Source code

001package org.hl7.fhir.r4.terminologies;
002
003import static org.apache.commons.lang3.StringUtils.isNotBlank;
004
005import java.io.FileNotFoundException;
006import java.io.IOException;
007
008/*
009 * Copyright (c) 2011+, HL7, Inc
010 * All rights reserved.
011 * 
012 * Redistribution and use in source and binary forms, with or without modification,
013 * are permitted provided that the following conditions are met:
014 * 
015 * Redistributions of source code must retain the above copyright notice, this
016 * list of conditions and the following disclaimer.
017 * Redistributions in binary form must reproduce the above copyright notice,
018 * this list of conditions and the following disclaimer in the documentation
019 * and/or other materials provided with the distribution.
020 * Neither the name of HL7 nor the names of its contributors may be used to
021 * endorse or promote products derived from this software without specific
022 * prior written permission.
023 * 
024 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
025 * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
026 * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
027 * IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
028 * INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
029 * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
030 * PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
031 * WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
032 * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
033 * POSSIBILITY OF SUCH DAMAGE.
034 * 
035 */
036
037import java.util.ArrayList;
038import java.util.HashMap;
039import java.util.HashSet;
040import java.util.List;
041import java.util.Map;
042import java.util.Set;
043import java.util.UUID;
044
045import org.apache.commons.lang3.NotImplementedException;
046import org.hl7.fhir.r4.context.IWorkerContext;
047import org.hl7.fhir.r4.model.BackboneElement;
048import org.hl7.fhir.r4.model.Base;
049import org.hl7.fhir.r4.model.CodeSystem;
050import org.hl7.fhir.r4.model.CodeSystem.CodeSystemContentMode;
051import org.hl7.fhir.r4.model.CodeSystem.ConceptDefinitionComponent;
052import org.hl7.fhir.r4.model.CodeSystem.ConceptDefinitionDesignationComponent;
053import org.hl7.fhir.r4.model.DateTimeType;
054import org.hl7.fhir.r4.model.ExpansionProfile;
055import org.hl7.fhir.r4.model.Factory;
056import org.hl7.fhir.r4.model.PrimitiveType;
057import org.hl7.fhir.r4.model.Type;
058import org.hl7.fhir.r4.model.UriType;
059import org.hl7.fhir.r4.model.ValueSet;
060import org.hl7.fhir.r4.model.ValueSet.ConceptReferenceComponent;
061import org.hl7.fhir.r4.model.ValueSet.ConceptReferenceDesignationComponent;
062import org.hl7.fhir.r4.model.ValueSet.ConceptSetComponent;
063import org.hl7.fhir.r4.model.ValueSet.ConceptSetFilterComponent;
064import org.hl7.fhir.r4.model.ValueSet.FilterOperator;
065import org.hl7.fhir.r4.model.ValueSet.ValueSetComposeComponent;
066import org.hl7.fhir.r4.model.ValueSet.ValueSetExpansionComponent;
067import org.hl7.fhir.r4.model.ValueSet.ValueSetExpansionContainsComponent;
068import org.hl7.fhir.r4.model.ValueSet.ValueSetExpansionParameterComponent;
069import org.hl7.fhir.r4.utils.ToolingExtensions;
070import org.hl7.fhir.exceptions.FHIRException;
071import org.hl7.fhir.exceptions.FHIRFormatError;
072import org.hl7.fhir.exceptions.NoTerminologyServiceException;
073import org.hl7.fhir.exceptions.TerminologyServiceException;
074import org.hl7.fhir.utilities.Utilities;
075
076public class ValueSetExpanderSimple implements ValueSetExpander {
077
078  private List<ValueSetExpansionContainsComponent> codes = new ArrayList<ValueSet.ValueSetExpansionContainsComponent>();
079  private List<ValueSetExpansionContainsComponent> roots = new ArrayList<ValueSet.ValueSetExpansionContainsComponent>();
080  private Map<String, ValueSetExpansionContainsComponent> map = new HashMap<String, ValueSet.ValueSetExpansionContainsComponent>();
081  private IWorkerContext context;
082  private boolean canBeHeirarchy = true;
083  private Set<String> excludeKeys = new HashSet<String>();
084  private Set<String> excludeSystems = new HashSet<String>();
085  private ValueSetExpanderFactory factory;
