001package org.hl7.fhir.r5.terminologies.expansion; 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 */ 031 032 033 034import static org.apache.commons.lang3.StringUtils.isNotBlank; 035 036import java.io.FileNotFoundException; 037import java.io.IOException; 038import java.text.MessageFormat; 039 040/* 041 * Copyright (c) 2011+, HL7, Inc 042 * All rights reserved. 043 * 044 * Redistribution and use in source and binary forms, with or without modification, 045 * are permitted provided that the following conditions are met: 046 * 047 * Redistributions of source code must retain the above copyright notice, this 048 * list of conditions and the following disclaimer. 049 * Redistributions in binary form must reproduce the above copyright notice, 050 * this list of conditions and the following disclaimer in the documentation 051 * and/or other materials provided with the distribution. 052 * Neither the name of HL7 nor the names of its contributors may be used to 053 * endorse or promote products derived from this software without specific 054 * prior written permission. 055 * 056 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 057 * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 058 * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. 059 * IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, 060 * INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT 061 * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR 062 * PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, 063 * WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) 064 * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE 065 * POSSIBILITY OF SUCH DAMAGE. 066 * 067 */ 068 069import java.util.ArrayList; 070import java.util.Calendar; 071import java.util.Collection; 072import java.util.GregorianCalendar; 073import java.util.HashSet; 074import java.util.List; 075import java.util.Set; 076 077import org.hl7.fhir.exceptions.FHIRException; 078import org.hl7.fhir.exceptions.FHIRFormatError; 079import org.hl7.fhir.exceptions.NoTerminologyServiceException; 080import org.hl7.fhir.exceptions.TerminologyServiceException; 081import org.hl7.fhir.r5.context.IWorkerContext; 082import org.hl7.fhir.r5.elementmodel.LanguageUtils; 083import org.hl7.fhir.r5.extensions.ExtensionConstants; 084import org.hl7.fhir.r5.extensions.ExtensionsUtils; 085import org.hl7.fhir.r5.model.BooleanType; 086import org.hl7.fhir.r5.model.CanonicalType; 087import org.hl7.fhir.r5.model.CodeSystem; 088import org.hl7.fhir.r5.model.CodeSystem.ConceptDefinitionComponent; 089import org.hl7.fhir.r5.model.CodeSystem.ConceptDefinitionDesignationComponent; 090import org.hl7.fhir.r5.model.CodeSystem.ConceptPropertyComponent; 091import org.hl7.fhir.r5.model.CodeSystem.PropertyComponent; 092import org.hl7.fhir.r5.model.CodeType; 093import org.hl7.fhir.r5.model.Coding; 094import org.hl7.fhir.r5.model.DataType; 095import org.hl7.fhir.r5.model.DateTimeType; 096import org.hl7.fhir.r5.model.DecimalType; 097import org.hl7.fhir.r5.model.Enumerations.CodeSystemContentMode; 098import org.hl7.fhir.r5.model.Enumerations.FilterOperator; 099import org.hl7.fhir.r5.model.OperationOutcome.IssueType; 100import org.hl7.fhir.r5.model.OperationOutcome.OperationOutcomeIssueComponent; 101import org.hl7.fhir.r5.model.Extension; 102import org.hl7.fhir.r5.model.Factory; 103import org.hl7.fhir.r5.model.IntegerType; 104import org.hl7.fhir.r5.model.PackageInformation; 105import org.hl7.fhir.r5.model.Parameters; 106import org.hl7.fhir.r5.model.Parameters.ParametersParameterComponent; 107import org.hl7.fhir.r5.model.PrimitiveType; 108import org.hl7.fhir.r5.model.Resource; 109import org.hl7.fhir.r5.model.StringType; 110import org.hl7.fhir.r5.model.UriType; 111import org.hl7.fhir.r5.model.ValueSet; 112import org.hl7.fhir.r5.model.ValueSet.ConceptReferenceComponent; 113import org.hl7.fhir.r5.model.ValueSet.ConceptReferenceDesignationComponent; 114import org.hl7.fhir.r5.model.ValueSet.ConceptSetComponent; 115import org.hl7.fhir.r5.model.ValueSet.ConceptSetFilterComponent; 116import org.hl7.fhir.r5.model.ValueSet.ValueSetComposeComponent; 117import org.hl7.fhir.r5.model.ValueSet.ValueSetExpansionComponent; 118import org.hl7.fhir.r5.model.ValueSet.ValueSetExpansionContainsComponent; 119import org.hl7.fhir.r5.model.ValueSet.ValueSetExpansionParameterComponent; 120import org.hl7.fhir.r5.model.ValueSet.ValueSetExpansionPropertyComponent; 121import org.hl7.fhir.r5.terminologies.CodeSystemUtilities; 122import org.hl7.fhir.r5.terminologies.ValueSetUtilities; 123import org.hl7.fhir.r5.terminologies.expansion.ValueSetExpander.UnknownValueSetException; 124import org.hl7.fhir.r5.terminologies.providers.CodeSystemProvider; 125import org.hl7.fhir.r5.terminologies.providers.CodeSystemProviderExtension; 126import org.hl7.fhir.r5.terminologies.utilities.TerminologyOperationContext; 127import org.hl7.fhir.r5.terminologies.utilities.TerminologyOperationContext.TerminologyServiceProtectionException; 128import org.hl7.fhir.r5.terminologies.utilities.ValueSetProcessBase.OpIssueCode; 129import org.hl7.fhir.r5.terminologies.utilities.ValueSetProcessBase.TerminologyOperationDetails; 130import org.hl7.fhir.r5.terminologies.validation.VSCheckerException; 131import org.hl7.fhir.r5.terminologies.utilities.TerminologyServiceErrorClass; 132import org.hl7.fhir.r5.terminologies.utilities.ValueSetProcessBase; 133import org.hl7.fhir.r5.utils.ToolingExtensions; 134import org.hl7.fhir.r5.utils.UserDataNames; 135import org.hl7.fhir.r5.utils.client.EFhirClientException; 136import org.hl7.fhir.utilities.CommaSeparatedStringBuilder; 137import org.hl7.fhir.utilities.MarkedToMoveToAdjunctPackage; 138import org.hl7.fhir.utilities.Utilities; 139import org.hl7.fhir.utilities.i18n.AcceptLanguageHeader; 140import org.hl7.fhir.utilities.i18n.AcceptLanguageHeader.LanguagePreference; 141import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity; 142import org.hl7.fhir.utilities.i18n.I18nConstants; 143 144@MarkedToMoveToAdjunctPackage 145public class ValueSetExpander extends ValueSetProcessBase { 146 147 148 public class UnknownValueSetException extends FHIRException { 149 150 protected UnknownValueSetException() { 151 super(); 152 } 153 154 protected UnknownValueSetException(String message, Throwable cause) { 155 super(message, cause); 156 } 157 158 protected UnknownValueSetException(String message) { 159 super(message); 160 } 161 162 protected UnknownValueSetException(Throwable cause) { 163 super(cause); 164 } 165 166 } 167 168 public class Token { 169 private String system; 170 private String code; 171 public Token(String system, String code) { 172 super(); 173 this.system = system; 174 this.code = code; 175 } 176 public String getSystem() { 177 return system; 178 } 179 public String getCode() { 180 return code; 181 } 182 public boolean matches(Coding use) { 183 return system.equals(use.getSystem()) && code.equals(use.getCode()); 184 } 185 public boolean matchesLang(String language) { 186 return system.equals("urn:ietf:bcp:47") && code.equals(language); 187 } 188 } 189 190 private static final boolean REPORT_VERSION_ANYWAY = true; 191 192 private static final String VS_EXP_IMPORT_ERROR_TOO_COSTLY = null; 193 194 private ValueSet focus; 195 private List<String> allErrors = new ArrayList<>(); 196 private int maxExpansionSize = 1000; 197 private WorkingContext dwc = new WorkingContext(); 198 199 private boolean checkCodesWhenExpanding; 200 private boolean includeAbstract = true; 201 private boolean debug; 202 private Set<String> sources = new HashSet<>(); 203 204 private AcceptLanguageHeader langs; 205 private List<Token> designations = new ArrayList<>(); 206 207 public ValueSetExpander(IWorkerContext context, TerminologyOperationContext opContext) { 208 super(context, opContext); 209 } 210 211 public ValueSetExpander(IWorkerContext context, TerminologyOperationContext opContext, List<String> allErrors) { 212 super(context, opContext); 213 this.allErrors = allErrors; 214 } 215 216 public void setMaxExpansionSize(int theMaxExpansionSize) { 217 maxExpansionSize = theMaxExpansionSize; 218 } 219 220 private ValueSetExpansionContainsComponent addCode(WorkingContext wc, String system, String code, String display, String dispLang, ValueSetExpansionContainsComponent parent, List<ConceptDefinitionDesignationComponent> designations, Parameters expParams, 221 boolean isAbstract, boolean inactive, List<ValueSet> filters, boolean noInactive, boolean deprecated, List<ValueSetExpansionPropertyComponent> vsProp, 222 List<ConceptPropertyComponent> csProps, CodeSystem cs, List<org.hl7.fhir.r5.model.ValueSet.ConceptPropertyComponent> expProps, List<Extension> csExtList, List<Extension> vsExtList, ValueSetExpansionComponent exp) throws ETooCostly { 223 opContext.deadCheck("addCode"+code); 224 225 if (filters != null && !filters.isEmpty() && !filterContainsCode(filters, system, code, exp)) 226 return null; 227 if (noInactive && inactive) { 228 return null; 229 } 230 231 ValueSetExpansionContainsComponent n = new ValueSet.ValueSetExpansionContainsComponent(); 232 n.setSystem(system); 233 n.setCode(code); 234 if (isAbstract) { 235 n.setAbstract(true); 236 } 237 if (inactive) { 238 n.setInactive(true); 239 } 240 if (deprecated) { 241 ValueSetUtilities.setDeprecated(vsProp, n); 242 } 243 if (ExtensionsUtils.hasExtension(csExtList, "http://hl7.org/fhir/StructureDefinition/codesystem-label")) { 244 ValueSetUtilities.addProperty(focus, n, "http://hl7.org/fhir/concept-properties#label", "label", ExtensionsUtils.getExtensionValue(csExtList, "http://hl7.org/fhir/StructureDefinition/codesystem-label")); 245 } 246 if (ExtensionsUtils.hasExtension(vsExtList, "http://hl7.org/fhir/StructureDefinition/valueset-label")) { 247 ValueSetUtilities.addProperty(focus, n, "http://hl7.org/fhir/concept-properties#label", "label", ExtensionsUtils.getExtensionValue(vsExtList, "http://hl7.org/fhir/StructureDefinition/valueset-label")); 248 } 249 if (ExtensionsUtils.hasExtension(csExtList, "http://hl7.org/fhir/StructureDefinition/codesystem-conceptOrder")) { 250 ValueSetUtilities.addProperty(focus, n, "http://hl7.org/fhir/concept-properties#order", "order", convertToDecimal(ExtensionsUtils.getExtensionValue(csExtList, "http://hl7.org/fhir/StructureDefinition/codesystem-conceptOrder"))); 251 } 252 if (ExtensionsUtils.hasExtension(vsExtList, "http://hl7.org/fhir/StructureDefinition/valueset-conceptOrder")) { 253 ValueSetUtilities.addProperty(focus, n, "http://hl7.org/fhir/concept-properties#order", "order", convertToDecimal(ExtensionsUtils.getExtensionValue(vsExtList, "http://hl7.org/fhir/StructureDefinition/valueset-conceptOrder"))); 254 } 255 if (ExtensionsUtils.hasExtension(csExtList, "http://hl7.org/fhir/StructureDefinition/itemWeight")) { 256 ValueSetUtilities.addProperty(focus, n, "http://hl7.org/fhir/concept-properties#itemWeight", "weight", ExtensionsUtils.getExtensionValue(csExtList, "http://hl7.org/fhir/StructureDefinition/itemWeight")); 257 } 258 if (ExtensionsUtils.hasExtension(vsExtList, "http://hl7.org/fhir/StructureDefinition/itemWeight")) { 259 ValueSetUtilities.addProperty(focus, n, "http://hl7.org/fhir/concept-properties#itemWeight", "weight", ExtensionsUtils.getExtensionValue(vsExtList, "http://hl7.org/fhir/StructureDefinition/itemWeight")); 260 } 261 ExtensionsUtils.copyExtensions(csExtList, n.getExtension(), 262 "http://hl7.org/fhir/StructureDefinition/coding-sctdescid", 263 "http://hl7.org/fhir/StructureDefinition/rendering-style", 264 "http://hl7.org/fhir/StructureDefinition/rendering-xhtml", 265 "http://hl7.org/fhir/StructureDefinition/codesystem-alternate"); 266 267 ExtensionsUtils.copyExtensions(vsExtList, n.getExtension(), 268 "http://hl7.org/fhir/StructureDefinition/valueset-supplement", 269 "http://hl7.org/fhir/StructureDefinition/valueset-deprecated", 270 "http://hl7.org/fhir/StructureDefinition/valueset-concept-definition", 271 "http://hl7.org/fhir/StructureDefinition/coding-sctdescid", 272 "http://hl7.org/fhir/StructureDefinition/rendering-style", 273 "http://hl7.org/fhir/StructureDefinition/rendering-xhtml"); 274 275 // display and designations 276 ConceptDefinitionDesignationComponent pref = null; 277 if (langs == null) { 278 n.setDisplay(display); 279 } else { 280 if (designations == null) { 281 designations = new ArrayList<>(); 282 } 283 designations.add(new ConceptDefinitionDesignationComponent().setLanguage(dispLang).setValue(display).setUse(new Coding().setSystem("http://terminology.hl7.org/CodeSystem/designation-usage").setCode("display"))); 284 pref = findMatchingDesignation(designations); 285 if (pref != null) { 286 n.setDisplay(pref.getValue()); 287 } 288 } 289 if (!n.hasDisplay() && display != null && langs != null && (langs.matches(dispLang) || Utilities.existsInList(langs.getSource(), "en", "en-US"))) { 290 n.setDisplay(display); 291 } 292 293 if (expParams.getParameterBool("includeDesignations") && designations != null) { 294 295 for (ConceptDefinitionDesignationComponent t : designations) { 296 if (t != pref && (t.hasLanguage() || t.hasUse()) && t.getValue() != null && passesDesignationFilter(t)) { 297 ConceptReferenceDesignationComponent d = n.addDesignation(); 298 if (t.getLanguage() != null) { 299 d.setLanguage(t.getLanguage().trim()); 300 } 301 if (t.getValue() != null) { 302 d.setValue(t.getValue().trim()); 303 } 304 if (t.getUse() != null) { 305 d.setUse(t.getUse()); 306 } 307 for (Extension ext : t.getExtension()) { 308 if (Utilities.existsInList(ext.getUrl(), "http://hl7.org/fhir/StructureDefinition/coding-sctdescid")) { 309 d.addExtension(ext); 310 } 311 } 312 } 313 } 314 } 315 for (ParametersParameterComponent p : expParams.getParameter()) { 316 if ("property".equals(p.getName())) { 317 if (csProps != null && p.hasValue()) { 318 for (ConceptPropertyComponent cp : csProps) { 319 if (p.getValue().primitiveValue().equals(cp.getCode())) { 320 PropertyComponent pd = cs.getProperty(cp.getCode()); 321 String url = pd == null ? null : pd.getUri(); 322 if (url == null) { 323 if ("definition".equals(cp.getCode())) { 324 url = "http://hl7.org/fhir/concept-properties#definition"; 325 } else { 326 // ?? 327 } 328 } 329 ValueSetUtilities.addProperty(focus, n, url, cp.getCode(), cp.getValue()).copyExtensions(cp, "http://hl7.org/fhir/StructureDefinition/alternate-code-use", "http://hl7.org/fhir/StructureDefinition/alternate-code-status"); 330 } 331 } 332 } 333 if (expProps != null && p.hasValue()) { 334 for (org.hl7.fhir.r5.model.ValueSet.ConceptPropertyComponent cp : expProps) { 335 if (p.getValue().primitiveValue().equals(cp.getCode())) { 336 String url = null; 337 for (ValueSetExpansionPropertyComponent t : vsProp) { 338 if (t.hasCode() && t.getCode().equals(cp.getCode())) { 339 url = t.getUri(); 340 } 341 } 342 if (url == null) { 343 if ("definition".equals(cp.getCode())) { 344 url = "http://hl7.org/fhir/concept-properties#definition"; 345 } else { 346 // TODO: try looking it up from the code system 347 } 348 } 349 ValueSetUtilities.addProperty(focus, n, url, cp.getCode(), cp.getValue()).copyExtensions(cp, "http://hl7.org/fhir/StructureDefinition/alternate-code-use", "http://hl7.org/fhir/StructureDefinition/alternate-code-status"); 350 } 351 } 352 } 353 } 354 } 355 356 String s = key(n); 357 if (wc.getExcludeKeys().contains(s)) { 358 return null; 359 } else if (wc.getMap().containsKey(s)) { 360 wc.setCanBeHierarchy(false); 361 } else { 362 wc.getCodes().add(n); 363 wc.getMap().put(s, n); 364// if (wc == dwc && wc.getTotal() > maxExpansionSize) { 365// if (wc.getOffset()+wc.getCount() > 0 && wc.getTotal() > wc.getOffset()+wc.getCount()) { 366// wc.setTotal(-1); 367// throw new EFinished(); 368// } 369// throw failCostly(context.formatMessage(I18nConstants.VALUESET_TOO_COSTLY, focus.getUrl(), ">" + Integer.toString(maxExpansionSize))); 370// } 371 } 372 if (wc.isCanBeHierarchy() && parent != null) { 373 parent.getContains().add(n); 374 } else if (!wc.getRootMap().containsKey(s)) { 375 wc.getRootMap().put(s, n); 376 wc.getRoots().add(n); 377 } 378 return n; 379 } 380 381 private String findParamValue(List<ValueSetExpansionParameterComponent> list, String name) { 382 for (ValueSetExpansionParameterComponent p : list) { 383 if (name.equals(p.getName())) { 384 return p.getValue().primitiveValue(); 385 } 386 } 387 return null; 388 } 389 390 private DataType convertToDecimal(DataType v) { 391 if (v == null) { 392 return null; 393 } 394 if (v instanceof DecimalType) { 395 return v; 396 } 397 if (v instanceof IntegerType) { 398 return new DecimalType(((IntegerType) v).asStringValue()); 399 } 400 return null; 401 } 402 403 private boolean passesDesignationFilter(ConceptDefinitionDesignationComponent d) { 404 if (designations.isEmpty()) { 405 return true; 406 } 407 for (Token t : designations) { 408 if ((d.hasUse() && t.matches(d.getUse())) || t.matchesLang(d.getLanguage())) { 409 return true; 410 } 411 for (Coding c : d.getAdditionalUse()) { 412 if (t.matches(c)) { 413 return true; 414 } 415 } 416 } 417 return false; 418 } 419 420 private ConceptDefinitionDesignationComponent findMatchingDesignation(List<ConceptDefinitionDesignationComponent> designations) { 421 if (langs == null) { 422 return null; 423 } 424 // we have a list of languages in priority order 425 // we have a list of designations in no order 426 // language exact match is preferred 427 // display is always preferred 428 429 for (LanguagePreference lang : langs.getLangs()) { 430 if (lang.getValue() > 0) { 431 for (ConceptDefinitionDesignationComponent cd : designations) { 432 if (isDisplay(cd, false) && LanguageUtils.langsMatchExact(cd.getLanguage(), lang.getLang())) { 433 return cd; 434 } 435 } 436 for (ConceptDefinitionDesignationComponent cd : designations) { 437 if (isDisplay(cd, false) && LanguageUtils.langsMatch(lang.getLang(), cd.getLanguage())) { 438 return cd; 439 } 440 } 441 for (ConceptDefinitionDesignationComponent cd : designations) { 442 if (isDisplay(cd, false) && LanguageUtils.langsMatch(cd.getLanguage(), lang.getLang())) { 443 return cd; 444 } 445 } 446 for (ConceptDefinitionDesignationComponent cd : designations) { 447 if (isDisplay(cd, true) && LanguageUtils.langsMatchExact(cd.getLanguage(), lang.getLang())) { 448 return cd; 449 } 450 } 451 for (ConceptDefinitionDesignationComponent cd : designations) { 452 if (isDisplay(cd, true) && LanguageUtils.langsMatch(cd.getLanguage(), lang.getLang())) { 