biolockj.module

Interface DatabaseModule

All Superinterfaces:

BioModule

All Known Implementing Classes:

ClassifierModuleImpl, Humann2Classifier, KneadData, Kraken2Classifier, KrakenClassifier, Metaphlan2Classifier, QiimeClassifier, QiimeClosedRefClassifier, QiimeDeNovoClassifier, QiimeOpenRefClassifier, RdpClassifier

public interface DatabaseModule
extends BioModule

Interface for BioModules that use a reference database that is used by the DockerUtil to find the correct database directory to map to the container /db volume.

Field Summary

Fields inherited from interface biolockj.module.BioModule

LOG_DIR, MAIN_SCRIPT_PREFIX, NO_VERSION, OUTPUT_DIR, RES_DIR, TEMP_DIR

Method Summary

Modifier and Type	Method and Description
File	getDB() Return database directory, if multiple databases are configured, they must share a common parent directory and the common parent directory is returned by this method.

Methods inherited from interface biolockj.module.BioModule

checkDependencies, cleanUp, executeTask, getAlias, getDockerImageName, getDockerImageOwner, getDockerImageTag, getID, getInputFiles, getLogDir, getMetadata, getModuleDir, getOutputDir, getPostRequisiteModules, getPreRequisiteModules, getPropDefault, getResourceDir, getSummary, getTempDir, init, isValidInputModule, setAlias, version

Method Detail

getDB

File getDB()
    throws ConfigPathException,
           ConfigNotFoundException,
           DockerVolCreationException

Return database directory, if multiple databases are configured, they must share a common parent directory and the common parent directory is returned by this method.

Returns:

Database directory

Throws:

ConfigPathException - if path is defined but does not exists

ConfigNotFoundException - if DB property is undefined and the default DB is not included in the module runtime env

DockerVolCreationException