Package fr.ens.biologie.genomique.eoulsan

Class Settings

    • Method Detail

      • isSetting

        public boolean isSetting​(String key)
        Test if a setting key exists.
        Returns:
        true if the setting exist

      • isDebug

        public boolean isDebug()
        Test is the debug mode is enabled.
        Returns:
        true if the debug mode is enable

      • isPrintStackTrace

        public boolean isPrintStackTrace()
        Test is the debug mode is enabled.
        Returns:
        true if the debug mode is enable

      • getAWSAccessKey

        public String getAWSAccessKey()
        Get the AWS access key.
        Returns:
        the AWS access key

      • getAWSSecretKey

        public String getAWSSecretKey()
        Get the AWS secret key.
        Returns:
        the AWS secret key

      • getHadoopLogLevel

        public String getHadoopLogLevel()
        Get the Hadoop log level.
        Returns:
        the Hadoop log level

      • getClusterSchedulerName

        public String getClusterSchedulerName()
        Get the name of the cluster scheduler.
        Returns:
        the name of the cluster scheduler

      • getDefaultClusterMemoryRequired

        public int getDefaultClusterMemoryRequired()
        Get the default memory required for the steps in cluster mode.
        Returns:
        the default memory required for the cluster mode

      • isRServeServerEnabled

        public boolean isRServeServerEnabled()
        Test if RServe is enabled.
        Returns:
        true if the RServe server is enabled

      • isSaveRscripts

        public boolean isSaveRscripts()
        Test if save.r.script is true
        Returns:
        boolean with keep Rscripts values

      • getRServeServerName

        public String getRServeServerName()
        Get the RServe server name.
        Returns:
        The name of the RServe to use

      • isKeepRServeFiles

        public boolean isKeepRServeFiles()
        Test if save.r.keep.files is true
        Returns:
        boolean if the RServe files must be kept

      • getTempDirectory

        public String getTempDirectory()
        Get the temporary directory.
        Returns:
        The temporary directory

      • getTempDirectoryFile

        public File getTempDirectoryFile()
        Get the temporary directory File.
        Returns:
        The temporary directory as a File object

      • isUserDefinedTempDirectory

        public boolean isUserDefinedTempDirectory()
        Test if the temporary directory File has been defined by user.
        Returns:
        true id the temporary directory has defined by user

      • getExecutablesTempDirectory

        public String getExecutablesTempDirectory()
        Get the temporary directory for executables.
        Returns:
        The temporary directory for executables

      • getExecutablesTempDirectoryFile

        public File getExecutablesTempDirectoryFile()
        Get the temporary directory File for executables.
        Returns:
        The temporary directory for executables as a File object

      • isObfuscateDesign

        public boolean isObfuscateDesign()
        Test if design must be obfuscated
        Returns:
        true if design must be obfuscated

      • isObfuscateDesignRemoveReplicateInfo

        public boolean isObfuscateDesignRemoveReplicateInfo()
        Test if replicate information must be removed from design.
        Returns:
        true if replicate information must be removed

      • getLocalThreadsNumber

        public int getLocalThreadsNumber()
        Get the number of threads to use in Steps computation in local mode.
        Returns:
        the number of threads to use

      • getDefaultFastqFormat

        public fr.ens.biologie.genomique.kenetre.bio.FastqFormat getDefaultFastqFormat()
        Get the default fastq format.
        Returns:
        the default fastq format

      • isBypassPlatformChecking

        public boolean isBypassPlatformChecking()
        Test if the platform checking must be avoided at Eoulsan startup.
        Returns:
        true if the platform checking must be avoided

      • getGenomeMapperIndexStoragePath

        public String getGenomeMapperIndexStoragePath()
        Get the genome mapper index storage path.
        Returns:
        the path to genome mapper index storage path

      • getGenomeDescStoragePath

        public String getGenomeDescStoragePath()
        Get the genome description storage path.
        Returns:
        the path to genome description storage path

      • getGenomeStoragePath

        public String getGenomeStoragePath()
        Get the genome storage path.
        Returns:
        the path to genome storage path

      • getGFFStoragePath

        public String getGFFStoragePath()
        Get the GFF storage path.
        Returns:
        the path to GFF storage path

      • getGTFStoragePath

        public String getGTFStoragePath()
        Get the GTF storage path.
        Returns:
        the path to GTF storage path

      • getAdditionalAnnotationStoragePath

        public String getAdditionalAnnotationStoragePath()
        Get the additional annotation storage path.
        Returns:
        the path to the additional annotation storage path

      • getAdditionalAnnotationHypertextLinksPath

        public String getAdditionalAnnotationHypertextLinksPath()
        Get the additional annotation hypertext links path.
        Returns:
        the additional annotation hypertext links path

      • isSendResultMail

        public boolean isSendResultMail()
        Test if an email must be sent at the end of the analysis.
        Returns:
        true if an email must be sent at the end of the analysis

      • getResultMail

        public String getResultMail()
        Get the mail address for eoulsan results.
        Returns:
        the mail address as a string

      • getSMTPHost

        public String getSMTPHost()
        Get the name of the SMTP server host.
        Returns:
        the name of the SMTP server host

      • getZooKeeperConnectString

        public String getZooKeeperConnectString()
        Get the ZooKeeper connect string.
        Returns:
        the ZooKeeper connect string

      • getZooKeeperDefaultPort

        public int getZooKeeperDefaultPort()
        Get the ZooKeeper default port.
        Returns:
        the ZooKeeper default port

      • getZooKeeperSessionTimeout

        public int getZooKeeperSessionTimeout()
        Get the ZooKeeper session timeout.
        Returns:
        the ZooKeeper session timeout

      • isUseOldEoulsanResultFormat

        public boolean isUseOldEoulsanResultFormat()
        Test if Eoulsan result files must be written using the old format.
        Returns:
        true if Eoulsan result files must be written using the old format

      • getUIName

        public String getUIName()
        Get the UI name.
        Returns:
        the UI name

      • getDockerBackend

        public String getDockerBackend()
        Get the Docker backend name.
        Returns:
        the docker connection string

      • getDockerConnection

        public String getDockerConnection()
        Get the Docker connection string.
        Returns:
        the docker connection string

      • isDockerBySingularityEnabled

        public boolean isDockerBySingularityEnabled()
        Is Docker features are enabled using singularity.
        Returns:
        true if the Docker features are enabled using Singularity

      • getDockerSingularityStoragePath

        public String getDockerSingularityStoragePath()
        Get the Docker singularity storage path.
        Returns:
        the path to GFF storage path

      • isDockerConnectionDefined

        public boolean isDockerConnectionDefined()
        Test if a Docker connection has been set.
        Returns:
        true if a Docker connection has been set

      • isDockerMountNFSRoots

        public boolean isDockerMountNFSRoots()
        Test if when use Docker, NFS roots must been mounted instead of file paths.
        Returns:
        true if if when use Docker, NFS roots must been mounted instead of file paths

      • getDockerConnectionURI

        public URI getDockerConnectionURI()
        Get the Docker connection URI.
        Returns:
        the docker connection URI

      • getDataFormatPaths

        public List<String> getDataFormatPaths()
        Get the format paths.
        Returns:
        the format path

      • getGalaxyToolPaths

        public List<String> getGalaxyToolPaths()
        Get the Galaxy tool path.
        Returns:
        the Galaxy tool path

      • getOutputTreeType

        public String getOutputTreeType()
        Get the output tree type.
        Returns:
        the output tree type

      • isSaveWorkflowImage

        public boolean isSaveWorkflowImage()
        Test if an image of the workflow must be saved.
        Returns:
        true if an image of the workflow must be saved

      • isUseStandardExternalModules

        public boolean isUseStandardExternalModules()
        Test if standard external modules must be used.
        Returns:
        true if standard external modules must be used

      • getSetting

        public String getSetting​(String settingName)
        Get a setting value.
        Returns:
        settingName value as a String

      • getIntSetting

        public int getIntSetting​(String settingName)
                  throws EoulsanException
        Get the value of the setting as a integer value
        Returns:
        the value of the setting as an integer
        Throws:
        EoulsanException - if the value is not an integer

      • getDoubleSetting

        public double getDoubleSetting​(String settingName)
                        throws EoulsanException
        Get the value of the setting as a double value
        Returns:
        the value of the setting as an double
        Throws:
        EoulsanException - if the value is not an double

      • getBooleanSetting

        public boolean getBooleanSetting​(String settingName)
        Get the value of the setting as a boolean value
        Returns:
        the value of the setting as an integer

      • getSettingsNames

        public Set<String> getSettingsNames()
        Get a set of settings names.
        Returns:
        a set with all the name of the settings

      • setDebug

        public void setDebug​(boolean debug)
        Set the debug setting.
        Parameters:
        debug - value of the debug setting

      • setPrintStackTrace

        public void setPrintStackTrace​(boolean printStackTrace)
        Set the print stack trace setting.
        Parameters:
        printStackTrace - value of the print stack trace setting

      • setAWSAccessKey

        public void setAWSAccessKey​(String value)
        Set the AWS access key.
        Parameters:
        value - the AWS access key

      • setAWSSecretKey

        public void setAWSSecretKey​(String value)
        Set the AWS secret key.
        Parameters:
        value - the AWS secret key

