Config

java.lang.Object
- biolockj.Config

```
public class Config
extends Object
```
Provides type-safe, validated methods for storing/accessing system properties.
Initially populated by the properties in the Config file, several additional properties are created and stored in the the Config (to save system determined info such as: pipeline directory and name, has paired reads?, has multiplexed reads?, etc.).

Constructor Summary

Constructors
Constructor and Description

Config()

Constructors
Constructor and Description
`Config()`

Method Summary

All Methods Static Methods Concrete Methods
Modifier and Type	Method and Description
`static boolean`	`getBoolean(BioModule module, String property)` Parse property value (Y or N) to return boolean, if not found, return false;
`static String`	`getConfigFileExt()` Gets the configuration file extension (often ".properties")
`static String`	`getConfigFileName()` Gets the configuration file name
`static String`	`getConfigFilePath()` Gets the full Config file path passed to BioLockJ as a runtime parameter.
`static Double`	`getDoubleVal(BioModule module, String property)` Parse property for numeric (double) value
`static String`	`getExe(BioModule module, String property)` Get exe.* property name.
`static String`	`getExeParams(BioModule module, String property)` Call this function to get the parameters configured for this property. Make sure the last character for non-null results is an empty character for use in bash scripts calling the corresponding executable.
`static File`	`getExistingDir(BioModule module, String property)` Get a valid File directory or return null
`static File`	`getExistingFile(BioModule module, String property)` Get a valid File or return null.
`protected static File`	`getExistingFileObject(String filePath)` Build File using filePath.
`static TreeMap<String,String>`	`getInitialProperties()` Get initial properties ordered by property
`static List<String>`	`getList(BioModule module, String property)` Parse comma delimited property value to return list
`static String`	`getModuleProp(BioModule module, String prop)` Return module specific property if configured, otherwise use the given prop.
`static String`	`getModuleProp(String moduleName, String prop)` Return module specific property if configured, otherwise use the given prop.
`static Integer`	`getNonNegativeInteger(BioModule module, String property)` Parse property as non-negative integer value
`static Double`	`getPositiveDoubleVal(BioModule module, String property)` Parse property as positive double value
`static Integer`	`getPositiveInteger(BioModule module, String property)` Parse property as positive integer value
`static TreeMap<String,String>`	`getProperties()` Get current properties ordered by property
`static Set<String>`	`getSet(BioModule module, String property)` Parse comma-separated property value to build an unordered Set
`static String`	`getString(BioModule module, String property)` Get property value as String.
`static Set<String>`	`getTreeSet(BioModule module, String property)` Parse comma-separated property value to build an ordered Set
`static Map<String,String>`	`getUsedProps()` Cache of the properties used in this pipeline.
`static void`	`initialize()` Initialize `Config` by reading in properties from config runtime parameter.
`static boolean`	`isOnCluster()` Check if running on cluster
`static String`	`pipelineName()` Get the current pipeline name (root folder name)
`static String`	`pipelinePath()` Get the current pipeline absolute directory path (root folder path)
`static String`	`replaceEnvVar(String arg)` Interpret env variable if included in the arg string, otherwise return the arg.
`protected static Properties`	`replaceEnvVars(Properties properties)` Interpret env variables defined in the Config file and runtime env - for example These props are used in: $BLJ/resources/config/defult/docker.properties: BLJ_ROOT=/mnt/efs EFS_DB=${BLJ_ROOT}/db humann2.protDB=${EFS_DB}/uniref Therefore, getString( "humann2.protDB" ) returns "/mnt/efs/db/uniref" If not found, check runtiem env (i.e., $HOME/bash_profile)
`static boolean`	`requireBoolean(BioModule module, String property)` Required to return a valid boolean or
`static Double`	`requireDoubleVal(BioModule module, String property)` Requires valid double value
`static File`	`requireExistingDir(BioModule module, String property)` Requires valid existing directory.
`static List<File>`	`requireExistingDirs(BioModule module, String property)` Requires valid list of file directories
`static File`	`requireExistingFile(BioModule module, String property)` Require valid existing file
`static Integer`	`requireInteger(BioModule module, String property)` Requires valid integer value
`static List<String>`	`requireList(BioModule module, String property)` Require valid list property
`static Double`	`requirePositiveDouble(BioModule module, String property)` Require valid positive double value
`static Integer`	`requirePositiveInteger(BioModule module, String property)` Require valid positive integer value
`static Set<String>`	`requireSet(BioModule module, String property)` Require valid Set value
`static String`	`requireString(BioModule module, String property)` Require valid String value
`static void`	`setConfigProperty(String name, Collection<?> data)` Sets a property value in the props cache as a list
`static void`	`setConfigProperty(String name, String val)` Sets a property value in the props cache
`static void`	`setPipelineDir(File dir)` Set the root pipeline directory path
`protected static void`	`setPipelineRootDir()` Set Create a pipeline root directory if the pipeline is new.

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

- Constructor Detail
  - Config
```
public Config()
```
- Method Detail
  - getBoolean
```
public static boolean getBoolean(BioModule module,
                                 String property)
                          throws ConfigFormatException
```
    Parse property value (Y or N) to return boolean, if not found, return false;
    
    Parameters:
    
    module - Source BioModule calling this function
    
    property - Property name
    
    Returns:
    
    boolean value
    
    Throws:
    
    ConfigFormatException - if property value is not null but also not Y or N.
  - getConfigFileExt
```
public static String getConfigFileExt()
```
    Gets the configuration file extension (often ".properties")
    
    Returns:
    
    Config file extension
  - getConfigFileName
```
public static String getConfigFileName()
```
    Gets the configuration file name
    
    Returns:
    
    Config file name
  - getConfigFilePath
```
public static String getConfigFilePath()
```
    Gets the full Config file path passed to BioLockJ as a runtime parameter.
    
    Returns:
    
    Config file path
  - getDoubleVal
```
public static Double getDoubleVal(BioModule module,
                                  String property)
                           throws ConfigFormatException
```
    Parse property for numeric (double) value
    
    Parameters:
    
    module - BioModule to check for module-specific form of this property
    
    property - Property name
    
    Returns:
    
    Double value or null
    
    Throws:
    
    ConfigFormatException - if property is defined, but set with a non-numeric value
  - getExe
```
public static String getExe(BioModule module,
                            String property)
                     throws Exception
```
    Get exe.* property name. If null, return the property name (without the "exe." prefix)
    
    Parameters:
    
    module - BioModule to check for module-specific form of this property
    
    property - Property name
    
    Returns:
    
    String value of executable
    
    Throws:
    
    Exception - if property does not start with "exe."
  - getExeParams
```
public static String getExeParams(BioModule module,
                                  String property)
                           throws Exception
```
    Call this function to get the parameters configured for this property.
    Make sure the last character for non-null results is an empty character for use in bash scripts calling the corresponding executable.
    
    Parameters:
    
    module - Calling module
    
    property - exe parameter name
    
    Returns:
    
    Executable program parameters
    
    Throws:
    
    Exception - if errors occur
  - getExistingDir
```
public static File getExistingDir(BioModule module,
                                  String property)
                           throws Exception
```
    Get a valid File directory or return null
    
    Parameters:
    
    module - BioModule to check for module-specific form of this property
    
    property - Property name
    
    Returns:
    
    File directory or null
    
    Throws:
    
    Exception - if path is defined but is not an existing directory or other errors occur
  - getExistingFile
```
public static File getExistingFile(BioModule module,
                                   String property)
                            throws Exception
```
    Get a valid File or return null. If path is a directory containing exactly 1 file, return that file.
    
    Parameters:
    
    module - BioModule to check for module-specific form of this property
    
    property - Property name
    
    Returns:
    
    File (not directory) or null
    
    Throws:
    
    Exception - if path is defined but is not an existing file or if other errors occur
  - getInitialProperties
```
public static TreeMap<String,String> getInitialProperties()
```
    Get initial properties ordered by property
    
    Returns:
    
    map ordered by property
  - getList
```
public static List<String> getList(BioModule module,
                                   String property)
```
    Parse comma delimited property value to return list
    
    Parameters:
    
    module - BioModule to check for module-specific form of this property
    
    property - Property name
    
    Returns:
    
    List of String values (or an empty list)
  - getModuleProp
```
public static String getModuleProp(BioModule module,
                                   String prop)
```
    Return module specific property if configured, otherwise use the given prop.
    
    Parameters:
    
    module - BioModule
    
    prop - Property
    
    Returns:
    
    Config property
  - getModuleProp
```
public static String getModuleProp(String moduleName,
                                   String prop)
```
    Return module specific property if configured, otherwise use the given prop.
    
    Parameters:
    
    moduleName - BioModule name
    
    prop - Property
    
    Returns:
    
    property name
  - getNonNegativeInteger
```
public static Integer getNonNegativeInteger(BioModule module,
                                            String property)
                                     throws ConfigFormatException
```
    Parse property as non-negative integer value
    
    Parameters:
    
    module - BioModule to check for module-specific form of this property
    
    property - Property name
    
    Returns:
    
    Non-negative integer or null
    
    Throws:
    
    ConfigFormatException - if defined but is not a non-negative integer value
  - getPositiveDoubleVal
```
public static Double getPositiveDoubleVal(BioModule module,
                                          String property)
                                   throws ConfigFormatException
```
    Parse property as positive double value
    
    Parameters:
    
    module - BioModule to check for module-specific form of this property
    
    property - Property name
    
    Returns:
    
    Positive Double value or null
    
    Throws:
    
    ConfigFormatException - if property is defined, but not set with a positive number
  - getPositiveInteger
```
public static Integer getPositiveInteger(BioModule module,
                                         String property)
                                  throws ConfigFormatException
```
    Parse property as positive integer value
    
    Parameters:
    
    module - BioModule to check for module-specific form of this property
    
    property - Property name
    
    Returns:
    
    Positive Integer value or null
    
    Throws:
    
    ConfigFormatException - if property is defined, but not set with a positive integer
  - getProperties
```
public static TreeMap<String,String> getProperties()
```
    Get current properties ordered by property
    
    Returns:
    
    map ordered by property
  - getSet
```
public static Set<String> getSet(BioModule module,
                                 String property)
```
    Parse comma-separated property value to build an unordered Set
    
    Parameters:
    
    module - BioModule to check for module-specific form of this property
    
    property - Property name
    
    Returns:
    
    Set of values or an empty set (if no values)
  - getString
```
public static String getString(BioModule module,
                               String property)
```
    Get property value as String. Empty strings return null.
    
    Parameters:
    
    module - BioModule to check for module-specific form of this property
    
    property - Config file property name
    
    Returns:
    
    String or null
  - getTreeSet
```
public static Set<String> getTreeSet(BioModule module,
                                     String property)
```
    Parse comma-separated property value to build an ordered Set
    
    Parameters:
    
    module - BioModule to check for module-specific form of this property
    
    property - Property name
    
    Returns:
    
    Set of values or an empty set (if no values)
  - getUsedProps
```
public static Map<String,String> getUsedProps()
```
    Cache of the properties used in this pipeline.
    
    Returns:
    
    list of properties
  - initialize
```
public static void initialize()
                       throws Exception
```
    Initialize Config by reading in properties from config runtime parameter.
    
