public class Hello_Friends extends ScriptModuleImpl implements ApiModule
Modifier and Type | Field and Description |
---|---|
static String |
EXCITE_PROP
|
static String |
EXCITE_PROP_DESC |
static String |
NAME_PROP
"A name to use instead of \'world\'."; defaults to: "world"
|
static String |
NAME_PROP_DEFAULT |
static String |
NAME_PROP_DESC |
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 |
---|
Hello_Friends() |
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()
Be sure to touch any / all properties your module uses.
|
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.
|
List<String> |
getWorkerScriptFunctions()
Method returns bash script lines used to build the functions called by the worker scripts.
|
protected String |
howExciting()
Accesses the "hello.excitmentLevel" and creates a string with that many !s, or
just "." if the value is null.
|
Boolean |
isValidProp(String property)
Tests to see if the value val is valid for property prop; primarily tests format.
|
protected String |
makeMessage()
Create a message based on the modules properties.
|
buildScriptForPairedReads, executeTask, getJobParams, getMainScript, getRuntimeParams, getScriptDir, getScriptErrors, getSummary, getTimeout, hasScripts
addGeneralProperty, addGeneralProperty, addGeneralProperty, addNewProperty, addNewProperty, cacheInputFiles, cleanUp, compareTo, equals, findModuleInputFiles, getAlias, getDescription, getDockerImageOwner, getDockerImageTag, getFileCache, getID, getInputFiles, getLogDir, getMenuPlacement, getMetadata, getModuleDir, getOutputDir, getPostRequisiteModules, getPreRequisiteModules, getPropDefault, getPropDescMap, getPropType, getPropTypeMap, getResourceDir, getTempDir, getTitle, hashCode, init, isValidInputModule, listProps, setAlias, toString
clone, finalize, getClass, notify, notifyAll, wait, wait, wait
getDescription, getMenuPlacement, getPropType, getTitle, listProps
cleanUp, executeTask, getAlias, getDockerImageOwner, getDockerImageTag, getID, getInputFiles, getLogDir, getMetadata, getModuleDir, getOutputDir, getPostRequisiteModules, getPreRequisiteModules, getPropDefault, getResourceDir, getSummary, getTempDir, init, isValidInputModule, setAlias, version
public static final String NAME_PROP
public static final String NAME_PROP_DESC
public static final String NAME_PROP_DEFAULT
public static final String EXCITE_PROP
public static final String EXCITE_PROP_DESC
public void checkDependencies() throws Exception
isValidProp(String)
method to check
individual values. IF applicable, code additional tests here to make sure your properties are compatible.checkDependencies
in interface BioModule
checkDependencies
in class ScriptModuleImpl
Exception
- thrown if missing or invalid dependencies are foundpublic Boolean isValidProp(String property) throws Exception
ApiModule
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.isValidProp
in interface ApiModule
isValidProp
in class ScriptModuleImpl
Exception
public List<List<String>> buildScript(List<File> files) throws Exception
ScriptModuleImpl
buildScript
in interface ScriptModule
buildScript
in class ScriptModuleImpl
files
- Files in the input directory that contain only forward readsException
- if unable to generate script linespublic List<String> getWorkerScriptFunctions() throws Exception
ScriptModule
getWorkerScriptFunctions
in interface ScriptModule
getWorkerScriptFunctions
in class ScriptModuleImpl
Exception
- if errors occurprotected String makeMessage() throws ConfigFormatException
ConfigFormatException
protected String howExciting() throws ConfigFormatException
BioModuleImpl.isValidProp(String)
ConfigFormatException
public String getDockerImageName()
BioModule
getDockerImageName
in interface BioModule
public 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