* Add configurable filesystem binary storage (fix #860) * Refine binary storage configuration handling * Refine binary storage bean wiring * Refine binary storage conditional beans * Add integration coverage for binary storage configs * Exercise binary storage via REST integration tests * Update src/main/resources/application.yaml Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> --------- Co-authored-by: Ubuntu <ubuntu@ip-172-31-35-43.eu-west-2.compute.internal> Co-authored-by: Ubuntu <ubuntu@ip-172-31-10-131.eu-west-2.compute.internal> Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
This commit is contained in:
Shamus Husheer
GitHub
@@ -0,0 +1,324 @@
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package ca.uhn.fhir.jpa.starter;
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import ca.uhn.fhir.context.FhirContext;
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import ca.uhn.fhir.jpa.binstore.FilesystemBinaryStorageSvcImpl;
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import ca.uhn.fhir.jpa.dao.data.IBinaryStorageEntityDao;
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import ca.uhn.fhir.jpa.model.entity.BinaryStorageEntity;
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import ca.uhn.fhir.rest.client.api.IGenericClient;
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import ca.uhn.fhir.rest.client.api.ServerValidationModeEnum;
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import org.hl7.fhir.instance.model.api.IIdType;
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import org.hl7.fhir.r4.model.Patient;
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import org.junit.jupiter.api.AfterEach;
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import org.junit.jupiter.api.BeforeEach;
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import org.junit.jupiter.api.Test;
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import org.springframework.beans.factory.annotation.Autowired;
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import org.springframework.boot.test.context.SpringBootTest;
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import org.springframework.boot.test.web.server.LocalServerPort;
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import org.springframework.transaction.PlatformTransactionManager;
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import org.springframework.transaction.support.TransactionTemplate;
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import java.io.IOException;
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import java.io.UncheckedIOException;
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import java.nio.file.Files;
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import java.nio.file.Path;
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import java.nio.file.Paths;
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import java.util.ArrayList;
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import java.util.Comparator;
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import java.util.LinkedHashSet;
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import java.util.List;
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import java.util.Set;
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import java.util.UUID;
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import java.util.concurrent.ThreadLocalRandom;
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import java.util.stream.Collectors;
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import java.util.stream.Stream;
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import static org.assertj.core.api.Assertions.assertThat;
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abstract class BaseBinaryStorageIntegrationTest {
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protected static final String COMMON_CONFIG_LOCATION = "spring.config.location=classpath:/binary-storage-test-empty.yaml";
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protected static final String COMMON_H2_USERNAME = "spring.datasource.username=sa";
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protected static final String COMMON_H2_PASSWORD = "spring.datasource.password=";
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protected static final String COMMON_JPA_DDL = "spring.jpa.hibernate.ddl-auto=create-drop";
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protected static final String COMMON_HIBERNATE_DIALECT =
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"spring.jpa.properties.hibernate.dialect=ca.uhn.fhir.jpa.model.dialect.HapiFhirH2Dialect";
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protected static final String COMMON_HIBERNATE_SEARCH_DISABLED = "spring.jpa.properties.hibernate.search.enabled=false";
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protected static final String COMMON_FLYWAY_DISABLED = "spring.flyway.enabled=false";
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protected static final String COMMON_FHIR_VERSION = "hapi.fhir.fhir_version=r4";
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protected static final String COMMON_REPO_VALIDATION_DISABLED =
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"hapi.fhir.enable_repository_validating_interceptor=false";
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protected static final String COMMON_MDM_DISABLED = "hapi.fhir.mdm_enabled=false";
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protected static final String COMMON_CR_DISABLED = "hapi.fhir.cr_enabled=false";
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protected static final String COMMON_SUBSCRIPTION_WS_DISABLED = "hapi.fhir.subscription.websocket_enabled=false";
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protected static final String COMMON_BEAN_OVERRIDE_ALLOWED = "spring.main.allow-bean-definition-overriding=true";
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protected static final String COMMON_CIRCULAR_REFERENCES = "spring.main.allow-circular-references=true";
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protected static final String COMMON_MCP_DISABLED = "spring.ai.mcp.server.enabled=false";
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protected static final String CONTENT_TYPE = "application/octet-stream";
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@LocalServerPort
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protected int port;
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protected FhirContext fhirContext;
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protected IGenericClient client;
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private final List<IIdType> resourcesToDelete = new ArrayList<>();
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@BeforeEach
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void setUpClient() {
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fhirContext = FhirContext.forR4();
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fhirContext.getRestfulClientFactory().setServerValidationMode(ServerValidationModeEnum.NEVER);
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fhirContext.getRestfulClientFactory().setSocketTimeout(1200 * 1000);
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String serverBase = "http://localhost:" + port + "/fhir/";
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client = fhirContext.newRestfulGenericClient(serverBase);
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resourcesToDelete.clear();
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}
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@AfterEach
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void deleteCreatedResources() {
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for (IIdType id : resourcesToDelete) {
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try {
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client.delete().resourceById(id).execute();
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} catch (Exception ignored) {
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// Ignore cleanup failures to keep tests resilient
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}
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}
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}
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protected IIdType createPatientWithPhoto(String label, byte[] payload) {
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Patient patient = new Patient();
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patient.addIdentifier().setSystem("urn:binary-storage-test").setValue(label);
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patient.addName().setFamily(label);
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patient.addPhoto().setContentType(CONTENT_TYPE).setData(payload);
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IIdType id = client.create().resource(patient).execute().getId().toUnqualifiedVersionless();
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resourcesToDelete.add(id);
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return id;
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}
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protected String uniqueLabel(String prefix) {
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return prefix + "-" + UUID.randomUUID();
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}
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protected byte[] randomBytes(int size) {
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byte[] payload = new byte[size];
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ThreadLocalRandom.current().nextBytes(payload);
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return payload;
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}
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protected void assertRegularFileCount(Path baseDir, long expectedFileCount) throws IOException {
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assertThat(regularFileCount(baseDir)).isEqualTo(expectedFileCount);
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}
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protected void assertRegularFileCountGreaterThan(Path baseDir, long minimumFileCount) throws IOException {
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assertThat(regularFileCount(baseDir)).isGreaterThan(minimumFileCount);
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}
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protected Path ensureDirectory(Path directory) throws IOException {
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Files.createDirectories(directory);
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return directory;
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}
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protected void deleteDirectoryContents(Path baseDir) throws IOException {
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if (Files.notExists(baseDir)) {
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return;
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}
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try (Stream<Path> files = Files.walk(baseDir)) {
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files.sorted(Comparator.reverseOrder())
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.filter(path -> !path.equals(baseDir))
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.forEach(path -> {
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try {
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Files.deleteIfExists(path);
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} catch (IOException e) {
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throw new UncheckedIOException(e);
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}
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});
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}
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}
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private long regularFileCount(Path baseDir) throws IOException {
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if (Files.notExists(baseDir)) {
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return 0;
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}
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try (Stream<Path> files = Files.walk(baseDir)) {
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return files.filter(Files::isRegularFile).count();
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}
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}
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}
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@SpringBootTest(
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webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT,
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classes = Application.class,
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properties = {
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BaseBinaryStorageIntegrationTest.COMMON_CONFIG_LOCATION,
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"spring.datasource.url=jdbc:h2:mem:binary-storage-db;DB_CLOSE_DELAY=-1",
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BaseBinaryStorageIntegrationTest.COMMON_H2_USERNAME,
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BaseBinaryStorageIntegrationTest.COMMON_H2_PASSWORD,
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BaseBinaryStorageIntegrationTest.COMMON_JPA_DDL,
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BaseBinaryStorageIntegrationTest.COMMON_HIBERNATE_DIALECT,
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BaseBinaryStorageIntegrationTest.COMMON_HIBERNATE_SEARCH_DISABLED,
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BaseBinaryStorageIntegrationTest.COMMON_FLYWAY_DISABLED,
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BaseBinaryStorageIntegrationTest.COMMON_FHIR_VERSION,
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BaseBinaryStorageIntegrationTest.COMMON_REPO_VALIDATION_DISABLED,
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BaseBinaryStorageIntegrationTest.COMMON_MDM_DISABLED,
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BaseBinaryStorageIntegrationTest.COMMON_CR_DISABLED,
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BaseBinaryStorageIntegrationTest.COMMON_SUBSCRIPTION_WS_DISABLED,
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BaseBinaryStorageIntegrationTest.COMMON_BEAN_OVERRIDE_ALLOWED,
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BaseBinaryStorageIntegrationTest.COMMON_CIRCULAR_REFERENCES,
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BaseBinaryStorageIntegrationTest.COMMON_MCP_DISABLED,
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"hapi.fhir.binary_storage_enabled=true",
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"hapi.fhir.binary_storage_mode=DATABASE"
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}
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)
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class BinaryStorageDatabaseModeIT extends BaseBinaryStorageIntegrationTest {
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@Autowired
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private IBinaryStorageEntityDao binaryStorageEntityDao;
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@Autowired
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private PlatformTransactionManager transactionManager;
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private TransactionTemplate transactionTemplate;
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@BeforeEach
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void initTemplate() {
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transactionTemplate = new TransactionTemplate(transactionManager);
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}
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@Test
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void largeAttachmentStoredInDatabase() {
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Set<String> beforeIds = captureContentIds();
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createPatientWithPhoto(uniqueLabel("database"), randomBytes(150_000));
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Set<String> afterIds = captureContentIds();
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afterIds.removeAll(beforeIds);
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assertThat(afterIds).hasSize(1);
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String binaryId = afterIds.iterator().next();
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BinaryStorageEntity entity = transactionTemplate.execute(status ->
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binaryStorageEntityDao.findById(binaryId).orElseThrow());
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assertThat(entity.hasStorageContent()).isTrue();
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assertThat(entity.getStorageContentBin()).hasSize(150_000);
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transactionTemplate.execute(status -> {
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binaryStorageEntityDao.deleteById(binaryId);
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return null;
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});
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}
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private Set<String> captureContentIds() {
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return transactionTemplate.execute(status ->
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binaryStorageEntityDao.findAll().stream()
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.map(BinaryStorageEntity::getContentId)
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.collect(Collectors.toCollection(LinkedHashSet::new)));
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}
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}
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@SpringBootTest(
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webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT,
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classes = Application.class,
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properties = {
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BaseBinaryStorageIntegrationTest.COMMON_CONFIG_LOCATION,
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"spring.datasource.url=jdbc:h2:mem:binary-storage-fs-default;DB_CLOSE_DELAY=-1",
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BaseBinaryStorageIntegrationTest.COMMON_H2_USERNAME,
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BaseBinaryStorageIntegrationTest.COMMON_H2_PASSWORD,
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BaseBinaryStorageIntegrationTest.COMMON_JPA_DDL,
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BaseBinaryStorageIntegrationTest.COMMON_HIBERNATE_DIALECT,
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BaseBinaryStorageIntegrationTest.COMMON_HIBERNATE_SEARCH_DISABLED,
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BaseBinaryStorageIntegrationTest.COMMON_FLYWAY_DISABLED,
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BaseBinaryStorageIntegrationTest.COMMON_FHIR_VERSION,
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BaseBinaryStorageIntegrationTest.COMMON_REPO_VALIDATION_DISABLED,
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BaseBinaryStorageIntegrationTest.COMMON_MDM_DISABLED,
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BaseBinaryStorageIntegrationTest.COMMON_CR_DISABLED,
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BaseBinaryStorageIntegrationTest.COMMON_SUBSCRIPTION_WS_DISABLED,
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BaseBinaryStorageIntegrationTest.COMMON_BEAN_OVERRIDE_ALLOWED,
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BaseBinaryStorageIntegrationTest.COMMON_CIRCULAR_REFERENCES,
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BaseBinaryStorageIntegrationTest.COMMON_MCP_DISABLED,
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"hapi.fhir.binary_storage_enabled=true",
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"hapi.fhir.binary_storage_mode=FILESYSTEM",
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"hapi.fhir.binary_storage_filesystem_base_directory=target/test-binary-storage/filesystem-default"
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}
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)
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class BinaryStorageFilesystemDefaultIT extends BaseBinaryStorageIntegrationTest {
