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Change Consent Key Parsing To Enum #309

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3 changes: 2 additions & 1 deletion src/main/java/de/medizininformatikinitiative/torch/config/AppConfig.java
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Expand Up @@ -11,6 +11,7 @@
import de.medizininformatikinitiative.torch.consent.ConsentValidator;
import de.medizininformatikinitiative.torch.cql.CqlClient;
import de.medizininformatikinitiative.torch.cql.FhirHelper;
import de.medizininformatikinitiative.torch.exceptions.ValidationException;
import de.medizininformatikinitiative.torch.management.CompartmentManager;
import de.medizininformatikinitiative.torch.management.ProcessedGroupFactory;
import de.medizininformatikinitiative.torch.management.StructureDefinitionHandler;
Expand Down Expand Up @@ -257,7 +258,7 @@ public ObjectMapper objectMapper() {
}

@Bean
public ConsentCodeMapper consentCodeMapper(ObjectMapper objectMapper) throws IOException {
public ConsentCodeMapper consentCodeMapper(ObjectMapper objectMapper) throws IOException, ValidationException {
return new ConsentCodeMapper(torchProperties.mapping().consent(), objectMapper);
}

Expand Down
52 changes: 40 additions & 12 deletions src/main/java/de/medizininformatikinitiative/torch/consent/ConsentCodeMapper.java
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Expand Up @@ -2,35 +2,52 @@

import com.fasterxml.jackson.databind.JsonNode;
import com.fasterxml.jackson.databind.ObjectMapper;
import de.medizininformatikinitiative.torch.exceptions.ValidationException;
import de.medizininformatikinitiative.torch.model.mapping.ConsentKey;

import java.io.File;
import java.io.IOException;
import java.util.*;
import java.util.ArrayList;
import java.util.Collections;
import java.util.EnumMap;
import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.Objects;
import java.util.Set;


/**
* Provides a Map of all consent codes belonging to a consent key e.g. "yes-yes-yes-yes"
* Provides a Map of all consent codes belonging to a consent key e.g. "yes-yes-yes-yes" as
* defined in the mapping file.
*/
public class ConsentCodeMapper {

private final Map<String, List<String>> consentMap;
private final Map<ConsentKey, List<String>> consentMap;
private final ObjectMapper objectMapper;


public ConsentCodeMapper(String consentFilePath, ObjectMapper objectMapper) throws IOException {
this.consentMap = new HashMap<>();
/**
* @param consentFilePath Path to the mapping file e.g. consent-mappings_fhir.json
* @param objectMapper Objectmapper for Json Processing
* @throws IOException
* @throws ValidationException
*/
public ConsentCodeMapper(String consentFilePath, ObjectMapper objectMapper) throws IOException, ValidationException {
this.consentMap = new EnumMap<>(ConsentKey.class);
Objects.requireNonNull(objectMapper);
this.objectMapper = objectMapper;
buildConsentMap(consentFilePath);
}

// Method to build the map based on the JSON file
private void buildConsentMap(String filePath) throws IOException {
//Class get Resource as Stream
//init method
private void buildConsentMap(String filePath) throws IOException, ValidationException {
File file = new File(filePath);
JsonNode consentMappingData = objectMapper.readTree(file.getAbsoluteFile());
for (JsonNode consent : consentMappingData) {
String keyCode = consent.get("key").get("code").asText();

ConsentKey keyCode = ConsentKey.fromString(consent.get("key").get("code").asText());
List<String> relevantCodes = new ArrayList<>();

JsonNode fixedCriteria = consent.get("fixedCriteria");
Expand All @@ -43,12 +60,23 @@ private void buildConsentMap(String filePath) throws IOException {
}
}
}

consentMap.put(keyCode, relevantCodes);
}
if (consentMap.size() != ConsentKey.values().length) {
throw new ValidationException("Consent map size does not match ConsentKey enum size");
}
}

public Set<String> getRelevantCodes(String key) {
/**
* @param key Consentkey to be handled
* @return All codes associated with that key
* e.g. for "no-no-no-no" in the current version of the codesystem
* "urn:oid:2.16.840.1.113883.3.1937.777.24.5.3" the codes
* "2.16.840.1.113883.3.1937.777.24.5.3.47"
* "2.16.840.1.113883.3.1937.777.24.5.3.49"
* "2.16.840.1.113883.3.1937.777.24.5.3.9" will be returned
*/
public Set<String> getRelevantCodes(ConsentKey key) {
return new HashSet<>(consentMap.getOrDefault(key, Collections.emptyList()));
}
}
}
3 changes: 2 additions & 1 deletion src/main/java/de/medizininformatikinitiative/torch/consent/ConsentFetcher.java
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Expand Up @@ -8,6 +8,7 @@
import de.medizininformatikinitiative.torch.model.fhir.Query;
import de.medizininformatikinitiative.torch.model.management.PatientBatch;
import de.medizininformatikinitiative.torch.model.management.PatientResourceBundle;
import de.medizininformatikinitiative.torch.model.mapping.ConsentKey;
import de.medizininformatikinitiative.torch.service.DataStore;
import de.medizininformatikinitiative.torch.util.ResourceUtils;
import org.hl7.fhir.r4.model.Consent;
Expand Down Expand Up @@ -98,7 +99,7 @@ private static Map<String, Provisions> mergeAllProvisions(Map<String, Collection
* @param batch A list of patient IDs to process in this batch.
* @return A {@link Flux} emitting maps containing consent information structured by patient ID and consent codes.
*/
public Mono<PatientBatchWithConsent> buildConsentInfo(String key, PatientBatch batch) {
public Mono<PatientBatchWithConsent> buildConsentInfo(ConsentKey key, PatientBatch batch) {
logger.debug("Starting to build consent info for key {} and {} patients", key, batch.ids().size());

Set<String> codes = mapper.getRelevantCodes(key);
Expand Down
3 changes: 2 additions & 1 deletion src/main/java/de/medizininformatikinitiative/torch/consent/ConsentHandler.java
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Expand Up @@ -4,6 +4,7 @@
import de.medizininformatikinitiative.torch.model.consent.PatientBatchWithConsent;
import de.medizininformatikinitiative.torch.model.fhir.Query;
import de.medizininformatikinitiative.torch.model.management.PatientBatch;
import de.medizininformatikinitiative.torch.model.mapping.ConsentKey;
import de.medizininformatikinitiative.torch.service.DataStore;
import de.medizininformatikinitiative.torch.util.ResourceUtils;
import org.hl7.fhir.r4.model.Encounter;
Expand Down Expand Up @@ -73,7 +74,7 @@ private static Mono<Map<String, Collection<Encounter>>> groupEncounterByPatient(
* @param batch Batch of patient IDs.
* @return {@link Mono<PatientBatchWithConsent>} containing all required provisions by patient with valid times.
*/
public Mono<PatientBatchWithConsent> fetchAndBuildConsentInfo(String consentKey, PatientBatch batch) {
public Mono<PatientBatchWithConsent> fetchAndBuildConsentInfo(ConsentKey consentKey, PatientBatch batch) {
return consentFetcher.buildConsentInfo(consentKey, batch)
.flatMap(this::adjustConsentPeriodsByPatientEncounters);
}
Expand Down
18 changes: 7 additions & 11 deletions src/main/java/de/medizininformatikinitiative/torch/model/crtdl/Crtdl.java
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Expand Up @@ -3,8 +3,8 @@
import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
import com.fasterxml.jackson.annotation.JsonProperty;
import com.fasterxml.jackson.databind.JsonNode;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import de.medizininformatikinitiative.torch.exceptions.ValidationException;
import de.medizininformatikinitiative.torch.model.mapping.ConsentKey;

import java.util.Optional;

