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- append "flare" to method name "DirectSpringConfig.directWebClientFlare" to clarify that it is only associated with the flare client - replace custom "internal/json" media type from mock server response in DirectBrokerClientFlareIT and replace it with standard application/json header - replace HashMap with EnumMap in DirectBrokerClient.DirectQuery - rename SITE_1_NAME to SITE_NAME_LOCAL to be consistent with SITE_ID_LOCAL (and make both constants final) - make the fhirClient a local var in the setup method in DirectBrokerClientCqlIT - don't return anything from DirectBrokerClientCqlIT.createDummyPatient - catch and wrap BaseServerResponseException when trying to read measure report from fhir server - catch BaseServerResponseException instead of just FhirClientConnectionException when creating library and measure - throw SiteNotFoundException instead of returning an empty string when the site name for an invalid id is requested - add constructor for QueryDefinitionNotFoundException without QueryMediaType parameter to be thrown in DSFQueryManager, and change the queryMediaType Parameter from String to the respective enum - move Measure.json and Library.json (as well as the 2 cql "query" files) to the direct broker package and use getResourceAsStream - remove backendquery mapping from DirectBrokerClient and move the backendquery id directly to DirectBrokerClient.DirectQuery - extract fhir connection from DirectBrokerClientCql to separate class FhirConnector
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...va/de/numcodex/feasibility_gui_backend/query/broker/QueryDefinitionNotFoundException.java
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149 changes: 13 additions & 136 deletions
149
...n/java/de/numcodex/feasibility_gui_backend/query/broker/direct/DirectBrokerClientCql.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,184 +1,61 @@ | ||
| package de.numcodex.feasibility_gui_backend.query.broker.direct; | ||
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| import ca.uhn.fhir.context.FhirContext; | ||
| import ca.uhn.fhir.rest.client.api.IGenericClient; | ||
| import ca.uhn.fhir.rest.client.exceptions.FhirClientConnectionException; | ||
| import ca.uhn.fhir.rest.param.DateParam; | ||
| import ca.uhn.fhir.rest.param.StringParam; | ||
| import de.numcodex.feasibility_gui_backend.query.broker.BrokerClient; | ||
| import de.numcodex.feasibility_gui_backend.query.broker.QueryDefinitionNotFoundException; | ||
| import de.numcodex.feasibility_gui_backend.query.collect.QueryStatus; | ||
| import de.numcodex.feasibility_gui_backend.query.broker.QueryNotFoundException; | ||
| import java.io.InputStream; | ||
| import lombok.extern.slf4j.Slf4j; | ||
| import org.hl7.fhir.instance.model.api.IBaseResource; | ||
| import org.hl7.fhir.r4.model.Bundle; | ||
| import org.hl7.fhir.r4.model.Library; | ||
| import org.hl7.fhir.r4.model.Measure; | ||
| import org.hl7.fhir.r4.model.MeasureReport; | ||
| import org.hl7.fhir.r4.model.Parameters; | ||
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| import java.io.IOException; | ||
| import java.util.*; | ||
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| import static de.numcodex.feasibility_gui_backend.query.QueryMediaType.CQL; | ||
| import static de.numcodex.feasibility_gui_backend.query.collect.QueryStatus.COMPLETED; | ||
| import static de.numcodex.feasibility_gui_backend.query.collect.QueryStatus.FAILED; | ||
| import static java.nio.charset.StandardCharsets.UTF_8; | ||
| import static org.hl7.fhir.r4.model.Bundle.BundleType.TRANSACTION; | ||
| import static org.hl7.fhir.r4.model.Bundle.HTTPVerb.POST; | ||
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| /** | ||
| * A {@link BrokerClient} to be used to directly communicate with a CQL-capable FHIR Server instance | ||
