BioModuleImpl

java.lang.Object
- biolockj.module.BioModuleImpl

All Implemented Interfaces:

BioModule, Comparable<BioModule>

Direct Known Subclasses:

Email, ImportMetadata, ScriptModuleImpl
```
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
MAIN_SCRIPT_PREFIX, OUTPUT_DIR, TEMP_DIR

Constructor Summary

Constructors
Constructor and Description

BioModuleImpl()

Constructors
Constructor and Description
`BioModuleImpl()`

Method Summary

All Methods Instance Methods Abstract Methods Concrete Methods
Modifier and Type	Method and Description
`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()` By default, no cleanUp code is required.
`int`	`compareTo(BioModule module)`
`boolean`	`equals(Object o)` 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
`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`	`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`	`getSummary()` Returns summary message to be displayed by Email module so must not contain confidential info.
`File`	`getTempDir()` Returns moduleDir/temp for intermediate files.
`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.
`String`	`toString()`
`protected void`	`validateFileNameUnique(Set<String> fileNames, File file)` Validate files in `Constants.INPUT_DIRS` have unique names.

Methods inherited from class java.lang.Object
clone, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

- 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
  - 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
```
    By default, no cleanUp code is required.
    
    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 o)
```
    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
  - 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()
                         throws Exception
```
    BioModule getInputFiles() is called to initialize upon first call and cached.
    
    Specified by:
    
    getInputFiles in interface BioModule
    
    Returns:
    
    Input files
    
    Throws:
    
    Exception - if unable to obtain input files
  - 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.PIPELINE_DELETE_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
  - 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)
                        throws Exception
```
    Cache the input files for quick access on subsequent calls to getInputFiles()
    
    Parameters:
    
    files - Input files
    
    Throws:
    
    Exception - if errors occur
  - findModuleInputFiles
```
protected List<File> findModuleInputFiles()
                                   throws Exception
```
    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
    
    Throws:
    
    Exception - if errors occur
  - getFileCache
```
protected List<File> getFileCache()
```
    Get cached input files
    
    Returns:
    
    List of input files
  - validateFileNameUnique
```
protected void validateFileNameUnique(Set<String> fileNames,
                                      File file)
                               throws Exception
```
    Validate files in Constants.INPUT_DIRS have unique names. BioModules that expect duplicates must override this method.
    
    Parameters:
    
    fileNames - A registry of module input file names added so far
    
    file - Next file to validate
    
    Throws:
    
    Exception - if a duplicate file name found

Class BioModuleImpl

Field Summary

Fields inherited from interface biolockj.module.BioModule

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

GZIP_EXT

LOG_EXT

PDF_EXT

RETURN

SH_EXT

TAB_DELIM

TSV_EXT

TXT_EXT

Constructor Detail

BioModuleImpl

Method Detail

checkDependencies

cleanUp

compareTo

equals

executeTask

getID

getInputFiles

getModuleDir

getOutputDir

getPostRequisiteModules

getPreRequisiteModules

getSummary

getTempDir

init

isValidInputModule

toString

cacheInputFiles

findModuleInputFiles

getFileCache

validateFileNameUnique