Package net.sf.basedb.plugins.batchimport

Class RawBioAssayImporter

java.lang.Object

net.sf.basedb.core.plugin.AbstractPlugin

net.sf.basedb.plugins.AbstractFlatFileImporter

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

net.sf.basedb.plugins.batchimport.RawBioAssayImporter

All Implemented Interfaces:

AutoDetectingImporter, InteractivePlugin, Plugin, SignalTarget, ConfigureByExample

public class RawBioAssayImporter
extends AbstractItemImporter<RawBioAssay>

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

Version:

2.8

Author:

nicklas

Last modified

$Date: 2022-01-13 07:45:03 +0100 (Thu, 13 Jan 2022) $

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 PluginParameter<String>	arrayDesignColumnMapping
private Mapper	arrayDesignMapper
protected static PluginParameter<String>	bioAssayColumnMapping
private Mapper	bioAssayMapper
private String	dataDirectory
private DefaultItemFunction<ArrayDesign>	defaultArrayDesignFunction
private DefaultItemFunction<Protocol>	defaultProtocolFunction
private DefaultItemFunction<Software>	defaultSoftwareFunction
private Mapper	descriptionMapper
protected static PluginParameter<String>	extractColumnMapping
private Mapper	extractMapper
protected static PluginParameter<String>	fileColumnMapping
private Mapper	fileMapper
private Mapper	fileSpotsMapper
protected static PluginParameter<String>	fileSpotsMapping
protected static PluginParameter<String>	fileTypeColumnMapping
private Mapper	fileTypeMapper
private static Set<GuiContext>	guiContexts
private Mapper	nameMapper
protected static PluginParameter<String>	platformColumnMapping
private Mapper	platformMapper
private Mapper	protocolMapper
protected static PluginParameter<String>	rawDataTypeColumnMapping
private Mapper	rawDataTypeMapper
private Mapper	registeredMapper
protected static PluginParameter<String>	softwareColumnMapping
private Mapper	softwareMapper
protected static PluginParameter<String>	variantColumnMapping
private Mapper	variantMapper

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
RawBioAssayImporter()

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	addMoreJobParameters(List<PluginParameter<?>> parameters)	Add parameter for "Data directory" directory where data files may be located.
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 RawBioAssay	createItem(DbControl dc, FlatFileParser.Data data)	Create a new item and populate it with data from the current line.
protected ItemQuery<RawBioAssay>	createItemQuery()	Calls RawBioAssay.getQuery().
protected void	doneWithItem(DbControl dc, RawBioAssay rba, int numMultiLines)	Validate data files if they have been set.
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 void	updateItem(DbControl dc, RawBioAssay rba, FlatFileParser.Data data)	Update an item with data from the current line.
protected void	updateMultiLineItem(DbControl dc, RawBioAssay rba, FlatFileParser.Data data, int multiLineNum)	Add data files

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

addMoreErrorParameters, addMoreParsingParameters, begin, beginData, configure, createItemQuery, 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, 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

platformColumnMapping

protected static final PluginParameter<String> platformColumnMapping

variantColumnMapping

protected static final PluginParameter<String> variantColumnMapping

rawDataTypeColumnMapping

protected static final PluginParameter<String> rawDataTypeColumnMapping

softwareColumnMapping

protected static final PluginParameter<String> softwareColumnMapping

bioAssayColumnMapping

protected static final PluginParameter<String> bioAssayColumnMapping

extractColumnMapping

protected static final PluginParameter<String> extractColumnMapping

arrayDesignColumnMapping

protected static final PluginParameter<String> arrayDesignColumnMapping

fileTypeColumnMapping

protected static final PluginParameter<String> fileTypeColumnMapping

fileColumnMapping

protected static final PluginParameter<String> fileColumnMapping

fileSpotsMapping

protected static final PluginParameter<String> fileSpotsMapping

nameMapper

private Mapper nameMapper

descriptionMapper

private Mapper descriptionMapper

registeredMapper

private Mapper registeredMapper

protocolMapper

private Mapper protocolMapper

defaultProtocolFunction

private DefaultItemFunction<Protocol> defaultProtocolFunction

softwareMapper

private Mapper softwareMapper

defaultSoftwareFunction

private DefaultItemFunction<Software> defaultSoftwareFunction

bioAssayMapper

private Mapper bioAssayMapper

extractMapper

private Mapper extractMapper

arrayDesignMapper

private Mapper arrayDesignMapper

defaultArrayDesignFunction

private DefaultItemFunction<ArrayDesign> defaultArrayDesignFunction

platformMapper

private Mapper platformMapper

variantMapper

private Mapper variantMapper

rawDataTypeMapper

private Mapper rawDataTypeMapper

fileTypeMapper

private Mapper fileTypeMapper

fileMapper

private Mapper fileMapper

fileSpotsMapper

private Mapper fileSpotsMapper

dataDirectory

private String dataDirectory

Constructor Details

RawBioAssayImporter

public RawBioAssayImporter()

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<RawBioAssay>

getItemForAnnotationTypes

protected Item getItemForAnnotationTypes()

Enable annotations as item identifier.

Overrides:

getItemForAnnotationTypes in class AbstractItemImporter<RawBioAssay>

Returns:

An Item or null

addMoreJobParameters

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

Add parameter for "Data directory" directory where data files may be located.

Overrides:

addMoreJobParameters in class AbstractItemImporter<RawBioAssay>

Parameters:

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

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<RawBioAssay>

Parameters:

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

createItemQuery

protected ItemQuery<RawBioAssay> createItemQuery()

Calls RawBioAssay.getQuery().

Specified by:

createItemQuery in class AbstractItemImporter<RawBioAssay>

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<RawBioAssay>

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 RawBioAssay 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<RawBioAssay>

Parameters:

dc - The DbControl to use for database access

data - The current data line

Returns:

A new item

updateItem

protected void updateItem(DbControl dc,
RawBioAssay rba,
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<RawBioAssay>

Parameters:

dc - The DbControl to use for database access

rba - The item to update

data - The current data line

updateMultiLineItem

protected void updateMultiLineItem(DbControl dc,
RawBioAssay rba,
FlatFileParser.Data data,
int multiLineNum)

Add data files

Overrides:

updateMultiLineItem in class AbstractItemImporter<RawBioAssay>

Parameters:

dc - The DbControl to use for database access

rba - 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

doneWithItem

protected void doneWithItem(DbControl dc,
RawBioAssay rba,
int numMultiLines)

Validate data files if they have been set.

Overrides:

doneWithItem in class AbstractItemImporter<RawBioAssay>

Parameters:

dc - The DbControl to use for database access

rba - The item to update

numMultiLines - The number of the multi-line entries, starting with 1 for the first multi-line (0 for single-line entries)