biolockj

Class Properties

java.lang.Object

java.util.Dictionary<K,V>

java.util.Hashtable<Object,Object>

java.util.Properties

biolockj.Properties

All Implemented Interfaces:

Serializable, Cloneable, Map<Object,Object>

public class Properties
extends Properties

Load properties defined in the BioLockJ configuration file, including inherited properties from project.defaultProps

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
static String	BOOLEAN_TYPE
static String	EXE_PATH
static String	FILE_PATH
static String	FILE_PATH_LIST
static String	INTEGER_TYPE
static String[]	KNOWN_TYPES
static String	LIST_TYPE
static String	NO_BROAD_USE Added description for general properties that are not meant to be used in their general form.
static String	NUMERTIC_TYPE
static String	POS_INTEGER_TYPE
static String	REQUIRED Prefix for property types whose values cannot be null.
static String	STRING_TYPE

Fields inherited from class java.util.Properties

defaults

Constructor Summary

Constructors

Constructor and Description
Properties() Default constructor.
Properties(Properties defaultConfig) Constructor called when "pipeline.defaultProps" contains a valid file-path

Method Summary

Modifier and Type	Method and Description
protected static Properties	buildConfig(File propFile) Recursive method handles nested default Config files.
static String	deprecatedPropMessage(String prop) Returns a message telling the user that the property is deprecated.
protected static ArrayList<File>	getDefaultConfig(File propFile) Parse property file for the property "pipeline.defaultProps".
static String	getDescription(String prop)
static List<String>	getListedModules(File file)
static HashMap<String,String>	getPropDescMap() Allow the API to access the list of properties and descriptions.
static String	getPropertyType(String prop)
static HashMap<String,String>	getPropTypeMap() Allow the API to access the list of properties and descriptions.
static boolean	isDeprecatedProp(String prop) Determines if the given prop is in the list of deprecated properties.
static boolean	isValidExeProp(BioModule module, String property) Verify that a given exe property has a valid value.
static Boolean	isValidProp(String property) Check if a property has a value in a valid format.
protected void	load(FileInputStream fis) Load properties, adding escape characters where necessary.
static Properties	loadProperties(File file) Instantiate Properties via buildConfig(File)
protected static Properties	readProps(File propFile, Properties defaultProps) Read the properties defined in the required propFile and defaultProps (if included) to build Config. Properties in propFile will override the defaultProps.
static void	registerProp(String prop, String type, String desc) Allow utility classes to keep their props private but still register them with Properties for API.

Methods inherited from class java.util.Properties

getProperty, getProperty, list, list, load, load, loadFromXML, propertyNames, save, setProperty, store, store, storeToXML, storeToXML, stringPropertyNames

Methods inherited from class java.util.Hashtable

clear, clone, compute, computeIfAbsent, computeIfPresent, contains, containsKey, containsValue, elements, entrySet, equals, forEach, get, getOrDefault, hashCode, isEmpty, keys, keySet, merge, put, putAll, putIfAbsent, rehash, remove, remove, replace, replace, replaceAll, size, toString, values

Methods inherited from class java.lang.Object

finalize, getClass, notify, notifyAll, wait, wait, wait

Field Detail

REQUIRED

public static final String REQUIRED

Prefix for property types whose values cannot be null.

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Constant Field Values

NO_BROAD_USE

public static final String NO_BROAD_USE

Added description for general properties that are not meant to be used in their general form.

See Also:

Constant Field Values

STRING_TYPE

public static final String STRING_TYPE

See Also:

Constant Field Values

BOOLEAN_TYPE

public static final String BOOLEAN_TYPE

See Also:

Constant Field Values

FILE_PATH

public static final String FILE_PATH

See Also:

Constant Field Values

EXE_PATH

public static final String EXE_PATH

See Also:

Constant Field Values

LIST_TYPE

public static final String LIST_TYPE

See Also:

Constant Field Values

FILE_PATH_LIST

public static final String FILE_PATH_LIST

See Also:

Constant Field Values

INTEGER_TYPE

public static final String INTEGER_TYPE

See Also:

Constant Field Values

POS_INTEGER_TYPE

public static final String POS_INTEGER_TYPE

See Also:

Constant Field Values

NUMERTIC_TYPE

public static final String NUMERTIC_TYPE

See Also:

Constant Field Values

KNOWN_TYPES

public static final String[] KNOWN_TYPES

Constructor Detail

Properties

public Properties()

Default constructor.

