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Batch validation of codes in value sets

This commit is contained in:
Grahame Grieve 2020-07-30 11:57:11 +10:00
parent a154f454b4
commit ea52c4206f
7 changed files with 230 additions and 9 deletions
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11
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/txClient/TerminologyClientR2.java
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@ -35,8 +35,10 @@ import java.net.URISyntaxException;
import java.util.Map;
import org.hl7.fhir.convertors.VersionConvertor_10_50;
import org.hl7.fhir.convertors.VersionConvertor_40_50;
import org.hl7.fhir.dstu2.utils.client.FHIRToolingClient;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r5.model.Bundle;
import org.hl7.fhir.r5.model.CapabilityStatement;
import org.hl7.fhir.r5.model.Parameters;
import org.hl7.fhir.r5.model.TerminologyCapabilities;
@ -116,6 +118,11 @@ public class TerminologyClientR2 implements TerminologyClient {
public int getRetryCount() throws FHIRException {
return client.getRetryCount();
}
@Override
public Bundle validateBatch(Bundle batch) {
return (Bundle) VersionConvertor_10_50.convertResource(client.transaction((org.hl7.fhir.dstu2.model.Bundle) VersionConvertor_10_50.convertResource(batch)));
}
}

10
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/txClient/TerminologyClientR3.java
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@ -35,8 +35,10 @@ import java.net.URISyntaxException;
import java.util.Map;
import org.hl7.fhir.convertors.VersionConvertor_30_50;
import org.hl7.fhir.convertors.VersionConvertor_40_50;
import org.hl7.fhir.dstu3.utils.client.FHIRToolingClient;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r5.model.Bundle;
import org.hl7.fhir.r5.model.CapabilityStatement;
import org.hl7.fhir.r5.model.Parameters;
import org.hl7.fhir.r5.model.TerminologyCapabilities;
@ -116,5 +118,11 @@ public class TerminologyClientR3 implements TerminologyClient {
public int getRetryCount() throws FHIRException {
return client.getRetryCount();
}
@Override
public Bundle validateBatch(Bundle batch) {
return (Bundle) VersionConvertor_30_50.convertResource(client.transaction((org.hl7.fhir.dstu3.model.Bundle) VersionConvertor_30_50.convertResource(batch, false)), false);
}
}

8
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/txClient/TerminologyClientR4.java
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@ -38,6 +38,7 @@ import org.hl7.fhir.convertors.VersionConvertor_40_50;
import org.hl7.fhir.convertors.conv40_50.TerminologyCapabilities40_50;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r4.utils.client.FHIRToolingClient;
import org.hl7.fhir.r5.model.Bundle;
import org.hl7.fhir.r5.model.CapabilityStatement;
import org.hl7.fhir.r5.model.Parameters;
import org.hl7.fhir.r5.model.TerminologyCapabilities;
@ -117,5 +118,10 @@ public class TerminologyClientR4 implements TerminologyClient {
public int getRetryCount() throws FHIRException {
return client.getRetryCount();
}
@Override
public Bundle validateBatch(Bundle batch) {
return (Bundle) VersionConvertor_40_50.convertResource(client.transaction((org.hl7.fhir.r4.model.Bundle) VersionConvertor_40_50.convertResource(batch)));
}
}

6
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/txClient/TerminologyClientR5.java
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@ -35,6 +35,7 @@ import java.net.URISyntaxException;
import java.util.Map;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r5.model.Bundle;
import org.hl7.fhir.r5.model.CapabilityStatement;
import org.hl7.fhir.r5.model.CodeSystem;
import org.hl7.fhir.r5.model.Parameters;
@ -110,4 +111,9 @@ public class TerminologyClientR5 implements TerminologyClient {
return client.getRetryCount();
}
@Override
public Bundle validateBatch(Bundle batch) {
return client.transaction(batch);
}
}

