org.hl7.fhir.r4b.context.BaseWorkerContext Maven / Gradle / Ivy
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package org.hl7.fhir.r4b.context;
import java.io.File;
/*
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.util.ArrayList;
import java.util.Collections;
import java.util.Comparator;
import java.util.Date;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Locale;
import java.util.Map;
import java.util.Set;
import org.apache.commons.lang3.StringUtils;
import org.fhir.ucum.UcumService;
import org.hl7.fhir.exceptions.DefinitionException;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.NoTerminologyServiceException;
import org.hl7.fhir.exceptions.TerminologyServiceException;
import org.hl7.fhir.r4b.conformance.ProfileUtilities;
import org.hl7.fhir.r4b.context.BaseWorkerContext.ResourceProxy;
import org.hl7.fhir.r4b.context.CanonicalResourceManager.CanonicalResourceProxy;
import org.hl7.fhir.r4b.context.IWorkerContext.PackageVersion;
import org.hl7.fhir.r4b.context.IWorkerContext.ILoggingService.LogCategory;
import org.hl7.fhir.r4b.context.TerminologyCache.CacheToken;
import org.hl7.fhir.r4b.model.BooleanType;
import org.hl7.fhir.r4b.model.Bundle;
import org.hl7.fhir.r4b.model.CanonicalResource;
import org.hl7.fhir.r4b.model.CanonicalType;
import org.hl7.fhir.r4b.model.CapabilityStatement;
import org.hl7.fhir.r4b.model.CodeSystem;
import org.hl7.fhir.r4b.model.CodeSystem.CodeSystemContentMode;
import org.hl7.fhir.r4b.model.CodeSystem.ConceptDefinitionComponent;
import org.hl7.fhir.r4b.model.CodeSystem.ConceptPropertyComponent;
import org.hl7.fhir.r4b.model.CodeableConcept;
import org.hl7.fhir.r4b.model.Coding;
import org.hl7.fhir.r4b.model.ConceptMap;
import org.hl7.fhir.r4b.model.Constants;
import org.hl7.fhir.r4b.model.ElementDefinition;
import org.hl7.fhir.r4b.model.ElementDefinition.ElementDefinitionBindingComponent;
import org.hl7.fhir.r4b.model.Enumerations.PublicationStatus;
import org.hl7.fhir.r4b.model.Identifier;
import org.hl7.fhir.r4b.model.ImplementationGuide;
import org.hl7.fhir.r4b.model.Library;
import org.hl7.fhir.r4b.model.Measure;
import org.hl7.fhir.r4b.model.NamingSystem;
import org.hl7.fhir.r4b.model.NamingSystem.NamingSystemIdentifierType;
import org.hl7.fhir.r4b.model.NamingSystem.NamingSystemUniqueIdComponent;
import org.hl7.fhir.r4b.model.OperationDefinition;
import org.hl7.fhir.r4b.model.OperationOutcome;
import org.hl7.fhir.r4b.model.Parameters;
import org.hl7.fhir.r4b.model.Parameters.ParametersParameterComponent;
import org.hl7.fhir.r4b.model.PlanDefinition;
import org.hl7.fhir.r4b.model.Questionnaire;
import org.hl7.fhir.r4b.model.Reference;
import org.hl7.fhir.r4b.model.Resource;
import org.hl7.fhir.r4b.model.SearchParameter;
import org.hl7.fhir.r4b.model.StringType;
import org.hl7.fhir.r4b.model.StructureDefinition;
import org.hl7.fhir.r4b.model.StructureDefinition.TypeDerivationRule;
import org.hl7.fhir.r4b.model.StructureMap;
import org.hl7.fhir.r4b.model.TerminologyCapabilities;
import org.hl7.fhir.r4b.model.TerminologyCapabilities.TerminologyCapabilitiesCodeSystemComponent;
import org.hl7.fhir.r4b.model.TerminologyCapabilities.TerminologyCapabilitiesExpansionParameterComponent;
import org.hl7.fhir.r4b.model.UriType;
import org.hl7.fhir.r4b.model.ValueSet;
import org.hl7.fhir.r4b.model.Bundle.BundleEntryComponent;
import org.hl7.fhir.r4b.model.Bundle.BundleType;
import org.hl7.fhir.r4b.model.Bundle.HTTPVerb;
import org.hl7.fhir.r4b.model.ValueSet.ConceptSetComponent;
import org.hl7.fhir.r4b.model.ValueSet.ValueSetComposeComponent;
import org.hl7.fhir.r4b.renderers.OperationOutcomeRenderer;
import org.hl7.fhir.r4b.terminologies.CodeSystemUtilities;
import org.hl7.fhir.r4b.terminologies.TerminologyClient;
import org.hl7.fhir.r4b.terminologies.ValueSetCheckerSimple;
import org.hl7.fhir.r4b.terminologies.ValueSetExpander.TerminologyServiceErrorClass;
import org.hl7.fhir.r4b.terminologies.ValueSetExpander.ValueSetExpansionOutcome;
import org.hl7.fhir.r4b.terminologies.ValueSetExpanderSimple;
import org.hl7.fhir.r4b.utils.ToolingExtensions;
import org.hl7.fhir.r4b.utils.validation.ValidationContextCarrier;
import org.hl7.fhir.utilities.OIDUtils;
import org.hl7.fhir.utilities.TimeTracker;
import org.hl7.fhir.utilities.ToolingClientLogger;
import org.hl7.fhir.utilities.TranslationServices;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.VersionUtilities;
import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
import org.hl7.fhir.utilities.i18n.I18nBase;
import org.hl7.fhir.utilities.i18n.I18nConstants;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueType;
import org.hl7.fhir.utilities.validation.ValidationOptions;
import com.google.gson.JsonObject;
import ca.uhn.fhir.model.valueset.BundleEntrySearchModeEnum;
public abstract class BaseWorkerContext extends I18nBase implements IWorkerContext {
public class ResourceProxy {
private Resource resource;
private CanonicalResourceProxy proxy;
public ResourceProxy(Resource resource) {
super();
this.resource = resource;
}
public ResourceProxy(CanonicalResourceProxy proxy) {
super();
this.proxy = proxy;
}
public Resource getResource() {
return resource != null ? resource : proxy.getResource();
}
public String getUrl() {
if (resource == null) {
return proxy.getUrl();
} else if (resource instanceof CanonicalResource) {
return ((CanonicalResource) resource).getUrl();
} else {
return null;
}
}
}
public class MetadataResourceVersionComparator implements Comparator {
private List list;
public MetadataResourceVersionComparator(List list) {
this.list = list;
}
@Override
public int compare(T arg1, T arg2) {
String v1 = arg1.getVersion();
String v2 = arg2.getVersion();
if (v1 == null && v2 == null) {
return Integer.compare(list.indexOf(arg1), list.indexOf(arg2)); // retain original order
} else if (v1 == null) {
return -1;
} else if (v2 == null) {
return 1;
} else {
String mm1 = VersionUtilities.getMajMin(v1);
String mm2 = VersionUtilities.getMajMin(v2);
if (mm1 == null || mm2 == null) {
return v1.compareTo(v2);
} else {
return mm1.compareTo(mm2);
}
}
}
}
private Object lock = new Object(); // used as a lock for the data that follows
protected String version; // although the internal resources are all R5, the version of FHIR they describe
// may not be
private String cacheId;
private boolean isTxCaching;
private Set cached = new HashSet<>();
private Map> allResourcesById = new HashMap>();
// all maps are to the full URI
private CanonicalResourceManager codeSystems = new CanonicalResourceManager(false);
private Set supportedCodeSystems = new HashSet();
private Set unsupportedCodeSystems = new HashSet(); // know that the terminology server doesn't
// support them
private CanonicalResourceManager valueSets = new CanonicalResourceManager(false);
private CanonicalResourceManager maps = new CanonicalResourceManager(false);
protected CanonicalResourceManager transforms = new CanonicalResourceManager(false);
private CanonicalResourceManager structures = new CanonicalResourceManager(
false);
private CanonicalResourceManager measures = new CanonicalResourceManager(false);
private CanonicalResourceManager libraries = new CanonicalResourceManager(false);
private CanonicalResourceManager guides = new CanonicalResourceManager(
false);
private CanonicalResourceManager capstmts = new CanonicalResourceManager(
false);
private CanonicalResourceManager searchParameters = new CanonicalResourceManager(
false);
private CanonicalResourceManager questionnaires = new CanonicalResourceManager(false);
private CanonicalResourceManager operations = new CanonicalResourceManager(
false);
private CanonicalResourceManager plans = new CanonicalResourceManager(false);
private CanonicalResourceManager systems = new CanonicalResourceManager(false);
private UcumService ucumService;
protected Map binaries = new HashMap();
protected Map oidCache = new HashMap<>();
protected Map> validationCache = new HashMap>();
protected String tsServer;
protected String name;
private boolean allowLoadingDuplicates;
protected TerminologyClient txClient;
private Set codeSystemsUsed = new HashSet<>();
protected ToolingClientLogger txLog;
private TerminologyCapabilities txcaps;
private boolean canRunWithoutTerminology;
protected boolean noTerminologyServer;
private int expandCodesLimit = 1000;
protected ILoggingService logger;
protected Parameters expParameters;
private TranslationServices translator = new NullTranslator();
protected TerminologyCache txCache;
protected TimeTracker clock;
private boolean tlogging = true;
private ICanonicalResourceLocator locator;
protected String userAgent;
public BaseWorkerContext() throws FileNotFoundException, IOException, FHIRException {
txCache = new TerminologyCache(lock, null);
setValidationMessageLanguage(getLocale());
clock = new TimeTracker();
}