Properties

public Properties(Properties defaultConfig)

Constructor called when "pipeline.defaultProps" contains a valid file-path

Parameters:

defaultConfig - Config built from "pipeline.defaultProps" property

Method Detail

load

protected void load(FileInputStream fis)
             throws IOException

Load properties, adding escape characters where necessary.

Parameters:

fis - FileInputStream

Throws:

IOException - if unable to convert escape characters

loadProperties

public static Properties loadProperties(File file)
                                 throws Exception

Instantiate Properties via buildConfig(File)

Parameters:

file - of Properties file

Returns:

Properties Config properties loaded from files

Throws:

Exception - if unable to extract properties from filePath

buildConfig

protected static Properties buildConfig(File propFile)
                                 throws Exception

Recursive method handles nested default Config files. Default props are overridden by parent level props.
Standard properties are always imported 1st: "${BLJ}/resources/config/default/standard.properties"
Docker properties are always imported 2nd if in a Docker container: "${BLJ}/resources/config/default/docker.properties"
Then nested default Config files defined by property: "pipeline.defaultProps"
The project Config file is read last to ensure properties are not overridden in the default Config files.

Parameters:

propFile - BioLockJ Configuration file

Returns:

Properties including default props

Throws:

Exception - if errors occur

getDefaultConfig

protected static ArrayList<File> getDefaultConfig(File propFile)
                                           throws BioLockJException,
                                                  IOException

Parse property file for the property "pipeline.defaultProps".

Parameters:

propFile - BioLockJ Config file

Returns:

nested default prop file or null

Throws:

BioLockJException

IOException - if FileReader reader fails to close.

Exception - if errors occur

readProps

protected static Properties readProps(File propFile,
                                      Properties defaultProps)
                               throws FileNotFoundException,
                                      IOException

Read the properties defined in the required propFile and defaultProps (if included) to build Config.
Properties in propFile will override the defaultProps.

Parameters:

propFile - BioLockJ configuration file

defaultProps - Default properties

Returns:

Properties instance

Throws:

FileNotFoundException - thrown if propFile is not a valid file path

IOException - thrown if propFile or defaultProps cannot be parsed to read in properties

getListedModules

public static List<String> getListedModules(File file)
                                     throws Exception

Throws:

Exception

registerProp

public static void registerProp(String prop,
                                String type,
                                String desc)
                         throws API_Exception

Allow utility classes to keep their props private but still register them with Properties for API.

Parameters:

prop - a property

type - The expected type of value for that property, must be one of the recognized types in Properties class

desc - Human readable string for users guide and similar uses.

Throws:

API_Exception

getPropDescMap

public static HashMap<String,String> getPropDescMap()
                                             throws API_Exception

Allow the API to access the list of properties and descriptions.

Returns:

Throws:

API_Exception

getDescription

public static String getDescription(String prop)
                             throws API_Exception

Throws:

API_Exception

getPropTypeMap

public static HashMap<String,String> getPropTypeMap()
                                             throws API_Exception

Allow the API to access the list of properties and descriptions.

Returns:

Throws:

API_Exception

getPropertyType

public static String getPropertyType(String prop)
                              throws API_Exception

Throws:

API_Exception

isValidExeProp

public static boolean isValidExeProp(BioModule module,
                                     String property)

Verify that a given exe property has a valid value.

Parameters:

property -

Returns:

isValidProp

public static Boolean isValidProp(String property)
                           throws API_Exception

Check if a property has a value in a valid format.

Parameters:

property -

Returns:

null if the property is no recognized, true if the property has a valid value, false otherwise.

Throws:

API_Exception

isDeprecatedProp

public static boolean isDeprecatedProp(String prop)

Determines if the given prop is in the list of deprecated properties.

Parameters:

prop -

Returns:

deprecatedPropMessage

public static String deprecatedPropMessage(String prop)

Returns a message telling the user that the property is deprecated. If there

Parameters:

prop -

Returns: