Source code

001package org.hl7.fhir.r4.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
032import java.util.ArrayList;
033import java.util.Calendar;
034import java.util.Collections;
035import java.util.Comparator;
036import java.util.List;
037
038import lombok.extern.slf4j.Slf4j;
039import org.hl7.fhir.exceptions.FHIRException;
040import org.hl7.fhir.exceptions.FHIRFormatError;
041import org.hl7.fhir.r4.model.BooleanType;
042import org.hl7.fhir.r4.model.CanonicalType;
043import org.hl7.fhir.r4.model.CodeSystem;
044import org.hl7.fhir.r4.model.CodeSystem.ConceptDefinitionComponent;
045import org.hl7.fhir.r4.model.CodeSystem.ConceptPropertyComponent;
046import org.hl7.fhir.r4.model.CodeSystem.PropertyComponent;
047import org.hl7.fhir.r4.model.CodeSystem.PropertyType;
048import org.hl7.fhir.r4.model.CodeType;
049import org.hl7.fhir.r4.model.DateTimeType;
050import org.hl7.fhir.r4.model.Enumerations.PublicationStatus;
051import org.hl7.fhir.r4.model.Identifier;
052import org.hl7.fhir.r4.model.Meta;
053import org.hl7.fhir.r4.model.Type;
054import org.hl7.fhir.r4.model.UriType;
055import org.hl7.fhir.r4.utils.ToolingExtensions;
056import org.hl7.fhir.r4.model.Coding;
057import org.hl7.fhir.utilities.StandardsStatus;
058import org.hl7.fhir.utilities.Utilities;
059
060@Slf4j
061public class CodeSystemUtilities {
062
063  public static boolean isNotSelectable(CodeSystem cs, ConceptDefinitionComponent def) {
064    for (ConceptPropertyComponent p : def.getProperty()) {
065      if (p.getCode().equals("notSelectable") && p.hasValue() && p.getValue() instanceof BooleanType)
066        return ((BooleanType) p.getValue()).getValue();
067    }
068    return false;
069  }
070
071  public static void setNotSelectable(CodeSystem cs, ConceptDefinitionComponent concept) throws FHIRFormatError {
072    defineNotSelectableProperty(cs);
073    ConceptPropertyComponent p = getProperty(concept, "abstract");
074    if (p != null)
075      p.setValue(new BooleanType(true));
076    else
077      concept.addProperty().setCode("notSelectable").setValue(new BooleanType(true));
078  }
079
080  public static void defineNotSelectableProperty(CodeSystem cs) {
081    defineCodeSystemProperty(cs, "notSelectable",
082        "Indicates that the code is abstract - only intended to be used as a selector for other concepts",
083        PropertyType.BOOLEAN);
084  }
085
086
087  public static Coding readCoding(String jurisdiction) {    
088    return jurisdiction == null || !jurisdiction.contains("#") ?  null : new Coding().setCode(jurisdiction.substring(jurisdiction.indexOf("#")+1)).setSystem(jurisdiction.substring(0, jurisdiction.indexOf("#")));
089  }
090
091  public enum ConceptStatus {
092    Active, Experimental, Deprecated, Retired;
093
094    public String toCode() {
095      switch (this) {
096      case Active:
097        return "active";
098      case Experimental:
099        return "experimental";
100      case Deprecated:
101        return "deprecated";
102      case Retired:
103        return "retired";
104      default:
105        return null;
106      }
107    }
108  }
109
110  public static void setStatus(CodeSystem cs, ConceptDefinitionComponent concept, ConceptStatus status)
111      throws FHIRFormatError {
112    defineStatusProperty(cs);
113    ConceptPropertyComponent p = getProperty(concept, "status");
114    if (p != null)
115      p.setValue(new CodeType(status.toCode()));
116    else
117      concept.addProperty().setCode("status").setValue(new CodeType(status.toCode()));
118  }
119
120  public static void defineStatusProperty(CodeSystem cs) {
121    defineCodeSystemProperty(cs, "status",
122        "A property that indicates the status of the concept. One of active, experimental, deprecated, retired",
123        PropertyType.CODE);
124  }
125
126  private static void defineDeprecatedProperty(CodeSystem cs) {
127    defineCodeSystemProperty(cs, "deprecationDate",
128        "The date at which a concept was deprecated. Concepts that are deprecated but not inactive can still be used, but their use is discouraged",
129        PropertyType.DATETIME);
130  }
131
132  public static void defineParentProperty(CodeSystem cs) {
133    defineCodeSystemProperty(cs, "parent",
134        "The concept identified in this property is a parent of the concept on which it is a property. The property type will be 'code'. The meaning of parent/child relationships is defined by the hierarchyMeaning attribute",
135        PropertyType.CODE);
136  }
137
138  public static void defineChildProperty(CodeSystem cs) {
139    defineCodeSystemProperty(cs, "child",
140        "The concept identified in this property is a child of the concept on which it is a property. The property type will be 'code'. The meaning of parent/child relationships is defined by the hierarchyMeaning attribute",
141        PropertyType.CODE);
142  }
143
144  public static boolean isDeprecated(CodeSystem cs, ConceptDefinitionComponent def) {
145    try {
146      for (ConceptPropertyComponent p : def.getProperty()) {
147        if (p.getCode().equals("status") && p.hasValue() && p.hasValueCodeType()
148            && p.getValueCodeType().getCode().equals("deprecated"))
149          return true;
150        // this, though status should also be set
151        if (p.getCode().equals("deprecationDate") && p.hasValue() && p.getValue() instanceof DateTimeType)
152          return ((DateTimeType) p.getValue()).before(new DateTimeType(Calendar.getInstance()));
153        // legacy
154        if (p.getCode().equals("deprecated") && p.hasValue() && p.getValue() instanceof BooleanType)
155          return ((BooleanType) p.getValue()).getValue();
156      }
157      return false;
158    } catch (FHIRException e) {
159      return false;
160    }
161  }
162
163  public static void setDeprecated(CodeSystem cs, ConceptDefinitionComponent concept, DateTimeType date)
164      throws FHIRFormatError {
165    setStatus(cs, concept, ConceptStatus.Deprecated);
166    defineDeprecatedProperty(cs);
167    concept.addProperty().setCode("deprecationDate").setValue(date);
168  }
169
170  public static boolean isInactive(CodeSystem cs, ConceptDefinitionComponent def) throws FHIRException {
171    for (ConceptPropertyComponent p : def.getProperty()) {
172      if (p.getCode().equals("status") && p.hasValueStringType())
173        return "inactive".equals(p.getValueStringType());
174    }
175    return false;
176  }
177
178  public static boolean isInactive(CodeSystem cs, String code) throws FHIRException {
179    ConceptDefinitionComponent def = findCode(cs.getConcept(), code);
180    if (def == null)
181      return true;
182    return isInactive(cs, def);
183  }
184
185  public static PropertyComponent defineCodeSystemProperty(CodeSystem cs, String code, String description,
186      PropertyType type) {
187    for (PropertyComponent p : cs.getProperty()) {
188      if (p.getCode().equals(code))
189        return p;
190    }
191    PropertyComponent p = cs.addProperty();
192    p.setCode(code).setDescription(description).setType(type).setUri("http://hl7.org/fhir/concept-properties#" + code);
193    return p;
194  }
195
196  public static String getCodeDefinition(CodeSystem cs, String code) {
197    return getCodeDefinition(cs.getConcept(), code);
198  }
199
200  private static String getCodeDefinition(List<ConceptDefinitionComponent> list, String code) {
201    for (ConceptDefinitionComponent c : list) {
202      if (c.hasCode() && c.getCode().equals(code))
203        return c.getDefinition();
204      String s = getCodeDefinition(c.getConcept(), code);
205      if (s != null)
206        return s;
207    }
208    return null;
209  }
210
211  public static CodeSystem makeShareable(CodeSystem cs) {
212    if (!cs.hasMeta())
213      cs.setMeta(new Meta());
214    for (UriType t : cs.getMeta().getProfile())
215      if (t.getValue().equals("http://hl7.org/fhir/StructureDefinition/shareablecodesystem"))
216        return cs;
217    cs.getMeta().getProfile().add(new CanonicalType("http://hl7.org/fhir/StructureDefinition/shareablecodesystem"));
218    return cs;
219  }
220
221  public static void setOID(CodeSystem cs, String oid) {
222    if (!oid.startsWith("urn:oid:"))
223      oid = "urn:oid:" + oid;
224    if (!cs.hasIdentifier())
225      cs.addIdentifier(new Identifier().setSystem("urn:ietf:rfc:3986").setValue(oid));
226    else if ("urn:ietf:rfc:3986".equals(cs.getIdentifierFirstRep().getSystem()) && cs.getIdentifierFirstRep().hasValue()
227        && cs.getIdentifierFirstRep().getValue().startsWith("urn:oid:"))
228      cs.getIdentifierFirstRep().setValue(oid);
229    else
230      throw new Error("unable to set OID on code system");
231
232  }
233
234  public static boolean hasOID(CodeSystem cs) {
235    return getOID(cs) != null;
236  }
237
238  public static String getOID(CodeSystem cs) {
239    if (cs.hasIdentifier() && "urn:ietf:rfc:3986".equals(cs.getIdentifierFirstRep().getSystem())
240        && cs.getIdentifierFirstRep().hasValue() && cs.getIdentifierFirstRep().getValue().startsWith("urn:oid:"))
241      return cs.getIdentifierFirstRep().getValue().substring(8);
242    return null;
243  }
244
245  public static ConceptDefinitionComponent findCode(List<ConceptDefinitionComponent> list, String code) {
246    for (ConceptDefinitionComponent c : list) {
247      if (c.getCode().equals(code))
248        return c;
249      ConceptDefinitionComponent s = findCode(c.getConcept(), code);
250      if (s != null)
251        return s;
252    }
253    return null;
254  }
255
256  public static void markStatus(CodeSystem cs, String wg, StandardsStatus status, String pckage, String fmm,
257      String normativeVersion) throws FHIRException {
258    if (wg != null) {
259      if (!ToolingExtensions.hasExtension(cs, ToolingExtensions.EXT_WORKGROUP)
260          || (Utilities.existsInList(ToolingExtensions.readStringExtension(cs, ToolingExtensions.EXT_WORKGROUP), "fhir",
261              "vocab") && !Utilities.existsInList(wg, "fhir", "vocab"))) {
262        ToolingExtensions.setCodeExtension(cs, ToolingExtensions.EXT_WORKGROUP, wg);
263      }
264    }
265    if (status != null) {
266      StandardsStatus ss = ToolingExtensions.getStandardsStatus(cs);
267      if (ss == null || ss.isLowerThan(status))
268        ToolingExtensions.setStandardsStatus(cs, status, normativeVersion);
269      if (pckage != null) {
270        if (!cs.hasUserData("ballot.package"))
271          cs.setUserData("ballot.package", pckage);
272        else if (!pckage.equals(cs.getUserString("ballot.package")))
273          if (!"infrastructure".equals(cs.getUserString("ballot.package")))
274            log.warn("Code System " + cs.getUrl() + ": ownership clash " + pckage + " vs "
275                + cs.getUserString("ballot.package"));
276      }
277      if (status == StandardsStatus.NORMATIVE) {
278        cs.setExperimental(false);
279        cs.setStatus(PublicationStatus.ACTIVE);
280      }
281    }
282    if (fmm != null) {
283      String sfmm = ToolingExtensions.readStringExtension(cs, ToolingExtensions.EXT_FMM_LEVEL);
284      if (Utilities.noString(sfmm) || Integer.parseInt(sfmm) < Integer.parseInt(fmm))
285        ToolingExtensions.setIntegerExtension(cs, ToolingExtensions.EXT_FMM_LEVEL, Integer.parseInt(fmm));
286    }
287  }
288
289  public static Type readProperty(ConceptDefinitionComponent concept, String code) {
290    for (ConceptPropertyComponent p : concept.getProperty())
291      if (p.getCode().equals(code))
292        return p.getValue();
293    return null;
294  }
295
296  public static ConceptPropertyComponent getProperty(ConceptDefinitionComponent concept, String code) {
297    for (ConceptPropertyComponent p : concept.getProperty())
298      if (p.getCode().equals(code))
299        return p;
300    return null;
301  }
302
303  // see http://hl7.org/fhir/R4/codesystem.html#hierachy
304  // returns additional parents not in the hierarchy
305  public static List<String> getOtherChildren(CodeSystem cs, ConceptDefinitionComponent c) {
306    List<String> res = new ArrayList<String>();
307    for (ConceptPropertyComponent p : c.getProperty()) {
308      if ("parent".equals(p.getCode())) {
309        res.add(p.getValue().primitiveValue());
310      }
311    }
312    return res;
313  }
314
315  // see http://hl7.org/fhir/R4/codesystem.html#hierachy
316  public static void addOtherChild(CodeSystem cs, ConceptDefinitionComponent owner, String code) {
317    defineChildProperty(cs);
318    owner.addProperty().setCode("child").setValue(new CodeType(code));
319  }
320
321  public static class ConceptDefinitionComponentSorter implements Comparator<ConceptDefinitionComponent> {
322
323    @Override
324    public int compare(ConceptDefinitionComponent o1, ConceptDefinitionComponent o2) {
325      return o1.getCode().compareToIgnoreCase(o2.getCode());
326    }
327
328  }
329
330  public static void sortAllCodes(CodeSystem cs) {
331    sortAllCodes(cs.getConcept());
332  }
333
334  public static void sortAllCodes(List<ConceptDefinitionComponent> list) {
335    Collections.sort(list, new ConceptDefinitionComponentSorter());
336    for (ConceptDefinitionComponent cd : list) {
337      if (cd.hasConcept()) {
338        sortAllCodes(cd.getConcept());
339      }
340    }
341  }
342
343}