Package net.sf.basedb.plugins

Class PlateFlatFileImporter

java.lang.Object

net.sf.basedb.core.plugin.AbstractPlugin

net.sf.basedb.plugins.AbstractFlatFileImporter

net.sf.basedb.plugins.PlateFlatFileImporter

All Implemented Interfaces:

AutoDetectingImporter, InteractivePlugin, Plugin, SignalTarget, ConfigureByExample

public class PlateFlatFileImporter
extends AbstractFlatFileImporter
implements InteractivePlugin, ConfigureByExample

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 static final PluginParameter<String>	barcodeColumnMapping
private Mapper	barcodeMapper
private static final PluginParameter<String>	columnColumnMapping
private Mapper	columnMapper
private RequestInformation	configureJob
private RequestInformation	configurePlugin
private DbControl	dc
private boolean	errorIfNotFound
private FlatFileParser	ffp
private static final Set<GuiContext>	guiContexts
protected static final PluginParameter<String>	missingReporterErrorParameter
private static final PluginParameter<String>	nameColumnMapping
private Mapper	nameMapper
private PluginParameter<Integer>	namePaddingParameter
private int	numPlates
private int	numWells
private static final Set<Permissions>	permissions
private Integer	plateNamePadding
private String	plateNamePrefix
private PluginParameter<String>	plateNamePrefixParameter
private HashMap<String,Plate>	plates
private PlateType	plateType
private PluginParameter<PlateType>	plateTypeParameter
private ItemParameterType<PlateType>	plateTypeType
private ReporterBatcher	reporterBatcher
private static final PluginParameter<String>	reporterColumnMapping
private Mapper	reporterMapper
private String	reporterPrefix
private PluginParameter<String>	reporterPrefixParameter
private static final 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
PlateFlatFileImporter()

Method Summary

Modifier and Type	Method	Description
protected void	begin(FlatFileParser ffp)	Create a DbControl and a RawDataBatcher.
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 and DbControl.
private List<PluginParameter<String>>	getAllColumnMappings()
private RequestInformation	getConfigureJobParameters(GuiContext context)
private RequestInformation	getConfigurePluginParameters(GuiContext context)
Set<GuiContext>	getGuiContexts()	Get a set containing all items that the plugin handles.
Collection<Permissions>	getPermissions()	Request create access to Plate:s, use access to PlateType:s and read access to Reporter:s, PlateGeometry: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 plates 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)	Always null, since plugin doesn't operate on individual items.
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

columnColumnMapping

private static final PluginParameter<String> columnColumnMapping

rowColumnMapping

private static final PluginParameter<String> rowColumnMapping

reporterColumnMapping

private static final PluginParameter<String> reporterColumnMapping

nameColumnMapping

private static final PluginParameter<String> nameColumnMapping

barcodeColumnMapping

private static final PluginParameter<String> barcodeColumnMapping

plateNamePrefixParameter

private PluginParameter<String> plateNamePrefixParameter

reporterPrefixParameter

private PluginParameter<String> reporterPrefixParameter

namePaddingParameter

private PluginParameter<Integer> namePaddingParameter

missingReporterErrorParameter

protected static final PluginParameter<String> missingReporterErrorParameter

plateTypeType

private ItemParameterType<PlateType> plateTypeType

plateTypeParameter

private PluginParameter<PlateType> plateTypeParameter

allColumnMappings

private List<PluginParameter<String>> allColumnMappings

configurePlugin

private RequestInformation configurePlugin

configureJob

private RequestInformation configureJob

dc

private DbControl dc

ffp

private FlatFileParser ffp

numPlates

private int numPlates

numWells

private int numWells

plateType

private PlateType plateType

plateNamePrefix

private String plateNamePrefix

plateNamePadding

private Integer plateNamePadding

reporterPrefix

private String reporterPrefix

reporterMapper

private Mapper reporterMapper

nameMapper

private Mapper nameMapper

barcodeMapper

private Mapper barcodeMapper

rowMapper

private Mapper rowMapper

columnMapper

private Mapper columnMapper

reporterBatcher

private ReporterBatcher reporterBatcher

errorIfNotFound

private boolean errorIfNotFound

plates

private HashMap<String,Plate> plates

Constructor Details

PlateFlatFileImporter

public PlateFlatFileImporter()

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 access to Plate:s, use access to PlateType:s and read access to Reporter:s, PlateGeometry: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()

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

isInContext

public String isInContext(GuiContext context,
 Object item)

Always null, since plugin doesn't operate on individual items.

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

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 what PlateType the plates in the file has.

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 RawDataBatcher. Load the RawBioAssay that 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 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 plates inserted.

Overrides:

getSuccessMessage in class AbstractFlatFileImporter

Parameters:

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

getConfigurePluginParameters

private RequestInformation getConfigurePluginParameters(GuiContext context)

getConfigureJobParameters

private RequestInformation getConfigureJobParameters(GuiContext context)

getAllColumnMappings

private List<PluginParameter<String>> getAllColumnMappings()