biolockj.module

Class BioModuleImpl

java.lang.Object

biolockj.module.BioModuleImpl

All Implemented Interfaces:

BioModule, Comparable<BioModule>

Direct Known Subclasses:

Email, ImportMetadata, ScriptModuleImpl, Stop

public abstract class BioModuleImpl
extends Object
implements BioModule, Comparable<BioModule>

Superclass for standard BioModules (classifiers, parsers, etc). Sets standard behavior for many of the BioModule interface methods.

Field Summary

Fields

Modifier and Type	Field and Description
static String	GZIP_EXT BioLockJ gzip file extension constant: ".gz"
static String	LOG_EXT BioLockJ log file extension constant: ".log"
static String	PDF_EXT BioLockJ PDF file extension constant: ".pdf"
static String	RETURN Return character constant *backslash-n*
static String	SH_EXT BioLockJ shell script file extension constant: ".sh"
static String	TAB_DELIM BioLockJ tab character constant: "\t"
static String	TSV_EXT BioLockJ tab delimited text file extension constant: ".tsv"
static String	TXT_EXT BioLockJ tab delimited text file extension constant: ".txt"

Fields inherited from interface biolockj.module.BioModule

LOG_DIR, MAIN_SCRIPT_PREFIX, NO_VERSION, OUTPUT_DIR, RES_DIR, TEMP_DIR

Constructor Summary

Constructors

Constructor and Description
BioModuleImpl()

Method Summary

Modifier and Type	Method and Description
protected void	addGeneralProperty(String prop)
protected void	addGeneralProperty(String prop, String additionalDescription)
protected void	addGeneralProperty(String prop, String type, String additionalDescription)
protected void	addNewProperty(String prop, String type, String desc)
protected void	addNewProperty(String prop, String type, String desc, String defaultValue)
protected void	cacheInputFiles(Collection<File> files) Cache the input files for quick access on subsequent calls to getInputFiles()
abstract void	checkDependencies() If restarting or running a direct pipeline execute the cleanup for completed modules.
void	cleanUp() If metadata exists in module output directory, refresh MetaUtil.
int	compareTo(BioModule module)
boolean	equals(Object obj) Compared based on ID
abstract void	executeTask() This is the main method called when it is time for the BioModule to complete its task.
protected List<File>	findModuleInputFiles() Called upon first access of input files to return sorted list of files from all Config."input.dirPaths" Hidden files (starting with ".") are ignored Call isValidInputModule(BioModule) on each previous module until acceptable input files are found
String	getAlias() Some BioModules may be added to a pipeline multiple times. The user may provide an alias for a module in the run order, thus allowing the user direct properties to an individual instance of a module.
String	getDescription(String prop)
String	getDetails()
String	getDockerImageOwner() Get the name of the docker hub user that owns the image to use for this module.
String	getDockerImageTag() Get the version / tag to use for the docker image.
protected List<File>	getFileCache() Get cached input files
Integer	getID() Some BioModules may be added to a pipeline multiple times so must be identified by an ID. This is the same value as the directory folder prefix when run. The 1st module ID is 0 (or 00 if there are more than 10 modules.
List<File>	getInputFiles() BioModule getInputFiles() is called to initialize upon first call and cached.
File	getLogDir() Returns moduleDir/temp for intermediate files.
List<String>	getMenuPlacement()
File	getMetadata() Updated/new metadata files are saved to the module output directory (if created by the module).
File	getModuleDir() All BioModule work must be contained within the scope of its root directory.
File	getOutputDir() Returns moduleDir/output which will be used as the next module's input.
List<String>	getPostRequisiteModules() By default, no post-requisites are required.
List<String>	getPreRequisiteModules() By default, no prerequisites are required.
String	getPropDefault(String prop) If a property is null based on the config files (including all defaults and standard.properties) but a module is passed to the Config class as the context for getting that module, the Config class can query the module for a value for the property.
protected HashMap<String,String>	getPropDescMap()
String	getPropType(String prop)
protected HashMap<String,String>	getPropTypeMap()
File	getResourceDir() Returns moduleDir/temp for intermediate files.
String	getSummary() Returns summary message to be displayed by Email module so must not contain confidential info.
File	getTempDir() Returns moduleDir/temp for intermediate files.
String	getTitle()
int	hashCode()
void	init() This method must be called immediately upon instantiation.
boolean	isValidInputModule(BioModule module) In the early stages of the pipeline, starting with the very 1st module ImportMetadata, most modules expect sequence files as input.
Boolean	isValidProp(String property)
List<String>	listProps()
void	setAlias(String alias)
String	toString()

Methods inherited from class java.lang.Object

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

Methods inherited from interface biolockj.module.BioModule

getDockerImageName, version

Field Detail

GZIP_EXT

public static final String GZIP_EXT

BioLockJ gzip file extension constant: ".gz"

See Also:

Constant Field Values

LOG_EXT

public static final String LOG_EXT

BioLockJ log file extension constant: ".log"

See Also:

Constant Field Values

PDF_EXT

public static final String PDF_EXT

BioLockJ PDF file extension constant: ".pdf"

See Also:

Constant Field Values

RETURN

public static final String RETURN

Return character constant *backslash-n*

See Also:

Constant Field Values

SH_EXT

public static final String SH_EXT

BioLockJ shell script file extension constant: ".sh"

See Also:

Constant Field Values

TAB_DELIM

public static final String TAB_DELIM

BioLockJ tab character constant: "\t"

See Also:

Constant Field Values

TSV_EXT

public static final String TSV_EXT

BioLockJ tab delimited text file extension constant: ".tsv"

See Also:

Constant Field Values

TXT_EXT

public static final String TXT_EXT

BioLockJ tab delimited text file extension constant: ".txt"

See Also:

Constant Field Values

Constructor Detail

BioModuleImpl

public BioModuleImpl()

Method Detail

addNewProperty

protected final void addNewProperty(String prop,
                                    String type,
                                    String desc)

addNewProperty

protected final void addNewProperty(String prop,
                                    String type,
                                    String desc,
                                    String defaultValue)

addGeneralProperty

protected final void addGeneralProperty(String prop)

addGeneralProperty

protected final void addGeneralProperty(String prop,
                                        String additionalDescription)

addGeneralProperty

protected final void addGeneralProperty(String prop,
                                        String type,
                                        String additionalDescription)

getPropDefault

public final String getPropDefault(String prop)

Description copied from interface: BioModule

If a property is null based on the config files (including all defaults and standard.properties) but a module is passed to the Config class as the context for getting that module, the Config class can query the module for a value for the property. In general, this is used for the properties defined in this module, but it CAN also be used for general properties.

Specified by:

getPropDefault in interface BioModule

Returns:

checkDependencies

public abstract void checkDependencies()
                                throws Exception

If restarting or running a direct pipeline execute the cleanup for completed modules.

Specified by:

checkDependencies in interface BioModule

Throws:

Exception - thrown if missing or invalid dependencies are found

cleanUp

public void cleanUp()
             throws Exception

If metadata exists in module output directory, refresh MetaUtil.

Specified by:

cleanUp in interface BioModule

Throws:

Exception - thrown if any runtime error occurs

compareTo

public int compareTo(BioModule module)

Specified by:

compareTo in interface Comparable<BioModule>

equals

public boolean equals(Object obj)

Compared based on ID

Overrides:

equals in class Object

executeTask

public abstract void executeTask()
                          throws Exception

Description copied from interface: BioModule

This is the main method called when it is time for the BioModule to complete its task.

Specified by:

executeTask in interface BioModule

Throws:

Exception - thrown if the module is unable to complete is task

getAlias

public String getAlias()

Description copied from interface: BioModule

Some BioModules may be added to a pipeline multiple times.
The user may provide an alias for a module in the run order, thus allowing the user direct properties to an individual instance of a module.

Specified by:

getAlias in interface BioModule

Returns:

Module ID

setAlias

public void setAlias(String alias)
              throws PipelineFormationException

Specified by:

setAlias in interface BioModule

Throws:

PipelineFormationException

getID

public Integer getID()

Description copied from interface: BioModule

Some BioModules may be added to a pipeline multiple times so must be identified by an ID.
This is the same value as the directory folder prefix when run.
The 1st module ID is 0 (or 00 if there are more than 10 modules.

Specified by:

getID in interface BioModule

Returns:

Module ID

getInputFiles

public List<File> getInputFiles()

BioModule getInputFiles() is called to initialize upon first call and cached.

Specified by:

getInputFiles in interface BioModule

Returns:

Input files

getMetadata

public File getMetadata()

Description copied from interface: BioModule

Updated/new metadata files are saved to the module output directory (if created by the module). Use param = FALSE to return an empty file objects in preparation for building a new metadata file.

Specified by:

getMetadata in interface BioModule

Returns:

Updated or new module/metadata/metadataFile.tsv is created, otherwise null

getModuleDir

public File getModuleDir()

All BioModule work must be contained within the scope of its root directory.

Specified by:

getModuleDir in interface BioModule

Returns:

BioModule root directory

getOutputDir

public File getOutputDir()

Returns moduleDir/output which will be used as the next module's input.

Specified by:

getOutputDir in interface BioModule

Returns:

File directory containing the primary BioModule output

getPostRequisiteModules

public List<String> getPostRequisiteModules()
                                     throws Exception

By default, no post-requisites are required.

Specified by:

getPostRequisiteModules in interface BioModule

Returns:

List of BioModules

Throws:

Exception - if invalid Class names are returned as post-requisites

getPreRequisiteModules

public List<String> getPreRequisiteModules()
                                    throws Exception

By default, no prerequisites are required.

Specified by:

getPreRequisiteModules in interface BioModule

Returns:

List of BioModule Class Names

Throws:

Exception - if invalid Class names are returned as prerequisites

getSummary

public String getSummary()
                  throws Exception

Returns summary message to be displayed by Email module so must not contain confidential info. ModuleUtil provides summary metrics on output files

Specified by:

getSummary in interface BioModule

Returns:

Summary of BioModule execution

Throws:

Exception - if any error occurs

getTempDir

public File getTempDir()

Returns moduleDir/temp for intermediate files. If Constants.RM_TEMP_FILES = "Y", this directory is deleted after pipeline completes successfully.

Specified by:

getTempDir in interface BioModule

Returns:

File directory of files typically not useful long term

getLogDir

public File getLogDir()

Returns moduleDir/temp for intermediate files. If Constants.RM_TEMP_FILES = "Y", this directory is deleted after pipeline completes successfully.

Specified by:

getLogDir in interface BioModule

Returns:

getResourceDir

public File getResourceDir()

Returns moduleDir/temp for intermediate files. If Constants.RM_TEMP_FILES = "Y", this directory is deleted after pipeline completes successfully.

Specified by:

getResourceDir in interface BioModule

Returns:

hashCode

public int hashCode()

Overrides:

hashCode in class Object

init

public void init()
          throws Exception

This method must be called immediately upon instantiation.

Specified by:

init in interface BioModule

Throws:

Exception - if errors occur

isValidInputModule

public boolean isValidInputModule(BioModule module)

In the early stages of the pipeline, starting with the very 1st module ImportMetadata, most modules expect sequence files as input. This method returns false if the previousModule only produced a new metadata file, such as ImportMetadata or RegisterNumReads. When getInputFiles() is called, this method determines if the previousModule output is valid input for the current BioModule. The default implementation of this method returns FALSE if the previousModule only generates a new metadata file.

Specified by:

isValidInputModule in interface BioModule

Parameters:

module - BioModule that ran before the current BioModule

Returns:

boolean TRUE if the previousModule output is acceptable input for the current BioModule

toString

public String toString()

Overrides:

toString in class Object

cacheInputFiles

protected void cacheInputFiles(Collection<File> files)

Cache the input files for quick access on subsequent calls to getInputFiles()

Parameters:

files - Input files

findModuleInputFiles

protected List<File> findModuleInputFiles()

Called upon first access of input files to return sorted list of files from all Config."input.dirPaths"
Hidden files (starting with ".") are ignored
Call isValidInputModule(BioModule) on each previous module until acceptable input files are found

Returns:

Set of input files

getFileCache

protected List<File> getFileCache()

Get cached input files

Returns:

List of input files

getTitle

public String getTitle()

getMenuPlacement

public List<String> getMenuPlacement()

getPropDescMap

protected final HashMap<String,String> getPropDescMap()

getDescription

public final String getDescription(String prop)
                            throws API_Exception

Throws:

API_Exception

listProps

public final List<String> listProps()

getPropTypeMap

protected final HashMap<String,String> getPropTypeMap()

getPropType

public final String getPropType(String prop)
                         throws API_Exception

Throws:

API_Exception

isValidProp

public Boolean isValidProp(String property)
                    throws Exception

Throws:

Exception

getDetails

public String getDetails()
                  throws API_Exception

Throws:

API_Exception

getDockerImageOwner

public String getDockerImageOwner()

Description copied from interface: BioModule

Get the name of the docker hub user that owns the image to use for this module. Docker images from docker hub are specified using this syntax: /:

Specified by:

getDockerImageOwner in interface BioModule

Returns:

getDockerImageTag

public String getDockerImageTag()

Description copied from interface: BioModule

Get the version / tag to use for the docker image. Docker images from docker hub are specified using this syntax: /:

Specified by:

getDockerImageTag in interface BioModule

Returns: