net.sf.basedb.plugins
Class Base1PluginExecuter

java.lang.Object
  net.sf.basedb.core.plugin.AbstractPlugin
      net.sf.basedb.core.plugin.AbstractAnalysisPlugin
          net.sf.basedb.plugins.Base1PluginExecuter

All Implemented Interfaces:

InteractivePlugin, Plugin, SignalTarget

public class Base1PluginExecuter
extends AbstractAnalysisPlugin
implements InteractivePlugin, SignalTarget

This plug-in executes a plug-in from the Base1 system. It takes a base1 configuration file to create its configuration.

Version:

2.2

Author:

Johan Enell

Last modified

$Date: 2011-03-15 14:19:25 +0100 (Tue, 15 Mar 2011) $

Nested Class Summary

private static class	Base1PluginExecuter.Base1JobParameterType
private class	Base1PluginExecuter.JobParameter

Nested classes/interfaces inherited from interface net.sf.basedb.core.plugin.Plugin

Plugin.MainType

Field Summary

private static About	about Plugin description
private static String	COMMAND_MANUAL_CONFIG This command is used if the user decides to configure the plugin by hand.
private RequestInformation	configureJob Holds info about a job configuration request.
private RequestInformation	configureManual Holds information about a manual plugin configuration request.
private RequestInformation	configurePlugin Holds information about a plugin configuration request.
private static URL	dtdFile
private File	execDirectory This is the directory where the plugin will generate its output.
private PluginParameter<String>	execNameParameter The name of the executable.
private static PluginParameter<String>	execPathParameter The path to where the plug-in executer can find the executables.
private static PluginParameter<File>	fileParameter Parameter definition that asks for the configuration file that should be imported.
private PluginParameter<Boolean>	geneAveragesParameter If the data should be exported averaged per gene.
private List<PluginParameter<?>>	jobParameters This list holds the job parameters derived from the configuration file.
private PluginParameter<String>	jobParametersParameter This parameter describes the job parameters that the base1 plugin needs.
private PluginParameter<Boolean>	leaveStdinParameter If the plug-in should leave the stdin.txt after execution.
private PluginParameter<Boolean>	leaveStdoutParameter If the plug-in should leave the stdout.txt after execution.
private PluginParameter<Integer>	maxChannelsParameter The maximum number of channels, 0 means unlimited.
private PluginParameter<Integer>	minChannelsParameter The minimum number of channels.
private static Set<Permissions>	permissions The plug-in permissions.
private PluginParameter<String>	pluginDirectoryParameter The directory where the plug-in will store it's output.
private PluginParameter<Boolean>	serialFormatParameter This parameter describes if the data should be exported in serial format or in matrix.
private ThreadSignalHandler	signalHandler
private PluginParameter<String>	usedColumnsParameter The reporter fields that should be exported as a tab separated string of column headers.
private PluginParameter<String>	usedFieldsParameter The spot fields that should be exported as a tab separated string of column headers.
private PluginParameter<String>	versionNumberParameter The version number of the plug-in.

Fields inherited from class net.sf.basedb.core.plugin.AbstractAnalysisPlugin

CHILD_DESCRIPTION, CHILD_NAME, CONTEXT_BIOASSAYS, CONTEXT_BIOASSAYSET, defaultGuiContexts, nameType, optionalNameType, SOURCE_BIOASSAYS, SOURCE_BIOASSAYSET, TRANSFORMATION_NAME

Fields inherited from class net.sf.basedb.core.plugin.AbstractPlugin

annotationSection, configuration, COPY_ANNOTATIONS, job, OVERWRITE_ANNOTATIONS, sc

Constructor Summary

Base1PluginExecuter()

Method Summary

private void	associateFiles(DbControl dc, Transformation trans, Directory homeDirectory)
void	configure(GuiContext context, Request request, Response response) Configure the plugin.
private void	copy(File f, File d) Copies the content from a File to a directory on the file system.
private boolean	deleteDir(File dir) Deletes all files and sub directories under dir.
private File	exportData(DbControl dc, Directory workingDirectory, ProgressReporter progress) Export the bioassay set to a file called 'stdin.txt' in the plugin directory.
About	getAbout() Get information about the plugin, such as name, version, authors, etc.
private List<AnnotationType>	getAnnotationTypes() Get the experimental factors connected to a experiment.
private Boolean	getBoolean(String s) Creates a boolean from a string.
private RequestInformation	getConfigureJobParameters() Creates the information needed for job configuration and initiates the parameters.
private RequestInformation	getConfigurePluginParameters() Creates the information needed for plugin configuration and initiates the parameters.
private File	getExecDirectory() Get the exec directory as a java.io.File.
private String	getExecLine()
private FlatFileParser	getInitializedFlatFileParser(InputStream stream, String charset) Creates a FlatFileParser for a plugin configuration file.
private Map<String,Base1PluginExecuter.JobParameter>	getJobParameterObjectsFromXML(String xml, boolean hideRemoved)
private List<PluginParameter<?>>	getJobParameters() Reads the configuration file an creates the parameters found there.
private List<PluginParameter<?>>	getJobParametersFromXML(String xml, boolean hideRemoved)
private RequestInformation	getManualConfigureParameters() Creates the information needed for manual configuration and initiates the parameters.
private Map<String,String>	getParametersFromBaseFile(File f) Get the data from the configuration file.
Collection<Permissions>	getPermissions() Return null, which gives the plugin the same permissions as the logged in user.
private Directory	getPluginDirectory(DbControl dc, String pathName) Get a directory
RequestInformation	getRequestInformation(GuiContext context, String command) This method will return the RequestInformation for a given command, i.e.
SignalHandler	getSignalHandler() Get the signal handler that is handling signals on behalf of this object.
private BioAssaySet	importData(DbControl dc, File stdout, Transformation t, IntensityTransform resultTransform, ProgressReporter progress) Imports the data from the file stdout.txt in the execution directory.
private void	importTempFiles(DbControl dc, File[] files, Directory d)
String	isInContext(GuiContext context, Object item) Checks if the BioAssaySet has the number of channels specified by the configuration and that it has the extra values.
boolean	requiresConfiguration() Returns FALSE, since that is how the plugins used to work before this method was introduced.
void	run(Request request, Response response, ProgressReporter progress) Run the plugin.
boolean	supportsConfigurations() Returns TRUE, since that is how the plugins used to work before this method was introduced.

Methods inherited from class net.sf.basedb.core.plugin.AbstractAnalysisPlugin

getChildDescriptionParameter, getChildNameParameter, getCurrentBioAssaySet, getCurrentExperiment, getGuiContexts, getMainType, getSourceBioAssays, getSourceBioAssaySet, getSourceBioAssaySetParameter, getSourceBioAssaysParameter, getTransformationName, getTransformationNameParameter, restrictSource

Methods inherited from class net.sf.basedb.core.plugin.AbstractPlugin

checkInterrupted, cloneParameterWithDefaultValue, closeLogFile, createLogFile, done, getCopyAnnotationsParmeter, getCurrentConfiguration, getCurrentJob, getJobOrConfigurationValue, getOverwriteAnnotationsParameters, init, log, log, storeValue, storeValue, storeValues, validateRequestParameters

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface net.sf.basedb.core.plugin.InteractivePlugin

getGuiContexts

Methods inherited from interface net.sf.basedb.core.plugin.Plugin

done, getMainType, init

Field Detail

about

private static final About about

Plugin description

permissions

private static final Set<Permissions> permissions

The plug-in permissions.

dtdFile

private static final URL dtdFile

fileParameter

private static final PluginParameter<File> fileParameter

Parameter definition that asks for the configuration file that should be imported.

execPathParameter

private static PluginParameter<String> execPathParameter

The path to where the plug-in executer can find the executables. In Base1 this was default to /usr/local/base/plugins.

serialFormatParameter

private PluginParameter<Boolean> serialFormatParameter

This parameter describes if the data should be exported in serial format or in matrix.

versionNumberParameter

private PluginParameter<String> versionNumberParameter

The version number of the plug-in.

execNameParameter

private PluginParameter<String> execNameParameter

The name of the executable.

geneAveragesParameter

private PluginParameter<Boolean> geneAveragesParameter

If the data should be exported averaged per gene.

minChannelsParameter

private PluginParameter<Integer> minChannelsParameter

The minimum number of channels.

maxChannelsParameter

private PluginParameter<Integer> maxChannelsParameter

The maximum number of channels, 0 means unlimited.

leaveStdinParameter

private PluginParameter<Boolean> leaveStdinParameter

If the plug-in should leave the stdin.txt after execution.

leaveStdoutParameter

private PluginParameter<Boolean> leaveStdoutParameter

If the plug-in should leave the stdout.txt after execution.

usedColumnsParameter

private PluginParameter<String> usedColumnsParameter

The reporter fields that should be exported as a tab separated string of column headers.

usedFieldsParameter

private PluginParameter<String> usedFieldsParameter

The spot fields that should be exported as a tab separated string of column headers.

jobParametersParameter

private PluginParameter<String> jobParametersParameter

This parameter describes the job parameters that the base1 plugin needs.

pluginDirectoryParameter

private PluginParameter<String> pluginDirectoryParameter

The directory where the plug-in will store it's output.

COMMAND_MANUAL_CONFIG

private static final String COMMAND_MANUAL_CONFIG

This command is used if the user decides to configure the plugin by hand.

See Also:

Constant Field Values

configureJob

private RequestInformation configureJob

Holds info about a job configuration request.

configurePlugin

private RequestInformation configurePlugin

Holds information about a plugin configuration request.

configureManual

private RequestInformation configureManual

Holds information about a manual plugin configuration request.

jobParameters

private List<PluginParameter<?>> jobParameters

This list holds the job parameters derived from the configuration file.

execDirectory

private File execDirectory

This is the directory where the plugin will generate its output.

signalHandler

private ThreadSignalHandler signalHandler

Constructor Detail

Base1PluginExecuter

public Base1PluginExecuter()

Method Detail

isInContext

public String isInContext(GuiContext context,
                          Object item)

Checks if the BioAssaySet has the number of channels specified by the configuration and that it has the extra values.

Specified by:

isInContext in interface InteractivePlugin

Overrides:

isInContext in class AbstractAnalysisPlugin

Parameters:

context - The context from where the plugin is invoked.

item - The item that should be checked if it is in context.

Returns:

null if the item is in context, otherwise an error message.

See Also:

AbstractAnalysisPlugin.isInContext(net.sf.basedb.core.plugin.GuiContext, java.lang.Object)

getRequestInformation

public RequestInformation getRequestInformation(GuiContext context,
                                                String command)
                                         throws BaseException

Description copied from interface: InteractivePlugin

This method will return the RequestInformation for a given command, i.e. the list of parameters and some nice help text.

Specified by:

getRequestInformation in interface InteractivePlugin

Parameters:

context - The current context of the client application, it is one of the values found in set returned by InteractivePlugin.getGuiContexts()

command - The command

Returns:

The RequestInformation for the command

Throws:

BaseException - if there is an error

configure

public void configure(GuiContext context,
                      Request request,
                      Response response)

Description copied from interface: InteractivePlugin

Configure the plugin. Hopefully the client is supplying values for the parameters specified by InteractivePlugin.getRequestInformation(GuiContext, String).

Specified by:

configure in interface InteractivePlugin

Parameters:

context - The current context of the client application, it is one of the values found in set returned by InteractivePlugin.getGuiContexts()

request - Request object with the command and parameters

response - Response object in for the plugin to response through

copy

private void copy(File f,
                  File d)
           throws IOException

Copies the content from a File to a directory on the file system.

Parameters:

f - The file to be copied.

d - The directory where the file will be written.

Throws:

IOException - If there is any error with target.

deleteDir

private boolean deleteDir(File dir)

Deletes all files and sub directories under dir.

Parameters:

dir -

Returns:

true if all deletions were successful

getPermissions

public Collection<Permissions> getPermissions()

Description copied from class: AbstractPlugin

Return null, which gives the plugin the same permissions as the logged in user.

Specified by:

getPermissions in interface Plugin

Overrides:

getPermissions in class AbstractPlugin

Returns:

A collection of permissions or null to not use permissions

getAbout

public About getAbout()

Description copied from interface: Plugin

Get information about the plugin, such as name, version, authors, etc.

Specified by:

getAbout in interface Plugin

Returns:

An About object

supportsConfigurations

public boolean supportsConfigurations()

Description copied from class: AbstractPlugin

Returns TRUE, since that is how the plugins used to work before this method was introduced.

Specified by:

supportsConfigurations in interface Plugin

Overrides:

supportsConfigurations in class AbstractPlugin

Returns:

TRUE or FALSE

requiresConfiguration

public boolean requiresConfiguration()

Description copied from class: AbstractPlugin

Returns FALSE, since that is how the plugins used to work before this method was introduced.