public BaseWorkerContext(Locale locale) throws FileNotFoundException, IOException, FHIRException {
txCache = new TerminologyCache(lock, null);
setValidationMessageLanguage(locale);
clock = new TimeTracker();
}
public BaseWorkerContext(CanonicalResourceManager codeSystems,
CanonicalResourceManager valueSets, CanonicalResourceManager maps,
CanonicalResourceManager profiles, CanonicalResourceManager guides)
throws FileNotFoundException, IOException, FHIRException {
this();
this.codeSystems = codeSystems;
this.valueSets = valueSets;
this.maps = maps;
this.structures = profiles;
this.guides = guides;
clock = new TimeTracker();
}
protected void copy(BaseWorkerContext other) {
synchronized (other.lock) { // tricky, because you need to lock this as well, but it's really not in use yet
allResourcesById.putAll(other.allResourcesById);
translator = other.translator;
codeSystems.copy(other.codeSystems);
txcaps = other.txcaps;
valueSets.copy(other.valueSets);
maps.copy(other.maps);
transforms.copy(other.transforms);
structures.copy(other.structures);
searchParameters.copy(other.searchParameters);
plans.copy(other.plans);
questionnaires.copy(other.questionnaires);
operations.copy(other.operations);
systems.copy(other.systems);
guides.copy(other.guides);
capstmts.copy(other.capstmts);
measures.copy(other.measures);
libraries.copy(libraries);
allowLoadingDuplicates = other.allowLoadingDuplicates;
tsServer = other.tsServer;
name = other.name;
txClient = other.txClient;
txLog = other.txLog;
txcaps = other.txcaps;
canRunWithoutTerminology = other.canRunWithoutTerminology;
noTerminologyServer = other.noTerminologyServer;
if (other.txCache != null)
txCache = other.txCache.copy();
expandCodesLimit = other.expandCodesLimit;
logger = other.logger;
expParameters = other.expParameters;
}
}
public void cacheResource(Resource r) throws FHIRException {
cacheResourceFromPackage(r, null);
}
public void registerResourceFromPackage(CanonicalResourceProxy r, PackageVersion packageInfo) throws FHIRException {
synchronized (lock) {
Map map = allResourcesById.get(r.getType());
if (map == null) {
map = new HashMap();
allResourcesById.put(r.getType(), map);
}
if ((packageInfo == null || !packageInfo.isExamplesPackage()) || !map.containsKey(r.getId())) {
map.put(r.getId(), new ResourceProxy(r));
}
String url = r.getUrl();
if (!allowLoadingDuplicates && hasResource(r.getType(), url)) {
// spcial workaround for known problems with existing packages
if (Utilities.existsInList(url, "http://hl7.org/fhir/SearchParameter/example")) {
return;
}
throw new DefinitionException(formatMessage(I18nConstants.DUPLICATE_RESOURCE_, url));
}
switch (r.getType()) {
case "StructureDefinition":
if ("1.4.0".equals(version)) {
StructureDefinition sd = (StructureDefinition) r.getResource();
fixOldSD(sd);
}
structures.register(r, packageInfo);
break;
case "ValueSet":
valueSets.register(r, packageInfo);
break;
case "CodeSystem":
codeSystems.register(r, packageInfo);
break;
case "ImplementationGuide":
guides.register(r, packageInfo);
break;
case "CapabilityStatement":
capstmts.register(r, packageInfo);
break;
case "Measure":
measures.register(r, packageInfo);
break;
case "Library":
libraries.register(r, packageInfo);
break;
case "SearchParameter":
searchParameters.register(r, packageInfo);
break;
case "PlanDefinition":
plans.register(r, packageInfo);
break;
case "OperationDefinition":
operations.register(r, packageInfo);
break;
case "Questionnaire":
questionnaires.register(r, packageInfo);
break;
case "ConceptMap":
maps.register(r, packageInfo);
break;
case "StructureMap":
transforms.register(r, packageInfo);
break;
case "NamingSystem":
systems.register(r, packageInfo);
break;
}
}
}
public void cacheResourceFromPackage(Resource r, PackageVersion packageInfo) throws FHIRException {
synchronized (lock) {
Map map = allResourcesById.get(r.fhirType());
if (map == null) {
map = new HashMap();
allResourcesById.put(r.fhirType(), map);
}
if ((packageInfo == null || !packageInfo.isExamplesPackage()) || !map.containsKey(r.getId())) {
map.put(r.getId(), new ResourceProxy(r));
} else {
System.out.println("Ignore " + r.fhirType() + "/" + r.getId() + " from package " + packageInfo.toString());
}
if (r instanceof CodeSystem || r instanceof NamingSystem) {
oidCache.clear();
}
if (r instanceof CanonicalResource) {
CanonicalResource m = (CanonicalResource) r;
String url = m.getUrl();
if (!allowLoadingDuplicates && hasResource(r.getClass(), url)) {
// spcial workaround for known problems with existing packages
if (Utilities.existsInList(url, "http://hl7.org/fhir/SearchParameter/example")) {
return;
}
throw new DefinitionException(formatMessage(I18nConstants.DUPLICATE_RESOURCE_, url));
}
if (r instanceof StructureDefinition) {
StructureDefinition sd = (StructureDefinition) m;
if ("1.4.0".equals(version)) {
fixOldSD(sd);
}
structures.see(sd, packageInfo);
} else if (r instanceof ValueSet) {
valueSets.see((ValueSet) m, packageInfo);
} else if (r instanceof CodeSystem) {
CodeSystemUtilities.crossLinkCodeSystem((CodeSystem) r);
codeSystems.see((CodeSystem) m, packageInfo);
} else if (r instanceof ImplementationGuide) {
guides.see((ImplementationGuide) m, packageInfo);
} else if (r instanceof CapabilityStatement) {
capstmts.see((CapabilityStatement) m, packageInfo);
} else if (r instanceof Measure) {
measures.see((Measure) m, packageInfo);
} else if (r instanceof Library) {
libraries.see((Library) m, packageInfo);
} else if (r instanceof SearchParameter) {
searchParameters.see((SearchParameter) m, packageInfo);
} else if (r instanceof PlanDefinition) {
plans.see((PlanDefinition) m, packageInfo);
} else if (r instanceof OperationDefinition) {
operations.see((OperationDefinition) m, packageInfo);
} else if (r instanceof Questionnaire) {
questionnaires.see((Questionnaire) m, packageInfo);
} else if (r instanceof ConceptMap) {
maps.see((ConceptMap) m, packageInfo);
} else if (r instanceof StructureMap) {
transforms.see((StructureMap) m, packageInfo);
} else if (r instanceof NamingSystem) {
systems.see((NamingSystem) m, packageInfo);
}
}
}
}
public void fixOldSD(StructureDefinition sd) {
if (sd.getDerivation() == TypeDerivationRule.CONSTRAINT && sd.getType().equals("Extension")
&& sd.getUrl().startsWith("http://hl7.org/fhir/StructureDefinition/")) {
sd.setSnapshot(null);
}
for (ElementDefinition ed : sd.getDifferential().getElement()) {
if (ed.getPath().equals("Extension.url") || ed.getPath().endsWith(".extension.url")) {
ed.setMin(1);
if (ed.hasBase()) {
ed.getBase().setMin(1);
}
}
if ("extension".equals(ed.getSliceName())) {
ed.setSliceName(null);
}
}
}
/*
* Compare business versions, returning "true" if the candidate newer version is
* in fact newer than the oldVersion Comparison will work for strictly numeric
* versions as well as multi-level versions separated by ., -, _, : or space
* Failing that, it will do unicode-based character ordering. E.g. 1.5.3 <
* 1.14.3 2017-3-10 < 2017-12-7 A3 < T2
*/
private boolean laterVersion(String newVersion, String oldVersion) {
// Compare business versions, retur
newVersion = newVersion.trim();
oldVersion = oldVersion.trim();
if (StringUtils.isNumeric(newVersion) && StringUtils.isNumeric(oldVersion)) {
return Double.parseDouble(newVersion) > Double.parseDouble(oldVersion);
} else if (hasDelimiter(newVersion, oldVersion, ".")) {
return laterDelimitedVersion(newVersion, oldVersion, "\\.");
} else if (hasDelimiter(newVersion, oldVersion, "-")) {
return laterDelimitedVersion(newVersion, oldVersion, "\\-");
} else if (hasDelimiter(newVersion, oldVersion, "_")) {
return laterDelimitedVersion(newVersion, oldVersion, "\\_");
} else if (hasDelimiter(newVersion, oldVersion, ":")) {
return laterDelimitedVersion(newVersion, oldVersion, "\\:");
} else if (hasDelimiter(newVersion, oldVersion, " ")) {
return laterDelimitedVersion(newVersion, oldVersion, "\\ ");
} else {
return newVersion.compareTo(oldVersion) > 0;
}
}
/*
* Returns true if both strings include the delimiter and have the same number
* of occurrences of it
*/
private boolean hasDelimiter(String s1, String s2, String delimiter) {
return s1.contains(delimiter) && s2.contains(delimiter) && s1.split(delimiter).length == s2.split(delimiter).length;
}
private boolean laterDelimitedVersion(String newVersion, String oldVersion, String delimiter) {
String[] newParts = newVersion.split(delimiter);
String[] oldParts = oldVersion.split(delimiter);
for (int i = 0; i < newParts.length; i++) {
if (!newParts[i].equals(oldParts[i])) {
return laterVersion(newParts[i], oldParts[i]);
}
}
// This should never happen
throw new Error(formatMessage(I18nConstants.DELIMITED_VERSIONS_HAVE_EXACT_MATCH_FOR_DELIMITER____VS_, delimiter,
newParts, oldParts));
}
protected void seeMetadataResource(T r, Map map, List list, boolean addId)
throws FHIRException {
// if (addId)
// map.put(r.getId(), r); // todo: why?
list.add(r);
if (r.hasUrl()) {
// first, this is the correct reosurce for this version (if it has a version)
if (r.hasVersion()) {
map.put(r.getUrl() + "|" + r.getVersion(), r);
}
// if we haven't get anything for this url, it's the correct version
if (!map.containsKey(r.getUrl())) {
map.put(r.getUrl(), r);
} else {
List rl = new ArrayList();
for (T t : list) {
if (t.getUrl().equals(r.getUrl()) && !rl.contains(t)) {
rl.add(t);
}
}
Collections.sort(rl, new MetadataResourceVersionComparator(list));
map.put(r.getUrl(), rl.get(rl.size() - 1));
T latest = null;
for (T t : rl) {
if (VersionUtilities.versionsCompatible(t.getVersion(), r.getVersion())) {
latest = t;
}
}
if (latest != null) { // might be null if it's not using semver
map.put(r.getUrl() + "|" + VersionUtilities.getMajMin(latest.getVersion()), rl.get(rl.size() - 1));
}
}
}
}
@Override
public CodeSystem fetchCodeSystem(String system) {
if (system == null) {
return null;
}
if (system.contains("|")) {
String s = system.substring(0, system.indexOf("|"));
String v = system.substring(system.indexOf("|") + 1);
return fetchCodeSystem(s, v);
}
CodeSystem cs;
synchronized (lock) {
cs = codeSystems.get(system);
}
if (cs == null && locator != null) {
locator.findResource(this, system);
synchronized (lock) {
cs = codeSystems.get(system);
}
}
return cs;
}
public CodeSystem fetchCodeSystem(String system, String version) {
if (version == null) {
return fetchCodeSystem(system);
}
CodeSystem cs;
synchronized (lock) {
cs = codeSystems.get(system, version);
}
if (cs == null && locator != null) {
locator.findResource(this, system);
synchronized (lock) {
cs = codeSystems.get(system);
}
}
return cs;
}
@Override
public boolean supportsSystem(String system) throws TerminologyServiceException {
synchronized (lock) {
if (codeSystems.has(system) && codeSystems.get(system).getContent() != CodeSystemContentMode.NOTPRESENT) {
return true;
} else if (supportedCodeSystems.contains(system)) {
return true;
} else if (system.startsWith("http://example.org") || system.startsWith("http://acme.com")
|| system.startsWith("http://hl7.org/fhir/valueset-") || system.startsWith("urn:oid:")) {
return false;
} else {
if (noTerminologyServer) {
return false;
}
if (txcaps == null) {
try {
log("Terminology server: Check for supported code systems for " + system);
setTxCaps(txClient.getTerminologyCapabilities());
} catch (Exception e) {
if (canRunWithoutTerminology) {
noTerminologyServer = true;
log("==============!! Running without terminology server !! ==============");
if (txClient != null) {
log("txServer = " + txClient.getAddress());
log("Error = " + e.getMessage() + "");
}
log("=====================================================================");
return false;
} else {
e.printStackTrace();
throw new TerminologyServiceException(e);
}
}
if (supportedCodeSystems.contains(system)) {
return true;
}
}
}
return false;
}
}
private void log(String message) {
if (logger != null) {
logger.logMessage(message);
} else {
System.out.println(message);
}
}
protected void tlog(String msg) {
if (tlogging) {
if (logger != null) {
logger.logDebugMessage(LogCategory.TX, msg);
} else {
System.out.println("-tx: " + msg);
}
}
}
// --- expansion support
// ------------------------------------------------------------------------------------------------------------
public int getExpandCodesLimit() {
return expandCodesLimit;
}
public void setExpandCodesLimit(int expandCodesLimit) {
this.expandCodesLimit = expandCodesLimit;
}
@Override
public ValueSetExpansionOutcome expandVS(ElementDefinitionBindingComponent binding, boolean cacheOk,
boolean heirarchical) throws FHIRException {
ValueSet vs = null;
vs = fetchResource(ValueSet.class, binding.getValueSet());
if (vs == null) {
throw new FHIRException(formatMessage(I18nConstants.UNABLE_TO_RESOLVE_VALUE_SET_, binding.getValueSet()));
}
return expandVS(vs, cacheOk, heirarchical);
}
@Override
public ValueSetExpansionOutcome expandVS(ConceptSetComponent inc, boolean hierarchical)
throws TerminologyServiceException {
ValueSet vs = new ValueSet();
vs.setStatus(PublicationStatus.ACTIVE);
vs.setCompose(new ValueSetComposeComponent());
vs.getCompose().getInclude().add(inc);
CacheToken cacheToken = txCache.generateExpandToken(vs, hierarchical);
ValueSetExpansionOutcome res;
res = txCache.getExpansion(cacheToken);
if (res != null) {
return res;
}
Parameters p = expParameters.copy();
p.setParameter("includeDefinition", false);
p.setParameter("excludeNested", !hierarchical);
boolean cached = addDependentResources(p, vs);
if (cached) {
p.addParameter().setName("cache-id").setValue(new StringType(cacheId));
}
for (ConceptSetComponent incl : vs.getCompose().getInclude()) {
codeSystemsUsed.add(incl.getSystem());
}
for (ConceptSetComponent incl : vs.getCompose().getExclude()) {
codeSystemsUsed.add(incl.getSystem());
}
if (noTerminologyServer) {
return new ValueSetExpansionOutcome(
formatMessage(I18nConstants.ERROR_EXPANDING_VALUESET_RUNNING_WITHOUT_TERMINOLOGY_SERVICES),
TerminologyServiceErrorClass.NOSERVICE);
}
Map params = new HashMap();
params.put("_limit", Integer.toString(expandCodesLimit));
params.put("_incomplete", "true");
tlog("$expand on " + txCache.summary(vs));
try {
ValueSet result = txClient.expandValueset(vs, p, params);
res = new ValueSetExpansionOutcome(result).setTxLink(txLog.getLastId());
} catch (Exception e) {
res = new ValueSetExpansionOutcome(e.getMessage() == null ? e.getClass().getName() : e.getMessage(),
TerminologyServiceErrorClass.UNKNOWN);
if (txLog != null) {
res.setTxLink(txLog.getLastId());
}
}
txCache.cacheExpansion(cacheToken, res, TerminologyCache.PERMANENT);
return res;
}
@Override
public ValueSetExpansionOutcome expandVS(ValueSet vs, boolean cacheOk, boolean heirarchical) {
if (expParameters == null)
throw new Error(formatMessage(I18nConstants.NO_EXPANSION_PARAMETERS_PROVIDED));
Parameters p = expParameters.copy();
return expandVS(vs, cacheOk, heirarchical, false, p);
}
@Override
public ValueSetExpansionOutcome expandVS(ValueSet vs, boolean cacheOk, boolean heirarchical, boolean incompleteOk) {
if (expParameters == null)
throw new Error(formatMessage(I18nConstants.NO_EXPANSION_PARAMETERS_PROVIDED));
Parameters p = expParameters.copy();
return expandVS(vs, cacheOk, heirarchical, incompleteOk, p);
}
public ValueSetExpansionOutcome expandVS(ValueSet vs, boolean cacheOk, boolean heirarchical, boolean incompleteOk,
Parameters p) {
if (p == null) {
throw new Error(formatMessage(I18nConstants.NO_PARAMETERS_PROVIDED_TO_EXPANDVS));
}
if (vs.hasExpansion()) {
return new ValueSetExpansionOutcome(vs.copy());
}
if (!vs.hasUrl()) {
throw new Error(formatMessage(I18nConstants.NO_VALUE_SET_IN_URL));
}
for (ConceptSetComponent inc : vs.getCompose().getInclude()) {
codeSystemsUsed.add(inc.getSystem());
}
for (ConceptSetComponent inc : vs.getCompose().getExclude()) {
codeSystemsUsed.add(inc.getSystem());
}
CacheToken cacheToken = txCache.generateExpandToken(vs, heirarchical);
ValueSetExpansionOutcome res;
if (cacheOk) {
res = txCache.getExpansion(cacheToken);
if (res != null) {
return res;
}
}
p.setParameter("includeDefinition", false);
p.setParameter("excludeNested", !heirarchical);
if (incompleteOk) {
p.setParameter("incomplete-ok", true);
}
List allErrors = new ArrayList<>();
// ok, first we try to expand locally
ValueSetExpanderSimple vse = new ValueSetExpanderSimple(this);
try {
res = vse.expand(vs, p);
allErrors.addAll(vse.getAllErrors());
if (res.getValueset() != null) {
if (!res.getValueset().hasUrl()) {
throw new Error(formatMessage(I18nConstants.NO_URL_IN_EXPAND_VALUE_SET));
}
txCache.cacheExpansion(cacheToken, res, TerminologyCache.TRANSIENT);
return res;
}
} catch (Exception e) {
allErrors.addAll(vse.getAllErrors());
e.printStackTrace();
}
// if that failed, we try to expand on the server
if (addDependentResources(p, vs)) {
p.addParameter().setName("cache-id").setValue(new StringType(cacheId));
}
if (noTerminologyServer) {
return new ValueSetExpansionOutcome(
formatMessage(I18nConstants.ERROR_EXPANDING_VALUESET_RUNNING_WITHOUT_TERMINOLOGY_SERVICES),
TerminologyServiceErrorClass.NOSERVICE, allErrors);
}
Map params = new HashMap();
params.put("_limit", Integer.toString(expandCodesLimit));
params.put("_incomplete", "true");
tlog("$expand on " + txCache.summary(vs));
try {
ValueSet result = txClient.expandValueset(vs, p, params);
if (result != null) {
if (!result.hasUrl()) {
result.setUrl(vs.getUrl());
}
if (!result.hasUrl()) {
throw new Error(formatMessage(I18nConstants.NO_URL_IN_EXPAND_VALUE_SET_2));
}
}
res = new ValueSetExpansionOutcome(result).setTxLink(txLog.getLastId());
} catch (Exception e) {
res = new ValueSetExpansionOutcome(e.getMessage() == null ? e.getClass().getName() : e.getMessage(),
TerminologyServiceErrorClass.UNKNOWN, allErrors).setTxLink(txLog == null ? null : txLog.getLastId());
}
txCache.cacheExpansion(cacheToken, res, TerminologyCache.PERMANENT);
return res;
}
private boolean hasTooCostlyExpansion(ValueSet valueset) {
return valueset != null && valueset.hasExpansion()
&& ToolingExtensions.hasExtension(valueset.getExpansion(), ToolingExtensions.EXT_EXP_TOOCOSTLY);
}
// --- validate code
// -------------------------------------------------------------------------------
@Override
public ValidationResult validateCode(ValidationOptions options, String system, String version, String code,
String display) {
assert options != null;
Coding c = new Coding(system, version, code, display);
return validateCode(options, c, null);
}
@Override
public ValidationResult validateCode(ValidationOptions options, String system, String version, String code,
String display, ValueSet vs) {
assert options != null;
Coding c = new Coding(system, version, code, display);
return validateCode(options, c, vs);
}
@Override
public ValidationResult validateCode(ValidationOptions options, String code, ValueSet vs) {
assert options != null;
Coding c = new Coding(null, code, null);
return validateCode(options.withGuessSystem(), c, vs);
}
@Override
public void validateCodeBatch(ValidationOptions options, List codes, ValueSet vs) {
if (options == null) {
options = ValidationOptions.defaults();
}
// 1st pass: what is in the cache?
// 2nd pass: What can we do internally
// 3rd pass: hit the server
for (CodingValidationRequest t : codes) {
t.setCacheToken(txCache != null ? txCache.generateValidationToken(options, t.getCoding(), vs) : null);
if (t.getCoding().hasSystem()) {
codeSystemsUsed.add(t.getCoding().getSystem());
}
if (txCache != null) {
t.setResult(txCache.getValidation(t.getCacheToken()));
}
}
if (options.isUseClient()) {
for (CodingValidationRequest t : codes) {
if (!t.hasResult()) {
try {
ValueSetCheckerSimple vsc = new ValueSetCheckerSimple(options, vs, this);
ValidationResult res = vsc.validateCode(t.getCoding());
if (txCache != null) {
txCache.cacheValidation(t.getCacheToken(), res, TerminologyCache.TRANSIENT);
}
t.setResult(res);
} catch (Exception e) {
}
}
}
}
for (CodingValidationRequest t : codes) {
if (!t.hasResult()) {
String codeKey = t.getCoding().hasVersion() ? t.getCoding().getSystem() + "|" + t.getCoding().getVersion()
: t.getCoding().getSystem();
if (!options.isUseServer()) {
t.setResult(new ValidationResult(IssueSeverity.WARNING,
formatMessage(I18nConstants.UNABLE_TO_VALIDATE_CODE_WITHOUT_USING_SERVER),
TerminologyServiceErrorClass.BLOCKED_BY_OPTIONS));
} else if (unsupportedCodeSystems.contains(codeKey)) {
t.setResult(new ValidationResult(IssueSeverity.ERROR,
formatMessage(I18nConstants.UNKNOWN_CODESYSTEM, t.getCoding().getSystem()),
TerminologyServiceErrorClass.CODESYSTEM_UNSUPPORTED));
} else if (noTerminologyServer) {
t.setResult(new ValidationResult(IssueSeverity.ERROR,
formatMessage(I18nConstants.ERROR_VALIDATING_CODE_RUNNING_WITHOUT_TERMINOLOGY_SERVICES, t.getCoding().getCode(), t.getCoding().getSystem()),
TerminologyServiceErrorClass.NOSERVICE));
}
}
}
if (expParameters == null)
throw new Error(formatMessage(I18nConstants.NO_EXPANSIONPROFILE_PROVIDED));
// for those that that failed, we try to validate on the server
Bundle batch = new Bundle();
batch.setType(BundleType.BATCH);
Set systems = new HashSet<>();
for (CodingValidationRequest t : codes) {
if (!t.hasResult()) {
Parameters pIn = new Parameters();
pIn.addParameter().setName("coding").setValue(t.getCoding());
if (options.isGuessSystem()) {
pIn.addParameter().setName("inferSystem").setValue(new BooleanType(true));
}
if (vs != null) {
pIn.addParameter().setName("valueSet").setResource(vs);
}
pIn.addParameter().setName("profile").setResource(expParameters);
setTerminologyOptions(options, pIn);
BundleEntryComponent be = batch.addEntry();
be.setResource(pIn);
be.getRequest().setMethod(HTTPVerb.POST);
be.getRequest().setUrl("CodeSystem/$validate-code");
be.setUserData("source", t);
systems.add(t.getCoding().getSystem());
}
}
if (batch.getEntry().size() > 0) {
tlog("$batch validate for " + batch.getEntry().size() + " codes on systems " + systems.toString());
if (txClient == null) {
throw new FHIRException(
formatMessage(I18nConstants.ATTEMPT_TO_USE_TERMINOLOGY_SERVER_WHEN_NO_TERMINOLOGY_SERVER_IS_AVAILABLE));
}
if (txLog != null) {
txLog.clearLastId();
}
Bundle resp = txClient.validateBatch(batch);
for (int i = 0; i < batch.getEntry().size(); i++) {
CodingValidationRequest t = (CodingValidationRequest) batch.getEntry().get(i).getUserData("source");
BundleEntryComponent r = resp.getEntry().get(i);
if (r.getResource() instanceof Parameters) {
t.setResult(processValidationResult((Parameters) r.getResource()));
if (txCache != null) {
txCache.cacheValidation(t.getCacheToken(), t.getResult(), TerminologyCache.PERMANENT);
}
} else {
t.setResult(new ValidationResult(IssueSeverity.ERROR, getResponseText(r.getResource()))
.setTxLink(txLog == null ? null : txLog.getLastId()));
}
}
}
}
private String getResponseText(Resource resource) {
if (resource instanceof OperationOutcome) {
return OperationOutcomeRenderer.toString((OperationOutcome) resource);
}
return "Todo";
}
@Override
public ValidationResult validateCode(ValidationOptions options, Coding code, ValueSet vs) {
ValidationContextCarrier ctxt = new ValidationContextCarrier();
return validateCode(options, code, vs, ctxt);
}
@Override
public ValidationResult validateCode(ValidationOptions options, Coding code, ValueSet vs,
ValidationContextCarrier ctxt) {
if (options == null) {
options = ValidationOptions.defaults();
}
if (code.hasSystem()) {
codeSystemsUsed.add(code.getSystem());
}
CacheToken cacheToken = txCache != null ? txCache.generateValidationToken(options, code, vs) : null;
ValidationResult res = null;
if (txCache != null) {
res = txCache.getValidation(cacheToken);
}
if (res != null) {
return res;
}
if (options.isUseClient()) {
// ok, first we try to validate locally
try {
ValueSetCheckerSimple vsc = new ValueSetCheckerSimple(options, vs, this, ctxt);
if (!vsc.isServerSide(code.getSystem())) {
res = vsc.validateCode(code);
if (txCache != null) {
txCache.cacheValidation(cacheToken, res, TerminologyCache.TRANSIENT);
}
return res;
}
} catch (Exception e) {
}
}
String codeKey = code.hasVersion() ? code.getSystem() + "|" + code.getVersion() : code.getSystem();
if (!options.isUseServer()) {
return new ValidationResult(IssueSeverity.WARNING,
formatMessage(I18nConstants.UNABLE_TO_VALIDATE_CODE_WITHOUT_USING_SERVER),
TerminologyServiceErrorClass.BLOCKED_BY_OPTIONS);
}
if (unsupportedCodeSystems.contains(codeKey)) {
return new ValidationResult(IssueSeverity.ERROR,
formatMessage(I18nConstants.UNKNOWN_CODESYSTEM, code.getSystem()),
TerminologyServiceErrorClass.CODESYSTEM_UNSUPPORTED);
}
// if that failed, we try to validate on the server
if (noTerminologyServer) {
return new ValidationResult(IssueSeverity.ERROR,
formatMessage(I18nConstants.ERROR_VALIDATING_CODE_RUNNING_WITHOUT_TERMINOLOGY_SERVICES, code.getCode(), code.getSystem()),
TerminologyServiceErrorClass.NOSERVICE);
}
String csumm = txCache != null ? txCache.summary(code) : null;
if (txCache != null) {
tlog("$validate " + csumm + " for " + txCache.summary(vs));
