Examples with ResourceURI com.b2international.snowowl.core.ResourceURI used on opensource projects

Example 16 with ResourceURI

use of com.b2international.snowowl.core.ResourceURI in project snow-owl by b2ihealthcare.

the class ValueSetMemberSearchSnomedReferenceSetTest method filterByRefsetUri.

@Test
public void filterByRefsetUri() throws Exception {
    SnomedReferenceSetMembers members = SnomedRequests.prepareSearchMember().all().filterByRefSet(Concepts.REFSET_DESCRIPTION_TYPE).build(CODESYSTEM).execute(Services.bus()).getSync(1, TimeUnit.MINUTES);
    ValueSetMembers setMembers = CodeSystemRequests.prepareSearchMembers().all().filterByValueSet(ComponentURI.of(CODESYSTEM, SnomedConcept.REFSET_TYPE, Concepts.REFSET_DESCRIPTION_TYPE).toString()).buildAsync().execute(Services.bus()).getSync(1, TimeUnit.MINUTES);
    assertThat(setMembers.getTotal()).isEqualTo(members.getTotal());
    assertThat(setMembers.stream().allMatch(m -> SnomedContentRule.SNOMEDCT.equals(m.getReferencedComponentURI().resourceUri())));
    Set<String> setMemberSourceCodes = FluentIterable.from(setMembers).transform(m -> m.getReferencedComponentURI().identifier()).toSet();
    Set<String> setMemberSourceTerms = FluentIterable.from(setMembers).transform(m -> m.getReferencedComponentURI().identifier()).toSet();
    assertThat(setMemberSourceCodes.contains(Concepts.TEXT_DEFINITION));
    assertThat(setMemberSourceCodes.contains(Concepts.FULLY_SPECIFIED_NAME));
    assertThat(setMemberSourceCodes.contains(Concepts.SYNONYM));
    assertThat(setMemberSourceTerms.contains(DEFINITION));
    assertThat(setMemberSourceTerms.contains(FSN));
    assertThat(setMemberSourceTerms.contains(SYNONYM));
}

Example 17 with ResourceURI

use of com.b2international.snowowl.core.ResourceURI in project snow-owl by b2ihealthcare.

the class SnomedConceptMapSearchRequestEvaluator method toCollectionResource.

private ConceptMapMappings toCollectionResource(SnomedReferenceSetMembers referenceSetMembers, ResourceURI uri, ServiceProvider context, Options search, SnomedDisplayTermType snomedDisplayTermType) {
    final Set<String> refSetsToFetch = referenceSetMembers.stream().map(SnomedReferenceSetMember::getRefsetId).collect(Collectors.toSet());
    final Map<String, SnomedConcept> refSetsById = SnomedRequests.prepareSearchConcept().all().filterByIds(refSetsToFetch).setLocales(search.getList(OptionKey.LOCALES, ExtendedLocale.class)).setExpand("pt(),referenceSet()").build(uri).execute(context.service(IEventBus.class)).getSync(1, TimeUnit.MINUTES).stream().collect(Collectors.toMap(SnomedConcept::getId, concept -> concept));
    final Map<String, ComponentURI> targetComponentsByRefSetId = getTargetComponentsByRefSetId(context, refSetsById);
    List<ConceptMapMapping> mappings = referenceSetMembers.stream().filter(m -> SnomedConcept.TYPE.equals(m.getReferencedComponent().getComponentType())).map(m -> {
        return toMapping(m, uri, targetComponentsByRefSetId.get(m.getRefsetId()), snomedDisplayTermType, refSetsById);
    }).collect(Collectors.toList());
    if (!mappings.isEmpty()) {
        final Map<String, Concept> conceptsById = Multimaps.index(mappings, mapping -> mapping.getTargetComponentURI().resourceUri()).asMap().entrySet().stream().filter(entry -> !TerminologyRegistry.UNSPECIFIED.equals(entry.getKey().getResourceId())).map(entry -> {
            final Set<String> idsToFetch = entry.getValue().stream().map(map -> map.getTargetComponentURI().identifier()).collect(Collectors.toSet());
            return CodeSystemRequests.prepareSearchConcepts().all().filterByCodeSystemUri(entry.getKey()).filterByIds(idsToFetch).buildAsync().execute(context.service(IEventBus.class)).getSync(5, TimeUnit.MINUTES).stream().collect(Collectors.toMap(Concept::getId, c -> c));
        }).flatMap(map -> map.entrySet().stream()).collect(Collectors.toMap(entry -> entry.getKey(), entry -> entry.getValue(), (concept1, concept2) -> concept1));
        mappings = mappings.stream().map(mapping -> {
            final String mapTargetId = mapping.getTargetComponentURI().identifier();
            if (conceptsById.containsKey(mapTargetId) && !mapping.getTargetComponentURI().isUnspecified()) {
                final Concept concept = conceptsById.get(mapTargetId);
                return mapping.toBuilder().targetTerm(concept.getTerm()).targetIconId(concept.getIconId()).build();
            } else {
                return mapping;
            }
        }).collect(Collectors.toList());
    }
    return new ConceptMapMappings(mappings, referenceSetMembers.getSearchAfter(), referenceSetMembers.getLimit(), referenceSetMembers.getTotal());
}

Example 18 with ResourceURI

use of com.b2international.snowowl.core.ResourceURI in project snow-owl by b2ihealthcare.

the class ValidateRequest method doValidate.

private ValidationResult doValidate(BranchContext context, Writer index) throws IOException {
    final String branchPath = context.path();
    ValidationRuleSearchRequestBuilder req = ValidationRequests.rules().prepareSearch();
    TerminologyResource resource = context.service(TerminologyResource.class);
    ResourceURI resourceURI = resource.getResourceURI(branchPath);
    if (!CompareUtils.isEmpty(ruleIds)) {
        req.filterByIds(ruleIds);
    }
    final ValidationRules rules = req.all().build().execute(context);
    final ValidationThreadPool pool = context.service(ValidationThreadPool.class);
    final BlockingQueue<IssuesToPersist> issuesToPersistQueue = Queues.newLinkedBlockingDeque();
    final List<Promise<Object>> validationPromises = Lists.newArrayList();
    // evaluate selected rules
    for (ValidationRule rule : rules) {
        checkArgument(rule.getCheckType() != null, "CheckType is missing for rule " + rule.getId());
        final ValidationRuleEvaluator evaluator = ValidationRuleEvaluator.Registry.get(rule.getType());
        if (evaluator != null) {
            validationPromises.add(pool.submit(rule.getCheckType(), () -> {
                Stopwatch w = Stopwatch.createStarted();
                try {
                    LOG.info("Executing rule '{}'...", rule.getId());
                    final List<?> evaluationResponse = evaluator.eval(context, rule, ruleParameters);
                    issuesToPersistQueue.offer(new IssuesToPersist(rule.getId(), evaluationResponse));
                    LOG.info("Execution of rule '{}' successfully completed in '{}'.", rule.getId(), w);
                // TODO report successfully executed validation rule
                } catch (Exception e) {
                    // TODO report failed validation rule
                    LOG.error("Execution of rule '{}' failed after '{}'.", rule.getId(), w, e);
                }
            }));
        }
    }
    final Set<String> ruleIds = rules.stream().map(ValidationRule::getId).collect(Collectors.toSet());
    final Multimap<String, ComponentIdentifier> whiteListedEntries = fetchWhiteListEntries(context, ruleIds);
    final Promise<List<Object>> promise = Promise.all(validationPromises);
    while (!promise.isDone() || !issuesToPersistQueue.isEmpty()) {
        if (!issuesToPersistQueue.isEmpty()) {
            final Collection<IssuesToPersist> issuesToPersist = newArrayList();
            issuesToPersistQueue.drainTo(issuesToPersist);
            if (!issuesToPersist.isEmpty()) {
                final List<String> rulesToPersist = issuesToPersist.stream().map(itp -> itp.ruleId).collect(Collectors.toList());
                LOG.info("Persisting issues generated by rules '{}'...", rulesToPersist);
                // persist new issues generated by rules so far, extending them using the Issue Extension API
                int persistedIssues = 0;
                final Multimap<String, ValidationIssue> issuesToExtendWithDetailsByToolingId = HashMultimap.create();
                for (IssuesToPersist ruleIssues : Iterables.consumingIterable(issuesToPersist)) {
                    final String ruleId = ruleIssues.ruleId;
                    final List<ValidationIssue> existingRuleIssues = ValidationRequests.issues().prepareSearch().all().filterByResourceUri(resourceURI).filterByRule(ruleId).build().execute(context).getItems();
                    final Set<String> issueIdsToDelete = Sets.newHashSet();
                    final Map<ComponentIdentifier, ValidationIssue> existingIsssuesByComponentIdentifier = new HashMap<>();
                    for (ValidationIssue issue : existingRuleIssues) {
                        if (existingIsssuesByComponentIdentifier.containsKey(issue.getAffectedComponent())) {
                            issueIdsToDelete.add(issue.getId());
                        } else {
                            existingIsssuesByComponentIdentifier.put(issue.getAffectedComponent(), issue);
                        }
                    }
                    // remove all processed whitelist entries
                    final Collection<ComponentIdentifier> ruleWhiteListEntries = whiteListedEntries.removeAll(ruleId);
                    final String toolingId = rules.stream().filter(rule -> ruleId.equals(rule.getId())).findFirst().get().getToolingId();
                    for (ValidationIssueDetails issueDetails : ruleIssues.issueDetails) {
                        final ValidationIssue validationIssue;
                        ComponentIdentifier componentIdentifier = issueDetails.affectedComponentId;
                        if (!existingIsssuesByComponentIdentifier.containsKey(componentIdentifier)) {
                            validationIssue = new ValidationIssue(UUID.randomUUID().toString(), ruleId, ComponentURI.of(resourceURI, componentIdentifier), ruleWhiteListEntries.contains(componentIdentifier));
                        } else {
                            final ValidationIssue issueToCopy = existingIsssuesByComponentIdentifier.get(componentIdentifier);
                            validationIssue = new ValidationIssue(issueToCopy.getId(), issueToCopy.getRuleId(), ComponentURI.of(resourceURI, issueToCopy.getAffectedComponent()), ruleWhiteListEntries.contains(issueToCopy.getAffectedComponent()));
                            existingIsssuesByComponentIdentifier.remove(componentIdentifier);
                        }
                        validationIssue.setDetails(ValidationIssueDetails.HIGHLIGHT_DETAILS, issueDetails.stylingDetails);
                        issuesToExtendWithDetailsByToolingId.put(toolingId, validationIssue);
                        persistedIssues++;
                    }
                    existingRuleIssues.stream().filter(issue -> existingIsssuesByComponentIdentifier.containsKey(issue.getAffectedComponent())).forEach(issue -> issueIdsToDelete.add(issue.getId()));
                    if (!issueIdsToDelete.isEmpty()) {
                        index.removeAll(Collections.singletonMap(ValidationIssue.class, issueIdsToDelete));
                    }
                }
                for (String toolingId : issuesToExtendWithDetailsByToolingId.keySet()) {
                    final ValidationIssueDetailExtension extensions = context.service(ValidationIssueDetailExtensionProvider.class).getExtensions(toolingId);
                    final Collection<ValidationIssue> issues = issuesToExtendWithDetailsByToolingId.removeAll(toolingId);
                    extensions.extendIssues(context, issues, ruleParameters);
                    for (ValidationIssue issue : issues) {
                        index.put(issue);
                    }
                }
                index.commit();
                LOG.info("Persisted '{}' issues generated by rules '{}'.", persistedIssues, rulesToPersist);
            }
        } else {
            try {
                // wait at least number of rules * 50ms for the next responses
                Thread.sleep(Math.min(((long) ruleIds.size()) * 100, POLL_INTERVAL_MAX));
            } catch (InterruptedException e) {
                throw new SnowowlRuntimeException(e);
            }
        }
    }
    // TODO return ValidationResult object with status and new issue IDs as set
    return new ValidationResult(context.info().id(), context.path());
}

Example 19 with ResourceURI

use of com.b2international.snowowl.core.ResourceURI in project snow-owl by b2ihealthcare.

the class ComponentURI method of.

public static ComponentURI of(String uri) {
    if (Strings.isNullOrEmpty(uri)) {
        return ComponentURI.UNSPECIFIED;
    }
    final List<String> parts = SLASH_SPLITTER.splitToList(uri);
    if (parts.size() < 4) {
        throw new BadRequestException("A component uri consists of at least four parts (resourceType/resourceId/componentType/componentId). Arg was: %s", uri);
    }
    int terminologyComponentTypeIndex = parts.size() - 2;
    int componentIdIndex = parts.size() - 1;
    ResourceURI resourceURI = new ResourceURI(SLASH_JOINER.join(parts.subList(0, terminologyComponentTypeIndex)));
    String componentType = parts.get(terminologyComponentTypeIndex);
    String componentId = parts.get(componentIdIndex);
    return new ComponentURI(resourceURI, componentType, componentId);
}

Example 20 with ResourceURI

use of com.b2international.snowowl.core.ResourceURI in project snow-owl by b2ihealthcare.

the class SnomedContentRule method createCodeSystemIfNotExist.

private void createCodeSystemIfNotExist() {
    final IEventBus eventBus = Services.bus();
    final CodeSystems codeSystems = CodeSystemRequests.prepareSearchCodeSystem().setLimit(0).filterById(codeSystemId.getResourceId()).buildAsync().execute(eventBus).getSync();
    if (codeSystems.getTotal() > 0) {
        return;
    }
    final ResourceURI extensionOf = Optional.ofNullable(this.extensionOf).or(() -> {
        return ResourceRequests.prepareSearchVersion().filterByResource(SNOMEDCT).sortBy(Sort.fieldDesc(VersionDocument.Fields.EFFECTIVE_TIME)).setLimit(1).buildAsync().execute(eventBus).getSync().first().map(Version::getVersionResourceURI);
    }).orElse(null);
    CodeSystemRequests.prepareNewCodeSystem().setId(codeSystemId.getResourceId()).setBranchPath(SNOMEDCT.equals(codeSystemId) ? Branch.MAIN_PATH : null).setUrl(SNOMEDCT.equals(codeSystemId) ? SnomedTerminologyComponentConstants.SNOMED_URI_SCT + "/" + Concepts.MODULE_SCT_CORE : SnomedTerminologyComponentConstants.SNOMED_URI_SCT + "/" + codeSystemId.getResourceId()).setDescription("description").setExtensionOf(extensionOf).setLanguage("ENG").setTitle(codeSystemId.getResourceId()).setOid("oid:" + codeSystemId).setOwner("https://b2i.sg").setToolingId(SnomedTerminologyComponentConstants.TOOLING_ID).setSettings(Map.of(SnomedTerminologyComponentConstants.CODESYSTEM_LANGUAGE_CONFIG_KEY, List.of(Map.of("languageTag", "en", "languageRefSetIds", Lists.newArrayList(Concepts.REFSET_LANGUAGE_TYPE_UK, Concepts.REFSET_LANGUAGE_TYPE_US))))).build(RestExtensions.USER, String.format("Create code system %s", codeSystemId)).execute(eventBus).getSync(1, TimeUnit.MINUTES);
}