Specified by:

requiresConfiguration in interface Plugin

Overrides:

requiresConfiguration in class AbstractPlugin

Returns:

TRUE or FALSE

run

public void run(Request request,
                Response response,
                ProgressReporter progress)

Description copied from interface: Plugin

Run the plugin. If a progress reporter object is passed it is recommended that the plugin makes use of it.

Specified by:

run in interface Plugin

Parameters:

request - Request object with the command and parameters

response - Response object in for the plugin to response through

progress - A ProgressReporter where the plugin can report its progess, can be null

getSignalHandler

public SignalHandler getSignalHandler()

Description copied from interface: SignalTarget

Get the signal handler that is handling signals on behalf of this object. Multiple invokations of this method may receive the same or different objects. Null may be returned if, for some reason, the current object instance doesn't want to receive signals. Returning null is the same as not implementing this interface.

Specified by:

getSignalHandler in interface SignalTarget

Returns:

A SignalHandler object, or null if the current instance doesn't support signals

exportData

private File exportData(DbControl dc,
                        Directory workingDirectory,
                        ProgressReporter progress)

Export the bioassay set to a file called 'stdin.txt' in the plugin directory.

Parameters:

dc - DbControl used to access the database

workingDirectory - Where in base' file system the exported BASEFile should be stored.

Returns:

The file where the data is exported to.

getAnnotationTypes

private List<AnnotationType> getAnnotationTypes()

Get the experimental factors connected to a experiment.

Returns:

A list of AnnotationType:s

getParametersFromBaseFile

private Map<String,String> getParametersFromBaseFile(File f)
                                              throws IOException

Get the data from the configuration file.

Parameters:

f - The file.

Returns:

A map of name->value pairs.

Throws:

IOException - If there i any problem reading from file.

getJobParameterObjectsFromXML

private Map<String,Base1PluginExecuter.JobParameter> getJobParameterObjectsFromXML(String xml,
                                                                                   boolean hideRemoved)

getJobParametersFromXML

private List<PluginParameter<?>> getJobParametersFromXML(String xml,
                                                         boolean hideRemoved)

getBoolean

private Boolean getBoolean(String s)

Creates a boolean from a string.

Parameters:

s - The string.

Returns:

false if s.equals("0") else true.

getManualConfigureParameters

private RequestInformation getManualConfigureParameters()

Creates the information needed for manual configuration and initiates the parameters. The parameters added are: versionNumber, usedColumns, usedFields, execName, geneAverages, SerialFormat, leaveStdin, leaveStdout, minChannel and maxCannel.

Returns:

The RequestInformation.

getConfigureJobParameters

private RequestInformation getConfigureJobParameters()

Creates the information needed for job configuration and initiates the parameters. The parameters added are: bioAssaySet and the parameters found in the configuration file.

Returns:

The RequestInformation

getConfigurePluginParameters

private RequestInformation getConfigurePluginParameters()

Creates the information needed for plugin configuration and initiates the parameters. The parameters added are: file and execPath.

Returns:

The RequestInformation.

getExecDirectory

private File getExecDirectory()
                       throws IOException

Get the exec directory as a java.io.File. The exec directory is a sub directory in "java.io.tmpdir".

Returns:

the directory.

Throws:

IOException

getExecLine

private String getExecLine()

getInitializedFlatFileParser

private FlatFileParser getInitializedFlatFileParser(InputStream stream,
                                                    String charset)

Creates a FlatFileParser for a plugin configuration file.

Parameters:

stream - The stream that the parser should read from.

Returns:

The initialised parser

getJobParameters

private List<PluginParameter<?>> getJobParameters()
                                           throws BaseException

Reads the configuration file an creates the parameters found there.

Returns:

A list of PluginParameter:s

Throws:

BaseException

getPluginDirectory

private Directory getPluginDirectory(DbControl dc,
                                     String pathName)

Get a directory

importData

private BioAssaySet importData(DbControl dc,
                               File stdout,
                               Transformation t,
                               IntensityTransform resultTransform,
                               ProgressReporter progress)
                        throws SQLException,
                               IOException

Imports the data from the file stdout.txt in the execution directory.

Throws:

IOException - if there is any error reading from stdout.txt

SQLException

associateFiles

private void associateFiles(DbControl dc,
                            Transformation trans,
                            Directory homeDirectory)

importTempFiles

private void importTempFiles(DbControl dc,
                             File[] files,
                             Directory d)