Package net.sf.basedb.plugins

Class ReporterFlatFileImporter

java.lang.Object

net.sf.basedb.core.plugin.AbstractPlugin

net.sf.basedb.plugins.AbstractFlatFileImporter

net.sf.basedb.plugins.ReporterFlatFileImporter

All Implemented Interfaces:

AutoDetectingImporter, InteractivePlugin, Plugin, SignalTarget, ConfigureByExample

Direct Known Subclasses:

GtfReporterImporter

public class ReporterFlatFileImporter
extends AbstractFlatFileImporter
implements InteractivePlugin, ConfigureByExample

A plugin that imports reporter from a flat file.

Version:

2.0

Author:

Nicklas

Last modified

$Date: 2019-03-21 12:50:52 +0100 (tors, 21 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 ReporterBatcher	batcher
private RequestInformation	configureJob
private RequestInformation	configurePlugin
private boolean	createMissing
private DbControl	dc
private Map<String,Float>	deferred
private Set<String>	deleted
private boolean	deleteMode
private static final PluginParameter<String>	descriptionColumnMapping
private Mapper	descriptionMapper
private Map<ExtendedProperty,Mapper>	extendedMappers
private boolean	failIfUsed
private FlatFileParser	ffp
private static final Set<GuiContext>	guiContexts
private Mapper	idMapper
private static final PluginParameter<String>	nameColumnMapping
private Mapper	nameMapper
private boolean	nullIfException
private int	numAddedToList
private int	numDeleted
private int	numExists
private int	numInserted
private int	numNotFound
private int	numUpdated
private int	numUsed
private static final StringParameterType	optionalColumnMapping
private static final Set<Permissions>	permissions
private static final PluginParameter<String>	reporterIdColumnMapping
protected static final PluginParameter<String>	reporterIsUsedErrorParameter
private ReporterList	reporterList
private PluginParameter<ReporterList>	reporterListParameter
private ReporterType	reporterType
private static final PluginParameter<String>	reporterTypeColumnMapping
private Mapper	reporterTypeMapper
private PluginParameter<ReporterType>	reporterTypeParameter
private Map<String,ReporterType>	reporterTypes
private static final StringParameterType	requiredColumnMapping
private static final PluginParameter<String>	scoreColumnMapping
private Mapper	scoreMapper
private static final PluginParameter<String>	symbolColumnMapping
private Mapper	symbolMapper
private boolean	updateExisting

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
ReporterFlatFileImporter()	Create a new importer.

Method Summary

Modifier and Type	Method	Description
protected void	begin(FlatFileParser ffp)	Create a DbControl and a ReporterBatcher.
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 ReporterBatcher and DbControl.
private List<PluginParameter<String>>	getAllColumnMappings(boolean reporterListContext)
private RequestInformation	getConfigureJobParameters(GuiContext context)
private RequestInformation	getConfigurePluginParameters(GuiContext context)
Set<GuiContext>	getGuiContexts()	Return a set containing the context:s [REPORTER, LIST], [REPORTERLIST, ITEM], [REPORTERSCORE, LIST].
Collection<Permissions>	getPermissions()	Request create, write and delete access to Reporter:s, write access to ReporterList:s and read access to File:s and ReporterType:s.
private ReporterType	getReporterType(String name)
RequestInformation	getRequestInformation(GuiContext context, String command)	The Request.COMMAND_CONFIGURE_PLUGIN command will ask for parser regular expressions, column mappings and the reporter type.
protected String	getSuccessMessage(int skippedLines)	Return x new reporters; y updated reporters; z reporters added to list.
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)	Null if the context is Item.REPORTERLIST and the item is a ReporterList.
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

nameColumnMapping

private static final PluginParameter<String> nameColumnMapping

reporterIdColumnMapping

private static final PluginParameter<String> reporterIdColumnMapping

descriptionColumnMapping

private static final PluginParameter<String> descriptionColumnMapping

symbolColumnMapping

private static final PluginParameter<String> symbolColumnMapping

scoreColumnMapping

private static final PluginParameter<String> scoreColumnMapping

reporterTypeColumnMapping

private static final PluginParameter<String> reporterTypeColumnMapping

reporterIsUsedErrorParameter

protected static final PluginParameter<String> reporterIsUsedErrorParameter

reporterTypeParameter

private PluginParameter<ReporterType> reporterTypeParameter

reporterListParameter

private PluginParameter<ReporterList> reporterListParameter

allColumnMappings

private List<PluginParameter<String>> allColumnMappings

configurePlugin

private RequestInformation configurePlugin

configureJob

private RequestInformation configureJob

dc

private DbControl dc

batcher

private ReporterBatcher batcher

idMapper

private Mapper idMapper

nameMapper

private Mapper nameMapper

symbolMapper

private Mapper symbolMapper

descriptionMapper

private Mapper descriptionMapper

scoreMapper

private Mapper scoreMapper

reporterTypeMapper

private Mapper reporterTypeMapper

extendedMappers

private Map<ExtendedProperty,Mapper> extendedMappers

reporterType

private ReporterType reporterType

reporterTypes

private Map<String,ReporterType> reporterTypes

reporterList

private ReporterList reporterList

updateExisting

private boolean updateExisting

createMissing

private boolean createMissing

deleteMode

private boolean deleteMode

numInserted

private int numInserted

numUpdated

private int numUpdated

numExists

private int numExists

numAddedToList

private int numAddedToList

numNotFound

private int numNotFound

numUsed

private int numUsed

numDeleted

private int numDeleted

deferred

private Map<String,Float> deferred

deleted

private Set<String> deleted

ffp

private FlatFileParser ffp

nullIfException

private boolean nullIfException

failIfUsed

private boolean failIfUsed

Constructor Details

ReporterFlatFileImporter

public ReporterFlatFileImporter()

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 create, write and delete access to Reporter:s, write access to ReporterList:s and read access to File:s and ReporterType: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 [REPORTER, LIST], [REPORTERLIST, ITEM], [REPORTERSCORE, LIST]. The first context is for importing reporters only, and the last two for importing reporters to a reporter 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)

Null if the context is Item.REPORTERLIST and the item is a ReporterList.

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 user doesn't have write permission to the reporter list

getRequestInformation

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

The Request.COMMAND_CONFIGURE_PLUGIN command will ask for parser regular expressions, column mappings and the reporter type. The Request.COMMAND_CONFIGURE_JOB command will ask for a file and if existing reporters should be updated or ignored.

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 ReporterBatcher. Load the ReporterType if one has been specified.

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

end

protected void end(boolean success)
            throws BaseException

Close and commit/rollback the ReporterBatcher 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)

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

getSuccessMessage

protected String getSuccessMessage(int skippedLines)

Return x new reporters; y updated reporters; z reporters added to list.

Overrides:

getSuccessMessage in class AbstractFlatFileImporter

Parameters:

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

getAllColumnMappings

private List<PluginParameter<String>> getAllColumnMappings(boolean reporterListContext)

getConfigureJobParameters

private RequestInformation getConfigureJobParameters(GuiContext context)

getConfigurePluginParameters

private RequestInformation getConfigurePluginParameters(GuiContext context)

getReporterType

private ReporterType getReporterType(String name)