Source code

001package org.hl7.fhir.r5.renderers;
002
003import java.io.IOException;
004import java.io.UnsupportedEncodingException;
005import java.util.ArrayList;
006import java.util.List;
007import java.util.Map;
008
009import org.hl7.fhir.exceptions.DefinitionException;
010import org.hl7.fhir.exceptions.FHIRFormatError;
011import org.hl7.fhir.r5.model.Bundle.BundleEntryComponent;
012import org.hl7.fhir.r5.model.CanonicalResource;
013import org.hl7.fhir.r5.model.CodeSystem;
014import org.hl7.fhir.r5.model.CodeSystem.ConceptDefinitionComponent;
015import org.hl7.fhir.r5.model.CodeSystem.PropertyComponent;
016import org.hl7.fhir.r5.model.ConceptMap;
017import org.hl7.fhir.r5.model.ConceptMap.ConceptMapGroupComponent;
018import org.hl7.fhir.r5.model.ConceptMap.SourceElementComponent;
019import org.hl7.fhir.r5.model.ConceptMap.TargetElementComponent;
020import org.hl7.fhir.r5.model.Questionnaire;
021import org.hl7.fhir.r5.model.Resource;
022import org.hl7.fhir.r5.model.StructureDefinition;
023import org.hl7.fhir.r5.model.ValueSet;
024import org.hl7.fhir.r5.model.ValueSet.ConceptSetComponent;
025import org.hl7.fhir.r5.renderers.utils.BaseWrappers.ResourceWrapper;
026import org.hl7.fhir.r5.renderers.utils.RenderingContext;
027import org.hl7.fhir.r5.renderers.utils.Resolver.ResourceContext;
028import org.hl7.fhir.r5.terminologies.CodeSystemUtilities;
029import org.hl7.fhir.r5.terminologies.utilities.ValidationResult;
030import org.hl7.fhir.r5.utils.ToolingExtensions;
031import org.hl7.fhir.utilities.Utilities;
032import org.hl7.fhir.utilities.xhtml.XhtmlNode;
033
034public abstract class TerminologyRenderer extends ResourceRenderer {
035  
036  private static final boolean DEBUG = false;
037
038
039  public TerminologyRenderer(RenderingContext context) {
040    super(context);
041  }
042
043  public TerminologyRenderer(RenderingContext context, ResourceContext rcontext) {
044    super(context, rcontext);
045  }
046
047  public String display(Resource r) throws UnsupportedEncodingException, IOException {
048    return ((CanonicalResource) r).present();
049  }
050
051  public String display(ResourceWrapper r) throws UnsupportedEncodingException, IOException {
052    if (r.has("title")) {
053      return r.children("title").get(0).getBase().primitiveValue();
054    }
055    if (r.has("name")) {
056      return r.children("name").get(0).getBase().primitiveValue();
057    }
058    return "??";
059  }
060
061  protected class TargetElementComponentWrapper {
062    protected ConceptMapGroupComponent group;
063    protected TargetElementComponent comp;
064    protected TargetElementComponentWrapper(ConceptMapGroupComponent group, TargetElementComponent comp) {
065      super();
066      this.group = group;
067      this.comp = comp;
068    }
069
070  }
071
072  public class UsedConceptMap {
073
074    private ConceptMapRenderInstructions details;
075    private String link;
076    private ConceptMap map;
077    public UsedConceptMap(ConceptMapRenderInstructions details, String link, ConceptMap map) {
078      super();
079      this.details = details;
080      this.link = link;
081      this.map = map;
082    }
083    public ConceptMapRenderInstructions getDetails() {
084      return details;
085    }
086    public ConceptMap getMap() {
087      return map;
088    }
089    public String getLink() {
090      return link;
091    }    
092  }
093
094  public class ConceptMapRenderInstructions {
095    private String name;
096    private String url;
097    private boolean doDescription;
098    public ConceptMapRenderInstructions(String name, String url, boolean doDescription) {
099      super();
100      this.name = name;
101      this.url = url;
102      this.doDescription = doDescription;
103    }
104    public String getName() {
105      return name;
106    }
107    public String getUrl() {
108      return url;
109    }
110    public boolean isDoDescription() {
111      return doDescription;
112    }
113  }
114
115
116  protected XhtmlNode addMapHeaders(XhtmlNode tr, List<UsedConceptMap> maps) throws FHIRFormatError, DefinitionException, IOException {
117    for (UsedConceptMap m : maps) {
118      XhtmlNode td = tr.td();
119      XhtmlNode b = td.b();
120      String link = m.getLink();
121      XhtmlNode a = b.ah(link);
122      a.addText(m.getDetails().getName());
123      if (m.getDetails().isDoDescription() && m.getMap().hasDescription())