| * without the need for using any middleware (Aktin or DSF). | ||
| */ | ||
| @Slf4j | ||
| public class DirectBrokerClientCql extends DirectBrokerClient { | ||
| private final FhirContext fhirContext; | ||
| private final IGenericClient fhirClient; | ||
| private final FhirConnector fhirConnector; | ||
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| /** | ||
| * Creates a new {@link DirectBrokerClientCql} instance that uses the given web client to | ||
| * communicate with a CQL capable FHIR server instance. | ||
| * | ||
| * @param fhirContext A FHIR context. | ||
| * @param fhirClient A FHIR client, configured with the correct url | ||
| * @param fhirConnector A FHIR connector. | ||
| */ | ||
| public DirectBrokerClientCql(FhirContext fhirContext, IGenericClient fhirClient) { | ||
| this.fhirContext = Objects.requireNonNull(fhirContext); | ||
| this.fhirClient = Objects.requireNonNull(fhirClient); | ||
| public DirectBrokerClientCql(FhirConnector fhirConnector) { | ||
| this.fhirConnector = Objects.requireNonNull(fhirConnector); | ||
| listeners = new ArrayList<>(); | ||
| brokerQueries = new HashMap<>(); | ||
| brokerToBackendQueryIdMapping = new HashMap<>(); | ||
| } | ||
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| @Override | ||
| public void publishQuery(String brokerQueryId) | ||
| throws QueryNotFoundException, IOException, QueryDefinitionNotFoundException { | ||
| var query = findQuery(brokerQueryId); | ||
| var queryContent = Optional.ofNullable(query.getQueryDefinition(CQL)) | ||
| .orElseThrow(() -> new QueryDefinitionNotFoundException(query.getQueryId(), | ||
| CQL.getRepresentation()) | ||
| ); | ||
| var queryContent = query.getQueryDefinition(CQL); | ||
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| updateQueryStatus(query, QueryStatus.EXECUTING); | ||
| String measureUri; | ||
| var libraryUri = "urn:uuid" + UUID.randomUUID(); | ||
| var measureUri = "urn:uuid" + UUID.randomUUID(); | ||
| MeasureReport measureReport; | ||
| try { | ||
| measureUri = createMeasureAndLibrary(queryContent); | ||
| Bundle bundle = fhirConnector.createBundle(queryContent, libraryUri, measureUri); | ||
| fhirConnector.transmitBundle(bundle); | ||
| measureReport = fhirConnector.evaluateMeasure(measureUri); | ||
| } catch (IOException e) { | ||
| updateQueryStatus(query, FAILED); | ||
| throw new IOException( | ||
| "An error occurred while publishing the query with ID: " + query.getQueryId() | ||
| + " while trying to create measure and library", e); | ||
| throw (e); | ||
| } | ||
| var measureReport = evaluateMeasure(measureUri); | ||
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| var resultCount = measureReport.getGroupFirstRep().getPopulationFirstRep().getCount(); | ||
| query.setResult(obfuscateResultCount ? obfuscate(resultCount) : resultCount); | ||
| updateQueryStatus(query, COMPLETED); | ||
| } | ||
|
|
||
| /** | ||
| * Create FHIR {@link Measure} and {@link Library} resources and transmit them in a bundled transaction. | ||
| * @param cql the plaintext cql definition | ||
| * @return the randomly generated identifier of the {@link Measure} resource | ||
| */ | ||
| private String createMeasureAndLibrary(String cql) throws IOException { | ||
| var libraryUri = "urn:uuid" + UUID.randomUUID(); | ||
| var library = appendCql(parseResource(Library.class, | ||
| getResourceFileAsString("query/cql/Library.json")).setUrl(libraryUri), cql); | ||
| var measureUri = "urn:uuid" + UUID.randomUUID(); | ||
| var measure = parseResource(Measure.class, | ||
| getResourceFileAsString("query/cql/Measure.json")) | ||
| .setUrl(measureUri) | ||
| .addLibrary(libraryUri); | ||
| var bundle = createBundle(library, measure); | ||
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| try { | ||
| fhirClient.transaction().withBundle(bundle).execute(); | ||