086  private ValueSet focus;
087  private int maxExpansionSize = 500;
088
089  private int total;
090
091  public ValueSetExpanderSimple(IWorkerContext context, ValueSetExpanderFactory factory) {
092    super();
093    this.context = context;
094    this.factory = factory;
095  }
096
097  public void setMaxExpansionSize(int theMaxExpansionSize) {
098    maxExpansionSize = theMaxExpansionSize;
099  }
100
101  private ValueSetExpansionContainsComponent addCode(String system, String code, String display, ValueSetExpansionContainsComponent parent, List<ConceptDefinitionDesignationComponent> designations,
102      ExpansionProfile profile, boolean isAbstract, boolean inactive, List<ValueSet> filters) {
103 
104    if (filters != null && !filters.isEmpty() && !filterContainsCode(filters, system, code))
105      return null;
106    ValueSetExpansionContainsComponent n = new ValueSet.ValueSetExpansionContainsComponent();
107    n.setSystem(system);
108    n.setCode(code);
109    if (isAbstract)
110      n.setAbstract(true);
111    if (inactive)
112      n.setInactive(true);
113
114    if (profile.getIncludeDesignations() && designations != null) {
115      for (ConceptDefinitionDesignationComponent t : designations) {
116        ToolingExtensions.addLanguageTranslation(n, t.getLanguage(), t.getValue());
117      }
118    }
119    ConceptDefinitionDesignationComponent t = profile.hasLanguage() ? getMatchingLang(designations, profile.getLanguage()) : null;
120    if (t == null)
121      n.setDisplay(display);
122    else
123      n.setDisplay(t.getValue());
124
125    String s = key(n);
126    if (map.containsKey(s) || excludeKeys.contains(s)) {
127      canBeHeirarchy = false;
128    } else {
129      codes.add(n);
130      map.put(s, n);
131      total++;
132    }
133    if (canBeHeirarchy && parent != null) {
134      parent.getContains().add(n);
135    } else {
136      roots.add(n);
137    }
138    return n;
139  }
140
141  private boolean filterContainsCode(List<ValueSet> filters, String system, String code) {
142    for (ValueSet vse : filters)
143      if (expansionContainsCode(vse.getExpansion().getContains(), system, code))
144        return true;
145    return false;
146  }
147
148  private boolean expansionContainsCode(List<ValueSetExpansionContainsComponent> contains, String system, String code) {
149    for (ValueSetExpansionContainsComponent cc : contains) {
150      if (system.equals(cc.getSystem()) && code.equals(cc.getCode()))
151        return true;
152      if (expansionContainsCode(cc.getContains(), system, code))
153        return true;
154    }
155    return false;
156  }
157
158  private ConceptDefinitionDesignationComponent getMatchingLang(List<ConceptDefinitionDesignationComponent> list, String lang) {
159    for (ConceptDefinitionDesignationComponent t : list)
160      if (t.getLanguage().equals(lang))
161        return t;
162    for (ConceptDefinitionDesignationComponent t : list)
163      if (t.getLanguage().startsWith(lang))
164        return t;
165    return null;
166  }
167
168  private void addCodeAndDescendents(CodeSystem cs, String system, ConceptDefinitionComponent def, ValueSetExpansionContainsComponent parent, ExpansionProfile profile, List<ValueSet> filters)
169      throws FHIRException {
170    if (!CodeSystemUtilities.isDeprecated(cs, def)) {
171      ValueSetExpansionContainsComponent np = null;
172      boolean abs = CodeSystemUtilities.isNotSelectable(cs, def);
173      boolean inc = CodeSystemUtilities.isInactive(cs, def);
174      if (canBeHeirarchy || !abs)
175        np = addCode(system, def.getCode(), def.getDisplay(), parent, def.getDesignation(), profile, abs, inc, filters);
176      for (ConceptDefinitionComponent c : def.getConcept())
177        addCodeAndDescendents(cs, system, c, np, profile, filters);
178    } else {
179      for (ConceptDefinitionComponent c : def.getConcept())
180        addCodeAndDescendents(cs, system, c, null, profile, filters);
181    }
182
183  }
184
185  private void addCodes(ValueSetExpansionComponent expand, List<ValueSetExpansionParameterComponent> params, ExpansionProfile profile, List<ValueSet> filters) throws ETooCostly, FHIRException {
