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.stopPipeline" to Y to stop the pipeline if expectations are not met. Be default ("validation.stopPipeline"=N), the utility will 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`	`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`	`HALT_PIPELINE` `Config` boolean property "validation.stopPipeline".
`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`	`MD5`
`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`	`SIZE`
`protected static String`	`SIZE_WITHIN_PERCENT` `Config` property "validation.sizeWithinPercent" giving the percentage by which size is allow to deviate and still be considered a valid match for the expectation.
`protected static String[]`	`statusStrings`
`protected static String`	`VALIDATION_FOLDER`

Constructor Summary

Constructors
Constructor and Description

ValidationUtil()

Constructors
Constructor and Description
`ValidationUtil()`

Method Summary

All Methods Static Methods Concrete Methods
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.
`protected static List<String>`	`getValidationAttributes()`
`static File`	`getValidationDir()`
`static boolean`	`hasStrictValidation(boolean printStdOut)` Print a message (and return boolean) to indicate that this pipeline has validation enabled.
`static void`	`registerProps()`
`static void`	`validateModule(BioModule module)`

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - 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
  - 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
  - FAIL
```
protected static final int FAIL
```
    See Also:
    
    Constant Field Values
  - HALT_PIPELINE
```
protected static final String HALT_PIPELINE
```
    Config boolean property "validation.stopPipeline". If the output files do not meet expectation, stop the 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
  - MD5
```
protected static final String MD5
```
    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
  - 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
  - SIZE
```
protected static final String SIZE
```
    See Also:
    
    Constant Field Values
  - SIZE_WITHIN_PERCENT
```
protected static final String SIZE_WITHIN_PERCENT
```
    Config property "validation.sizeWithinPercent" giving the percentage by which size is allow to deviate and still be considered a valid match for the expectation.
    
    See Also:
    
    Constant Field Values
  - 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
  - getValidationDir
```
public static File getValidationDir()
```
  - validateModule
```
public static void validateModule(BioModule module)
                           throws BioLockJException
```
    Throws:
    
    BioLockJException
  - getValidationAttributes
```
protected static List<String> getValidationAttributes()
```
  - hasStrictValidation
```
public static boolean hasStrictValidation(boolean printStdOut)
```
    Print a message (and return boolean) to indicate that this pipeline has validation enabled. This makes a biolockj_complete much more meaningful, because we know the pipeline met some expectation regarding the output it produced.
    
    Parameters:
    
    printStdOut -
    
    Returns:
  - registerProps
```
public static void registerProps()
                          throws API_Exception
```
    Throws:
    
    API_Exception

Class ValidationUtil

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

EXPECTATION_FILE

COMPARE_ON

FAIL

HALT_PIPELINE

MATCHED_EXPECTATION

MD5

NAME

OUTPUT_FILE_SUFFIX

PASS

REPORT

REPORT_ON

SIZE

SIZE_WITHIN_PERCENT

statusStrings

VALIDATION_FOLDER

Constructor Detail

ValidationUtil

Method Detail

checkDependencies

getValidationDir

validateModule

getValidationAttributes

hasStrictValidation

registerProps