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Significant improvement to performance rendering value sets, and only use server side caching if the server declares it supports it

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This commit is contained in:
Grahame Grieve 2020-08-14 08:09:02 +10:00
parent 7021969ea2
commit 7771c7f231
5 changed files with 82 additions and 38 deletions
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2
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/VersionConvertor_10_50.java
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@ -3439,6 +3439,8 @@ public class VersionConvertor_10_50 {
for (ParametersParameterComponent p : src.getParameter()) {
if (p.getName().equals("system"))
res.addCodeSystem().setUri(p.getValue().primitiveValue());
if (p.getName().equals("expansion.parameter"))
res.getExpansion().addParameter().setName(p.getValue().primitiveValue());
}
return res;
}

2
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/VersionConvertor_30_50.java
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@ -5539,6 +5539,8 @@ public class VersionConvertor_30_50 {
for (ParametersParameterComponent p : src.getParameter()) {
if (p.getName().equals("system"))
res.addCodeSystem().setUri(p.getValue().primitiveValue());
if (p.getName().equals("expansion.parameter"))
res.getExpansion().addParameter().setName(p.getValue().primitiveValue());
}
return res;
}

40
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/context/BaseWorkerContext.java
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@ -90,6 +90,7 @@ import org.hl7.fhir.r5.model.StructureDefinition.TypeDerivationRule;
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.TerminologyCapabilities.TerminologyCapabilitiesExpansionParameterComponent;
import org.hl7.fhir.r5.model.UriType;
import org.hl7.fhir.r5.model.ValueSet;
import org.hl7.fhir.r5.model.Bundle.BundleEntryComponent;
@ -156,6 +157,7 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
private Object lock = new Object(); // used as a lock for the data that follows
protected String version;
private String cacheId;
private boolean isTxCaching;
private Set<String> cached = new HashSet<>();
private Map<String, Map<String, Resource>> allResourcesById = new HashMap<String, Map<String, Resource>>();
@ -504,7 +506,7 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
if (txcaps == null) {
try {
log("Terminology server: Check for supported code systems for "+system);
txcaps = txClient.getTerminologyCapabilities();
setTxCaps(txClient.getTerminologyCapabilities());
} catch (Exception e) {
if (canRunWithoutTerminology) {
noTerminologyServer = true;
@ -520,11 +522,6 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
throw new TerminologyServiceException(e);
}
}
if (txcaps != null) {
for (TerminologyCapabilitiesCodeSystemComponent tccs : txcaps.getCodeSystem()) {
supportedCodeSystems.add(tccs.getUri());
}
}
if (supportedCodeSystems.contains(system)) {
return true;
}
@ -588,7 +585,7 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
Parameters p = expParameters.copy();
p.setParameter("includeDefinition", false);
p.setParameter("excludeNested", !hierarchical);
if (cacheId != null) {
if (isTxCaching && cacheId != null) {
p.addParameter().setName("cache-id").setValue(new StringType(cacheId));
}
addDependentResources(p, vs);
@ -663,7 +660,7 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
}
// if that failed, we try to expand on the server
if (cacheId != null) {
if (isTxCaching && cacheId != null) {
p.addParameter().setName("cache-id").setValue(new StringType(cacheId));
}
addDependentResources(p, vs);
@ -927,11 +924,11 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
}
private ValidationResult validateOnServer(ValueSet vs, Parameters pin) throws FHIRException {
if (cacheId != null) {
if (isTxCaching && cacheId != null) {
pin.addParameter().setName("cache-id").setValue(new StringType(cacheId));
}
if (vs != null) {
if (cacheId != null && cached.contains(vs.getUrl()+"|"+vs.getVersion())) {
if (isTxCaching && cacheId != null && cached.contains(vs.getUrl()+"|"+vs.getVersion())) {
pin.addParameter().setName("url").setValue(new UriType(vs.getUrl()+"|"+vs.getVersion()));
} else {
pin.addParameter().setName("valueSet").setResource(vs);
@ -976,7 +973,7 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
for (CanonicalType c : inc.getValueSet()) {
ValueSet vs = fetchResource(ValueSet.class, c.getValue());
if (vs != null) {
if (cacheId == null || !cached.contains(vs.getVUrl())) {
if (isTxCaching && cacheId == null || !cached.contains(vs.getVUrl())) {
pin.addParameter().setName("tx-resource").setResource(vs);
cached.add(vs.getVUrl());
}
@ -985,7 +982,7 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
}
CodeSystem cs = fetchResource(CodeSystem.class, inc.getSystem());
if (cs != null) {
if (cacheId == null || !cached.contains(cs.getVUrl())) {
if (isTxCaching && cacheId == null || !cached.contains(cs.getVUrl())) {
pin.addParameter().setName("tx-resource").setResource(cs);
cached.add(cs.getVUrl());
}
@ -1859,4 +1856,23 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
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());
}
}
}
}

5
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/context/SimpleWorkerContext.java
View File

@ -63,6 +63,7 @@ import org.hl7.fhir.r5.formats.XmlParser;
import org.hl7.fhir.r5.model.Bundle;
import org.hl7.fhir.r5.model.Bundle.BundleEntryComponent;
import org.hl7.fhir.r5.model.CanonicalResource;
import org.hl7.fhir.r5.model.CapabilityStatement;
import org.hl7.fhir.r5.model.ElementDefinition.ElementDefinitionBindingComponent;
import org.hl7.fhir.r5.model.Questionnaire;
import org.hl7.fhir.r5.model.Resource;
@ -293,7 +294,9 @@ public class SimpleWorkerContext extends BaseWorkerContext implements IWorkerCon
txLog = new HTMLClientLogger(log);
}
txClient.setLogger(txLog);
return txClient.getCapabilitiesStatementQuick().getSoftware().getVersion();
CapabilityStatement cps = txClient.getCapabilitiesStatementQuick();
setTxCaps(txClient.getTerminologyCapabilities());
return cps.getSoftware().getVersion();
} catch (Exception e) {
throw new FHIRException(formatMessage(I18nConstants.UNABLE_TO_CONNECT_TO_TERMINOLOGY_SERVER_USE_PARAMETER_TX_NA_TUN_RUN_WITHOUT_USING_TERMINOLOGY_SERVICES_TO_VALIDATE_LOINC_SNOMED_ICDX_ETC_ERROR__, e.getMessage()), e);
}

