biolockj.module.diy

Class Rmarkdown

java.lang.Object

biolockj.module.BioModuleImpl

biolockj.module.ScriptModuleImpl

biolockj.module.diy.Rmarkdown

All Implemented Interfaces:

ApiModule, BioModule, ScriptModule, Comparable<BioModule>

public class Rmarkdown
extends ScriptModuleImpl
implements ApiModule

Field Summary

Fields

Modifier and Type	Field and Description
protected static String	RESOURCES Config property: "rmarkdown.resources"
protected static String	RMD_FILE Config property: "rmarkdown.rmarkdown"

Fields inherited from class biolockj.module.BioModuleImpl

GZIP_EXT, LOG_EXT, PDF_EXT, RETURN, SH_EXT, TAB_DELIM, TSV_EXT, TXT_EXT

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
Rmarkdown()

Method Summary

Modifier and Type	Method and Description
List<List<String>>	buildScript(List<File> files) Return an inner list of lines to execute for each sample.
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
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.
String	getDockerImageName() Get the docker image to use for this module.
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.
String	getSummary() Returns summary message to be displayed by Email module so must not contain confidential info.
List<String>	getWorkerScriptFunctions() Method returns bash script lines used to build the functions called by the worker scripts.
Boolean	isValidProp(String property) Tests to see if the value val is valid for property prop; primarily tests format.
protected String	transferMarkdown()
protected void	transferResources()

Methods inherited from class biolockj.module.ScriptModuleImpl

buildScriptForPairedReads, executeTask, getJobParams, getMainScript, getRuntimeParams, getScriptDir, getScriptErrors, getTimeout, hasScripts

Methods inherited from class biolockj.module.BioModuleImpl

addGeneralProperty, addGeneralProperty, addGeneralProperty, addNewProperty, addNewProperty, cacheInputFiles, cleanUp, compareTo, equals, findModuleInputFiles, getAlias, getDescription, getFileCache, getID, getInputFiles, getLogDir, getMenuPlacement, getMetadata, getModuleDir, getOutputDir, getPostRequisiteModules, getPreRequisiteModules, getPropDefault, getPropDescMap, getPropType, getPropTypeMap, getResourceDir, getTempDir, getTitle, hashCode, init, isValidInputModule, listProps, setAlias, toString

Methods inherited from class java.lang.Object

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

Methods inherited from interface biolockj.api.ApiModule

getDescription, getMenuPlacement, getPropType, getTitle, listProps

Methods inherited from interface biolockj.module.BioModule

cleanUp, executeTask, getAlias, getID, getInputFiles, getLogDir, getMetadata, getModuleDir, getOutputDir, getPostRequisiteModules, getPreRequisiteModules, getPropDefault, getResourceDir, getTempDir, init, isValidInputModule, setAlias, version

Field Detail

RMD_FILE

protected static final String RMD_FILE

Config property: "rmarkdown.rmarkdown"

See Also:

Constant Field Values

RESOURCES

protected static final String RESOURCES

Config property: "rmarkdown.resources"

See Also:

Constant Field Values

Constructor Detail

Rmarkdown

public Rmarkdown()

Method Detail

checkDependencies

public void checkDependencies()
                       throws Exception

Description copied from class: ScriptModuleImpl

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

Specified by:

checkDependencies in interface BioModule

Overrides:

checkDependencies in class ScriptModuleImpl

Throws:

Exception - thrown if missing or invalid dependencies are found

isValidProp

public Boolean isValidProp(String property)
                    throws Exception

Description copied from interface: ApiModule

Tests to see if the value val is valid for property prop; primarily tests format. This is designed for individual properties. To make sure property values are compatible, use BioModule.checkDependencies(). Using switch/case or a stack of if/else is recommended. Within each case, call any/all method that is used by this module to access the value from the config file, leveraging the checks in the Config.get* methods. This method should never actually return false. If the value is not valid, it should throw an exception that includes a helpful message about whats not valid. As part of a throwable, that message is passed along to wherever the call started. Any time that "false" is actually the desired form, this method should be wrapped in a try/catch.

Specified by:

isValidProp in interface ApiModule

Overrides:

isValidProp in class ScriptModuleImpl

Returns:

true if value is recognized and good, false/Exception if it is recognized and invalid, null if prop is not recognized.

Throws:

Exception

buildScript

public List<List<String>> buildScript(List<File> files)
                               throws Exception

Description copied from class: ScriptModuleImpl

Return an inner list of lines to execute for each sample. Return these as a list (outer list)

Specified by:

buildScript in interface ScriptModule

Specified by:

buildScript in class ScriptModuleImpl

Parameters:

files - Files in the input directory that contain only forward reads

Returns:

Nested list of bash scripts lines

Throws:

Exception - if unable to generate script lines

getWorkerScriptFunctions

public List<String> getWorkerScriptFunctions()
                                      throws Exception

Description copied from interface: ScriptModule

Method returns bash script lines used to build the functions called by the worker scripts.

Specified by:

getWorkerScriptFunctions in interface ScriptModule

Overrides:

getWorkerScriptFunctions in class ScriptModuleImpl

Returns:

Bash script lines for the functions

Throws:

Exception - if errors occur

getSummary

public String getSummary()
                  throws Exception

Description copied from class: ScriptModuleImpl

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

Overrides:

getSummary in class ScriptModuleImpl

Returns:

Summary of BioModule execution

Throws:

Exception - if any error occurs

transferMarkdown

protected String transferMarkdown()
                           throws ConfigPathException,
                                  IOException,
                                  Exception

Throws:

ConfigPathException

IOException

Exception

transferResources

protected void transferResources()
                          throws ConfigPathException,
                                 IOException,
                                 Exception

Throws:

ConfigPathException

IOException

Exception

getDescription

public String getDescription()

Description copied from interface: ApiModule

Briefly describe what this module does. A more detailed description may be returned by getDetails.

Specified by:

getDescription in interface ApiModule

Returns:

getDetails

public String getDetails()
                  throws API_Exception

Description copied from interface: ApiModule

A extension of getDescription. Beyond the brief description, give details such as the interaction between properties.

Specified by:

getDetails in interface ApiModule

Overrides:

getDetails in class BioModuleImpl

Returns:

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

Overrides:

getDockerImageOwner in class BioModuleImpl

Returns:

getDockerImageName

public String getDockerImageName()

Description copied from interface: BioModule

Get the docker image to use for this module. The owner and version/tag are specificed separately; this is just the image name. Docker images from docker hub are specified using this syntax: /:

Specified by:

getDockerImageName 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

Overrides:

getDockerImageTag in class BioModuleImpl

Returns:

getCitationString

public String getCitationString()

Description copied from interface: ApiModule

At a minimum, this should return the name and/or url for the wrapped tool. For BioLockJ home-grown modules, it can cite BioLockJ and give the current version. Ideally this will include the version for the wrapped tool. Tool version may require using a stored variable that can be filled in during execution; and the string that is returned pre-execution may not have the version.

Specified by:

getCitationString in interface ApiModule

Returns: