Examples with Function java.util.function.Function used on opensource projects

Example 91 with Function

use of java.util.function.Function in project gatk by broadinstitute.

the class ReadsDataSourceUnitTest method testManuallySpecifiedIndicesWithCustomReaderFactoryAndNullWrappers.

@Test(dataProvider = "manuallySpecifiedIndexTestData")
public void testManuallySpecifiedIndicesWithCustomReaderFactoryAndNullWrappers(final List<Path> bams, final List<Path> indices) {
    final SamReaderFactory customFactory = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.STRICT);
    // ReadsDataSource should not be using the wrapper since the files are not on the Google cloud.
    // So we pass this invalid wrapper: if the code tries to use it, it'll blow up.
    Function<SeekableByteChannel, SeekableByteChannel> nullWrapper = (SeekableByteChannel) -> null;
    try (final ReadsDataSource readsSource = new ReadsDataSource(bams, indices, customFactory, nullWrapper, nullWrapper)) {
        Assert.assertTrue(readsSource.indicesAvailable(), "Explicitly-provided indices not detected for bams: " + bams);
        final Iterator<GATKRead> queryReads = readsSource.query(new SimpleInterval("1", 1, 300));
        int queryCount = 0;
        while (queryReads.hasNext()) {
            ++queryCount;
            queryReads.next();
        }
        Assert.assertEquals(queryCount, 5, "Wrong number of reads returned in query");
    }
}

Example 92 with Function

use of java.util.function.Function in project ddf by codice.

the class Historian method version.

/**
     * Versions updated {@link Metacard}s and {@link ContentItem}s.
     *
     * @param streamUpdateRequest   Needed to pass {@link ddf.catalog.core.versioning.MetacardVersion#SKIP_VERSIONING}
     *                              flag into downstream update
     * @param updateStorageResponse Versions this response's updated items
     * @return the update response originally passed in
     * @throws UnsupportedQueryException
     * @throws SourceUnavailableException
     * @throws IngestException
     */
public UpdateStorageResponse version(UpdateStorageRequest streamUpdateRequest, UpdateStorageResponse updateStorageResponse, UpdateResponse updateResponse) throws UnsupportedQueryException, SourceUnavailableException, IngestException {
    if (doSkip(updateStorageResponse)) {
        return updateStorageResponse;
    }
    setSkipFlag(streamUpdateRequest);
    setSkipFlag(updateStorageResponse);
    List<Metacard> updatedMetacards = updateStorageResponse.getUpdatedContentItems().stream().filter(ci -> StringUtils.isBlank(ci.getQualifier())).map(ContentItem::getMetacard).filter(Objects::nonNull).filter(isNotVersionNorDeleted).collect(Collectors.toList());
    Map<String, Metacard> originalMetacards = query(forIds(updatedMetacards.stream().map(Metacard::getId).collect(Collectors.toList())));
    Collection<ReadStorageRequest> ids = getReadStorageRequests(updatedMetacards);
    Map<String, List<ContentItem>> content = getContent(ids);
    Function<String, Action> getAction = (id) -> content.containsKey(id) ? Action.VERSIONED_CONTENT : Action.VERSIONED;
    Map<String, Metacard> versionMetacards = getVersionMetacards(originalMetacards.values(), getAction, (Subject) updateResponse.getProperties().get(SecurityConstants.SECURITY_SUBJECT));
    CreateStorageResponse createStorageResponse = versionContentItems(content, versionMetacards);
    if (createStorageResponse == null) {
        LOGGER.debug("Could not version content items.");
        return updateStorageResponse;
    }
    setResourceUriForContent(/*mutable*/
    versionMetacards, createStorageResponse);
    storeVersionMetacards(versionMetacards);
    return updateStorageResponse;
}

Example 93 with Function

use of java.util.function.Function in project ddf by codice.

the class Historian method version.

/**
     * Versions deleted {@link Metacard}s.
     *
     * @param deleteResponse Versions this responses deleted metacards
     */
public DeleteResponse version(DeleteResponse deleteResponse) throws SourceUnavailableException, IngestException {
    if (doSkip(deleteResponse)) {
        return deleteResponse;
    }
    setSkipFlag(deleteResponse);
    List<Metacard> deletedMetacards = deleteResponse.getDeletedMetacards().stream().filter(isNotVersionNorDeleted).collect(Collectors.toList());
    // [ContentItem.getId: content items]
    Map<String, List<ContentItem>> contentItems = getContent(getReadStorageRequests(deletedMetacards));
    Function<String, Action> getAction = (id) -> contentItems.containsKey(id) ? Action.DELETED_CONTENT : Action.DELETED;
    // [MetacardVersion.VERSION_OF_ID: versioned metacard]
    Map<String, Metacard> versionedMap = getVersionMetacards(deletedMetacards, getAction, (Subject) deleteResponse.getRequest().getProperties().get(SecurityConstants.SECURITY_SUBJECT));
    CreateStorageResponse createStorageResponse = versionContentItems(contentItems, versionedMap);
    if (createStorageResponse != null) {
        setResourceUriForContent(/*Mutable*/
        versionedMap, createStorageResponse);
    }
    executeAsSystem(() -> catalogProvider().create(new CreateRequestImpl(new ArrayList<>(versionedMap.values()))));
    String emailAddress = SubjectUtils.getEmailAddress((Subject) deleteResponse.getProperties().get(SecurityConstants.SECURITY_SUBJECT));
    List<Metacard> deletionMetacards = versionedMap.entrySet().stream().map(s -> new DeletedMetacardImpl(uuidGenerator.generateUuid(), s.getKey(), emailAddress, s.getValue().getId(), MetacardVersionImpl.toMetacard(s.getValue(), metacardTypes))).collect(Collectors.toList());
    executeAsSystem(() -> catalogProvider().create(new CreateRequestImpl(deletionMetacards, new HashMap<>())));
    return deleteResponse;
}

Example 94 with Function

use of java.util.function.Function in project ddf by codice.

the class MetacardApplication method patchMetacards.

protected UpdateResponse patchMetacards(List<MetacardChanges> metacardChanges) throws SourceUnavailableException, IngestException, FederationException, UnsupportedQueryException {
    Set<String> changedIds = metacardChanges.stream().flatMap(mc -> mc.getIds().stream()).collect(Collectors.toSet());
    Map<String, Result> results = util.getMetacards(changedIds, "*");
    for (MetacardChanges changeset : metacardChanges) {
        for (AttributeChange attributeChange : changeset.getAttributes()) {
            for (String id : changeset.getIds()) {
                List<String> values = attributeChange.getValues();
                Metacard result = results.get(id).getMetacard();
                Function<Serializable, Serializable> mapFunc = Function.identity();
                if (isChangeTypeDate(attributeChange, result)) {
                    mapFunc = mapFunc.andThen(util::parseDate);
                }
                result.setAttribute(new AttributeImpl(attributeChange.getAttribute(), values.stream().filter(Objects::nonNull).map(mapFunc).collect(Collectors.toList())));
            }
        }
    }
    List<Metacard> changedMetacards = results.values().stream().map(Result::getMetacard).collect(Collectors.toList());
    return catalogFramework.update(new UpdateRequestImpl(changedMetacards.stream().map(Metacard::getId).collect(Collectors.toList()).toArray(new String[0]), changedMetacards));
}

Example 95 with Function

use of java.util.function.Function in project dhis2-core by dhis2.

the class QueryPlannerTest method planQueryStartEndDateQueryGrouperB.

/**
     * Splits in 4 queries for each period to satisfy optimal for a total
     * of 4 queries, because all queries have different periods.
     */
@Test
public void planQueryStartEndDateQueryGrouperB() {
    DataQueryParams params = DataQueryParams.newBuilder().withDataElements(getList(deA, deB)).withOrganisationUnits(getList(ouA)).withFilterPeriods(getList(createPeriod("200101"), createPeriod("200102"), createPeriod("200103"), createPeriod("200104"))).build();
    List<Function<DataQueryParams, List<DataQueryParams>>> queryGroupers = Lists.newArrayList();
    queryGroupers.add(q -> queryPlanner.groupByStartEndDate(q));
    QueryPlannerParams plannerParams = QueryPlannerParams.newBuilder().withOptimalQueries(4).withTableName(ANALYTICS_TABLE_NAME).withQueryGroupers(queryGroupers).build();
    DataQueryGroups queryGroups = queryPlanner.planQuery(params, plannerParams);
    List<DataQueryParams> queries = queryGroups.getAllQueries();
    assertEquals(2, queries.size());
    assertEquals(1, queryGroups.getSequentialQueries().size());
    assertEquals(2, queryGroups.getLargestGroupSize());
    for (DataQueryParams query : queries) {
        assertNotNull(query.getStartDate());
        assertNotNull(query.getEndDate());
        assertDimensionNameNotNull(query);
        assertNull(query.getFilter(PERIOD_DIM_ID));
    }
}