Expand All @@ -17,32 +17,28 @@ public record Crtdl(
@JsonProperty(required = true)
DataExtraction dataExtraction
) {
private static final Logger logger = LoggerFactory.getLogger(Crtdl.class);

public Crtdl {
requireNonNull(cohortDefinition);
requireNonNull(dataExtraction);
}

public Optional<String> consentKey() {
public Optional<ConsentKey> consentKey() throws ValidationException {
JsonNode inclusionCriteria = cohortDefinition.get("inclusionCriteria");
if (inclusionCriteria != null && inclusionCriteria.isArray()) {
for (JsonNode criteriaGroup : inclusionCriteria) {
for (JsonNode criteria : criteriaGroup) {
JsonNode context = criteria.get("context");
if (context != null && "Einwilligung".equals(context.get("code").asText())) {
JsonNode termcodes = criteria.get("termCodes");
if (termcodes != null && termcodes.isArray()) {
JsonNode firstTermcode = termcodes.get(0);
if (firstTermcode != null && firstTermcode.has("code")) {
return Optional.of(firstTermcode.get("code").asText());
}
JsonNode firstTermcode = criteria.get("termCodes").get(0);
if (firstTermcode != null && firstTermcode.has("code")) {
String code = firstTermcode.get("code").asText();
return Optional.of(ConsentKey.fromString(code));
}
}
}
}
}
return Optional.empty();
}

}
28 changes: 4 additions & 24 deletions src/main/java/de/medizininformatikinitiative/torch/model/crtdl/annotated/AnnotatedCrtdl.java
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@@ -1,38 +1,18 @@
package de.medizininformatikinitiative.torch.model.crtdl.annotated;

import com.fasterxml.jackson.databind.JsonNode;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import de.medizininformatikinitiative.torch.model.mapping.ConsentKey;

import java.util.Optional;

import static java.util.Objects.requireNonNull;

public record AnnotatedCrtdl(JsonNode cohortDefinition, AnnotatedDataExtraction dataExtraction) {
public record AnnotatedCrtdl(JsonNode cohortDefinition, AnnotatedDataExtraction dataExtraction,
Optional<ConsentKey> consentKey) {

public AnnotatedCrtdl {
requireNonNull(cohortDefinition);
requireNonNull(dataExtraction);
}

public Optional<String> consentKey() {
JsonNode inclusionCriteria = cohortDefinition.get("inclusionCriteria");
if (inclusionCriteria != null && inclusionCriteria.isArray()) {
for (JsonNode criteriaGroup : inclusionCriteria) {
for (JsonNode criteria : criteriaGroup) {
JsonNode context = criteria.get("context");
if (context != null && "Einwilligung".equals(context.get("code").asText())) {
JsonNode termcodes = criteria.get("termCodes");
if (termcodes != null && termcodes.isArray()) {
JsonNode firstTermcode = termcodes.get(0);
if (firstTermcode != null && firstTermcode.has("code")) {
return Optional.of(firstTermcode.get("code").asText());
}
}
}
}
}
}
return Optional.empty();
requireNonNull(consentKey);
}
}
11 changes: 11 additions & 0 deletions src/main/java/de/medizininformatikinitiative/torch/model/mapping/ConsentKey.java
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@@ -1,5 +1,7 @@
package de.medizininformatikinitiative.torch.model.mapping;

import de.medizininformatikinitiative.torch.exceptions.ValidationException;

import static java.util.Objects.requireNonNull;

public enum ConsentKey {
Expand Down Expand Up @@ -31,4 +33,13 @@ public enum ConsentKey {
public String toString() {
return s;
}

public static ConsentKey fromString(String value) throws ValidationException {
for (ConsentKey key : values()) {
if (key.toString().equalsIgnoreCase(value)) {
return key;
}
}
throw new ValidationException("Unknown consent key: " + value);
}
}
13 changes: 8 additions & 5 deletions src/main/java/de/medizininformatikinitiative/torch/service/CrtdlValidatorService.java
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Expand Up @@ -9,6 +9,7 @@
import de.medizininformatikinitiative.torch.model.crtdl.annotated.AnnotatedAttributeGroup;
import de.medizininformatikinitiative.torch.model.crtdl.annotated.AnnotatedCrtdl;
import de.medizininformatikinitiative.torch.model.crtdl.annotated.AnnotatedDataExtraction;
import de.medizininformatikinitiative.torch.model.mapping.ConsentKey;
import de.medizininformatikinitiative.torch.util.CompiledStructureDefinition;
import de.medizininformatikinitiative.torch.util.FhirPathBuilder;
import org.hl7.fhir.r4.model.ElementDefinition;
Expand All @@ -20,6 +21,7 @@
import java.util.HashSet;
import java.util.List;
import java.util.Objects;
import java.util.Optional;
import java.util.Set;
import java.util.function.Predicate;

Expand All @@ -45,26 +47,27 @@ public CrtdlValidatorService(StructureDefinitionHandler profileHandler, Standard
* @return the validated Crtdl or an error signal with ValidationException if a profile is unknown.
*/
public AnnotatedCrtdl validate(Crtdl crtdl) throws ValidationException {
Optional<ConsentKey> consentKey = crtdl.consentKey();
List<AnnotatedAttributeGroup> annotatedAttributeGroups = new ArrayList<>();
Set<String> linkedGroups = new HashSet<>();
Set<String> successfullyAnnotatedGroups = new HashSet<>();
boolean exactlyOnePatientGroup = false;
boolean patientGroupFound = false;
String patientAttributeGroupId = "";

for (AttributeGroup attributeGroup : crtdl.dataExtraction().attributeGroups()) {
CompiledStructureDefinition definition = profileHandler.getDefinition(attributeGroup.groupReference())
.orElseThrow(() -> new ValidationException("Unknown Profile: " + attributeGroup.groupReference()));
if (Objects.equals(definition.type(), "Patient")) {
if (exactlyOnePatientGroup) {
if (patientGroupFound) {
throw new ValidationException(" More than one Patient Attribute Group");
} else {
exactlyOnePatientGroup = true;
patientGroupFound = true;
patientAttributeGroupId = attributeGroup.id();
logger.debug("Found Patient Attribute Group {}", patientAttributeGroupId);
}
}
}
if (!exactlyOnePatientGroup) {
if (!patientGroupFound) {
throw new ValidationException("No Patient Attribute Group");
}

Expand All @@ -86,7 +89,7 @@ public AnnotatedCrtdl validate(Crtdl crtdl) throws ValidationException {
}


return new AnnotatedCrtdl(crtdl.cohortDefinition(), new AnnotatedDataExtraction(annotatedAttributeGroups));
return new AnnotatedCrtdl(crtdl.cohortDefinition(), new AnnotatedDataExtraction(annotatedAttributeGroups), consentKey);
}

private AnnotatedAttributeGroup annotateGroup(AttributeGroup attributeGroup, CompiledStructureDefinition
Expand Down
7 changes: 4 additions & 3 deletions src/test/java/de/medizininformatikinitiative/torch/ConsentFetcherIT.java
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Expand Up @@ -5,6 +5,7 @@
import de.medizininformatikinitiative.torch.exceptions.ConsentViolatedException;
import de.medizininformatikinitiative.torch.model.consent.PatientBatchWithConsent;
import de.medizininformatikinitiative.torch.model.management.PatientBatch;
import de.medizininformatikinitiative.torch.model.mapping.ConsentKey;
import org.hl7.fhir.r4.model.DateTimeType;
import org.hl7.fhir.r4.model.Observation;
import org.hl7.fhir.r4.model.Reference;
Expand Down Expand Up @@ -69,7 +70,7 @@ private void assertConsentFalse(PatientBatchWithConsent batch, String patientId,

@Test
void failsOnNoPatientMatchesConsentKeyBuildingConsent() {
var resultBatch = consentFetcher.buildConsentInfo("yes-no-no-yes", BATCH);
var resultBatch = consentFetcher.buildConsentInfo(ConsentKey.YES_NO_NO_YES, BATCH);

StepVerifier.create(resultBatch)
.expectErrorSatisfies(error -> assertThat(error)
Expand All @@ -80,7 +81,7 @@ void failsOnNoPatientMatchesConsentKeyBuildingConsent() {

@Test
void failsOnUnknownPatientBuildingConsent() {
var resultBatch = consentFetcher.buildConsentInfo("yes-yes-yes-yes", BATCH_UNKNOWN);
var resultBatch = consentFetcher.buildConsentInfo(ConsentKey.YES_YES_YES_YES, BATCH_UNKNOWN);

