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.).

Field Summary

Fields
Modifier and Type Field and Description

static String BLJ_BASH_VAR

static String BLJ_PROJ_VAR

(package private) static Properties props

Fields
Modifier and Type	Field and Description
`static String`	`BLJ_BASH_VAR`
`static String`	`BLJ_PROJ_VAR`
`(package private) static Properties`	`props`

Constructor Summary

Constructors
Constructor and Description

Config()

Constructors
Constructor and Description
`Config()`

Method Summary

All Methods Static Methods Concrete Methods Deprecated Methods
Modifier and Type	Method and Description
`static void`	`checkDependencies(BioModule module)`
`static String`	`convertRelativePath(String filePath, File CONFIG_DOT)` Given a relative path (ie, one that starts with "."), get the absolute path---even when runnig in docker.
`static String`	`convertWindowsPathForDocker(String path)`
`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`	`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 Map<String,String>`	`getEnvVarMap()` Return the String, String map of environment variables and their values.
`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.
`static List<File>`	`getExistingFileList(BioModule module, String property)`
`static File`	`getExistingFileObject(BioModule module, String property)` Build File using module and property name.
`static File`	`getExistingFileObjectFromPath(String filePath)` Build File using filePath.
`static File`	`getExistingFileObjectFromPath(String filePath, boolean convertRelativePath, boolean containerizePath)` Build File using filePath.
`static File`	`getFileObjectFromPath(String filePath, boolean convertRelativePath, boolean containerizePath)` Build File using filePath.
`static TreeMap<String,String>`	`getInitialProperties()` Get initial properties ordered by property
`static Integer`	`getIntegerProp(BioModule module, String property)` Parse property value as integer
`static List<String>`	`getList(BioModule module, String property)` Parse comma delimited property value to return list
`static File`	`getLocalConfigFile(String path)` Return file for path after modifying if running in a Docker container and/or interpreting bash env vars.
`static String`	`getModuleFormProp(BioModule module, String property)`
`static String`	`getModulePropName(BioModule module, String property)` Return property name after substituting the module name as its prefix.
`static Integer`	`getNonNegativeInteger(BioModule module, String property)` Parse property as non-negative integer value
`static File`	`getPipelineDir()` Deprecated. Use `BioLockJ.getPipelineDir()` instead
`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)`
`static String`	`getString(BioModule module, String property, String defaultVal)` 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`	`isInternalProperty(String property)`
`static boolean`	`isOnCluster()` Check if running on cluster
`static void`	`partiallyInitialize(File tempConfig)`
`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 environment 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`	`resetUsedProps()` Dump all of the properties stored for the current module into the allUsedProps set, and clear out the module-used-props to start with a clean slate.
`static void`	`saveModuleProps(BioModule module)`
`static void`	`setConfigProperty(String name, Collection<?> data)` Sets a property value in the props cache as a list
`static void`	`setConfigProperty(String name, Collection<?> data, BioModule module)` 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`	`setConfigProperty(String genericName, String val, BioModule module)` Sets a property value in the props cache
`static void`	`setFilePathProperty(String name, String val)`
`static void`	`setFilePathProperty(String name, String val, BioModule module)`
`static void`	`showUnusedProps()`

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

- Field Detail
  - BLJ_BASH_VAR
```
public static final String BLJ_BASH_VAR
```
    See Also:
    
    Constant Field Values
  - BLJ_PROJ_VAR
```
public static final String BLJ_PROJ_VAR
```
    See Also:
    
    Constant Field Values
  - props
```
static Properties props
```
- 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
  - 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 SpecialPropertiesException
```
    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:
    
    SpecialPropertiesException - if property name does not start with "exe." or if other exceptions are encountered
  - 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 ConfigPathException,
                                  DockerVolCreationException
```
    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:
    
    ConfigPathException - if path is defined but is not an existing file
    
    DockerVolCreationException
  - getExistingFile
```
public static File getExistingFile(BioModule module,
                                   String property)
                            throws ConfigPathException,
                                   DockerVolCreationException
```
    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:
    
    ConfigPathException - if path is defined but is not an existing file
    
    DockerVolCreationException
  - 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)
  - getLocalConfigFile
```
public static File getLocalConfigFile(String path)
                               throws ConfigPathException,
                                      DockerVolCreationException
```
    Return file for path after modifying if running in a Docker container and/or interpreting bash env vars.
    
    Parameters:
    
    path - File path
    
    Returns:
    
    Local File
    
    Throws:
    
    ConfigPathException - if the local path
    
    DockerVolCreationException
  - getModulePropName
```
public static String getModulePropName(BioModule module,
                                       String property)
```
    Return property name after substituting the module name as its prefix. Give first priority to a property that uses the module's alias, then one that uses the module name. If both of those are null, then use the property as given.
    
    Parameters:
    
    module - BioModule
    
    property - Property name
    
    Returns:
    
    BioModule specific property name
  - getModuleFormProp
```
public static String getModuleFormProp(BioModule module,
                                       String property)
```
  - 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
  - getPipelineDir
```
public static File getPipelineDir()
```
    Deprecated. Use BioLockJ.getPipelineDir() instead
    
    Get the pipeline directory if it is a valid directory on the file system.
    
    Returns:
    
    Pipeline directory (if it exists)
  - 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,
                               String defaultVal)
```
    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
  - getString
```
public static String getString(BioModule module,
                               String property)
```
  - 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. Save a copy of the primary Config to the pipeline root directory
    
    Throws:
    
    Exception - if unable to load Props
  - partiallyInitialize
```
public static void partiallyInitialize(File tempConfig)
                                throws Exception
```
    Throws:
    
    Exception
  - 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 environment variable if included in the arg string, otherwise return the arg. Variables are recognized if they are surrounded by ${ and }. For example: "dee ${VAR} da" becomes "fee doo da" IFF there is a variable "VAR" that is defined as "doo" either in the runtime environment, or in the config file. The special character "~" ("tilda") is changed to "${HOME}" and then processed IFF it is the first character in the string after removing any flanking white space.
    
    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 ConfigPathException,
                                      ConfigNotFoundException,
                                      DockerVolCreationException
```
    Requires valid existing directory.
    
    Parameters:
    
    module - BioModule to check for module-specific form of this property
    
    property - Property name
    
    Returns:
    
    File directory
    
    Throws:
    
    ConfigPathException - if path is defined but is not an existing file
    
    ConfigNotFoundException - if property is undefined
    
    DockerVolCreationException
  - requireExistingDirs
```
public static List<File> requireExistingDirs(BioModule module,
                                             String property)
                                      throws ConfigPathException,
                                             ConfigNotFoundException,
                                             DockerVolCreationException
```
    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:
    
    ConfigPathException - if directory paths are undefined or do not exist
    
    ConfigNotFoundException - if a required property is undefined
    
    DockerVolCreationException
  - requireExistingFile
```
public static File requireExistingFile(BioModule module,
                                       String property)
                                throws ConfigPathException,
                                       ConfigNotFoundException,
                                       DockerVolCreationException
```
    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:
    
