+++ /dev/null
-/*
- * Copyright (C) The Arvados Authors. All rights reserved.
- *
- * SPDX-License-Identifier: AGPL-3.0 OR Apache-2.0
- *
- */
-
-package org.arvados.client.facade;
-
-import com.google.common.collect.Lists;
-import org.arvados.client.api.client.CollectionsApiClient;
-import org.arvados.client.api.client.GroupsApiClient;
-import org.arvados.client.api.client.KeepWebApiClient;
-import org.arvados.client.api.client.UsersApiClient;
-import org.arvados.client.api.model.*;
-import org.arvados.client.api.model.argument.Filter;
-import org.arvados.client.api.model.argument.ListArgument;
-import org.arvados.client.config.FileConfigProvider;
-import org.arvados.client.config.ConfigProvider;
-import org.arvados.client.logic.collection.FileToken;
-import org.arvados.client.logic.collection.ManifestDecoder;
-import org.arvados.client.logic.keep.FileDownloader;
-import org.arvados.client.logic.keep.FileUploader;
-import org.arvados.client.logic.keep.KeepClient;
-import org.slf4j.Logger;
-
-import java.io.File;
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.List;
-
-public class ArvadosFacade {
-
- private final ConfigProvider config;
- private final Logger log = org.slf4j.LoggerFactory.getLogger(ArvadosFacade.class);
- private CollectionsApiClient collectionsApiClient;
- private GroupsApiClient groupsApiClient;
- private UsersApiClient usersApiClient;
- private FileDownloader fileDownloader;
- private FileUploader fileUploader;
- private static final String PROJECT = "project";
- private static final String SUBPROJECT = "sub-project";
-
- public ArvadosFacade(ConfigProvider config) {
- this.config = config;
- setFacadeFields();
- }
-
- public ArvadosFacade() {
- this.config = new FileConfigProvider();
- setFacadeFields();
- }
-
- private void setFacadeFields() {
- collectionsApiClient = new CollectionsApiClient(config);
- groupsApiClient = new GroupsApiClient(config);
- usersApiClient = new UsersApiClient(config);
- KeepClient keepClient = new KeepClient(config);
- ManifestDecoder manifestDecoder = new ManifestDecoder();
- KeepWebApiClient keepWebApiClient = new KeepWebApiClient(config);
- fileDownloader = new FileDownloader(keepClient, manifestDecoder, collectionsApiClient, keepWebApiClient);
- fileUploader = new FileUploader(keepClient, collectionsApiClient, config);
- }
-
- /**
- * This method downloads single file from collection using Arvados Keep-Web.
- * File is saved on a drive in specified location and returned.
- *
- * @param filePathName path to the file in collection. If requested file is stored
- * directly in collection (not within its subdirectory) this
- * would be just the name of file (ex. 'file.txt').
- * Otherwise full file path must be passed (ex. 'folder/file.txt')
- * @param collectionUuid uuid of collection containing requested file
- * @param pathToDownloadFolder path to location in which file should be saved.
- * Passed location must be a directory in which file of
- * that name does not already exist.
- * @return downloaded file
- */
- public File downloadFile(String filePathName, String collectionUuid, String pathToDownloadFolder) {
- return fileDownloader.downloadSingleFileUsingKeepWeb(filePathName, collectionUuid, pathToDownloadFolder);
- }
-
- /**
- * This method downloads all files from collection.
- * Directory named by collection uuid is created in specified location,
- * files are saved on a drive in this directory and list with downloaded
- * files is returned.
- *
- * @param collectionUuid uuid of collection from which files are downloaded
- * @param pathToDownloadFolder path to location in which files should be saved.
- * New folder named by collection uuid, containing
- * downloaded files, is created in this location.
- * Passed location must be a directory in which folder
- * of that name does not already exist.
- * @param usingKeepWeb if set to true files will be downloaded using Keep Web.
- * If set to false files will be downloaded using Keep Server API.
