org.hl7.fhir.dstu2.utils.BaseWorkerContext Maven / Gradle / Ivy
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package org.hl7.fhir.dstu2.utils;
/*
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.io.FileNotFoundException;
import java.io.IOException;
import java.text.MessageFormat;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Locale;
import java.util.Map;
import java.util.Objects;
import java.util.ResourceBundle;
import java.util.Set;
import org.hl7.fhir.dstu2.model.BooleanType;
import org.hl7.fhir.dstu2.model.CodeableConcept;
import org.hl7.fhir.dstu2.model.Coding;
import org.hl7.fhir.dstu2.model.ConceptMap;
import org.hl7.fhir.dstu2.model.Conformance;
import org.hl7.fhir.dstu2.model.Extension;
import org.hl7.fhir.dstu2.model.IntegerType;
import org.hl7.fhir.dstu2.model.Parameters;
import org.hl7.fhir.dstu2.model.Parameters.ParametersParameterComponent;
import org.hl7.fhir.dstu2.model.Reference;
import org.hl7.fhir.dstu2.model.StringType;
import org.hl7.fhir.dstu2.model.StructureDefinition;
import org.hl7.fhir.dstu2.model.UriType;
import org.hl7.fhir.dstu2.model.ValueSet;
import org.hl7.fhir.dstu2.model.ValueSet.ConceptDefinitionComponent;
import org.hl7.fhir.dstu2.model.ValueSet.ConceptDefinitionDesignationComponent;
import org.hl7.fhir.dstu2.model.ValueSet.ConceptSetComponent;
import org.hl7.fhir.dstu2.model.ValueSet.ValueSetComposeComponent;
import org.hl7.fhir.dstu2.model.ValueSet.ValueSetExpansionComponent;
import org.hl7.fhir.dstu2.model.ValueSet.ValueSetExpansionContainsComponent;
import org.hl7.fhir.dstu2.terminologies.ValueSetExpander.ETooCostly;
import org.hl7.fhir.dstu2.terminologies.ValueSetExpander.ValueSetExpansionOutcome;
import org.hl7.fhir.dstu2.terminologies.ValueSetExpanderFactory;
import org.hl7.fhir.dstu2.terminologies.ValueSetExpansionCache;
import org.hl7.fhir.dstu2.utils.client.FHIRToolingClient;
import org.hl7.fhir.utilities.CommaSeparatedStringBuilder;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.i18n.I18nBase;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
public abstract class BaseWorkerContext extends I18nBase implements IWorkerContext {
// all maps are to the full URI
protected Map codeSystems = new HashMap();
protected Map valueSets = new HashMap();
protected Map maps = new HashMap();
protected ValueSetExpanderFactory expansionCache = new ValueSetExpansionCache(this);
protected boolean cacheValidation; // if true, do an expansion and cache the expansion
private Set failed = new HashSet(); // value sets for which we don't try to do expansion, since the
// first attempt to get a comprehensive expansion was not
// successful
protected Map> validationCache = new HashMap>();
// private ValueSetExpansionCache expansionCache; //
protected FHIRToolingClient txServer;
private Locale locale;
private ResourceBundle i18Nmessages;
@Override
public ValueSet fetchCodeSystem(String system) {
return codeSystems.get(system);
}
@Override
public boolean supportsSystem(String system) {
if (codeSystems.containsKey(system))
return true;
else {
Conformance conf = txServer.getConformanceStatement();
for (Extension ex : ToolingExtensions.getExtensions(conf,
"http://hl7.org/fhir/StructureDefinition/conformance-supported-system")) {
if (system.equals(((UriType) ex.getValue()).getValue())) {
return true;
}
}
}
return false;
}
@Override
public ValueSetExpansionOutcome expandVS(ValueSet vs, boolean cacheOk) {
try {
Parameters params = new Parameters();
params.addParameter().setName("_limit").setValue(new IntegerType("10000"));
params.addParameter().setName("_incomplete").setValue(new BooleanType("true"));
params.addParameter().setName("profile").setValue(new UriType("http://www.healthintersections.com.au/fhir/expansion/no-details"));
ValueSet result = txServer.expandValueset(vs, params);
return new ValueSetExpansionOutcome(result);
} catch (Exception e) {
return new ValueSetExpansionOutcome("Error expanding ValueSet \"" + vs.getUrl() + ": " + e.getMessage());
}
}
private ValidationResult handleByCache(ValueSet vs, Coding coding, boolean tryCache) {
String cacheId = cacheId(coding);
Map cache = validationCache.get(vs.getUrl());
if (cache == null) {
cache = new HashMap();
validationCache.put(vs.getUrl(), cache);
}
if (cache.containsKey(cacheId))
return cache.get(cacheId);
if (!tryCache)
return null;
if (!cacheValidation)
return null;
if (failed.contains(vs.getUrl()))
return null;
ValueSetExpansionOutcome vse = expandVS(vs, true);
if (vse.getValueset() == null || notcomplete(vse.getValueset())) {
failed.add(vs.getUrl());
return null;
}
ValidationResult res = validateCode(coding, vse.getValueset());
cache.put(cacheId, res);
return res;
}
private boolean notcomplete(ValueSet vs) {
if (!vs.hasExpansion())
return true;
if (!vs.getExpansion().getExtensionsByUrl("http://hl7.org/fhir/StructureDefinition/valueset-unclosed").isEmpty())
return true;
if (!vs.getExpansion().getExtensionsByUrl("http://hl7.org/fhir/StructureDefinition/valueset-toocostly").isEmpty())
return true;
return false;
}
private ValidationResult handleByCache(ValueSet vs, CodeableConcept concept, boolean tryCache) {
String cacheId = cacheId(concept);
Map cache = validationCache.get(vs.getUrl());
if (cache == null) {
cache = new HashMap();
validationCache.put(vs.getUrl(), cache);
}
if (cache.containsKey(cacheId))
return cache.get(cacheId);
if (validationCache.containsKey(vs.getUrl()) && validationCache.get(vs.getUrl()).containsKey(cacheId))
return validationCache.get(vs.getUrl()).get(cacheId);
if (!tryCache)
return null;
if (!cacheValidation)
return null;
if (failed.contains(vs.getUrl()))
return null;
ValueSetExpansionOutcome vse = expandVS(vs, true);
if (vse.getValueset() == null || notcomplete(vse.getValueset())) {
failed.add(vs.getUrl());
return null;
}
ValidationResult res = validateCode(concept, vse.getValueset());
cache.put(cacheId, res);
return res;
}
private String cacheId(Coding coding) {
return "|" + coding.getSystem() + "|" + coding.getVersion() + "|" + coding.getCode() + "|" + coding.getDisplay();
}
private String cacheId(CodeableConcept cc) {
StringBuilder b = new StringBuilder();
for (Coding c : cc.getCoding()) {
b.append("#");
b.append(cacheId(c));
}
return b.toString();
}
private ValidationResult verifyCodeExternal(ValueSet vs, Coding coding, boolean tryCache) {
ValidationResult res = handleByCache(vs, coding, tryCache);
if (res != null)
return res;
Parameters pin = new Parameters();
pin.addParameter().setName("coding").setValue(coding);
pin.addParameter().setName("valueSet").setResource(vs);
res = serverValidateCode(pin);
Map cache = validationCache.get(vs.getUrl());
cache.put(cacheId(coding), res);
return res;
}
private ValidationResult verifyCodeExternal(ValueSet vs, CodeableConcept cc, boolean tryCache) {
ValidationResult res = handleByCache(vs, cc, tryCache);
if (res != null)
return res;
Parameters pin = new Parameters();
pin.addParameter().setName("codeableConcept").setValue(cc);
pin.addParameter().setName("valueSet").setResource(vs);
res = serverValidateCode(pin);
Map cache = validationCache.get(vs.getUrl());
cache.put(cacheId(cc), res);
return res;
}
private ValidationResult serverValidateCode(Parameters pin) {
Parameters pout = txServer.operateType(ValueSet.class, "validate-code", pin);
