Package net.sf.basedb.plugins.batchimport

Class SampleImporter

java.lang.Object

net.sf.basedb.core.plugin.AbstractPlugin

net.sf.basedb.plugins.AbstractFlatFileImporter

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

net.sf.basedb.plugins.batchimport.SampleImporter

All Implemented Interfaces:

AutoDetectingImporter, InteractivePlugin, Plugin, SignalTarget, ConfigureByExample

public class SampleImporter
extends AbstractItemImporter<Sample>

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

Version:

2.8

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>	bioPlateColumnMapping	Column mapping parameter for the bioplate
private Mapper	bioPlateMapper
protected static final PluginParameter<String>	bioWellColColumnMapping	Column mapping parameter for the biowell's column
private Mapper	bioWellColMapper
protected static final PluginParameter<String>	bioWellRowColumnMapping	Column mapping parameter for the biowell's row
private Mapper	bioWellRowMapper
protected static final PluginParameter<String>	createdColumnMapping	Column mapping parameter for the sample creation date.
private Mapper	createdMapper
private DefaultItemFunction<Protocol>	defaultPrototolFunction
private Mapper	descriptionMapper
private Mapper	externalIdMapper
private static final Set<GuiContext>	guiContexts
private Mapper	kitMapper
private Mapper	nameMapper
protected static final PluginParameter<String>	originalQuantityColumnMapping	Column mapping parameter for the original quantity.
private Mapper	originalQuantityMapper
protected static final PluginParameter<String>	parentColumnMapping	Column mapping parameter for the parent (biosource OR sample)
private Mapper	parentMapper
protected static final PluginParameter<String>	parentTypeColumnMapping	Column mapping parameter for the parent type.
private Mapper	parentTypeMapper
private Mapper	protocolMapper
private Mapper	registeredMapper
protected static final PluginParameter<String>	usedQuantityColumnMapping	Column mapping parameter for the used quantity from the parent.
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
SampleImporter()

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	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 Sample	createItem(DbControl dc, FlatFileParser.Data data)	Create a new item and populate it with data from the current line.
protected ItemQuery<Sample>	createItemQuery()	Calls Sample.getQuery().
Set<GuiContext>	getGuiContexts()	Get a set containing all items that the plugin handles.
protected IdMethod[]	getIdMethods()	Useable methods are: PropertyIdMethod.NAME PropertyIdMethod.EXTERNAL_ID 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, Sample sample, FlatFileParser.Data data)	Update an item with data from the current line.
protected void	updateMultiLineItem(DbControl dc, Sample sample, FlatFileParser.Data data, int multiLineNum)	If the sample is pooled, add the parent sample.

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, 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

createdColumnMapping

protected static final PluginParameter<String> createdColumnMapping

Column mapping parameter for the sample creation date.

originalQuantityColumnMapping

protected static final PluginParameter<String> originalQuantityColumnMapping

Column mapping parameter for the original quantity.

parentTypeColumnMapping

protected static final PluginParameter<String> parentTypeColumnMapping

Column mapping parameter for the parent type.

parentColumnMapping

protected static final PluginParameter<String> parentColumnMapping

Column mapping parameter for the parent (biosource OR sample)

usedQuantityColumnMapping

protected static final PluginParameter<String> usedQuantityColumnMapping

Column mapping parameter for the used quantity from the parent.

bioPlateColumnMapping

protected static final PluginParameter<String> bioPlateColumnMapping

Column mapping parameter for the bioplate

bioWellRowColumnMapping

protected static final PluginParameter<String> bioWellRowColumnMapping

Column mapping parameter for the biowell's row

bioWellColColumnMapping

protected static final PluginParameter<String> bioWellColColumnMapping

Column mapping parameter for the biowell's column

nameMapper

private Mapper nameMapper

descriptionMapper

private Mapper descriptionMapper

externalIdMapper

private Mapper externalIdMapper

originalQuantityMapper

private Mapper originalQuantityMapper

createdMapper

private Mapper createdMapper

registeredMapper

private Mapper registeredMapper

protocolMapper

private Mapper protocolMapper

kitMapper

private Mapper kitMapper

defaultPrototolFunction

private DefaultItemFunction<Protocol> defaultPrototolFunction

parentTypeMapper

private Mapper parentTypeMapper

parentMapper

private Mapper parentMapper

usedQuantityMapper

private UsedQuantityMapper usedQuantityMapper

bioPlateMapper

private Mapper bioPlateMapper

bioWellRowMapper

private Mapper bioWellRowMapper

bioWellColMapper

private Mapper bioWellColMapper

Constructor Details

SampleImporter

public SampleImporter()

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.EXTERNAL_ID
• InternalIdMethod.INTERNAL_ID
• FallbackIdMethod.NAME_OR_ID

Overrides:

getIdMethods in class AbstractItemImporter<Sample>

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<Sample>

Returns:

An Item or null

getItemForAnnotationTypes

protected Item getItemForAnnotationTypes()

Enable annotations as item identifier.

Overrides:

getItemForAnnotationTypes in class AbstractItemImporter<Sample>

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<Sample>

Parameters:

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

createItemQuery

protected ItemQuery<Sample> createItemQuery()

Calls Sample.getQuery().

Specified by:

createItemQuery in class AbstractItemImporter<Sample>

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<Sample>

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 Sample 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<Sample>

Parameters:

dc - The DbControl to use for database access

data - The current data line

Returns:

A new item

updateItem

protected void updateItem(DbControl dc,
 Sample sample,
 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<Sample>

Parameters:

dc - The DbControl to use for database access

sample - The item to update

data - The current data line

updateMultiLineItem

protected void updateMultiLineItem(DbControl dc,
 Sample sample,
 FlatFileParser.Data data,
 int multiLineNum)

If the sample is pooled, add the parent sample.

Overrides:

updateMultiLineItem in class AbstractItemImporter<Sample>

Parameters:

dc - The DbControl to use for database access

sample - 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