use of com.b2international.snowowl.core.attachments.AttachmentRegistry in project snow-owl by b2ihealthcare.
the class SnomedRf2ExportRequest method execute.
@Override
public Attachment execute(final BranchContext context) {
final String referenceBranch = context.path();
if (referenceBranch.contains(RevisionIndex.AT_CHAR) && !Rf2ReleaseType.SNAPSHOT.equals(releaseType)) {
throw new BadRequestException("Only snapshot export is allowed for point-in-time branch path '%s'.", referenceBranch);
}
if (referenceBranch.contains(RevisionIndex.REV_RANGE)) {
if (!Rf2ReleaseType.DELTA.equals(releaseType) || needsVersionBranchesForDeltaExport()) {
throw new BadRequestException("Only unpublished delta export is allowed for branch path range '%s'.", referenceBranch);
}
}
// register export start time for later use
final long exportStartTime = Instant.now().toEpochMilli();
// Step 1: check if the export reference branch is a working branch path descendant
final CodeSystem referenceCodeSystem = (CodeSystem) context.service(TerminologyResource.class);
if (!CompareUtils.isEmpty(referenceCodeSystem.getSettings())) {
if (Strings.isNullOrEmpty(countryNamespaceElement)) {
if (maintainerType == null) {
String maintainerType = (String) referenceCodeSystem.getSettings().get(SnomedTerminologyComponentConstants.CODESYSTEM_MAINTAINER_TYPE_CONFIG_KEY);
String nrcCountryCode = (String) referenceCodeSystem.getSettings().get(SnomedTerminologyComponentConstants.CODESYSTEM_NRC_COUNTRY_CODE_CONFIG_KEY);
if (!Strings.isNullOrEmpty(maintainerType)) {
String customCountryNamespaceElement = getCountryNamespaceElement(context, referenceCodeSystem, Rf2MaintainerType.getByNameIgnoreCase(maintainerType), Strings.nullToEmpty(nrcCountryCode));
countryNamespaceElement = customCountryNamespaceElement;
}
} else {
countryNamespaceElement = getCountryNamespaceElement(context, referenceCodeSystem, maintainerType, Strings.nullToEmpty(nrcCountryCode));
}
}
if (refSetExportLayout == null && referenceCodeSystem.getSettings().containsKey(SnomedTerminologyComponentConstants.CODESYSTEM_RF2_EXPORT_LAYOUT_CONFIG_KEY)) {
String refSetLayout = (String) referenceCodeSystem.getSettings().get(SnomedTerminologyComponentConstants.CODESYSTEM_RF2_EXPORT_LAYOUT_CONFIG_KEY);
Rf2RefSetExportLayout rf2RefSetExportLayout = Rf2RefSetExportLayout.getByNameIgnoreCase(refSetLayout);
refSetExportLayout = rf2RefSetExportLayout;
}
}
if (Strings.isNullOrEmpty(countryNamespaceElement)) {
countryNamespaceElement = getCountryNamespaceElement(context, referenceCodeSystem, DEFAULT_MAINTAINER_TYPE, "");
}
if (refSetExportLayout == null) {
refSetExportLayout = DEFAULT_RF2_EXPORT_LAYOUT;
}
// Step 2: retrieve code system versions that are visible from the reference branch
final TreeSet<Version> versionsToExport = getAllExportableCodeSystemVersions(context, referenceCodeSystem);
// Step 3: compute branches to export
final List<String> branchesToExport = computeBranchesToExport(referenceBranch, versionsToExport);
// Step 4: compute possible language codes
Multimap<String, String> availableLanguageCodes = getLanguageCodes(context, branchesToExport);
Path exportDirectory = null;
try {
final UUID exportId = UUID.randomUUID();
// create temporary export directory
exportDirectory = createExportDirectory(exportId);
// get archive effective time based on latest version effective / transient effective time / current date
final LocalDateTime archiveEffectiveDate = getArchiveEffectiveTime(context, versionsToExport);
final String archiveEffectiveDateShort = EffectiveTimes.format(archiveEffectiveDate.toLocalDate(), DateFormats.SHORT);
// create main folder including release status and archive effective date
final Path releaseDirectory = createReleaseDirectory(exportDirectory, archiveEffectiveDate);
final Set<String> visitedComponentEffectiveTimes = newHashSet();
final long effectiveTimeStart = startEffectiveTime != null ? EffectiveTimes.getEffectiveTime(startEffectiveTime) : 0;
final long effectiveTimeEnd = endEffectiveTime != null ? EffectiveTimes.getEffectiveTime(endEffectiveTime) : Long.MAX_VALUE;
// export content from the pre-computed version branches
for (String branch : branchesToExport) {
exportBranch(releaseDirectory, context, branch, archiveEffectiveDateShort, effectiveTimeStart, effectiveTimeEnd, visitedComponentEffectiveTimes, availableLanguageCodes.get(branch));
}
// export content from reference branch
if (includePreReleaseContent) {
// If a special branch path was given, use it directly
final String referenceBranchToExport = containsSpecialCharacter(referenceBranch) ? referenceBranch : RevisionIndex.toBranchAtPath(referenceBranch, exportStartTime);
exportBranch(releaseDirectory, context, referenceBranchToExport, archiveEffectiveDateShort, EffectiveTimes.UNSET_EFFECTIVE_TIME, EffectiveTimes.UNSET_EFFECTIVE_TIME, visitedComponentEffectiveTimes, availableLanguageCodes.get(referenceBranch));
}
// Step 6: compress to archive and upload to the file registry
final AttachmentRegistry fileRegistry = context.service(AttachmentRegistry.class);
registerResult(fileRegistry, exportId, exportDirectory);
final String fileName = releaseDirectory.getFileName() + ".zip";
return new Attachment(exportId, fileName);
} catch (final Exception e) {
throw new SnowowlRuntimeException("Failed to export terminology content to RF2.", e);
} finally {
if (exportDirectory != null) {
FileUtils.deleteDirectory(exportDirectory.toFile());
}
}
}
use of com.b2international.snowowl.core.attachments.AttachmentRegistry in project snow-owl by b2ihealthcare.
the class ResourcesImportRequest method execute.
@Override
public ImportResponse execute(ServiceProvider context) {
final InternalAttachmentRegistry attachmentRegistry = (InternalAttachmentRegistry) context.service(AttachmentRegistry.class);
final File file = attachmentRegistry.getAttachment(sourceFile.getAttachmentId());
try {
final List<R> sourceFileContent = loadSourceFileContent(context, file);
final Map<String, R> existingResources = newHashMap(loadExistingResources(context, sourceFileContent));
final ImportDefectAcceptor defectAcceptor = new ImportDefectAcceptor(sourceFile.getFileName());
validateSourceFileContent(context, sourceFileContent, existingResources, defectAcceptor);
List<ImportDefect> defects = defectAcceptor.getDefects();
// Content with validation errors can not be imported
ImportResponse validationResponse = ImportResponse.defects(defects);
if (!validationResponse.getErrors().isEmpty()) {
return validationResponse;
}
final Set<ComponentURI> visitedComponents = Sets.newHashSet();
// Import each resource present in the source file, along with its content
for (final R resource : sourceFileContent) {
final String id = resource.getId();
ComponentURI importedResource = importResource(context, resource, existingResources.get(id));
if (importedResource != null) {
visitedComponents.add(importedResource);
}
visitedComponents.addAll(importContent(context, resource, existingResources.get(id)));
}
return ImportResponse.success(visitedComponents, defects);
} catch (final ApiException e) {
throw e;
} catch (final Exception e) {
String error = "Unexpected error happened during the import of the source file: " + sourceFile.getFileName();
context.log().error(error, e);
return ImportResponse.error(error);
} finally {
if (sourceFile != null && attachmentRegistry != null) {
attachmentRegistry.delete(sourceFile.getAttachmentId());
}
}
}
use of com.b2international.snowowl.core.attachments.AttachmentRegistry in project snow-owl by b2ihealthcare.
the class OntologyExportRequest method execute.
@Override
public String execute(final BranchContext context) {
final RevisionSearcher revisionSearcher = context.service(RevisionSearcher.class);
TerminologyResource resource = context.service(TerminologyResource.class);
@SuppressWarnings("unchecked") final Set<String> reasonerExcludedModuleIds = Collections3.toImmutableSet((Iterable) resource.getSettings().getOrDefault(REASONER_EXCLUDE_MODULE_IDS, Collections.emptySet()));
final SnomedCoreConfiguration configuration = context.service(SnomedCoreConfiguration.class);
final boolean concreteDomainSupportEnabled = configuration.isConcreteDomainSupported();
final ReasonerTaxonomyBuilder taxonomyBuilder = new ReasonerTaxonomyBuilder(reasonerExcludedModuleIds);
taxonomyBuilder.addActiveConceptIds(revisionSearcher);
taxonomyBuilder.finishConcepts();
taxonomyBuilder.addFullySpecifiedNames(revisionSearcher);
taxonomyBuilder.addConceptFlags(revisionSearcher);
taxonomyBuilder.addActiveStatedEdges(revisionSearcher);
taxonomyBuilder.addActiveStatedRelationships(revisionSearcher);
taxonomyBuilder.addNeverGroupedTypeIds(revisionSearcher);
taxonomyBuilder.addActiveAxioms(revisionSearcher);
if (concreteDomainSupportEnabled) {
taxonomyBuilder.addActiveConcreteDomainMembers(revisionSearcher);
}
final ReasonerTaxonomy taxonomy = taxonomyBuilder.build();
final OWLOntologyManager ontologyManager = OWLManager.createOWLOntologyManager();
ontologyManager.getOntologyFactories().add(new DelegateOntologyFactory(taxonomy));
final IRI ontologyIRI = IRI.create(DelegateOntology.NAMESPACE_SCTM + ontologyModuleId);
try {
final OWLOntology ontology = ontologyManager.createOntology(ontologyIRI);
OWLOntology ontologyToExport = ontologyManager.createOntology();
ontology.getAxioms().forEach(axiom -> {
ontologyManager.addAxiom(ontologyToExport, axiom);
});
final OWLDocumentFormat documentFormat = getOWLDocumentFormat();
final AttachmentRegistry fileRegistry = context.service(AttachmentRegistry.class);
final UUID id = UUID.randomUUID();
final PipedOutputStream os = new PipedOutputStream();
final PipedInputStream is = new PipedInputStream(os, PIPE_SIZE);
final ForkJoinTask<?> uploadTask = ForkJoinTask.adapt(() -> fileRegistry.upload(id, is));
final ForkJoinTask<?> saveTask = ForkJoinTask.adapt(() -> {
try {
ontologyManager.saveOntology(ontologyToExport, documentFormat, os);
} catch (final OWLOntologyStorageException e) {
throw createExportFailedException(context, e);
} finally {
try {
os.close();
} catch (final IOException e) {
throw createExportFailedException(context, e);
}
}
});
ForkJoinTask.invokeAll(saveTask, uploadTask);
return id.toString();
} catch (final OWLOntologyCreationException e) {
throw createExportFailedException(context, e);
} catch (final IOException e) {
throw createExportFailedException(context, e);
} finally {
// invalidate static cache entries :'(
ontologyManager.getOntologies().forEach(o -> {
ontologyManager.applyChange(new SetOntologyID(o, new OWLOntologyID()));
});
}
}
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