org.hl7.fhir.r5.terminologies.expansion.ValueSetExpander Maven / Gradle / Ivy
package org.hl7.fhir.r5.terminologies.expansion;
/*
Copyright (c) 2011+, HL7, Inc.
All rights reserved.
Redistribution and use in source and binary forms, with or without modification,
are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
* Neither the name of HL7 nor the names of its contributors may be used to
endorse or promote products derived from this software without specific
prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
POSSIBILITY OF SUCH DAMAGE.
*/
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.text.MessageFormat;
/*
* Copyright (c) 2011+, HL7, Inc
* All rights reserved.
*
* Redistribution and use in source and binary forms, with or without modification,
* are permitted provided that the following conditions are met:
*
* Redistributions of source code must retain the above copyright notice, this
* list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright notice,
* this list of conditions and the following disclaimer in the documentation
* and/or other materials provided with the distribution.
* Neither the name of HL7 nor the names of its contributors may be used to
* endorse or promote products derived from this software without specific
* prior written permission.
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
* ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
* WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
* IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
* INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
* NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
* PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
* WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
* ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
* POSSIBILITY OF SUCH DAMAGE.
*
*/
import java.util.ArrayList;
import java.util.Calendar;
import java.util.Collection;
import java.util.GregorianCalendar;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.exceptions.NoTerminologyServiceException;
import org.hl7.fhir.exceptions.TerminologyServiceException;
import org.hl7.fhir.r5.context.IWorkerContext;
import org.hl7.fhir.r5.elementmodel.LanguageUtils;
import org.hl7.fhir.r5.extensions.ExtensionConstants;
import org.hl7.fhir.r5.extensions.ExtensionsUtils;
import org.hl7.fhir.r5.model.BooleanType;
import org.hl7.fhir.r5.model.CanonicalType;
import org.hl7.fhir.r5.model.CodeSystem;
import org.hl7.fhir.r5.model.CodeSystem.ConceptDefinitionComponent;
import org.hl7.fhir.r5.model.CodeSystem.ConceptDefinitionDesignationComponent;
import org.hl7.fhir.r5.model.CodeSystem.ConceptPropertyComponent;
import org.hl7.fhir.r5.model.CodeSystem.PropertyComponent;
import org.hl7.fhir.r5.model.CodeType;
import org.hl7.fhir.r5.model.Coding;
import org.hl7.fhir.r5.model.DataType;
import org.hl7.fhir.r5.model.DateTimeType;
import org.hl7.fhir.r5.model.DecimalType;
import org.hl7.fhir.r5.model.Enumerations.CodeSystemContentMode;
import org.hl7.fhir.r5.model.Enumerations.FilterOperator;
import org.hl7.fhir.r5.model.OperationOutcome.IssueType;
import org.hl7.fhir.r5.model.OperationOutcome.OperationOutcomeIssueComponent;
import org.hl7.fhir.r5.model.Extension;
import org.hl7.fhir.r5.model.Factory;
import org.hl7.fhir.r5.model.IntegerType;
import org.hl7.fhir.r5.model.PackageInformation;
import org.hl7.fhir.r5.model.Parameters;
import org.hl7.fhir.r5.model.Parameters.ParametersParameterComponent;
import org.hl7.fhir.r5.model.PrimitiveType;
import org.hl7.fhir.r5.model.Resource;
import org.hl7.fhir.r5.model.StringType;
import org.hl7.fhir.r5.model.UriType;
import org.hl7.fhir.r5.model.ValueSet;
import org.hl7.fhir.r5.model.ValueSet.ConceptReferenceComponent;
import org.hl7.fhir.r5.model.ValueSet.ConceptReferenceDesignationComponent;
import org.hl7.fhir.r5.model.ValueSet.ConceptSetComponent;
import org.hl7.fhir.r5.model.ValueSet.ConceptSetFilterComponent;
import org.hl7.fhir.r5.model.ValueSet.ValueSetComposeComponent;
import org.hl7.fhir.r5.model.ValueSet.ValueSetExpansionComponent;
import org.hl7.fhir.r5.model.ValueSet.ValueSetExpansionContainsComponent;
import org.hl7.fhir.r5.model.ValueSet.ValueSetExpansionParameterComponent;
import org.hl7.fhir.r5.model.ValueSet.ValueSetExpansionPropertyComponent;
import org.hl7.fhir.r5.terminologies.CodeSystemUtilities;
import org.hl7.fhir.r5.terminologies.ValueSetUtilities;
import org.hl7.fhir.r5.terminologies.expansion.ValueSetExpander.UnknownValueSetException;
import org.hl7.fhir.r5.terminologies.providers.CodeSystemProvider;
import org.hl7.fhir.r5.terminologies.providers.CodeSystemProviderExtension;
import org.hl7.fhir.r5.terminologies.utilities.TerminologyOperationContext;
import org.hl7.fhir.r5.terminologies.utilities.TerminologyOperationContext.TerminologyServiceProtectionException;
import org.hl7.fhir.r5.terminologies.utilities.ValueSetProcessBase.OpIssueCode;
import org.hl7.fhir.r5.terminologies.utilities.ValueSetProcessBase.TerminologyOperationDetails;
import org.hl7.fhir.r5.terminologies.validation.VSCheckerException;
import org.hl7.fhir.r5.terminologies.utilities.TerminologyServiceErrorClass;
import org.hl7.fhir.r5.terminologies.utilities.ValueSetProcessBase;
import org.hl7.fhir.r5.utils.ToolingExtensions;
import org.hl7.fhir.r5.utils.UserDataNames;
import org.hl7.fhir.r5.utils.client.EFhirClientException;
import org.hl7.fhir.utilities.CommaSeparatedStringBuilder;
import org.hl7.fhir.utilities.MarkedToMoveToAdjunctPackage;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.i18n.AcceptLanguageHeader;
import org.hl7.fhir.utilities.i18n.AcceptLanguageHeader.LanguagePreference;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
import org.hl7.fhir.utilities.i18n.I18nConstants;
@MarkedToMoveToAdjunctPackage
public class ValueSetExpander extends ValueSetProcessBase {
public class UnknownValueSetException extends FHIRException {
protected UnknownValueSetException() {
super();
}
protected UnknownValueSetException(String message, Throwable cause) {
super(message, cause);
}
protected UnknownValueSetException(String message) {
super(message);
}
protected UnknownValueSetException(Throwable cause) {
super(cause);
}
}
public class Token {
private String system;
private String code;
public Token(String system, String code) {
super();
this.system = system;
this.code = code;
}
public String getSystem() {
return system;
}
public String getCode() {
return code;
}
public boolean matches(Coding use) {
return system.equals(use.getSystem()) && code.equals(use.getCode());
}
public boolean matchesLang(String language) {
return system.equals("urn:ietf:bcp:47") && code.equals(language);
}
}
private static final boolean REPORT_VERSION_ANYWAY = true;
private static final String VS_EXP_IMPORT_ERROR_TOO_COSTLY = null;
private ValueSet focus;
private List allErrors = new ArrayList<>();
private int maxExpansionSize = 1000;
private WorkingContext dwc = new WorkingContext();
private boolean checkCodesWhenExpanding;
private boolean includeAbstract = true;
private boolean debug;
private Set sources = new HashSet<>();
private AcceptLanguageHeader langs;
private List designations = new ArrayList<>();
public ValueSetExpander(IWorkerContext context, TerminologyOperationContext opContext) {
super(context, opContext);
}
public ValueSetExpander(IWorkerContext context, TerminologyOperationContext opContext, List allErrors) {
super(context, opContext);
this.allErrors = allErrors;
}
public void setMaxExpansionSize(int theMaxExpansionSize) {
