Package net.sf.basedb.plugins.batchimport

Class PhysicalBioAssayImporter

java.lang.Object

net.sf.basedb.core.plugin.AbstractPlugin

net.sf.basedb.plugins.AbstractFlatFileImporter

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

net.sf.basedb.plugins.batchimport.PhysicalBioAssayImporter

All Implemented Interfaces:

AutoDetectingImporter, InteractivePlugin, Plugin, SignalTarget, ConfigureByExample

public class PhysicalBioAssayImporter
extends AbstractItemImporter<PhysicalBioAssay>

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

Since:

3.0

Author:

nicklas

Last modified

$Date: 2024-12-19 08:20:15 +0100 (Thu, 19 Dec 2024) $

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>	arraySlideColumnMapping
private Mapper	arraySlideMapper
private Mapper	createdMapper
private DefaultItemFunction<Hardware>	defaultHardwareFunction
private DefaultItemFunction<Protocol>	defaultProtocolFunction
private Mapper	descriptionMapper
protected static final PluginParameter<String>	extractPositionColumnMapping
private Mapper	extractPositionMapper
private boolean	failIfMultiplePositions
private static final Set<GuiContext>	guiContexts
protected static final PluginParameter<String>	hardwareColumnMapping
private Mapper	hardwareMapper
private Mapper	kitMapper
private static final PluginParameter<String>	multiplePositionsError
private Mapper	nameMapper
private Mapper	parentMapper
private Mapper	protocolMapper
private Mapper	registeredMapper
protected static final PluginParameter<String>	sizeColumnMapping
private Mapper	sizeMapper
private UsedQuantityMapper	usedQuantityMapper

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
PhysicalBioAssayImporter()

Method Summary

Modifier and Type	Method	Description
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 PhysicalBioAssay	createItem(DbControl dc, FlatFileParser.Data data)	Create a new item and populate it with data from the current line.
protected ItemQuery<PhysicalBioAssay>	createItemQuery()	Calls PhysicalBioAssay.getQuery().
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 Item	getItemForAnnotationTypes()	Enable annotations as item identifier.
protected Item	getItemForSubtypes()	Does the importer want to use item subtypes when importing?
protected void	updateItem(DbControl dc, PhysicalBioAssay pba, FlatFileParser.Data data)	Update an item with data from the current line.
protected void	updateMultiLineItem(DbControl dc, PhysicalBioAssay pba, FlatFileParser.Data data, int multiLineNum)	Add parent extracts and the used quantities

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

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, getProjectDefaultPlatform, getProjectDefaultRawDataType, getProjectDefaultVariant, getRequestInformation, getSuccessMessage, handleData, initReferenceQuery, isInContext, parseDate, requiresConfiguration, setOrAddFile, setUpErrorHandling, supportsConfigurations, updateItemSubtype, 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

hardwareColumnMapping

protected static final PluginParameter<String> hardwareColumnMapping

arraySlideColumnMapping

protected static final PluginParameter<String> arraySlideColumnMapping

sizeColumnMapping

protected static final PluginParameter<String> sizeColumnMapping

extractPositionColumnMapping

protected static final PluginParameter<String> extractPositionColumnMapping

multiplePositionsError

private static final PluginParameter<String> multiplePositionsError

nameMapper

private Mapper nameMapper

descriptionMapper

private Mapper descriptionMapper

sizeMapper

private Mapper sizeMapper

createdMapper

private Mapper createdMapper

registeredMapper

private Mapper registeredMapper

protocolMapper

private Mapper protocolMapper

defaultProtocolFunction

private DefaultItemFunction<Protocol> defaultProtocolFunction

hardwareMapper

private Mapper hardwareMapper

defaultHardwareFunction

private DefaultItemFunction<Hardware> defaultHardwareFunction

kitMapper

private Mapper kitMapper

parentMapper

private Mapper parentMapper

usedQuantityMapper

private UsedQuantityMapper usedQuantityMapper

extractPositionMapper

private Mapper extractPositionMapper

arraySlideMapper

private Mapper arraySlideMapper

failIfMultiplePositions

private boolean failIfMultiplePositions

Constructor Details

PhysicalBioAssayImporter

public PhysicalBioAssayImporter()

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
• InternalIdMethod.INTERNAL_ID
• FallbackIdMethod.NAME_OR_ID

Overrides:

getIdMethods in class AbstractItemImporter<PhysicalBioAssay>

getItemForSubtypes

protected Item getItemForSubtypes()

Description copied from class: AbstractItemImporter

Does the importer want to use item subtypes when importing? If this method returns a non-null, this class will add a parameter in the "Item identification" section that makes it possible to select which subtypes the importer should use to limit the search for existing items. The default implementation returns null.

Overrides:

getItemForSubtypes in class AbstractItemImporter<PhysicalBioAssay>

Returns:

An Item or null

getItemForAnnotationTypes

protected Item getItemForAnnotationTypes()

Enable annotations as item identifier.

Overrides:

getItemForAnnotationTypes in class AbstractItemImporter<PhysicalBioAssay>

Returns:

An Item or null

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<PhysicalBioAssay>

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<PhysicalBioAssay>

Parameters:

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

createItemQuery

protected ItemQuery<PhysicalBioAssay> createItemQuery()

Calls PhysicalBioAssay.getQuery().

Specified by:

createItemQuery in class AbstractItemImporter<PhysicalBioAssay>

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<PhysicalBioAssay>

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 PhysicalBioAssay 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<PhysicalBioAssay>

Parameters:

dc - The DbControl to use for database access

data - The current data line

Returns:

A new item

updateItem

protected void updateItem(DbControl dc,
 PhysicalBioAssay pba,
 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<PhysicalBioAssay>

Parameters:

dc - The DbControl to use for database access

pba - The item to update

data - The current data line

updateMultiLineItem

protected void updateMultiLineItem(DbControl dc,
 PhysicalBioAssay pba,
 FlatFileParser.Data data,
 int multiLineNum)

Add parent extracts and the used quantities

Overrides:

updateMultiLineItem in class AbstractItemImporter<PhysicalBioAssay>

Parameters:

dc - The DbControl to use for database access

pba - 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