Exception
subclasses specific to BioLockJ.See: Description
Class | Description |
---|---|
FatalExceptionHandler |
FatalExceptionHandler saves logs somewhere the user can access if failures occur before the log file is generated.
|
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 |
Exception
subclasses specific to BioLockJ.