Package net.sf.basedb.plugins.batchimport

Class BioPlateImporter

java.lang.Object

net.sf.basedb.core.plugin.AbstractPlugin

net.sf.basedb.plugins.AbstractFlatFileImporter

net.sf.basedb.plugins.batchimport.AbstractItemImporter<BioPlate>

net.sf.basedb.plugins.batchimport.BioPlateImporter

All Implemented Interfaces:

AutoDetectingImporter, InteractivePlugin, Plugin, SignalTarget, ConfigureByExample

public class BioPlateImporter
extends AbstractItemImporter<BioPlate>

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

Since:

2.16

Author:

nicklas

Last modified

$Date: 2019-03-21 08:45:42 +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
protected static final PluginParameter<String>	barcodeColumnMapping
private Mapper	barcodeMapper
protected static final PluginParameter<String>	bioPlateTypeColumnMapping
private Mapper	bioPlateTypeMapper
private Mapper	createdMapper
private DefaultItemFunction<Hardware>	defaultHardwareFunction
private Mapper	descriptionMapper
private static final Set<GuiContext>	guiContexts
protected static final PluginParameter<String>	hardwareColumnMapping
private Mapper	hardwareMapper
private Mapper	nameMapper
protected static final PluginParameter<String>	plateGeometryColumnMapping
private Mapper	plateGeometryMapper
protected static final PluginParameter<String>	positionColumnMapping
private Mapper	positionMapper
private Mapper	registeredMapper
protected static final PluginParameter<String>	sectionColumnMapping
private Mapper	sectionMapper
protected static final PluginParameter<String>	trayColumnMapping
private Mapper	trayMapper

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

addMembersMode, createMode, defaultsSection, descriptionColumnMapping, externalIdColumnMapping, idAnnotationColumnMapping, identificationSection, internalIdColumnMapping, kitColumnMapping, nameColumnMapping, optionalColumnMapping, permissionTemplateColumnMapping, protocolColumnMapping, registeredColumnMapping, removeMembersMode, requiredColumnMapping, subtypeColumnMapping, updateMode

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
BioPlateImporter()

Method Summary

Modifier and Type	Method	Description
protected void	addMoreColumnMappingParameters(List<PluginParameter<?>> parameters)	Adds column mappings for name, description, plate type, plate geometry, barcode and freezer.
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 BioPlate	createItem(DbControl dc, FlatFileParser.Data data)	Create a new item and populate it with data from the current line.
protected ItemQuery<BioPlate>	createItemQuery()	Calls BioPlate.getQuery().
Set<GuiContext>	getGuiContexts()	Get a set containing all items that the plugin handles.
protected IdMethod[]	getIdMethods()	Useable methods are: PropertyIdMethod.NAME PropertyIdMethod.BARCODE InternalIdMethod.INTERNAL_ID FallbackIdMethod.NAME_OR_ID
protected Item	getItemForAnnotationTypes()	Enable annotations as item identifier.
protected void	updateItem(DbControl dc, BioPlate plate, FlatFileParser.Data data)	Update an item with data from the current line.

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

addMoreErrorParameters, addMoreJobParameters, addMoreParsingParameters, begin, beginData, configure, createItemQuery, doneWithItem, end, findAnnotationTypeCategory, findArrayBatch, findArrayDesign, findArraySlide, findBioPlate, findBioPlateType, findBioSource, findBioSource, findBioWell, findDataFileType, findDerivedBioAssay, findExtract, findExtract, findFileServer, findHardware, findHardware, findHybridization, findItemSubtype, findItemSubtype, findKit, findLabeledExtract, findPermissionTemplate, findPhysicalBioAssay, findPlateGeometry, findPlatform, findProtocol, findProtocol, findRawDataType, findReferencedItem, findReferencedItemWithSubtype, findSample, findSample, findSoftware, findSoftware, findTag, findTag, findUnit, findVariant, getAnnotationIdMethods, getConfigureOptionsParameters, getConfigureParserParameters, getDefaultItemFunction, getIdMethod, getItemForSubtypes, getProjectDefaultPlatform, getProjectDefaultRawDataType, getProjectDefaultVariant, getRequestInformation, getSuccessMessage, handleData, initReferenceQuery, isInContext, parseDate, requiresConfiguration, setOrAddFile, setUpErrorHandling, supportsConfigurations, updateItemSubtype, updateMultiLineItem, updatePermissions

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, start, wrapInputStream

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

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

Field Details

guiContexts

private static final Set<GuiContext> guiContexts

bioPlateTypeColumnMapping

protected static final PluginParameter<String> bioPlateTypeColumnMapping

plateGeometryColumnMapping

protected static final PluginParameter<String> plateGeometryColumnMapping

hardwareColumnMapping

protected static final PluginParameter<String> hardwareColumnMapping

sectionColumnMapping

protected static final PluginParameter<String> sectionColumnMapping

trayColumnMapping

protected static final PluginParameter<String> trayColumnMapping

positionColumnMapping

protected static final PluginParameter<String> positionColumnMapping

barcodeColumnMapping

protected static final PluginParameter<String> barcodeColumnMapping

nameMapper

private Mapper nameMapper

descriptionMapper

private Mapper descriptionMapper

bioPlateTypeMapper

private Mapper bioPlateTypeMapper

plateGeometryMapper

private Mapper plateGeometryMapper

createdMapper

private Mapper createdMapper

registeredMapper

private Mapper registeredMapper

hardwareMapper

private Mapper hardwareMapper

defaultHardwareFunction

private DefaultItemFunction<Hardware> defaultHardwareFunction

sectionMapper

private Mapper sectionMapper

trayMapper

private Mapper trayMapper

positionMapper

private Mapper positionMapper

barcodeMapper

private Mapper barcodeMapper

Constructor Details

BioPlateImporter

public BioPlateImporter()

Method Details

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
• PropertyIdMethod.BARCODE
• InternalIdMethod.INTERNAL_ID
• FallbackIdMethod.NAME_OR_ID

Overrides:

getIdMethods in class AbstractItemImporter<BioPlate>

getItemForAnnotationTypes

protected Item getItemForAnnotationTypes()

Enable annotations as item identifier.

Overrides:

getItemForAnnotationTypes in class AbstractItemImporter<BioPlate>

Returns:

An Item or null

addMoreColumnMappingParameters

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

Adds column mappings for name, description, plate type, plate geometry, barcode and freezer.

Overrides:

addMoreColumnMappingParameters in class AbstractItemImporter<BioPlate>

Parameters:

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

createItemQuery

protected ItemQuery<BioPlate> createItemQuery()

Calls BioPlate.getQuery().

Specified by:

createItemQuery in class AbstractItemImporter<BioPlate>

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<BioPlate>

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 BioPlate 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<BioPlate>

Parameters:

dc - The DbControl to use for database access

data - The current data line

Returns:

A new item

updateItem

protected void updateItem(DbControl dc,
 BioPlate plate,
 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<BioPlate>

Parameters:

dc - The DbControl to use for database access

plate - The item to update

data - The current data line