    Throws:
    
    Exception - if unable to load Props
  - isOnCluster
```
public static boolean isOnCluster()
```
    Check if running on cluster
    
    Returns:
    
    TRUE if running on the cluster
  - pipelineName
```
public static String pipelineName()
```
    Get the current pipeline name (root folder name)
    
    Returns:
    
    Pipeline name
  - pipelinePath
```
public static String pipelinePath()
```
    Get the current pipeline absolute directory path (root folder path)
    
    Returns:
    
    Pipeline directory path
  - replaceEnvVar
```
public static String replaceEnvVar(String arg)
```
    Interpret env variable if included in the arg string, otherwise return the arg.
    
    Parameters:
    
    arg - Property or runtime argument
    
    Returns:
    
    Updated arg value after replacing env variables
  - requireBoolean
```
public static boolean requireBoolean(BioModule module,
                                     String property)
                              throws ConfigNotFoundException,
                                     ConfigFormatException
```
    Required to return a valid boolean or
    
    Parameters:
    
    module - BioModule to check for module-specific form of this property
    
    property - Property name
    
    Returns:
    
    boolean or
    
    Throws:
    
    ConfigNotFoundException - if propertyName is undefined
    
    ConfigFormatException - if property is defined, but not set to a boolean value
  - requireDoubleVal
```
public static Double requireDoubleVal(BioModule module,
                                      String property)
                               throws ConfigNotFoundException,
                                      ConfigFormatException
```
    Requires valid double value
    
    Parameters:
    
    module - BioModule to check for module-specific form of this property
    
    property - Property name
    
    Returns:
    
    Double value
    
    Throws:
    
    ConfigNotFoundException - if property is undefined
    
    ConfigFormatException - if property is defined, but set with a non-numeric value
  - requireExistingDir
```
public static File requireExistingDir(BioModule module,
                                      String property)
                               throws Exception
```
    Requires valid existing directory.
    
    Parameters:
    
    module - BioModule to check for module-specific form of this property
    
    property - Property name
    
    Returns:
    
    File directory
    
    Throws:
    
    Exception - if property is undefined or if property is not a valid directory path
  - requireExistingDirs
```
public static List<File> requireExistingDirs(BioModule module,
                                             String property)
                                      throws Exception
```
    Requires valid list of file directories
    
    Parameters:
    
    module - BioModule to check for module-specific form of this property
    
    property - Property name
    
    Returns:
    
    List of File directories
    
    Throws:
    
    Exception - if errors occur
  - requireExistingFile
```
public static File requireExistingFile(BioModule module,
                                       String property)
                                throws Exception
```
    Require valid existing file
    
    Parameters:
    
    module - BioModule to check for module-specific form of this property
    
    property - Property name
    
    Returns:
    
    File with filename defined by property
    
    Throws:
    
    Exception - if property is undefined or if property is not a valid file path
  - requireInteger
```
public static Integer requireInteger(BioModule module,
                                     String property)
                              throws ConfigNotFoundException,
                                     ConfigFormatException
```
    Requires valid integer value
    
    Parameters:
    
    module - BioModule to check for module-specific form of this property
    
    property - Property name
    
    Returns:
    
    Integer value
    
    Throws:
    
    ConfigNotFoundException - if property is undefined
    
    ConfigFormatException - if property is not a valid integer
  - requireList
```
public static List<String> requireList(BioModule module,
                                       String property)
                                throws ConfigNotFoundException
```
    Require valid list property
    
    Parameters:
    
    module - BioModule to check for module-specific form of this property
    
    property - Property name
    
    Returns:
    
    List
    
    Throws:
    
    ConfigNotFoundException - if property is undefined
  - requirePositiveDouble
```
public static Double requirePositiveDouble(BioModule module,
                                           String property)
                                    throws ConfigNotFoundException,
                                           ConfigFormatException
```
    Require valid positive double value
    
    Parameters:
    
    module - BioModule to check for module-specific form of this property
    
    property - Property name
    
    Returns:
    
    Positive Double
    
    Throws:
    
    ConfigNotFoundException - if property is undefined
    
    ConfigFormatException - if property is defined, but not set to a positive numeric value
  - requirePositiveInteger
```
public static Integer requirePositiveInteger(BioModule module,
                                             String property)
                                      throws ConfigNotFoundException,
                                             ConfigFormatException
```
    Require valid positive integer value
    
    Parameters:
    
    module - BioModule to check for module-specific form of this property
    
    property - Property name
    
    Returns:
    
    Positive Integer
    
    Throws:
    
    ConfigNotFoundException - if property is undefined
    
    ConfigFormatException - if property is defined, but not set to a positive integer value
  - requireSet
```
public static Set<String> requireSet(BioModule module,
                                     String property)
                              throws ConfigNotFoundException
```
    Require valid Set value
    
    Parameters:
    
    module - BioModule to check for module-specific form of this property
    
    property - Property name
    
    Returns:
    
    Set of values
    
    Throws:
    
    ConfigNotFoundException - if property is undefined
  - requireString
```
public static String requireString(BioModule module,
                                   String property)
                            throws ConfigNotFoundException
```
    Require valid String value
    
    Parameters:
    
    module - BioModule to check for module-specific form of this property
    
    property - Property name
    
    Returns:
    
    String value
    
    Throws:
    
    ConfigNotFoundException - if property is undefined
  - setConfigProperty
```
public static void setConfigProperty(String name,
                                     Collection<?> data)
```
    Sets a property value in the props cache as a list
    
    Parameters:
    
    name - Property name
    
    data - Collection of data to store using the key = property
  - setConfigProperty
```
public static void setConfigProperty(String name,
                                     String val)
```
    Sets a property value in the props cache
    
    Parameters:
    
    name - Property name
    
    val - Value to assign to property
  - setPipelineDir
```
public static void setPipelineDir(File dir)
```
    Set the root pipeline directory path
    
    Parameters:
    
    dir - Pipeline directory path
  - getExistingFileObject
```
protected static File getExistingFileObject(String filePath)
                                     throws Exception
```
    Build File using filePath.
    
    Parameters:
    
    filePath - File path
    
    Returns:
    
    File or null
    
    Throws:
    
    Exception - if path is defined but is not found on the file system or other errors occur
  - replaceEnvVars
```
protected static Properties replaceEnvVars(Properties properties)
```
    Interpret env variables defined in the Config file and runtime env - for example
    These props are used in: $BLJ/resources/config/defult/docker.properties:
    - BLJ_ROOT=/mnt/efs
    - EFS_DB=${BLJ_ROOT}/db
    - humann2.protDB=${EFS_DB}/uniref
    Therefore, getString( "humann2.protDB" ) returns "/mnt/efs/db/uniref"
    If not found, check runtiem env (i.e., $HOME/bash_profile)
    Parameters:
    
    properties - All Config Properties
    
    Returns:
    
    Properties after replacing env variables
  - setPipelineRootDir
```
protected static void setPipelineRootDir()
                                  throws Exception
```
    Set Create a pipeline root directory if the pipeline is new.
    
    Throws:
    
    Exception - if any errors occur

Class Config

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

Config

Method Detail

getBoolean

getConfigFileExt

getConfigFileName

getConfigFilePath

getDoubleVal

getExe

getExeParams

getExistingDir

getExistingFile

getInitialProperties

getList

getModuleProp

getModuleProp

getNonNegativeInteger

getPositiveDoubleVal

getPositiveInteger

getProperties

getSet

getString

getTreeSet

getUsedProps

initialize

isOnCluster

pipelineName

pipelinePath

replaceEnvVar

requireBoolean

requireDoubleVal

requireExistingDir

requireExistingDirs

requireExistingFile

requireInteger

requireList

requirePositiveDouble

requirePositiveInteger

requireSet

requireString

setConfigProperty

setConfigProperty

setPipelineDir

getExistingFileObject

replaceEnvVars

setPipelineRootDir