public class RdpHierParser extends JavaModuleImpl implements ApiModule
BLJ_OPTIONS
GZIP_EXT, LOG_EXT, PDF_EXT, RETURN, SH_EXT, TAB_DELIM, TSV_EXT, TXT_EXT
LOG_DIR, MAIN_SCRIPT_PREFIX, NO_VERSION, OUTPUT_DIR, RES_DIR, TEMP_DIR
Constructor and Description |
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RdpHierParser() |
Modifier and Type | Method and Description |
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void |
checkDependencies()
Validate module dependencies:
Require
Config . exists
Require Config . is positive integer
Require Config . is positive integer
Verify Config . is positive integer if set
Start the AWS DB sync to S3 if a novel DB has been configure and
"aws.copyDbToS3" is enabled
|
void |
executeTask()
JavaModules run pure Java code.
If in Direct mode, execute JavaModuleImpl.runModule() to run the module functionality; another BioLockJ instance
is the manager that has launched this instance to run this module.Otherwise, this instance is the manager, If Config ."pipeline.detachJavaModules"="Y" execute
BioModule.executeTask() to build the bash scripts to launch a secondary instance in direct mode to run this module.Otherwise (if "pipeline.detachJavaModules"="N"), execute JavaModuleImpl.runModule() to run the Java code to execute module functionality within the manager instance. |
String |
getCitationString()
At a minimum, this should return the name and/or url for the wrapped tool.
|
String |
getDescription()
Briefly describe what this module does.
|
String |
getDetails()
A extension of
getDescription . |
List<File> |
getInputFiles()
BioModule
BioModuleImpl.getInputFiles() is called to initialize upon first call and cached. |
List<String> |
getPreRequisiteModules()
By default, no prerequisites are required.
|
boolean |
isValidInputModule(BioModule module)
If module is a
SeqModule input must contain sequence data. |
static void |
main(String[] args)
For stand-alone testing outside of a BioLockJ pipeline.
arg 0 - comma-separated list of taxonomic levels arg 1 - comma-separated list of input files (one or more) arg 2 - path/to/dir where the outputs will be saved |
void |
runModule()
This method executes the modules primary Java routine.
|
String |
version()
Changes to a module class should be accompanied by a increment in version.
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buildScript, getDockerImageName, getDockerImageOwner, getDockerImageTag, getWorkerScriptFunctions, markStatus, moduleComplete, moduleFailed, runBioLockJ_CMD
buildScriptForPairedReads, getJobParams, getMainScript, getRuntimeParams, getScriptDir, getScriptErrors, getSummary, getTimeout, hasScripts, isValidProp
addGeneralProperty, addGeneralProperty, addGeneralProperty, addNewProperty, addNewProperty, cacheInputFiles, cleanUp, compareTo, equals, findModuleInputFiles, getAlias, getDescription, getFileCache, getID, getLogDir, getMenuPlacement, getMetadata, getModuleDir, getOutputDir, getPostRequisiteModules, getPropDefault, getPropDescMap, getPropType, getPropTypeMap, getResourceDir, getTempDir, getTitle, hashCode, init, listProps, setAlias, toString
clone, finalize, getClass, notify, notifyAll, wait, wait, wait
getDescription, getMenuPlacement, getPropType, getTitle, isValidProp, listProps
cleanUp, getAlias, getDockerImageName, getDockerImageOwner, getDockerImageTag, getID, getLogDir, getMetadata, getModuleDir, getOutputDir, getPostRequisiteModules, getPropDefault, getResourceDir, getSummary, getTempDir, init, setAlias
buildScriptForPairedReads, getJobParams, getMainScript, getScriptDir, getScriptErrors, getTimeout
public void checkDependencies() throws Exception
ScriptModuleImpl
Config
. exists
Config
. is positive integer
Config
. is positive integer
Config
. is positive integer if set
checkDependencies
in interface BioModule
checkDependencies
in class ScriptModuleImpl
Exception
- thrown if missing or invalid dependencies are foundpublic static void main(String[] args) throws Exception
args
- Exception
public void runModule() throws Exception
JavaModule
runModule
in interface JavaModule
runModule
in class JavaModuleImpl
Exception
- thrown if any runtime error occurspublic void executeTask() throws Exception
JavaModuleImpl
JavaModuleImpl.runModule()
to run the module functionality; another BioLockJ instance
is the manager that has launched this instance to run this module.Config
."pipeline.detachJavaModules"="Y" execute
BioModule.executeTask()
to build the bash scripts to launch a secondary instance in direct mode to run this module.JavaModuleImpl.runModule()
to run the Java code to execute module functionality within the manager instance.executeTask
in interface BioModule
executeTask
in class JavaModuleImpl
Exception
- thrown if the module is unable to complete is taskpublic List<File> getInputFiles()
BioModuleImpl
BioModuleImpl.getInputFiles()
is called to initialize upon first call and cached.getInputFiles
in interface BioModule
getInputFiles
in class BioModuleImpl
public boolean isValidInputModule(BioModule module)
JavaModuleImpl
SeqModule
input must contain sequence data.isValidInputModule
in interface BioModule
isValidInputModule
in class JavaModuleImpl
module
- BioModule that ran before the current BioModulepublic List<String> getPreRequisiteModules() throws Exception
BioModuleImpl
getPreRequisiteModules
in interface BioModule
getPreRequisiteModules
in class BioModuleImpl
Exception
- if invalid Class names are returned as prerequisitespublic String getDescription()
ApiModule
getDetails
.getDescription
in interface ApiModule
public String getDetails()
ApiModule
getDescription
. Beyond the brief description, give details such as
the interaction between properties.getDetails
in interface ApiModule
getDetails
in class BioModuleImpl
public String getCitationString()
ApiModule
getCitationString
in interface ApiModule