Source code

001package org.hl7.fhir.r4.elementmodel;
002
003/*-
004 * #%L
005 * org.hl7.fhir.r4
006 * %%
007 * Copyright (C) 2014 - 2019 Health Level 7
008 * %%
009 * Licensed under the Apache License, Version 2.0 (the "License");
010 * you may not use this file except in compliance with the License.
011 * You may obtain a copy of the License at
012 * 
013 *      http://www.apache.org/licenses/LICENSE-2.0
014 * 
015 * Unless required by applicable law or agreed to in writing, software
016 * distributed under the License is distributed on an "AS IS" BASIS,
017 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
018 * See the License for the specific language governing permissions and
019 * limitations under the License.
020 * #L%
021 */
022
023
024import java.io.IOException;
025import java.io.InputStream;
026import java.io.OutputStream;
027import java.util.HashSet;
028import java.util.List;
029import java.util.Set;
030
031import org.hl7.fhir.exceptions.FHIRException;
032import org.hl7.fhir.exceptions.FHIRFormatError;
033import org.hl7.fhir.r4.context.IWorkerContext;
034import org.hl7.fhir.r4.elementmodel.Element.SpecialElement;
035import org.hl7.fhir.r4.formats.IParser.OutputStyle;
036import org.hl7.fhir.r4.model.ElementDefinition.TypeRefComponent;
037import org.hl7.fhir.r4.model.StructureDefinition;
038import org.hl7.fhir.r4.utils.SnomedExpressions;
039import org.hl7.fhir.r4.utils.SnomedExpressions.Expression;
040import org.hl7.fhir.r4.utils.formats.Turtle;
041import org.hl7.fhir.r4.utils.formats.Turtle.Complex;
042import org.hl7.fhir.r4.utils.formats.Turtle.Section;
043import org.hl7.fhir.r4.utils.formats.Turtle.Subject;
044import org.hl7.fhir.r4.utils.formats.Turtle.TTLComplex;
045import org.hl7.fhir.r4.utils.formats.Turtle.TTLList;
046import org.hl7.fhir.r4.utils.formats.Turtle.TTLLiteral;
047import org.hl7.fhir.r4.utils.formats.Turtle.TTLObject;
048import org.hl7.fhir.r4.utils.formats.Turtle.TTLURL;
049import org.hl7.fhir.utilities.TextFile;
050import org.hl7.fhir.utilities.Utilities;
051import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
052import org.hl7.fhir.utilities.validation.ValidationMessage.IssueType;
053
054
055public class TurtleParser extends ParserBase {
056
057  private String base;
058
059  public static String FHIR_URI_BASE = "http://hl7.org/fhir/";
060  public static String FHIR_VERSION_BASE = "http://build.fhir.org/";
061
062  public TurtleParser(IWorkerContext context) {
063    super(context);
064  }
065  @Override
066  public Element parse(InputStream input) throws IOException, FHIRException {
067    Turtle src = new Turtle();
068    if (policy == ValidationPolicy.EVERYTHING) {
069      try {
070        src.parse(TextFile.streamToString(input));
071      } catch (Exception e) {  
072        logError(-1, -1, "(document)", IssueType.INVALID, "Error parsing Turtle: "+e.getMessage(), IssueSeverity.FATAL);
073        return null;
074      }
075      return parse(src);  
076    } else {
077    src.parse(TextFile.streamToString(input));
078      return parse(src);  
079    } 
080  }
081  
082  private Element parse(Turtle src) throws FHIRException {
083    // we actually ignore the stated URL here
084    for (TTLComplex cmp : src.getObjects().values()) {
085      for (String p : cmp.getPredicates().keySet()) {
086        if ((FHIR_URI_BASE + "nodeRole").equals(p) && cmp.getPredicates().get(p).hasValue(FHIR_URI_BASE + "treeRoot")) {
087          return parse(src, cmp);
088        }
089      }
090    }
091    // still here: well, we didn't find a start point
092    String msg = "Error parsing Turtle: unable to find any node maked as the entry point (where " + FHIR_URI_BASE + "nodeRole = " + FHIR_URI_BASE + "treeRoot)";
093    if (policy == ValidationPolicy.EVERYTHING) {
094      logError(-1, -1, "(document)", IssueType.INVALID, msg, IssueSeverity.FATAL);
095      return null;
096    } else {
097      throw new FHIRFormatError(msg);
098    } 
099  }
100  
101  private Element parse(Turtle src, TTLComplex cmp) throws FHIRException {
102    TTLObject type = cmp.getPredicates().get("http://www.w3.org/2000/01/rdf-schema#type");
103    if (type == null) {
104      logError(cmp.getLine(), cmp.getCol(), "(document)", IssueType.INVALID, "Unknown resource type (missing rdfs:type)", IssueSeverity.FATAL);
105      return null;
106    }
107    if (type instanceof TTLList) {
108      // this is actually broken - really we have to look through the structure definitions at this point
109      for (TTLObject obj : ((TTLList) type).getList()) {
110        if (obj instanceof TTLURL && ((TTLURL) obj).getUri().startsWith(FHIR_URI_BASE)) {
111          type = obj;
112          break;
113        }
114      }
115    }
116    if (!(type instanceof TTLURL)) {
117      logError(cmp.getLine(), cmp.getCol(), "(document)", IssueType.INVALID, "Unexpected datatype for rdfs:type)", IssueSeverity.FATAL);
118      return null;
119    }
120    String name = ((TTLURL) type).getUri();
121    String ns = name.substring(0, name.lastIndexOf("/"));
122    name = name.substring(name.lastIndexOf("/")+1);
123    String path = "/"+name;
124
125    StructureDefinition sd = getDefinition(cmp.getLine(), cmp.getCol(), ns, name);
126    if (sd == null)
127      return null;
128
129    Element result = new Element(name, new Property(context, sd.getSnapshot().getElement().get(0), sd));
130    result.markLocation(cmp.getLine(), cmp.getCol());
131    result.setType(name);
132    parseChildren(src, path, cmp, result, false);
133    result.numberChildren();
134    return result;  
135  }
136  
137  private void parseChildren(Turtle src, String path, TTLComplex object, Element context, boolean primitive) throws FHIRException {
138
139    List<Property> properties = context.getProperty().getChildProperties(context.getName(), null);
140    Set<String> processed = new HashSet<String>();
141    if (primitive)
142      processed.add(FHIR_URI_BASE + "value");
143
144    // note that we do not trouble ourselves to maintain the wire format order here - we don't even know what it was anyway
145    // first pass: process the properties
146    for (Property property : properties) {
147      if (property.isChoice()) {
148        for (TypeRefComponent type : property.getDefinition().getType()) {
149          String eName = property.getName().substring(0, property.getName().length()-3) + Utilities.capitalize(type.getCode());
150          parseChild(src, object, context, processed, property, path, getFormalName(property, eName));
151        }
152      } else  {
153        parseChild(src, object, context, processed, property, path, getFormalName(property));
154      } 
155    }
156
157    // second pass: check for things not processed
158    if (policy != ValidationPolicy.NONE) {
159      for (String u : object.getPredicates().keySet()) {
160        if (!processed.contains(u)) {
161          TTLObject n = object.getPredicates().get(u);
162          logError(n.getLine(), n.getCol(), path, IssueType.STRUCTURE, "Unrecognised predicate '"+u+"'", IssueSeverity.ERROR);         
163        }
164      }
165    }
166  }
167  
168  private void parseChild(Turtle src, TTLComplex object, Element context, Set<String> processed, Property property, String path, String name) throws FHIRException {
169    processed.add(name);
170    String npath = path+"/"+property.getName();
171    TTLObject e = object.getPredicates().get(FHIR_URI_BASE + name);
172    if (e == null)
173      return;
174    if (property.isList() && (e instanceof TTLList)) {
175      TTLList arr = (TTLList) e;
176      for (TTLObject am : arr.getList()) {
177        parseChildInstance(src, npath, object, context, property, name, am);
178      }
179    } else {
180      parseChildInstance(src, npath, object, context, property, name, e);
181    }
182  }
183
184  private void parseChildInstance(Turtle src, String npath, TTLComplex object, Element context, Property property, String name, TTLObject e) throws FHIRException {
185    if (property.isResource())
186      parseResource(src, npath, object, context, property, name, e);
187    else  if (e instanceof TTLComplex) {
188      TTLComplex child = (TTLComplex) e;
189      Element n = new Element(tail(name), property).markLocation(e.getLine(), e.getCol());
190      context.getChildren().add(n);
191      if (property.isPrimitive(property.getType(tail(name)))) {
192        parseChildren(src, npath, child, n, true);
193        TTLObject val = child.getPredicates().get(FHIR_URI_BASE + "value");
194        if (val != null) {
195          if (val instanceof TTLLiteral) {
196            String value = ((TTLLiteral) val).getValue();
197            String type = ((TTLLiteral) val).getType();
198            // todo: check type
199            n.setValue(value);
200          } else
201            logError(object.getLine(), object.getCol(), npath, IssueType.INVALID, "This property must be a Literal, not a "+e.getClass().getName(), IssueSeverity.ERROR);
202        }
203      } else 
204        parseChildren(src, npath, child, n, false);
205
206    } else 
207      logError(object.getLine(), object.getCol(), npath, IssueType.INVALID, "This property must be a URI or bnode, not a "+e.getClass().getName(), IssueSeverity.ERROR);
208  }
209
210
211  private String tail(String name) {
212    return name.substring(name.lastIndexOf(".")+1);
213  }
214
215  private void parseResource(Turtle src, String npath, TTLComplex object, Element context, Property property, String name, TTLObject e) throws FHIRException {
216    TTLComplex obj;
217    if (e instanceof TTLComplex) 
218      obj = (TTLComplex) e;
219    else if (e instanceof TTLURL) {
220      String url = ((TTLURL) e).getUri();
221      obj = src.getObject(url);
222      if (obj == null) {
223        logError(e.getLine(), e.getCol(), npath, IssueType.INVALID, "reference to "+url+" cannot be resolved", IssueSeverity.FATAL);
224        return;
225      }
226    } else
227      throw new FHIRFormatError("Wrong type for resource");
228      
229    TTLObject type = obj.getPredicates().get("http://www.w3.org/2000/01/rdf-schema#type");
230    if (type == null) {
231      logError(object.getLine(), object.getCol(), npath, IssueType.INVALID, "Unknown resource type (missing rdfs:type)", IssueSeverity.FATAL);
232      return;
233  }
234    if (type instanceof TTLList) {
235      // this is actually broken - really we have to look through the structure definitions at this point
236      for (TTLObject tobj : ((TTLList) type).getList()) {
237        if (tobj instanceof TTLURL && ((TTLURL) tobj).getUri().startsWith(FHIR_URI_BASE)) {
238          type = tobj;
239          break;
240        }
241      }
242    }
243    if (!(type instanceof TTLURL)) {
244      logError(object.getLine(), object.getCol(), npath, IssueType.INVALID, "Unexpected datatype for rdfs:type)", IssueSeverity.FATAL);
245      return;
246    }
247    String rt = ((TTLURL) type).getUri();
248    String ns = rt.substring(0, rt.lastIndexOf("/"));
249    rt = rt.substring(rt.lastIndexOf("/")+1);
250    
251    StructureDefinition sd = getDefinition(object.getLine(), object.getCol(), ns, rt);
252    if (sd == null)
253      return;
254    
255    Element n = new Element(tail(name), property).markLocation(object.getLine(), object.getCol());
256    context.getChildren().add(n);
257    n.updateProperty(new Property(this.context, sd.getSnapshot().getElement().get(0), sd), SpecialElement.fromProperty(n.getProperty()), property);
258    n.setType(rt);
259    parseChildren(src, npath, obj, n, false);
260  }
261  
262  private String getFormalName(Property property) {
263    String en = property.getDefinition().getBase().getPath();
264    if (en == null) 
265      en = property.getDefinition().getPath();
266//    boolean doType = false;
267//      if (en.endsWith("[x]")) {
268//        en = en.substring(0, en.length()-3);
269//        doType = true;        
270//      }
271//     if (doType || (element.getProperty().getDefinition().getType().size() > 1 && !allReference(element.getProperty().getDefinition().getType())))
272//       en = en + Utilities.capitalize(element.getType());
273    return en;
274  }
275  
276  private String getFormalName(Property property, String elementName) {
277    String en = property.getDefinition().getBase().getPath();
278    if (en == null)
279      en = property.getDefinition().getPath();
280    if (!en.endsWith("[x]")) 
281      throw new Error("Attempt to replace element name for a non-choice type");
282    return en.substring(0, en.lastIndexOf(".")+1)+elementName;
283  }
284  
285  
286  @Override
287  public void compose(Element e, OutputStream stream, OutputStyle style, String base) throws IOException, FHIRException {
288    this.base = base;
289    
290                Turtle ttl = new Turtle();
291                compose(e, ttl, base);
292                ttl.commit(stream, false);
293  }
294
295
296
297  public void compose(Element e, Turtle ttl, String base) throws FHIRException {
298    ttl.prefix("fhir", FHIR_URI_BASE);
299    ttl.prefix("rdfs", "http://www.w3.org/2000/01/rdf-schema#");
300    ttl.prefix("owl", "http://www.w3.org/2002/07/owl#");
301    ttl.prefix("xsd", "http://www.w3.org/2001/XMLSchema#");
302
303
304    Section section = ttl.section("resource");
305    String subjId = genSubjectId(e);
306
307    String ontologyId = subjId.replace(">", ".ttl>");
308    Section ontology = ttl.section("ontology header");
309    ontology.triple(ontologyId, "a", "owl:Ontology");
310    ontology.triple(ontologyId, "owl:imports", "fhir:fhir.ttl");
311    if(ontologyId.startsWith("<" + FHIR_URI_BASE))
312      ontology.triple(ontologyId, "owl:versionIRI", ontologyId.replace(FHIR_URI_BASE, FHIR_VERSION_BASE));
313
314    Subject subject = section.triple(subjId, "a", "fhir:" + e.getType());
315                subject.linkedPredicate("fhir:nodeRole", "fhir:treeRoot", linkResolver == null ? null : linkResolver.resolvePage("rdf.html#tree-root"));
316
317                for (Element child : e.getChildren()) {
318                        composeElement(section, subject, child, null);
319                }
320
321  }
322  
323  protected String getURIType(String uri) {
324    if(uri.startsWith("<" + FHIR_URI_BASE))
325      if(uri.substring(FHIR_URI_BASE.length() + 1).contains("/"))
326        return uri.substring(FHIR_URI_BASE.length() + 1, uri.indexOf('/', FHIR_URI_BASE.length() + 1));
327    return null;
328  }
329
330  protected String getReferenceURI(String ref) {
331    if (ref != null && (ref.startsWith("http://") || ref.startsWith("https://")))
332      return "<" + ref + ">";
333    else if (base != null && ref != null && ref.contains("/"))
334      return "<" + Utilities.appendForwardSlash(base) + ref + ">";
335    else
336      return null;
337    }
338
339  protected void decorateReference(Complex t, Element coding) {
340    String refURI = getReferenceURI(coding.getChildValue("reference"));
341    if(refURI != null)
342      t.linkedPredicate("fhir:link", refURI, linkResolver == null ? null : linkResolver.resolvePage("rdf.html#reference"));
343  }
344  
345  protected void decorateCanonical(Complex t, Element canonical) {
346    String refURI = getReferenceURI(canonical.primitiveValue());
347    if(refURI != null)
348      t.linkedPredicate("fhir:link", refURI, linkResolver == null ? null : linkResolver.resolvePage("rdf.html#reference"));
349  }
350  
351  private String genSubjectId(Element e) {
352    String id = e.getChildValue("id");
353    if (base == null || id == null)
354      return "";
355    else if (base.endsWith("#"))
356      return "<" + base + e.getType() + "-" + id + ">";
357    else
358      return "<" + Utilities.pathURL(base, e.getType(), id) + ">";
359  }
360
361        private String urlescape(String s) {
362          StringBuilder b = new StringBuilder();
363          for (char ch : s.toCharArray()) {
364            if (Utilities.charInSet(ch,  ':', ';', '=', ','))
365              b.append("%"+Integer.toHexString(ch));
366            else
367              b.append(ch);
368          }
369          return b.toString();
370  }
371
372  private void composeElement(Section section, Complex ctxt, Element element, Element parent) throws FHIRException {
373//    "Extension".equals(element.getType())?
374//            (element.getProperty().getDefinition().getIsModifier()? "modifierExtension" : "extension") ; 
375    String en = getFormalName(element);
376
377          Complex t;
378          if (element.getSpecial() == SpecialElement.BUNDLE_ENTRY && parent != null && parent.getNamedChildValue("fullUrl") != null) {
379            String url = "<"+parent.getNamedChildValue("fullUrl")+">";
380            ctxt.linkedPredicate("fhir:"+en, url, linkResolver == null ? null : linkResolver.resolveProperty(element.getProperty()));
381            t = section.subject(url);
382          } else {
383            t = ctxt.linkedPredicate("fhir:"+en, linkResolver == null ? null : linkResolver.resolveProperty(element.getProperty()));
384          }
385    if (element.getSpecial() != null)
386      t.linkedPredicate("a", "fhir:"+element.fhirType(), linkResolver == null ? null : linkResolver.resolveType(element.fhirType()));
387          if (element.hasValue())
388                t.linkedPredicate("fhir:value", ttlLiteral(element.getValue(), element.getType()), linkResolver == null ? null : linkResolver.resolveType(element.getType()));
389          if (element.getProperty().isList() && (!element.isResource() || element.getSpecial() == SpecialElement.CONTAINED))
390                t.linkedPredicate("fhir:index", Integer.toString(element.getIndex()), linkResolver == null ? null : linkResolver.resolvePage("rdf.html#index"));
391
392          if ("Coding".equals(element.getType()))
393                decorateCoding(t, element, section);
394    if (Utilities.existsInList(element.getType(), "Reference"))
395      decorateReference(t, element);
396    else if (Utilities.existsInList(element.getType(), "canonical"))
397      decorateCanonical(t, element);
398                        
399    if("canonical".equals(element.getType())) {
400      String refURI = element.primitiveValue();
401      if (refURI != null) {
402        String uriType = getURIType(refURI);
403        if(uriType != null && !section.hasSubject(refURI))
404          section.triple(refURI, "a", "fhir:" + uriType);
405      }
406    }
407
408    if("Reference".equals(element.getType())) {
409      String refURI = getReferenceURI(element.getChildValue("reference"));
410      if (refURI != null) {
411        String uriType = getURIType(refURI);
412        if(uriType != null && !section.hasSubject(refURI))
413          section.triple(refURI, "a", "fhir:" + uriType);
414      }
415    }
416
417                for (Element child : element.getChildren()) {
418      if ("xhtml".equals(child.getType())) {
419        String childfn = getFormalName(child);
420        t.predicate("fhir:" + childfn, ttlLiteral(child.getValue(), child.getType()));
421      } else
422                        composeElement(section, t, child, element);
423                }
424        }
425
426  private String getFormalName(Element element) {
427    String en = null;
428    if (element.getSpecial() == null) {
429      if (element.getProperty().getDefinition().hasBase())
430        en = element.getProperty().getDefinition().getBase().getPath();
431    }
432    else if (element.getSpecial() == SpecialElement.BUNDLE_ENTRY)
433      en = "Bundle.entry.resource";
434    else if (element.getSpecial() == SpecialElement.BUNDLE_OUTCOME)
435      en = "Bundle.entry.response.outcome";
436    else if (element.getSpecial() == SpecialElement.PARAMETER)
437      en = element.getElementProperty().getDefinition().getPath();
438    else // CONTAINED
439      en = "DomainResource.contained";
440
441    if (en == null)
442      en = element.getProperty().getDefinition().getPath();
443    boolean doType = false;
444      if (en.endsWith("[x]")) {
445        en = en.substring(0, en.length()-3);
446        doType = true;
447      }
448     if (doType || (element.getProperty().getDefinition().getType().size() > 1 && !allReference(element.getProperty().getDefinition().getType())))
449       en = en + Utilities.capitalize(element.getType());
450    return en;
451  }
452
453        private boolean allReference(List<TypeRefComponent> types) {
454          for (TypeRefComponent t : types) {
455            if (!t.getCode().equals("Reference"))
456              return false;
457          }
