Package ca.corefacility.bioinformatics.irida.pipeline.upload.galaxy

Class GalaxyLibrariesService

java.lang.Object

ca.corefacility.bioinformatics.irida.pipeline.upload.galaxy.GalaxyLibrariesService

public class GalaxyLibrariesService
extends java.lang.Object

A service class for dealing with Galaxy libraries.

Constructor Summary

Constructors

Constructor	Description
GalaxyLibrariesService(com.github.jmchilton.blend4j.galaxy.LibrariesClient librariesClient, int libraryPollingTime, int libraryUploadTimeout, int threadPoolSize)	Builds a new GalaxyLibrariesService with the given LibrariesClient.

Method Summary

Modifier and Type	Method	Description
com.github.jmchilton.blend4j.galaxy.beans.Library	buildEmptyLibrary(GalaxyProjectName libraryName)	Builds a new empty library with the given name.
void	deleteLibrary(java.lang.String libraryId)	Deletes the Galaxy library with the given id.
java.util.Map<java.nio.file.Path,java.lang.String>	filesToLibraryWait(java.util.Set<java.nio.file.Path> paths, com.github.jmchilton.blend4j.galaxy.beans.Library library, DataStorage dataStorage)	Uploads a set of files to a given library, waiting until all uploads are complete.
java.lang.String	fileToLibrary(java.nio.file.Path path, InputFileType fileType, com.github.jmchilton.blend4j.galaxy.beans.Library library, DataStorage dataStorage)	Uploads the given file to a library with the given information.

Methods inherited from class java.lang.Object

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

Constructor Detail

GalaxyLibrariesService

public GalaxyLibrariesService(com.github.jmchilton.blend4j.galaxy.LibrariesClient librariesClient,
                              int libraryPollingTime,
                              int libraryUploadTimeout,
                              int threadPoolSize)

Builds a new GalaxyLibrariesService with the given LibrariesClient.

Parameters:

librariesClient - The LibrariesClient used to interact with Galaxy libraries.

libraryPollingTime - The time (in seconds) for polling a Galaxy library.

libraryUploadTimeout - The timeout (in seconds) for waiting for files to be uploaded to a library.

threadPoolSize - The thread pool size for parallel polling of Galaxy to check if uploads are finished.

Method Detail

buildEmptyLibrary

public com.github.jmchilton.blend4j.galaxy.beans.Library buildEmptyLibrary(GalaxyProjectName libraryName)
                                                                    throws CreateLibraryException

Builds a new empty library with the given name.

Parameters:

libraryName - The name of the new library.

Returns:

A Library object for the newly created library.

Throws:

CreateLibraryException - If no library could be created.

fileToLibrary

public java.lang.String fileToLibrary(java.nio.file.Path path,
                                      InputFileType fileType,
                                      com.github.jmchilton.blend4j.galaxy.beans.Library library,
                                      DataStorage dataStorage)
                               throws UploadException

Uploads the given file to a library with the given information.

Parameters:

path - The path of the file to upload.

fileType - The type of the file to upload.

library - The library to upload the file into.

dataStorage - The DataStorage method to apply to this dataset.

Returns:

A dataset id for the dataset in this library.

Throws:

UploadException - If there was an issue uploading the file to the library.

filesToLibraryWait

public java.util.Map<java.nio.file.Path,java.lang.String> filesToLibraryWait(java.util.Set<java.nio.file.Path> paths,
                                                                                   com.github.jmchilton.blend4j.galaxy.beans.Library library,
                                                                                   DataStorage dataStorage)
                                                                            throws UploadException

Uploads a set of files to a given library, waiting until all uploads are complete.

Parameters:

paths - The set of paths to upload.

library - The library to initially upload the file into.

dataStorage - The type of DataStorage strategy to use.

Returns:

An @{link Map} of paths and ids for each dataset object in this library.

Throws:

UploadException - If there was an issue uploading the file to Galaxy.

deleteLibrary

public void deleteLibrary(java.lang.String libraryId)
                   throws DeleteGalaxyObjectFailedException

Deletes the Galaxy library with the given id.

Parameters:

libraryId - The id of the library to delete.

Throws:

DeleteGalaxyObjectFailedException - If there was a failure to delete the library.