} else {
tlog("$validate " + csumm + " before cache exists");
}
try {
Parameters pIn = new Parameters();
pIn.addParameter().setName("coding").setValue(code);
if (options.isGuessSystem()) {
pIn.addParameter().setName("inferSystem").setValue(new BooleanType(true));
}
setTerminologyOptions(options, pIn);
res = validateOnServer(vs, pIn, options);
} catch (Exception e) {
res = new ValidationResult(IssueSeverity.ERROR, e.getMessage() == null ? e.getClass().getName() : e.getMessage())
.setTxLink(txLog == null ? null : txLog.getLastId()).setErrorClass(TerminologyServiceErrorClass.SERVER_ERROR);
}
if (res.getErrorClass() == TerminologyServiceErrorClass.CODESYSTEM_UNSUPPORTED && !code.hasVersion()) {
unsupportedCodeSystems.add(codeKey);
} else if (txCache != null) { // we never cache unsuppoted code systems - we always keep trying (but only once
// per run)
txCache.cacheValidation(cacheToken, res, TerminologyCache.PERMANENT);
}
return res;
}
private void setTerminologyOptions(ValidationOptions options, Parameters pIn) {
if (options.hasLanguages()) {
pIn.addParameter("displayLanguage", options.getLanguages().toString());
}
if (options.isMembershipOnly()) {
pIn.addParameter("valueset-membership-only", true);
}
if (options.isDisplayWarningMode()) {
pIn.addParameter("lenient-display-validation", true);
}
if (options.isVersionFlexible()) {
pIn.addParameter("default-to-latest-version", true);
}
}
@Override
public ValidationResult validateCode(ValidationOptions options, CodeableConcept code, ValueSet vs) {
CacheToken cacheToken = txCache.generateValidationToken(options, code, vs);
ValidationResult res = txCache.getValidation(cacheToken);
if (res != null) {
return res;
}
for (Coding c : code.getCoding()) {
if (c.hasSystem()) {
codeSystemsUsed.add(c.getSystem());
}
}
if (options.isUseClient()) {
// ok, first we try to validate locally
try {
ValueSetCheckerSimple vsc = new ValueSetCheckerSimple(options, vs, this);
res = vsc.validateCode(code);
txCache.cacheValidation(cacheToken, res, TerminologyCache.TRANSIENT);
return res;
} catch (Exception e) {
if (e instanceof NoTerminologyServiceException) {
return new ValidationResult(IssueSeverity.ERROR, "No Terminology Service",
TerminologyServiceErrorClass.NOSERVICE);
}
}
}
if (!options.isUseServer()) {
return new ValidationResult(IssueSeverity.WARNING, "Unable to validate code without using server",
TerminologyServiceErrorClass.BLOCKED_BY_OPTIONS);
}
// if that failed, we try to validate on the server
if (noTerminologyServer) {
return new ValidationResult(IssueSeverity.ERROR, "Error validating code: running without terminology services",
TerminologyServiceErrorClass.NOSERVICE);
}
tlog("$validate " + txCache.summary(code) + " for " + txCache.summary(vs));
try {
Parameters pIn = new Parameters();
pIn.addParameter().setName("codeableConcept").setValue(code);
setTerminologyOptions(options, pIn);
res = validateOnServer(vs, pIn, options);
} catch (Exception e) {
res = new ValidationResult(IssueSeverity.ERROR, e.getMessage() == null ? e.getClass().getName() : e.getMessage())
.setTxLink(txLog.getLastId());
}
txCache.cacheValidation(cacheToken, res, TerminologyCache.PERMANENT);
return res;
}
private ValidationResult validateOnServer(ValueSet vs, Parameters pin, ValidationOptions options)
throws FHIRException {
boolean cache = false;
if (vs != null) {
for (ConceptSetComponent inc : vs.getCompose().getInclude()) {
codeSystemsUsed.add(inc.getSystem());
}
for (ConceptSetComponent inc : vs.getCompose().getExclude()) {
codeSystemsUsed.add(inc.getSystem());
}
}
if (vs != null) {
if (isTxCaching && cacheId != null && vs.getUrl() != null
&& cached.contains(vs.getUrl() + "|" + vs.getVersion())) {
pin.addParameter().setName("url")
.setValue(new UriType(vs.getUrl() + (vs.hasVersion() ? "|" + vs.getVersion() : "")));
} else if (options.getVsAsUrl()) {
pin.addParameter().setName("url").setValue(new StringType(vs.getUrl()));
} else {
pin.addParameter().setName("valueSet").setResource(vs);
if (vs.getUrl() != null) {
cached.add(vs.getUrl() + "|" + vs.getVersion());
}
}
cache = true;
addDependentResources(pin, vs);
}
if (cache) {
pin.addParameter().setName("cache-id").setValue(new StringType(cacheId));
}
for (ParametersParameterComponent pp : pin.getParameter()) {
if (pp.getName().equals("profile")) {
throw new Error(formatMessage(I18nConstants.CAN_ONLY_SPECIFY_PROFILE_IN_THE_CONTEXT));
}
}
if (expParameters == null) {
throw new Error(formatMessage(I18nConstants.NO_EXPANSIONPROFILE_PROVIDED));
}
pin.addParameter().setName("profile").setResource(expParameters);
if (txLog != null) {
txLog.clearLastId();
}
if (txClient == null) {
throw new FHIRException(
formatMessage(I18nConstants.ATTEMPT_TO_USE_TERMINOLOGY_SERVER_WHEN_NO_TERMINOLOGY_SERVER_IS_AVAILABLE));
}
Parameters pOut;
if (vs == null) {
pOut = txClient.validateCS(pin);
} else {
pOut = txClient.validateVS(pin);
}
return processValidationResult(pOut);
}
private boolean addDependentResources(Parameters pin, ValueSet vs) {
boolean cache = false;
for (ConceptSetComponent inc : vs.getCompose().getInclude()) {
cache = addDependentResources(pin, inc) || cache;
}
for (ConceptSetComponent inc : vs.getCompose().getExclude()) {
cache = addDependentResources(pin, inc) || cache;
}
return cache;
}
private boolean addDependentResources(Parameters pin, ConceptSetComponent inc) {
boolean cache = false;
for (CanonicalType c : inc.getValueSet()) {
ValueSet vs = fetchResource(ValueSet.class, c.getValue());
if (vs != null) {
pin.addParameter().setName("tx-resource").setResource(vs);
if (isTxCaching && cacheId == null || !cached.contains(vs.getVUrl())) {
cached.add(vs.getVUrl());
cache = true;
}
addDependentResources(pin, vs);
}
}
CodeSystem cs = fetchResource(CodeSystem.class, inc.getSystem());
if (cs != null) {
pin.addParameter().setName("tx-resource").setResource(cs);
if (isTxCaching && cacheId == null || !cached.contains(cs.getVUrl())) {
cached.add(cs.getVUrl());
cache = true;
}
// todo: supplements
}
return cache;
}
public ValidationResult processValidationResult(Parameters pOut) {
boolean ok = false;
String message = "No Message returned";
String display = null;
String system = null;
String code = null;
TerminologyServiceErrorClass err = TerminologyServiceErrorClass.UNKNOWN;
for (ParametersParameterComponent p : pOut.getParameter()) {
if (p.hasValue()) {
if (p.getName().equals("result")) {
ok = ((BooleanType) p.getValue()).getValue().booleanValue();
} else if (p.getName().equals("message")) {
message = p.getValue().primitiveValue();
} else if (p.getName().equals("display")) {
display = p.getValue().primitiveValue();
} else if (p.getName().equals("system")) {
system = p.getValue().primitiveValue();
} else if (p.getName().equals("code")) {
code = p.getValue().primitiveValue();
} else if (p.getName().equals("cause")) {
try {
IssueType it = IssueType.fromCode(((StringType) p.getValue()).getValue());
if (it == IssueType.UNKNOWN) {
err = TerminologyServiceErrorClass.UNKNOWN;
} else if (it == IssueType.NOTFOUND) {
err = TerminologyServiceErrorClass.CODESYSTEM_UNSUPPORTED;
} else if (it == IssueType.NOTSUPPORTED) {
err = TerminologyServiceErrorClass.VALUESET_UNSUPPORTED;
} else {
err = null;
}
} catch (FHIRException e) {
}
}
}
}
if (!ok) {
return new ValidationResult(IssueSeverity.ERROR, message + " (from " + txClient.getAddress() + ")", err)
.setTxLink(txLog.getLastId());
} else if (message != null && !message.equals("No Message returned")) {
return new ValidationResult(IssueSeverity.WARNING, message + " (from " + txClient.getAddress() + ")", system,
new ConceptDefinitionComponent().setDisplay(display).setCode(code)).setTxLink(txLog.getLastId());
} else if (display != null) {
return new ValidationResult(system, new ConceptDefinitionComponent().setDisplay(display).setCode(code))
.setTxLink(txLog.getLastId());
} else {
return new ValidationResult(system, new ConceptDefinitionComponent().setCode(code)).setTxLink(txLog.getLastId());
}
}
