com.pacbio.secondary.vis.common.utils

Class RuntimeConfigUtils

java.lang.Object

com.pacbio.secondary.vis.common.utils.RuntimeConfigUtils

public class RuntimeConfigUtils
extends java.lang.Object

Author:

mmilletti

Constructor Summary

Constructors

Constructor and Description
RuntimeConfigUtils()

Method Summary

Methods

Modifier and Type	Method and Description
static java.lang.String	ensureAbsolutePathToJobMetadata(java.lang.String job_path) Resolves path of job file
static java.lang.String	getConfiguredHostName()
static java.lang.String	getConfiguredHttpPort()
protected static java.lang.String	getConfigXMLFilePath()
protected static java.lang.String	getJobsRootDirectory()
protected static java.lang.String	getPathToReferenceIndexFile()
static java.lang.String	getPathToReferenceMetadataFromID(java.lang.String reference_id) Resolves path of reference metafile using: - absolute reference id - relative path to reference.info.xml to support portability of reference files - runtime environment variable and config.xml pointing to root of seymour reference repository instance
protected static java.lang.String	getReferenceMetadataFromID(org.w3c.dom.Document xDoc, java.lang.String refID)
protected static java.lang.String	getReferencesRootDirectory()
protected static java.lang.String	getRootDirectory(java.lang.String target)
static java.lang.String	getSeymourHome() Returns value of SEYMOUR_HOME env variable
static java.lang.String	getSmrtAnalysisHome() Get equivalent of SEYMOUR_HOME by looking up into directory of .aar file...
static java.lang.String	getSMRTAnalysisVersion()
protected static java.lang.String	getSystemInfo(java.lang.String target)
static java.lang.String	getUserHome() Returns value of USER_HOME env variable
protected static java.lang.String	getVioletContentRootDirectory()
static java.lang.String	getVioletUserDataRootDirectory()
static void	main(java.lang.String[] args)

Methods inherited from class java.lang.Object

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

Constructor Detail

RuntimeConfigUtils

public RuntimeConfigUtils()

Method Detail

getSmrtAnalysisHome

public static java.lang.String getSmrtAnalysisHome()

Get equivalent of SEYMOUR_HOME by looking up into directory of .aar file...

Returns:

getSeymourHome

public static java.lang.String getSeymourHome()

Returns value of SEYMOUR_HOME env variable

Returns:

getUserHome

public static java.lang.String getUserHome()

Returns value of USER_HOME env variable

Returns:

getPathToReferenceMetadataFromID

public static java.lang.String getPathToReferenceMetadataFromID(java.lang.String reference_id)

Resolves path of reference metafile using: - absolute reference id - relative path to reference.info.xml to support portability of reference files - runtime environment variable and config.xml pointing to root of seymour reference repository instance

Parameters:

reference_id - id of reference of full path to metadata file

Returns:

absolute filename based on runtime config

getVioletUserDataRootDirectory

public static java.lang.String getVioletUserDataRootDirectory()

ensureAbsolutePathToJobMetadata

public static java.lang.String ensureAbsolutePathToJobMetadata(java.lang.String job_path)

Resolves path of job file

Parameters:

job_path - relative or absolute filename

Returns:

absolute filename based on runtime config

getSMRTAnalysisVersion

public static java.lang.String getSMRTAnalysisVersion()

getConfiguredHostName

public static java.lang.String getConfiguredHostName()

getConfiguredHttpPort

public static java.lang.String getConfiguredHttpPort()

getPathToReferenceIndexFile

protected static java.lang.String getPathToReferenceIndexFile()

getReferencesRootDirectory

protected static java.lang.String getReferencesRootDirectory()

getVioletContentRootDirectory

protected static java.lang.String getVioletContentRootDirectory()

getJobsRootDirectory

protected static java.lang.String getJobsRootDirectory()

getRootDirectory

protected static java.lang.String getRootDirectory(java.lang.String target)

getSystemInfo

protected static java.lang.String getSystemInfo(java.lang.String target)

Parameters:

target -

Returns:

getConfigXMLFilePath

protected static java.lang.String getConfigXMLFilePath()

getReferenceMetadataFromID

protected static java.lang.String getReferenceMetadataFromID(org.w3c.dom.Document xDoc,
                                          java.lang.String refID)

main

public static void main(java.lang.String[] args)

Parameters:

args -