biolockj.util

Class ValidationUtil

java.lang.Object

biolockj.util.ValidationUtil

public class ValidationUtil
extends Object

This utility measures attributes of the files in the output directory of each module as it completes. If there is no expectation file, the utility reports the values for these attributes and saves a file in the "validation" folder which can be used as an expectation in future runs. If there is an expectation file, the values for the current outputs will be compared with the expected values and the utility will stop the pipeline if the files do not meet expectations. Set "validation.alwaysPass" to Y to report on the comparison but not stop the pipeline. This is an easy way to verify that the outputs of a pipeline are the same as a previous run, which is particularly helpful after software has been updated, or after any other changes that are not expected to alter results. To provide an expectation file, use Config property "validation.expectationFile" and give the file path to the "validation" folder of the run that you want to match. To specify which file attributes are reported, use Config property "validation.reportOn". To specify which file attributes are used for the comparison, use use Config property "validation.compareOn".

Author:

Ivory

Field Summary

Fields

Modifier and Type	Field and Description
protected static String	ALWAYS_PASS Config boolean property.
protected static ArrayList<String>	availableAttributes
protected static String	COMPARE_ON Config set property giving the file metrics to use in comparing to the expectation.
static String	EXPECTATION_FILE Config String property giving the file path that gives the expected values for file metrics.
protected static int	FAIL
protected static String	MATCHED_EXPECTATION The last column in a the output file, "MATCHED_EXPECTATION", indicates if the referenced file met all expectations (PASS), or not (FAIL), or was not compared to any expectations (REPORT).
protected static String	NAME The first column in an expectation file must be "name"
protected static String	OUTPUT_FILE_SUFFIX Append the String "_validation.txt" to the name of the validated module to get the output file name.
protected static int	PASS
protected static int	REPORT
protected static String	REPORT_ON Config property "validation.reportOn" giving the set of file metrics to use report.
protected static String[]	statusStrings
protected static String	VALIDATION_FOLDER

Constructor Summary

Constructors

Constructor and Description
ValidationUtil()

Method Summary

Modifier and Type	Method and Description
static void	checkDependencies(BioModule module) This method calls the methods that are used by executeTask to get the validation input.
static void	executeTask(BioModule module)
static File	getValidationDir()

Methods inherited from class java.lang.Object

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

Field Detail

ALWAYS_PASS

protected static final String ALWAYS_PASS

Config boolean property. Even if the files do not meet expectation, just record this, do not halt the pipeline.

See Also:

Constant Field Values

COMPARE_ON

protected static final String COMPARE_ON

Config set property giving the file metrics to use in comparing to the expectation. Default is to use all metrics in the expectation file.

See Also:

Constant Field Values

EXPECTATION_FILE

public static final String EXPECTATION_FILE

Config String property giving the file path that gives the expected values for file metrics. Probably generated by a previous run of the same pipeline.

See Also:

Constant Field Values

MATCHED_EXPECTATION

protected static final String MATCHED_EXPECTATION

The last column in a the output file, "MATCHED_EXPECTATION", indicates if the referenced file met all expectations (PASS), or not (FAIL), or was not compared to any expectations (REPORT). The value "MATCHED_EXPECTATION" is hard-coded in the FileSummary.getAtt() method. If this is a column in the expectation file, it is ignored.

See Also:

Constant Field Values

NAME

protected static final String NAME

The first column in an expectation file must be "name"

See Also:

Constant Field Values

OUTPUT_FILE_SUFFIX

protected static final String OUTPUT_FILE_SUFFIX

Append the String "_validation.txt" to the name of the validated module to get the output file name.

See Also:

Constant Field Values

FAIL

protected static final int FAIL

See Also:

Constant Field Values

PASS

protected static final int PASS

See Also:

Constant Field Values

REPORT

protected static final int REPORT

See Also:

Constant Field Values

REPORT_ON

protected static final String REPORT_ON

Config property "validation.reportOn" giving the set of file metrics to use report. Default is to use all currently available metrics.

See Also:

Constant Field Values

availableAttributes

protected static final ArrayList<String> availableAttributes

statusStrings

protected static final String[] statusStrings

VALIDATION_FOLDER

protected static final String VALIDATION_FOLDER

See Also:

Constant Field Values

Constructor Detail

ValidationUtil

public ValidationUtil()

Method Detail

checkDependencies

public static void checkDependencies(BioModule module)
                              throws Exception

This method calls the methods that are used by executeTask to get the validation input. The goal is to ensure that IF the validation utility is going to fail due to any kind of problem with the validation input, it fails before the pipeline starts so it can be corrected immediately.

Parameters:

module - BioModule to check validation dependencies for

Throws:

Exception - if errors occur

executeTask

public static void executeTask(BioModule module)
                        throws Exception

Throws:

Exception

getValidationDir

public static File getValidationDir()