Examples with Request com.b2international.snowowl.core.events.Request used on opensource projects

Example 1 with Request

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

the class SnomedRf2ExportRequest method getIdentifierConcepts.

private List<SnomedConcept> getIdentifierConcepts(final RepositoryContext context, final String currentVersion) {
    final Collection<String> refSetsToLoad;
    if (refSets == null) {
        // Retrieve all reference sets if refSets is null
        final Request<BranchContext, SnomedReferenceSets> refSetRequest = SnomedRequests.prepareSearchRefSet().all().build();
        final SnomedReferenceSets allReferenceSets = execute(context, currentVersion, refSetRequest);
        refSetsToLoad = allReferenceSets.stream().map(r -> r.getId()).collect(Collectors.toSet());
    } else {
        refSetsToLoad = refSets;
    }
    final SnomedConceptSearchRequestBuilder refSetRequestBuilder = SnomedRequests.prepareSearchConcept().all().filterByIds(refSetsToLoad).setExpand("pt(),referenceSet()").setLocales(locales());
    final Request<BranchContext, SnomedConcepts> request = refSetRequestBuilder.build();
    final SnomedConcepts referenceSets = execute(context, currentVersion, request);
    // Return only the identifier concepts which have an existing reference set on this branch
    return referenceSets.stream().filter(c -> c.getReferenceSet() != null).collect(Collectors.toList());
}

Example 2 with Request

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

the class DescriptionChangeConverter method expand.

@Override
public void expand(final List<DescriptionChange> results) {
    if (!expand().containsKey(DescriptionChange.Expand.DESCRIPTION)) {
        return;
    }
    /*
		 * Depending on the CD member change search request, we might need to issue
		 * SNOMED CT searches against multiple branches; find out which ones we have.
		 */
    final Multimap<String, DescriptionChange> itemsByBranch = getItemsByBranch(results);
    // Check if we only need to load inferred CD members in their entirety
    final Options expandOptions = expand().getOptions(DescriptionChange.Expand.DESCRIPTION);
    final boolean inferredOnly = expandOptions.getBoolean("inferredOnly");
    final Options descriptionExpandOptions = expandOptions.getOptions("expand");
    final Options conceptOptions = descriptionExpandOptions.getOptions("concept");
    final boolean needsConcept = descriptionExpandOptions.keySet().contains("concept");
    for (final String branch : itemsByBranch.keySet()) {
        final Collection<DescriptionChange> itemsForCurrentBranch = itemsByBranch.get(branch);
        /*
			 * Expand concept on "new" descriptions via a separate search request, they will
			 * be different from the concept on the "origin" description.
			 */
        if (needsConcept) {
            final List<ReasonerDescription> blankDescriptions = itemsForCurrentBranch.stream().filter(c -> ChangeNature.NEW.equals(c.getChangeNature())).map(DescriptionChange::getDescription).collect(Collectors.toList());
            final Multimap<String, ReasonerDescription> descriptionsByConceptId = FluentIterable.from(blankDescriptions).index(ReasonerDescription::getConceptId);
            final Set<String> conceptIds = descriptionsByConceptId.keySet();
            final Request<BranchContext, SnomedConcepts> conceptSearchRequest = SnomedRequests.prepareSearchConcept().filterByIds(conceptIds).setLimit(conceptIds.size()).setExpand(conceptOptions.get("expand", Options.class)).setLocales(locales()).build();
            final SnomedConcepts concepts = new BranchRequest<>(branch, new RevisionIndexReadRequest<>(conceptSearchRequest)).execute(context());
            for (final SnomedConcept concept : concepts) {
                final String conceptId = concept.getId();
                final Collection<ReasonerDescription> descriptionsForConcept = descriptionsByConceptId.get(conceptId);
                for (final ReasonerDescription description : descriptionsForConcept) {
                    description.setConcept(concept);
                }
            }
        }
        /*
			 * Then fetch all the required descriptions. Note that the same "origin"
			 * description might be used for multiple eg. "new" counterparts.
			 */
        final Set<String> descriptionIds = itemsForCurrentBranch.stream().filter(c -> !inferredOnly || ChangeNature.NEW.equals(c.getChangeNature())).map(c -> c.getDescription().getOriginDescriptionId()).collect(Collectors.toSet());
        final Request<BranchContext, SnomedDescriptions> descriptionSearchRequest = SnomedRequests.prepareSearchDescription().filterByIds(descriptionIds).setLimit(descriptionIds.size()).setExpand(descriptionExpandOptions).setLocales(locales()).build();
        final SnomedDescriptions descriptions = new BranchRequest<>(branch, new RevisionIndexReadRequest<>(descriptionSearchRequest)).execute(context());
        final Map<String, SnomedDescription> descriptionsById = Maps.uniqueIndex(descriptions, SnomedDescription::getId);
        for (final DescriptionChange item : itemsForCurrentBranch) {
            final ReasonerDescription reasonerDescription = item.getDescription();
            final String descriptionId = reasonerDescription.getOriginDescriptionId();
            switch(item.getChangeNature()) {
                case NEW:
                    {
                        final SnomedDescription expandedDescription = descriptionsById.get(descriptionId);
                        reasonerDescription.setAcceptabilityMap(expandedDescription.getAcceptabilityMap());
                        reasonerDescription.setCaseSignificanceId(expandedDescription.getCaseSignificanceId());
                        // reasonerDescription.setConcept(...) is already set earlier (or expanded)
                        reasonerDescription.setLanguageCode(expandedDescription.getLanguageCode());
                        // reasonerMember.setReleased(...) is already set
                        reasonerDescription.setTerm(expandedDescription.getTerm());
                        reasonerDescription.setType(expandedDescription.getType());
                    }
                    break;
                case REDUNDANT:
                    if (!inferredOnly) {
                        final SnomedDescription expandedDescription = descriptionsById.get(descriptionId);
                        reasonerDescription.setAcceptabilityMap(expandedDescription.getAcceptabilityMap());
                        reasonerDescription.setCaseSignificanceId(expandedDescription.getCaseSignificanceId());
                        reasonerDescription.setConcept(expandedDescription.getConcept());
                        reasonerDescription.setLanguageCode(expandedDescription.getLanguageCode());
                        // reasonerMember.setReleased(...) is already set
                        reasonerDescription.setTerm(expandedDescription.getTerm());
                        reasonerDescription.setType(expandedDescription.getType());
                    }
                    break;
                default:
                    throw new IllegalStateException(String.format("Unexpected description change '%s' found with SCTID '%s'.", item.getChangeNature(), item.getDescription().getOriginDescriptionId()));
            }
        }
    }
}

Example 3 with Request

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

the class CommitInfoRequestTest method getCommitInfoByComment.

private CommitInfo getCommitInfoByComment(final String comment) {
    Request<RepositoryContext, CommitInfos> req = RepositoryRequests.commitInfos().prepareSearchCommitInfo().filterByComment(comment).build();
    final CommitInfos commitInfos = new ResourceRepositoryRequestBuilder<CommitInfos>() {

        @Override
        public Request<RepositoryContext, CommitInfos> build() {
            return req;
        }
    }.buildAsync().execute(bus).getSync();
    assertEquals(commitInfos.getTotal(), 1);
    return Iterables.getOnlyElement(commitInfos);
}

Example 4 with Request

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

the class AuthorizedRequest method execute.

@Override
public R execute(ServiceProvider context) {
    final RequestHeaders requestHeaders = context.service(RequestHeaders.class);
    final String authorizationToken = requestHeaders.header(AUTHORIZATION_HEADER);
    final IdentityProvider identityProvider = context.service(IdentityProvider.class);
    final Collection<Request<?, ?>> requests = getNestedRequests();
    final User user;
    // if there is no authentication configured
    if (IdentityProvider.NOOP == identityProvider) {
        // allow execution as SYSTEM user
        user = User.SYSTEM;
    } else if (Strings.isNullOrEmpty(authorizationToken)) {
        // allow login requests in
        if (requests.stream().allMatch(req -> req.getClass().isAnnotationPresent(Unprotected.class))) {
            user = User.SYSTEM;
        } else {
            // if there is authentication configured, but no authorization token found prevent execution and throw UnauthorizedException
            if (PlatformUtil.isDevVersion()) {
                Request<?, ?> request = Iterables.getFirst(requests, null);
                System.err.println(request);
            }
            throw new UnauthorizedException("Missing authorization token");
        }
    } else {
        // verify authorization header value
        user = context.service(AuthorizationHeaderVerifier.class).auth(authorizationToken);
        if (user == null) {
            throw new UnauthorizedException("Incorrect authorization token");
        }
    }
    ServiceProvider userContext = context.inject().bind(User.class, user).bind(IEventBus.class, new AuthorizedEventBus(context.service(IEventBus.class), requestHeaders.headers())).build();
    if (!User.SYSTEM.equals(user) && !user.isAdministrator()) {
        // authorize user whether it is permitted to execute the request(s) or not
        requests.stream().filter(AccessControl.class::isInstance).map(AccessControl.class::cast).flatMap(ac -> {
            List<Permission> permissions = ac.getPermissions(userContext, next());
            if (permissions.isEmpty()) {
                context.log().warn("No permissions required to execute request '{}'.", MonitoredRequest.toJson(context, next(), Map.of()));
            }
            return permissions.stream();
        }).forEach(permissionRequirement -> {
            if (!user.hasPermission(permissionRequirement)) {
                throw new ForbiddenException("Operation not permitted. '%s' permission is required. User has '%s'.", permissionRequirement.getPermission(), user.getPermissions());
            }
        });
    }
    return next(userContext);
}

Example 5 with Request

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

the class CommitInfoRequestTest method getCommitInfo.

@Test
public void getCommitInfo() {
    final String oid = UUID.randomUUID().toString();
    final String shortName = UUID.randomUUID().toString();
    final String comment = "Code system for commit info 1";
    createCodeSystem(oid, shortName, comment);
    final String id = getCommitInfoByComment(comment).getId();
    Request<RepositoryContext, CommitInfo> req = RepositoryRequests.commitInfos().prepareGetCommitInfo(id).build();
    CommitInfo commitInfo = new ResourceRepositoryRequestBuilder<CommitInfo>() {

        @Override
        public Request<RepositoryContext, CommitInfo> build() {
            return req;
        }
    }.buildAsync().execute(bus).getSync();
    assertEquals(id, commitInfo.getId());
    assertEquals(comment, commitInfo.getComment());
    assertEquals(BRANCH, commitInfo.getBranch());
    assertEquals(USER_ID, commitInfo.getAuthor());
}