BioModule

All Known Subinterfaces:: ClassifierModule, DatabaseModule, JavaModule, ParserModule, ScriptModule, SeqModule

All Known Implementing Classes:: AddMetadataToPathwayTables, AddMetadataToTaxaTables, AwkFastaConverter, BioModuleImpl, BuildQiimeMapping, BuildTaxaTables, ClassifierModuleImpl, CompileOtuCounts, Demultiplexer, Email, Gunzipper, Humann2Classifier, Humann2CountModule, Humann2Parser, ImportMetadata, JavaModuleImpl, JsonReport, KneadData, Kraken2Classifier, Kraken2Parser, KrakenClassifier, KrakenParser, LogTransformTaxaTables, MergeQiimeOtuTables, Metaphlan2Classifier, Metaphlan2Parser, Multiplexer, NormalizeTaxaTables, OtuCountModule, ParserModuleImpl, PearMergeReads, QiimeClassifier, QiimeClosedRefClassifier, QiimeDeNovoClassifier, QiimeOpenRefClassifier, QiimeParser, R_CalculateStats, R_Module, R_PlotEffectSize, R_PlotMds, R_PlotOtus, R_PlotPvalHistograms, RarefyOtuCounts, RarefySeqs, RdpClassifier, RdpParser, RegisterNumReads, RemoveLowOtuCounts, RemoveLowPathwayCounts, RemoveScarceOtuCounts, RemoveScarcePathwayCounts, ScriptModuleImpl, SeqFileValidator, SeqModuleImpl, TaxaCountModule, TrimPrimers

public interface BioModule

Classes that implement this interface are eligible to be included in a BioLockJ pipeline.
Use the #BioModule tag with the class name in the Config file to include a module.
The Pipeline class executes BioModules in the order provided in the Config file.

BioModule Directory Structure

Directory	Description
output	Contains all module output files
temp	Holds intermediate files generated by the module, but are not to be passed on to the next module. This directory will deleted after pipeline execution if "pipeline.deleteTempFiles" = "Y"

Field Summary

Fields
Modifier and Type	Field and Description
`static String`	`MAIN_SCRIPT_PREFIX` Script prefix appended to start of file name to indicate the main script in the script directory.
`static String`	`OUTPUT_DIR` Name of the output sub-directory
`static String`	`TEMP_DIR` Name of the temporary sub-directory

Method Summary

All Methods Instance Methods Abstract Methods
Modifier and Type	Method and Description
`void`	`checkDependencies()` During pipeline initialization, all configured BioModules will run this method to validate dependencies.
`void`	`cleanUp()` This method executes after execution to update Config modified by the module or other cleanup operations.
`void`	`executeTask()` This is the main method called when it is time for the BioModule to complete its task.
`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()` Each BioModule takes the previous BioModule output as input: BioModule[ n ].getInputFiles() = BioModule[ n - 1 ].getOutputDir().listFiles() Special cases: The 1st BioModule return all files in "input.dirPaths" If previous BioModule BioModule[ n - 1 ] is a MetadataModule, forward it's input + output file: BioModule[ n ].getInputFiles() = BioModule[ n -1 ].getInputFiles() + BioModule[ n -1 ].getOutputFiles()
`File`	`getModuleDir()` Each BioModule generates sub-directory under $DOCKER_PROJ
`File`	`getOutputDir()` Output files destined as input for the next BioModule is created in this directory.
`List<String>`	`getPostRequisiteModules()` `Pipeline` calls this method when building the list of pipeline BioModules to execute.
`List<String>`	`getPreRequisiteModules()` `Pipeline` calls this method when building the list of pipeline BioModules to execute.
`String`	`getSummary()` Gets the BioModule execution summary, this is sent as part of the notification email, if configured. Summary should not include data content, to avoid unintentional publication of confidential information. However, meta-data such as number/size of files can be helpful during debug.
`File`	`getTempDir()` Contains intermediate files generated by the module but not used by the next BioModule. The files may contain supplementary information or data that may be helpful during debug or recovery. If "pipeline.deleteTempFiles" = "Y", successful pipelines delete this directory.
`void`	`init()` Initialize a new module to generate a unique ID and module directory.
`boolean`	`isValidInputModule(BioModule previousModule)` BioModules `getInputFiles()` method typically, but not always, return the previousModule output files.

- Field Detail
  - MAIN_SCRIPT_PREFIX
```
static final String MAIN_SCRIPT_PREFIX
```
    Script prefix appended to start of file name to indicate the main script in the script directory. BioModules that generate scripts must create exactly one main script.
    
    See Also:
    
    Constant Field Values
  - OUTPUT_DIR
```
static final String OUTPUT_DIR
```
    Name of the output sub-directory
    
    See Also:
    
    Constant Field Values
  - TEMP_DIR
```
static final String TEMP_DIR
```
    Name of the temporary sub-directory
    
    See Also:
    
    Constant Field Values
- Method Detail
  - checkDependencies
```
void checkDependencies()
                throws Exception
```
    During pipeline initialization, all configured BioModules will run this method to validate dependencies.
    
    Throws:
    
    Exception - thrown if missing or invalid dependencies are found
  - cleanUp
```
void cleanUp()
      throws Exception
```
    This method executes after execution to update Config modified by the module or other cleanup operations.
    
    Throws:
    
    Exception - thrown if any runtime error occurs
  - executeTask
```
void executeTask()
          throws Exception
```
    This is the main method called when it is time for the BioModule to complete its task.
    
    Throws:
    
    Exception - thrown if the module is unable to complete is task
  - getID
```
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.
    
    Returns:
    
    Module ID
  - getInputFiles
```
List<File> getInputFiles()
                  throws Exception
```
    Each BioModule takes the previous BioModule output as input:
    BioModule[ n ].getInputFiles() = BioModule[ n - 1 ].getOutputDir().listFiles()
    Special cases:
    - The 1st BioModule return all files in "input.dirPaths"
    - If previous BioModule BioModule[ n - 1 ] is a MetadataModule, forward it's input + output file: BioModule[ n ].getInputFiles() = BioModule[ n -1 ].getInputFiles() + BioModule[ n -1 ].getOutputFiles()
    Returns:
    
    Input files
    
    Throws:
    
    Exception - if unable to obtain input files
  - getModuleDir
```
File getModuleDir()
```
    Each BioModule generates sub-directory under $DOCKER_PROJ
    
    Returns:
    
    BioModule root directory
  - getOutputDir
```
File getOutputDir()
```
    Output files destined as input for the next BioModule is created in this directory.
    
    Returns:
    
    File directory containing the primary BioModule output
  - getPostRequisiteModules
```
List<String> getPostRequisiteModules()
                              throws Exception
```
    Pipeline calls this method when building the list of pipeline BioModules to execute. Any BioModules returned by this method will be added to the pipeline after the current BioModule. If multiple post-requisites are found, the modules will be added in the order listed.
    
    Returns:
    
    List of BioModules
    
    Throws:
    
    Exception - if invalid Class names are returned as post-requisites
  - getPreRequisiteModules
```
List<String> getPreRequisiteModules()
                             throws Exception
```
    Pipeline calls this method when building the list of pipeline BioModules to execute. Any BioModules returned by this method will be added to the pipeline before the current BioModule. If multiple prerequisites are returned, the modules will be added in the order listed.
    
    Returns:
    
    List of BioModule Class Names
    
    Throws:
    
    Exception - if invalid Class names are returned as prerequisites
  - getSummary
```
String getSummary()
           throws Exception
```
    Gets the BioModule execution summary, this is sent as part of the notification email, if configured.
    Summary should not include data content, to avoid unintentional publication of confidential information.
    However, meta-data such as number/size of files can be helpful during debug.
    
    Returns:
    
    Summary of BioModule execution
    
    Throws:
    
    Exception - if any error occurs
  - getTempDir
```
File getTempDir()
```
    Contains intermediate files generated by the module but not used by the next BioModule.
    The files may contain supplementary information or data that may be helpful during debug or recovery.
    If "pipeline.deleteTempFiles" = "Y", successful pipelines delete this directory.
    
    Returns:
    
    File directory of files typically not useful long term
  - init
```
void init()
   throws Exception
```
    Initialize a new module to generate a unique ID and module directory.
    
    Throws:
    
    Exception - if errors occur
  - isValidInputModule
```
boolean isValidInputModule(BioModule previousModule)
```
    BioModules getInputFiles() method typically, but not always, return the previousModule output files. This method checks the output directory from the previous module to check for input deemed acceptable by the current module. The conditions coded in this method will be checked on each previous module in the pipeline until acceptable input is found. If no previous module produced acceptable input, the files under Config."input.dirPaths" are returned.
    
    This method can be overridden by modules that need input files generated prior to the previous module.
    
    Parameters:
    
    previousModule - BioModule that ran before the current BioModule
    
    Returns:
    
    boolean TRUE if the previousModule output is acceptable input for the current BioModule

Interface BioModule

Field Summary

Method Summary

Field Detail

MAIN_SCRIPT_PREFIX

OUTPUT_DIR

TEMP_DIR

Method Detail

checkDependencies

cleanUp

executeTask

getID

getInputFiles

getModuleDir

getOutputDir

getPostRequisiteModules

getPreRequisiteModules

getSummary

getTempDir

init

isValidInputModule