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Eliminating possible NPE + adding safer try--with-resources version + small code cleanup #364

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merged 2 commits into from
Nov 7, 2023
Merged

Eliminating possible NPE + adding safer try--with-resources version + small code cleanup #364

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1a59a82
eliminating possible NPE + small code cleanup
Nov 7, 2023
7fb7d5d
applying a safer and more concise version of try-catch -> try-with-re…
Nov 7, 2023
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2 changes: 1 addition & 1 deletion ...-translator/src/main/java/uk/nhs/adaptors/pss/translator/mapper/AgentDirectoryMapper.java
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Original file line number Diff line number Diff line change
Expand Up @@ -63,7 +63,7 @@ public List<? extends DomainResource> mapAgentDirectory(RCMRMT030101UK04AgentDir
return agentResources;
}

return null;
return List.of();
}

private void mapAgent(RCCTMT120101UK01Agent agent, List<DomainResource> agentResourceList) {
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2 changes: 1 addition & 1 deletion ...anslator/src/main/java/uk/nhs/adaptors/pss/translator/mapper/DocumentReferenceMapper.java
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Expand Up @@ -238,6 +238,6 @@ private Integer getAttachmentSize(List<PatientAttachmentLog> patientAttachmentLo
// stubbed method for abstract class
public List<DocumentReference> mapResources(RCMRMT030101UK04EhrExtract ehrExtract, Patient patient,
List<Encounter> encounterList, String practiseCode) {
return null;
return List.of();
}
}
14 changes: 6 additions & 8 deletions ...-translator/src/main/java/uk/nhs/adaptors/pss/translator/storage/AzureStorageService.java
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Expand Up @@ -82,23 +82,21 @@ private BlockBlobClient createBlobBlockClient(String filename) {
}

private void addFileStringToMainContainer(String filename, byte[] fileAsString) throws StorageException, IOException {
try {
try (InputStream dataStream = new ByteArrayInputStream(fileAsString)) {
BlockBlobClient blobClient = createBlobBlockClient(filename);
InputStream dataStream = new ByteArrayInputStream(fileAsString);
blobClient.upload(dataStream, fileAsString.length);
dataStream.close();
} catch (IOException e) {
throw new StorageException("Failed to upload blob to Azure Blob storage", e);
}
}

private ByteArrayOutputStream downloadFileToStream(String filename) throws StorageException {
try {
BlockBlobClient blobClient = createBlobBlockClient(filename);
int dataSize = (int) blobClient.getProperties().getBlobSize();
ByteArrayOutputStream outputStream = new ByteArrayOutputStream(dataSize);

BlockBlobClient blobClient = createBlobBlockClient(filename);
int dataSize = (int) blobClient.getProperties().getBlobSize();

try (ByteArrayOutputStream outputStream = new ByteArrayOutputStream(dataSize)) {
blobClient.downloadStream(outputStream);
outputStream.close();
return outputStream;
} catch (IOException e) {
throw new StorageException("Failed to download blob from Azure Blob storage", e);
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6 changes: 2 additions & 4 deletions gp2gp-translator/src/main/java/uk/nhs/adaptors/pss/translator/util/ObservationUtil.java
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Expand Up @@ -138,10 +138,8 @@ public static Object getEffective(IVLTS effectiveTime, TS availabilityTime) {
effectivePeriod.setEndElement(DateFormatUtil.parseToDateTimeType(effectiveTime.getHigh().getValue()));
}

if (availabilityTimeHasValue(availabilityTime) && effectivePeriod.getStart() == null) {
if (effectivePeriod.getEnd() != null) {
effectivePeriod.setStartElement(DateFormatUtil.parseToDateTimeType(availabilityTime.getValue()));
}
if (availabilityTimeHasValue(availabilityTime) && effectivePeriod.getStart() == null && effectivePeriod.getEnd() != null) {
effectivePeriod.setStartElement(DateFormatUtil.parseToDateTimeType(availabilityTime.getValue()));
}

if (effectivePeriod.hasStart() || effectivePeriod.hasEnd()) {
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18 changes: 0 additions & 18 deletions ...p-translator/src/main/java/uk/nhs/adaptors/pss/translator/util/ResourceReferenceUtil.java
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Expand Up @@ -4,8 +4,6 @@
import static uk.nhs.adaptors.pss.translator.util.ResourceFilterUtil.isBloodPressure;
import static uk.nhs.adaptors.pss.translator.util.ResourceFilterUtil.isDiagnosticReport;
import static uk.nhs.adaptors.pss.translator.util.ResourceFilterUtil.isDocumentReference;
import static uk.nhs.adaptors.pss.translator.util.ResourceFilterUtil.isTemplate;

import java.util.List;

import org.hl7.fhir.dstu3.model.IdType;
Expand Down Expand Up @@ -57,14 +55,6 @@ public void extractChildReferencesFromCompoundStatement(RCMRMT030101UK04Compound
addDiagnosticReportEntry(compoundStatement, entryReferences);
} else {

// NIAD_2190 the section below appears to be for Questionnaire Response links and the observation
// created that goes with it. Since Questionnaires have been removed, the contents of the addTemplateEntry function has
// been commented out while it is tested more in depth. It can be removed following the effect investigation
// - Scott Alexander 21072022
if (isTemplate(compoundStatement)) {
addTemplateEntry(compoundStatement, entryReferences);
}

compoundStatement.getComponent().forEach(component -> {
addObservationStatementEntry(
component.getObservationStatement(), entryReferences, compoundStatement);
Expand Down Expand Up @@ -108,14 +98,6 @@ private static boolean isNotIgnoredResource(RCMRMT030101UK04CompoundStatement co
|| !references.contains(OBSERVATION_REFERENCE.formatted(compoundStatement.getId().get(0).getRoot()));
}

private static void addTemplateEntry(RCMRMT030101UK04CompoundStatement compoundStatement,
List<Reference> entryReferences) {
// entryReferences.add(createResourceReference(ResourceType.QuestionnaireResponse.name(),
// QUESTIONNAIRE_ID.formatted(compoundStatement.getId().get(0).getRoot())));
// entryReferences.add(createResourceReference(ResourceType.Observation.name(),
// compoundStatement.getId().get(0).getRoot()));
}

private void addObservationStatementEntry(RCMRMT030101UK04ObservationStatement observationStatement,
List<Reference> entryReferences, RCMRMT030101UK04CompoundStatement compoundStatement) {
if (observationStatement != null && isNotIgnoredResource(compoundStatement, entryReferences)) {
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