biolockj.util

Class DownloadUtil

java.lang.Object

biolockj.util.DownloadUtil

public final class DownloadUtil
extends Object

This utility is used to validate the metadata to help ensure the format is valid R script input.

Field Summary

Fields

Modifier and Type	Field and Description
protected static String	DOWNLOAD_DIR Config String property: "pipeline.downloadDir" Sets the local directory targeted by the scp command.
static String	DOWNLOAD_LIST Name of the file holding the list of pipeline files to include when running DownloadUtil

Method Summary

Modifier and Type	Method and Description
protected static List<File>	buildDownloadList(Collection<File> files) Add files to "downloadList.txt" in pipeline root directory.
protected static String	getClusterUser() If System.user.home is a file path (like /usr/home/johnDoe), return last directory name (johnDoe).
protected static org.apache.commons.io.filefilter.IOFileFilter	getDirFilter(boolean includeOutput, boolean includeScript, boolean includeTemp) Get a directory name filter to include module sub-directories.
static String	getDownloadCmd() If running on cluster, build command for user to download pipeline analysis.
static String	getDownloadDirPath() Get validated Config."pipeline.downloadDir" if running on cluster, otherwise return null
static File	getDownloadListFile() Get the download list file.
protected static List<BioModule>	getDownloadModules() Get the modules to download.
protected static BigInteger	getDownloadSize(List<File> files) Get the total size of all files included for download.
protected static File	makeRunAllScript(List<BioModule> modules) This script allows a user to run all R scripts together from a single script.

Methods inherited from class java.lang.Object

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

Field Detail

DOWNLOAD_LIST

public static final String DOWNLOAD_LIST

Name of the file holding the list of pipeline files to include when running DownloadUtil

See Also:

Constant Field Values

DOWNLOAD_DIR

protected static final String DOWNLOAD_DIR

Config String property: "pipeline.downloadDir"
Sets the local directory targeted by the scp command.

See Also:

Constant Field Values

Method Detail

getDownloadCmd

public static String getDownloadCmd()
                             throws Exception

If running on cluster, build command for user to download pipeline analysis.

The pipeline analysis is extracted from the last module output directory (except Email).
Download target = ModuleUtil.getDownloadDir() on the local workstation.
Example download command: scp -rp johnDoe@myUniversity.usa.edu:"dir1, dir2, file1" /Users/johnDoe/projects/downloads

Returns:

String (scp command) or null

Throws:

Exception - if Config parameters are missing or invalid

getDownloadDirPath

public static String getDownloadDirPath()

Get validated Config."pipeline.downloadDir" if running on cluster, otherwise return null

Returns:

String download directory file or null

getDownloadListFile

public static File getDownloadListFile()

Get the download list file.

Returns:

File containing list of files to download

buildDownloadList

protected static List<File> buildDownloadList(Collection<File> files)
                                       throws Exception

Add files to "downloadList.txt" in pipeline root directory.

Parameters:

files - - files to add to the download list

Returns:

List of files for download

Throws:

Exception - if errors occur

getClusterUser

protected static String getClusterUser()

If System.user.home is a file path (like /usr/home/johnDoe), return last directory name (johnDoe). Otherwise return System.user.home value.

Returns:

The userId

getDirFilter

protected static org.apache.commons.io.filefilter.IOFileFilter getDirFilter(boolean includeOutput,
                                                                            boolean includeScript,
                                                                            boolean includeTemp)

Get a directory name filter to include module sub-directories.

Parameters:

includeOutput - include the output directory

includeScript - include the script directory

includeTemp - include the temp directory

Returns:

a file name filter

getDownloadModules

protected static List<BioModule> getDownloadModules()

Get the modules to download. The following are downloaded if found in the pipeline:

• AddMetadataToTaxaTables
• AddMetadataToPathwayTables
• JsonReport
• Any module that inherits from R_Module

If pipeline contains R_PlotEffectSize and Config."r_PlotEffectSize.disableFoldChange"="N" include additional modules:

• Humann2Parser
• BuildTaxaTables

Returns:

BioModules to download

getDownloadSize

protected static BigInteger getDownloadSize(List<File> files)

Get the total size of all files included for download.

Parameters:

files - List of download files

Returns:

BigInteger total download size

makeRunAllScript

protected static File makeRunAllScript(List<BioModule> modules)
                                throws Exception

This script allows a user to run all R scripts together from a single script.

Parameters:

modules - BioModules

Returns:

File Run_All.R script

Throws:

Exception - if errors occur