453 return cd; 454 } 455 } 456 for (ConceptDefinitionDesignationComponent cd : designations) { 457 if (isDisplay(cd, true) && LanguageUtils.langsMatch(lang.getLang(), cd.getLanguage())) { 458 return cd; 459 } 460 } 461 for (ConceptDefinitionDesignationComponent cd : designations) { 462 if (LanguageUtils.langsMatchExact(cd.getLanguage(), lang.getLang())) { 463 return cd; 464 } 465 } 466 for (ConceptDefinitionDesignationComponent cd : designations) { 467 if (LanguageUtils.langsMatch(cd.getLanguage(), lang.getLang())) { 468 return cd; 469 } 470 } 471 for (ConceptDefinitionDesignationComponent cd : designations) { 472 if (LanguageUtils.langsMatch(lang.getLang(), cd.getLanguage())) { 473 return cd; 474 } 475 } 476 } 477 } 478 return null; 479 } 480 481 private boolean isDisplay(ConceptDefinitionDesignationComponent cd, boolean def) { 482 return (def && !cd.hasUse()) || (cd.hasUse() && cd.getUse().is("http://terminology.hl7.org/CodeSystem/designation-usage", "display")); 483 } 484 485 private boolean filterContainsCode(List<ValueSet> filters, String system, String code, ValueSetExpansionComponent exp) { 486 for (ValueSet vse : filters) { 487 checkCanonical(exp, vse, focus); 488 if (expansionContainsCode(vse.getExpansion().getContains(), system, code)) 489 return true; 490 } 491 return false; 492 } 493 494 private boolean expansionContainsCode(List<ValueSetExpansionContainsComponent> contains, String system, String code) { 495 for (ValueSetExpansionContainsComponent cc : contains) { 496 if (system.equals(cc.getSystem()) && code.equals(cc.getCode())) 497 return true; 498 if (expansionContainsCode(cc.getContains(), system, code)) 499 return true; 500 } 501 return false; 502 } 503 504 private ConceptDefinitionDesignationComponent getMatchingLang(List<ConceptDefinitionDesignationComponent> list, AcceptLanguageHeader langs) { 505 for (ConceptDefinitionDesignationComponent t : list) { 506 if (LanguageUtils.langsMatchExact(langs, t.getLanguage())) { 507 return t; 508 } 509 } 510 for (ConceptDefinitionDesignationComponent t : list) { 511 if (LanguageUtils.langsMatch(langs, t.getLanguage())) { 512 return t; 513 } 514 } 515 return null; 516 } 517 518 private void addCodeAndDescendents(WorkingContext wc, ValueSetExpansionContainsComponent focus, ValueSetExpansionContainsComponent parent, Parameters expParams, List<ValueSet> filters, boolean noInactive, List<ValueSetExpansionPropertyComponent> vsProps, ValueSet vsSrc, ValueSetExpansionComponent exp, String langDisplay) throws FHIRException, ETooCostly { 519 opContext.deadCheck("addCodeAndDescendents"); 520 focus.checkNoModifiers("Expansion.contains", "expanding"); 521 ValueSetExpansionContainsComponent np = null; 522 for (String code : getCodesForConcept(focus, expParams)) { 523 ValueSetExpansionContainsComponent t = addCode(wc, focus.getSystem(), code, focus.getDisplay(), langDisplay, parent, 524 convert(focus.getDesignation()), expParams, focus.getAbstract(), focus.getInactive(), filters, noInactive, false, vsProps, makeCSProps(focus.getExtensionString(ToolingExtensions.EXT_DEFINITION), null), null, focus.getProperty(), null, focus.getExtension(), exp); 525 if (np == null) { 526 np = t; 527 } 528 } 529 for (ValueSetExpansionContainsComponent c : focus.getContains()) 530 addCodeAndDescendents(wc, c, np, expParams, filters, noInactive, vsProps, vsSrc, exp, langDisplay); 531 } 532 533 private String getLang(ValueSet vsSrc) { 534 if (vsSrc.hasLanguage()) { 535 return vsSrc.getLanguage(); 536 } 537 for (ValueSetExpansionParameterComponent p : vsSrc.getExpansion().getParameter()) { 538 if ("displayLanguage".equals(p.getName())) { 539 return p.getValue().primitiveValue(); 540 } 541 } 542 return null; 543 } 544 545 private List<ConceptPropertyComponent> makeCSProps(String definition, List<ConceptPropertyComponent> list) { 546 List<ConceptPropertyComponent> res = new ArrayList<>(); 547 if (!Utilities.noString(definition)) { 548 res.add(new ConceptPropertyComponent("definition", new StringType(definition))); 549 } 550 if (list != null) { 551 res.addAll(list); 552 } 553 return res; 554 } 555 556 private List<String> getCodesForConcept(ValueSetExpansionContainsComponent focus, Parameters expParams) { 557 List<String> codes = new ArrayList<>(); 558 codes.add(focus.getCode()); 559 for (org.hl7.fhir.r5.model.ValueSet.ConceptPropertyComponent p : focus.getProperty()) { 560 if ("alternateCode".equals(p.getCode()) && (altCodeParams.passes(p.getExtension())) && p.getValue().isPrimitive()) { 561 codes.add(p.getValue().primitiveValue()); 562 } 563 } 564 return codes; 565 } 566 567 private List<ConceptDefinitionDesignationComponent> convert(List<ConceptReferenceDesignationComponent> designations) { 568 List<ConceptDefinitionDesignationComponent> list = new ArrayList<ConceptDefinitionDesignationComponent>(); 569 for (ConceptReferenceDesignationComponent d : designations) { 570 ConceptDefinitionDesignationComponent n = new ConceptDefinitionDesignationComponent(); 571 n.setLanguage(d.getLanguage()); 572 if (d.hasUse()) { 573 n.setUse(d.getUse()); 574 } 575 n.setValue(d.getValue()); 576 list.add(n); 577 } 578 return list; 579 } 580 581 private void addCodeAndDescendents(WorkingContext wc, CodeSystem cs, String system, ConceptDefinitionComponent def, ValueSetExpansionContainsComponent parent, Parameters expParams, List<ValueSet> filters, 582 ConceptDefinitionComponent exclusion, ConceptFilter filterFunc, boolean noInactive, List<ValueSetExpansionPropertyComponent> vsProps, List<WorkingContext> otherFilters, ValueSetExpansionComponent exp) throws FHIRException, ETooCostly { 583 opContext.deadCheck("addCodeAndDescendents"); 584 def.checkNoModifiers("Code in Code System", "expanding"); 585 if (exclusion != null) { 586 if (exclusion.getCode().equals(def.getCode())) 587 return; // excluded. 588 } 589 ValueSetExpansionContainsComponent np = null; 590 boolean abs = CodeSystemUtilities.isNotSelectable(cs, def); 591 boolean inc = CodeSystemUtilities.isInactive(cs, def); 592 boolean dep = CodeSystemUtilities.isDeprecated(cs, def, false); 593 if ((includeAbstract || !abs) && filterFunc.includeConcept(cs, def) && passesOtherFilters(otherFilters, cs, def.getCode())) { 594 for (String code : getCodesForConcept(def, expParams)) { 595 ValueSetExpansionContainsComponent t = addCode(wc, system, code, def.getDisplay(), cs.getLanguage(), parent, def.getDesignation(), expParams, abs, inc, filters, noInactive, dep, vsProps, makeCSProps(def.getDefinition(), def.getProperty()), cs, null, def.getExtension(), null, exp); 596 if (np == null) { 597 np = t; 598 } 599 } 600 } 601 for (ConceptDefinitionComponent c : def.getConcept()) { 602 addCodeAndDescendents(wc, cs, system, c, np, expParams, filters, exclusion, filterFunc, noInactive, vsProps, otherFilters, exp); 603 } 604 if (def.hasUserData(CodeSystemUtilities.USER_DATA_CROSS_LINK)) { 605 List<ConceptDefinitionComponent> children = (List<ConceptDefinitionComponent>) def.getUserData(CodeSystemUtilities.USER_DATA_CROSS_LINK); 606 for (ConceptDefinitionComponent c : children) 607 addCodeAndDescendents(wc, cs, system, c, np, expParams, filters, exclusion, filterFunc, noInactive, vsProps, otherFilters, exp); 608 } 609 } 610 611 612 private void excludeCodeAndDescendents(WorkingContext wc, CodeSystem cs, String system, ConceptDefinitionComponent def, Parameters expParams, List<ValueSet> filters, 613 ConceptDefinitionComponent exclusion, ConceptFilter filterFunc, List<WorkingContext> otherFilters, ValueSetExpansionComponent exp) throws FHIRException, ETooCostly { 614 opContext.deadCheck("excludeCodeAndDescendents"); 615 def.checkNoModifiers("Code in Code System", "expanding"); 616 if (exclusion != null) { 617 if (exclusion.getCode().equals(def.getCode())) 618 return; // excluded. 619 } 620 boolean abs = CodeSystemUtilities.isNotSelectable(cs, def); 621 if ((includeAbstract || !abs) && filterFunc.includeConcept(cs, def) && passesOtherFilters(otherFilters, cs, def.getCode())) { 622 for (String code : getCodesForConcept(def, expParams)) { 623 if (!(filters != null && !filters.isEmpty() && !filterContainsCode(filters, system, code, exp))) 624 excludeCode(wc, system, code); 625 } 626 } 627 for (ConceptDefinitionComponent c : def.getConcept()) { 628 excludeCodeAndDescendents(wc, cs, system, c, expParams, filters, exclusion, filterFunc, otherFilters, exp); 629 } 630 if (def.hasUserData(CodeSystemUtilities.USER_DATA_CROSS_LINK)) { 631 List<ConceptDefinitionComponent> children = (List<ConceptDefinitionComponent>) def.getUserData(CodeSystemUtilities.USER_DATA_CROSS_LINK); 632 for (ConceptDefinitionComponent c : children) 633 excludeCodeAndDescendents(wc, cs, system, c, expParams, filters, exclusion, filterFunc, otherFilters, exp); 634 } 635 } 636 637 638 private List<String> getCodesForConcept(ConceptDefinitionComponent focus, Parameters expParams) { 639 List<String> codes = new ArrayList<>(); 640 codes.add(focus.getCode()); 641 for (ConceptPropertyComponent p : focus.getProperty()) { 642 if ("alternateCode".equals(p.getCode()) && (altCodeParams.passes(p.getExtension())) && p.getValue().isPrimitive()) { 643 codes.add(p.getValue().primitiveValue()); 644 } 645 } 646 return codes; 647 } 648 649 private static boolean hasUse(ConceptPropertyComponent p, List<String> uses) { 650 for (Extension ext : p.getExtensionsByUrl(ToolingExtensions.EXT_CS_ALTERNATE_USE)) { 651 if (ext.hasValueCoding() && Utilities.existsInList(ext.getValueCoding().getCode(), uses)) { 652 return true; 653 } 654 } 655 return false; 656 } 657 658 659 660 private void addCodes(ValueSetExpansionComponent expand, List<ValueSetExpansionParameterComponent> params, Parameters expParams, List<ValueSet> filters, boolean noInactive, List<ValueSetExpansionPropertyComponent> vsProps, ValueSet vsSrc, ValueSetExpansionComponent exp) throws ETooCostly, FHIRException { 661 if (expand != null) { 662 if (expand.getContains().size() > maxExpansionSize) 663 throw failCostly(context.formatMessage(I18nConstants.VALUESET_TOO_COSTLY, vsSrc.getUrl(), ">" + Integer.toString(expand.getContains().size()))); 664 for (ValueSetExpansionParameterComponent p : expand.getParameter()) { 665 if (!existsInParams(params, p.getName(), p.getValue())) 666 params.add(p); 667 } 668 669 copyImportContains(expand.getContains(), null, expParams, filters, noInactive, vsProps, vsSrc, exp); 670 } 671 } 672 673 private void excludeCode(WorkingContext wc, String theSystem, String theCode) { 674 ValueSetExpansionContainsComponent n = new ValueSet.ValueSetExpansionContainsComponent(); 675 n.setSystem(theSystem); 676 n.setCode(theCode); 677 String s = key(n); 678 wc.getExcludeKeys().add(s); 679 } 680 681 private void excludeCodes(WorkingContext wc, ConceptSetComponent exc, Parameters expParams, ValueSetExpansionComponent exp, ValueSet vs, String vspath) throws FHIRException, FileNotFoundException, ETooCostly, IOException { 682 opContext.deadCheck("excludeCodes"); 683 exc.checkNoModifiers("Compose.exclude", "expanding"); 684 if (exc.hasSystem() && exc.getConcept().size() == 0 && exc.getFilter().size() == 0) { 685 wc.getExcludeSystems().add(exc.getSystem()); 686 } 687 688 for (UriType imp : exc.getValueSet()) { 689 excludeCodes(wc, importValueSetForExclude(wc, imp.getValue(), exp, expParams, false, vs).getExpansion()); 690 } 691 692 if (exc.hasSystem()) { 693 CodeSystem cs = context.fetchSupplementedCodeSystem(exc.getSystem()); 694 if ((cs == null || cs.getContent() != CodeSystemContentMode.COMPLETE) && context.supportsSystem(exc.getSystem(), opContext.getOptions().getFhirVersion())) { 695 ValueSetExpansionOutcome vse = context.expandVS(new TerminologyOperationDetails(requiredSupplements), exc, false, false); 696 ValueSet valueset = vse.getValueset(); 697 if (valueset.hasUserData(UserDataNames.VS_EXPANSION_SOURCE)) { 698 sources.add(valueset.getUserString(UserDataNames.VS_EXPANSION_SOURCE)); 699 } 700 if (valueset == null) 701 throw failTSE("Error Expanding ValueSet: "+vse.getError()); 702 excludeCodes(wc, valueset.getExpansion()); 703 return; 704 } 705 706 for (ConceptReferenceComponent c : exc.getConcept()) { 707 excludeCode(wc, exc.getSystem(), c.getCode()); 708 } 709 710 if (exc.getFilter().size() > 0) { 711 if (cs.getContent() == CodeSystemContentMode.FRAGMENT) { 712 addFragmentWarning(exp, cs); 713 } 714 List<WorkingContext> filters = new ArrayList<>(); 715 for (int i = 1; i < exc.getFilter().size(); i++) { 716 WorkingContext wc1 = new WorkingContext(); 717 filters.add(wc1); 718 processFilter(exc, exp, expParams, null, cs, false, exc.getFilter().get(i), wc1, null, true, vspath+".filter["+i+"]"); 719 } 720 ConceptSetFilterComponent fc = exc.getFilter().get(0); 721 WorkingContext wc1 = dwc; 722 processFilter(exc, exp, expParams, null, cs, false, fc, wc1, filters, true, vspath+".filter[0]"); 723 } 724 } 725 } 726 727 private void excludeCodes(WorkingContext wc, ValueSetExpansionComponent expand) { 728 opContext.deadCheck("excludeCodes"); 729 for (ValueSetExpansionContainsComponent c : expand.getContains()) { 730 excludeCode(wc, c.getSystem(), c.getCode()); 731 } 732 } 733 734 private boolean existsInParams(List<ValueSetExpansionParameterComponent> params, String name, DataType value) { 735 for (ValueSetExpansionParameterComponent p : params) { 736 if (p.getName().equals(name) && PrimitiveType.compareDeep(p.getValue(), value, false)) { 737 return true; 738 } 739 } 740 return false; 741 } 742 743 public ValueSetExpansionOutcome expand(ValueSet source, Parameters expParams) { 744 allErrors.clear(); 745 try { 746 opContext.seeContext(source.getVersionedUrl()); 747 748 return expandInternal(source, expParams); 749 } catch (NoTerminologyServiceException e) { 750 // well, we couldn't expand, so we'll return an interface to a checker that can check membership of the set 751 // that might fail too, but it might not, later. 752 return new ValueSetExpansionOutcome(e.getMessage(), TerminologyServiceErrorClass.NOSERVICE, allErrors, false); 753 } catch (CodeSystemProviderExtension e) { 754 // well, we couldn't expand, so we'll return an interface to a checker that can check membership of the set 755 // that might fail too, but it might not, later. 756 return new ValueSetExpansionOutcome(e.getMessage(), TerminologyServiceErrorClass.INTERNAL_ERROR, allErrors, false); 757 } catch (TerminologyServiceProtectionException e) { 758 if (opContext.isOriginal()) { 759 return new ValueSetExpansionOutcome(e.getMessage(), e.getError(), allErrors, false); 760 } else { 761 throw e; 762 } 763 } catch (ETooCostly e) { 764 return new ValueSetExpansionOutcome(e.getMessage(), TerminologyServiceErrorClass.TOO_COSTLY, allErrors, false); 765 } catch (UnknownValueSetException e) { 766 return new ValueSetExpansionOutcome(e.getMessage(), TerminologyServiceErrorClass.VALUESET_UNKNOWN, allErrors, false); 767 } catch (VSCheckerException e) { 768 return new ValueSetExpansionOutcome(e.getMessage(), TerminologyServiceErrorClass.UNKNOWN, allErrors, e.getIssues()); 769 } catch (Exception e) { 770 if (debug) { 771 e.printStackTrace(); 772 } 773 return new ValueSetExpansionOutcome(e.getMessage(), TerminologyServiceErrorClass.UNKNOWN, allErrors, e instanceof EFhirClientException || e instanceof TerminologyServiceException); 774 } 775 } 776 777 public ValueSetExpansionOutcome expandInternal(ValueSet source, Parameters expParams) throws FHIRException, FileNotFoundException, ETooCostly, IOException, CodeSystemProviderExtension { 778 if (expParams == null) 779 expParams = makeDefaultExpansion(); 780 altCodeParams.seeParameters(expParams); 781 altCodeParams.seeValueSet(source); 782 source.checkNoModifiers("ValueSet", "expanding"); 783 focus = source.copy(); 784 focus.setIdBase(null); 785 focus.setExpansion(new ValueSet.ValueSetExpansionComponent()); 786 focus.getExpansion().setTimestampElement(DateTimeType.now()); 787 focus.getExpansion().setIdentifier(Factory.createUUID()); 788 checkCanonical(focus.getExpansion(), focus, focus); 789 for (Extension ext : focus.getCompose().getExtensionsByUrl("http://hl7.org/fhir/tools/StructureDefinion/valueset-expansion-param")) { 790 processParameter(ext.getExtensionString("name"), ext.getExtensionByUrl("value").getValue()); 791 } 792 for (ParametersParameterComponent p : expParams.getParameter()) { 793 processParameter(p.getName(), p.getValue()); 794 } 795 for (Extension s : focus.getExtensionsByUrl(ExtensionConstants.EXT_VSSUPPLEMENT)) { 796 requiredSupplements.add(s.getValue().primitiveValue()); 797 } 798 if (langs == null && focus.hasLanguage()) { 799 langs = new AcceptLanguageHeader(focus.getLanguage(), true); 800 } 801 802 try { 803 if (source.hasCompose()) { 804 // ExtensionsUtils.stripExtensions(focus.getCompose()); - disabled 23/05/2023 GDG - why was this ever thought to be a good idea? 805 handleCompose(source.getCompose(), focus.getExpansion(), expParams, source.getUrl(), focus.getExpansion().getExtension(), source); 806 } 807 } catch (EFinished e) { 808 // nothing - we intended to trap this here 809 } 810 811 if (dwc.getCount() > maxExpansionSize && dwc.getOffsetParam() + dwc.getCountParam() == 0) { 812 if (dwc.isNoTotal()) { 813 throw failCostly(context.formatMessage(I18nConstants.VALUESET_TOO_COSTLY, focus.getVersionedUrl(), ">" + MessageFormat.format("{0,number,#}", maxExpansionSize))); 814 } else { 815 throw failCostly(context.formatMessage(I18nConstants.VALUESET_TOO_COSTLY_COUNT, focus.getVersionedUrl(), ">" + MessageFormat.format("{0,number,#}", maxExpansionSize), MessageFormat.format("{0,number,#}", dwc.getCount()))); 816 } 817 } else if (dwc.isCanBeHierarchy() && ((dwc.getCountParam() == 0) || dwc.getCountParam() > dwc.getCodes().size())) { 818 for (ValueSetExpansionContainsComponent c : dwc.getRoots()) { 819 focus.getExpansion().getContains().add(c); 820 } 821 } else { 822 int i = 0; 823 int cc = 0; 824 for (ValueSetExpansionContainsComponent c : dwc.getCodes()) { 825 c.getContains().clear(); // make sure any hierarchy is wiped 826 if (dwc.getMap().containsKey(key(c)) && (includeAbstract || !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 827 if (dwc.getOffsetParam() == 0 || i >= dwc.getOffsetParam()) { 828 focus.getExpansion().getContains().add(c); 829 cc++; 830 if (cc == dwc.getCountParam()) { 831 break; 832 } 833 } 834 i++; 835 } 836 } 837 } 838 839 if (dwc.hasOffsetParam()) { 840 focus.getExpansion().setOffset(dwc.getOffsetParam()); 841 } 842 if (!dwc.isNoTotal()) { 843 focus.getExpansion().setTotal(dwc.getStatedTotal()); 844 } 845 if (!requiredSupplements.isEmpty()) { 846 return new ValueSetExpansionOutcome(context.formatMessagePlural(requiredSupplements.size(), I18nConstants.VALUESET_SUPPLEMENT_MISSING, CommaSeparatedStringBuilder.build(requiredSupplements)), TerminologyServiceErrorClass.BUSINESS_RULE, allErrors, false); 847 } 848 if (!expParams.hasParameter("includeDefinition") || !expParams.getParameterBool("includeDefinition")) { 849 focus.setCompose(null); 850 focus.getExtension().clear(); 851 focus.setPublisher(null); 852 focus.setDescription(null); 853 focus.setPurpose(null); 854 focus.getContact().clear(); 855 focus.setCopyright(null); 856 focus.setText(null); 857 } 858 return new ValueSetExpansionOutcome(focus); 859 } 860 861 private void processParameter(String name, DataType value) { 862 if (Utilities.existsInList(name, "includeDesignations", "excludeNested", "activeOnly", "offset", "count")) { 863 focus.getExpansion().getParameter().removeIf(p -> p.getName().equals(name)); 864 focus.getExpansion().addParameter().setName(name).setValue(value); 865 } 866 if ("displayLanguage".equals(name)) { 867 this.langs = new AcceptLanguageHeader(value.primitiveValue(), true); 868 focus.getExpansion().getParameter().removeIf(p -> p.getName().equals(name)); 869 focus.getExpansion().addParameter().setName(name).setValue(new CodeType(value.primitiveValue())); 870 } 871 if ("designation".equals(name)) { 872 String[] v = value.primitiveValue().split("\\|"); 873 if (v.length != 2 || !Utilities.isAbsoluteUrl(v[0]) || Utilities.noString(v[1])) { 874 throw new NoTerminologyServiceException("Unable to understand designation parameter "+value.primitiveValue()); 875 } 876 this.designations.add(new Token(v[0], v[1])); 877 focus.getExpansion().addParameter().setName(name).setValue(new StringType(value.primitiveValue())); 878 } 879 if ("offset".equals(name) && value instanceof IntegerType) { 880 focus.getExpansion().getParameter().removeIf(p -> p.getName().equals(name)); 881 focus.getExpansion().addParameter().setName(name).setValue(value); 882 dwc.setOffsetParam(((IntegerType) value).getValue()); 883 if (dwc.getOffsetParam() < 0) { 884 dwc.setOffsetParam(0); 885 } 886 } 887 if ("count".equals(name)) { 888 focus.getExpansion().getParameter().removeIf(p -> p.getName().equals(name)); 889 focus.getExpansion().addParameter().setName(name).setValue(value); 890 dwc.setCountParam(((IntegerType) value).getValue()); 891 if (dwc.getCountParam() < 0) { 892 dwc.setCountParam(0); 893 } 894 } 895 } 896 897 public ValueSetExpansionOutcome doExpand(ValueSet source, Parameters expParams) throws FHIRException, ETooCostly, FileNotFoundException, IOException, CodeSystemProviderExtension { 898 if (expParams == null) 899 expParams = makeDefaultExpansion(); 900 altCodeParams.seeParameters(expParams); 901 altCodeParams.seeValueSet(source); 902 source.checkNoModifiers("ValueSet", "expanding"); 903 focus = source.copy(); 904 focus.setIdBase(null); 905 focus.setExpansion(new ValueSet.ValueSetExpansionComponent()); 906 focus.getExpansion().setTimestampElement(DateTimeType.now()); 907 focus.getExpansion().setIdentifier(Factory.createUUID()); 908 checkCanonical(focus.getExpansion(), focus, focus); 909 for (Extension ext : focus.getCompose().getExtensionsByUrl("http://hl7.org/fhir/tools/StructureDefinion/valueset-expansion-param")) { 910 processParameter(ext.getExtensionString("name"), ext.getExtensionByUrl("value").getValue()); 911 } 912 for (ParametersParameterComponent p : expParams.getParameter()) { 913 processParameter(p.getName(), p.getValue()); 914 } 915 for (Extension s : focus.getExtensionsByUrl(ExtensionConstants.EXT_VSSUPPLEMENT)) { 916 requiredSupplements.add(s.getValue().primitiveValue()); 917 } 918 if (langs == null && focus.hasLanguage()) { 919 langs = new AcceptLanguageHeader(focus.getLanguage(), true); 920 } 921 922 try { 923 if (source.hasCompose()) { 924// ExtensionsUtils.stripExtensions(focus.getCompose()); - disabled 23/05/2023 GDG - why was this ever thought to be a good idea? 925 handleCompose(source.getCompose(), focus.getExpansion(), expParams, source.getUrl(), focus.getExpansion().getExtension(), source); 926 } 927 } catch (EFinished e) { 928 // nothing - we intended to trap this here 929 } 930 931 if (dwc.getCount() > maxExpansionSize && dwc.getOffsetParam() + dwc.getCountParam() == 0) { 932 if (dwc.isNoTotal()) { 933 throw failCostly(context.formatMessage(I18nConstants.VALUESET_TOO_COSTLY, focus.getVersionedUrl(), ">" + MessageFormat.format("{0,number,#}", maxExpansionSize))); 934 } else { 935 throw failCostly(context.formatMessage(I18nConstants.VALUESET_TOO_COSTLY_COUNT, focus.getVersionedUrl(), ">" + MessageFormat.format("{0,number,#}", maxExpansionSize), MessageFormat.format("{0,number,#}", dwc.getCount()))); 936 } 937 } else if (dwc.isCanBeHierarchy() && ((dwc.getCountParam() == 0) || dwc.getCountParam() > dwc.getCodes().size())) { 938 for (ValueSetExpansionContainsComponent c : dwc.getRoots()) { 939 focus.getExpansion().getContains().add(c); 940 } 941 } else { 942 int i = 0; 943 int cc = 0; 944 for (ValueSetExpansionContainsComponent c : dwc.getCodes()) { 945 c.getContains().clear(); // make sure any hierarchy is wiped 946 if (dwc.getMap().containsKey(key(c)) && (includeAbstract || !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 947 if (dwc.getOffsetParam() == 0 || i >= dwc.getOffsetParam()) { 948 focus.getExpansion().getContains().add(c); 949 cc++; 950 if (cc == dwc.getCountParam()) { 951 break; 952 } 953 } 954 i++; 955 } 956 } 957 } 958 959 if (dwc.hasOffsetParam()) { 960 focus.getExpansion().setOffset(dwc.getOffsetParam()); 961 } 962 if (!dwc.isNoTotal()) { 963 focus.getExpansion().setTotal(dwc.getStatedTotal()); 964 } 965 if (!requiredSupplements.isEmpty()) { 966 return new ValueSetExpansionOutcome(context.formatMessagePlural(requiredSupplements.size(), I18nConstants.VALUESET_SUPPLEMENT_MISSING, CommaSeparatedStringBuilder.build(requiredSupplements)), TerminologyServiceErrorClass.BUSINESS_RULE, allErrors, false); 967 } 968 if (!expParams.hasParameter("includeDefinition") || !expParams.getParameterBool("includeDefinition")) { 969 focus.setCompose(null); 970 focus.getExtension().clear(); 971 focus.setPublisher(null); 972 focus.setDescription(null); 973 focus.setPurpose(null); 974 focus.getContact().clear(); 975 focus.setCopyright(null); 976 focus.setText(null); 977 } 978 return new ValueSetExpansionOutcome(focus); 979 } 980 981 982 private Parameters makeDefaultExpansion() { 983 Parameters res = new Parameters(); 984 res.addParameter("excludeNested", true); 985 res.addParameter("includeDesignations", false); 986 return res; 987 } 988 989 private ConceptDefinitionComponent getConceptForCode(List<ConceptDefinitionComponent> clist, String code) { 990 for (ConceptDefinitionComponent c : clist) { 991 if (code.equals(c.getCode())) 992 return c; 993 ConceptDefinitionComponent v = getConceptForCode(c.getConcept(), code); 994 if (v != null) 995 return v; 996 } 997 return null; 998 } 999 1000 private void handleCompose(ValueSetComposeComponent compose, ValueSetExpansionComponent exp, Parameters expParams, String ctxt, List<Extension> extensions, ValueSet valueSet) 1001 throws ETooCostly, FileNotFoundException, IOException, FHIRException, CodeSystemProviderExtension { 1002 compose.checkNoModifiers("ValueSet.compose", "expanding"); 1003 String vspath = "ValueSet["+valueSet.getVersionedUrl()+"].compose"; 1004 1005 // Exclude comes first because we build up a map of things to exclude 1006 int c = 0; 1007 for (ConceptSetComponent inc : compose.getExclude()) { 1008 excludeCodes(dwc, inc, expParams, exp, valueSet, vspath+".include["+c+"]"); 1009 c++; 1010 } 1011 dwc.setCanBeHierarchy(!expParams.getParameterBool("excludeNested") && dwc.getExcludeKeys().isEmpty() && dwc.getExcludeSystems().isEmpty() && dwc.getOffsetParam() == 0); 1012 includeAbstract = !expParams.getParameterBool("excludeNotForUI"); 1013 boolean first = true; 1014 c = 0; 1015 for (ConceptSetComponent inc : compose.getInclude()) { 1016 if (first == true) 1017 first = false; 1018 else 1019 dwc.setCanBeHierarchy(false); 1020 includeCodes(inc, exp, expParams, dwc.isCanBeHierarchy(), compose.hasInactive() ? !compose.getInactive() : checkNoInActiveFromParam(expParams), extensions, valueSet, vspath+".include["+c+"]"); 1021 c++; 1022 } 1023 } 1024 1025 /** 1026 * returns true if activeOnly = true 1027 * @param expParams 1028 * @return 1029 */ 1030 private boolean checkNoInActiveFromParam(Parameters expParams) { 1031 for (ParametersParameterComponent p : expParams.getParameter()) { 1032 if (p.getName().equals("activeOnly")) { 1033 return p.getValueBooleanType().getValue(); 1034 } 1035 } 1036 return false; 1037 } 1038 1039 private ValueSet importValueSet(WorkingContext wc, String value, ValueSetExpansionComponent exp, Parameters expParams, boolean noInactive, ValueSet valueSet) throws ETooCostly, TerminologyServiceException, FileNotFoundException, IOException, FHIRFormatError { 1040 if (value == null) 1041 throw fail(I18nConstants.VS_EXP_IMPORT_NULL, true); 