// --------------------------------------------------------------------------------------------------------------------------------------------------------
public void initTS(String cachePath) throws Exception {
if (!ManagedFileAccess.file(cachePath).exists()) {
Utilities.createDirectory(cachePath);
}
txCache = new TerminologyCache(lock, cachePath);
}
public void clearTSCache(String url) throws Exception {
txCache.removeCS(url);
}
public void clearTS() {
txCache.clear();
}
@Override
public List findMapsForSource(String url) throws FHIRException {
synchronized (lock) {
List res = new ArrayList();
for (ConceptMap map : maps.getList()) {
if (((Reference) map.getSource()).getReference().equals(url)) {
res.add(map);
}
}
return res;
}
}
public boolean isCanRunWithoutTerminology() {
return canRunWithoutTerminology;
}
public void setCanRunWithoutTerminology(boolean canRunWithoutTerminology) {
this.canRunWithoutTerminology = canRunWithoutTerminology;
}
public void setLogger(ILoggingService logger) {
this.logger = logger;
}
public Parameters getExpansionParameters() {
return expParameters;
}
public void setExpansionProfile(Parameters expParameters) {
this.expParameters = expParameters;
}
@Override
public boolean isNoTerminologyServer() {
return noTerminologyServer;
}
public void setNoTerminologyServer(boolean noTerminologyServer) {
this.noTerminologyServer = noTerminologyServer;
}
public String getName() {
return name;
}
public void setName(String name) {
this.name = name;
}
@Override
public Set getResourceNamesAsSet() {
Set res = new HashSet();
res.addAll(getResourceNames());
return res;
}
public boolean isAllowLoadingDuplicates() {
return allowLoadingDuplicates;
}
public void setAllowLoadingDuplicates(boolean allowLoadingDuplicates) {
this.allowLoadingDuplicates = allowLoadingDuplicates;
}
@Override
public T fetchResourceWithException(Class class_, String uri) throws FHIRException {
return fetchResourceWithException(class_, uri, null);
}
public T fetchResourceWithException(String cls, String uri) throws FHIRException {
return fetchResourceWithException(cls, uri, null);
}
public T fetchResourceWithException(Class class_, String uri, CanonicalResource source)
throws FHIRException {
return fetchResourceWithException(class_, uri, null, source);
}
@SuppressWarnings("unchecked")
public T fetchResourceWithException(Class class_, String uri, String version,
CanonicalResource source) throws FHIRException {
if (uri == null) {
return null;
}
if (class_ == StructureDefinition.class) {
uri = ProfileUtilities.sdNs(uri, getOverrideVersionNs());
}
synchronized (lock) {
if (uri.contains("|")) {
version = uri.substring(uri.lastIndexOf("|") + 1);
uri = uri.substring(0, uri.lastIndexOf("|"));
}
if (uri.contains("#")) {
uri = uri.substring(0, uri.indexOf("#"));
}
if (class_ == Resource.class || class_ == null) {
if (structures.has(uri)) {
return (T) structures.get(uri, version);
}
if (guides.has(uri)) {
return (T) guides.get(uri, version);
}
if (capstmts.has(uri)) {
return (T) capstmts.get(uri, version);
}
if (measures.has(uri)) {
return (T) measures.get(uri, version);
}
if (libraries.has(uri)) {
return (T) libraries.get(uri, version);
}
if (valueSets.has(uri)) {
return (T) valueSets.get(uri, version);
}
if (codeSystems.has(uri)) {
return (T) codeSystems.get(uri, version);
}
if (operations.has(uri)) {
return (T) operations.get(uri, version);
}
if (searchParameters.has(uri)) {
return (T) searchParameters.get(uri, version);
}
if (plans.has(uri)) {
return (T) plans.get(uri, version);
}
if (maps.has(uri)) {
return (T) maps.get(uri, version);
}
if (transforms.has(uri)) {
return (T) transforms.get(uri, version);
}
if (questionnaires.has(uri)) {
return (T) questionnaires.get(uri, version);
}
if (uri.matches(Constants.URI_REGEX) && !uri.contains("ValueSet")) {
return null;
}
// it might be a special URL.
if (Utilities.isAbsoluteUrl(uri) || uri.startsWith("ValueSet/")) {
Resource res = null; // findTxValueSet(uri);
if (res != null) {
return (T) res;
}
}
for (Map rt : allResourcesById.values()) {
for (ResourceProxy r : rt.values()) {
if (uri.equals(r.getUrl())) {
if (version == null || version == r.getResource().getMeta().getVersionId()) {
return (T) r.getResource();
}
}
}
}
return null;
} else if (class_ == ImplementationGuide.class) {
return (T) guides.get(uri, version);
} else if (class_ == CapabilityStatement.class) {
return (T) capstmts.get(uri, version);
} else if (class_ == Measure.class) {
return (T) measures.get(uri, version);
} else if (class_ == Library.class) {
return (T) libraries.get(uri, version);
} else if (class_ == StructureDefinition.class) {
return (T) structures.get(uri, version);
} else if (class_ == StructureMap.class) {
return (T) transforms.get(uri, version);
} else if (class_ == ValueSet.class) {
return (T) valueSets.get(uri, version);
} else if (class_ == CodeSystem.class) {
return (T) codeSystems.get(uri, version);
} else if (class_ == ConceptMap.class) {
return (T) maps.get(uri, version);
} else if (class_ == PlanDefinition.class) {
return (T) plans.get(uri, version);
} else if (class_ == OperationDefinition.class) {
OperationDefinition od = operations.get(uri, version);
return (T) od;
} else if (class_ == Questionnaire.class) {
return (T) questionnaires.get(uri, version);
} else if (class_ == SearchParameter.class) {
SearchParameter res = searchParameters.get(uri, version);
return (T) res;
}
if (class_ == CodeSystem.class && codeSystems.has(uri)) {
return (T) codeSystems.get(uri, version);
}
if (class_ == ValueSet.class && valueSets.has(uri)) {
return (T) valueSets.get(uri, version);
}
if (class_ == Questionnaire.class) {
return (T) questionnaires.get(uri, version);
}
if (supportedCodeSystems.contains(uri)) {
return null;
}
throw new FHIRException(formatMessage(I18nConstants.NOT_DONE_YET_CANT_FETCH_, uri));
}
}
public PackageVersion getPackageForUrl(String uri) {
if (uri == null) {
return null;
}
uri = ProfileUtilities.sdNs(uri, getOverrideVersionNs());
synchronized (lock) {
String version = null;
if (uri.contains("|")) {
version = uri.substring(uri.lastIndexOf("|") + 1);
uri = uri.substring(0, uri.lastIndexOf("|"));
}
if (uri.contains("#")) {
uri = uri.substring(0, uri.indexOf("#"));
}
if (structures.has(uri)) {
return structures.getPackageInfo(uri, version);
}
if (guides.has(uri)) {
return guides.getPackageInfo(uri, version);
}
if (capstmts.has(uri)) {
return capstmts.getPackageInfo(uri, version);
}
if (measures.has(uri)) {
return measures.getPackageInfo(uri, version);
}
if (libraries.has(uri)) {
return libraries.getPackageInfo(uri, version);
}
if (valueSets.has(uri)) {
return valueSets.getPackageInfo(uri, version);
}
if (codeSystems.has(uri)) {
return codeSystems.getPackageInfo(uri, version);
}
if (operations.has(uri)) {
return operations.getPackageInfo(uri, version);
}
if (searchParameters.has(uri)) {
return searchParameters.getPackageInfo(uri, version);
}
if (plans.has(uri)) {
return plans.getPackageInfo(uri, version);
}
if (maps.has(uri)) {
return maps.getPackageInfo(uri, version);
}
if (transforms.has(uri)) {
return transforms.getPackageInfo(uri, version);
}
if (questionnaires.has(uri)) {
return questionnaires.getPackageInfo(uri, version);
}
return null;
}
}
@SuppressWarnings("unchecked")
public T fetchResourceWithException(String cls, String uri, CanonicalResource source)
throws FHIRException {
if (uri == null) {
return null;
}
if ("StructureDefinition".equals(cls)) {
uri = ProfileUtilities.sdNs(uri, getOverrideVersionNs());
}
synchronized (lock) {
String version = null;
if (uri.contains("|")) {
version = uri.substring(uri.lastIndexOf("|") + 1);
uri = uri.substring(0, uri.lastIndexOf("|"));
}
if (uri.contains("#")) {
uri = uri.substring(0, uri.indexOf("#"));
}
if (cls == null || "Resource".equals(cls)) {
if (structures.has(uri)) {
return (T) structures.get(uri, version);
}
if (guides.has(uri)) {
return (T) guides.get(uri, version);
}
if (capstmts.has(uri)) {
return (T) capstmts.get(uri, version);
}
if (measures.has(uri)) {
return (T) measures.get(uri, version);