maxExpansionSize = theMaxExpansionSize;
}
private ValueSetExpansionContainsComponent addCode(WorkingContext wc, String system, String code, String display, String dispLang, ValueSetExpansionContainsComponent parent, List designations, Parameters expParams,
boolean isAbstract, boolean inactive, List filters, boolean noInactive, boolean deprecated, List vsProp,
List csProps, CodeSystem cs, List expProps, List csExtList, List vsExtList, ValueSetExpansionComponent exp) throws ETooCostly {
opContext.deadCheck("addCode"+code);
if (filters != null && !filters.isEmpty() && !filterContainsCode(filters, system, code, exp))
return null;
if (noInactive && inactive) {
return null;
}
ValueSetExpansionContainsComponent n = new ValueSet.ValueSetExpansionContainsComponent();
n.setSystem(system);
n.setCode(code);
if (isAbstract) {
n.setAbstract(true);
}
if (inactive) {
n.setInactive(true);
}
if (deprecated) {
ValueSetUtilities.setDeprecated(vsProp, n);
}
if (ExtensionsUtils.hasExtension(csExtList, "http://hl7.org/fhir/StructureDefinition/codesystem-label")) {
ValueSetUtilities.addProperty(focus, n, "http://hl7.org/fhir/concept-properties#label", "label", ExtensionsUtils.getExtensionValue(csExtList, "http://hl7.org/fhir/StructureDefinition/codesystem-label"));
}
if (ExtensionsUtils.hasExtension(vsExtList, "http://hl7.org/fhir/StructureDefinition/valueset-label")) {
ValueSetUtilities.addProperty(focus, n, "http://hl7.org/fhir/concept-properties#label", "label", ExtensionsUtils.getExtensionValue(vsExtList, "http://hl7.org/fhir/StructureDefinition/valueset-label"));
}
if (ExtensionsUtils.hasExtension(csExtList, "http://hl7.org/fhir/StructureDefinition/codesystem-conceptOrder")) {
ValueSetUtilities.addProperty(focus, n, "http://hl7.org/fhir/concept-properties#order", "order", convertToDecimal(ExtensionsUtils.getExtensionValue(csExtList, "http://hl7.org/fhir/StructureDefinition/codesystem-conceptOrder")));
}
if (ExtensionsUtils.hasExtension(vsExtList, "http://hl7.org/fhir/StructureDefinition/valueset-conceptOrder")) {
ValueSetUtilities.addProperty(focus, n, "http://hl7.org/fhir/concept-properties#order", "order", convertToDecimal(ExtensionsUtils.getExtensionValue(vsExtList, "http://hl7.org/fhir/StructureDefinition/valueset-conceptOrder")));
}
if (ExtensionsUtils.hasExtension(csExtList, "http://hl7.org/fhir/StructureDefinition/itemWeight")) {
ValueSetUtilities.addProperty(focus, n, "http://hl7.org/fhir/concept-properties#itemWeight", "weight", ExtensionsUtils.getExtensionValue(csExtList, "http://hl7.org/fhir/StructureDefinition/itemWeight"));
}
if (ExtensionsUtils.hasExtension(vsExtList, "http://hl7.org/fhir/StructureDefinition/itemWeight")) {
ValueSetUtilities.addProperty(focus, n, "http://hl7.org/fhir/concept-properties#itemWeight", "weight", ExtensionsUtils.getExtensionValue(vsExtList, "http://hl7.org/fhir/StructureDefinition/itemWeight"));
}
ExtensionsUtils.copyExtensions(csExtList, n.getExtension(),
"http://hl7.org/fhir/StructureDefinition/coding-sctdescid",
"http://hl7.org/fhir/StructureDefinition/rendering-style",
"http://hl7.org/fhir/StructureDefinition/rendering-xhtml",
"http://hl7.org/fhir/StructureDefinition/codesystem-alternate");
ExtensionsUtils.copyExtensions(vsExtList, n.getExtension(),
"http://hl7.org/fhir/StructureDefinition/valueset-supplement",
"http://hl7.org/fhir/StructureDefinition/valueset-deprecated",
"http://hl7.org/fhir/StructureDefinition/valueset-concept-definition",
"http://hl7.org/fhir/StructureDefinition/coding-sctdescid",
"http://hl7.org/fhir/StructureDefinition/rendering-style",
"http://hl7.org/fhir/StructureDefinition/rendering-xhtml");
// display and designations
ConceptDefinitionDesignationComponent pref = null;
if (langs == null) {
n.setDisplay(display);
} else {
if (designations == null) {
designations = new ArrayList<>();
}
designations.add(new ConceptDefinitionDesignationComponent().setLanguage(dispLang).setValue(display).setUse(new Coding().setSystem("http://terminology.hl7.org/CodeSystem/designation-usage").setCode("display")));
pref = findMatchingDesignation(designations);
if (pref != null) {
n.setDisplay(pref.getValue());
}
}
if (!n.hasDisplay() && display != null && langs != null && (langs.matches(dispLang) || Utilities.existsInList(langs.getSource(), "en", "en-US"))) {
n.setDisplay(display);
}
if (expParams.getParameterBool("includeDesignations") && designations != null) {
for (ConceptDefinitionDesignationComponent t : designations) {
if (t != pref && (t.hasLanguage() || t.hasUse()) && t.getValue() != null && passesDesignationFilter(t)) {
ConceptReferenceDesignationComponent d = n.addDesignation();
if (t.getLanguage() != null) {
d.setLanguage(t.getLanguage().trim());
}
if (t.getValue() != null) {
d.setValue(t.getValue().trim());
}
if (t.getUse() != null) {
d.setUse(t.getUse());
}
for (Extension ext : t.getExtension()) {
if (Utilities.existsInList(ext.getUrl(), "http://hl7.org/fhir/StructureDefinition/coding-sctdescid")) {
d.addExtension(ext);
}
}
}
}
}
for (ParametersParameterComponent p : expParams.getParameter()) {
if ("property".equals(p.getName())) {
if (csProps != null && p.hasValue()) {
for (ConceptPropertyComponent cp : csProps) {
if (p.getValue().primitiveValue().equals(cp.getCode())) {
PropertyComponent pd = cs.getProperty(cp.getCode());
String url = pd == null ? null : pd.getUri();
if (url == null) {
if ("definition".equals(cp.getCode())) {
url = "http://hl7.org/fhir/concept-properties#definition";
} else {
// ??
}
}
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");
}
}
}
if (expProps != null && p.hasValue()) {
for (org.hl7.fhir.r5.model.ValueSet.ConceptPropertyComponent cp : expProps) {
if (p.getValue().primitiveValue().equals(cp.getCode())) {
String url = null;
for (ValueSetExpansionPropertyComponent t : vsProp) {
if (t.hasCode() && t.getCode().equals(cp.getCode())) {
url = t.getUri();
}
}
if (url == null) {
if ("definition".equals(cp.getCode())) {
url = "http://hl7.org/fhir/concept-properties#definition";
} else {
// TODO: try looking it up from the code system
}
}
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");
}
}
}
}
}
String s = key(n);
if (wc.getExcludeKeys().contains(s)) {
return null;
} else if (wc.getMap().containsKey(s)) {
wc.setCanBeHierarchy(false);
} else {
wc.getCodes().add(n);
wc.getMap().put(s, n);
// if (wc == dwc && wc.getTotal() > maxExpansionSize) {
// if (wc.getOffset()+wc.getCount() > 0 && wc.getTotal() > wc.getOffset()+wc.getCount()) {
// wc.setTotal(-1);
// throw new EFinished();
// }
// throw failCostly(context.formatMessage(I18nConstants.VALUESET_TOO_COSTLY, focus.getUrl(), ">" + Integer.toString(maxExpansionSize)));
// }
}
if (wc.isCanBeHierarchy() && parent != null) {
parent.getContains().add(n);
} else if (!wc.getRootMap().containsKey(s)) {
wc.getRootMap().put(s, n);
wc.getRoots().add(n);
}
return n;
}
private String findParamValue(List list, String name) {
for (ValueSetExpansionParameterComponent p : list) {
if (name.equals(p.getName())) {
return p.getValue().primitiveValue();
}
}
return null;
}
private DataType convertToDecimal(DataType v) {
if (v == null) {
return null;
}
if (v instanceof DecimalType) {
return v;
}
if (v instanceof IntegerType) {
return new DecimalType(((IntegerType) v).asStringValue());
}
return null;
}
private boolean passesDesignationFilter(ConceptDefinitionDesignationComponent d) {
if (designations.isEmpty()) {
return true;
}
for (Token t : designations) {
if ((d.hasUse() && t.matches(d.getUse())) || t.matchesLang(d.getLanguage())) {
return true;
}
for (Coding c : d.getAdditionalUse()) {
if (t.matches(c)) {
return true;
}
}
}
return false;
}
private ConceptDefinitionDesignationComponent findMatchingDesignation(List designations) {
if (langs == null) {
return null;
}
// we have a list of languages in priority order
// we have a list of designations in no order
// language exact match is preferred
// display is always preferred
for (LanguagePreference lang : langs.getLangs()) {
if (lang.getValue() > 0) {
for (ConceptDefinitionDesignationComponent cd : designations) {
if (isDisplay(cd, false) && LanguageUtils.langsMatchExact(cd.getLanguage(), lang.getLang())) {
return cd;
}
}
for (ConceptDefinitionDesignationComponent cd : designations) {
if (isDisplay(cd, false) && LanguageUtils.langsMatch(lang.getLang(), cd.getLanguage())) {
return cd;
}
}
for (ConceptDefinitionDesignationComponent cd : designations) {
if (isDisplay(cd, false) && LanguageUtils.langsMatch(cd.getLanguage(), lang.getLang())) {
return cd;
}
}
for (ConceptDefinitionDesignationComponent cd : designations) {
if (isDisplay(cd, true) && LanguageUtils.langsMatchExact(cd.getLanguage(), lang.getLang())) {
return cd;
}
}
for (ConceptDefinitionDesignationComponent cd : designations) {
if (isDisplay(cd, true) && LanguageUtils.langsMatch(cd.getLanguage(), lang.getLang())) {
return cd;
}
}
for (ConceptDefinitionDesignationComponent cd : designations) {
if (isDisplay(cd, true) && LanguageUtils.langsMatch(lang.getLang(), cd.getLanguage())) {
return cd;
}
}
for (ConceptDefinitionDesignationComponent cd : designations) {
if (LanguageUtils.langsMatchExact(cd.getLanguage(), lang.getLang())) {
return cd;
}
}
for (ConceptDefinitionDesignationComponent cd : designations) {
if (LanguageUtils.langsMatch(cd.getLanguage(), lang.getLang())) {
return cd;
}
}
for (ConceptDefinitionDesignationComponent cd : designations) {
if (LanguageUtils.langsMatch(lang.getLang(), cd.getLanguage())) {
return cd;
}
}
}
}
return null;
}
private boolean isDisplay(ConceptDefinitionDesignationComponent cd, boolean def) {
return (def && !cd.hasUse()) || (cd.hasUse() && cd.getUse().is("http://terminology.hl7.org/CodeSystem/designation-usage", "display"));
}
private boolean filterContainsCode(List filters, String system, String code, ValueSetExpansionComponent exp) {
for (ValueSet vse : filters) {
checkCanonical(exp, vse, focus);
if (expansionContainsCode(vse.getExpansion().getContains(), system, code))
return true;
}
return false;
}
private boolean expansionContainsCode(List contains, String system, String code) {
for (ValueSetExpansionContainsComponent cc : contains) {
if (system.equals(cc.getSystem()) && code.equals(cc.getCode()))
return true;
if (expansionContainsCode(cc.getContains(), system, code))
return true;
}
return false;
}
private ConceptDefinitionDesignationComponent getMatchingLang(List list, AcceptLanguageHeader langs) {
for (ConceptDefinitionDesignationComponent t : list) {
if (LanguageUtils.langsMatchExact(langs, t.getLanguage())) {
return t;
}
}
for (ConceptDefinitionDesignationComponent t : list) {
if (LanguageUtils.langsMatch(langs, t.getLanguage())) {
return t;
}
}
return null;
}
private void addCodeAndDescendents(WorkingContext wc, ValueSetExpansionContainsComponent focus, ValueSetExpansionContainsComponent parent, Parameters expParams, List filters, boolean noInactive, List vsProps, ValueSet vsSrc, ValueSetExpansionComponent exp, String langDisplay) throws FHIRException, ETooCostly {
opContext.deadCheck("addCodeAndDescendents");
focus.checkNoModifiers("Expansion.contains", "expanding");
ValueSetExpansionContainsComponent np = null;
for (String code : getCodesForConcept(focus, expParams)) {
ValueSetExpansionContainsComponent t = addCode(wc, focus.getSystem(), code, focus.getDisplay(), langDisplay, parent,
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);
if (np == null) {
np = t;
}
}
for (ValueSetExpansionContainsComponent c : focus.getContains())
addCodeAndDescendents(wc, c, np, expParams, filters, noInactive, vsProps, vsSrc, exp, langDisplay);
}
private String getLang(ValueSet vsSrc) {
if (vsSrc.hasLanguage()) {
return vsSrc.getLanguage();
}
for (ValueSetExpansionParameterComponent p : vsSrc.getExpansion().getParameter()) {
if ("displayLanguage".equals(p.getName())) {
return p.getValue().primitiveValue();
}
}
return null;
}
private List makeCSProps(String definition, List list) {
List res = new ArrayList<>();
if (!Utilities.noString(definition)) {
res.add(new ConceptPropertyComponent("definition", new StringType(definition)));
}
if (list != null) {
res.addAll(list);
}
return res;
}
private List getCodesForConcept(ValueSetExpansionContainsComponent focus, Parameters expParams) {
List codes = new ArrayList<>();
codes.add(focus.getCode());
for (org.hl7.fhir.r5.model.ValueSet.ConceptPropertyComponent p : focus.getProperty()) {
if ("alternateCode".equals(p.getCode()) && (altCodeParams.passes(p.getExtension())) && p.getValue().isPrimitive()) {
codes.add(p.getValue().primitiveValue());
}
}
return codes;
}
private List convert(List designations) {
List list = new ArrayList();
for (ConceptReferenceDesignationComponent d : designations) {
ConceptDefinitionDesignationComponent n = new ConceptDefinitionDesignationComponent();
n.setLanguage(d.getLanguage());
if (d.hasUse()) {
n.setUse(d.getUse());
}
n.setValue(d.getValue());
list.add(n);
}
return list;
}
private void addCodeAndDescendents(WorkingContext wc, CodeSystem cs, String system, ConceptDefinitionComponent def, ValueSetExpansionContainsComponent parent, Parameters expParams, List filters,
ConceptDefinitionComponent exclusion, ConceptFilter filterFunc, boolean noInactive, List vsProps, List otherFilters, ValueSetExpansionComponent exp) throws FHIRException, ETooCostly {
opContext.deadCheck("addCodeAndDescendents");
def.checkNoModifiers("Code in Code System", "expanding");
if (exclusion != null) {
if (exclusion.getCode().equals(def.getCode()))
return; // excluded.
}
ValueSetExpansionContainsComponent np = null;
boolean abs = CodeSystemUtilities.isNotSelectable(cs, def);
boolean inc = CodeSystemUtilities.isInactive(cs, def);
boolean dep = CodeSystemUtilities.isDeprecated(cs, def, false);
if ((includeAbstract || !abs) && filterFunc.includeConcept(cs, def) && passesOtherFilters(otherFilters, cs, def.getCode())) {
for (String code : getCodesForConcept(def, expParams)) {
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);
if (np == null) {
np = t;
}
}
}
for (ConceptDefinitionComponent c : def.getConcept()) {
addCodeAndDescendents(wc, cs, system, c, np, expParams, filters, exclusion, filterFunc, noInactive, vsProps, otherFilters, exp);
}
if (def.hasUserData(CodeSystemUtilities.USER_DATA_CROSS_LINK)) {
List children = (List) def.getUserData(CodeSystemUtilities.USER_DATA_CROSS_LINK);
for (ConceptDefinitionComponent c : children)
addCodeAndDescendents(wc, cs, system, c, np, expParams, filters, exclusion, filterFunc, noInactive, vsProps, otherFilters, exp);
}
}
private void excludeCodeAndDescendents(WorkingContext wc, CodeSystem cs, String system, ConceptDefinitionComponent def, Parameters expParams, List filters,
ConceptDefinitionComponent exclusion, ConceptFilter filterFunc, List otherFilters, ValueSetExpansionComponent exp) throws FHIRException, ETooCostly {
opContext.deadCheck("excludeCodeAndDescendents");
def.checkNoModifiers("Code in Code System", "expanding");
if (exclusion != null) {
if (exclusion.getCode().equals(def.getCode()))
return; // excluded.