186    if (expand.getContains().size() > maxExpansionSize)
187      throw new ETooCostly("Too many codes to display (>" + Integer.toString(expand.getContains().size()) + ")");
188    for (ValueSetExpansionParameterComponent p : expand.getParameter()) {
189      if (!existsInParams(params, p.getName(), p.getValue()))
190        params.add(p);
191    }
192
193    copyImportContains(expand.getContains(), null, profile, filters);
194  }
195
196  private void excludeCode(String theSystem, String theCode) {
197    ValueSetExpansionContainsComponent n = new ValueSet.ValueSetExpansionContainsComponent();
198    n.setSystem(theSystem);
199    n.setCode(theCode);
200    String s = key(n);
201    excludeKeys.add(s);
202  }
203
204  private void excludeCodes(ConceptSetComponent exc, List<ValueSetExpansionParameterComponent> params, String ctxt) throws FHIRException {
205    exc.checkNoModifiers("Compose.exclude", "expanding");
206    if (exc.hasSystem() && exc.getConcept().size() == 0 && exc.getFilter().size() == 0) {
207      excludeSystems.add(exc.getSystem());
208    }
209
210    if (exc.hasValueSet())
211      throw new Error("Processing Value set references in exclude is not yet done in "+ctxt);
212    // importValueSet(imp.getValue(), params, profile);
213
214    CodeSystem cs = context.fetchCodeSystem(exc.getSystem());
215    if ((cs == null || cs.getContent() != CodeSystemContentMode.COMPLETE) && context.supportsSystem(exc.getSystem())) {
216      excludeCodes(context.expandVS(exc, false), params);
217      return;
218    }
219
220    for (ConceptReferenceComponent c : exc.getConcept()) {
221      excludeCode(exc.getSystem(), c.getCode());
222    }
223
224    if (exc.getFilter().size() > 0)
225      throw new NotImplementedException("not done yet");
226  }
227
228  private void excludeCodes(ValueSetExpansionComponent expand, List<ValueSetExpansionParameterComponent> params) {
229    for (ValueSetExpansionContainsComponent c : expand.getContains()) {
230      excludeCode(c.getSystem(), c.getCode());
231    }
232  }
233
234  private boolean existsInParams(List<ValueSetExpansionParameterComponent> params, String name, Type value) {
235    for (ValueSetExpansionParameterComponent p : params) {
236      if (p.getName().equals(name) && PrimitiveType.compareDeep(p.getValue(), value, false))
237        return true;
238    }
239    return false;
240  }
241
242  @Override
243  public ValueSetExpansionOutcome expand(ValueSet source, ExpansionProfile profile) {
244
245    if (profile == null)
246      profile = makeDefaultExpansion();
247    try {
248      source.checkNoModifiers("ValueSet", "expanding");
249      focus = source.copy();
250      focus.setExpansion(new ValueSet.ValueSetExpansionComponent());
251      focus.getExpansion().setTimestampElement(DateTimeType.now());
252      focus.getExpansion().setIdentifier(Factory.createUUID());
253      if (!profile.getUrl().startsWith("urn:uuid:"))
254        focus.getExpansion().addParameter().setName("profile").setValue(new UriType(profile.getUrl()));
255
256      if (source.hasCompose())
257        handleCompose(source.getCompose(), focus.getExpansion().getParameter(), profile, source.getUrl());
258
259      if (canBeHeirarchy) {
260        for (ValueSetExpansionContainsComponent c : roots) {
261          focus.getExpansion().getContains().add(c);
262        }
263      } else {
264        for (ValueSetExpansionContainsComponent c : codes) {
265          if (map.containsKey(key(c)) && !c.getAbstract()) { // we may have added abstract codes earlier while we still thought it might be heirarchical, but later we gave up, so now ignore them
266            focus.getExpansion().getContains().add(c);
267            c.getContains().clear(); // make sure any heirarchy is wiped
268          }
269        }
270      }
271
272      if (total > 0) {
273        focus.getExpansion().setTotal(total);
274      }
275
276      return new ValueSetExpansionOutcome(focus);
277    } catch (RuntimeException e) {
278      // TODO: we should put something more specific instead of just Exception below, since
279      // it swallows bugs.. what would be expected to be caught there?
