Uses of Class
fr.ens.biologie.genomique.aozan.aozan3.Aozan3Exception
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Uses of Aozan3Exception in fr.ens.biologie.genomique.aozan.aozan3
Methods in fr.ens.biologie.genomique.aozan.aozan3 that throw Aozan3Exception Modifier and Type Method Description void
Configuration. load(Path file)
Load configuration.void
Configuration. load(Path file, boolean aozan2Compatibility)
Load configuration.RunId
DefaultRunIdGenerator. newRunId(RunId runId, Map<String,String> constants)
RunId
RunIdGenerator. newRunId(RunId runId, Map<String,String> contants)
Create a new run id for the output of a processor.EmailMessage
TemplateEmailMessage. toEmailMessage(long id, String subject, Map<String,String> variables)
Generate EmailMessage object.EmailMessage
TemplateEmailMessage. toEmailMessage(String subject, Map<String,String> variables)
Generate EmailMessage object.Constructors in fr.ens.biologie.genomique.aozan.aozan3 that throw Aozan3Exception Constructor Description SendMail(Configuration conf, fr.ens.biologie.genomique.kenetre.log.GenericLogger logger)
Public constructor. -
Uses of Aozan3Exception in fr.ens.biologie.genomique.aozan.aozan3.dataprocessor
Methods in fr.ens.biologie.genomique.aozan.aozan3.dataprocessor that throw Aozan3Exception Modifier and Type Method Description EmailMessage
DataProcessorTemplateEmailMessage. endDataProcessorEmail(String subject, RunId runId, Path outputDirectory, long startTime, long endTime, long outputSize, long diskFree, Map<String,String> variables)
Create an end of step message.void
AbstractIlluminaDemuxDataProcessor. init(Configuration conf, fr.ens.biologie.genomique.kenetre.log.GenericLogger logger)
void
Aozan2QCDataProcessor. init(Configuration conf, fr.ens.biologie.genomique.kenetre.log.GenericLogger logger)
void
DataProcessor. init(Configuration conf, fr.ens.biologie.genomique.kenetre.log.GenericLogger logger)
Initialize the processor.void
DiscoverNewIlluminaRunDataProcessor. init(Configuration conf, fr.ens.biologie.genomique.kenetre.log.GenericLogger logger)
void
DoradoONTBasecallingDataProcessor. init(Configuration conf, fr.ens.biologie.genomique.kenetre.log.GenericLogger logger)
void
EndIlluminaRunDataProcessor. init(Configuration conf, fr.ens.biologie.genomique.kenetre.log.GenericLogger logger)
void
GuppyONTBasecallingDataProcessor. init(Configuration conf, fr.ens.biologie.genomique.kenetre.log.GenericLogger logger)
void
SyncDataProcessor. init(Configuration conf, fr.ens.biologie.genomique.kenetre.log.GenericLogger logger)
DataProcessor.ProcessResult
AbstractIlluminaDemuxDataProcessor. process(InputData inputData, RunConfiguration runConf)
DataProcessor.ProcessResult
Aozan2QCDataProcessor. process(InputData inputData, RunConfiguration runConf)
DataProcessor.ProcessResult
DataProcessor. process(InputData inputData, RunConfiguration conf)
Process data.DataProcessor.ProcessResult
DiscoverNewIlluminaRunDataProcessor. process(InputData inputData, RunConfiguration conf)
DataProcessor.ProcessResult
DoradoONTBasecallingDataProcessor. process(InputData inputData, RunConfiguration runConf)
DataProcessor.ProcessResult
EndIlluminaRunDataProcessor. process(InputData inputData, RunConfiguration conf)
DataProcessor.ProcessResult
GuppyONTBasecallingDataProcessor. process(InputData inputData, RunConfiguration runConf)
DataProcessor.ProcessResult
SyncDataProcessor. process(InputData input, RunConfiguration runConf)
protected void
AbstractIlluminaDemuxDataProcessor. processSampleSheet(fr.ens.biologie.genomique.kenetre.illumina.samplesheet.SampleSheet samplesheet)
Process sample sheet.protected void
BclConvertIlluminaDemuxDataProcessor. processSampleSheet(fr.ens.biologie.genomique.kenetre.illumina.samplesheet.SampleSheet samplesheet)