}
boolean abs = CodeSystemUtilities.isNotSelectable(cs, def);
if ((includeAbstract || !abs) && filterFunc.includeConcept(cs, def) && passesOtherFilters(otherFilters, cs, def.getCode())) {
for (String code : getCodesForConcept(def, expParams)) {
if (!(filters != null && !filters.isEmpty() && !filterContainsCode(filters, system, code, exp)))
excludeCode(wc, system, code);
}
}
for (ConceptDefinitionComponent c : def.getConcept()) {
excludeCodeAndDescendents(wc, cs, system, c, expParams, filters, exclusion, filterFunc, otherFilters, exp);
}
if (def.hasUserData(CodeSystemUtilities.USER_DATA_CROSS_LINK)) {
List children = (List) def.getUserData(CodeSystemUtilities.USER_DATA_CROSS_LINK);
for (ConceptDefinitionComponent c : children)
excludeCodeAndDescendents(wc, cs, system, c, expParams, filters, exclusion, filterFunc, otherFilters, exp);
}
}
private List getCodesForConcept(ConceptDefinitionComponent focus, Parameters expParams) {
List codes = new ArrayList<>();
codes.add(focus.getCode());
for (ConceptPropertyComponent p : focus.getProperty()) {
if ("alternateCode".equals(p.getCode()) && (altCodeParams.passes(p.getExtension())) && p.getValue().isPrimitive()) {
codes.add(p.getValue().primitiveValue());
}
}
return codes;
}
private static boolean hasUse(ConceptPropertyComponent p, List uses) {
for (Extension ext : p.getExtensionsByUrl(ToolingExtensions.EXT_CS_ALTERNATE_USE)) {
if (ext.hasValueCoding() && Utilities.existsInList(ext.getValueCoding().getCode(), uses)) {
return true;
}
}
return false;
}
private void addCodes(ValueSetExpansionComponent expand, List params, Parameters expParams, List filters, boolean noInactive, List vsProps, ValueSet vsSrc, ValueSetExpansionComponent exp) throws ETooCostly, FHIRException {
if (expand != null) {
if (expand.getContains().size() > maxExpansionSize)
throw failCostly(context.formatMessage(I18nConstants.VALUESET_TOO_COSTLY, vsSrc.getUrl(), ">" + Integer.toString(expand.getContains().size())));
for (ValueSetExpansionParameterComponent p : expand.getParameter()) {
if (!existsInParams(params, p.getName(), p.getValue()))
params.add(p);
}
copyImportContains(expand.getContains(), null, expParams, filters, noInactive, vsProps, vsSrc, exp);
}
}
private void excludeCode(WorkingContext wc, String theSystem, String theCode) {
ValueSetExpansionContainsComponent n = new ValueSet.ValueSetExpansionContainsComponent();
n.setSystem(theSystem);
n.setCode(theCode);
String s = key(n);
wc.getExcludeKeys().add(s);
}
private void excludeCodes(WorkingContext wc, ConceptSetComponent exc, Parameters expParams, ValueSetExpansionComponent exp, ValueSet vs, String vspath) throws FHIRException, FileNotFoundException, ETooCostly, IOException {
opContext.deadCheck("excludeCodes");
exc.checkNoModifiers("Compose.exclude", "expanding");
if (exc.hasSystem() && exc.getConcept().size() == 0 && exc.getFilter().size() == 0) {
wc.getExcludeSystems().add(exc.getSystem());
}
for (UriType imp : exc.getValueSet()) {
excludeCodes(wc, importValueSetForExclude(wc, imp.getValue(), exp, expParams, false, vs).getExpansion());
}
if (exc.hasSystem()) {
CodeSystem cs = context.fetchSupplementedCodeSystem(exc.getSystem());
if ((cs == null || cs.getContent() != CodeSystemContentMode.COMPLETE) && context.supportsSystem(exc.getSystem(), opContext.getOptions().getFhirVersion())) {
ValueSetExpansionOutcome vse = context.expandVS(new TerminologyOperationDetails(requiredSupplements), exc, false, false);
ValueSet valueset = vse.getValueset();
if (valueset.hasUserData(UserDataNames.VS_EXPANSION_SOURCE)) {
sources.add(valueset.getUserString(UserDataNames.VS_EXPANSION_SOURCE));
}
if (valueset == null)
throw failTSE("Error Expanding ValueSet: "+vse.getError());
excludeCodes(wc, valueset.getExpansion());
return;
}
for (ConceptReferenceComponent c : exc.getConcept()) {
excludeCode(wc, exc.getSystem(), c.getCode());
}
if (exc.getFilter().size() > 0) {
if (cs.getContent() == CodeSystemContentMode.FRAGMENT) {
addFragmentWarning(exp, cs);
}
List filters = new ArrayList<>();
for (int i = 1; i < exc.getFilter().size(); i++) {
WorkingContext wc1 = new WorkingContext();
filters.add(wc1);
processFilter(exc, exp, expParams, null, cs, false, exc.getFilter().get(i), wc1, null, true, vspath+".filter["+i+"]");
}
ConceptSetFilterComponent fc = exc.getFilter().get(0);
WorkingContext wc1 = dwc;
processFilter(exc, exp, expParams, null, cs, false, fc, wc1, filters, true, vspath+".filter[0]");
}
}
}
private void excludeCodes(WorkingContext wc, ValueSetExpansionComponent expand) {
opContext.deadCheck("excludeCodes");
for (ValueSetExpansionContainsComponent c : expand.getContains()) {
excludeCode(wc, c.getSystem(), c.getCode());
}
}
private boolean existsInParams(List params, String name, DataType value) {
for (ValueSetExpansionParameterComponent p : params) {
if (p.getName().equals(name) && PrimitiveType.compareDeep(p.getValue(), value, false)) {
return true;
}
}
return false;
}
public ValueSetExpansionOutcome expand(ValueSet source, Parameters expParams) {
allErrors.clear();
try {
opContext.seeContext(source.getVersionedUrl());
return expandInternal(source, expParams);
} catch (NoTerminologyServiceException e) {
// well, we couldn't expand, so we'll return an interface to a checker that can check membership of the set
// that might fail too, but it might not, later.
return new ValueSetExpansionOutcome(e.getMessage(), TerminologyServiceErrorClass.NOSERVICE, allErrors, false);
} catch (CodeSystemProviderExtension e) {
// well, we couldn't expand, so we'll return an interface to a checker that can check membership of the set
// that might fail too, but it might not, later.
return new ValueSetExpansionOutcome(e.getMessage(), TerminologyServiceErrorClass.INTERNAL_ERROR, allErrors, false);
} catch (TerminologyServiceProtectionException e) {
if (opContext.isOriginal()) {
return new ValueSetExpansionOutcome(e.getMessage(), e.getError(), allErrors, false);
} else {
throw e;
}
} catch (ETooCostly e) {
return new ValueSetExpansionOutcome(e.getMessage(), TerminologyServiceErrorClass.TOO_COSTLY, allErrors, false);
} catch (UnknownValueSetException e) {
return new ValueSetExpansionOutcome(e.getMessage(), TerminologyServiceErrorClass.VALUESET_UNKNOWN, allErrors, false);
} catch (VSCheckerException e) {
return new ValueSetExpansionOutcome(e.getMessage(), TerminologyServiceErrorClass.UNKNOWN, allErrors, e.getIssues());
} catch (Exception e) {
if (debug) {
e.printStackTrace();
}
return new ValueSetExpansionOutcome(e.getMessage(), TerminologyServiceErrorClass.UNKNOWN, allErrors, e instanceof EFhirClientException || e instanceof TerminologyServiceException);
}
}
public ValueSetExpansionOutcome expandInternal(ValueSet source, Parameters expParams) throws FHIRException, FileNotFoundException, ETooCostly, IOException, CodeSystemProviderExtension {
if (expParams == null)
expParams = makeDefaultExpansion();
altCodeParams.seeParameters(expParams);
altCodeParams.seeValueSet(source);
source.checkNoModifiers("ValueSet", "expanding");
focus = source.copy();
focus.setIdBase(null);
focus.setExpansion(new ValueSet.ValueSetExpansionComponent());
focus.getExpansion().setTimestampElement(DateTimeType.now());
focus.getExpansion().setIdentifier(Factory.createUUID());
checkCanonical(focus.getExpansion(), focus, focus);
for (Extension ext : focus.getCompose().getExtensionsByUrl("http://hl7.org/fhir/tools/StructureDefinion/valueset-expansion-param")) {
processParameter(ext.getExtensionString("name"), ext.getExtensionByUrl("value").getValue());
}
for (ParametersParameterComponent p : expParams.getParameter()) {
processParameter(p.getName(), p.getValue());
}
for (Extension s : focus.getExtensionsByUrl(ExtensionConstants.EXT_VSSUPPLEMENT)) {
requiredSupplements.add(s.getValue().primitiveValue());
}
if (langs == null && focus.hasLanguage()) {
langs = new AcceptLanguageHeader(focus.getLanguage(), true);
}
try {
if (source.hasCompose()) {
// ExtensionsUtils.stripExtensions(focus.getCompose()); - disabled 23/05/2023 GDG - why was this ever thought to be a good idea?
