Examples with BaseEntity com.epam.pipeline.entity.BaseEntity used on opensource projects

Example 1 with BaseEntity

use of com.epam.pipeline.entity.BaseEntity in project cloud-pipeline by epam.

the class ParameterMapper method resolveConfigurations.

public List<ResolvedConfiguration> resolveConfigurations(AnalysisConfiguration<? extends AbstractRunConfigurationEntry> configuration) {
    FolderWithMetadata project = folderManager.getProject(configuration.getConfigurationId(), AclClass.CONFIGURATION);
    Map<String, PipeConfValue> projectData = project == null ? new HashMap<>() : project.getData();
    List<? extends AbstractRunConfigurationEntry> entries = configuration.getEntries();
    if (CollectionUtils.isEmpty(configuration.getEntitiesIds())) {
        return Collections.singletonList(resolveParameters(entries, projectData));
    }
    // In case of array references one entity may be expanded to
    // list of references entities, e.g. SampleSet is expanded
    // to list of Sample entities
    // TODO: The only reason to store it as map - is to add association to run
    // TODO: to initial entity, from which link comes. Find better solution.
    Map<Long, List<MetadataEntity>> targetEntities = fetchAndExpandInputEntities(configuration);
    // resolve all parameter references in configurations
    Map<Long, ResolvedConfiguration> resolvedConfigurations = targetEntities.values().stream().flatMap(Collection::stream).collect(Collectors.toMap(BaseEntity::getId, entity -> resolveParameters(entity, entries, projectData)));
    return targetEntities.entrySet().stream().map(idToEntities -> idToEntities.getValue().stream().map(entity -> {
        ResolvedConfiguration currentConfiguration = resolvedConfigurations.get(entity.getId());
        currentConfiguration.getAssociatedEntityIds().add(idToEntities.getKey());
        return currentConfiguration;
    }).collect(Collectors.toList())).flatMap(Collection::stream).collect(Collectors.toList());
}

Example 2 with BaseEntity

use of com.epam.pipeline.entity.BaseEntity in project cloud-pipeline by epam.

the class FirecloudRunner method runAnalysis.

@Override
public List<PipelineRun> runAnalysis(AnalysisConfiguration<FirecloudRunConfigurationEntry> configuration) {
    Assert.state(CollectionUtils.isNotEmpty(configuration.getEntitiesIds()), "Entities are required to run analysis in Firecloud");
    FolderWithMetadata project = folderManager.getProject(configuration.getConfigurationId(), AclClass.CONFIGURATION);
    Assert.notNull(project, "Project folder must be specified to run analysis in Firecloud.");
    List<Long> entities = parameterMapper.fetchAndExpandInputEntities(configuration).values().stream().flatMap(Collection::stream).map(BaseEntity::getId).collect(Collectors.toList());
    // TODO: after merge - add check that FC class is filled
    configuration.getEntries().forEach(this::validateFirecloudConfiguration);
    FirecloudConfiguration settings = buildFirecloudConfig(configuration.getRefreshToken());
    return configuration.getEntries().stream().map(entry -> runFirecloudAnalysis(settings, entry, configuration.getConfigurationId(), entities, project.getId())).collect(Collectors.toList());
}

Example 3 with BaseEntity

use of com.epam.pipeline.entity.BaseEntity in project cloud-pipeline by epam.

the class GrantPermissionManager method loadAllEntitiesPermissions.

public EntityWithPermissionVO loadAllEntitiesPermissions(AclClass aclClass, Integer page, Integer pageSize, boolean expandGroups, Integer filterMask) {
    EntityWithPermissionVO result = new EntityWithPermissionVO();
    Collection<? extends AbstractSecuredEntity> entities = entityManager.loadAllWithParents(aclClass, page, pageSize);
    Map<AbstractSecuredEntity, List<AclPermissionEntry>> allPermissions = getEntitiesPermissions(entities);
    result.setTotalCount(entityManager.loadTotalCount(aclClass));
    List<EntityPermission> permissions = entities.stream().distinct().sorted(Comparator.comparingLong(BaseEntity::getId)).map(entity -> getEntityPermission(allPermissions, entity)).collect(toList());
    if (expandGroups) {
        expandGroups(permissions);
        if (filterMask != null) {
            permissions.forEach(entry -> {
                Set<AclPermissionEntry> filtered = SetUtils.emptyIfNull(entry.getPermissions()).stream().filter(permission -> permissionsService.isMaskBitSet(permission.getMask(), filterMask)).collect(toSet());
                entry.setPermissions(filtered);
            });
        }
    }
    result.setEntityPermissions(permissions);
    return result;
}

Example 4 with BaseEntity

use of com.epam.pipeline.entity.BaseEntity in project cloud-pipeline by epam.

the class ConfigurationEntryMapper method getContentBuilder.

private XContentBuilder getContentBuilder(final EntityContainer<ConfigurationEntryDoc> container) {
    RunConfiguration configuration = container.getEntity().getConfiguration();
    try (XContentBuilder jsonBuilder = XContentFactory.jsonBuilder()) {
        jsonBuilder.startObject();
        AbstractRunConfigurationEntry entry = container.getEntity().getEntry();
        jsonBuilder.field(DOC_TYPE_FIELD, SearchDocumentType.CONFIGURATION.name()).field("id", container.getEntity().getId()).field("name", Optional.ofNullable(entry).map(AbstractRunConfigurationEntry::getName).orElse(configuration.getName())).field("description", configuration.getName() + " " + StringUtils.defaultIfBlank(configuration.getDescription(), StringUtils.EMPTY)).field("createdDate", parseDataToString(configuration.getCreatedDate())).field("parentId", Optional.ofNullable(configuration.getParent()).map(BaseEntity::getId).orElse(null));
        buildUserContent(container.getOwner(), jsonBuilder);
        buildMetadata(container.getMetadata(), jsonBuilder);
        buildPermissions(container.getPermissions(), jsonBuilder);
        if (entry != null) {
            buildConfigurationEntry(entry, container.getEntity().getPipeline(), jsonBuilder);
        }
        jsonBuilder.endObject();
        return jsonBuilder;
    } catch (IOException e) {
        throw new IllegalArgumentException("Failed to create elasticsearch document for run configuration: ", e);
    }
}