static void
DoradoONTBasecallingDataProcessor. run(Path inputTar, Path outputPath, Path modelsPath, String runId, String doradoVersion, Path tmpPath, String flowcellType, String kit, String barcodeKits, boolean trimBarcodes, String minQscore, String model, String cudaDevice, int batchSize, int chunkSize, boolean keepTemporaryFiles, fr.ens.biologie.genomique.kenetre.log.GenericLogger logger)
static void
GuppyONTBasecallingDataProcessor. run(Path inputTar, Path outputPath, String runId, String guppyVersion, Path tmpPath, String flowcellType, String kit, String barcodeKits, boolean trimBarcodes, String minQscore, String config, String cudaDevice, int gpuRunnersPerDevice, int chunksPerRunner, boolean fast5Output, boolean keepTemporaryFiles, fr.ens.biologie.genomique.kenetre.log.GenericLogger logger)
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Uses of Aozan3Exception in fr.ens.biologie.genomique.aozan.aozan3.dataprovider
Methods in fr.ens.biologie.genomique.aozan.aozan3.dataprovider that throw Aozan3Exception Modifier and Type Method Description void
EmptyRunDataProvider. init(DataStorage storage, Configuration conf, fr.ens.biologie.genomique.kenetre.log.GenericLogger logger)
void
IlluminaProcessedRunDataProvider. init(DataStorage storage, Configuration conf, fr.ens.biologie.genomique.kenetre.log.GenericLogger logger)
void
IlluminaRawRunDataProvider. init(DataStorage storage, Configuration conf, fr.ens.biologie.genomique.kenetre.log.GenericLogger logger)
void
RunDataProvider. init(DataStorage storage, Configuration conf, fr.ens.biologie.genomique.kenetre.log.GenericLogger logger)
Initialize the provider. -
Uses of Aozan3Exception in fr.ens.biologie.genomique.aozan.aozan3.legacy
Methods in fr.ens.biologie.genomique.aozan.aozan3.legacy that throw Aozan3Exception Modifier and Type Method Description void
RunIdStorage. add(RunId runId)
Add a run id to the storagevoid
AozanLock. createLock()
Create the lock file.Set<RunId>
RunIdStorage. load()
Load run ids.void
AozanLock. unlock()
Remove the lock file.Constructors in fr.ens.biologie.genomique.aozan.aozan3.legacy that throw Aozan3Exception Constructor Description LegacyRecipes(Configuration conf, fr.ens.biologie.genomique.kenetre.log.GenericLogger logger, Path aozan2ConfFile)
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Uses of Aozan3Exception in fr.ens.biologie.genomique.aozan.aozan3.log
Methods in fr.ens.biologie.genomique.aozan.aozan3.log that throw Aozan3Exception Modifier and Type Method Description static fr.ens.biologie.genomique.kenetre.log.GenericLogger
AozanLoggerFactory. newLogger(Configuration conf, fr.ens.biologie.genomique.kenetre.log.GenericLogger oldLogger)
Configure logger. -
Uses of Aozan3Exception in fr.ens.biologie.genomique.aozan.aozan3.recipe
Methods in fr.ens.biologie.genomique.aozan.aozan3.recipe that throw Aozan3Exception Modifier and Type Method Description void
Recipe. addDataProvider(String providerName, String storageName, boolean inProgress, Configuration conf)
Add a data provider.Set<RunId>
Recipe. availableRuns()
Get available runs.Set<RunId>
Recipe. availableRuns(Collection<RunId> excludedRunIds)
Get available runs.void
Recipe. execute()
Use the recipe to process run provided by the run data providerboolean
Recipe. execute(String runId)
Execute the recipe for a run.Set<RunId>
Recipe. execute(List<String> runIds)
Execute a list of run Ids.DataStorage
DataStorageRegistry. get(String name)
Get a data storage from its nameList<String>
Recipe. getAvalaibleRuns()
Get the list of available runs.List<RecipeFinder.RecipePath>
RecipeFinder. getRecipes()
Get the recipes existing in the directory.void
Recipe. init()
Initialize the steps of the recipevoid
Step. init()
Initialize the step.protected Configuration
ConfigurationXMLParser. parse(NodeList nList, String source)
protected Recipe
RecipeXMLParser. parse(NodeList nList, String source)
protected List<Step>
StepsXMLParser. parse(NodeList nList, String source)
protected Void
StoragesXMLParser. parse(NodeList nList, String source)
DataProcessor.ProcessResult
Step. process(InputData inputData)
Process input data.Constructors in fr.ens.biologie.genomique.aozan.aozan3.recipe that throw Aozan3Exception Constructor Description Recipe(String recipeName, String description, Configuration conf, fr.ens.biologie.genomique.kenetre.log.GenericLogger logger)
Public constructor.RecipeFinder(Path directory)
Constructor. -
Uses of Aozan3Exception in fr.ens.biologie.genomique.aozan.aozan3.runconfigurationprovider
Methods in fr.ens.biologie.genomique.aozan.aozan3.runconfigurationprovider that throw Aozan3Exception Modifier and Type Method Description RunConfiguration
IlluminaSamplesheetRunConfigurationProvider. getRunConfiguration(RunData runData)
RunConfiguration
RunConfigurationProvider. getRunConfiguration(RunData runData)
Get the run configuration for a run datavoid
EmptyRunConfigurationProvider. init(Configuration conf, fr.ens.biologie.genomique.kenetre.log.GenericLogger logger)
void
IlluminaSamplesheetRunConfigurationProvider. init(Configuration conf, fr.ens.biologie.genomique.kenetre.log.GenericLogger logger)
void
RunConfigurationProvider. init(Configuration conf, fr.ens.biologie.genomique.kenetre.log.GenericLogger logger)
Initialize the run configurator provider. -
Uses of Aozan3Exception in fr.ens.biologie.genomique.aozan.aozan3.samplesheetconverter
Methods in fr.ens.biologie.genomique.aozan.aozan3.samplesheetconverter with parameters of type Aozan3Exception Modifier and Type Method Description void
AbstractSampleSheetConverter. saveError(Aozan3Exception e)
Save error message.Methods in fr.ens.biologie.genomique.aozan.aozan3.samplesheetconverter that throw Aozan3Exception Modifier and Type Method Description protected abstract void
AbstractSampleSheetConverter. checkSampleSheet(List<String> warnings)
Check the samplesheet.protected void
IlluminaSampleSheetConverter. checkSampleSheet(List<String> warnings)
protected void
NanoporeSampleSheetConverter. checkSampleSheet(List<String> warnings)
void
AbstractSampleSheetConverter. convert()
Convert the samplesheet.protected abstract void
AbstractSampleSheetConverter. fixSampleSheet(List<String> warnings)
Fix the samplesheet.protected void
IlluminaSampleSheetConverter. fixSampleSheet(List<String> warnings)
protected void
NanoporeSampleSheetConverter. fixSampleSheet(List<String> warnings)
protected abstract void
AbstractSampleSheetConverter. loadSampleSheet()
Load the samplesheet.protected void
IlluminaSampleSheetConverter. loadSampleSheet()
protected void
NanoporeSampleSheetConverter. loadSampleSheet()
protected abstract void
AbstractSampleSheetConverter. saveSampleSheet()
Save the samplesheet.protected void
IlluminaSampleSheetConverter. saveSampleSheet()
protected void
NanoporeSampleSheetConverter. saveSampleSheet()
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Uses of Aozan3Exception in fr.ens.biologie.genomique.aozan.aozan3.util
Methods in fr.ens.biologie.genomique.aozan.aozan3.util that throw Aozan3Exception Modifier and Type Method Description void
Tar. execute()
Execute tar.void
UnTar. execute()
Execute untar.Constructors in fr.ens.biologie.genomique.aozan.aozan3.util that throw Aozan3Exception Constructor Description Tar(Path inputDirectoryPath, Path outputArchive)
Constructor.UnTar(Path inputArchive, Path outputDirectoryPath)
Constructor.
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