1000 == 0)
192        System.out.print(".");
193      String code = col(row, "LOINC_NUM");
194      String comp = col(row, "COMPONENT");
195//                              DataElement de = new DataElement();
196//                              de.setId("loinc-"+code);
197//                  de.setMeta(new Meta().setLastUpdatedElement(InstantType.now()));
198//                              bundle.getEntry().add(new BundleEntryComponent().setResource(de));
199//                              Identifier id = new Identifier();
200//                              id.setSystem("http://hl7.org/fhir/commondataelement/loinc");
201//                              id.setValue(code);
202//                              de.addIdentifier(id);
203//                              de.setPublisher("Regenstrief + FHIR Project Team");
204//                              if (!col(row, "STATUS").equals("ACTIVE"))
205//                                      de.setStatus(PublicationStatus.DRAFT); // till we get good at this
206//                              else
207//                                      de.setStatus(PublicationStatus.RETIRED);
208//                              de.setDateElement(DateTimeType.now());
209//                              de.setName(comp);
210//                              ElementDefinition dee = de.addElement();
211//
212//                              // PROPERTY     ignore
213//                              // TIME_ASPCT   
214//                              // SYSTEM       
215//                              // SCALE_TYP    
216//                              // METHOD_TYP   
217//                              // dee.getCategory().add(new CodeableConcept().setText(col(row, "CLASS")));
218//                              // SOURCE       
219//                              // DATE_LAST_CHANGED - should be in ?   
220//                              // CHNG_TYPE    
221//                              dee.setComment(col(row , "COMMENTS"));
222//                              if (hasCol(row, "CONSUMER_NAME"))
223//                                      dee.addAlias(col(row, "CONSUMER_NAME"));        
224//                              // MOLAR_MASS   
225//                              // CLASSTYPE    
226//                              // FORMULA      
227//                              // SPECIES      
228//                              // EXMPL_ANSWERS        
229//                              // ACSSYM       
230//                              // BASE_NAME - ? this is a relationship 
231//                              // NAACCR_ID    
232//                              // ---------- CODE_TABLE todo   
233//                              // SURVEY_QUEST_TEXT    
234//                              // SURVEY_QUEST_SRC     
235//                              if (hasCol(row, "RELATEDNAMES2")) {
236//              String n = col(row, "RELATEDNAMES2");
237//              for (String s : n.split("\\;")) {
238//                                              if (!Utilities.noString(s))
239//                                                      dee.addAlias(s);        
240//              }
241//                              }
242//                              dee.addAlias(col(row, "SHORTNAME"));    
243//                              // ORDER_OBS    
244//                              // CDISC Code   
245//                              // HL7_FIELD_SUBFIELD_ID        
246//                              //  ------------------ EXTERNAL_COPYRIGHT_NOTICE todo   
247//                              dee.setDefinition(col(row, "LONG_COMMON_NAME"));        
248//                              // HL7_V2_DATATYPE      
249//                              String cc = makeType(col(row, "HL7_V3_DATATYPE"), code);
250//                              if (cc != null)
251//                                dee.addType().setCode(cc);    
252//                              // todo... CURATED_RANGE_AND_UNITS      
253//                              // todo: DOCUMENT_SECTION       
254//                              // STATUS_REASON        
255//                              // STATUS_TEXT  
256//                              // CHANGE_REASON_PUBLIC 
257//                              // COMMON_TEST_RANK     
258//                              // COMMON_ORDER_RANK    
259//                              // COMMON_SI_TEST_RANK  
260//                              // HL7_ATTACHMENT_STRUCTURE
261//
262//                              // units:
263//                              // UNITSREQUIRED        
264//                              // SUBMITTED_UNITS
265//                              ToolingExtensions.setAllowableUnits(dee, makeUnits(col(row, "EXAMPLE_UNITS"), col(row, "EXAMPLE_UCUM_UNITS")));
266//                              // EXAMPLE_SI_UCUM_UNITS        
267
268      row = XMLUtil.getNextSibling(row);
269    }
270    System.out.println("done");
271  }
272
273  private String makeType(String type, String id) {
274    if (Utilities.noString(type))
275      return null;
276    if (type.equals("PQ"))
277      return "Quantity";
278    else if (type.equals("ED"))
279      return "Attachment";
280    else if (type.equals("TS"))
281      return "dateTime";
282    else if (type.equals("ST"))
283      return "string";
284    else if (type.equals("II"))
285      return "Identifier";
286    else if (type.equals("CWE"))
287      return "CodeableConcept";
288    else if (type.equals("CD") || type.equals("CO"))
289      return "CodeableConcept";
290    else if (type.equals("PN"))
291      return "HumanName";
292    else if (type.equals("EN"))
293      return "HumanName";
294    else if (type.equals("AD"))
295      return "Address";
296    else if (type.equals("BL"))
297      return "boolean";
298    else if (type.equals("GTS"))
299      return "Schedule";
300    else if (type.equals("INT"))
301      return "integer";
302    else if (type.equals("CS"))
303      return "code";
304    else if (type.equals("IVL_TS"))
305      return "Period";
306    else if (type.equals("MMAT") || type.equals("PRF") || type.equals("TX") || type.equals("DT") || type.equals("FT"))
307      return null;
308    else
309      throw new Error("unmapped type " + type + " for LOINC code " + id);
310  } // 18606-4: MMAT. 18665-0: PRF. 18671-8: TX. 55400-6: DT; 8251-1: FT
311
312  private CodeableConcept makeUnits(String text, String ucum) {
313    if (Utilities.noString(text) && Utilities.noString(ucum))
314      return null;
315    CodeableConcept cc = new CodeableConcept();
316    cc.setText(text);
317    cc.getCoding().add(new Coding().setCode(ucum).setSystem("http://unitsofmeasure.org"));
318    return cc;
319  }
320
321  public Bundle getBundle() {
322    return bundle;
323  }
324}