103
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/context/BaseWorkerContext.java
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@ -55,6 +55,7 @@ import org.hl7.fhir.r5.context.CanonicalResourceManager.CanonicalResourceProxy;
import org.hl7.fhir.r5.context.IWorkerContext.ILoggingService.LogCategory;
import org.hl7.fhir.r5.context.TerminologyCache.CacheToken;
import org.hl7.fhir.r5.model.BooleanType;
import org.hl7.fhir.r5.model.Bundle;
import org.hl7.fhir.r5.model.CanonicalResource;
import org.hl7.fhir.r5.model.CapabilityStatement;
import org.hl7.fhir.r5.model.CodeSystem;
@ -88,6 +89,8 @@ import org.hl7.fhir.r5.model.StructureMap;
import org.hl7.fhir.r5.model.TerminologyCapabilities;
import org.hl7.fhir.r5.model.TerminologyCapabilities.TerminologyCapabilitiesCodeSystemComponent;
import org.hl7.fhir.r5.model.ValueSet;
import org.hl7.fhir.r5.model.Bundle.BundleEntryComponent;
import org.hl7.fhir.r5.model.Bundle.BundleType;
import org.hl7.fhir.r5.model.ValueSet.ConceptSetComponent;
import org.hl7.fhir.r5.model.ValueSet.ValueSetComposeComponent;
import org.hl7.fhir.r5.terminologies.CodeSystemUtilities;
@ -111,6 +114,8 @@ import org.hl7.fhir.utilities.validation.ValidationOptions.ValueSetMode;
import com.google.gson.JsonObject;
import ca.uhn.fhir.model.valueset.BundleEntrySearchModeEnum;
public abstract class BaseWorkerContext extends I18nBase implements IWorkerContext{
public class MetadataResourceVersionComparator<T extends CanonicalResource> implements Comparator<T> {
@ -685,10 +690,99 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
return validateCode(options.guessSystem(), c, vs);
}
@Override
public void validateCodeBatch(ValidationOptions options, List<? extends CodingValidationRequest> 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 (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()) {
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(t.getCoding().getSystem())) {
t.setResult(new ValidationResult(IssueSeverity.ERROR,formatMessage(I18nConstants.TERMINOLOGY_TX_SYSTEM_NOTKNOWN, t.getCoding().getSystem()), TerminologyServiceErrorClass.CODESYSTEM_UNSUPPORTED));
} else if (noTerminologyServer) {
t.setResult(new ValidationResult(IssueSeverity.ERROR,formatMessage(I18nConstants.ERROR_VALIDATING_CODE_RUNNING_WITHOUT_TERMINOLOGY_SERVICES), 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<String> 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("implySystem").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().setUrl("ValueSet/$validate-code");
be.setUserData("source", t);
systems.add(t.getCoding().getSystem());
}
}
if (batch.getEntry().size() > 0) {
tlog("$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.getResponse().getStatus().startsWith("2")) {
t.setResult(new ValidationResult(IssueSeverity.ERROR, getResponseText(r.getResource())).setTxLink(txLog == null ? null : txLog.getLastId()));
} else {
t.setResult(processValidationResult((Parameters) r.getResource()));
}
}
}
}
private String getResponseText(Resource resource) {
return "Todo";
}
@Override
public ValidationResult validateCode(ValidationOptions options, Coding code, ValueSet vs) {
assert options != null;
if (options == null) {
options = ValidationOptions.defaults();
}
@ -813,6 +907,10 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
pOut = txClient.validateCS(pin);
else
pOut = txClient.validateVS(pin);
return processValidationResult(pOut);
}
public ValidationResult processValidationResult(Parameters pOut) {
boolean ok = false;
String message = "No Message returned";
String display = null;
@ -1622,4 +1720,5 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
return txClient;
}
}

51
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/context/IWorkerContext.java
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@ -44,6 +44,8 @@ import org.fhir.ucum.UcumService;
import org.hl7.fhir.exceptions.DefinitionException;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.TerminologyServiceException;
import org.hl7.fhir.r5.context.IWorkerContext.CodingValidationRequest;
import org.hl7.fhir.r5.context.TerminologyCache.CacheToken;
import org.hl7.fhir.r5.formats.IParser;
import org.hl7.fhir.r5.formats.ParserType;
import org.hl7.fhir.r5.model.Bundle;
@ -93,6 +95,53 @@ import com.google.gson.JsonSyntaxException;
*/
public interface IWorkerContext {
public class CodingValidationRequest {
private Coding coding;
private ValidationResult result;
private CacheToken cacheToken;
public CodingValidationRequest(Coding coding) {
super();
this.coding = coding;
}
public ValidationResult getResult() {
return result;
}
public void setResult(ValidationResult result) {
this.result = result;
}
public Coding getCoding() {
return coding;
}
public boolean hasResult() {
return result != null;
}
/**
* internal logic; external users of batch validation should ignore this property
*
* @return
*/
public CacheToken getCacheToken() {
return cacheToken;
}
/**
* internal logic; external users of batch validation should ignore this property
*
* @param cacheToken
*/
public void setCacheToken(CacheToken cacheToken) {
this.cacheToken = cacheToken;
}
}
public class PackageVersion {
private String id;
private String version;
@ -619,6 +668,8 @@ public interface IWorkerContext {
* @return
*/
public ValidationResult validateCode(ValidationOptions options, Coding code, ValueSet vs);
public void validateCodeBatch(ValidationOptions options, List<? extends CodingValidationRequest> codes, ValueSet vs);
/**
* returns the recommended tla for the type (from the structure definitions)

50
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/type/ValueSetValidator.java
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@ -1,9 +1,11 @@
package org.hl7.fhir.validation.instance.type;
import java.util.ArrayList;
import java.util.List;
import org.hl7.fhir.r5.model.ValueSet;
import org.hl7.fhir.r5.context.IWorkerContext;
import org.hl7.fhir.r5.context.IWorkerContext.CodingValidationRequest;
import org.hl7.fhir.r5.context.IWorkerContext.ValidationResult;
import org.hl7.fhir.r5.elementmodel.Element;
import org.hl7.fhir.r5.model.CodeSystem;
@ -19,10 +21,26 @@ import org.hl7.fhir.utilities.validation.ValidationMessage.Source;
import org.hl7.fhir.utilities.validation.ValidationOptions;
import org.hl7.fhir.validation.BaseValidator;
import org.hl7.fhir.validation.TimeTracker;
import org.hl7.fhir.validation.instance.type.ValueSetValidator.VSCodingValidationRequest;
import org.hl7.fhir.validation.instance.utils.NodeStack;
public class ValueSetValidator extends BaseValidator {
public class VSCodingValidationRequest extends CodingValidationRequest {
private NodeStack stack;
public VSCodingValidationRequest(NodeStack stack, Coding code) {
super(code);
this.stack = stack;
}
public NodeStack getStack() {
return stack;
}
}
public ValueSetValidator(IWorkerContext context, TimeTracker timeTracker) {
super(context);
source = Source.InstanceValidator;
@ -58,7 +76,6 @@ public class ValueSetValidator extends BaseValidator {
private void validateValueSetInclude(List<ValidationMessage> errors, Element include, NodeStack stack) {
String system = include.getChildValue("system");
String version = include.getChildValue("version");
boolean systemOk = true;
List<Element> valuesets = include.getChildrenByName("valueSet");
int i = 0;
for (Element ve : valuesets) {
@ -79,13 +96,31 @@ public class ValueSetValidator extends BaseValidator {
List<Element> concepts = include.getChildrenByName("concept");
List<Element> filters = include.getChildrenByName("filter");
if (!Utilities.noString(system)) {
boolean systemOk = true;
int cc = 0;
List<VSCodingValidationRequest> batch = new ArrayList<>();
boolean first = true;
for (Element concept : concepts) {
if (systemOk && !validateValueSetIncludeConcept(errors, concept, stack.push(concept, cc, null, null), system, version)) {
systemOk = false;
// we treat the first differently because we want to know if tbe system is worth validating. if it is, then we batch the rest
if (first) {
systemOk = validateValueSetIncludeConcept(errors, concept, stack.push(concept, cc, null, null), system, version);
first = false;
} else if (systemOk) {
batch.add(prepareValidateValueSetIncludeConcept(errors, concept, stack.push(concept, cc, null, null), system, version));
}
cc++;
}
if (batch.size() > 0) {
context.validateCodeBatch(ValidationOptions.defaults(), batch, null);
for (VSCodingValidationRequest cv : batch) {
if (version == null) {
warning(errors, IssueType.BUSINESSRULE, cv.getStack().getLiteralPath(), cv.getResult().isOk(), I18nConstants.VALUESET_INCLUDE_INVALID_CONCEPT_CODE, system, cv.getCoding().getCode());
} else {
warning(errors, IssueType.BUSINESSRULE, cv.getStack().getLiteralPath(), cv.getResult().isOk(), I18nConstants.VALUESET_INCLUDE_INVALID_CONCEPT_CODE_VER, system, version, cv.getCoding().getCode());
}
}
}
int cf = 0;
for (Element filter : filters) {
if (systemOk && !validateValueSetIncludeFilter(errors, include, stack.push(filter, cf, null, null), system, version)) {
@ -121,6 +156,15 @@ public class ValueSetValidator extends BaseValidator {
return true;
}
private VSCodingValidationRequest prepareValidateValueSetIncludeConcept(List<ValidationMessage> errors, Element concept, NodeStack stack, String system, String version) {
String code = concept.getChildValue("code");
Coding c = new Coding(system, code, null);
if (version != null) {
c.setVersion(version);
}
return new VSCodingValidationRequest(stack, c);
}
private boolean validateValueSetIncludeFilter(List<ValidationMessage> errors, Element include, NodeStack push, String system, String version) {
return true;
}