handleCompose(source.getCompose(), focus.getExpansion(), expParams, source.getUrl(), focus.getExpansion().getExtension(), source);
}
} catch (EFinished e) {
// nothing - we intended to trap this here
}
if (dwc.getCount() > maxExpansionSize && dwc.getOffsetParam() + dwc.getCountParam() == 0) {
if (dwc.isNoTotal()) {
throw failCostly(context.formatMessage(I18nConstants.VALUESET_TOO_COSTLY, focus.getVersionedUrl(), ">" + MessageFormat.format("{0,number,#}", maxExpansionSize)));
} else {
throw failCostly(context.formatMessage(I18nConstants.VALUESET_TOO_COSTLY_COUNT, focus.getVersionedUrl(), ">" + MessageFormat.format("{0,number,#}", maxExpansionSize), MessageFormat.format("{0,number,#}", dwc.getCount())));
}
} else if (dwc.isCanBeHierarchy() && ((dwc.getCountParam() == 0) || dwc.getCountParam() > dwc.getCodes().size())) {
for (ValueSetExpansionContainsComponent c : dwc.getRoots()) {
focus.getExpansion().getContains().add(c);
}
} else {
int i = 0;
int cc = 0;
for (ValueSetExpansionContainsComponent c : dwc.getCodes()) {
c.getContains().clear(); // make sure any hierarchy is wiped
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
if (dwc.getOffsetParam() == 0 || i >= dwc.getOffsetParam()) {
focus.getExpansion().getContains().add(c);
cc++;
if (cc == dwc.getCountParam()) {
break;
}
}
i++;
}
}
}
if (dwc.hasOffsetParam()) {
focus.getExpansion().setOffset(dwc.getOffsetParam());
}
if (!dwc.isNoTotal()) {
focus.getExpansion().setTotal(dwc.getStatedTotal());
}
if (!requiredSupplements.isEmpty()) {
return new ValueSetExpansionOutcome(context.formatMessagePlural(requiredSupplements.size(), I18nConstants.VALUESET_SUPPLEMENT_MISSING, CommaSeparatedStringBuilder.build(requiredSupplements)), TerminologyServiceErrorClass.BUSINESS_RULE, allErrors, false);
}
if (!expParams.hasParameter("includeDefinition") || !expParams.getParameterBool("includeDefinition")) {
focus.setCompose(null);
focus.getExtension().clear();
focus.setPublisher(null);
focus.setDescription(null);
focus.setPurpose(null);
focus.getContact().clear();
focus.setCopyright(null);
focus.setText(null);
}
return new ValueSetExpansionOutcome(focus);
}
private void processParameter(String name, DataType value) {
if (Utilities.existsInList(name, "includeDesignations", "excludeNested", "activeOnly", "offset", "count")) {
focus.getExpansion().getParameter().removeIf(p -> p.getName().equals(name));
focus.getExpansion().addParameter().setName(name).setValue(value);
}
if ("displayLanguage".equals(name)) {
this.langs = new AcceptLanguageHeader(value.primitiveValue(), true);
focus.getExpansion().getParameter().removeIf(p -> p.getName().equals(name));
focus.getExpansion().addParameter().setName(name).setValue(new CodeType(value.primitiveValue()));
}
if ("designation".equals(name)) {
String[] v = value.primitiveValue().split("\\|");
if (v.length != 2 || !Utilities.isAbsoluteUrl(v[0]) || Utilities.noString(v[1])) {
throw new NoTerminologyServiceException("Unable to understand designation parameter "+value.primitiveValue());
}
this.designations.add(new Token(v[0], v[1]));
focus.getExpansion().addParameter().setName(name).setValue(new StringType(value.primitiveValue()));
}
if ("offset".equals(name) && value instanceof IntegerType) {
focus.getExpansion().getParameter().removeIf(p -> p.getName().equals(name));
focus.getExpansion().addParameter().setName(name).setValue(value);
dwc.setOffsetParam(((IntegerType) value).getValue());
if (dwc.getOffsetParam() < 0) {
dwc.setOffsetParam(0);
}
}
if ("count".equals(name)) {
focus.getExpansion().getParameter().removeIf(p -> p.getName().equals(name));
focus.getExpansion().addParameter().setName(name).setValue(value);
dwc.setCountParam(((IntegerType) value).getValue());
if (dwc.getCountParam() < 0) {
dwc.setCountParam(0);
}
}
}
public ValueSetExpansionOutcome doExpand(ValueSet source, Parameters expParams) throws FHIRException, ETooCostly, FileNotFoundException, IOException, CodeSystemProviderExtension {
if (expParams == null)
expParams = makeDefaultExpansion();
altCodeParams.seeParameters(expParams);
altCodeParams.seeValueSet(source);
source.checkNoModifiers("ValueSet", "expanding");
focus = source.copy();
focus.setIdBase(null);
focus.setExpansion(new ValueSet.ValueSetExpansionComponent());
focus.getExpansion().setTimestampElement(DateTimeType.now());
focus.getExpansion().setIdentifier(Factory.createUUID());
checkCanonical(focus.getExpansion(), focus, focus);
for (Extension ext : focus.getCompose().getExtensionsByUrl("http://hl7.org/fhir/tools/StructureDefinion/valueset-expansion-param")) {
processParameter(ext.getExtensionString("name"), ext.getExtensionByUrl("value").getValue());
}
for (ParametersParameterComponent p : expParams.getParameter()) {
processParameter(p.getName(), p.getValue());
}
for (Extension s : focus.getExtensionsByUrl(ExtensionConstants.EXT_VSSUPPLEMENT)) {
requiredSupplements.add(s.getValue().primitiveValue());
}
if (langs == null && focus.hasLanguage()) {
langs = new AcceptLanguageHeader(focus.getLanguage(), true);
}
try {
if (source.hasCompose()) {
// ExtensionsUtils.stripExtensions(focus.getCompose()); - disabled 23/05/2023 GDG - why was this ever thought to be a good idea?
handleCompose(source.getCompose(), focus.getExpansion(), expParams, source.getUrl(), focus.getExpansion().getExtension(), source);
}
} catch (EFinished e) {
// nothing - we intended to trap this here
}
if (dwc.getCount() > maxExpansionSize && dwc.getOffsetParam() + dwc.getCountParam() == 0) {
if (dwc.isNoTotal()) {
throw failCostly(context.formatMessage(I18nConstants.VALUESET_TOO_COSTLY, focus.getVersionedUrl(), ">" + MessageFormat.format("{0,number,#}", maxExpansionSize)));
} else {
throw failCostly(context.formatMessage(I18nConstants.VALUESET_TOO_COSTLY_COUNT, focus.getVersionedUrl(), ">" + MessageFormat.format("{0,number,#}", maxExpansionSize), MessageFormat.format("{0,number,#}", dwc.getCount())));
}
} else if (dwc.isCanBeHierarchy() && ((dwc.getCountParam() == 0) || dwc.getCountParam() > dwc.getCodes().size())) {
for (ValueSetExpansionContainsComponent c : dwc.getRoots()) {
focus.getExpansion().getContains().add(c);
}
} else {
int i = 0;
int cc = 0;
for (ValueSetExpansionContainsComponent c : dwc.getCodes()) {
c.getContains().clear(); // make sure any hierarchy is wiped
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
if (dwc.getOffsetParam() == 0 || i >= dwc.getOffsetParam()) {
focus.getExpansion().getContains().add(c);
cc++;
if (cc == dwc.getCountParam()) {
break;
}
}
i++;
}
}
}
if (dwc.hasOffsetParam()) {
focus.getExpansion().setOffset(dwc.getOffsetParam());
}
if (!dwc.isNoTotal()) {
focus.getExpansion().setTotal(dwc.getStatedTotal());
}
if (!requiredSupplements.isEmpty()) {
return new ValueSetExpansionOutcome(context.formatMessagePlural(requiredSupplements.size(), I18nConstants.VALUESET_SUPPLEMENT_MISSING, CommaSeparatedStringBuilder.build(requiredSupplements)), TerminologyServiceErrorClass.BUSINESS_RULE, allErrors, false);
}
if (!expParams.hasParameter("includeDefinition") || !expParams.getParameterBool("includeDefinition")) {
focus.setCompose(null);
focus.getExtension().clear();
focus.setPublisher(null);
focus.setDescription(null);
focus.setPurpose(null);
focus.getContact().clear();
focus.setCopyright(null);
focus.setText(null);
}
return new ValueSetExpansionOutcome(focus);
}
private Parameters makeDefaultExpansion() {
Parameters res = new Parameters();
res.addParameter("excludeNested", true);
res.addParameter("includeDesignations", false);
return res;
}
private ConceptDefinitionComponent getConceptForCode(List clist, String code) {
for (ConceptDefinitionComponent c : clist) {
if (code.equals(c.getCode()))
return c;
ConceptDefinitionComponent v = getConceptForCode(c.getConcept(), code);
if (v != null)
return v;
}
return null;
}
private void handleCompose(ValueSetComposeComponent compose, ValueSetExpansionComponent exp, Parameters expParams, String ctxt, List extensions, ValueSet valueSet)
throws ETooCostly, FileNotFoundException, IOException, FHIRException, CodeSystemProviderExtension {
compose.checkNoModifiers("ValueSet.compose", "expanding");
String vspath = "ValueSet["+valueSet.getVersionedUrl()+"].compose";
// Exclude comes first because we build up a map of things to exclude
int c = 0;
for (ConceptSetComponent inc : compose.getExclude()) {
excludeCodes(dwc, inc, expParams, exp, valueSet, vspath+".include["+c+"]");
c++;
}
dwc.setCanBeHierarchy(!expParams.getParameterBool("excludeNested") && dwc.getExcludeKeys().isEmpty() && dwc.getExcludeSystems().isEmpty() && dwc.getOffsetParam() == 0);
includeAbstract = !expParams.getParameterBool("excludeNotForUI");
boolean first = true;
c = 0;
for (ConceptSetComponent inc : compose.getInclude()) {
if (first == true)
first = false;
else
dwc.setCanBeHierarchy(false);
includeCodes(inc, exp, expParams, dwc.isCanBeHierarchy(), compose.hasInactive() ? !compose.getInactive() : checkNoInActiveFromParam(expParams), extensions, valueSet, vspath+".include["+c+"]");
c++;
}
}
/**
* returns true if activeOnly = true
* @param expParams
* @return
*/
private boolean checkNoInActiveFromParam(Parameters expParams) {