boolean ok = false;
String message = "No Message returned";
String display = null;
for (ParametersParameterComponent p : pout.getParameter()) {
if (p.getName().equals("result"))
ok = ((BooleanType) p.getValue()).getValue().booleanValue();
else if (p.getName().equals("message"))
message = ((StringType) p.getValue()).getValue();
else if (p.getName().equals("display"))
display = ((StringType) p.getValue()).getValue();
}
if (!ok)
return new ValidationResult(IssueSeverity.ERROR, message);
else if (display != null)
return new ValidationResult(new ConceptDefinitionComponent().setDisplay(display));
else
return new ValidationResult(null);
}
@Override
public ValueSetExpansionComponent expandVS(ConceptSetComponent inc) {
ValueSet vs = new ValueSet();
vs.setCompose(new ValueSetComposeComponent());
vs.getCompose().getInclude().add(inc);
ValueSetExpansionOutcome vse = expandVS(vs, true);
return vse.getValueset().getExpansion();
}
@Override
public ValidationResult validateCode(String system, String code, String display) {
try {
if (codeSystems.containsKey(system))
return verifyCodeInternal(codeSystems.get(system), system, code, display);
else
return verifyCodeExternal(null, new Coding().setSystem(system).setCode(code).setDisplay(display), true);
} catch (Exception e) {
return new ValidationResult(IssueSeverity.FATAL,
"Error validating code \"" + code + "\" in system \"" + system + "\": " + e.getMessage());
}
}
@Override
public ValidationResult validateCode(Coding code, ValueSet vs) {
try {
if (codeSystems.containsKey(code.getSystem()) || vs.hasExpansion())
return verifyCodeInternal(codeSystems.get(code.getSystem()), code.getSystem(), code.getCode(),
code.getDisplay());
else
return verifyCodeExternal(vs, code, true);
} catch (Exception e) {
return new ValidationResult(IssueSeverity.FATAL,
"Error validating code \"" + code + "\" in system \"" + code.getSystem() + "\": " + e.getMessage());
}
}
@Override
public ValidationResult validateCode(CodeableConcept code, ValueSet vs) {
try {
if (vs.hasCodeSystem() || vs.hasExpansion())
return verifyCodeInternal(vs, code);
else
return verifyCodeExternal(vs, code, true);
} catch (Exception e) {
return new ValidationResult(IssueSeverity.FATAL,
"Error validating code \"" + code.toString() + "\": " + e.getMessage());
}
}
@Override
public ValidationResult validateCode(String system, String code, String display, ValueSet vs) {
try {
if (system == null && vs.hasCodeSystem())
return verifyCodeInternal(vs, vs.getCodeSystem().getSystem(), code, display);
else if (codeSystems.containsKey(system) || vs.hasExpansion())
return verifyCodeInternal(vs, system, code, display);
else
return verifyCodeExternal(vs, new Coding().setSystem(system).setCode(code).setDisplay(display), true);
} catch (Exception e) {
return new ValidationResult(IssueSeverity.FATAL,
"Error validating code \"" + code + "\" in system \"" + system + "\": " + e.getMessage());
}
}
@Override
public ValidationResult validateCode(String system, String code, String display, ConceptSetComponent vsi) {
try {
ValueSet vs = new ValueSet().setUrl(Utilities.makeUuidUrn());
vs.getCompose().addInclude(vsi);
return verifyCodeExternal(vs, new Coding().setSystem(system).setCode(code).setDisplay(display), true);
} catch (Exception e) {
return new ValidationResult(IssueSeverity.FATAL,
"Error validating code \"" + code + "\" in system \"" + system + "\": " + e.getMessage());
}
}
@Override
public List findMapsForSource(String url) {
List res = new ArrayList();
for (ConceptMap map : maps.values())
if (((Reference) map.getSource()).getReference().equals(url))
res.add(map);
return res;
}
private ValidationResult verifyCodeInternal(ValueSet vs, CodeableConcept code)
throws FileNotFoundException, ETooCostly, IOException {
for (Coding c : code.getCoding()) {
ValidationResult res = verifyCodeInternal(vs, c.getSystem(), c.getCode(), c.getDisplay());
if (res.isOk())
return res;
}
if (code.getCoding().isEmpty())
return new ValidationResult(IssueSeverity.ERROR, "None code provided");
else
return new ValidationResult(IssueSeverity.ERROR, "None of the codes are in the specified value set");
}
private ValidationResult verifyCodeInternal(ValueSet vs, String system, String code, String display)
throws FileNotFoundException, ETooCostly, IOException {
if (vs.hasExpansion())
return verifyCodeInExpansion(vs, system, code, display);
else if (vs.hasCodeSystem() && !vs.hasCompose())
return verifyCodeInCodeSystem(vs, system, code, display);
else {
ValueSetExpansionOutcome vse = expansionCache.getExpander().expand(vs);
if (vse.getValueset() != null)
return verifyCodeExternal(vs, new Coding().setSystem(system).setCode(code).setDisplay(display), false);
else
return verifyCodeInExpansion(vse.getValueset(), system, code, display);
}
}
private ValidationResult verifyCodeInCodeSystem(ValueSet vs, String system, String code, String display) {
ConceptDefinitionComponent cc = findCodeInConcept(vs.getCodeSystem().getConcept(), code);
if (cc == null)
return new ValidationResult(IssueSeverity.ERROR,
"Unknown Code " + code + " in " + vs.getCodeSystem().getSystem());
if (display == null)
return new ValidationResult(cc);
CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder();
if (cc.hasDisplay()) {
b.append(cc.getDisplay());
if (display.equalsIgnoreCase(cc.getDisplay()))
return new ValidationResult(cc);
}
for (ConceptDefinitionDesignationComponent ds : cc.getDesignation()) {
b.append(ds.getValue());
if (display.equalsIgnoreCase(ds.getValue()))
return new ValidationResult(cc);
}
return new ValidationResult(IssueSeverity.ERROR,
"Display Name for " + code + " must be one of '" + b.toString() + "'");
}
private ValidationResult verifyCodeInExpansion(ValueSet vs, String system, String code, String display) {
ValueSetExpansionContainsComponent cc = findCode(vs.getExpansion().getContains(), code);
if (cc == null)
return new ValidationResult(IssueSeverity.ERROR,
"Unknown Code " + code + " in " + vs.getCodeSystem().getSystem());
if (display == null)
return new ValidationResult(new ConceptDefinitionComponent().setCode(code).setDisplay(cc.getDisplay()));
if (cc.hasDisplay()) {
if (display.equalsIgnoreCase(cc.getDisplay()))
return new ValidationResult(new ConceptDefinitionComponent().setCode(code).setDisplay(cc.getDisplay()));
return new ValidationResult(IssueSeverity.ERROR,
"Display Name for " + code + " must be '" + cc.getDisplay() + "'");
}
return null;
}
private ValueSetExpansionContainsComponent findCode(List contains, String code) {
for (ValueSetExpansionContainsComponent cc : contains) {
if (code.equals(cc.getCode()))
return cc;
ValueSetExpansionContainsComponent c = findCode(cc.getContains(), code);
if (c != null)
return c;
}
return null;
}
private ConceptDefinitionComponent findCodeInConcept(List concept, String code) {
for (ConceptDefinitionComponent cc : concept) {
if (code.equals(cc.getCode()))
return cc;
ConceptDefinitionComponent c = findCodeInConcept(cc.getConcept(), code);
if (c != null)
return c;
}
return null;
}
@Override
public StructureDefinition fetchTypeDefinition(String typeName) {
return fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/" + typeName);
}
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