    ConfigPathException - if path is defined but is not an existing file
    
    ConfigNotFoundException - if property is undefined
    
    DockerVolCreationException
  - 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,
                                     BioModule module)
                              throws DockerVolCreationException
```
    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
    
    module - if module is not null, and the props already include a module-specific form of this property, save the new value to the module specific form.
    
    Throws:
    
    DockerVolCreationException
  - setConfigProperty
```
public static void setConfigProperty(String name,
                                     Collection<?> data)
                              throws DockerVolCreationException
```
    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
    
    Throws:
    
    DockerVolCreationException
  - setFilePathProperty
```
public static void setFilePathProperty(String name,
                                       String val,
                                       BioModule module)
                                throws DockerVolCreationException
```
    Throws:
    
    DockerVolCreationException
  - setFilePathProperty
```
public static void setFilePathProperty(String name,
                                       String val)
                                throws DockerVolCreationException
```
    Throws:
    
    DockerVolCreationException
  - setConfigProperty
```
public static void setConfigProperty(String genericName,
                                     String val,
                                     BioModule module)
```
    Sets a property value in the props cache
    
    Parameters:
    
    name - Property name
    
    val - Value to assign to property
    
    module - if module is not null, and the props already include a module-specific form of this property, save the new value to the module specific form.
  - 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
  - getFileObjectFromPath
```
public static File getFileObjectFromPath(String filePath,
                                         boolean convertRelativePath,
                                         boolean containerizePath)
                                  throws DockerVolCreationException
```
    Build File using filePath.
    
    Parameters:
    
    filePath - File path
    
    Returns:
    
    File or null
    
    Throws:
    
    ConfigPathException - if path is defined but is not found on the file system
    
    DockerVolCreationException
  - getExistingFileObjectFromPath
```
public static File getExistingFileObjectFromPath(String filePath)
                                          throws ConfigPathException,
                                                 DockerVolCreationException
```
    Build File using filePath.
    
    Parameters:
    
    filePath - File path
    
    Returns:
    
    File or null
    
    Throws:
    
    ConfigPathException - if path is defined but is not found on the file system
    
    DockerVolCreationException
  - getExistingFileObjectFromPath
```
public static File getExistingFileObjectFromPath(String filePath,
                                                 boolean convertRelativePath,
                                                 boolean containerizePath)
                                          throws ConfigPathException,
                                                 DockerVolCreationException
```
    Build File using filePath. In some internal cases, it may be best to avoid converting relative paths, or to the docker conversion. If the path is null, return null. If the path does not lead to a valid file, throw exception.
    
    Parameters:
    
    filePath -
    
    convertRelativePath - - should the "./" be converted to be relative to the config file
    
    containerizePath - - should this be converted from host-path form to in-docker-container form.
    
    Returns:
    
    Throws:
    
    ConfigPathException
    
    DockerVolCreationException
  - getExistingFileObject
```
public static File getExistingFileObject(BioModule module,
                                         String property)
                                  throws ConfigPathException,
                                         DockerVolCreationException
```
    Build File using module and property name.
    
    Parameters:
    
    module - A BioModule, can be null
    
    property - A string property name.
    
    Returns:
    
    File or null
    
    Throws:
    
    ConfigPathException - if path is defined but is not found on the file system
    
    DockerVolCreationException
  - getExistingFileList
```
public static List<File> getExistingFileList(BioModule module,
                                             String property)
                                      throws ConfigPathException,
                                             DockerVolCreationException
```
    Throws:
    
    ConfigPathException
    
    DockerVolCreationException
  - convertWindowsPathForDocker
```
public static String convertWindowsPathForDocker(String path)
```
  - convertRelativePath
```
public static String convertRelativePath(String filePath,
                                         File CONFIG_DOT)
                                  throws DockerVolCreationException
```
    Given a relative path (ie, one that starts with "."), get the absolute path---even when runnig in docker. In the config file, users can use ./ to reference files in the same directory as the config file. And by extension, "../" can reference the parent of that directory. We tell users to use host paths in their config file, so when we replace the . or .., it is important that replace it with the HOST path to the config file directory.
    
    Parameters:
    
    filePath -
    
    Returns:
    
    Throws:
    
    DockerVolCreationException
  - 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
  - getIntegerProp
```
public static Integer getIntegerProp(BioModule module,
                                     String property)
                              throws ConfigFormatException
```
    Parse property value as integer
    
    Parameters:
    
    property - Property name
    
    Returns:
    
    integer value or null
    
    Throws:
    
    ConfigFormatException - if property is defined, but does not return an integer
  - isInternalProperty
```
public static boolean isInternalProperty(String property)
```
  - resetUsedProps
```
public static void resetUsedProps()
```
    Dump all of the properties stored for the current module into the allUsedProps set, and clear out the module-used-props to start with a clean slate.
  - saveModuleProps
```
public static void saveModuleProps(BioModule module)
                            throws IOException
```
    Throws:
    
    IOException
  - showUnusedProps
```
public static void showUnusedProps()
                            throws FileNotFoundException,
                                   IOException
```
    Throws:
    
    FileNotFoundException
    
    IOException
  - getEnvVarMap
```
public static Map<String,String> getEnvVarMap()
                                       throws ConfigNotFoundException
```
    Return the String, String map of environment variables and their values. This map will only include variables that are referenced in the config file using the ${VAR} format.
    
    Returns:
    
    Throws:
    
    ConfigNotFoundException
  - checkDependencies
```
public static void checkDependencies(BioModule module)
                              throws ConfigNotFoundException,
                                     ConfigFormatException
```
    Throws:
    
    ConfigNotFoundException
    
    ConfigFormatException

Class Config

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

BLJ_BASH_VAR

BLJ_PROJ_VAR

props

Constructor Detail

Config

Method Detail

getBoolean

getConfigFileExt

getConfigFilePath

getDoubleVal

getExe

getExeParams

getExistingDir

getExistingFile

getInitialProperties

getList

getLocalConfigFile

getModulePropName

getModuleFormProp

getNonNegativeInteger

getPipelineDir

getPositiveDoubleVal

getPositiveInteger

getProperties

getSet

getString

getString

getTreeSet

getUsedProps

initialize

partiallyInitialize

isOnCluster

pipelineName

pipelinePath

replaceEnvVar

requireBoolean

requireDoubleVal

requireExistingDir

requireExistingDirs

requireExistingFile

requireInteger

requireList

requirePositiveDouble

requirePositiveInteger

requireSet

requireString

setConfigProperty

setConfigProperty

setFilePathProperty

setFilePathProperty

setConfigProperty

setConfigProperty

getFileObjectFromPath

getExistingFileObjectFromPath

getExistingFileObjectFromPath

getExistingFileObject

getExistingFileList

convertWindowsPathForDocker

convertRelativePath

replaceEnvVars

getIntegerProp

isInternalProperty

resetUsedProps

saveModuleProps

showUnusedProps

getEnvVarMap

checkDependencies