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