biolockj.api

Interface ApiModule

All Superinterfaces:

BioModule

All Known Implementing Classes:

AddMetadataToTaxaTables, AddPseudoCount, AwkFastaConverter, BuildTaxaTables, Demultiplexer, DESeq2, EdgeR, Email, ForEachFile, ForEachLevel, ForEachLoop, ForEachSample, GenMod, GenomeAssembly, Gunzipper, Hello_Friends, Hello_World, Humann2Classifier, Humann2Parser, ImportMetadata, KneadData, Kraken2Classifier, Kraken2Parser, KrakenClassifier, KrakenParser, LogTransformTaxaTables, Metaphlan2Classifier, Multiplexer, NormalizeByReadsPerMillion, NormalizeTaxaTables, PearMergeReads, QiimeClosedRefClassifier, QiimeDeNovoClassifier, QiimeOpenRefClassifier, R_CalculateStats, R_PlotEffectSize, R_PlotMds, R_PlotOtus, R_PlotPvalHistograms, RarefyOtuCounts, RarefySeqs, RdpClassifier, RdpHierParser, RdpParser, RemoveLowOtuCounts, Rmarkdown, SeqFileValidator, ShannonDiversity, SraDownload, SraMetaData, SraMetaDB, SrpSrrConverter, Step2, Step3, Step4, Step5, Stop, TrimPrimers

public interface ApiModule
extends BioModule

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
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.

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

isValidProp

Boolean isValidProp(String property)
             throws Exception

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.

Parameters:

property -

value -

Returns:

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

Throws:

Exception

listProps

List<String> listProps()

List properties that this module uses, including those called by any super class.

Returns:

getTitle

String getTitle()

Get a human readable name for this module.

Returns:

getMenuPlacement

List<String> getMenuPlacement()

Get a list of Strings describing the menu structure that should be used in the GUI. By default (BioModuleImpl) this is the just the package structure of the module class. The option to override the this method is a way to de-couple developers organization from the presentation to the user.

getDescription

String getDescription()

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

Returns:

getDescription

String getDescription(String prop)
               throws API_Exception

Describe a given property / how it is used (including how it is used by a super class)

Returns:

Throws:

API_Exception

getDetails

String getDetails()
           throws API_Exception

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

Returns:

Throws:

API_Exception

getPropType

String getPropType(String prop)
            throws API_Exception

Get the type for a given property.

Returns:

Throws:

API_Exception

getCitationString

String getCitationString()

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.

Returns: