biolockj.util

Class SummaryUtil

java.lang.Object

biolockj.util.SummaryUtil

public class SummaryUtil
extends Object

This module builds an execution summary for the pipeline which is printed to the log file and is be sent to the user if the Email module is configured.

Field Summary

Fields

Modifier and Type	Field and Description
static String	PIPELINE_STATUS

Constructor Summary

Constructors

Constructor and Description
SummaryUtil()

Method Summary

Modifier and Type	Method and Description
static void	addSummaryFooterForFailedPipeline() Called when pipeline fails to add summary details to summary file, if possible.
static String	displayAsciiArt() Print the application name *bigly* with some ASCII art :-)
static String	getCountSummary(Map<String,String> map, String label, boolean addTotal) Return the min/max/mean/median summary stats for the given metadata numeric column
static Double	getDoubleRatio(Double num, Double denom) Return a num/denom ratio
static String	getFooter() Print the final lines of the summary with overall status, runtime, and the download scp command if applicable.
static String	getInputSummary(BioModule module) Build a summary of the input files for the given module
static Long	getLongRatio(Double num, Double denom) Return a num/denom ratio floor value (do not round up)
static String	getMean(Collection<?> vals, boolean isDouble) Return the mean value
static String	getMedian(Collection<?> vals, boolean isDouble) Return the median value
static String	getModuleRunTime(BioModule module) Return duration module ran based on modified data of started file, formatted for display (as hours, minutes, seconds).
static String	getOutputDirSummary(BioModule module) Return summary of BioModule output directory, with metrics: Number of output files Mean output file size Path of new metadata file if any created
static int	getPad(String label) Summary count label padding as label length + 18
static String	getRunTime(long duration) Get runtime message (formatted as hours, minutes, seconds) based on startTime passed.
static String	getScriptDirSummary(ScriptModule module) Return summary of the ScriptModule script directory with metrics: Print main script name Number of worker scripts run Number of worker scripts successful/failed/incomplete Average worker script run time Longest running worker script names/duration Longest running workers script names/duration
protected static String	getScriptRunTime(Long duration) Get the script runtime in hours and minutes
static String	getSummary() Pipeline execution summary.
static File	getSummaryFile() Getter for the summary file.
static void	reportFailure(Exception ex) Report exception details in the summary
static void	reportSuccess(BioModule module) After each module completes, this method is called to track the execution summary. If module is null, the pipeline is complete/successful.
protected static void	resetModuleSummary(BioModule module) Modules can be forced to reset to incomplete status.
protected static void	saveSummary(String summary) Save the summary generated to the pipeline root directory.
static boolean	sendHostInfo(File pipelineDir) Write the system host info.
static void	touchSystemInfo() Save information about the system, such as OS name and version.
static void	updateNumAttempts() Update the number of attempts in the summary file (called from restart)

Methods inherited from class java.lang.Object

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

Field Detail

PIPELINE_STATUS

public static final String PIPELINE_STATUS

See Also:

Constant Field Values

Constructor Detail

SummaryUtil

public SummaryUtil()

Method Detail

touchSystemInfo

public static void touchSystemInfo()

Save information about the system, such as OS name and version.

sendHostInfo

public static boolean sendHostInfo(File pipelineDir)

Write the system host info. This is used when an instance of BioLockJ running outside of a container creates the system info record. The instance inside the container will see the container info, not the host.

Parameters:

pipelineDir -

addSummaryFooterForFailedPipeline

public static void addSummaryFooterForFailedPipeline()

Called when pipeline fails to add summary details to summary file, if possible.

displayAsciiArt

public static String displayAsciiArt()

Print the application name *bigly* with some ASCII art :-)

Returns:

My beautiful artwork

getCountSummary

public static String getCountSummary(Map<String,String> map,
                                     String label,
                                     boolean addTotal)
                              throws Exception

Return the min/max/mean/median summary stats for the given metadata numeric column

Parameters:

map - Map(sampleId,count)

label - Context label

addTotal - Boolean if should include total count

Returns:

Summary lines

Throws:

Exception - if errors occur

getDoubleRatio

public static Double getDoubleRatio(Double num,
                                    Double denom)

Return a num/denom ratio

Parameters:

num - Numerator

denom - Denominator

Returns:

num/denom Double value

getFooter

public static String getFooter()
                        throws Exception

Print the final lines of the summary with overall status, runtime, and the download scp command if applicable.

Returns:

Summary info

Throws:

Exception - if any error occurs

getInputSummary

public static String getInputSummary(BioModule module)

Build a summary of the input files for the given module

Parameters:

module - BioModule to summarize

Returns:

module input summary

getLongRatio

public static Long getLongRatio(Double num,
                                Double denom)

Return a num/denom ratio floor value (do not round up)

Parameters:

num - Numerator

denom - Denominator

Returns:

num/denom Long floor value

getMean

public static String getMean(Collection<?> vals,
                             boolean isDouble)

Return the mean value

Parameters:

vals - Collection of values

isDouble - if the Collection holds Double values

Returns:

mean value

getMedian

public static String getMedian(Collection<?> vals,
                               boolean isDouble)

Return the median value

Parameters:

vals - Collection of values

isDouble - if the Collection holds Double values

Returns:

median value

getModuleRunTime

public static String getModuleRunTime(BioModule module)

Return duration module ran based on modified data of started file, formatted for display (as hours, minutes, seconds).

Parameters:

module - BioModule

Returns:

Formatted module runtime

getOutputDirSummary

public static String getOutputDirSummary(BioModule module)

Return summary of BioModule output directory, with metrics:

• Number of output files
• Mean output file size
• Path of new metadata file if any created

Parameters:

module - BioModule to summarize

Returns:

Summary of module output directory

getPad

public static int getPad(String label)

Summary count label padding as label length + 18

Parameters:

label - Label

Returns:

padding length

getRunTime

public static String getRunTime(long duration)

Get runtime message (formatted as hours, minutes, seconds) based on startTime passed.

Parameters:

duration - Milliseconds of run time

Returns:

Formatted runtime as XX hours : XX minutes: XX seconds

getScriptDirSummary

public static String getScriptDirSummary(ScriptModule module)

Return summary of the ScriptModule script directory with metrics:

• Print main script name
• Number of worker scripts run
• Number of worker scripts successful/failed/incomplete
• Average worker script run time
• Longest running worker script names/duration
• Longest running workers script names/duration

Parameters:

module - ScriptModule to summarize

Returns:

Summary of module script directory

getSummary

public static String getSummary()

Pipeline execution summary.

Returns:

Pipeline summary

getSummaryFile

public static File getSummaryFile()

Getter for the summary file.

Returns:

summary file

reportFailure

public static void reportFailure(Exception ex)
                          throws Exception

Report exception details in the summary

Parameters:

ex - Exception thrown causing application runtime failure

Throws:

Exception - if unable to save the updates summary

reportSuccess

public static void reportSuccess(BioModule module)
                          throws Exception

After each module completes, this method is called to track the execution summary.
If module is null, the pipeline is complete/successful.

Parameters:

module - Completed module

Throws:

Exception - if unable to build the summary

updateNumAttempts

public static void updateNumAttempts()
                              throws Exception

Update the number of attempts in the summary file (called from restart)

Throws:

Exception - if unable to update the summary file

getScriptRunTime

protected static String getScriptRunTime(Long duration)

Get the script runtime in hours and minutes

Parameters:

duration - in milliseconds

Returns:

Formatted runtime description

resetModuleSummary

protected static void resetModuleSummary(BioModule module)
                                  throws Exception

Modules can be forced to reset to incomplete status. In this scenario, this method will remove the summary for completed modules that are rerun.

Parameters:

module - Rerun module

Throws:

Exception - if unable to reset the summary

saveSummary

protected static void saveSummary(String summary)
                           throws Exception

Save the summary generated to the pipeline root directory.

Parameters:

summary - Pipeline summary

Throws:

Exception - if file processing errors occur