- * @return list containing downloaded files
- */
- public List<File> downloadCollectionFiles(String collectionUuid, String pathToDownloadFolder, boolean usingKeepWeb) {
- if (usingKeepWeb)
- return fileDownloader.downloadFilesFromCollectionUsingKeepWeb(collectionUuid, pathToDownloadFolder);
- return fileDownloader.downloadFilesFromCollection(collectionUuid, pathToDownloadFolder);
- }
-
- /**
- * Lists all FileTokens (objects containing information about files) for
- * specified collection.
- * Information in each FileToken includes file path, name, size and position
- * in data stream
- *
- * @param collectionUuid uuid of collection for which FileTokens are listed
- * @return list containing FileTokens for each file in specified collection
- */
- public List<FileToken> listFileInfoFromCollection(String collectionUuid) {
- return fileDownloader.listFileInfoFromCollection(collectionUuid);
- }
-
- /**
- * Creates and uploads new collection containing passed files.
- * Created collection has a default name and is uploaded to user's 'Home' project.
- *
- * @see ArvadosFacade#upload(List, String, String)
- */
- public Collection upload(List<File> files) {
- return upload(files, null, null);
- }
-
- /**
- * Creates and uploads new collection containing a single file.
- * Created collection has a default name and is uploaded to user's 'Home' project.
- *
- * @see ArvadosFacade#upload(List, String, String)
- */
- public Collection upload(File file) {
- return upload(Collections.singletonList(file), null, null);
- }
-
- /**
- * Uploads new collection with specified name and containing selected files
- * to an existing project.
- *
- * @param sourceFiles list of files to be uploaded within new collection
- * @param collectionName name for the newly created collection.
- * Collection with that name cannot be already created
- * in specified project. If null is passed
- * then collection name is set to default, containing
- * phrase 'New Collection' and a timestamp.
- * @param projectUuid uuid of the project in which created collection is to be included.
- * If null is passed then collection is uploaded to user's 'Home' project.
- * @return collection object mapped from JSON that is returned from server after successful upload
- */
- public Collection upload(List<File> sourceFiles, String collectionName, String projectUuid) {
- return fileUploader.upload(sourceFiles, collectionName, projectUuid);
- }
-
- /**
- * Uploads a file to a specified collection.
- *
- * @see ArvadosFacade#uploadToExistingCollection(List, String)
- */
- public Collection uploadToExistingCollection(File file, String collectionUUID) {
- return fileUploader.uploadToExistingCollection(Collections.singletonList(file), collectionUUID);
- }
-
- /**
- * Uploads multiple files to an existing collection.
- *
- * @param files list of files to be uploaded to existing collection.
- * File names must be unique - both within passed list and
- * in comparison with files already existing within collection.
- * @param collectionUUID UUID of collection to which files should be uploaded
- * @return collection object mapped from JSON that is returned from server after successful upload
- */
- public Collection uploadToExistingCollection(List<File> files, String collectionUUID) {
- return fileUploader.uploadToExistingCollection(files, collectionUUID);
- }
-
- /**
- * Creates and uploads new empty collection to specified project.
- *
- * @param collectionName name for the newly created collection.
- * Collection with that name cannot be already created
- * in specified project.
- * @param projectUuid uuid of project that will contain uploaded empty collection.
- * To select home project pass current user's uuid from getCurrentUser()
- * @return collection object mapped from JSON that is returned from server after successful upload
- * @see ArvadosFacade#getCurrentUser()
- */
- public Collection createEmptyCollection(String collectionName, String projectUuid) {
- Collection collection = new Collection();
- collection.setOwnerUuid(projectUuid);
- collection.setName(collectionName);
- return collectionsApiClient.create(collection);
- }
-
- /**
- * Returns current user information based on Api Token provided via configuration
- *
- * @return user object mapped from JSON that is returned from server based on provided Api Token.
- * It contains information about user who has this token assigned.
- */
- public User getCurrentUser() {
- return usersApiClient.current();
- }
-
- /**
- * Gets uuid of current user based on api Token provided in configuration and uses it to list all
- * projects that this user owns in Arvados.
- *
- * @return GroupList containing all groups that current user is owner of.
- * @see ArvadosFacade#getCurrentUser()
- */
- public GroupList showGroupsOwnedByCurrentUser() {
- ListArgument listArgument = ListArgument.builder()
- .filters(Arrays.asList(
- Filter.of("owner_uuid", Filter.Operator.LIKE, getCurrentUser().getUuid()),
- Filter.of("group_class", Filter.Operator.IN, Lists.newArrayList(PROJECT, SUBPROJECT)
- )))
- .build();
- GroupList groupList = groupsApiClient.list(listArgument);
- log.debug("Groups owned by user:");
- groupList.getItems().forEach(m -> log.debug(m.getUuid() + " -- " + m.getName()));
-
- return groupList;
- }
-
- /**
- * Gets uuid of current user based on api Token provided in configuration and uses it to list all
- * projects that this user has read access to in Arvados.
- *
- * @return GroupList containing all groups that current user has read access to.
- */
- public GroupList showGroupsAccessibleByCurrentUser() {
- ListArgument listArgument = ListArgument.builder()
- .filters(Collections.singletonList(
- Filter.of("group_class", Filter.Operator.IN, Lists.newArrayList(PROJECT, SUBPROJECT)
- )))
- .build();
- GroupList groupList = groupsApiClient.list(listArgument);
- log.debug("Groups accessible by user:");
- groupList.getItems().forEach(m -> log.debug(m.getUuid() + " -- " + m.getName()));
-
- return groupList;
- }
-
- /**
- * Filters all collections from selected project and returns list of those that contain passed String in their name.
- * Operator "LIKE" is used so in order to obtain certain collection it is sufficient to pass just part of its name.
- * Returned collections in collectionList are ordered by date of creation (starting from oldest one).
- *
- * @param collectionName collections containing this param in their name will be returned.
- * Passing a wildcard is possible - for example passing "a%" searches for
- * all collections starting with "a".
- * @param projectUuid uuid of project in which will be searched for collections with given name. To search home
- * project provide user uuid (from getCurrentUser())
- * @return object CollectionList containing all collections matching specified name criteria
- * @see ArvadosFacade#getCurrentUser()
- */
- public CollectionList getCollectionsFromProjectByName(String collectionName, String projectUuid) {
- ListArgument listArgument = ListArgument.builder()
- .filters(Arrays.asList(
- Filter.of("owner_uuid", Filter.Operator.LIKE, projectUuid),
- Filter.of("name", Filter.Operator.LIKE, collectionName)
- ))
- .order(Collections.singletonList("created_at"))
- .build();
-
- return collectionsApiClient.list(listArgument);
- }
-
- /**
- * Creates new project that will be a subproject of "home" for current user.
- *
- * @param projectName name for the newly created project
- * @return Group object containing information about created project
- * (mapped from JSON returned from server after creating the project)
- */
- public Group createNewProject(String projectName) {
- Group project = new Group();
- project.setName(projectName);
- project.setGroupClass(PROJECT);
- Group createdProject = groupsApiClient.create(project);
- log.debug("Project " + createdProject.getName() + " created with UUID: " + createdProject.getUuid());
- return createdProject;
- }
-
- /**
- * Deletes collection with specified uuid.
- *
- * @param collectionUuid uuid of collection to be deleted. User whose token is provided in configuration
- * must be authorized to delete such collection.
- * @return collection object with deleted collection (mapped from JSON returned from server after deleting the collection)
- */
- public Collection deleteCollection(String collectionUuid) {
- Collection deletedCollection = collectionsApiClient.delete(collectionUuid);
- log.debug("Collection: " + collectionUuid + " deleted.");
- return deletedCollection;
- }
-}
projects / arvados.git / blobdiff
