Package net.sf.basedb.plugins

Class ReporterMapFlatFileImporter

java.lang.Object

net.sf.basedb.core.plugin.AbstractPlugin

net.sf.basedb.plugins.AbstractFlatFileImporter

net.sf.basedb.plugins.ReporterMapFlatFileImporter

All Implemented Interfaces:

AutoDetectingImporter, InteractivePlugin, Plugin, SignalTarget, ConfigureByExample

Direct Known Subclasses:

GtfReporterMapImporter

public class ReporterMapFlatFileImporter
extends AbstractFlatFileImporter
implements InteractivePlugin, ConfigureByExample

A plugin that imports features to an ArrayDesign from a flat file. The ArrayDesign will not have any connections to plates.

Version:

2.0

Author:

Enell

Last modified

$Date: 2019-03-20 16:21:26 +0100 (ons, 20 mars 2019) $

Nested Class Summary

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

Plugin.MainType

Field Summary

Fields

Modifier and Type	Field	Description
private List<PluginParameter<String>>	allColumnMappings
private ArrayDesign	arrayDesign
private PluginParameter<ArrayDesign>	arrayDesignParameter
private ItemParameterType<ArrayDesign>	arrayDesignType
private FeatureBatcher	batcher
protected static PluginParameter<String>	blockColumnMapping
private Mapper	blockMapper
private Map<BlockInfo,ArrayDesignBlock>	blocks
protected static PluginParameter<String>	columnColumnMapping
private Mapper	columnMapper
private RequestInformation	configureJob
private RequestInformation	configurePlugin
private DbControl	dc
protected static PluginParameter<String>	duplicateFeatureErrorParameter
private boolean	errorIfNotFound
protected static PluginParameter<String>	featureIdColumnMapping
protected static PluginParameter<String>	featureIdentificationParameter
private Mapper	featureIdMapper
private FlatFileParser	ffp
private static Set<GuiContext>	guiContexts
protected static PluginParameter<String>	metaGridXColumnMapping
private Mapper	metaGridXMapper
protected static PluginParameter<String>	metaGridYColumnMapping
private Mapper	metaGridYMapper
protected static PluginParameter<String>	missingReporterErrorParameter
private int	numBlocks
private int	numFeatures
private static StringParameterType	optionalColumnMapping
private static Set<Permissions>	permissions
protected static PluginParameter<String>	positionColumnMapping
private Mapper	positionMapper
private ReporterBatcher	reporterBatcher
protected static PluginParameter<String>	reporterIdColumnMapping
private FileSetMember	reporterMapMember
private Mapper	reporterMapper
private static StringParameterType	requiredColumnMapping
protected static PluginParameter<String>	rowColumnMapping
private Mapper	rowMapper

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

complexMappings, dataFooterRegexpParameter, dataHeaderRegexpParameter, dataSplitterRegexpParameter, defaultErrorParameter, errorSection, excelSheetParameter, 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

Constructors

Constructor	Description
ReporterMapFlatFileImporter()	Create a new importer.

Method Summary

Modifier and Type	Method	Description
protected void	begin(FlatFileParser ffp)	Create a DbControl and a FeatureBatcher.
protected void	beginData()	Initialise column Mapper:s.
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 FeatureBatcher and DbControl.
private List<PluginParameter<String>>	getAllColumnMappings()
private RequestInformation	getConfigureJobParameters(GuiContext context)
private RequestInformation	getConfigurePluginParameters(GuiContext context)
Set<GuiContext>	getGuiContexts()	Return a set containing the element [ARRAYDESIGN, ITEM].
Collection<Permissions>	getPermissions()	Request write access to ArrayDesign:s, read access to 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)	Return x features inserted; y blocks inserted.
protected void	handleData(FlatFileParser.Data data)	Called by the parser for every line in the file that is a data line.
String	isInContext(GuiContext context, Object item)	Returns null if the item is a ArrayDesign that doesn't already have any features and is using a supported platform/variant.
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, getDateFormatter, getDecimalSeparator, getErrorHandler, getErrorOption, getFileIterator, getInitializedFlatFileParser, getInitializedFlatFileParser, getMainType, getMapper, getMapper, getNumberFormat, getNumBytes, getPattern, getPattern, getProgress, getSignalHandler, getTimestampFormatter, 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, isLogging, 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 Details

guiContexts

private static final Set<GuiContext> guiContexts

permissions

private static final Set<Permissions> permissions

requiredColumnMapping

private static final StringParameterType requiredColumnMapping

optionalColumnMapping

private static final StringParameterType optionalColumnMapping

featureIdentificationParameter

protected static final PluginParameter<String> featureIdentificationParameter

reporterIdColumnMapping

protected static final PluginParameter<String> reporterIdColumnMapping

featureIdColumnMapping

protected static final PluginParameter<String> featureIdColumnMapping

positionColumnMapping

protected static final PluginParameter<String> positionColumnMapping

blockColumnMapping

protected static final PluginParameter<String> blockColumnMapping

metaGridXColumnMapping

protected static final PluginParameter<String> metaGridXColumnMapping

metaGridYColumnMapping

protected static final PluginParameter<String> metaGridYColumnMapping

columnColumnMapping

protected static final PluginParameter<String> columnColumnMapping

rowColumnMapping

protected static final PluginParameter<String> rowColumnMapping

missingReporterErrorParameter

protected static final PluginParameter<String> missingReporterErrorParameter

duplicateFeatureErrorParameter

protected static final PluginParameter<String> duplicateFeatureErrorParameter

configurePlugin

private RequestInformation configurePlugin

configureJob

private RequestInformation configureJob

dc

private DbControl dc

batcher

private FeatureBatcher batcher

reporterBatcher

private ReporterBatcher reporterBatcher

reporterMapMember

private FileSetMember reporterMapMember

arrayDesign

private ArrayDesign arrayDesign

blocks

private Map<BlockInfo,ArrayDesignBlock> blocks

ffp

private FlatFileParser ffp

arrayDesignType

private ItemParameterType<ArrayDesign> arrayDesignType

arrayDesignParameter

private PluginParameter<ArrayDesign> arrayDesignParameter

allColumnMappings

private List<PluginParameter<String>> allColumnMappings

errorIfNotFound

private boolean errorIfNotFound

reporterMapper

private Mapper reporterMapper

featureIdMapper

private Mapper featureIdMapper

positionMapper

private Mapper positionMapper

blockMapper

private Mapper blockMapper

columnMapper

private Mapper columnMapper

rowMapper

private Mapper rowMapper

metaGridXMapper

private Mapper metaGridXMapper

metaGridYMapper

private Mapper metaGridYMapper

numFeatures

private int numFeatures

numBlocks

private int numBlocks

Constructor Details

ReporterMapFlatFileImporter

public ReporterMapFlatFileImporter()

Create a new importer.

Method Details

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 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

getGuiContexts

public Set<GuiContext> getGuiContexts()

Return a set containing the element [ARRAYDESIGN, ITEM].

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)

Returns null if the item is a ArrayDesign that doesn't already have any features and is using a supported platform/variant.

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

Throws:

PermissionDeniedException - If the array design already has features or if the logged in user doesn't have write permission

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:

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)

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

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)

beginData

protected void beginData()

Initialise column Mapper:s.

Overrides:

beginData in class AbstractFlatFileImporter

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

Close and commit/rollback the FeatureBatcher and 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 x features inserted; y blocks inserted.

Overrides:

getSuccessMessage in class AbstractFlatFileImporter

Parameters:

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

getAllColumnMappings

private List<PluginParameter<String>> getAllColumnMappings()

getConfigureJobParameters

private RequestInformation getConfigureJobParameters(GuiContext context)

getConfigurePluginParameters

private RequestInformation getConfigurePluginParameters(GuiContext context)