71
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/renderers/ValueSetRenderer.java
View File

@ -6,17 +6,23 @@ import java.text.SimpleDateFormat;
import java.util.ArrayList;
import java.util.Collections;
import java.util.Date;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
import org.hl7.fhir.exceptions.DefinitionException;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.exceptions.TerminologyServiceException;
import org.hl7.fhir.r5.context.IWorkerContext.CodingValidationRequest;
import org.hl7.fhir.r5.context.IWorkerContext.ValidationResult;
import org.hl7.fhir.r5.model.BooleanType;
import org.hl7.fhir.r5.model.CanonicalResource;
import org.hl7.fhir.r5.model.CodeSystem;
import org.hl7.fhir.r5.model.CodeSystem.ConceptDefinitionComponent;
import org.hl7.fhir.r5.model.Coding;
import org.hl7.fhir.r5.model.ConceptMap;
import org.hl7.fhir.r5.model.DataType;
import org.hl7.fhir.r5.model.DomainResource;
@ -182,7 +188,7 @@ public class ValueSetRenderer extends TerminologyRenderer {
p.addText(" and may be missing codes, or include codes that are not valid");
}
}
generateVersionNotice(x, vs.getExpansion());
CodeSystem allCS = null;
@ -737,6 +743,9 @@ public class ValueSetRenderer extends TerminologyRenderer {
li.code(inc.getVersion());
}
// for performance reasons, we do all the fetching in one batch
Map<String, ConceptDefinitionComponent> definitions = getConceptsForCodes(e, inc);
XhtmlNode t = li.table("none");
boolean hasComments = false;
boolean hasDefinition = false;
@ -750,7 +759,7 @@ public class ValueSetRenderer extends TerminologyRenderer {
for (ConceptReferenceComponent c : inc.getConcept()) {
XhtmlNode tr = t.tr();
XhtmlNode td = tr.td();
ConceptDefinitionComponent cc = getConceptForCode(e, c.getCode(), inc);
ConceptDefinitionComponent cc = definitions.get(c.getCode());
addCodeToTable(false, inc.getSystem(), c.getCode(), c.hasDisplay()? c.getDisplay() : cc != null ? cc.getDisplay() : "", td);
td = tr.td();
@ -844,24 +853,13 @@ public class ValueSetRenderer extends TerminologyRenderer {
}
private ConceptDefinitionComponent getConceptForCode(CodeSystem e, String code, ConceptSetComponent inc) {
if (code == null) {
return null;
private Map<String, ConceptDefinitionComponent> getConceptsForCodes(CodeSystem e, ConceptSetComponent inc) {
if (e == null) {
e = getContext().getWorker().fetchCodeSystem(inc.getSystem());
}
// first, look in the code systems
if (e == null)
e = getContext().getWorker().fetchCodeSystem(inc.getSystem());
if (e != null) {
ConceptDefinitionComponent v = getConceptForCode(e.getConcept(), code);
if (v != null)
return v;
}
if (context.isNoSlowLookup())
return null;
if (!getContext().getWorker().hasCache()) {
ValueSetExpansionComponent vse;
ValueSetExpansionComponent vse = null;
if (!context.isNoSlowLookup() && !getContext().getWorker().hasCache()) {
try {
ValueSetExpansionOutcome vso = getContext().getWorker().expandVS(inc, false);
ValueSet valueset = vso.getValueset();
@ -872,16 +870,39 @@ public class ValueSetRenderer extends TerminologyRenderer {
} catch (TerminologyServiceException e1) {
return null;
}
if (vse != null) {
ConceptDefinitionComponent v = getConceptForCodeFromExpansion(vse.getContains(), code);
if (v != null)
return v;
}
Map<String, ConceptDefinitionComponent> results = new HashMap<>();
List<CodingValidationRequest> serverList = new ArrayList<>();
// 1st pass, anything we can resolve internally
for (ConceptReferenceComponent cc : inc.getConcept()) {
String code = cc.getCode();
ConceptDefinitionComponent v = null;
if (e != null) {
v = getConceptForCode(e.getConcept(), code);
}
if (v == null && vse != null) {
v = getConceptForCodeFromExpansion(vse.getContains(), code);
}
if (v != null) {
results.put(code, v);
} else {
serverList.add(new CodingValidationRequest(new Coding(inc.getSystem(), code, null)));
}
}
return getContext().getWorker().validateCode(getContext().getTerminologyServiceOptions(), inc.getSystem(), code, null).asConceptDefinition();
if (!context.isNoSlowLookup() && !serverList.isEmpty()) {
getContext().getWorker().validateCodeBatch(getContext().getTerminologyServiceOptions(), serverList, null);
for (CodingValidationRequest vr : serverList) {
ConceptDefinitionComponent v = vr.getResult().asConceptDefinition();
if (v != null) {
results.put(vr.getCoding().getCode(), v);
}
}
}
return results;
}
private ConceptDefinitionComponent getConceptForCode(List<ConceptDefinitionComponent> list, String code) {
for (ConceptDefinitionComponent c : list) {
if (code.equals(c.getCode()))