net.sf.basedb.plugins
Class PlateMappingImporter

java.lang.Object
  net.sf.basedb.core.plugin.AbstractPlugin
      net.sf.basedb.plugins.AbstractFlatFileImporter
          net.sf.basedb.plugins.PlateMappingImporter

All Implemented Interfaces:

AutoDetectingImporter, InteractivePlugin, Plugin, SignalTarget

public class PlateMappingImporter
extends AbstractFlatFileImporter
implements InteractivePlugin

Importer for plate mappings. It has a fixed file format:

Source plates=1
Source rows=3
Source columns=3
Destination plates=1
Destination rows=3
Destination columns=3
Source plate    Source row      Source column   Destination plate       Destination row Destination column
0       0       0       0       0       0
0       0       1       0       1       0
0       0       2       0       2       0
0       1       0       0       0       1
0       1       1       0       1       1
0       1       2       0       2       1
0       2       0       0       0       2
0       2       1       0       1       2
0       2       2       0       2       2

Version:

2.0

Author:

nicklas

Last modified

$Date: 2011-04-18 13:23:57 +0200 (Mon, 18 Apr 2011) $

Nested Class Summary

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

Plugin.MainType

Field Summary

private RequestInformation	configureJob
private DbControl	dc
private static PluginParameter<String>	descriptionParameter
private Mapper	destColumnMapper
private Mapper	destPlateMapper
private Mapper	destRowMapper
private FlatFileParser	ffp
private static Set<GuiContext>	guiContexts
private static PluginParameter<String>	nameParameter
private static Set<Permissions>	permissions
private PlateMapping	pm
private static StringParameterType	requiredStringParameter
private Mapper	sourceColumnMapper
private Mapper	sourcePlateMapper
private Mapper	sourceRowMapper

Fields inherited from class net.sf.basedb.plugins.AbstractFlatFileImporter

complexMappings, dataFooterRegexpParameter, dataHeaderRegexpParameter, dataSplitterRegexpParameter, defaultErrorParameter, errorSection, fileParameter, fileType, headerRegexpParameter, ignoreRegexpParameter, invalidUseOfNullErrorParameter, mappingSection, maxDataColumnsParameter, minDataColumnsParameter, numberFormatErrorParameter, numberOutOfRangeErrorParameter, numDataColumnsType, optionalRegexpType, parserSection, requiredRegexpType, sectionRegexpParameter, stringTooLongErrorParameter, trimQuotesParameter

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

annotationSection, configuration, COPY_ANNOTATIONS, job, OVERWRITE_ANNOTATIONS, sc

Constructor Summary

PlateMappingImporter()
Create a new importer.

Method Summary

protected void	begin(FlatFileParser ffp) Save reference to parser.
protected void	beginData() Create a DbControl and a new PlateMapping.
void	configure(GuiContext context, Request request, Response response) Store configuration settings for Request.COMMAND_CONFIGURE_PLUGIN and Request.COMMAND_CONFIGURE_JOB.
protected void	end(boolean success) Close and commit/rollback the DbControl.
private PlateGeometry	findGeometry(DbControl dc, int rows, int columns)
private RequestInformation	getConfigureJobParameters(GuiContext context)
Set<GuiContext>	getGuiContexts() Return a set containing the context:s [PLATEMAPPING, LIST].
protected FlatFileParser	getInitializedFlatFileParser() Create and initialise a flat file parser by setting all regular expressions and other options.
Collection<Permissions>	getPermissions() Request create and write access to PlateMapping:s, create and use access to PlateGeometries and read access to File:s.
RequestInformation	getRequestInformation(GuiContext context, String command) This method will return the RequestInformation for a given command, i.e.
protected String	getSuccessMessage(int skippedLines) Return Platemapping 'name' created.
protected void	handleData(FlatFileParser.Data data) Add a mapping detail.
String	isInContext(GuiContext context, Object item) Always null.
boolean	requiresConfiguration() Return TRUE, since the implementation requires it for finding the regular expressions used by the FlatFileParser.
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.plugins.AbstractFlatFileImporter

addErrorHandler, checkColumnMapping, checkColumnMapping, continueWithNextFileAfterError, doImport, finish, getCharset, getCharset, getDecimalSeparator, getErrorHandler, getErrorOption, getFileIterator, getMainType, getMapper, getMapper, getNumberFormat, getNumBytes, getProgress, getSignalHandler, getTotalFileSize, handleHeader, handleSection, isImportable, isImportable, log, log, log, log, run, setUpErrorHandling, start, wrapInputStream

