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
BioModule s 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 |
Modifier and Type | Method and Description |
---|---|
protected static ArrayList<File> |
Properties.getDefaultConfig(File propFile)
Parse property file for the property "pipeline.defaultProps".
|
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 |
Constructor and Description |
---|
SpecialPropertiesException(String property,
BioLockJException bljEx) |
Modifier and Type | Method and Description |
---|---|
(package private) static void |
Launcher.handleBioLockJException(BioLockJException ex) |
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.
|
Modifier and Type | Method and Description |
---|---|
protected File |
R_Module.getFunctionLib() |
static File |
R_Module.getFunctionLib(BioModule module) |
protected File |
R_Module.getModuleRScript() |
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) |
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.
|