280      throw e;
281    } catch (NoTerminologyServiceException e) {
282      // well, we couldn't expand, so we'll return an interface to a checker that can check membership of the set
283      // that might fail too, but it might not, later.
284      return new ValueSetExpansionOutcome(new ValueSetCheckerSimple(source, factory, context), e.getMessage(), TerminologyServiceErrorClass.NOSERVICE);
285    } catch (Exception e) {
286      // well, we couldn't expand, so we'll return an interface to a checker that can check membership of the set
287      // that might fail too, but it might not, later.
288      return new ValueSetExpansionOutcome(new ValueSetCheckerSimple(source, factory, context), e.getMessage(), TerminologyServiceErrorClass.UNKNOWN);
289    }
290  }
291
292  private ExpansionProfile makeDefaultExpansion() {
293    ExpansionProfile res = new ExpansionProfile();
294    res.setUrl("urn:uuid:" + UUID.randomUUID().toString().toLowerCase());
295    res.setExcludeNested(true);
296    res.setIncludeDesignations(false);
297    return res;
298  }
299
300  private void addToHeirarchy(List<ValueSetExpansionContainsComponent> target, List<ValueSetExpansionContainsComponent> source) {
301    for (ValueSetExpansionContainsComponent s : source) {
302      target.add(s);
303    }
304  }
305
306  private String getCodeDisplay(CodeSystem cs, String code) throws TerminologyServiceException {
307    ConceptDefinitionComponent def = getConceptForCode(cs.getConcept(), code);
308    if (def == null)
309      throw new TerminologyServiceException("Unable to find code '" + code + "' in code system " + cs.getUrl());
310    return def.getDisplay();
311  }
312
313  private ConceptDefinitionComponent getConceptForCode(List<ConceptDefinitionComponent> clist, String code) {
314    for (ConceptDefinitionComponent c : clist) {
315      if (code.equals(c.getCode()))
316        return c;
317      ConceptDefinitionComponent v = getConceptForCode(c.getConcept(), code);
318      if (v != null)
319        return v;
320    }
321    return null;
322  }
323
324  private void handleCompose(ValueSetComposeComponent compose, List<ValueSetExpansionParameterComponent> params, ExpansionProfile profile, String ctxt)
325      throws ETooCostly, FileNotFoundException, IOException, FHIRException {
326    compose.checkNoModifiers("ValueSet.compose", "expanding");
327    // Exclude comes first because we build up a map of things to exclude
328    for (ConceptSetComponent inc : compose.getExclude())
329      excludeCodes(inc, params, ctxt);
330    canBeHeirarchy = !profile.getExcludeNested() && excludeKeys.isEmpty() && excludeSystems.isEmpty();
331    boolean first = true;
332    for (ConceptSetComponent inc : compose.getInclude()) {
333      if (first == true)
334        first = false;
335      else
336        canBeHeirarchy = false;
337      includeCodes(inc, params, profile);
338    }
339
340  }
341
342  private ValueSet importValueSet(String value, List<ValueSetExpansionParameterComponent> params, ExpansionProfile profile)
343      throws ETooCostly, TerminologyServiceException, FileNotFoundException, IOException, FHIRFormatError {
344    if (value == null)
345      throw new TerminologyServiceException("unable to find value set with no identity");
346    ValueSet vs = context.fetchResource(ValueSet.class, value);
347    if (vs == null)
348      throw new TerminologyServiceException("Unable to find imported value set " + value);
349    ValueSetExpansionOutcome vso = factory.getExpander().expand(vs, profile);
350    if (vso.getError() != null)
351      throw new TerminologyServiceException("Unable to expand imported value set: " + vso.getError());
352    if (vso.getService() != null)
353      throw new TerminologyServiceException("Unable to expand imported value set " + value);
354    if (vs.hasVersion())
355      if (!existsInParams(params, "version", new UriType(vs.getUrl() + "|" + vs.getVersion())))
356        params.add(new ValueSetExpansionParameterComponent().setName("version").setValue(new UriType(vs.getUrl() + "|" + vs.getVersion())));
357    for (ValueSetExpansionParameterComponent p : vso.getValueset().getExpansion().getParameter()) {
358      if (!existsInParams(params, p.getName(), p.getValue()))
359        params.add(p);
360    }
361    canBeHeirarchy = false; // if we're importing a value set, we have to be combining, so we won't try for a heirarchy
362    return vso.getValueset();
363  }
364
365  private void copyImportContains(List<ValueSetExpansionContainsComponent> list, ValueSetExpansionContainsComponent parent, ExpansionProfile profile, List<ValueSet> filter) throws FHIRException {
366    for (ValueSetExpansionContainsComponent c : list) {
367      c.checkNoModifiers("Imported Expansion in Code System", "expanding");
368      ValueSetExpansionContainsComponent np = addCode(c.getSystem(), c.getCode(), c.getDisplay(), parent, null, profile, c.getAbstract(), c.getInactive(), filter);
369      copyImportContains(c.getContains(), np, profile, filter);
370    }
371  }
372
373  private void includeCodes(ConceptSetComponent inc, List<ValueSetExpansionParameterComponent> params, ExpansionProfile profile) throws ETooCostly, FileNotFoundException, IOException, FHIRException {
374    inc.checkNoModifiers("Compose.include", "expanding");
375    List<ValueSet> imports = new ArrayList<ValueSet>();
376    for (UriType imp : inc.getValueSet()) {
377      imports.add(importValueSet(imp.getValue(), params, profile));
378    }
379
380    if (!inc.hasSystem()) {
381      if (imports.isEmpty()) // though this is not supposed to be the case
382        return;
383      ValueSet base = imports.get(0);
384      imports.remove(0);
385      base.checkNoModifiers("Imported ValueSet", "expanding");
386      copyImportContains(base.getExpansion().getContains(), null, profile, imports);
387    } else {
388      CodeSystem cs = context.fetchCodeSystem(inc.getSystem());
389      if ((cs == null || cs.getContent() != CodeSystemContentMode.COMPLETE) && context.supportsSystem(inc.getSystem())) {
390        addCodes(context.expandVS(inc, canBeHeirarchy), params, profile, imports);
391        return;
392      }
393
394      if (cs == null) {
395        if (context.isNoTerminologyServer())
396          throw new NoTerminologyServiceException("unable to find code system " + inc.getSystem().toString());
397        else
398          throw new TerminologyServiceException("unable to find code system " + inc.getSystem().toString());
399      }
400      cs.checkNoModifiers("Code System", "expanding");
401      if (cs.getContent() != CodeSystemContentMode.COMPLETE)
402        throw new TerminologyServiceException("Code system " + inc.getSystem().toString() + " is incomplete");
403      if (cs.hasVersion())
404        if (!existsInParams(params, "version", new UriType(cs.getUrl() + "|" + cs.getVersion())))
405          params.add(new ValueSetExpansionParameterComponent().setName("version").setValue(new UriType(cs.getUrl() + "|" + cs.getVersion())));
406
407      if (inc.getConcept().size() == 0 && inc.getFilter().size() == 0) {
408        // special case - add all the code system
409        for (ConceptDefinitionComponent def : cs.getConcept()) {
410          addCodeAndDescendents(cs, inc.getSystem(), def, null, profile, imports);
411        }
412      }
413
414      if (!inc.getConcept().isEmpty()) {
415        canBeHeirarchy = false;
416        for (ConceptReferenceComponent c : inc.getConcept()) {
417          c.checkNoModifiers("Code in Code System", "expanding");
418          addCode(inc.getSystem(), c.getCode(), Utilities.noString(c.getDisplay()) ? getCodeDisplay(cs, c.getCode()) : c.getDisplay(), null, convertDesignations(c.getDesignation()), profile, false,
419              CodeSystemUtilities.isInactive(cs, c.getCode()), imports);
420        }
421      }
422      if (inc.getFilter().size() > 1) {
423        canBeHeirarchy = false; // which will bt the case if we get around to supporting this
424        throw new TerminologyServiceException("Multiple filters not handled yet"); // need to and them, and this isn't done yet. But this shouldn't arise in non loinc and snomed value sets
425      }
426      if (inc.getFilter().size() == 1) {
427        ConceptSetFilterComponent fc = inc.getFilter().get(0);
428        if ("concept".equals(fc.getProperty()) && fc.getOp() == FilterOperator.ISA) {
429          // special: all codes in the target code system under the value
430          ConceptDefinitionComponent def = getConceptForCode(cs.getConcept(), fc.getValue());
431          if (def == null)
432            throw new TerminologyServiceException("Code '" + fc.getValue() + "' not found in system '" + inc.getSystem() + "'");
433          addCodeAndDescendents(cs, inc.getSystem(), def, null, profile, imports);
434        } else if ("concept".equals(fc.getProperty()) && fc.getOp() == FilterOperator.DESCENDENTOF) {
435          // special: all codes in the target code system under the value
436          ConceptDefinitionComponent def = getConceptForCode(cs.getConcept(), fc.getValue());
437          if (def == null)
438            throw new TerminologyServiceException("Code '" + fc.getValue() + "' not found in system '" + inc.getSystem() + "'");
439          for (ConceptDefinitionComponent c : def.getConcept())
440            addCodeAndDescendents(cs, inc.getSystem(), c, null, profile, imports);
441        } else if ("display".equals(fc.getProperty()) && fc.getOp() == FilterOperator.EQUAL) {
442          // gg; note: wtf is this: if the filter is display=v, look up the code 'v', and see if it's diplsay is 'v'?
443          canBeHeirarchy = false;
444          ConceptDefinitionComponent def = getConceptForCode(cs.getConcept(), fc.getValue());
445          if (def != null) {
446            if (isNotBlank(def.getDisplay()) && isNotBlank(fc.getValue())) {
447              if (def.getDisplay().contains(fc.getValue())) {
448                addCode(inc.getSystem(), def.getCode(), def.getDisplay(), null, def.getDesignation(), profile, CodeSystemUtilities.isNotSelectable(cs, def), CodeSystemUtilities.isInactive(cs, def),
449                    imports);
450              }
451            }
452          }
453        } else
454          throw new NotImplementedException("Search by property[" + fc.getProperty() + "] and op[" + fc.getOp() + "] is not supported yet");
455      }
456    }
457  }
458
459  private List<ConceptDefinitionDesignationComponent> convertDesignations(List<ConceptReferenceDesignationComponent> list) {
460    List<ConceptDefinitionDesignationComponent> res = new ArrayList<CodeSystem.ConceptDefinitionDesignationComponent>();
461    for (ConceptReferenceDesignationComponent t : list) {
462      ConceptDefinitionDesignationComponent c = new ConceptDefinitionDesignationComponent();
463      c.setLanguage(t.getLanguage());
464      c.setUse(t.getUse());
465      c.setValue(t.getValue());
466    }
467    return res;
468  }
469
470  private String key(String uri, String code) {
471    return "{" + uri + "}" + code;
472  }
473
474  private String key(ValueSetExpansionContainsComponent c) {
475    return key(c.getSystem(), c.getCode());
476  }
477
478}