Package biolockj.exception

This package contains Exception subclasses specific to BioLockJ.

See: Description

Class Summary

Class	Description
FatalExceptionHandler	FatalExceptionHandler saves logs somewhere the user can access if failures occur before the log file is generated.

Exception Summary

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

Package biolockj.exception Description

This package contains Exception subclasses specific to BioLockJ.