public class LogTransformTaxaTables extends TransformTaxaTables implements ApiModule
Modifier and Type | Field and Description |
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protected static String |
LOG_10
Log 10 display string a supported value for: "report.logBase"
|
protected static String |
LOG_E
Log e display string a supported value for: "report.logBase"
|
BLJ_OPTIONS
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 |
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LogTransformTaxaTables() |
Modifier and Type | Method and Description |
---|---|
void |
checkDependencies()
Verify
Config ."report.logBase" property is valid (if defined) with a
value = (e or 10). |
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.
|
protected String |
getLogBase()
Get the Log base (10 or e)
|
protected String |
getProcessSuffix() |
String |
getSummary()
Returns summary message to be displayed by Email module so must not contain confidential info.
|
Boolean |
isValidProp(String property)
Tests to see if the value val is valid for property prop; primarily tests format.
|
protected TaxaLevelTable |
transform(TaxaLevelTable inputData,
List<String> filteredSampleIDs,
List<String> filteredTaxaIDs)
Log transform the data
|
filterSamples, filterTaxa, getOutputFile, runModule
filterByProcessLevel, getDetails, getInputFiles, getPreRequisiteModules, isTaxaModule, isValidInputModule
buildScript, executeTask, getDockerImageName, getDockerImageOwner, getDockerImageTag, getWorkerScriptFunctions, markStatus, moduleComplete, moduleFailed, runBioLockJ_CMD
buildScriptForPairedReads, getJobParams, getMainScript, getRuntimeParams, getScriptDir, getScriptErrors, getTimeout, hasScripts
addGeneralProperty, addGeneralProperty, addGeneralProperty, addNewProperty, addNewProperty, cacheInputFiles, cleanUp, compareTo, equals, findModuleInputFiles, getAlias, getDescription, getFileCache, getID, getLogDir, getMenuPlacement, getMetadata, getModuleDir, getOutputDir, getPostRequisiteModules, getPropDefault, getPropDescMap, getPropType, getPropTypeMap, getResourceDir, getTempDir, getTitle, hashCode, init, listProps, setAlias, toString
clone, finalize, getClass, notify, notifyAll, wait, wait, wait
getDescription, getDetails, getMenuPlacement, getPropType, getTitle, listProps
cleanUp, executeTask, getAlias, getDockerImageName, getDockerImageOwner, getDockerImageTag, getID, getInputFiles, getLogDir, getMetadata, getModuleDir, getOutputDir, getPostRequisiteModules, getPreRequisiteModules, getPropDefault, getResourceDir, getTempDir, init, isValidInputModule, setAlias, version
buildScriptForPairedReads, getJobParams, getMainScript, getScriptDir, getScriptErrors, getTimeout
protected static final String LOG_10
protected static final String LOG_E
public void checkDependencies() throws Exception
Config
."report.logBase" property is valid (if defined) with a
value = (e or 10).checkDependencies
in interface BioModule
checkDependencies
in class ScriptModuleImpl
ConfigFormatException
- if REPORT_LOG_BASE is not set to a valid option (e or 10)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
protected TaxaLevelTable transform(TaxaLevelTable inputData, List<String> filteredSampleIDs, List<String> filteredTaxaIDs) throws Exception
transform
in class TransformTaxaTables
otuTable
- OTU raw count tableException
- if unable to construct LogTransformTaxaTablesprotected String getProcessSuffix()
getProcessSuffix
in class TransformTaxaTables
protected String getLogBase()
public String getSummary() throws Exception
ScriptModuleImpl
getSummary
in interface BioModule
getSummary
in class ScriptModuleImpl
Exception
- if any error occurspublic String getDescription()
ApiModule
getDetails
.getDescription
in interface ApiModule
public String getCitationString()
ApiModule
getCitationString
in interface ApiModule