1042 String url = getCu().pinValueSet(value, expParams); 1043 ValueSet vs = context.findTxResource(ValueSet.class, url, valueSet); 1044 if (vs == null) { 1045 boolean pinned = !url.equals(value); 1046 String ver = pinned ? url.substring(value.length()+1) : null; 1047 if (context.fetchResource(CodeSystem.class, url, valueSet) != null) { 1048 throw failNotFound(pinned ? I18nConstants.VS_EXP_IMPORT_CS_PINNED : I18nConstants.VS_EXP_IMPORT_CS, true, value, ver); 1049 } else { 1050 throw failNotFound(pinned ? I18nConstants.VS_EXP_IMPORT_UNK_PINNED : I18nConstants.VS_EXP_IMPORT_UNK, true, value, ver); 1051 } 1052 } 1053 checkCanonical(exp, vs, focus); 1054 if (noInactive) { 1055 expParams = expParams.copy(); 1056 expParams.addParameter("activeOnly", true); 1057 } 1058 ValueSetExpander expander = new ValueSetExpander(context, opContext.copy(), allErrors); 1059 ValueSetExpansionOutcome vso = expander.expand(vs, expParams); 1060 if (vso.getError() != null) { 1061 addErrors(vso.getAllErrors()); 1062 if (vso.getErrorClass() == TerminologyServiceErrorClass.VALUESET_UNKNOWN) { 1063 throw failUnk(I18nConstants.VS_EXP_IMPORT_ERROR, true, vs.getUrl(), vso.getError()); 1064 } else { 1065 throw fail(I18nConstants.VS_EXP_IMPORT_ERROR, true, vs.getUrl(), vso.getError()); 1066 } 1067 } else if (vso.getValueset() == null) { 1068 throw fail(I18nConstants.VS_EXP_IMPORT_FAIL, true, vs.getUrl()); 1069 } 1070 sources.addAll(expander.sources); 1071 if (vs.hasVersion() || REPORT_VERSION_ANYWAY) { 1072 UriType u = new UriType(vs.getUrl() + (vs.hasVersion() ? "|"+vs.getVersion() : "")); 1073 if (!existsInParams(exp.getParameter(), "used-valueset", u)) 1074 exp.getParameter().add(new ValueSetExpansionParameterComponent().setName("used-valueset").setValue(u)); 1075 } 1076 ValueSetExpansionComponent evs = vso.getValueset().getExpansion(); 1077 for (Extension ex : evs.getExtension()) { 1078 if (ex.getUrl().equals(ToolingExtensions.EXT_EXP_TOOCOSTLY)) { 1079 if (ex.getValue() instanceof BooleanType) { 1080 exp.getExtension().add(new Extension(ToolingExtensions.EXT_EXP_TOOCOSTLY).setValue(new CanonicalType(value))); 1081 } else { 1082 exp.getExtension().add(ex); 1083 } 1084 } 1085 } 1086 if (!evs.hasTotal()) { 1087 // because if there's no total, we can't know if we got everything 1088 dwc.setNoTotal(true); 1089 } 1090 for (ValueSetExpansionParameterComponent p : evs.getParameter()) { 1091 if (!existsInParams(exp.getParameter(), p.getName(), p.getValue())) 1092 exp.getParameter().add(p); 1093 } 1094 if (isValueSetUnionImports(valueSet)) { 1095 copyExpansion(wc, evs.getContains()); 1096 } 1097 wc.setCanBeHierarchy(false); // if we're importing a value set, we have to be combining, so we won't try for a hierarchy 1098 return vso.getValueset(); 1099 } 1100 1101 1102 1103 private ValueSet importValueSetForExclude(WorkingContext wc, String value, ValueSetExpansionComponent exp, Parameters expParams, boolean noInactive, ValueSet valueSet) throws ETooCostly, TerminologyServiceException, FileNotFoundException, IOException, FHIRFormatError { 1104 if (value == null) 1105 throw fail(I18nConstants.VS_EXP_IMPORT_NULL_X, true); 1106 String url = getCu().pinValueSet(value, expParams); 1107 ValueSet vs = context.findTxResource(ValueSet.class, url, valueSet); 1108 if (vs == null) { 1109 boolean pinned = !url.equals(value); 1110 String ver = pinned ? url.substring(value.length()+1) : null; 1111 if (context.fetchResource(CodeSystem.class, url, valueSet) != null) { 1112 throw fail(pinned ? I18nConstants.VS_EXP_IMPORT_CS_PINNED_X : I18nConstants.VS_EXP_IMPORT_CS_X, true, value, ver); 1113 } else { 1114 throw fail(pinned ? I18nConstants.VS_EXP_IMPORT_UNK_PINNED_X : I18nConstants.VS_EXP_IMPORT_UNK_X, true, value, ver); 1115 } 1116 } 1117 checkCanonical(exp, vs, focus); 1118 if (noInactive) { 1119 expParams = expParams.copy(); 1120 expParams.addParameter("activeOnly", true); 1121 } 1122 ValueSetExpander expander = new ValueSetExpander(context, opContext.copy(), allErrors); 1123 ValueSetExpansionOutcome vso = expander.expand(vs, expParams); 1124 sources.addAll(expander.sources); 1125 if (vso.getError() != null) { 1126 addErrors(vso.getAllErrors()); 1127 throw fail(I18nConstants.VS_EXP_IMPORT_ERROR_X, true, vs.getUrl(), vso.getError()); 1128 } else if (vso.getValueset() == null) { 1129 throw fail(I18nConstants.VS_EXP_IMPORT_FAIL_X, true, vs.getUrl()); 1130 } 1131 1132 if (vs.hasVersion() || REPORT_VERSION_ANYWAY) { 1133 UriType u = new UriType(vs.getUrl() + (vs.hasVersion() ? "|"+vs.getVersion() : "")); 1134 if (!existsInParams(exp.getParameter(), "used-valueset", u)) 1135 exp.getParameter().add(new ValueSetExpansionParameterComponent().setName("used-valueset").setValue(u)); 1136 } 1137 for (Extension ex : vso.getValueset().getExpansion().getExtension()) { 1138 if (ex.getUrl().equals(ToolingExtensions.EXT_EXP_TOOCOSTLY)) { 1139 throw fail(VS_EXP_IMPORT_ERROR_TOO_COSTLY, true, vs.getUrl()); 1140 } 1141 } 1142 return vso.getValueset(); 1143 } 1144 1145 protected boolean isValueSetUnionImports(ValueSet valueSet) { 1146 PackageInformation p = valueSet.getSourcePackage(); 1147 if (p != null) { 1148 return p.getDate().before(new GregorianCalendar(2022, Calendar.MARCH, 31).getTime()); 1149 } else { 1150 return false; 1151 } 1152 } 1153 1154 public void copyExpansion(WorkingContext wc,List<ValueSetExpansionContainsComponent> list) { 1155 opContext.deadCheck("copyExpansion"); 1156 for (ValueSetExpansionContainsComponent cc : list) { 1157 ValueSetExpansionContainsComponent n = new ValueSet.ValueSetExpansionContainsComponent(); 1158 n.setSystem(cc.getSystem()); 1159 n.setCode(cc.getCode()); 1160 n.setAbstract(cc.getAbstract()); 1161 n.setInactive(cc.getInactive()); 1162 n.setDisplay(cc.getDisplay()); 1163 n.getDesignation().addAll(cc.getDesignation()); 1164 1165 String s = key(n); 1166 if (!wc.getMap().containsKey(s) && !wc.getExcludeKeys().contains(s)) { 1167 wc.getCodes().add(n); 1168 wc.getMap().put(s, n); 1169 } 1170 copyExpansion(wc, cc.getContains()); 1171 } 1172 } 1173 1174 private void addErrors(List<String> errs) { 1175 for (String s : errs) { 1176 if (!allErrors.contains(s)) { 1177 allErrors.add(s); 1178 } 1179 } 1180 } 1181 1182 private int copyImportContains(List<ValueSetExpansionContainsComponent> list, ValueSetExpansionContainsComponent parent, Parameters expParams, List<ValueSet> filter, boolean noInactive, List<ValueSetExpansionPropertyComponent> vsProps, ValueSet vsSrc, ValueSetExpansionComponent exp) throws FHIRException, ETooCostly { 1183 int count = 0; 1184 opContext.deadCheck("copyImportContains"); 1185 1186 String lang = vsSrc.getLanguage(); 1187 if (lang == null) { 1188 lang = findParamValue(vsSrc.getExpansion().getParameter(), "displayLanguage"); 1189 } 1190 for (ValueSetExpansionContainsComponent c : list) { 1191 c.checkNoModifiers("Imported Expansion in Code System", "expanding"); 1192 ValueSetExpansionContainsComponent np = addCode(dwc, c.getSystem(), c.getCode(), c.getDisplay(), lang, parent, translateDesignations(c), expParams, c.getAbstract(), c.getInactive(), 1193 filter, noInactive, false, vsProps, makeCSProps(c.getExtensionString(ToolingExtensions.EXT_DEFINITION), null), null, c.getProperty(), null, c.getExtension(), exp); 1194 if (np != null) { 1195 count++; 1196 } 1197 count = count + copyImportContains(c.getContains(), np, expParams, filter, noInactive, vsProps, vsSrc, exp); 1198 } 1199 return count; 1200 } 1201 1202 private List<ConceptDefinitionDesignationComponent> translateDesignations(ValueSetExpansionContainsComponent c) { 1203 if (!c.hasDesignation()) { 1204 return null; 1205 } 1206 List<ConceptDefinitionDesignationComponent> list = new ArrayList<>(); 1207 for (ConceptReferenceDesignationComponent d : c.getDesignation()) { 1208 ConceptDefinitionDesignationComponent d2 = new ConceptDefinitionDesignationComponent(); 1209 d2.setLanguage(d.getLanguage()); 1210 d2.setUse(d.getUse()); 1211 d2.setAdditionalUse(d.getAdditionalUse()); 1212 d2.setValue(d.getValue()); 1213 list.add(d2); 1214 } 1215 return list; 1216 } 1217 1218 private void includeCodes(ConceptSetComponent inc, ValueSetExpansionComponent exp, Parameters expParams, boolean heirarchical, boolean noInactive, List<Extension> extensions, ValueSet valueSet, String vspath) throws ETooCostly, FileNotFoundException, IOException, FHIRException, CodeSystemProviderExtension { 1219 opContext.deadCheck("includeCodes"); 1220 inc.checkNoModifiers("Compose.include", "expanding"); 1221 List<ValueSet> imports = new ArrayList<ValueSet>(); 1222 for (CanonicalType imp : inc.getValueSet()) { 1223 imports.add(importValueSet(dwc, imp.getValue(), exp, expParams, noInactive, valueSet)); 1224 } 1225 1226 if (!inc.hasSystem()) { 1227 if (imports.isEmpty()) // though this is not supposed to be the case 1228 return; 1229 ValueSet base = imports.get(0); 1230 checkCanonical(exp, base, focus); 1231 imports.remove(0); 1232 base.checkNoModifiers("Imported ValueSet", "expanding"); 1233 copyImportContains(base.getExpansion().getContains(), null, expParams, imports, noInactive, base.getExpansion().getProperty(), base, exp); 1234 } else { 1235 CodeSystem cs = context.fetchSupplementedCodeSystem(inc.getSystem()); 1236 if (ValueSetUtilities.isServerSide(inc.getSystem()) || (cs == null || (cs.getContent() != CodeSystemContentMode.COMPLETE && cs.getContent() != CodeSystemContentMode.FRAGMENT))) { 1237 doServerIncludeCodes(inc, heirarchical, exp, imports, expParams, extensions, noInactive, valueSet.getExpansion().getProperty()); 1238 } else { 1239 if (cs.hasUserData(UserDataNames.tx_known_supplements)) { 1240 for (String s : cs.getUserString(UserDataNames.tx_known_supplements).split("\\,")) { 1241 requiredSupplements.remove(s); 1242 } 1243 } 1244 doInternalIncludeCodes(inc, exp, expParams, imports, cs, noInactive, valueSet, vspath); 1245 } 1246 } 1247 } 1248 1249 private void doServerIncludeCodes(ConceptSetComponent inc, boolean heirarchical, ValueSetExpansionComponent exp, List<ValueSet> imports, Parameters expParams, List<Extension> extensions, boolean noInactive, List<ValueSetExpansionPropertyComponent> vsProps) throws FHIRException, CodeSystemProviderExtension, ETooCostly { 1250 opContext.deadCheck("doServerIncludeCodes"); 1251 CodeSystemProvider csp = CodeSystemProvider.factory(inc.getSystem()); 1252 if (csp != null) { 1253 csp.includeCodes(inc, heirarchical, exp, imports, expParams, extensions, noInactive, vsProps); 1254 return; 1255 } 1256 1257 ValueSetExpansionOutcome vso = context.expandVS(new TerminologyOperationDetails(requiredSupplements), inc, heirarchical, noInactive); 1258 if (vso.getError() != null) { 1259 throw failTSE("Unable to expand imported value set: " + vso.getError()); 1260 } 1261 ValueSet vs = vso.getValueset(); 1262 if (vs.hasUserData(UserDataNames.VS_EXPANSION_SOURCE)) { 1263 sources.add(vs.getUserString(UserDataNames.VS_EXPANSION_SOURCE)); 1264 } 1265 if (vs.hasVersion() || REPORT_VERSION_ANYWAY) { 1266 UriType u = new UriType(vs.getUrl() + (vs.hasVersion() ? "|"+vs.getVersion() : "")); 1267 if (!existsInParams(exp.getParameter(), "used-valueset", u)) { 1268 exp.getParameter().add(new ValueSetExpansionParameterComponent().setName("used-valueset").setValue(u)); 1269 } 1270 } 1271 if (vs.getExpansion().hasTotal()) { 1272 // 0 for now... dwc.incExtraCount(!vs.getExpansion().getTotal()); 1273 } else { 1274 dwc.setNoTotal(true); 1275 } 1276 for (ValueSetExpansionParameterComponent p : vso.getValueset().getExpansion().getParameter()) { 1277 if (!existsInParams(exp.getParameter(), p.getName(), p.getValue())) { 1278 exp.getParameter().add(p); 1279 } 1280 } 1281 for (Extension ex : vs.getExpansion().getExtension()) { 1282 if (Utilities.existsInList(ex.getUrl(), ToolingExtensions.EXT_EXP_TOOCOSTLY, "http://hl7.org/fhir/StructureDefinition/valueset-unclosed")) { 1283 if (!ExtensionsUtils.hasExtension(extensions, ex.getUrl())) { 1284 extensions.add(ex); 1285 } 1286 } 1287 } 1288 for (ValueSetExpansionContainsComponent cc : vs.getExpansion().getContains()) { 1289 addCodeAndDescendents(dwc, cc, null, expParams, imports, noInactive, vsProps, vs, exp, getLang(vs)); 1290 } 1291 } 1292 1293 1294 public void doInternalIncludeCodes(ConceptSetComponent inc, ValueSetExpansionComponent exp, Parameters expParams, List<ValueSet> imports, CodeSystem cs, boolean noInactive, Resource vsSrc, String vspath) throws NoTerminologyServiceException, TerminologyServiceException, FHIRException, ETooCostly { 1295 opContext.deadCheck("doInternalIncludeCodes"); 1296 if (cs == null) { 1297 if (context.isNoTerminologyServer()) 1298 throw failTSE("Unable to find code system " + inc.getSystem().toString()); 1299 else 1300 throw failTSE("Unable to find code system " + inc.getSystem().toString()); 1301 } 1302 checkCanonical(exp, cs, focus); 1303 cs.checkNoModifiers("Code System", "expanding"); 1304 if (cs.getContent() != CodeSystemContentMode.COMPLETE && cs.getContent() != CodeSystemContentMode.FRAGMENT) 1305 throw failTSE("Code system " + inc.getSystem().toString() + " is incomplete"); 1306 if (cs.hasVersion() || REPORT_VERSION_ANYWAY) { 1307 UriType u = new UriType(cs.getUrl() + (cs.hasVersion() ? "|"+cs.getVersion() : "")); 1308 if (!existsInParams(exp.getParameter(), "used-codesystem", u)) 1309 exp.getParameter().add(new ValueSetExpansionParameterComponent().setName("used-codesystem").setValue(u)); 1310 if (cs.hasUserData(UserDataNames.tx_known_supplements)) { 1311 for (String s : cs.getUserString(UserDataNames.tx_known_supplements).split("\\,")) { 1312 u = new UriType(s); 1313 if (!existsInParams(exp.getParameter(), "used-supplement", u)) { 1314 exp.getParameter().add(new ValueSetExpansionParameterComponent().setName("used-supplement").setValue(u)); 1315 } 1316 } 1317 } 1318 } 1319 if (inc.getConcept().size() == 0 && inc.getFilter().size() == 0) { 1320 // special case - add all the code system 1321 for (ConceptDefinitionComponent def : cs.getConcept()) { 1322 addCodeAndDescendents(dwc, cs, inc.getSystem(), def, null, expParams, imports, null, new AllConceptsFilter(allErrors), noInactive, exp.getProperty(), null, exp); 1323 } 1324 if (cs.getContent() == CodeSystemContentMode.FRAGMENT) { 1325 addFragmentWarning(exp, cs); 1326 } 1327 if (cs.getContent() == CodeSystemContentMode.EXAMPLE) { 1328 addExampleWarning(exp, cs); 1329 } 1330 } 1331 1332 if (!inc.getConcept().isEmpty()) { 1333 dwc.setCanBeHierarchy(false); 1334 for (ConceptReferenceComponent c : inc.getConcept()) { 1335 c.checkNoModifiers("Code in Value Set", "expanding"); 1336 ConceptDefinitionComponent def = CodeSystemUtilities.findCodeOrAltCode(cs.getConcept(), c.getCode(), null); 1337 boolean inactive = false; // default is true if we're a fragment and 1338 boolean isAbstract = false; 1339 if (def == null) { 1340 if (cs.getContent() == CodeSystemContentMode.FRAGMENT) { 1341 addFragmentWarning(exp, cs); 1342 } else if (cs.getContent() == CodeSystemContentMode.EXAMPLE) { 1343 addExampleWarning(exp, cs); 1344 } else { 1345 if (checkCodesWhenExpanding) { 1346 throw failTSE("Unable to find code '" + c.getCode() + "' in code system " + cs.getUrl()); 1347 } 1348 } 1349 } else { 1350 def.checkNoModifiers("Code in Code System", "expanding"); 1351 inactive = CodeSystemUtilities.isInactive(cs, def); 1352 isAbstract = CodeSystemUtilities.isNotSelectable(cs, def); 1353 addCode(dwc, inc.getSystem(), c.getCode(), !Utilities.noString(c.getDisplay()) ? c.getDisplay() : def.getDisplay(), c.hasDisplay() ? vsSrc.getLanguage() : cs.getLanguage(), null, mergeDesignations(def, convertDesignations(c.getDesignation())), 1354 expParams, isAbstract, inactive, imports, noInactive, false, exp.getProperty(), makeCSProps(def.getDefinition(), def.getProperty()), cs, null, def.getExtension(), c.getExtension(), exp); 1355 } 1356 } 1357 } 1358 if (inc.getFilter().size() > 0) { 1359 if (inc.getFilter().size() > 1) { 1360 dwc.setCanBeHierarchy(false); // which will be the case if we get around to supporting this 1361 } 1362 if (cs.getContent() == CodeSystemContentMode.FRAGMENT) { 1363 addFragmentWarning(exp, cs); 1364 } 1365 List<WorkingContext> filters = new ArrayList<>(); 1366 for (int i = 1; i < inc.getFilter().size(); i++) { 1367 WorkingContext wc = new WorkingContext(); 1368 filters.add(wc); 1369 processFilter(inc, exp, expParams, imports, cs, noInactive, inc.getFilter().get(i), wc, null, false, vspath+".filter["+i+"]"); 1370 } 1371 ConceptSetFilterComponent fc = inc.getFilter().get(0); 1372 WorkingContext wc = dwc; 1373 processFilter(inc, exp, expParams, imports, cs, noInactive, fc, wc, filters, false, vspath+".filter[0]"); 1374 } 1375 } 1376 1377 private void processFilter(ConceptSetComponent inc, ValueSetExpansionComponent exp, Parameters expParams, List<ValueSet> imports, CodeSystem cs, boolean noInactive, 1378 ConceptSetFilterComponent fc, WorkingContext wc, List<WorkingContext> filters, boolean exclude, String vspath) 1379 throws ETooCostly { 1380 1381 if (!fc.hasValue() || fc.getValue() == null) { 1382 List<OperationOutcomeIssueComponent> issues = new ArrayList<>(); 1383 issues.addAll(makeIssue(IssueSeverity.ERROR, IssueType.INVALID, vspath+".value", context.formatMessage(I18nConstants.UNABLE_TO_HANDLE_SYSTEM_FILTER_WITH_NO_VALUE, cs.getUrl(), fc.getProperty(), fc.getOp().toCode()), OpIssueCode.VSProcessing, null)); 1384 throw new VSCheckerException(context.formatMessage(I18nConstants.UNABLE_TO_HANDLE_SYSTEM_FILTER_WITH_NO_VALUE, cs.getUrl(), fc.getProperty(), fc.getOp().toCode()), issues, TerminologyServiceErrorClass.INTERNAL_ERROR); 1385 } 1386 opContext.deadCheck("processFilter"); 1387 if ("concept".equals(fc.getProperty()) && fc.getOp() == FilterOperator.ISA) { 1388 // special: all codes in the target code system under the value 1389 ConceptDefinitionComponent def = getConceptForCode(cs.getConcept(), fc.getValue()); 1390 if (def == null) 1391 throw failTSE("Code '" + fc.getValue() + "' not found in system '" + inc.getSystem() + "'"); 1392 if (exclude) { 1393 excludeCodeAndDescendents(wc, cs, inc.getSystem(), def, null, imports, null, new AllConceptsFilter(allErrors), filters, exp); 1394 } else { 1395 addCodeAndDescendents(wc, cs, inc.getSystem(), def, null, expParams, imports, null, new AllConceptsFilter(allErrors), noInactive, exp.getProperty(), filters, exp); 1396 } 1397 } else if ("concept".equals(fc.getProperty()) && fc.getOp() == FilterOperator.ISNOTA) { 1398 // special: all codes in the target code system that are not under the value 1399 ConceptDefinitionComponent defEx = getConceptForCode(cs.getConcept(), fc.getValue()); 1400 if (defEx == null) 1401 throw failTSE("Code '" + fc.getValue() + "' not found in system '" + inc.getSystem() + "'"); 1402 for (ConceptDefinitionComponent def : cs.getConcept()) { 1403 if (exclude) { 1404 excludeCodeAndDescendents(wc, cs, inc.getSystem(), def, null, imports, defEx, new AllConceptsFilter(allErrors), filters, exp); 1405 } else { 1406 addCodeAndDescendents(wc, cs, inc.getSystem(), def, null, expParams, imports, defEx, new AllConceptsFilter(allErrors), noInactive, exp.getProperty(), filters, exp); 1407 } 1408 } 1409 } else if ("concept".equals(fc.getProperty()) && fc.getOp() == FilterOperator.DESCENDENTOF) { 1410 // special: all codes in the target code system under the value 1411 ConceptDefinitionComponent def = getConceptForCode(cs.getConcept(), fc.getValue()); 1412 if (def == null) 1413 throw failTSE("Code '" + fc.getValue() + "' not found in system '" + inc.getSystem() + "'"); 1414 for (ConceptDefinitionComponent c : def.getConcept()) 1415 if (exclude) { 1416 excludeCodeAndDescendents(wc, cs, inc.getSystem(), c, null, imports, null, new AllConceptsFilter(allErrors), filters, exp); 1417 } else { 1418 addCodeAndDescendents(wc, cs, inc.getSystem(), c, null, expParams, imports, null, new AllConceptsFilter(allErrors), noInactive, exp.getProperty(), filters, exp); 1419 } 1420 if (def.hasUserData(CodeSystemUtilities.USER_DATA_CROSS_LINK)) { 1421 List<ConceptDefinitionComponent> children = (List<ConceptDefinitionComponent>) def.getUserData(CodeSystemUtilities.USER_DATA_CROSS_LINK); 1422 for (ConceptDefinitionComponent c : children) { 1423 if (exclude) { 1424 excludeCodeAndDescendents(wc, cs, inc.getSystem(), c, null, imports, null, new AllConceptsFilter(allErrors), filters, exp); 1425 } else { 1426 addCodeAndDescendents(wc, cs, inc.getSystem(), c, null, expParams, imports, null, new AllConceptsFilter(allErrors), noInactive, exp.getProperty(), filters, exp); 1427 } 1428 } 1429 } 1430 1431 } else if ("display".equals(fc.getProperty()) && fc.getOp() == FilterOperator.EQUAL) { 1432 // gg; note: wtf is this: if the filter is display=v, look up the code 'v', and see if it's display is 'v'? 1433 dwc.setCanBeHierarchy(false); 1434 ConceptDefinitionComponent def = getConceptForCode(cs.getConcept(), fc.getValue()); 1435 if (def != null) { 1436 if (isNotBlank(def.getDisplay()) && isNotBlank(fc.getValue())) { 1437 if (def.getDisplay().contains(fc.getValue()) && passesOtherFilters(filters, cs, def.getCode())) { 1438 for (String code : getCodesForConcept(def, expParams)) { 1439 opContext.deadCheck("processFilter2"); 1440 if (exclude) { 1441 excludeCode(wc, inc.getSystem(), code); 1442 } else { 1443 addCode(wc, inc.getSystem(), code, def.getDisplay(), cs.getLanguage(), null, def.getDesignation(), expParams, CodeSystemUtilities.isNotSelectable(cs, def), CodeSystemUtilities.isInactive(cs, def), 1444 imports, noInactive, false, exp.getProperty(), makeCSProps(def.getDefinition(), def.getProperty()), cs, null, def.getExtension(), null, exp); 1445 } 1446 } 1447 } 1448 } 1449 } 1450 } else if (CodeSystemUtilities.isDefinedProperty(cs, fc.getProperty())) { 1451 for (ConceptDefinitionComponent def : cs.getConcept()) { 1452 PropertyFilter pf = new PropertyFilter(allErrors, fc, CodeSystemUtilities.getPropertyDefinition(cs, fc.getProperty())); 1453 if (exclude) { 1454 excludeCodeAndDescendents(wc, cs, inc.getSystem(), def, null, imports, null, pf, filters, exp); 1455 } else { 1456 addCodeAndDescendents(wc, cs, inc.getSystem(), def, null, expParams, imports, null, pf, noInactive, exp.getProperty(), filters, exp); 1457 } 1458 } 1459 } else if (isKnownProperty(fc.getProperty(), cs)) { 1460 for (ConceptDefinitionComponent def : cs.getConcept()) { 1461 KnownPropertyFilter pf = new KnownPropertyFilter(allErrors, fc, fc.getProperty()); 1462 if (exclude) { 1463 excludeCodeAndDescendents(wc, cs, inc.getSystem(), def, null, imports, null, pf, filters, exp); 1464 } else { 1465 addCodeAndDescendents(wc, cs, inc.getSystem(), def, null, expParams, imports, null, pf, noInactive, exp.getProperty(), filters, exp); 1466 } 1467 } 1468 } else if ("code".equals(fc.getProperty()) && fc.getOp() == FilterOperator.REGEX) { 1469 for (ConceptDefinitionComponent def : cs.getConcept()) { 1470 if (exclude) { 1471 excludeCodeAndDescendents(wc, cs, inc.getSystem(), def, null, imports, null, new RegexFilter(allErrors, fc.getValue()), filters, exp); 1472 } else { 1473 addCodeAndDescendents(wc, cs, inc.getSystem(), def, null, expParams, imports, null, new RegexFilter(allErrors, fc.getValue()), noInactive, exp.getProperty(), filters, exp); 1474 } 1475 } 1476 } else { 1477 throw fail(I18nConstants.VS_EXP_FILTER_UNK, true, focus.getVersionedUrl(), fc.getProperty(), fc.getOp()); 1478 } 1479 } 1480 1481 private boolean isKnownProperty(String property, CodeSystem cs) { 1482 return Utilities.existsInList(property, "notSelectable"); 1483 } 1484 1485 private List<ConceptDefinitionDesignationComponent> mergeDesignations(ConceptDefinitionComponent def, 1486 List<ConceptDefinitionDesignationComponent> list) { 1487 List<ConceptDefinitionDesignationComponent> res = new ArrayList<>(); 1488 if (def != null) { 1489 res.addAll(def.getDesignation()); 1490 } 1491 res.addAll(list); 1492 return res; 1493 } 1494 1495 1496 1497 private void addFragmentWarning(ValueSetExpansionComponent exp, CodeSystem cs) { 1498 String url = cs.getVersionedUrl(); 1499 for (ValueSetExpansionParameterComponent p : exp.getParameter()) { 1500 if ("fragment".equals(p.getName()) && p.hasValueUriType() && url.equals(p.getValue().primitiveValue())) { 1501 return; 1502 } 1503 } 1504 exp.addParameter().setName("fragment").setValue(new CanonicalType(url)); 1505 } 1506 1507 private void addExampleWarning(ValueSetExpansionComponent exp, CodeSystem cs) { 1508 String url = cs.getVersionedUrl(); 1509 for (ValueSetExpansionParameterComponent p : exp.getParameter()) { 1510 if ("example".equals(p.getName()) && p.hasValueUriType() && url.equals(p.getValue().primitiveValue())) { 1511 return; 1512 } 1513 } 1514 exp.addParameter().setName("example").setValue(new CanonicalType(url)); 1515 } 1516 1517 private List<ConceptDefinitionDesignationComponent> convertDesignations(List<ConceptReferenceDesignationComponent> list) { 1518 List<ConceptDefinitionDesignationComponent> res = new ArrayList<CodeSystem.ConceptDefinitionDesignationComponent>(); 1519 for (ConceptReferenceDesignationComponent t : list) { 1520 ConceptDefinitionDesignationComponent c = new ConceptDefinitionDesignationComponent(); 1521 c.setLanguage(t.getLanguage()); 1522 if (t.hasUse()) { 1523 c.setUse(t.getUse()); 1524 } 1525 c.setValue(t.getValue()); 1526 c.getExtension().addAll(t.getExtension()); 1527 res.add(c); 1528 } 1529 return res; 1530 } 1531 1532 private String key(String uri, String code) { 1533 return "{" + uri + "}" + code; 1534 } 1535 1536 private String key(ValueSetExpansionContainsComponent c) { 1537 return key(c.getSystem(), c.getCode()); 1538 } 1539 1540 private FHIRException fail(String msgId, boolean check, Object... params) { 1541 String msg = context.formatMessage(msgId, params); 1542 allErrors.add(msg); 1543 return new FHIRException(msg); 1544 } 1545 1546 private UnknownValueSetException failUnk(String msgId, boolean check, Object... params) { 1547 String msg = context.formatMessage(msgId, params); 1548 allErrors.add(msg); 1549 return new UnknownValueSetException(msg); 1550 } 1551 1552 private UnknownValueSetException failNotFound(String msgId, boolean check, Object... params) { 1553 String msg = context.formatMessage(msgId, params); 1554 allErrors.add(msg); 1555 return new UnknownValueSetException(msg); 1556 } 1557 1558 private ETooCostly failCostly(String msg) { 1559 allErrors.add(msg); 1560 return new ETooCostly(msg); 1561 } 1562 1563 private TerminologyServiceException failTSE(String msg) { 1564 allErrors.add(msg); 1565 return new TerminologyServiceException(msg); 1566 } 1567 1568 public Collection<? extends String> getAllErrors() { 1569 return allErrors; 1570 } 1571 1572 public boolean isCheckCodesWhenExpanding() { 1573 return checkCodesWhenExpanding; 1574 } 1575 1576 public void setCheckCodesWhenExpanding(boolean checkCodesWhenExpanding) { 1577 this.checkCodesWhenExpanding = checkCodesWhenExpanding; 1578 } 1579 1580 private boolean passesOtherFilters(List<WorkingContext> otherFilters, CodeSystem cs, String code) { 1581 if (otherFilters == null) { 1582 return true; 1583 } 1584 String key = key(cs.getUrl(), code); 1585 for (WorkingContext wc : otherFilters) { 1586 if (!wc.getMap().containsKey(key)) { 1587 return false; 1588 } 1589 } 1590 return true; 1591 } 1592 1593 public boolean isDebug() { 1594 return debug; 1595 } 1596 1597 public ValueSetExpander setDebug(boolean debug) { 1598 this.debug = debug; 1599 return this; 1600 } 1601 1602 public String getSource() { 1603 if (sources.isEmpty()) { 1604 return "internal"; 1605 } else { 1606 return CommaSeparatedStringBuilder.join(", ", Utilities.sorted(sources)); 1607 } 1608 } 1609 1610 1611}