public interface ApiModule extends BioModule
LOG_DIR, MAIN_SCRIPT_PREFIX, NO_VERSION, OUTPUT_DIR, RES_DIR, TEMP_DIR
Modifier and Type | Method and Description |
---|---|
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 |
getDescription(String prop)
Describe a given property / how it is used (including how it is used by a super class)
|
String |
getDetails()
A extension of
getDescription . |
List<String> |
getMenuPlacement()
Get a list of Strings describing the menu structure that should be used in the GUI.
|
String |
getPropType(String prop)
Get the type for a given property.
|
String |
getTitle()
Get a human readable name for this module.
|
Boolean |
isValidProp(String property)
Tests to see if the value val is valid for property prop; primarily tests format.
|
List<String> |
listProps()
List properties that this module uses, including those called by any super class.
|
checkDependencies, cleanUp, executeTask, getAlias, getDockerImageName, getDockerImageOwner, getDockerImageTag, getID, getInputFiles, getLogDir, getMetadata, getModuleDir, getOutputDir, getPostRequisiteModules, getPreRequisiteModules, getPropDefault, getResourceDir, getSummary, getTempDir, init, isValidInputModule, setAlias, version
Boolean isValidProp(String property) throws Exception
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.property
- value
- Exception
List<String> listProps()
String getTitle()
List<String> getMenuPlacement()
String getDescription()
getDetails
.String getDescription(String prop) throws API_Exception
API_Exception
String getDetails() throws API_Exception
getDescription
. Beyond the brief description, give details such as
the interaction between properties.API_Exception
String getPropType(String prop) throws API_Exception
API_Exception
String getCitationString()