}
if (libraries.has(uri)) {
return (T) libraries.get(uri, version);
}
if (valueSets.has(uri)) {
return (T) valueSets.get(uri, version);
}
if (codeSystems.has(uri)) {
return (T) codeSystems.get(uri, version);
}
if (operations.has(uri)) {
return (T) operations.get(uri, version);
}
if (searchParameters.has(uri)) {
return (T) searchParameters.get(uri, version);
}
if (plans.has(uri)) {
return (T) plans.get(uri, version);
}
if (maps.has(uri)) {
return (T) maps.get(uri, version);
}
if (transforms.has(uri)) {
return (T) transforms.get(uri, version);
}
if (questionnaires.has(uri)) {
return (T) questionnaires.get(uri, version);
}
for (Map rt : allResourcesById.values()) {
for (ResourceProxy r : rt.values()) {
if (uri.equals(r.getUrl())) {
return (T) r.getResource();
}
}
}
} else if ("ImplementationGuide".equals(cls)) {
return (T) guides.get(uri, version);
} else if ("CapabilityStatement".equals(cls)) {
return (T) capstmts.get(uri, version);
} else if ("Measure".equals(cls)) {
return (T) measures.get(uri, version);
} else if ("Library".equals(cls)) {
return (T) libraries.get(uri, version);
} else if ("StructureDefinition".equals(cls)) {
return (T) structures.get(uri, version);
} else if ("StructureMap".equals(cls)) {
return (T) transforms.get(uri, version);
} else if ("ValueSet".equals(cls)) {
return (T) valueSets.get(uri, version);
} else if ("CodeSystem".equals(cls)) {
return (T) codeSystems.get(uri, version);
} else if ("NamingSystem".equals(cls)) {
return (T) systems.get(uri, version);
} else if ("ConceptMap".equals(cls)) {
return (T) maps.get(uri, version);
} else if ("PlanDefinition".equals(cls)) {
return (T) plans.get(uri, version);
} else if ("OperationDefinition".equals(cls)) {
OperationDefinition od = operations.get(uri, version);
return (T) od;
} else if ("Questionnaire".equals(cls)) {
return (T) questionnaires.get(uri, version);
} else if ("SearchParameter".equals(cls)) {
SearchParameter res = searchParameters.get(uri, version);
return (T) res;
}
if ("CodeSystem".equals(cls) && codeSystems.has(uri)) {
return (T) codeSystems.get(uri, version);
}
if ("ValueSet".equals(cls) && valueSets.has(uri)) {
return (T) valueSets.get(uri, version);
}
if ("Questionnaire".equals(cls)) {
return (T) questionnaires.get(uri, version);
}
if (cls == null) {
if (uri.matches(Constants.URI_REGEX) && !uri.contains("ValueSet")) {
return null;
}
// it might be a special URL.
if (Utilities.isAbsoluteUrl(uri) || uri.startsWith("ValueSet/")) {
Resource res = null; // findTxValueSet(uri);
if (res != null) {
return (T) res;
}
}
return null;
}
if (supportedCodeSystems.contains(uri)) {
return null;
}
throw new FHIRException(formatMessage(I18nConstants.NOT_DONE_YET_CANT_FETCH_, uri));
}
}
private Set notCanonical = new HashSet();
private String overrideVersionNs;
@Override
public Resource fetchResourceById(String type, String uri) {
synchronized (lock) {
String[] parts = uri.split("\\/");
if (!Utilities.noString(type) && parts.length == 1) {
if (allResourcesById.containsKey(type)) {
return allResourcesById.get(type).get(parts[0]).getResource();
} else {
return null;
}
}
if (parts.length >= 2) {
if (!Utilities.noString(type)) {
if (!type.equals(parts[parts.length - 2])) {
throw new Error(formatMessage(I18nConstants.RESOURCE_TYPE_MISMATCH_FOR___, type, uri));
}
}
return allResourcesById.get(parts[parts.length - 2]).get(parts[parts.length - 1]).getResource();
} else {
throw new Error(formatMessage(I18nConstants.UNABLE_TO_PROCESS_REQUEST_FOR_RESOURCE_FOR___, type, uri));
}
}
}
public T fetchResource(Class class_, String uri, CanonicalResource source) {
try {
return fetchResourceWithException(class_, uri, source);
} catch (FHIRException e) {
throw new Error(e);
}
}
public T fetchResource(Class class_, String uri) {
try {
return fetchResourceWithException(class_, uri, null);
} catch (FHIRException e) {
throw new Error(e);
}
}
public T fetchResource(Class class_, String uri, String version) {
try {
return fetchResourceWithException(class_, uri, version, null);
} catch (FHIRException e) {
throw new Error(e);
}
}
@Override
public boolean hasResource(Class class_, String uri) {
try {
return fetchResourceWithException(class_, uri) != null;
} catch (Exception e) {
return false;
}
}
public boolean hasResource(String cls, String uri) {
try {
return fetchResourceWithException(cls, uri) != null;
} catch (Exception e) {
return false;
}
}
public TranslationServices translator() {
return translator;
}
public void setTranslator(TranslationServices translator) {
this.translator = translator;
}
public class NullTranslator implements TranslationServices {
@Override
public String translate(String context, String value, String targetLang) {
return value;
}
@Override
public String translate(String context, String value) {
return value;
}
@Override
public String toStr(float value) {
return null;
}
@Override
public String toStr(Date value) {
return null;
}
@Override
public String translateAndFormat(String contest, String lang, String value, Object... args) {
return String.format(value, args);
}
@Override
public Map translations(String value) {
// TODO Auto-generated method stub
return null;
}
@Override
public Set listTranslations(String category) {
// TODO Auto-generated method stub
return null;
}
}
public void reportStatus(JsonObject json) {
synchronized (lock) {
json.addProperty("codeystem-count", codeSystems.size());
json.addProperty("valueset-count", valueSets.size());
json.addProperty("conceptmap-count", maps.size());
json.addProperty("transforms-count", transforms.size());
json.addProperty("structures-count", structures.size());
json.addProperty("guides-count", guides.size());
json.addProperty("statements-count", capstmts.size());
json.addProperty("measures-count", measures.size());
json.addProperty("libraries-count", libraries.size());
}
}
public void dropResource(Resource r) throws FHIRException {
dropResource(r.fhirType(), r.getId());
}
public void dropResource(String fhirType, String id) {
synchronized (lock) {
Map map = allResourcesById.get(fhirType);
if (map == null) {
map = new HashMap();
allResourcesById.put(fhirType, map);
}
if (map.containsKey(id)) {
map.remove(id); // this is a challenge because we might have more than one resource with this id
// (different versions)
}
if (fhirType.equals("StructureDefinition")) {
structures.drop(id);
} else if (fhirType.equals("ImplementationGuide")) {
guides.drop(id);
} else if (fhirType.equals("CapabilityStatement")) {
capstmts.drop(id);
} else if (fhirType.equals("Measure")) {
measures.drop(id);
} else if (fhirType.equals("Library")) {
libraries.drop(id);
} else if (fhirType.equals("ValueSet")) {
valueSets.drop(id);
} else if (fhirType.equals("CodeSystem")) {
codeSystems.drop(id);
} else if (fhirType.equals("OperationDefinition")) {
operations.drop(id);
} else if (fhirType.equals("Questionnaire")) {
questionnaires.drop(id);
} else if (fhirType.equals("ConceptMap")) {
maps.drop(id);
} else if (fhirType.equals("StructureMap")) {
transforms.drop(id);
} else if (fhirType.equals("NamingSystem")) {
systems.drop(id);
}
}
}
private void dropMetadataResource(Map map, String id) {
T res = map.get(id);
if (res != null) {
map.remove(id);
if (map.containsKey(res.getUrl())) {
map.remove(res.getUrl());
}
if (res.getVersion() != null) {
if (map.containsKey(res.getUrl() + "|" + res.getVersion())) {
map.remove(res.getUrl() + "|" + res.getVersion());
}
}
}
}
@Override
public List allConformanceResources() {
synchronized (lock) {
List result = new ArrayList();
structures.listAllM(result);
guides.listAllM(result);
capstmts.listAllM(result);
measures.listAllM(result);
libraries.listAllM(result);
codeSystems.listAllM(result);
valueSets.listAllM(result);
maps.listAllM(result);
transforms.listAllM(result);
plans.listAllM(result);
questionnaires.listAllM(result);
systems.listAllM(result);
return result;
}
}
public String listSupportedSystems() {
synchronized (lock) {
String sl = null;
for (String s : supportedCodeSystems) {
sl = sl == null ? s : sl + "\r\n" + s;
}
return sl;
}
}
public int totalCount() {
synchronized (lock) {
return valueSets.size() + maps.size() + structures.size() + transforms.size();
}
}
public List listMaps() {
List m = new ArrayList();
synchronized (lock) {
maps.listAll(m);
}
return m;
}
public List listTransforms() {
List m = new ArrayList();
synchronized (lock) {
transforms.listAll(m);
}
return m;
}
public StructureMap getTransform(String code) {
synchronized (lock) {
return transforms.get(code);
}
}
public List listStructures() {
List m = new ArrayList();
synchronized (lock) {
structures.listAll(m);
}
return m;
}
public StructureDefinition getStructure(String code) {
synchronized (lock) {
return structures.get(code);
}
}
@Override
public String oid2Uri(String oid) {
synchronized (lock) {
if (oid != null && oid.startsWith("urn:oid:")) {
oid = oid.substring(8);
}
if (oidCache.containsKey(oid)) {
return oidCache.get(oid);
}
String uri = OIDUtils.getUriForOid(oid);
if (uri != null) {
oidCache.put(oid, uri);
return uri;
}
CodeSystem cs = fetchCodeSystem("http://terminology.hl7.org/CodeSystem/v2-tables");
if (cs != null) {
for (ConceptDefinitionComponent cc : cs.getConcept()) {
for (ConceptPropertyComponent cp : cc.getProperty()) {
if (Utilities.existsInList(cp.getCode(), "v2-table-oid", "v2-cs-oid")
&& oid.equals(cp.getValue().primitiveValue())) {
for (ConceptPropertyComponent cp2 : cc.getProperty()) {
if ("v2-cs-uri".equals(cp2.getCode())) {
oidCache.put(oid, cp2.getValue().primitiveValue());
return cp2.getValue().primitiveValue();
}
}
}
}
}
}
for (CodeSystem css : codeSystems.getList()) {
if (("urn:oid:" + oid).equals(css.getUrl())) {
oidCache.put(oid, css.getUrl());
return css.getUrl();
}
for (Identifier id : css.getIdentifier()) {
if ("urn:ietf:rfc:3986".equals(id.getSystem()) && ("urn:oid:" + oid).equals(id.getValue())) {
oidCache.put(oid, css.getUrl());
return css.getUrl();
}
}
}
for (NamingSystem ns : systems.getList()) {
if (hasOid(ns, oid)) {
uri = getUri(ns);
if (uri != null) {
oidCache.put(oid, null);
return null;
}
}
}
}
oidCache.put(oid, null);
return null;
}
private String getUri(NamingSystem ns) {
for (NamingSystemUniqueIdComponent id : ns.getUniqueId()) {
if (id.getType() == NamingSystemIdentifierType.URI) {
return id.getValue();
}
}
return null;
}
private boolean hasOid(NamingSystem ns, String oid) {
for (NamingSystemUniqueIdComponent id : ns.getUniqueId()) {
if (id.getType() == NamingSystemIdentifierType.OID && id.getValue().equals(oid)) {
return true;
}
}
return false;
}
public void cacheVS(JsonObject json, Map t) {
synchronized (lock) {
validationCache.put(json.get("url").getAsString(), t);
}
}
public SearchParameter getSearchParameter(String code) {
synchronized (lock) {
return searchParameters.get(code);
}
}
@Override
public String getOverrideVersionNs() {
return overrideVersionNs;
}
@Override
public void setOverrideVersionNs(String value) {
overrideVersionNs = value;
}
@Override
public ILoggingService getLogger() {
return logger;
}
@Override
public StructureDefinition fetchTypeDefinition(String typeName) {
if (Utilities.isAbsoluteUrl(typeName)) {
return fetchResource(StructureDefinition.class, typeName);
} else {
return fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/" + typeName);
}
}
public boolean isTlogging() {
return tlogging;
}
public void setTlogging(boolean tlogging) {
this.tlogging = tlogging;
}
public UcumService getUcumService() {
return ucumService;
}
public void setUcumService(UcumService ucumService) {
this.ucumService = ucumService;
}
@Override
public List getStructures() {
List res = new ArrayList<>();
synchronized (lock) { // tricky, because you need to lock this as well, but it's really not in use yet
structures.listAll(res);
}
return res;
}
public String getLinkForUrl(String corePath, String url) {
if (url == null) {
return null;
}
if (codeSystems.has(url)) {
return codeSystems.get(url).getUserString("path");
}
if (valueSets.has(url)) {
return valueSets.get(url).getUserString("path");
}
if (maps.has(url)) {
return maps.get(url).getUserString("path");
}
if (transforms.has(url)) {
return transforms.get(url).getUserString("path");
}
if (structures.has(url)) {
return structures.get(url).getUserString("path");
}
if (guides.has(url)) {
return guides.get(url).getUserString("path");
}
if (capstmts.has(url)) {
return capstmts.get(url).getUserString("path");
}
if (measures.has(url)) {
return measures.get(url).getUserString("path");
}
if (libraries.has(url)) {
return libraries.get(url).getUserString("path");
}
if (searchParameters.has(url)) {
return searchParameters.get(url).getUserString("path");
}
if (questionnaires.has(url)) {
return questionnaires.get(url).getUserString("path");
}
if (operations.has(url)) {
return operations.get(url).getUserString("path");
}
if (plans.has(url)) {
return plans.get(url).getUserString("path");
}
if (url.equals("http://loinc.org")) {
return corePath + "loinc.html";
}
if (url.equals("http://unitsofmeasure.org")) {
return corePath + "ucum.html";
}
if (url.equals("http://snomed.info/sct")) {
return corePath + "snomed.html";
}
return null;
}
public List allImplementationGuides() {
List res = new ArrayList<>();
guides.listAll(res);
return res;
}
@Override
public Map getBinaries() {
return binaries;
}
public void finishLoading() {
for (StructureDefinition sd : listStructures()) {
try {
if (sd.getSnapshot().isEmpty()) {
generateSnapshot(sd);
// new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(Utilities.path("[tmp]", "snapshot", tail(sd.getUrl())+".xml")), sd);
}
} catch (Exception e) {
// System.out.println("Unable to generate snapshot for "+tail(sd.getUrl()) +" from "+tail(sd.getBaseDefinition())+" because "+e.getMessage());
}
}
}
protected String tail(String url) {
if (Utilities.noString(url)) {
return "noname";
}
if (url.contains("/")) {
return url.substring(url.lastIndexOf("/") + 1);
}
return url;
}
public int getClientRetryCount() {
return txClient == null ? 0 : txClient.getRetryCount();
}
public IWorkerContext setClientRetryCount(int value) {
if (txClient != null) {
txClient.setRetryCount(value);
}
return this;
}
public String getTxCache() {
return txCache.getFolder();
}
public TerminologyClient getTxClient() {
return txClient;
}
public String getCacheId() {
return cacheId;
}
public void setCacheId(String cacheId) {
this.cacheId = cacheId;
}
public TerminologyCapabilities getTxCaps() {
return txcaps;
}
public void setTxCaps(TerminologyCapabilities txCaps) {
this.txcaps = txCaps;
if (txCaps != null) {
for (TerminologyCapabilitiesExpansionParameterComponent t : txcaps.getExpansion().getParameter()) {
if ("cache-id".equals(t.getName())) {
isTxCaching = true;
}
}
for (TerminologyCapabilitiesCodeSystemComponent tccs : txcaps.getCodeSystem()) {
supportedCodeSystems.add(tccs.getUri());
}
}
}
public TimeTracker clock() {
return clock;
}
public int countAllCaches() {
return codeSystems.size() + valueSets.size() + maps.size() + transforms.size() + structures.size() + measures.size()
+ libraries.size() + guides.size() + capstmts.size() + searchParameters.size() + questionnaires.size()
+ operations.size() + plans.size() + systems.size();
}
public Set getCodeSystemsUsed() {
return codeSystemsUsed;
}
public String getSpecUrl() {
String v = getVersion();
switch (VersionUtilities.getMajMin(v)) {
case "1.0":
return "http://hl7.org/fhir/DSTU1";
case "1.4":
return "http://hl7.org/fhir/DSTU2";
case "3.0":
return "http://hl7.org/fhir/STU3";
case "4.0":
return "http://hl7.org/fhir/R4";
case "4.5":
return "http://build.fhir.org";
case "5.0":
return "http://build.fhir.org";
default:
return "http://hl7.org/fhir";
}
}
public ICanonicalResourceLocator getLocator() {
return locator;
}
public void setLocator(ICanonicalResourceLocator locator) {
this.locator = locator;
}
public String getUserAgent() {
return userAgent;
}
public void setUserAgent(String userAgent) {
this.userAgent = userAgent;
if (txClient != null)
txClient.setUserAgent(userAgent);
}
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