StepVerifier.create(resultBatch)
.expectErrorSatisfies(error -> assertThat(error)
Expand All @@ -91,7 +92,7 @@ void failsOnUnknownPatientBuildingConsent() {

@Test
void successBuildingConsent() {
var resultBatch = consentFetcher.buildConsentInfo("yes-yes-yes-yes", BATCH);
var resultBatch = consentFetcher.buildConsentInfo(ConsentKey.YES_YES_YES_YES, BATCH);

StepVerifier.create(resultBatch)
.assertNext(batch -> {
Expand Down
3 changes: 2 additions & 1 deletion src/test/java/de/medizininformatikinitiative/torch/ConsentHandlerIT.java
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Expand Up @@ -4,6 +4,7 @@
import de.medizininformatikinitiative.torch.consent.ConsentValidator;
import de.medizininformatikinitiative.torch.model.consent.PatientBatchWithConsent;
import de.medizininformatikinitiative.torch.model.management.PatientBatch;
import de.medizininformatikinitiative.torch.model.mapping.ConsentKey;
import org.hl7.fhir.r4.model.DateTimeType;
import org.hl7.fhir.r4.model.Observation;
import org.hl7.fhir.r4.model.Reference;
Expand Down Expand Up @@ -67,7 +68,7 @@ private void assertConsentFalse(PatientBatchWithConsent batch, String patientId,

@Test
void successAfterEncounterUpdatesProvisions() {
var resultBatch = consentHandler.fetchAndBuildConsentInfo("yes-yes-yes-yes", BATCH);
var resultBatch = consentHandler.fetchAndBuildConsentInfo(ConsentKey.YES_YES_YES_YES, BATCH);

StepVerifier.create(resultBatch)
.assertNext(batch -> {
Expand Down
9 changes: 5 additions & 4 deletions src/test/java/de/medizininformatikinitiative/torch/ConsentHandlerTest.java
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Expand Up @@ -4,6 +4,7 @@
import de.medizininformatikinitiative.torch.consent.ConsentHandler;
import de.medizininformatikinitiative.torch.exceptions.ConsentViolatedException;
import de.medizininformatikinitiative.torch.model.management.PatientBatch;
import de.medizininformatikinitiative.torch.model.mapping.ConsentKey;
import de.medizininformatikinitiative.torch.service.DataStore;
import org.junit.jupiter.api.Test;
import org.mockito.Mockito;
Expand All @@ -26,10 +27,10 @@ public class ConsentHandlerTest {

@Test
void failsOnNoPatientMatchesConsentKeyBuildingConsent() {
when(consentFetcher.buildConsentInfo("yes-no-no-yes", BATCH))
when(consentFetcher.buildConsentInfo(ConsentKey.YES_NO_NO_YES, BATCH))
.thenReturn(Mono.error(new ConsentViolatedException("No valid provisions found for any patients in batch")));

var resultBatch = consentHandler.fetchAndBuildConsentInfo("yes-no-no-yes", BATCH);
var resultBatch = consentHandler.fetchAndBuildConsentInfo(ConsentKey.YES_NO_NO_YES, BATCH);

StepVerifier.create(resultBatch)
.expectErrorSatisfies(error -> assertThat(error)
Expand All @@ -40,10 +41,10 @@ void failsOnNoPatientMatchesConsentKeyBuildingConsent() {

@Test
void failsOnUnknownPatientBuildingConsent() {
when(consentFetcher.buildConsentInfo("yes-yes-yes-yes", BATCH_UNKNOWN))
when(consentFetcher.buildConsentInfo(ConsentKey.YES_YES_YES_YES, BATCH_UNKNOWN))
.thenReturn(Mono.error(new ConsentViolatedException("No valid provisions found for any patients in batch")));

var resultBatch = consentHandler.fetchAndBuildConsentInfo("yes-yes-yes-yes", BATCH_UNKNOWN);
var resultBatch = consentHandler.fetchAndBuildConsentInfo(ConsentKey.YES_YES_YES_YES, BATCH_UNKNOWN);

StepVerifier.create(resultBatch)
.expectErrorSatisfies(error -> assertThat(error)
Expand Down
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