org.arvados.client.facade

Class ArvadosFacade

java.lang.Object

org.arvados.client.facade.ArvadosFacade

public class ArvadosFacade
extends java.lang.Object

Constructor Summary

Constructors

Constructor and Description
ArvadosFacade()
ArvadosFacade(ConfigProvider config)

Method Summary

Modifier and Type	Method and Description
Collection	createEmptyCollection(java.lang.String collectionName, java.lang.String projectUuid) Creates and uploads new empty collection to specified project.
Group	createNewProject(java.lang.String projectName) Creates new project that will be a subproject of "home" for current user.
Collection	deleteCollection(java.lang.String collectionUuid) Deletes collection with specified uuid.
java.util.List<java.io.File>	downloadCollectionFiles(java.lang.String collectionUuid, java.lang.String pathToDownloadFolder, boolean usingKeepWeb) This method downloads all files from collection.
java.io.File	downloadFile(java.lang.String filePathName, java.lang.String collectionUuid, java.lang.String pathToDownloadFolder) This method downloads single file from collection using Arvados Keep-Web.
CollectionList	getCollectionsFromProjectByName(java.lang.String collectionName, java.lang.String projectUuid) Filters all collections from selected project and returns list of those that contain passed String in their name.
User	getCurrentUser() Returns current user information based on Api Token provided via configuration
Group	getProjectByUuid(java.lang.String projectUuid) Gets project details by uuid.
java.util.List<FileToken>	listFileInfoFromCollection(java.lang.String collectionUuid) Lists all FileTokens (objects containing information about files) for specified collection.
GroupList	showGroupsAccessibleByCurrentUser() 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.
GroupList	showGroupsOwnedByCurrentUser() 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.
Collection	upload(java.io.File file) Creates and uploads new collection containing a single file.
Collection	upload(java.util.List<java.io.File> files) Creates and uploads new collection containing passed files.
Collection	upload(java.util.List<java.io.File> sourceFiles, java.lang.String collectionName, java.lang.String projectUuid) Uploads new collection with specified name and containing selected files to an existing project.
Collection	uploadToExistingCollection(java.io.File file, java.lang.String collectionUUID) Uploads a file to a specified collection.
Collection	uploadToExistingCollection(java.util.List<java.io.File> files, java.lang.String collectionUUID) Uploads multiple files to an existing collection.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

ArvadosFacade

public ArvadosFacade(ConfigProvider config)

ArvadosFacade

public ArvadosFacade()

Method Detail

downloadFile

public java.io.File downloadFile(java.lang.String filePathName,
                                 java.lang.String collectionUuid,
                                 java.lang.String pathToDownloadFolder)

This method downloads single file from collection using Arvados Keep-Web. File is saved on a drive in specified location and returned.

Parameters:

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')

collectionUuid - uuid of collection containing requested file

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.

Returns:

downloaded file

downloadCollectionFiles

public java.util.List<java.io.File> downloadCollectionFiles(java.lang.String collectionUuid,
                                                            java.lang.String pathToDownloadFolder,
                                                            boolean usingKeepWeb)

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.

Parameters:

collectionUuid - uuid of collection from which files are downloaded

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.

usingKeepWeb - if set to true files will be downloaded using Keep Web. If set to false files will be downloaded using Keep Server API.

Returns:

list containing downloaded files

listFileInfoFromCollection

public java.util.List<FileToken> listFileInfoFromCollection(java.lang.String collectionUuid)

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

Parameters:

collectionUuid - uuid of collection for which FileTokens are listed

Returns:

list containing FileTokens for each file in specified collection

upload

public Collection upload(java.util.List<java.io.File> files)

Creates and uploads new collection containing passed files. Created collection has a default name and is uploaded to user's 'Home' project.

Parameters:

files - list of files to be uploaded within new collection

Returns:

collection object mapped from JSON that is returned from server after successful upload

See Also:

upload(List, String, String)

upload

public Collection upload(java.io.File file)

Creates and uploads new collection containing a single file. Created collection has a default name and is uploaded to user's 'Home' project.

Parameters:

file - file to be uploaded

Returns:

collection object mapped from JSON that is returned from server after successful upload

See Also:

upload(List, String, String)

upload

public Collection upload(java.util.List<java.io.File> sourceFiles,
                         java.lang.String collectionName,
                         java.lang.String projectUuid)

Uploads new collection with specified name and containing selected files to an existing project.

Parameters:

sourceFiles - list of files to be uploaded within new collection

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.

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.

Returns:

collection object mapped from JSON that is returned from server after successful upload

uploadToExistingCollection

public Collection uploadToExistingCollection(java.io.File file,
                                             java.lang.String collectionUUID)

Uploads a file to a specified collection.

Parameters:

file - file to be uploaded to existing collection. Filenames must be unique in comparison with files already existing within collection.

collectionUUID - UUID of collection to which files should be uploaded

Returns:

collection object mapped from JSON that is returned from server after successful upload

See Also:

uploadToExistingCollection(List, String)

uploadToExistingCollection

public Collection uploadToExistingCollection(java.util.List<java.io.File> files,
                                             java.lang.String collectionUUID)

Uploads multiple files to an existing collection.

Parameters:

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.

collectionUUID - UUID of collection to which files should be uploaded

Returns:

collection object mapped from JSON that is returned from server after successful upload

createEmptyCollection

public Collection createEmptyCollection(java.lang.String collectionName,
                                        java.lang.String projectUuid)

Creates and uploads new empty collection to specified project.

Parameters:

collectionName - name for the newly created collection. Collection with that name cannot be already created in specified project.

projectUuid - uuid of project that will contain uploaded empty collection. To select home project pass current user's uuid from getCurrentUser()

Returns:

collection object mapped from JSON that is returned from server after successful upload

See Also:

getCurrentUser()

getCurrentUser

public User getCurrentUser()

Returns current user information based on Api Token provided via configuration

Returns:

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.

showGroupsOwnedByCurrentUser

public GroupList showGroupsOwnedByCurrentUser()

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.

Returns:

GroupList containing all groups that current user is owner of.

See Also:

getCurrentUser()

showGroupsAccessibleByCurrentUser

public GroupList showGroupsAccessibleByCurrentUser()

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.

Returns:

GroupList containing all groups that current user has read access to.

getCollectionsFromProjectByName

public CollectionList getCollectionsFromProjectByName(java.lang.String collectionName,
                                                      java.lang.String projectUuid)

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).

Parameters:

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".

projectUuid - uuid of project in which will be searched for collections with given name. To search home project provide user uuid (from getCurrentUser())

Returns:

object CollectionList containing all collections matching specified name criteria

See Also:

getCurrentUser()

getProjectByUuid

public Group getProjectByUuid(java.lang.String projectUuid)

Gets project details by uuid.

Parameters:

projectUuid - uuid of project

Returns:

Group object containing information about project

createNewProject

public Group createNewProject(java.lang.String projectName)

Creates new project that will be a subproject of "home" for current user.

Parameters:

projectName - name for the newly created project

Returns:

Group object containing information about created project (mapped from JSON returned from server after creating the project)

deleteCollection

public Collection deleteCollection(java.lang.String collectionUuid)

Deletes collection with specified uuid.

Parameters:

collectionUuid - uuid of collection to be deleted. User whose token is provided in configuration must be authorized to delete such collection.

Returns:

collection object with deleted collection (mapped from JSON returned from server after deleting the collection)