net.sf.basedb.plugins
Class PrintMapFlatFileImporter

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

All Implemented Interfaces:

AutoDetectingImporter, InteractivePlugin, Plugin, SignalTarget

public class PrintMapFlatFileImporter
extends AbstractFlatFileImporter
implements InteractivePlugin

A plugin that imports an ArrayDesign from a printmap. The formats supported are TAM and MwBr

Version:

2.0

Author:

Enell

Last modified

$Date: 2010-11-08 14:49:35 +0100 (Mon, 08 Nov 2010) $

Nested Class Summary

private static class	PrintMapFlatFileImporter.FormatType
private static class	PrintMapFlatFileImporter.MetaBlock
private static class	PrintMapFlatFileImporter.Section

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

Plugin.MainType

Field Summary

private static About	about
private ArrayDesign	arrayDesign
private PluginParameter<ArrayDesign>	arrayDesignParameter
private ItemParameterType<ArrayDesign>	arrayDesignType
private FeatureBatcher	batcher
private Map<BlockInfo,ArrayDesignBlock>	blocks
private RequestInformation	configureJob
private DbControl	dc
private int	expectedNumBlocks
private PrintMapFlatFileImporter.FormatType	formatType
private static Set<GuiContext>	guiContexts
private Map<Integer,PrintMapFlatFileImporter.MetaBlock>	metaBlocks
protected static PluginParameter<String>	missingWellErrorParameter
private int	numBlocks
private int	numFeatures
private static Set<Permissions>	permissions
private FileSetMember	printMapMember
private PrintMapFlatFileImporter.Section	section
private int	spotSize

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

CHARSET, charsetType, complexMappings, dataFooterRegexpParameter, dataHeaderRegexpParameter, dataSplitterRegexpParameter, DECIMAL_SEPARATOR, decimalSeparatorType, 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

PrintMapFlatFileImporter()

Method Summary

protected void	begin(FlatFileParser ffp) Create a DbControl and a FeatureBatcher.
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) Called just after the last line of the file has been parsed, or immediately after an error has ocurred.
private Well	findWell(int platePosition, int row, int column)
About	getAbout() Get information about the plugin, such as name, version, authors, etc.
private RequestInformation	getConfigureJobParameters(GuiContext context)
Set<GuiContext>	getGuiContexts() Get a set containing all items that the plugin handles.
protected FlatFileParser	getInitializedFlatFileParser() Create and initialise a flat file parser by setting all regular expressions and other options.
Collection<Permissions>	getPermissions() Request write access to ArrayDesign:s, read access to Plate:s, Reporter:s, DataFileType:s, Platform:s and File:s.
RequestInformation	getRequestInformation(GuiContext context, String command) The Request.COMMAND_CONFIGURE_PLUGIN command will ask for parser regular expressions and column mappings.
protected String	getSuccessMessage(int skippedLines) Called if the parsing was successful to let the subclass generate a simple message that is sent back to the core and user interface.
protected void	handleData(FlatFileParser.Data data) Called by the parser for every line in the file that is a data line.
protected void	handleHeader(FlatFileParser.Line line) Called by the parser for every line in the file that is a header line.
protected void	handleSection(FlatFileParser.Line line) Called by the parser for every line in the file that is a section line.
protected boolean	isImportable(FlatFileParser ffp) Check that the file is a TAM or MwBr file.
String	isInContext(GuiContext context, Object item) Returns null if the item is a ArrayDesign that doesn't already have any features and isn't an affy design.
boolean	requiresConfiguration() Return TRUE, since the implementation requires it for finding the regular expressions used by the FlatFileParser.
private void	setBlockValue(PrintMapFlatFileImporter.MetaBlock block, FlatFileParser.Line line)
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, beginData, checkColumnMapping, checkColumnMapping, continueWithNextFileAfterError, doImport, finish, getCharset, getCharset, getCharsetParameter, getDecimalSeparator, getDecimalSeparatorParameter, getErrorHandler, getErrorOption, getFileIterator, getMainType, getMapper, getNumberFormat, getNumBytes, getPrimaryLocationFilter, getProgress, getSignalHandler, getTotalFileSize, isImportable, log, log, log, log, run, setUpErrorHandling, start, wrapInputStream

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.Plugin

done, getMainType, init, run

Field Detail

about

private static final About about

guiContexts

private static final Set<GuiContext> guiContexts

permissions

private static final Set<Permissions> permissions

missingWellErrorParameter

protected static final PluginParameter<String> missingWellErrorParameter

configureJob

private RequestInformation configureJob

dc

private DbControl dc

batcher

private FeatureBatcher batcher

blocks

private Map<BlockInfo,ArrayDesignBlock> blocks

metaBlocks

private Map<Integer,PrintMapFlatFileImporter.MetaBlock> metaBlocks

arrayDesign

private ArrayDesign arrayDesign

printMapMember

private FileSetMember printMapMember

arrayDesignType

private ItemParameterType<ArrayDesign> arrayDesignType

arrayDesignParameter

private PluginParameter<ArrayDesign> arrayDesignParameter

numFeatures

private int numFeatures

numBlocks

private int numBlocks

section

private PrintMapFlatFileImporter.Section section

formatType

private PrintMapFlatFileImporter.FormatType formatType

expectedNumBlocks

private int expectedNumBlocks

spotSize

private int spotSize

Constructor Detail

PrintMapFlatFileImporter

public PrintMapFlatFileImporter()

Method Detail

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: 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 write access to ArrayDesign:s, read access to Plate:s, Reporter:s, DataFileType:s, Platform:s and File:s.

Specified by:

getPermissions in interface Plugin

Overrides:

getPermissions in class AbstractPlugin

Returns:

A collection of permissions or null to not use permissions

isInContext

public String isInContext(GuiContext context,
                          Object item)

Returns null if the item is a ArrayDesign that doesn't already have any features and isn't an affy design.

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

getGuiContexts

public Set<GuiContext> getGuiContexts()

Description copied from interface: InteractivePlugin

Get a set containing all items that the plugin handles. Ie. if the plugin imports reporters, return a set containing Item.REPORTER. This information is used by client applications to put the plugin in the proper place in the user interface.

Specified by:

getGuiContexts in interface InteractivePlugin

Returns:

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

getRequestInformation

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

The Request.COMMAND_CONFIGURE_PLUGIN command will ask for parser regular expressions and column mappings. The Request.COMMAND_CONFIGURE_JOB command will ask for a file and the array design that features should be added to.

Specified by:

getRequestInformation in interface InteractivePlugin

Parameters:

command - the command for the request

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

Returns:

The RequestInformation for the command

Throws:

BaseException - if there is an error

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

isImportable

protected boolean isImportable(FlatFileParser ffp)

Check that the file is a TAM or MwBr file.

Overrides:

isImportable in class AbstractFlatFileImporter

Parameters:

ffp - The FlatFileParser object used to parse the file

Returns:

TRUE if a FormatName header is present and contains "TAM" or "MwBr", FALSE otherwise

begin

protected void begin(FlatFileParser ffp)
              throws BaseException

Create a DbControl and a FeatureBatcher. Check that the ArrayDesign doesn't already have features.

Overrides:

begin in class AbstractFlatFileImporter

Throws:

BaseException

See Also:

AbstractFlatFileImporter.end(boolean)

handleHeader

protected void handleHeader(FlatFileParser.Line line)
                     throws BaseException

Description copied from class: AbstractFlatFileImporter

Called by the parser for every line in the file that is a header line.

Overrides:

handleHeader in class AbstractFlatFileImporter

Throws:

BaseException

handleSection

protected void handleSection(FlatFileParser.Line line)
                      throws BaseException

Description copied from class: AbstractFlatFileImporter

Called by the parser for every line in the file that is a section line.

Overrides:

handleSection in class AbstractFlatFileImporter

Throws:

BaseException

handleData

protected void handleData(FlatFileParser.Data data)
                   throws BaseException

Description copied from class: AbstractFlatFileImporter

Called by the parser for every line in the file that is a data line.

Specified by:

handleData in class AbstractFlatFileImporter

Throws:

BaseException

end

protected void end(boolean success)
            throws BaseException

Description copied from class: AbstractFlatFileImporter

Called just after the last line of the file has been parsed, or immediately after an error has ocurred. A subclass should clean up any resources aquired in the AbstractFlatFileImporter.begin(FlatFileParser) method here. Note that this metod is called once for every file returned by the AbstractFlatFileImporter.getFileIterator() iterator.

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)

Description copied from class: AbstractFlatFileImporter

Called if the parsing was successful to let the subclass generate a simple message that is sent back to the core and user interface. An example message might by: 178 reporters imported successfully. The default implementation always return null. Note that this method is called once for every file returned by AbstractFlatFileImporter.getFileIterator().

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)

findWell

private Well findWell(int platePosition,
                      int row,
                      int column)

setBlockValue

private void setBlockValue(PrintMapFlatFileImporter.MetaBlock block,
                           FlatFileParser.Line line)
                    throws BaseException

Throws:

BaseException