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

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.Plugin

done, getMainType, init, run

Field Detail

guiContexts

private static final Set<GuiContext> guiContexts

permissions

private static final Set<Permissions> permissions

requiredStringParameter

private static final StringParameterType requiredStringParameter

configureJob

private RequestInformation configureJob

nameParameter

private static final PluginParameter<String> nameParameter

descriptionParameter

private static final PluginParameter<String> descriptionParameter

dc

private DbControl dc

pm

private PlateMapping pm

sourcePlateMapper

private Mapper sourcePlateMapper

sourceRowMapper

private Mapper sourceRowMapper

sourceColumnMapper

private Mapper sourceColumnMapper

destPlateMapper

private Mapper destPlateMapper

destRowMapper

private Mapper destRowMapper

destColumnMapper

private Mapper destColumnMapper

ffp

private FlatFileParser ffp

Constructor Detail

PlateMappingImporter

public PlateMappingImporter()

Create a new importer.

Method Detail

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: AbstractFlatFileImporter

Return TRUE, since the implementation requires it for finding the regular expressions used by the FlatFileParser. If this method is overridden and returns FALSE, the subclass must also override the AbstractFlatFileImporter.getInitializedFlatFileParser() method and provide a parser with all regular expressions and other options set.

Specified by:

requiresConfiguration in interface Plugin

Overrides:

requiresConfiguration in class AbstractFlatFileImporter

Returns:

TRUE or FALSE

getPermissions

public Collection<Permissions> getPermissions()

Request create and write access to PlateMapping:s, create and use access to PlateGeometries and read access to File:s.

Specified by:

getPermissions in interface Plugin

Overrides:

getPermissions in class AbstractPlugin

Returns:

A collection of permissions or null to not use permissions

getGuiContexts

public Set<GuiContext> getGuiContexts()

Return a set containing the context:s [PLATEMAPPING, LIST].

Specified by:

getGuiContexts in interface InteractivePlugin

Returns:

A Set containing Item:s, or null if the plugin is not concerned about items

isInContext

public String isInContext(GuiContext context,
                          Object item)

Always null.

Specified by:

isInContext 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()

item - The currently active item, it's type should match the GuiContext.getItem() type, or null if the context is a list context

Returns:

Null if the plugin can use that item, or a warning-level message explaining why the plugin can't be used

configure

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

Store configuration settings for Request.COMMAND_CONFIGURE_PLUGIN and Request.COMMAND_CONFIGURE_JOB.

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

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

begin

protected void begin(FlatFileParser ffp)
              throws BaseException

Save reference to parser.

Overrides:

begin in class AbstractFlatFileImporter

Throws:

BaseException

See Also:

AbstractFlatFileImporter.end(boolean)

beginData

protected void beginData()

Create a DbControl and a new PlateMapping. Initialise column Mapper:s.

Overrides:

beginData in class AbstractFlatFileImporter

handleData

protected void handleData(FlatFileParser.Data data)
                   throws BaseException

Add a mapping detail.

Specified by:

handleData in class AbstractFlatFileImporter

Throws:

BaseException

end

protected void end(boolean success)
            throws BaseException

Close and commit/rollback the DbControl.

Overrides:

end in class AbstractFlatFileImporter

Parameters:

success - TRUE if the file was parsed successfully, FALSE otherwise

Throws:

BaseException

See Also:

AbstractFlatFileImporter.begin(FlatFileParser)

getSuccessMessage

protected String getSuccessMessage(int skippedLines)

Return Platemapping 'name' created..

Overrides:

getSuccessMessage in class AbstractFlatFileImporter

Parameters:

skippedLines - The number of data lines that were skipped due to errors

getInitializedFlatFileParser

protected FlatFileParser getInitializedFlatFileParser()
                                               throws BaseException

Description copied from class: AbstractFlatFileImporter

Create and initialise a flat file parser by setting all regular expressions and other options. This implementation gets all parameters from the AbstractPlugin.job or AbstractPlugin.configuration settings. If a subclass doesn't store the parameters there it must override this method and initialise the parser. Note that this method is called once for each file returned by the AbstractFlatFileImporter.getFileIterator() and that a new parser is needed for each file.

Overrides:

getInitializedFlatFileParser in class AbstractFlatFileImporter

Returns:

An intialised flat file parser

Throws:

BaseException

getConfigureJobParameters

private RequestInformation getConfigureJobParameters(GuiContext context)

findGeometry

private PlateGeometry findGeometry(DbControl dc,
                                   int rows,
                                   int columns)