124        addMarkdown(td, m.getMap().getDescription());
125    }
126    return tr;
127  }
128
129  protected String getHeader() {
130    int i = 3;
131    while (i <= getContext().getHeaderLevelContext())
132      i++;
133    if (i > 6)
134      i = 6;
135    return "h"+Integer.toString(i);
136  }
137
138  protected List<TargetElementComponentWrapper> findMappingsForCode(String code, ConceptMap map) {
139    List<TargetElementComponentWrapper> mappings = new ArrayList<TargetElementComponentWrapper>();
140
141    for (ConceptMapGroupComponent g : map.getGroup()) {
142      for (SourceElementComponent c : g.getElement()) {
143        if (c.getCode().equals(code))
144          for (TargetElementComponent cc : c.getTarget())
145            mappings.add(new TargetElementComponentWrapper(g, cc));
146      }
147    }
148    return mappings;
149  }
150
151
152
153  protected String getCharForRelationship(TargetElementComponent mapping) {
154    if (!mapping.hasRelationship())
155      return "";
156    switch (mapping.getRelationship()) {
157    case EQUIVALENT : return "~";
158    case SOURCEISNARROWERTHANTARGET : return "<";
159    case SOURCEISBROADERTHANTARGET : return ">";
160    case NOTRELATEDTO : return "!=";
161    default: return "?";
162    }
163  }
164
165  protected <T extends Resource> void addCsRef(ConceptSetComponent inc, XhtmlNode li, T cs) {
166    String ref = null;
167    boolean addHtml = true;
168    if (cs != null) {
169      ref = (String) cs.getUserData("external.url");
170      if (Utilities.noString(ref))
171        ref = (String) cs.getUserData("filename");
172      else
173        addHtml = false;
174      if (Utilities.noString(ref)) {
175        ref = (String) cs.getWebPath();
176        if (ref != null) {
177          addHtml = false;
178        }
179      }
180    }
181    String spec = getSpecialReference(inc.getSystem());
182    if (spec != null) {
183      XhtmlNode a = li.ah(spec);
184      a.code(inc.getSystem());
185    } else if (cs != null && ref != null) {
186      if (addHtml && !ref.contains(".html"))
187        ref = ref + ".html";
188      ref = context.fixReference(ref);
189      XhtmlNode a = li.ah(ref.replace("\\", "/"));
190      a.code(inc.getSystem());
191    } else {
192      li.code(inc.getSystem());
193    }
194  }
195
196
197  private String getSpecialReference(String system) {
198    if ("http://snomed.info/sct".equals(system))
199      return "http://www.snomed.org/";
200    if (Utilities.existsInList(system, "http://loinc.org", "http://unitsofmeasure.org", "http://www.nlm.nih.gov/research/umls/rxnorm", "http://ncimeta.nci.nih.gov", "http://fdasis.nlm.nih.gov", 
201        "http://www.radlex.org", "http://www.whocc.no/atc", "http://dicom.nema.org/resources/ontology/DCM", "http://www.genenames.org", "http://www.ensembl.org", "http://www.ncbi.nlm.nih.gov/nuccore", 
202        "http://www.ncbi.nlm.nih.gov/clinvar", "http://sequenceontology.org", "http://www.hgvs.org/mutnomen", "http://www.ncbi.nlm.nih.gov/projects/SNP", "http://cancer.sanger.ac.uk/cancergenome/projects/cosmic", 
203        "http://www.lrg-sequence.org", "http://www.omim.org", "http://www.ncbi.nlm.nih.gov/pubmed", "http://www.pharmgkb.org", "http://clinicaltrials.gov", "http://www.ebi.ac.uk/ipd/imgt/hla/")) 
204      return system;
205
206    return null;
207  }
208
209  protected XhtmlNode addTableHeaderRowStandard(XhtmlNode t, boolean hasHierarchy, boolean hasDisplay, boolean definitions, boolean comments, boolean version, boolean deprecated, List<PropertyComponent> properties, List<String> langs, Map<String, String> designations, boolean doDesignations) {
210    XhtmlNode tr = t.tr();
211    if (hasHierarchy) {
212      tr.td().b().tx(context.formatPhrase(RenderingContext.TERMINOLOGY_LVL));
213    }
214    tr.td().attribute("style", "white-space:nowrap").b().tx(formatPhrase(RenderingContext.GENERAL_CODE));
215    if (hasDisplay) {
216      tr.td().b().tx(formatPhrase(RenderingContext.TX_DISPLAY));
217    }
218    if (definitions) {
219      tr.td().b().tx(formatPhrase(RenderingContext.GENERAL_DEFINITION));
220    }
221    if (deprecated) {
222      tr.td().b().tx(formatPhrase(RenderingContext.CODESYSTEM_DEPRECATED));
223    }
224    if (comments) {
225      tr.td().b().tx(formatPhrase(RenderingContext.GENERAL_COMMENTS));
226    }
227    if (version) {
