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hhundhhund
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workaround for adding missing codes to expanded ValueSet
Fixes error with ValueSets https://www.netzwerk-universitaetsmedizin.de/fhir/ValueSet/rheumatological-immunological-diseases and https://www.netzwerk-universitaetsmedizin.de/fhir/ValueSet/vaccines-snomed
1 parent 19aa267 commit f27bb7b

5 files changed

Lines changed: 284 additions & 32 deletions

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‎codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/spring/config/ValidationConfig.java‎

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Original file line numberDiff line numberDiff line change
@@ -55,7 +55,9 @@
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import de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.validation.ValueSetExpansionClient;
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import de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.validation.ValueSetExpansionClientJersey;
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import de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.validation.ValueSetExpansionClientWithFileSystemCache;
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import de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.validation.ValueSetExpansionClientWithModifiers;
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import de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.validation.structure_definition.StructureDefinitionModifier;
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import de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.validation.value_set.ValueSetModifier;
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import de.rwh.utils.crypto.CertificateHelper;
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import de.rwh.utils.crypto.io.CertificateReader;
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import de.rwh.utils.crypto.io.PemIo;
@@ -198,6 +200,12 @@ public static enum TerminologyServerConnectionTestStatus
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@Value("${de.netzwerk.universitaetsmedizin.codex.gecco.validation.valueset.expansion.client.verbose:false}")
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private boolean valueSetExpansionClientVerbose;
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@ProcessDocumentation(description = "List of ValueSet modifier classes, modifiers are executed before atempting to expand a ValueSet and after", processNames = "wwwnetzwerk-universitaetsmedizinde_dataSend")
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@Value("#{'${de.netzwerk.universitaetsmedizin.codex.gecco.validation.valueset.expansion.modifierClasses:"
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+ "de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.validation.value_set.MissingEntriesIncluder"
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+ "}'.trim().split('(,[ ]?)|(\\n)')}")
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private List<String> valueSetModifierClasses;
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@ProcessDocumentation(description = "List of StructureDefinition modifier classes, modifiers are executed before atempting to generate a StructureDefinition snapshot", processNames = "wwwnetzwerk-universitaetsmedizinde_dataSend")
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@Value("#{'${de.netzwerk.universitaetsmedizin.codex.gecco.validation.structuredefinition.modifierClasses:"
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+ "de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.validation.structure_definition.ClosedTypeSlicingRemover,"
@@ -410,8 +418,29 @@ private ValidationPackageClientJersey validationPackageClientJersey()
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@Bean
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public ValueSetExpansionClient valueSetExpansionClient()
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{
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List<ValueSetModifier> modifiers = valueSetModifierClasses.stream().map(this::createValueSetModifier)
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.collect(Collectors.toList());
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return new ValueSetExpansionClientWithFileSystemCache(valueSetCacheFolder(), fhirContext,
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valueSetExpansionClientJersey());
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new ValueSetExpansionClientWithModifiers(valueSetExpansionClientJersey(), modifiers));
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}
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private ValueSetModifier createValueSetModifier(String className)
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{
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try
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{
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Class<?> modifierClass = Class.forName(className);
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if (ValueSetModifier.class.isAssignableFrom(modifierClass))
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return (ValueSetModifier) modifierClass.getConstructor().newInstance();
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else
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throw new IllegalArgumentException(
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"Class " + className + " not compatible with " + ValueSetModifier.class.getName());
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}
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catch (ClassNotFoundException | InstantiationException | IllegalAccessException | InvocationTargetException
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| NoSuchMethodException | SecurityException e)
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{
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throw new RuntimeException(e);
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}
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}
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@Bean

‎codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/validation/ValueSetExpansionClientWithModifiers.java‎

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Original file line numberDiff line numberDiff line change
@@ -0,0 +1,68 @@
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package de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.validation;
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import java.io.IOException;
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import java.util.ArrayList;
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import java.util.Arrays;
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import java.util.Collection;
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import java.util.List;
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import java.util.Objects;
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import javax.ws.rs.WebApplicationException;
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import org.hl7.fhir.r4.model.CapabilityStatement;
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import org.hl7.fhir.r4.model.ValueSet;
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import org.springframework.beans.factory.InitializingBean;
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import de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.validation.value_set.MissingEntriesIncluder;
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import de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.validation.value_set.ValueSetModifier;
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public class ValueSetExpansionClientWithModifiers implements ValueSetExpansionClient, InitializingBean
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{
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public static final ValueSetModifier MISSING_ENTRIES_INCLUDER = new MissingEntriesIncluder();
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private final ValueSetExpansionClient delegate;
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private final List<ValueSetModifier> valueSetModifiers = new ArrayList<>();
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public ValueSetExpansionClientWithModifiers(ValueSetExpansionClient delegate)
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{
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this(delegate, Arrays.asList(MISSING_ENTRIES_INCLUDER));
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}
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public ValueSetExpansionClientWithModifiers(ValueSetExpansionClient delegate,
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Collection<? extends ValueSetModifier> valueSetModifiers)
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{
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this.delegate = delegate;
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if (valueSetModifiers != null)
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this.valueSetModifiers.addAll(valueSetModifiers);
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}
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@Override
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public void afterPropertiesSet() throws Exception
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{
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Objects.requireNonNull(delegate, "delegate");
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}
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@Override
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public ValueSet expand(ValueSet valueSet) throws IOException, WebApplicationException
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{
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if (valueSet == null)
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return null;
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for (ValueSetModifier modifier : valueSetModifiers)
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valueSet = modifier.modifyPreExpansion(valueSet);
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ValueSet expandedValueSet = delegate.expand(valueSet);
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for (ValueSetModifier modifier : valueSetModifiers)
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expandedValueSet = modifier.modifyPostExpansion(valueSet, expandedValueSet);
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return expandedValueSet;
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}
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@Override
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public CapabilityStatement getMetadata() throws WebApplicationException
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{
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return delegate.getMetadata();
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}
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}

‎codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/validation/value_set/MissingEntriesIncluder.java‎

Lines changed: 69 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,69 @@
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package de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.validation.value_set;
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import java.util.Set;
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import java.util.stream.Collectors;
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import java.util.stream.Stream;
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import org.hl7.fhir.r4.model.ValueSet;
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import org.hl7.fhir.r4.model.ValueSet.ConceptSetComponent;
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import org.hl7.fhir.r4.model.ValueSet.ValueSetExpansionContainsComponent;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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public class MissingEntriesIncluder implements ValueSetModifier
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{
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private static final Logger logger = LoggerFactory.getLogger(MissingEntriesIncluder.class);
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@Override
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public ValueSet modifyPostExpansion(ValueSet vsWithComposition, ValueSet vsWithExpansion)
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{
20+
if (vsWithExpansion == null)
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return null;
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if (!vsWithExpansion.hasExpansion())
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return vsWithExpansion;
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if (vsWithComposition.hasCompose()
26+
&& vsWithComposition.getCompose().getInclude().stream().anyMatch(ConceptSetComponent::hasConcept))
27+
{
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Set<String> expandedEntries = vsWithExpansion.getExpansion().getContains().stream()
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.map(c -> toEntry(c.getSystem(), c.getVersion(), c.getCode())).distinct()
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.collect(Collectors.toSet());
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32+
vsWithComposition.getCompose().getInclude().stream().filter(ConceptSetComponent::hasConcept)
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.forEach(include ->
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{
35+
String system = include.getSystem();
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String version = include.getVersion();
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include.getConcept().forEach(concept ->
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{
40+
if (!expandedEntries.contains(toEntry(system, version, concept.getCode())))
41+
{
42+
if (version != null)
43+
logger.warn(
44+
"Adding missing concept to ValueSet {}|{}: system: '{}', version: '{}', code: '{}', display: '{}'",
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vsWithExpansion.getUrl(), vsWithExpansion.getVersion(), system, version,
46+
concept.getCode(), concept.getDisplay());
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else
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logger.warn(
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"Adding missing concept to ValueSet {}|{}: system: '{}', code: '{}', display: '{}'",
50+
vsWithExpansion.getUrl(), vsWithExpansion.getVersion(), system,
51+
concept.getCode(), concept.getDisplay());
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vsWithExpansion.getExpansion()
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.addContains(new ValueSetExpansionContainsComponent().setSystem(system)
55+
.setVersion(version).setCode(concept.getCode())
56+
.setDisplay(concept.getDisplay()));
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}
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});
59+
});
60+
}
61+
62+
return vsWithExpansion;
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}
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private String toEntry(String system, String version, String code)
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{
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return Stream.of(system, version, code).filter(e -> e != null).collect(Collectors.joining());
68+
}
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}

‎codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/validation/value_set/ValueSetModifier.java‎

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@@ -0,0 +1,16 @@
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package de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.validation.value_set;
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import org.hl7.fhir.r4.model.ValueSet;
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public interface ValueSetModifier
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{
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default ValueSet modifyPreExpansion(ValueSet vs)
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{
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return vs;
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}
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default ValueSet modifyPostExpansion(ValueSet vsWithComposition, ValueSet vsWithExpansion)
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{
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return vsWithExpansion;
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}
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}

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