Source code

001package org.hl7.fhir.dstu3.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
032
033
034import java.io.FileInputStream;
035import java.io.FileNotFoundException;
036import java.io.FileOutputStream;
037import java.io.IOException;
038
039import javax.xml.parsers.DocumentBuilder;
040import javax.xml.parsers.DocumentBuilderFactory;
041import javax.xml.parsers.ParserConfigurationException;
042
043import org.hl7.fhir.dstu3.formats.XmlParser;
044import org.hl7.fhir.dstu3.model.Bundle;
045import org.hl7.fhir.dstu3.model.Bundle.BundleEntryComponent;
046import org.hl7.fhir.dstu3.model.Bundle.BundleType;
047import org.hl7.fhir.dstu3.model.CodeableConcept;
048import org.hl7.fhir.dstu3.model.Coding;
049import org.hl7.fhir.dstu3.model.DataElement;
050import org.hl7.fhir.dstu3.model.DateTimeType;
051import org.hl7.fhir.dstu3.model.ElementDefinition;
052import org.hl7.fhir.dstu3.model.Enumerations.PublicationStatus;
053import org.hl7.fhir.dstu3.model.Identifier;
054import org.hl7.fhir.dstu3.model.InstantType;
055import org.hl7.fhir.dstu3.model.Meta;
056import org.hl7.fhir.dstu3.utils.ToolingExtensions;
057import org.hl7.fhir.exceptions.FHIRFormatError;
058import org.hl7.fhir.utilities.Utilities;
059import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
060import org.hl7.fhir.utilities.xml.XMLUtil;
061import org.w3c.dom.Document;
062import org.w3c.dom.Element;
063import org.xml.sax.SAXException;
064import org.xmlpull.v1.XmlPullParserException;
065
066/**
067 * This class converts the LOINC XML representation that the FHIR build tool uses internally to a set of DataElements in an atom feed
068 * 
069 * @author Grahame
070 *
071 */
072@Deprecated
073public class LoincToDEConvertor {
074
075        public static void main(String[] args) throws FHIRFormatError, IOException, XmlPullParserException, SAXException, ParserConfigurationException {
076                if (args.length == 0) {
077                        System.out.println("FHIR LOINC to CDE convertor. ");
078                        System.out.println("");
079                        System.out.println("This tool converts from LOINC to A set of DataElement definitions.");
080                        System.out.println("");
081                        System.out.println("Usage: [jar(path?)] [dest] (-defn [definitions]) where: ");
082                        System.out.println("* [dest] is a file name of the bundle to produce");
083                        System.out.println("* [definitions] is the file name of a file produced by exporting the main LOINC table from the mdb to XML");
084                        System.out.println("");
085                } else {
086                        LoincToDEConvertor exe = new LoincToDEConvertor();
087                        exe.setDest(args[0]);
088                        for (int i = 1; i < args.length; i++) {
089                                if (args[i].equals("-defn"))
090                                        exe.setDefinitions(args[i+1]);
091                        }
092                        exe.process();
093                }
094
095        }
096
097        private String dest;
098        private String definitions;
099        public String getDest() {
100                return dest;
101        }
102        public void setDest(String dest) {
103                this.dest = dest;
104        }
105        public String getDefinitions() {
106                return definitions;
107        }
108        public void setDefinitions(String definitions) {
109                this.definitions = definitions;
110        }
111
112        private Document xml;
113        private Bundle bundle;
114        private DateTimeType now;
115
116  public Bundle process(String sourceFile) 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() throws FHIRFormatError, IOException, XmlPullParserException, SAXException, ParserConfigurationException {
134                log("Begin. Produce Loinc CDEs in "+dest+" from "+definitions);
135                loadLoinc();
136                log("LOINC loaded");
137
138                now = DateTimeType.now();
139
140                bundle = new Bundle();
141                bundle.setId("http://hl7.org/fhir/commondataelement/loinc");
142    bundle.setMeta(new Meta().setLastUpdatedElement(InstantType.now()));
143
144                processLoincCodes();
145                if (dest != null) {
146                        log("Saving...");
147                        saveBundle();
148                }
149                log("Done");
150
151        }
152
153        private void log(String string) {
154                System.out.println(string);
155
156        }
157        private void loadLoinc() throws FileNotFoundException, SAXException, IOException, ParserConfigurationException {
158                DocumentBuilderFactory factory = XMLUtil.newXXEProtectedDocumentBuilderFactory();
159                factory.setNamespaceAware(true);
160                DocumentBuilder builder = factory.newDocumentBuilder();
161
162                xml = builder.parse(ManagedFileAccess.inStream(definitions)); 
163        }
164
165        private void saveBundle() throws FHIRFormatError, IOException, XmlPullParserException {
166                XmlParser xml = new XmlParser();
167                FileOutputStream s = ManagedFileAccess.outStream(dest);
168    xml.compose(s, bundle, true);
169    s.close();
170        }
171
172        private String col(Element row, String name) {
173                Element e = XMLUtil.getNamedChild(row, name);
174                if (e == null)
175                        return null;
176                String text = e.getTextContent();
177                return text;
178        }
179
180        private boolean hasCol(Element row, String name) {
181                return Utilities.noString(col(row, name));
182        }
183
184        private void processLoincCodes() {
185                Element row = XMLUtil.getFirstChild(xml.getDocumentElement());
186                int i = 0;
187                while (row != null) {
188                        i++;
189                        if (i % 1000 == 0)
190                                System.out.print(".");
191                                String code = col(row, "LOINC_NUM");
192                                String comp = col(row, "COMPONENT");
193                                DataElement de = new DataElement();
194                                de.setId("loinc-"+code);
195                    de.setMeta(new Meta().setLastUpdatedElement(InstantType.now()));
196                                bundle.getEntry().add(new BundleEntryComponent().setResource(de));
197                                Identifier id = new Identifier();
198                                id.setSystem("http://hl7.org/fhir/commondataelement/loinc");
199                                id.setValue(code);
200                                de.addIdentifier(id);
201                                de.setPublisher("Regenstrief + FHIR Project Team");
202                                if (!col(row, "STATUS").equals("ACTIVE"))
203                                        de.setStatus(PublicationStatus.DRAFT); // till we get good at this
204                                else
205                                        de.setStatus(PublicationStatus.RETIRED);
206                                de.setDateElement(DateTimeType.now());
207                                de.setName(comp);
208                                ElementDefinition dee = de.addElement();
209
210                                // PROPERTY     ignore
211                                // TIME_ASPCT   
212                                // SYSTEM       
213                                // SCALE_TYP    
214                                // METHOD_TYP   
215                                // dee.getCategory().add(new CodeableConcept().setText(col(row, "CLASS")));
216                                // SOURCE       
217                                // DATE_LAST_CHANGED - should be in ?   
218                                // CHNG_TYPE    
219                                dee.setComment(col(row , "COMMENTS"));
220                                if (hasCol(row, "CONSUMER_NAME"))
221                                        dee.addAlias(col(row, "CONSUMER_NAME"));        
222                                // MOLAR_MASS   
223                                // CLASSTYPE    
224                                // FORMULA      
225                                // SPECIES      
226                                // EXMPL_ANSWERS        
227                                // ACSSYM       
228                                // BASE_NAME - ? this is a relationship 
229                                // NAACCR_ID    
230                                // ---------- CODE_TABLE todo   
231                                // SURVEY_QUEST_TEXT    
232                                // SURVEY_QUEST_SRC     
233                                if (hasCol(row, "RELATEDNAMES2")) {
234                String n = col(row, "RELATEDNAMES2");
235                for (String s : n.split("\\;")) {
236                                                if (!Utilities.noString(s))
237                                                        dee.addAlias(s);        
238                }
239                                }
240                                dee.addAlias(col(row, "SHORTNAME"));    
241                                // ORDER_OBS    
242                                // CDISC Code   
243                                // HL7_FIELD_SUBFIELD_ID        
244                                //  ------------------ EXTERNAL_COPYRIGHT_NOTICE todo   
245                                dee.setDefinition(col(row, "LONG_COMMON_NAME"));        
246                                // HL7_V2_DATATYPE      
247                                String cc = makeType(col(row, "HL7_V3_DATATYPE"), code);
248                                if (cc != null)
249                                  dee.addType().setCode(cc);    
250                                // todo... CURATED_RANGE_AND_UNITS      
251                                // todo: DOCUMENT_SECTION       
252                                // STATUS_REASON        
253                                // STATUS_TEXT  
254                                // CHANGE_REASON_PUBLIC 
255                                // COMMON_TEST_RANK     
256                                // COMMON_ORDER_RANK    
257                                // COMMON_SI_TEST_RANK  
258                                // HL7_ATTACHMENT_STRUCTURE
259
260                                // units:
261                                // UNITSREQUIRED        
262                                // SUBMITTED_UNITS
263                                ToolingExtensions.setAllowableUnits(dee, makeUnits(col(row, "EXAMPLE_UNITS"), col(row, "EXAMPLE_UCUM_UNITS")));
264                                // EXAMPLE_SI_UCUM_UNITS        
265                        
266                        row = XMLUtil.getNextSibling(row);
267                }
268                System.out.println("done");
269        }
270
271        private String makeType(String type, String id) {
272                if (Utilities.noString(type))
273                        return null;
274                if (type.equals("PQ"))
275                        return "Quantity";
276                else if (type.equals("ED"))
277                  return "Attachment";
278                else if (type.equals("TS"))
279                  return "dateTime";
280                else if (type.equals("ST"))
281                  return "string";
282                else if (type.equals("II"))
283                  return "Identifier";
284                else if (type.equals("CWE"))
285                  return "CodeableConcept";
286                else if (type.equals("CD") || type.equals("CO"))
287                  return "CodeableConcept";
288                else if (type.equals("PN"))
289                  return "HumanName";
290                else if (type.equals("EN"))
291                  return "HumanName";
292                else if (type.equals("AD"))
293                  return "Address";
294                else if (type.equals("BL"))
295                  return "boolean";
296                else if (type.equals("GTS"))
297                  return "Schedule";
298                else if (type.equals("INT"))
299                  return "integer";
300                else if (type.equals("CS"))
301                  return "code";
302                else if (type.equals("IVL_TS"))
303                  return "Period";
304                else if (type.equals("MMAT") || type.equals("PRF") || type.equals("TX") || type.equals("DT") || type.equals("FT"))
305                  return null;
306                else
307                        throw new Error("unmapped type "+type+" for LOINC code "+id);
308        } // 18606-4: MMAT.  18665-0: PRF. 18671-8: TX. 55400-6: DT; 8251-1: FT 
309
310        private CodeableConcept makeUnits(String text, String ucum) {
311                if (Utilities.noString(text) && Utilities.noString(ucum))
312                        return null;
313                CodeableConcept cc = new CodeableConcept();
314                cc.setText(text);
315                cc.getCoding().add(new Coding().setCode(ucum).setSystem("http://unitsofmeasure.org"));
316                return cc;
317        }
318  public Bundle getBundle() {
319    return bundle;
320  }
321}