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static final Path BASE_DIRECTORY = Paths.get("target/test-binary-storage/filesystem-default").toAbsolutePath();
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@Autowired
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private FilesystemBinaryStorageSvcImpl filesystemBinaryStorageSvc;
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@BeforeEach
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void prepareDirectory() throws IOException {
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ensureDirectory(BASE_DIRECTORY);
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deleteDirectoryContents(BASE_DIRECTORY);
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}
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@Test
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void filesystemModeUsesDefaultThreshold() throws IOException {
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assertThat(filesystemBinaryStorageSvc.getMinimumBinarySize()).isEqualTo(102_400);
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assertRegularFileCount(BASE_DIRECTORY, 0);
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createPatientWithPhoto(uniqueLabel("fs-default-inline"), randomBytes(50_000));
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assertRegularFileCount(BASE_DIRECTORY, 0);
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createPatientWithPhoto(uniqueLabel("fs-default-offload"), randomBytes(150_000));
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assertRegularFileCountGreaterThan(BASE_DIRECTORY, 0);
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}
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@AfterEach
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void cleanUpDirectory() throws IOException {
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deleteDirectoryContents(BASE_DIRECTORY);
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}
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}
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@SpringBootTest(
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webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT,
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classes = Application.class,
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properties = {
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BaseBinaryStorageIntegrationTest.COMMON_CONFIG_LOCATION,
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"spring.datasource.url=jdbc:h2:mem:binary-storage-fs-custom;DB_CLOSE_DELAY=-1",
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BaseBinaryStorageIntegrationTest.COMMON_H2_USERNAME,
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BaseBinaryStorageIntegrationTest.COMMON_H2_PASSWORD,
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BaseBinaryStorageIntegrationTest.COMMON_JPA_DDL,
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BaseBinaryStorageIntegrationTest.COMMON_HIBERNATE_DIALECT,
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BaseBinaryStorageIntegrationTest.COMMON_HIBERNATE_SEARCH_DISABLED,
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BaseBinaryStorageIntegrationTest.COMMON_FLYWAY_DISABLED,
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BaseBinaryStorageIntegrationTest.COMMON_FHIR_VERSION,
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BaseBinaryStorageIntegrationTest.COMMON_REPO_VALIDATION_DISABLED,
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BaseBinaryStorageIntegrationTest.COMMON_MDM_DISABLED,
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BaseBinaryStorageIntegrationTest.COMMON_CR_DISABLED,
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BaseBinaryStorageIntegrationTest.COMMON_SUBSCRIPTION_WS_DISABLED,
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BaseBinaryStorageIntegrationTest.COMMON_BEAN_OVERRIDE_ALLOWED,
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BaseBinaryStorageIntegrationTest.COMMON_CIRCULAR_REFERENCES,
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BaseBinaryStorageIntegrationTest.COMMON_MCP_DISABLED,
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"hapi.fhir.binary_storage_enabled=true",
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"hapi.fhir.binary_storage_mode=FILESYSTEM",
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"hapi.fhir.binary_storage_filesystem_base_directory=target/test-binary-storage/filesystem-custom",
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"hapi.fhir.inline_resource_storage_below_size=32768"
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}
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)
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class BinaryStorageFilesystemCustomThresholdIT extends BaseBinaryStorageIntegrationTest {
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static final Path BASE_DIRECTORY = Paths.get("target/test-binary-storage/filesystem-custom").toAbsolutePath();
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@Autowired
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private FilesystemBinaryStorageSvcImpl filesystemBinaryStorageSvc;
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@BeforeEach
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void prepareDirectory() throws IOException {
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ensureDirectory(BASE_DIRECTORY);
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deleteDirectoryContents(BASE_DIRECTORY);
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}
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@Test
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void filesystemModeHonoursCustomThreshold() throws IOException {
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assertThat(filesystemBinaryStorageSvc.getMinimumBinarySize()).isEqualTo(32_768);
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assertRegularFileCount(BASE_DIRECTORY, 0);
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createPatientWithPhoto(uniqueLabel("fs-custom-inline"), randomBytes(30_000));
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assertRegularFileCount(BASE_DIRECTORY, 0);
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createPatientWithPhoto(uniqueLabel("fs-custom-offload"), randomBytes(40_000));
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assertRegularFileCountGreaterThan(BASE_DIRECTORY, 0);
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}
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@AfterEach
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void cleanUpDirectory() throws IOException {
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deleteDirectoryContents(BASE_DIRECTORY);
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}
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}
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@@ -0,0 +1,96 @@
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package ca.uhn.fhir.jpa.starter.common;
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import ca.uhn.fhir.jpa.binstore.DatabaseBinaryContentStorageSvcImpl;
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import ca.uhn.fhir.jpa.binstore.FilesystemBinaryStorageSvcImpl;
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import ca.uhn.fhir.jpa.binary.api.IBinaryStorageSvc;
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import ca.uhn.fhir.jpa.starter.AppProperties;
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import org.junit.jupiter.api.Test;
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import org.junit.jupiter.api.io.TempDir;
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import java.nio.file.Files;
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import java.nio.file.Path;
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import static org.assertj.core.api.Assertions.assertThat;
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import static org.assertj.core.api.Assertions.assertThatThrownBy;
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class FhirServerConfigCommonBinaryStorageTest {
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@TempDir
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Path tempDir;
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private FhirServerConfigCommon newConfig() {
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return new FhirServerConfigCommon(new AppProperties());
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}
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@Test
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void defaultsToDatabaseImplementation() {
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AppProperties props = new AppProperties();
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IBinaryStorageSvc svc = binaryStorageSvc(props);
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assertThat(svc).isInstanceOf(DatabaseBinaryContentStorageSvcImpl.class);
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}
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@Test
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void filesystemModeUsesDefaultMinimumWhenUnspecified() throws Exception {
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AppProperties props = new AppProperties();
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props.setBinary_storage_mode(AppProperties.BinaryStorageMode.FILESYSTEM);
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Path baseDir = tempDir.resolve("fs-default");
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Files.createDirectories(baseDir);
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props.setBinary_storage_filesystem_base_directory(baseDir.toString());
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FilesystemBinaryStorageSvcImpl svc = filesystemBinaryStorageSvc(props);
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assertThat(svc.getMinimumBinarySize()).isEqualTo(102_400);
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}
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@Test
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void filesystemModeHonoursExplicitMinimum() throws Exception {
|
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AppProperties props = new AppProperties();
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props.setBinary_storage_mode(AppProperties.BinaryStorageMode.FILESYSTEM);
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props.setInline_resource_storage_below_size(4096);
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Path baseDir = tempDir.resolve("fs-min-explicit");
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Files.createDirectories(baseDir);
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props.setBinary_storage_filesystem_base_directory(baseDir.toString());
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FilesystemBinaryStorageSvcImpl svc = filesystemBinaryStorageSvc(props);
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assertThat(svc.getMinimumBinarySize()).isEqualTo(4096);
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}
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@Test
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void filesystemModeSupportsZeroMinimumWhenExplicit() throws Exception {
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AppProperties props = new AppProperties();
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props.setBinary_storage_mode(AppProperties.BinaryStorageMode.FILESYSTEM);
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props.setInline_resource_storage_below_size(0);
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Path baseDir = tempDir.resolve("fs-zero");
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Files.createDirectories(baseDir);
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props.setBinary_storage_filesystem_base_directory(baseDir.toString());
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||||
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FilesystemBinaryStorageSvcImpl svc = filesystemBinaryStorageSvc(props);
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||||
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assertThat(svc.getMinimumBinarySize()).isZero();
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||||
}
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||||
|
||||
@Test
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void filesystemModeRequiresBaseDirectory() {
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||||
AppProperties props = new AppProperties();
|
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props.setBinary_storage_mode(AppProperties.BinaryStorageMode.FILESYSTEM);
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assertThatThrownBy(() -> filesystemBinaryStorageSvc(props))
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.isInstanceOf(IllegalArgumentException.class)
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.hasMessageContaining("binary_storage_filesystem_base_directory");
|
||||
}
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||||
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||||
private IBinaryStorageSvc binaryStorageSvc(AppProperties props) {
|
||||
FhirServerConfigCommon config = newConfig();
|
||||
if (props.getBinary_storage_mode() == AppProperties.BinaryStorageMode.FILESYSTEM) {
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||||
return config.filesystemBinaryStorageSvc(props);
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||||
}
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return config.databaseBinaryStorageSvc(props);
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||||
}
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||||
|
||||
private FilesystemBinaryStorageSvcImpl filesystemBinaryStorageSvc(AppProperties props) {
|
||||
return (FilesystemBinaryStorageSvcImpl) binaryStorageSvc(props);
|
||||
}
|
||||
}
|
||||
Reference in New Issue
Block a user