| } catch (FhirClientConnectionException e) { | ||
| throw new IOException(e); | ||
| } | ||
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| return measureUri; | ||
| } | ||
|
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| /** | ||
| * Get the {@link MeasureReport} for a previously transmitted {@link Measure} | ||
| * @param measureUri the identifier of the {@link Measure} | ||
| * @return the retrieved {@link MeasureReport} from the server | ||
| */ | ||
| private MeasureReport evaluateMeasure(String measureUri) { | ||
| return fhirClient.operation() | ||
| .onType(Measure.class) | ||
| .named("evaluate-measure") | ||
| .withSearchParameter(Parameters.class, "measure", new StringParam(measureUri)) | ||
| .andSearchParameter("periodStart", new DateParam("1900")) | ||
| .andSearchParameter("periodEnd", new DateParam("2100")) | ||
| .useHttpGet() | ||
| .returnResourceType(MeasureReport.class) | ||
| .execute(); | ||
| } | ||
|
|
||
| /** | ||
| * Read file contents as String | ||
| * @param fileName name of the resource file | ||
| * @return the String contents of the file | ||
| */ | ||
| public static String getResourceFileAsString(String fileName) throws IOException { | ||
| InputStream is = getResourceFileAsInputStream(fileName); | ||
| if (is != null) { | ||
| return new String(is.readAllBytes(), UTF_8); | ||
| } else { | ||
| throw new RuntimeException("File not found in classpath: " + fileName); | ||
| } | ||
| } | ||
|
|
||
| /** | ||
| * Read file contents as {@link InputStream} | ||
| * @param fileName name of the resource file | ||
| * @return an {@link InputStream} of the file | ||
| */ | ||
| public static InputStream getResourceFileAsInputStream(String fileName) { | ||
| ClassLoader classLoader = DirectBrokerClientCql.class.getClassLoader(); | ||
| return classLoader.getResourceAsStream(fileName); | ||
| } | ||
|
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| /** | ||
| * Parse a String as an {@link IBaseResource} implementation | ||
| * @param type the concrete {@link IBaseResource} implementation class to parse to | ||
| * @param input the {@link String} to parse | ||
| * @return the wanted {@link IBaseResource} implementation object | ||
| * @param <T> any implementation of {@link IBaseResource} | ||
| */ | ||
| private <T extends IBaseResource> T parseResource(Class<T> type, String input) { | ||
| var parser = fhirContext.newJsonParser(); | ||
| return type.cast(parser.parseResource(input)); | ||
| } | ||
|
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| /** | ||
| * Add the CQL query to a {@link Library} | ||
| * @param library the {@link Library} to add the CQL string to | ||
| * @param cql the CQL string to add | ||
| * @return the {@link Library} with the added CQL | ||
| */ | ||
| private Library appendCql(Library library, String cql) { | ||
| library.getContentFirstRep().setContentType(CQL.getRepresentation()); | ||
| library.getContentFirstRep().setData(cql.getBytes(UTF_8)); | ||
| return library; | ||
| } | ||
|
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| /** | ||
| * Create a {@link Bundle} of a {@link Library} and a {@link Measure} | ||
| * @param library the {@link Library} to add to the {@link Bundle} | ||
| * @param measure the {@link Measure} to add to the {@link Bundle} | ||
| * @return the {@link Bundle}, consisting of the given {@link Library} and {@link Measure} | ||
| */ | ||
| private static Bundle createBundle(Library library, Measure measure) { | ||
| var bundle = new Bundle(); | ||
| bundle.setType(TRANSACTION); | ||
| bundle.addEntry().setResource(library).getRequest().setMethod(POST).setUrl("Library"); | ||
| bundle.addEntry().setResource(measure).getRequest().setMethod(POST).setUrl("Measure"); | ||
| return bundle; | ||
| } | ||
|
|
||
| } |
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