Uses of Class
biolockj.exception.BioLockJException

Packages that use BioLockJException

Package	Description
biolockj	The root biolockj package contains core classes used by all BioLockJ pipelines.
biolockj.exception	This package contains Exception subclasses specific to BioLockJ.
biolockj.launch
biolockj.module.implicit	The modules in this package are implicitly added to pipelines as needed. These modules cannot be directly added to any pipeline unless overridden via pipeline.disableImplicitModules=Y.
biolockj.module.report.r	This package contains BioModules that build pipeline reports from the standard OTU abundance tables by generating R scripts to produce the summary statistics and data visualizations output to PDF files.
biolockj.util	Static utilities centralize and organize reusable core methods.
biolockj.util.paths

Uses of BioLockJException in biolockj

Methods in biolockj that throw BioLockJException

Modifier and Type	Method and Description
protected static ArrayList<File>	Properties.getDefaultConfig(File propFile) Parse property file for the property "pipeline.defaultProps".

Uses of BioLockJException in biolockj.exception

Subclasses of BioLockJException in biolockj.exception

Modifier and Type	Class and Description
class	BioLockJStatusException
class	ConfigConflictException
class	ConfigException ConfigException is the superclass for all BioLockJ configuration file Exceptions used to ensure message uniformity.
class	ConfigFormatException ConfigFormatException is thrown if property is defined but the format is invalid.
class	ConfigNotFoundException ConfigNotFoundException is thrown if a required Config property is undefined.
class	ConfigPathException ConfigPathException is thrown if property is invalid file paths are encountered when processing the BioLockJ configuration file.
class	ConfigViolationException ConfigViolationException is thrown at runtime due to application state violations caused by invalid module I/O (sequences or metadata) as defined by Config properties.
class	DirectModuleException Some module are run as secondary instances of the BioLockJ program.
class	DockerImageException
class	DockerVolCreationException
class	DockerVolumeException
class	ExpectationFileFormatException TODO : Add info
class	FileWithoutMetadataException
class	IntentionalStop Parent exception for BioLockJ Exception that arise when the user explicitly intended to make the pipeline stop.
class	InvalidPipelineException
class	MetadataException MetadataException is thrown if errors occur processing Metadata files.
class	MetadataWithoutFileException
class	OtuFileException OtuFileException is thrown if errors occur processing OTU files.
class	PipelineFormationException PipelineFormationException is thrown when there is a problem in setting up the modules to run.
class	PipelineScriptException PipelineScriptException is thrown by BashScriptBuilder if errors occur writing MASTER & WORKER scripts.
class	RequiredRPackageException
class	RuntimeParamException ConfigException is the superclass for all BioLockJ configuration file Exceptions used to ensure message uniformity.
class	SequnceFormatException SequnceFormatException is thrown if errors occur processing fasta/fastq sequence files.
class	SpecialPropertiesException This type of exception is thrown if an error occurs while processing a special type of property such as "exe." properties or defaultProps.
class	StopAfterPrecheck When running in "precheck" mode, this is the mechanism that stops a pipeline from running.
class	StopModuleException
class	ValidationException ValidationException is thrown at module runtime if the Validation module finds a discrepancy between the expectations given for one or more files and the files found in the previous module.
class	ValidationExecutionException ValidationException is thrown at module runtime if the ValidationUtil throws a non-BioLockJ error while validating module output.
class	ValidationUtilityException

Constructors in biolockj.exception with parameters of type BioLockJException

Constructor and Description
SpecialPropertiesException(String property, BioLockJException bljEx)

Uses of BioLockJException in biolockj.launch

Methods in biolockj.launch with parameters of type BioLockJException

Modifier and Type	Method and Description
(package private) static void	Launcher.handleBioLockJException(BioLockJException ex)

Uses of BioLockJException in biolockj.module.implicit

Methods in biolockj.module.implicit that throw BioLockJException

Modifier and Type	Method and Description
protected void	ImportMetadata.buildNewMetadataFile() Create a simple metadata file in the module output directory, with only the 1st column populated with Sample IDs.

Uses of BioLockJException in biolockj.module.report.r

Methods in biolockj.module.report.r that throw BioLockJException

Modifier and Type	Method and Description
protected File	R_Module.getFunctionLib()
static File	R_Module.getFunctionLib(BioModule module)
protected File	R_Module.getModuleRScript()

Uses of BioLockJException in biolockj.util

Methods in biolockj.util that throw BioLockJException

Modifier and Type	Method and Description
static void	DockerUtil.checkDependencies(BioModule module)
static File	MasterConfigUtil.getExistingMasterConfig(File pipelineRoot) Find the MASTER config file in an existing pipeline.
static File	TaxaUtil.getTaxonomyTableFile(File dir, String level, String suffix) Create File object of a taxonomy table at the given level, with the given suffix, in the given directory dir.
static TaxaLevelTable	TaxaUtil.readTaxaTable(File taxaTable) Read a table of counts, formatted with samples as rows (ids in first column) and taxa as columns (ids in header).
static void	ValidationUtil.validateModule(BioModule module)

Uses of BioLockJException in biolockj.util.paths

Methods in biolockj.util.paths that throw BioLockJException

Modifier and Type	Method and Description
String	PathMapper.asInnerPath(String path) Convert path to inner path form.
String	PathMapper.asOuterPath(String path) Convert path to outer path form.
Map<String,String>	PathMapper.getMap() The map at represents the connection of inner path to outer path.