net.sf.basedb.plugins.batchimport
Class HybridizationImporter

java.lang.Object
  net.sf.basedb.core.plugin.AbstractPlugin
      net.sf.basedb.plugins.AbstractFlatFileImporter
          net.sf.basedb.plugins.batchimport.AbstractItemImporter<Hybridization>
              net.sf.basedb.plugins.batchimport.HybridizationImporter

All Implemented Interfaces:

AutoDetectingImporter, InteractivePlugin, Plugin, SignalTarget, ConfigureByExample

public class HybridizationImporter
extends AbstractItemImporter<Hybridization>

Plug-in for importing hybridization items in a batch. The plug-in can create new items and updated existing items.

Version:

2.8

Author:

nicklas

Last modified

$Date: 2010-06-24 10:46:52 +0200 (Thu, 24 Jun 2010) $

Nested Class Summary

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

Plugin.MainType

Field Summary

private static About	about
protected static PluginParameter<String>	arrayIndexColumnMapping
private Mapper	arrayIndexMapper
protected static PluginParameter<String>	arraySlideColumnMapping
private Mapper	arraySlideMapper
private Mapper	createdMapper
private Mapper	descriptionMapper
private boolean	failIfMultipleArrayIndex
private static Set<GuiContext>	guiContexts
protected static PluginParameter<String>	hardwareColumnMapping
private Mapper	hardwareMapper
private static PluginParameter<String>	multipleArrayIndexErrorParameter
private Mapper	nameMapper
protected static PluginParameter<String>	numArraysColumnMapping
private Mapper	numArraysMapper
private Mapper	parentMapper
private Mapper	protocolMapper
private Mapper	usedQuantityMapper

Fields inherited from class net.sf.basedb.plugins.batchimport.AbstractItemImporter

defaultsSection, descriptionColumnMapping, externalIdColumnMapping, identificationSection, internalIdColumnMapping, nameColumnMapping, optionalColumnMapping, permissionTemplateColumnMapping, protocolColumnMapping, requiredColumnMapping

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

HybridizationImporter()

Method Summary

protected void	addMoreColumnMappingParameters(List<PluginParameter<?>> parameters) Adds column mappings for name, externalId, description, protocol, creation date, original quantity, pooled, parent and used quantity from parent.
protected void	addMoreErrorParameters(List<PluginParameter<?>> parameters) Add extra parameters to the "Error handling" section that the subclass needs.
protected void	createColumnMappers(FlatFileParser ffp, boolean cropStrings) Create mappers that can be used to extract data values from the file that is currently being parsed by the ffp FlatFileParser.
protected Hybridization	createItem(DbControl dc, FlatFileParser.Data data) Create a new item and populate it with data from the current line.
protected ItemQuery<Hybridization>	createItemQuery() Calls Hybridization.getQuery().
About	getAbout() Get information about the plugin, such as name, version, authors, etc.
Set<GuiContext>	getGuiContexts() Get a set containing all items that the plugin handles.
protected IdMethod[]	getIdMethods() Useable methods are: PropertyIdMethod.NAME InternalIdMethod.INTERNAL_ID FallbackIdMethod.NAME_OR_ID
protected void	updateItem(DbControl dc, Hybridization hyb, FlatFileParser.Data data) Update an item with data from the current line.
protected void	updateMultiLineItem(DbControl dc, Hybridization hyb, FlatFileParser.Data data, int multiLineNum) Add parent labeled extracts and the used quantities

Methods inherited from class net.sf.basedb.plugins.batchimport.AbstractItemImporter

addMoreJobParameters, addMoreParsingParameters, begin, beginData, configure, doneWithItem, end, findArrayBatch, findArrayDesign, findArraySlide, findBioPlate, findBioPlateType, findBioSource, findBioWell, findDataFileType, findExtract, findFeatureExtractionSoftware, findFreezer, findHybridization, findHybridizationStation, findImage, findLabel, findLabeledExtract, findPermissionTemplate, findPlateGeometry, findPlatform, findPrintRobot, findProtocol, findProtocol, findRawDataType, findReferencedItem, findSample, findScan, findScanner, findVariant, getConfigureOptionsParameters, getConfigureParserParameters, getIdMethod, getInitializedFlatFileParser, getInitializedFlatFileParser, getProjectDefaultPlatform, getProjectDefaultRawDataType, getProjectDefaultVariant, getRequestInformation, getSuccessMessage, handleData, initReferenceQuery, isInContext, parseDate, requiresConfiguration, setUpErrorHandling, supportsConfigurations, updatePermissions

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

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

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

checkInterrupted, cloneParameterWithDefaultValue, closeLogFile, createLogFile, done, getCopyAnnotationsParmeter, getCurrentConfiguration, getCurrentJob, getJobOrConfigurationValue, getOverwriteAnnotationsParameters, getPermissions, 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, getPermissions, init, run

Field Detail

guiContexts

private static final Set<GuiContext> guiContexts

about

private static final About about

hardwareColumnMapping

protected static final PluginParameter<String> hardwareColumnMapping

arraySlideColumnMapping

protected static final PluginParameter<String> arraySlideColumnMapping

numArraysColumnMapping

protected static final PluginParameter<String> numArraysColumnMapping

arrayIndexColumnMapping

protected static final PluginParameter<String> arrayIndexColumnMapping

multipleArrayIndexErrorParameter

private static final PluginParameter<String> multipleArrayIndexErrorParameter

nameMapper

private Mapper nameMapper

descriptionMapper

private Mapper descriptionMapper

numArraysMapper

private Mapper numArraysMapper

createdMapper

private Mapper createdMapper

protocolMapper

private Mapper protocolMapper

hardwareMapper

private Mapper hardwareMapper

parentMapper

private Mapper parentMapper

usedQuantityMapper

private Mapper usedQuantityMapper

arrayIndexMapper

private Mapper arrayIndexMapper

arraySlideMapper

private Mapper arraySlideMapper

failIfMultipleArrayIndex

private boolean failIfMultipleArrayIndex

Constructor Detail

HybridizationImporter

public HybridizationImporter()

Method Detail

getAbout

public About getAbout()

Description copied from interface: Plugin

Get information about the plugin, such as name, version, authors, etc.

Returns:

An About object

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.

Returns:

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

getIdMethods

protected IdMethod[] getIdMethods()

Useable methods are:

• PropertyIdMethod.NAME
• InternalIdMethod.INTERNAL_ID
• FallbackIdMethod.NAME_OR_ID

Overrides:

getIdMethods in class AbstractItemImporter<Hybridization>

addMoreColumnMappingParameters

protected void addMoreColumnMappingParameters(List<PluginParameter<?>> parameters)

Adds column mappings for name, externalId, description, protocol, creation date, original quantity, pooled, parent and used quantity from parent.

Overrides:

addMoreColumnMappingParameters in class AbstractItemImporter<Hybridization>

Parameters:

parameters - The list of parameters to add the column mapping parameters to

addMoreErrorParameters

protected void addMoreErrorParameters(List<PluginParameter<?>> parameters)

Description copied from class: AbstractItemImporter

Add extra parameters to the "Error handling" section that the subclass needs. This method is called during configuration of the plug-in and the default implementation does nothing.

Overrides:

addMoreErrorParameters in class AbstractItemImporter<Hybridization>

Parameters:

parameters - The list of parameters to add the column mapping parameters to

createItemQuery

protected ItemQuery<Hybridization> createItemQuery()

Calls Hybridization.getQuery().

Specified by:

createItemQuery in class AbstractItemImporter<Hybridization>

Returns:

A query

createColumnMappers

protected void createColumnMappers(FlatFileParser ffp,
                                   boolean cropStrings)

Description copied from class: AbstractItemImporter

Create mappers that can be used to extract data values from the file that is currently being parsed by the ffp FlatFileParser. This method is called during initialisation of the plug-in when the FlatFileParser.parseHeaders() has successfully found the start of data. Use the AbstractFlatFileImporter.getMapper(FlatFileParser, String, Integer, Mapper) to create column mappers. Example:

nameMapper = getMapper(ffp, job.getValue("nameColumnMapping"), 
   cropStrings ? Nameable.MAX_NAME_LENGTH : null, null);

Overrides:

createColumnMappers in class AbstractItemImporter<Hybridization>

Parameters:

ffp - The parser that is parsing the data file

cropStrings - If strings that are too long to fit in the database should be cropped or not (=generate an error)

createItem

protected Hybridization createItem(DbControl dc,
                                   FlatFileParser.Data data)

Description copied from class: AbstractItemImporter

Create a new item and populate it with data from the current line. Do not call DbControl.saveItem(BasicItem). This is done automatically by the core implementation.

BioSource bs = BioSource.getNew(dc);
// Set properties; see example on updateItem method
return bs;

If the current data line doesn't have data for all required properties, this method should throw an InvalidUseOfNullException exception.

This method is called during import when current item can be found and if the user has selected to create missing item.

Specified by:

createItem in class AbstractItemImporter<Hybridization>

Parameters:

dc - The DbControl to use for database access

data - The current data line

Returns:

A new item

updateItem

protected void updateItem(DbControl dc,
                          Hybridization hyb,
                          FlatFileParser.Data data)

Description copied from class: AbstractItemImporter

Update an item with data from the current line. Example:

if (nameMapper != null) item.setName(nameMapper.getValue(data));
if (descriptionMapper != null) item.setDescription(descriptionMapper.getValue(data));
...

This method is called during import to update an existing item.

Specified by:

updateItem in class AbstractItemImporter<Hybridization>

Parameters:

dc - The DbControl to use for database access

hyb - The item to update

data - The current data line

updateMultiLineItem

protected void updateMultiLineItem(DbControl dc,
                                   Hybridization hyb,
                                   FlatFileParser.Data data,
                                   int multiLineNum)

Add parent labeled extracts and the used quantities

Overrides:

updateMultiLineItem in class AbstractItemImporter<Hybridization>

Parameters:

dc - The DbControl to use for database access

hyb - The item to update

data - The current data line

multiLineNum - The number of the multi-line entry, starting with 1 for the first multi-line