for (ParametersParameterComponent p : expParams.getParameter()) {
if (p.getName().equals("activeOnly")) {
return p.getValueBooleanType().getValue();
}
}
return false;
}
private ValueSet importValueSet(WorkingContext wc, String value, ValueSetExpansionComponent exp, Parameters expParams, boolean noInactive, ValueSet valueSet) throws ETooCostly, TerminologyServiceException, FileNotFoundException, IOException, FHIRFormatError {
if (value == null)
throw fail(I18nConstants.VS_EXP_IMPORT_NULL, true);
String url = getCu().pinValueSet(value, expParams);
ValueSet vs = context.findTxResource(ValueSet.class, url, valueSet);
if (vs == null) {
boolean pinned = !url.equals(value);
String ver = pinned ? url.substring(value.length()+1) : null;
if (context.fetchResource(CodeSystem.class, url, valueSet) != null) {
throw failNotFound(pinned ? I18nConstants.VS_EXP_IMPORT_CS_PINNED : I18nConstants.VS_EXP_IMPORT_CS, true, value, ver);
} else {
throw failNotFound(pinned ? I18nConstants.VS_EXP_IMPORT_UNK_PINNED : I18nConstants.VS_EXP_IMPORT_UNK, true, value, ver);
}
}
checkCanonical(exp, vs, focus);
if (noInactive) {
expParams = expParams.copy();
expParams.addParameter("activeOnly", true);
}
ValueSetExpander expander = new ValueSetExpander(context, opContext.copy(), allErrors);
ValueSetExpansionOutcome vso = expander.expand(vs, expParams);
if (vso.getError() != null) {
addErrors(vso.getAllErrors());
if (vso.getErrorClass() == TerminologyServiceErrorClass.VALUESET_UNKNOWN) {
throw failUnk(I18nConstants.VS_EXP_IMPORT_ERROR, true, vs.getUrl(), vso.getError());
} else {
throw fail(I18nConstants.VS_EXP_IMPORT_ERROR, true, vs.getUrl(), vso.getError());
}
} else if (vso.getValueset() == null) {
throw fail(I18nConstants.VS_EXP_IMPORT_FAIL, true, vs.getUrl());
}
sources.addAll(expander.sources);
if (vs.hasVersion() || REPORT_VERSION_ANYWAY) {
UriType u = new UriType(vs.getUrl() + (vs.hasVersion() ? "|"+vs.getVersion() : ""));
if (!existsInParams(exp.getParameter(), "used-valueset", u))
exp.getParameter().add(new ValueSetExpansionParameterComponent().setName("used-valueset").setValue(u));
}
ValueSetExpansionComponent evs = vso.getValueset().getExpansion();
for (Extension ex : evs.getExtension()) {
if (ex.getUrl().equals(ToolingExtensions.EXT_EXP_TOOCOSTLY)) {
if (ex.getValue() instanceof BooleanType) {
exp.getExtension().add(new Extension(ToolingExtensions.EXT_EXP_TOOCOSTLY).setValue(new CanonicalType(value)));
} else {
exp.getExtension().add(ex);
}
}
}
if (!evs.hasTotal()) {
// because if there's no total, we can't know if we got everything
dwc.setNoTotal(true);
}
for (ValueSetExpansionParameterComponent p : evs.getParameter()) {
if (!existsInParams(exp.getParameter(), p.getName(), p.getValue()))
exp.getParameter().add(p);
}
if (isValueSetUnionImports(valueSet)) {
copyExpansion(wc, evs.getContains());
}
wc.setCanBeHierarchy(false); // if we're importing a value set, we have to be combining, so we won't try for a hierarchy
return vso.getValueset();
}
private ValueSet importValueSetForExclude(WorkingContext wc, String value, ValueSetExpansionComponent exp, Parameters expParams, boolean noInactive, ValueSet valueSet) throws ETooCostly, TerminologyServiceException, FileNotFoundException, IOException, FHIRFormatError {
if (value == null)
throw fail(I18nConstants.VS_EXP_IMPORT_NULL_X, true);
String url = getCu().pinValueSet(value, expParams);
ValueSet vs = context.findTxResource(ValueSet.class, url, valueSet);
if (vs == null) {
boolean pinned = !url.equals(value);
String ver = pinned ? url.substring(value.length()+1) : null;
if (context.fetchResource(CodeSystem.class, url, valueSet) != null) {
throw fail(pinned ? I18nConstants.VS_EXP_IMPORT_CS_PINNED_X : I18nConstants.VS_EXP_IMPORT_CS_X, true, value, ver);
} else {
throw fail(pinned ? I18nConstants.VS_EXP_IMPORT_UNK_PINNED_X : I18nConstants.VS_EXP_IMPORT_UNK_X, true, value, ver);
}
}
checkCanonical(exp, vs, focus);
if (noInactive) {
expParams = expParams.copy();
expParams.addParameter("activeOnly", true);
}
ValueSetExpander expander = new ValueSetExpander(context, opContext.copy(), allErrors);
ValueSetExpansionOutcome vso = expander.expand(vs, expParams);
sources.addAll(expander.sources);
if (vso.getError() != null) {
addErrors(vso.getAllErrors());
throw fail(I18nConstants.VS_EXP_IMPORT_ERROR_X, true, vs.getUrl(), vso.getError());
} else if (vso.getValueset() == null) {
throw fail(I18nConstants.VS_EXP_IMPORT_FAIL_X, true, vs.getUrl());
}
if (vs.hasVersion() || REPORT_VERSION_ANYWAY) {
UriType u = new UriType(vs.getUrl() + (vs.hasVersion() ? "|"+vs.getVersion() : ""));
if (!existsInParams(exp.getParameter(), "used-valueset", u))
exp.getParameter().add(new ValueSetExpansionParameterComponent().setName("used-valueset").setValue(u));
}
for (Extension ex : vso.getValueset().getExpansion().getExtension()) {
if (ex.getUrl().equals(ToolingExtensions.EXT_EXP_TOOCOSTLY)) {
throw fail(VS_EXP_IMPORT_ERROR_TOO_COSTLY, true, vs.getUrl());
}
}
return vso.getValueset();
}
protected boolean isValueSetUnionImports(ValueSet valueSet) {
PackageInformation p = valueSet.getSourcePackage();
if (p != null) {
return p.getDate().before(new GregorianCalendar(2022, Calendar.MARCH, 31).getTime());
} else {
return false;
}
}
public void copyExpansion(WorkingContext wc,List list) {
opContext.deadCheck("copyExpansion");
for (ValueSetExpansionContainsComponent cc : list) {
ValueSetExpansionContainsComponent n = new ValueSet.ValueSetExpansionContainsComponent();
n.setSystem(cc.getSystem());
n.setCode(cc.getCode());
n.setAbstract(cc.getAbstract());
n.setInactive(cc.getInactive());
n.setDisplay(cc.getDisplay());
n.getDesignation().addAll(cc.getDesignation());
String s = key(n);
if (!wc.getMap().containsKey(s) && !wc.getExcludeKeys().contains(s)) {
wc.getCodes().add(n);
wc.getMap().put(s, n);
}
copyExpansion(wc, cc.getContains());
}
}
private void addErrors(List errs) {
for (String s : errs) {
if (!allErrors.contains(s)) {
allErrors.add(s);
}
}
}
private int copyImportContains(List list, ValueSetExpansionContainsComponent parent, Parameters expParams, List filter, boolean noInactive, List vsProps, ValueSet vsSrc, ValueSetExpansionComponent exp) throws FHIRException, ETooCostly {
int count = 0;
opContext.deadCheck("copyImportContains");
String lang = vsSrc.getLanguage();
if (lang == null) {
lang = findParamValue(vsSrc.getExpansion().getParameter(), "displayLanguage");
}
for (ValueSetExpansionContainsComponent c : list) {
c.checkNoModifiers("Imported Expansion in Code System", "expanding");
ValueSetExpansionContainsComponent np = addCode(dwc, c.getSystem(), c.getCode(), c.getDisplay(), lang, parent, translateDesignations(c), expParams, c.getAbstract(), c.getInactive(),
filter, noInactive, false, vsProps, makeCSProps(c.getExtensionString(ToolingExtensions.EXT_DEFINITION), null), null, c.getProperty(), null, c.getExtension(), exp);
if (np != null) {
count++;
}
count = count + copyImportContains(c.getContains(), np, expParams, filter, noInactive, vsProps, vsSrc, exp);
}
return count;
}
private List translateDesignations(ValueSetExpansionContainsComponent c) {
if (!c.hasDesignation()) {
return null;
}
List list = new ArrayList<>();
for (ConceptReferenceDesignationComponent d : c.getDesignation()) {
ConceptDefinitionDesignationComponent d2 = new ConceptDefinitionDesignationComponent();
d2.setLanguage(d.getLanguage());
d2.setUse(d.getUse());
d2.setAdditionalUse(d.getAdditionalUse());
d2.setValue(d.getValue());
list.add(d2);
}
return list;
}
private void includeCodes(ConceptSetComponent inc, ValueSetExpansionComponent exp, Parameters expParams, boolean heirarchical, boolean noInactive, List extensions, ValueSet valueSet, String vspath) throws ETooCostly, FileNotFoundException, IOException, FHIRException, CodeSystemProviderExtension {
opContext.deadCheck("includeCodes");
inc.checkNoModifiers("Compose.include", "expanding");
List imports = new ArrayList();
for (CanonicalType imp : inc.getValueSet()) {
imports.add(importValueSet(dwc, imp.getValue(), exp, expParams, noInactive, valueSet));
}
if (!inc.hasSystem()) {
if (imports.isEmpty()) // though this is not supposed to be the case
return;
ValueSet base = imports.get(0);
checkCanonical(exp, base, focus);
imports.remove(0);
base.checkNoModifiers("Imported ValueSet", "expanding");
copyImportContains(base.getExpansion().getContains(), null, expParams, imports, noInactive, base.getExpansion().getProperty(), base, exp);
} else {
CodeSystem cs = context.fetchSupplementedCodeSystem(inc.getSystem());
if (ValueSetUtilities.isServerSide(inc.getSystem()) || (cs == null || (cs.getContent() != CodeSystemContentMode.COMPLETE && cs.getContent() != CodeSystemContentMode.FRAGMENT))) {
doServerIncludeCodes(inc, heirarchical, exp, imports, expParams, extensions, noInactive, valueSet.getExpansion().getProperty());
} else {
if (cs.hasUserData(UserDataNames.tx_known_supplements)) {
for (String s : cs.getUserString(UserDataNames.tx_known_supplements).split("\\,")) {
requiredSupplements.remove(s);
}
}
doInternalIncludeCodes(inc, exp, expParams, imports, cs, noInactive, valueSet, vspath);
}
}
}
private void doServerIncludeCodes(ConceptSetComponent inc, boolean heirarchical, ValueSetExpansionComponent exp, List imports, Parameters expParams, List extensions, boolean noInactive, List vsProps) throws FHIRException, CodeSystemProviderExtension, ETooCostly {
opContext.deadCheck("doServerIncludeCodes");
CodeSystemProvider csp = CodeSystemProvider.factory(inc.getSystem());
if (csp != null) {
csp.includeCodes(inc, heirarchical, exp, imports, expParams, extensions, noInactive, vsProps);
return;
}
ValueSetExpansionOutcome vso = context.expandVS(new TerminologyOperationDetails(requiredSupplements), inc, heirarchical, noInactive);
if (vso.getError() != null) {
throw failTSE("Unable to expand imported value set: " + vso.getError());
}
ValueSet vs = vso.getValueset();
if (vs.hasUserData(UserDataNames.VS_EXPANSION_SOURCE)) {
sources.add(vs.getUserString(UserDataNames.VS_EXPANSION_SOURCE));
}
if (vs.hasVersion() || REPORT_VERSION_ANYWAY) {
UriType u = new UriType(vs.getUrl() + (vs.hasVersion() ? "|"+vs.getVersion() : ""));
if (!existsInParams(exp.getParameter(), "used-valueset", u)) {
exp.getParameter().add(new ValueSetExpansionParameterComponent().setName("used-valueset").setValue(u));
}
}
if (vs.getExpansion().hasTotal()) {
// 0 for now... dwc.incExtraCount(!vs.getExpansion().getTotal());
} else {
dwc.setNoTotal(true);
}
for (ValueSetExpansionParameterComponent p : vso.getValueset().getExpansion().getParameter()) {
if (!existsInParams(exp.getParameter(), p.getName(), p.getValue())) {
exp.getParameter().add(p);
}
}
for (Extension ex : vs.getExpansion().getExtension()) {
if (Utilities.existsInList(ex.getUrl(), ToolingExtensions.EXT_EXP_TOOCOSTLY, "http://hl7.org/fhir/StructureDefinition/valueset-unclosed")) {
if (!ExtensionsUtils.hasExtension(extensions, ex.getUrl())) {
extensions.add(ex);
}
}
}
for (ValueSetExpansionContainsComponent cc : vs.getExpansion().getContains()) {
addCodeAndDescendents(dwc, cc, null, expParams, imports, noInactive, vsProps, vs, exp, getLang(vs));
}
}
public void doInternalIncludeCodes(ConceptSetComponent inc, ValueSetExpansionComponent exp, Parameters expParams, List imports, CodeSystem cs, boolean noInactive, Resource vsSrc, String vspath) throws NoTerminologyServiceException, TerminologyServiceException, FHIRException, ETooCostly {
opContext.deadCheck("doInternalIncludeCodes");
if (cs == null) {
if (context.isNoTerminologyServer())
throw failTSE("Unable to find code system " + inc.getSystem().toString());
else
throw failTSE("Unable to find code system " + inc.getSystem().toString());
}
checkCanonical(exp, cs, focus);
cs.checkNoModifiers("Code System", "expanding");
if (cs.getContent() != CodeSystemContentMode.COMPLETE && cs.getContent() != CodeSystemContentMode.FRAGMENT)
throw failTSE("Code system " + inc.getSystem().toString() + " is incomplete");
if (cs.hasVersion() || REPORT_VERSION_ANYWAY) {
UriType u = new UriType(cs.getUrl() + (cs.hasVersion() ? "|"+cs.getVersion() : ""));
if (!existsInParams(exp.getParameter(), "used-codesystem", u))
exp.getParameter().add(new ValueSetExpansionParameterComponent().setName("used-codesystem").setValue(u));
if (cs.hasUserData(UserDataNames.tx_known_supplements)) {
for (String s : cs.getUserString(UserDataNames.tx_known_supplements).split("\\,")) {
u = new UriType(s);
if (!existsInParams(exp.getParameter(), "used-supplement", u)) {
exp.getParameter().add(new ValueSetExpansionParameterComponent().setName("used-supplement").setValue(u));
}
}
}
}
if (inc.getConcept().size() == 0 && inc.getFilter().size() == 0) {
// special case - add all the code system
for (ConceptDefinitionComponent def : cs.getConcept()) {
addCodeAndDescendents(dwc, cs, inc.getSystem(), def, null, expParams, imports, null, new AllConceptsFilter(allErrors), noInactive, exp.getProperty(), null, exp);
}
if (cs.getContent() == CodeSystemContentMode.FRAGMENT) {
addFragmentWarning(exp, cs);
}
if (cs.getContent() == CodeSystemContentMode.EXAMPLE) {
addExampleWarning(exp, cs);
}
}
if (!inc.getConcept().isEmpty()) {
dwc.setCanBeHierarchy(false);
for (ConceptReferenceComponent c : inc.getConcept()) {
c.checkNoModifiers("Code in Value Set", "expanding");
ConceptDefinitionComponent def = CodeSystemUtilities.findCodeOrAltCode(cs.getConcept(), c.getCode(), null);
boolean inactive = false; // default is true if we're a fragment and
boolean isAbstract = false;
if (def == null) {
if (cs.getContent() == CodeSystemContentMode.FRAGMENT) {
addFragmentWarning(exp, cs);
} else if (cs.getContent() == CodeSystemContentMode.EXAMPLE) {
addExampleWarning(exp, cs);
} else {
if (checkCodesWhenExpanding) {
throw failTSE("Unable to find code '" + c.getCode() + "' in code system " + cs.getUrl());
}
}
} else {
def.checkNoModifiers("Code in Code System", "expanding");
inactive = CodeSystemUtilities.isInactive(cs, def);
isAbstract = CodeSystemUtilities.isNotSelectable(cs, def);
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())),
expParams, isAbstract, inactive, imports, noInactive, false, exp.getProperty(), makeCSProps(def.getDefinition(), def.getProperty()), cs, null, def.getExtension(), c.getExtension(), exp);
}
}
}
if (inc.getFilter().size() > 0) {
if (inc.getFilter().size() > 1) {
dwc.setCanBeHierarchy(false); // which will be the case if we get around to supporting this
}
if (cs.getContent() == CodeSystemContentMode.FRAGMENT) {
addFragmentWarning(exp, cs);
}
List filters = new ArrayList<>();
for (int i = 1; i < inc.getFilter().size(); i++) {
WorkingContext wc = new WorkingContext();
filters.add(wc);
processFilter(inc, exp, expParams, imports, cs, noInactive, inc.getFilter().get(i), wc, null, false, vspath+".filter["+i+"]");
}
ConceptSetFilterComponent fc = inc.getFilter().get(0);
WorkingContext wc = dwc;
processFilter(inc, exp, expParams, imports, cs, noInactive, fc, wc, filters, false, vspath+".filter[0]");
}
}
private void processFilter(ConceptSetComponent inc, ValueSetExpansionComponent exp, Parameters expParams, List imports, CodeSystem cs, boolean noInactive,
ConceptSetFilterComponent fc, WorkingContext wc, List filters, boolean exclude, String vspath)
throws ETooCostly {
if (!fc.hasValue() || fc.getValue() == null) {
List issues = new ArrayList<>();
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));
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);
}
opContext.deadCheck("processFilter");
if ("concept".equals(fc.getProperty()) && fc.getOp() == FilterOperator.ISA) {
// special: all codes in the target code system under the value
ConceptDefinitionComponent def = getConceptForCode(cs.getConcept(), fc.getValue());
if (def == null)
throw failTSE("Code '" + fc.getValue() + "' not found in system '" + inc.getSystem() + "'");
if (exclude) {
excludeCodeAndDescendents(wc, cs, inc.getSystem(), def, null, imports, null, new AllConceptsFilter(allErrors), filters, exp);
} else {
addCodeAndDescendents(wc, cs, inc.getSystem(), def, null, expParams, imports, null, new AllConceptsFilter(allErrors), noInactive, exp.getProperty(), filters, exp);
}
} else if ("concept".equals(fc.getProperty()) && fc.getOp() == FilterOperator.ISNOTA) {
// special: all codes in the target code system that are not under the value
ConceptDefinitionComponent defEx = getConceptForCode(cs.getConcept(), fc.getValue());
if (defEx == null)
throw failTSE("Code '" + fc.getValue() + "' not found in system '" + inc.getSystem() + "'");
for (ConceptDefinitionComponent def : cs.getConcept()) {
if (exclude) {
excludeCodeAndDescendents(wc, cs, inc.getSystem(), def, null, imports, defEx, new AllConceptsFilter(allErrors), filters, exp);
} else {
addCodeAndDescendents(wc, cs, inc.getSystem(), def, null, expParams, imports, defEx, new AllConceptsFilter(allErrors), noInactive, exp.getProperty(), filters, exp);
}
}
} else if ("concept".equals(fc.getProperty()) && fc.getOp() == FilterOperator.DESCENDENTOF) {
// special: all codes in the target code system under the value
ConceptDefinitionComponent def = getConceptForCode(cs.getConcept(), fc.getValue());
if (def == null)
throw failTSE("Code '" + fc.getValue() + "' not found in system '" + inc.getSystem() + "'");
for (ConceptDefinitionComponent c : def.getConcept())
if (exclude) {
excludeCodeAndDescendents(wc, cs, inc.getSystem(), c, null, imports, null, new AllConceptsFilter(allErrors), filters, exp);
} else {
addCodeAndDescendents(wc, cs, inc.getSystem(), c, null, expParams, imports, null, new AllConceptsFilter(allErrors), noInactive, exp.getProperty(), filters, exp);
}
if (def.hasUserData(CodeSystemUtilities.USER_DATA_CROSS_LINK)) {
List children = (List) def.getUserData(CodeSystemUtilities.USER_DATA_CROSS_LINK);
for (ConceptDefinitionComponent c : children) {
if (exclude) {
excludeCodeAndDescendents(wc, cs, inc.getSystem(), c, null, imports, null, new AllConceptsFilter(allErrors), filters, exp);
} else {
addCodeAndDescendents(wc, cs, inc.getSystem(), c, null, expParams, imports, null, new AllConceptsFilter(allErrors), noInactive, exp.getProperty(), filters, exp);
}
}
}
} else if ("display".equals(fc.getProperty()) && fc.getOp() == FilterOperator.EQUAL) {
// gg; note: wtf is this: if the filter is display=v, look up the code 'v', and see if it's display is 'v'?
dwc.setCanBeHierarchy(false);
ConceptDefinitionComponent def = getConceptForCode(cs.getConcept(), fc.getValue());
if (def != null) {
if (isNotBlank(def.getDisplay()) && isNotBlank(fc.getValue())) {
if (def.getDisplay().contains(fc.getValue()) && passesOtherFilters(filters, cs, def.getCode())) {
for (String code : getCodesForConcept(def, expParams)) {
opContext.deadCheck("processFilter2");
if (exclude) {
excludeCode(wc, inc.getSystem(), code);
} else {
addCode(wc, inc.getSystem(), code, def.getDisplay(), cs.getLanguage(), null, def.getDesignation(), expParams, CodeSystemUtilities.isNotSelectable(cs, def), CodeSystemUtilities.isInactive(cs, def),
imports, noInactive, false, exp.getProperty(), makeCSProps(def.getDefinition(), def.getProperty()), cs, null, def.getExtension(), null, exp);
}
}
}
}
}
} else if (CodeSystemUtilities.isDefinedProperty(cs, fc.getProperty())) {
for (ConceptDefinitionComponent def : cs.getConcept()) {
PropertyFilter pf = new PropertyFilter(allErrors, fc, CodeSystemUtilities.getPropertyDefinition(cs, fc.getProperty()));
if (exclude) {
excludeCodeAndDescendents(wc, cs, inc.getSystem(), def, null, imports, null, pf, filters, exp);
} else {
addCodeAndDescendents(wc, cs, inc.getSystem(), def, null, expParams, imports, null, pf, noInactive, exp.getProperty(), filters, exp);
}
}
} else if (isKnownProperty(fc.getProperty(), cs)) {
for (ConceptDefinitionComponent def : cs.getConcept()) {
KnownPropertyFilter pf = new KnownPropertyFilter(allErrors, fc, fc.getProperty());
if (exclude) {
excludeCodeAndDescendents(wc, cs, inc.getSystem(), def, null, imports, null, pf, filters, exp);
} else {
addCodeAndDescendents(wc, cs, inc.getSystem(), def, null, expParams, imports, null, pf, noInactive, exp.getProperty(), filters, exp);
}
}
} else if ("code".equals(fc.getProperty()) && fc.getOp() == FilterOperator.REGEX) {
for (ConceptDefinitionComponent def : cs.getConcept()) {
if (exclude) {
excludeCodeAndDescendents(wc, cs, inc.getSystem(), def, null, imports, null, new RegexFilter(allErrors, fc.getValue()), filters, exp);
} else {
addCodeAndDescendents(wc, cs, inc.getSystem(), def, null, expParams, imports, null, new RegexFilter(allErrors, fc.getValue()), noInactive, exp.getProperty(), filters, exp);
}
}
} else {
throw fail(I18nConstants.VS_EXP_FILTER_UNK, true, focus.getVersionedUrl(), fc.getProperty(), fc.getOp());
}
}
private boolean isKnownProperty(String property, CodeSystem cs) {
return Utilities.existsInList(property, "notSelectable");
}
private List mergeDesignations(ConceptDefinitionComponent def,
List list) {
List res = new ArrayList<>();
if (def != null) {
res.addAll(def.getDesignation());
}
res.addAll(list);
return res;
}
private void addFragmentWarning(ValueSetExpansionComponent exp, CodeSystem cs) {
String url = cs.getVersionedUrl();
for (ValueSetExpansionParameterComponent p : exp.getParameter()) {
if ("fragment".equals(p.getName()) && p.hasValueUriType() && url.equals(p.getValue().primitiveValue())) {
return;
}
}
exp.addParameter().setName("fragment").setValue(new CanonicalType(url));
}
private void addExampleWarning(ValueSetExpansionComponent exp, CodeSystem cs) {
String url = cs.getVersionedUrl();
for (ValueSetExpansionParameterComponent p : exp.getParameter()) {
if ("example".equals(p.getName()) && p.hasValueUriType() && url.equals(p.getValue().primitiveValue())) {
return;
}
}
exp.addParameter().setName("example").setValue(new CanonicalType(url));
}
private List convertDesignations(List list) {
List res = new ArrayList();
for (ConceptReferenceDesignationComponent t : list) {
ConceptDefinitionDesignationComponent c = new ConceptDefinitionDesignationComponent();
c.setLanguage(t.getLanguage());
if (t.hasUse()) {
c.setUse(t.getUse());
}
c.setValue(t.getValue());
c.getExtension().addAll(t.getExtension());
res.add(c);
}
return res;
}
private String key(String uri, String code) {
return "{" + uri + "}" + code;
}
private String key(ValueSetExpansionContainsComponent c) {
return key(c.getSystem(), c.getCode());
}
private FHIRException fail(String msgId, boolean check, Object... params) {
String msg = context.formatMessage(msgId, params);
allErrors.add(msg);
return new FHIRException(msg);
}
private UnknownValueSetException failUnk(String msgId, boolean check, Object... params) {
String msg = context.formatMessage(msgId, params);
allErrors.add(msg);
return new UnknownValueSetException(msg);
}
private UnknownValueSetException failNotFound(String msgId, boolean check, Object... params) {
String msg = context.formatMessage(msgId, params);
allErrors.add(msg);
return new UnknownValueSetException(msg);
}
private ETooCostly failCostly(String msg) {
allErrors.add(msg);
return new ETooCostly(msg);
}
private TerminologyServiceException failTSE(String msg) {
allErrors.add(msg);
return new TerminologyServiceException(msg);
}
public Collection getAllErrors() {
return allErrors;
}
public boolean isCheckCodesWhenExpanding() {
return checkCodesWhenExpanding;
}
public void setCheckCodesWhenExpanding(boolean checkCodesWhenExpanding) {
this.checkCodesWhenExpanding = checkCodesWhenExpanding;
}
private boolean passesOtherFilters(List otherFilters, CodeSystem cs, String code) {
if (otherFilters == null) {
return true;
}
String key = key(cs.getUrl(), code);
for (WorkingContext wc : otherFilters) {
if (!wc.getMap().containsKey(key)) {
return false;
}
}
return true;
}
public boolean isDebug() {
return debug;
}
public ValueSetExpander setDebug(boolean debug) {
this.debug = debug;
return this;
}
public String getSource() {
if (sources.isEmpty()) {
return "internal";
} else {
return CommaSeparatedStringBuilder.join(", ", Utilities.sorted(sources));
}
}
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