      • setHadoopLogLevel

        public void setHadoopLogLevel​(String value)
        Set the Hadoop log level.
        Parameters:
        value - the HAdoop log level

      • setClusterSchedulerName

        public void setClusterSchedulerName​(String schedulerName)
        Set the name of the cluster scheduler.
        Parameters:
        schedulerName - the name of the cluster scheduler

      • setDefaultClusterMemoryRequired

        public void setDefaultClusterMemoryRequired​(int memory)
        Set the default memory required for the steps in cluster mode.
        Parameters:
        memory - the required memory

      • setRServeServerEnabled

        public void setRServeServerEnabled​(boolean enable)
        Set if RServe is enabled.
        Parameters:
        enable - true if the RServe server is enable

      • setSaveRscript

        public void setSaveRscript​(boolean krs)
        Set if save Rscripts is true
        Parameters:
        krs - boolean

      • setKeepRServeFiles

        public void setKeepRServeFiles​(boolean keepRServeFiles)
        Set if save Rscripts is true
        Parameters:
        keepRServeFiles - true if Rserve file must be kept

      • setRServeServerName

        public void setRServeServerName​(String serverName)
        Set the RServe server name.
        Parameters:
        serverName - The name of the RServe to use

      • setTempDirectory

        public void setTempDirectory​(String tempDirectory)
        Set the temporary directory.
        Parameters:
        tempDirectory - The path to the temporary directory

      • setExecutablesTempDirectory

        public void setExecutablesTempDirectory​(String executablesTempDirectory)
        Set the temporary directory for executables.
        Parameters:
        executablesTempDirectory - The path to the temporary directory for executables

      • setObfuscateDesign

        public void setObfuscateDesign​(boolean obfuscate)
        Set if the design must be obfuscated
        Parameters:
        obfuscate - true if the design must be obfuscated

      • setObfuscateRemoveDesignInfo

        public void setObfuscateRemoveDesignInfo​(boolean remove)
        Set if the replicate information must be removed from the design.
        Parameters:
        remove - true if the replicate information must be remove

      • setLocalThreadsNumber

        public void setLocalThreadsNumber​(int threadsNumber)
        Set the number of threads to use in local mode.
        Parameters:
        threadsNumber - the number of threads to use in local mode

      • setDefaultFastqFormat

        public void setDefaultFastqFormat​(fr.ens.biologie.genomique.kenetre.bio.FastqFormat format)
        Set the Fastq format default value.
        Parameters:
        format - the value to set

      • setBypassPlatformChecking

        public void setBypassPlatformChecking​(boolean bypass)
        Set if the platform checking must be avoided.
        Parameters:
        bypass - true to bypass the platform checking

      • setGenomeMapperIndexStoragePath

        public void setGenomeMapperIndexStoragePath​(String genomeMapperIndexStoragePath)
        Set the genome index storage path.
        Parameters:
        genomeMapperIndexStoragePath - the path to genome index storage path

      • setGenomeDescStoragePath

        public void setGenomeDescStoragePath​(String genomeDescStoragePath)
        Set the genome description storage path.
        Parameters:
        genomeDescStoragePath - the path to genome index storage path

      • setGenomeStoragePath

        public void setGenomeStoragePath​(String genomeStoragePath)
        Set the genome storage path.
        Parameters:
        genomeStoragePath - the path to genome index storage path

      • setGFFStoragePath

        public void setGFFStoragePath​(String gffStoragePath)
        Set the GFF storage path.
        Parameters:
        gffStoragePath - the path to GFF index storage path

      • setGTFStoragePath

        public void setGTFStoragePath​(String gtfStoragePath)
        Set the GTF storage path.
        Parameters:
        gtfStoragePath - the path to GTF index storage path

      • setAdditionalAnnotationStoragePath

        public void setAdditionalAnnotationStoragePath​(String additionalAnnotationStoragePath)
        Set the additional annotation storage path.
        Parameters:
        additionalAnnotationStoragePath - the path to the additional annotation index storage path

      • setAdditionalAnnotationHypertextLinksPath

        public void setAdditionalAnnotationHypertextLinksPath​(String additionalAnnotationHypertextLinksPath)
        Set the additional annotation hypertext links path.
        Parameters:
        additionalAnnotationHypertextLinksPath - the path to the additional annotation hypertext links path

      • setSendResultMail

        public void setSendResultMail​(boolean enableSendResultMail)
        Set if an email must be sent at the end of the analysis.
        Parameters:
        enableSendResultMail - true if an email must be sent at the end of the analysis

      • setResultMail

        public void setResultMail​(String mail)
        Set the mail address for eoulsan results.
        Parameters:
        mail - the mail address as a string

      • setSMTPHost

        public void setSMTPHost​(String smtpHost)
        Set the SMTP server host.
        Parameters:
        smtpHost - the name of the SMTP server host

      • setZooKeeperConnectString

        public void setZooKeeperConnectString​(String connectString)
        Set the ZooKeeper connect string.
        Parameters:
        connectString - the ZooKeeper connect string

      • setZooKeeperDefaultPort

        public void setZooKeeperDefaultPort​(int port)
        Set the ZooKeeper default port.
        Parameters:
        port - the ZooKeeper default port

      • setZooKeeperSessionTimeout

        public void setZooKeeperSessionTimeout​(int timeout)
        Set the ZooKeeper session timeout.
        Parameters:
        timeout - the ZooKeeper session timeout

      • setUseOldEoulsanResultFormat

        public void setUseOldEoulsanResultFormat​(boolean useOldEoulsanResultFormat)
        Set if Eoulsan result files must be written using the old format.
        Parameters:
        useOldEoulsanResultFormat - true if Eoulsan result files must be written using the old format

      • setUIName

        public void setUIName​(String uiName)
        Set the UI name.
        Parameters:
        uiName - the UI name

      • setDockerBackEnd

        public void setDockerBackEnd​(String backend)
        Set the Docker URI.
        Parameters:
        backend - the Docker back-end

      • setDockerConnectionURI

        public void setDockerConnectionURI​(String uri)
        Set the Docker URI.
        Parameters:
        uri - the Docker URI

      • setDockerBySingularityEnabled

        public void setDockerBySingularityEnabled​(boolean enabled)
        Enable Docker features using Singularity
        Parameters:
        enabled - true to enable the feature

      • setDockerSingularityStoragePath

        public void setDockerSingularityStoragePath​(String storagePath)
        Set the Docker singularity storage path.
        Parameters:
        storagePath - the path to Docker singularity storage path

      • setDockerMountNFSRoots

        public void setDockerMountNFSRoots​(boolean enable)
        Set if when use Docker, NFS roots must been mounted instead of file paths. param value the value of the parameter

      • setDataFormatPath

        public void setDataFormatPath​(String path)
        Set the format path.
        Parameters:
        path - the format

      • setDataFormatPaths

        public void setDataFormatPaths​(List<String> paths)
        Set the data format paths
        Parameters:
        paths - the path to set

      • setGalaxyToolPath

        public void setGalaxyToolPath​(String path)
        Set the Galaxy tool path.
        Parameters:
        path - the format

      • setGalaxyToolsPaths

        public void setGalaxyToolsPaths​(List<String> paths)
        Set the Galaxy tools paths
        Parameters:
        paths - the path to set

      • setOutputTreeType

        public void setOutputTreeType​(String outputTreeType)
        Set the output tree type.
        Parameters:
        outputTreeType - the output tree type

      • setSaveWorkflowImage

        public void setSaveWorkflowImage​(boolean save)
        Set if an image of the workflow must be saved.
        Parameters:
        save - the value

      • setUseStandardExternalModules

        public void setUseStandardExternalModules​(boolean enable)
        Set if standard external modules must be used.
        Parameters:
        enable - the value

      • setSetting

        public void setSetting​(String settingName,
                       String settingValue)
        Set a setting value.
        Parameters:
        settingName - name of the setting to set
        settingValue - value of the setting to set

      • setSetting

        public void setSetting​(String settingName,
                       String settingValue,
                       boolean logChange)
        Set a setting value.
        Parameters:
        settingName - name of the setting to set
        settingValue - value of the setting to set
        logChange - if true the change will be logged

      • getConfigurationFilePath

        public static String getConfigurationFilePath()
        Get the configuration file path.
        Returns:
        the configuration file path

      • getJavaMailSMTPProperties

        public Properties getJavaMailSMTPProperties()
        Create a property object for javamail smtp configuration from the settings.
        Returns:
        a property object

      • saveSettings

        public void saveSettings()
                  throws IOException
        Save application options.
        Throws:
        IOException - if an error occurs while writing results

      • saveSettings

        public void saveSettings​(File file)
                  throws IOException
        Save application options.
        Parameters:
        file - File to save
        Throws:
        IOException - if an error occurs while writing settings

      • setSettings

        public void setSettings​(Settings settings)
        Set the values of the settings with another Settings object.
        Parameters:
        settings - Settings object which values must be set in the current object

      • logSettings

        public void logSettings()
        Add all the settings to the log.

      • getSettingsKeyToObfuscated

        public Set<String> getSettingsKeyToObfuscated()
        Get a set with the names of the settings to obfuscate.
        Returns:
        a set of strings with the name of the settings to obfuscate