use of org.ihtsdo.drools.validator.rf2.service.DroolsDescriptionService in project snomed-drools by IHTSDO.
the class DroolsRF2Validator method validateSnapshot.
public List<InvalidContent> validateSnapshot(InputStream snomedRf2EditionZip, Set<String> ruleSetNamesToRun) throws ReleaseImportException {
long start = new Date().getTime();
Assert.isTrue(ruleSetNamesToRun != null && !ruleSetNamesToRun.isEmpty(), "The name of at least one rule set must be specified.");
ReleaseImporter importer = new ReleaseImporter();
SnomedDroolsComponentRepository repository = new SnomedDroolsComponentRepository();
logger.info("Loading components from RF2");
LoadingProfile loadingProfile = LoadingProfile.complete;
loadingProfile.getIncludedReferenceSetFilenamePatterns().add(".*_cRefset_Language.*");
importer.loadSnapshotReleaseFiles(snomedRf2EditionZip, loadingProfile, new SnomedDroolsComponentFactory(repository));
logger.info("Components loaded");
DroolsConceptService conceptService = new DroolsConceptService(repository);
DroolsDescriptionService descriptionService = new DroolsDescriptionService(repository);
DroolsRelationshipService relationshipService = new DroolsRelationshipService(repository);
Collection<DroolsConcept> concepts = repository.getConcepts();
logger.info("Running tests");
List<InvalidContent> invalidContents = ruleExecutor.execute(ruleSetNamesToRun, concepts, conceptService, descriptionService, relationshipService, true, false);
logger.info("Tests complete. Total run time {} seconds", (new Date().getTime() - start) / 1000);
logger.info("invalidContent count {}", invalidContents.size());
return invalidContents;
}
use of org.ihtsdo.drools.validator.rf2.service.DroolsDescriptionService in project snomed-drools by IHTSDO.
the class DroolsRF2Validator method validateRF2Files.
/**
* @param extractedRF2FilesDirectories Paths to directories containing all extracted RF2 files. This can be the snapshot files of a single or multiple code systems and
* can also include delta files for the new release.
* @param previousReleaseDirectories Path to directories containing extracted RF2 files from the previous release. These are used to determine the released status of
* components, that is used in some assertions.
* @param ruleSetNamesToRun The assertion groups to run the rules of.
* @param currentEffectiveTime The current effectiveTime of the latest published files, used to determine the published flag on components.
* @param includedModules Optional filter to validate components only in specific modules.
* @param activeConceptsOnly Optional filter to return invalid content only for active concepts (ignore inactive concepts).
* @return A collections of invalid content according to the rules within the assertion groups selected.
* @throws ReleaseImportException Exception thrown when application fails to load the RF2 files to be validated.
*/
public List<InvalidContent> validateRF2Files(Set<String> extractedRF2FilesDirectories, Set<String> previousReleaseDirectories, Set<String> ruleSetNamesToRun, String currentEffectiveTime, Set<String> includedModules, boolean activeConceptsOnly) throws ReleaseImportException {
long start = new Date().getTime();
Assert.isTrue(ruleSetNamesToRun != null && !ruleSetNamesToRun.isEmpty(), "The name of at least one rule set must be specified.");
PreviousReleaseComponentFactory previousReleaseComponentFactory = null;
if (previousReleaseDirectories != null) {
previousReleaseComponentFactory = loadPreviousReleaseComponentIds(previousReleaseDirectories);
}
logger.info("Loading components from RF2");
SnomedDroolsComponentRepository repository = loadComponentsFromRF2(extractedRF2FilesDirectories, currentEffectiveTime, previousReleaseComponentFactory);
logger.info("Components loaded");
DroolsConceptService conceptService = new DroolsConceptService(repository);
DroolsDescriptionService descriptionService = new DroolsDescriptionService(repository, testResourceProvider);
DroolsRelationshipService relationshipService = new DroolsRelationshipService(repository);
Collection<DroolsConcept> concepts = repository.getConcepts();
logger.info("Running tests");
List<InvalidContent> invalidContents = ruleExecutor.execute(ruleSetNamesToRun, concepts, conceptService, descriptionService, relationshipService, true, false);
invalidContents.addAll(repository.getComponentLoadingErrors());
// Filter only invalid components that are in the specified modules list, if modules list is not specified, return all invalid components
if (includedModules != null && !includedModules.isEmpty()) {
logger.info("Filtering invalid contents for included module ids: {}", String.join(",", includedModules));
invalidContents = invalidContents.stream().filter(content -> includedModules.contains(content.getComponent().getModuleId())).collect(Collectors.toList());
}
// Filter only active concepts
if (activeConceptsOnly) {
invalidContents = invalidContents.stream().filter(c -> conceptService.isActive(c.getConceptId())).collect(Collectors.toList());
}
// Add concept FSN to invalid contents
for (InvalidContent invalidContent : invalidContents) {
if (invalidContent.getConceptId() != null && !invalidContent.getConceptId().isEmpty()) {
Set<String> fsnSet = descriptionService.getFSNs(Sets.newHashSet(invalidContent.getConceptId()));
if (!fsnSet.isEmpty()) {
invalidContent.setConceptFsn(fsnSet.iterator().next());
}
}
}
// Free resources after getting validation results
repository.cleanup();
descriptionService.getDroolsDescriptionIndex().cleanup();
logger.info("invalidContent count {}", invalidContents.size());
logger.info("Tests complete. Total run time {} seconds", (new Date().getTime() - start) / 1000);
return invalidContents;
}
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