228      tr.td().b().tx(formatPhrase(RenderingContext.GENERAL_VER));
229    }
230    if (properties != null) {
231      for (PropertyComponent pc : properties) {
232        String display = getDisplayForProperty(pc);
233        tr.td().b().tx(display);      
234      }
235    }
236    if (doDesignations) {
237      if (designations != null) {
238        for (String url : designations.keySet()) {
239          tr.td().b().addText(designations.get(url));
240        }
241      }
242      if (langs != null) {
243        for (String lang : langs) {
244          tr.td().b().addText(describeLang(lang));
245        }
246      }
247    }
248    return tr;
249  }
250
251  protected String getDisplayForProperty(PropertyComponent pc) {
252    String display = ToolingExtensions.getPresentation(pc, pc.getCodeElement());
253    if (display == null || display.equals(pc.getCode()) && pc.hasUri()) {
254      display = getDisplayForProperty(pc.getUri());
255      if (display == null) {
256        display = pc.getCode();
257      }
258    }
259    return display;
260  }
261
262
263  protected String getDisplayForProperty(String uri) {
264    if (Utilities.noString(uri)){
265      return null;
266    }
267    String code = null;
268    if (uri.contains("#")) {
269      code = uri.substring(uri.indexOf("#")+1);
270      uri = uri.substring(0, uri.indexOf("#"));
271    }
272    CodeSystem cs = getContext().getWorker().fetchCodeSystem(uri);
273    if (cs == null) {
274      return null;
275    }
276    ConceptDefinitionComponent cc = code == null ? null : CodeSystemUtilities.getCode(cs, code);
277    return cc == null ? null : cc.getDisplay();
278  }
279
280
281  protected void AddVsRef(String value, XhtmlNode li, Resource source) {
282    Resource res = null;
283    if (rcontext != null) {
284      BundleEntryComponent be = rcontext.resolve(value);
285      if (be != null) {
286        res = be.getResource(); 
287      }
288    }
289    if (res != null && !(res instanceof CanonicalResource)) {
290      li.addText(value);
291      return;      
292    }      
293    CanonicalResource vs = (CanonicalResource) res;
294    if (vs == null)
295      vs = getContext().getWorker().findTxResource(ValueSet.class, value, source);
296    if (vs == null)
297      vs = getContext().getWorker().fetchResource(StructureDefinition.class, value, source);
298    if (vs == null)
299      vs = getContext().getWorker().fetchResource(Questionnaire.class, value, source);
300    if (vs != null) {
301      String ref = (String) vs.getWebPath();
302
303      ref = context.fixReference(ref);
304      XhtmlNode a = li.ah(ref == null ? "?ngen-11?" : ref.replace("\\", "/"));
305      a.addText(vs.present());
306    } else {
307      CodeSystem cs = getContext().getWorker().fetchCodeSystem(value);
308      if (cs != null) {
309        String ref = (String) cs.getWebPath();
310        ref = context.fixReference(ref);
311        XhtmlNode a = li.ah(ref == null ? "?ngen-12?" : ref.replace("\\", "/"));
312        a.addText(value);
313      } else if (value.equals("http://snomed.info/sct") || value.equals("http://snomed.info/id")) {
314        XhtmlNode a = li.ah(value);
315        a.tx(context.formatPhrase(RenderingContext.STRUC_DEF_SNOMED));
316      }
317      else {
318        if (value.startsWith("http://hl7.org") && !Utilities.existsInList(value, "http://hl7.org/fhir/sid/icd-10-us")) {
319          if (DEBUG) {
320            System.out.println("Unable to resolve value set "+value);
321          }
322        }
323        li.addText(value);
324      }
325    }
326  }
327
328  protected String getDisplayForConcept(String system, String version, String value) {
329    if (value == null || system == null)
330      return null;
331    ValidationResult cl = getContext().getWorker().validateCode(getContext().getTerminologyServiceOptions().withVersionFlexible(true), system, version, value, null);
332    return cl == null ? null : cl.getDisplay();
333  }
334
335
336  protected void clipboard(XhtmlNode x, String img, String title, String source) {
337    XhtmlNode span = x.span("cursor: pointer", formatPhrase(RenderingContext.TERM_REND_COPY, title));
338    span.attribute("onClick", "navigator.clipboard.writeText('"+Utilities.escapeJson(source)+"');");
339    span.img(img, "btn").setAttribute("width", "24px").setAttribute("height", "16px");
340  }
341  
342
343  
344}