public abstract class Step3 extends Step2
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 |
---|
Step3() |
Modifier and Type | Method and Description |
---|---|
void |
checkDependencies()
Be sure to touch any / all properties your module uses.
|
Boolean |
isValidProp(String property)
Tests to see if the value val is valid for property prop; primarily tests format.
|
getCitationString, getDescription, getDetails
buildScript, buildScriptForPairedReads, executeTask, getJobParams, getMainScript, getRuntimeParams, getScriptDir, getScriptErrors, getSummary, getTimeout, getWorkerScriptFunctions, 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, getDockerImageName, 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