458    return true;
459  }
460
461  static public String ttlLiteral(String value, String type) {
462          String xst = "";
463          if (type.equals("boolean"))
464            xst = "^^xsd:boolean";
465    else if (type.equals("integer"))
466      xst = "^^xsd:integer";
467    else if (type.equals("unsignedInt"))
468      xst = "^^xsd:nonNegativeInteger";
469    else if (type.equals("positiveInt"))
470      xst = "^^xsd:positiveInteger";
471    else if (type.equals("decimal"))
472      xst = "^^xsd:decimal";
473    else if (type.equals("base64Binary"))
474      xst = "^^xsd:base64Binary";
475    else if (type.equals("instant"))
476      xst = "^^xsd:dateTime";
477    else if (type.equals("time"))
478      xst = "^^xsd:time";
479    else if (type.equals("date") || type.equals("dateTime") ) {
480      String v = value;
481      if (v.length() > 10) {
482        int i = value.substring(10).indexOf("-");
483        if (i == -1)
484          i = value.substring(10).indexOf("+");
485        v = i == -1 ? value : value.substring(0,  10+i);
486      }
487      if (v.length() > 10)
488        xst = "^^xsd:dateTime";
489      else if (v.length() == 10)
490        xst = "^^xsd:date";
491      else if (v.length() == 7)
492        xst = "^^xsd:gYearMonth";
493      else if (v.length() == 4)
494        xst = "^^xsd:gYear";
495    }
496          
497                return "\"" +Turtle.escape(value, true) + "\""+xst;
498        }
499
500  protected void decorateCoding(Complex t, Element coding, Section section) throws FHIRException {
501    String system = coding.getChildValue("system");
502    String code = coding.getChildValue("code");
503    
504    if (system == null || code == null)
505      return;
506    if ("http://snomed.info/sct".equals(system)) {
507      t.prefix("sct", "http://snomed.info/id/");
508      if (code.contains(":") || code.contains("="))
509        generateLinkedPredicate(t, code);
510      else
511        t.linkedPredicate("a", "sct:" + urlescape(code), null);
512    } else if ("http://loinc.org".equals(system)) {
513      t.prefix("loinc", "http://loinc.org/rdf#");
514      t.linkedPredicate("a", "loinc:"+urlescape(code).toUpperCase(), null);
515    }  
516  }
517  private void generateLinkedPredicate(Complex t, String code) throws FHIRException {
518    Expression expression = SnomedExpressions.parse(code);
519    
520  }
521
522
523//    128045006|cellulitis (disorder)|:{363698007|finding site|=56459004|foot structure|}
524//    Grahame Grieve: or
525//
526//    64572001|disease|:{116676008|associated morphology|=72704001|fracture|,363698007|finding site|=(12611008|bone structure of  tibia|:272741003|laterality|=7771000|left|)}
527//    Harold Solbrig:
528//    a sct:128045006,
529//      rdfs:subClassOf [
530//          a owl:Restriction;
531//          owl:onProperty sct:609096000 ;
532//          owl:someValuesFrom [
533//                a owl:Restriction;
534//                 owl:onProperty sct:363698007 ;
535//                owl:someValuesFrom sct:56459004 ] ] ;
536//    and
537//
538//    a sct:64572001,
539//       rdfs:subclassOf  [
540//           a owl:Restriction ;
541//           owl:onProperty sct:60909600 ;
542//           owl:someValuesFrom [ 
543//                 a owl:Class ;
544//                 owl:intersectionOf ( [
545//                      a owl:Restriction;
546//                      owl:onProperty sct:116676008;
547//                     owl:someValuesFrom sct:72704001 ] 
548//                 [  a owl:Restriction;
549//                      owl:onProperty sct:363698007 
550//                      owl:someValuesFrom [
551//                            a owl:Class ;
552//                            owl:intersectionOf(
553//                                 sct:12611008
554//                                 owl:someValuesFrom [
555//                                         a owl:Restriction;
556//                                         owl:onProperty sct:272741003;
557//                                         owl:someValuesFrom sct:7771000
558//                                  ] ) ] ] ) ] ]
559//    (an approximation -- I'll have to feed it into a translator to be sure I've got it 100% right)
560//
561  
562}