net.sf.basedb.plugins.batchimport
Class ScanImporter

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

All Implemented Interfaces:

AutoDetectingImporter, InteractivePlugin, Plugin, SignalTarget, ConfigureByExample

public class ScanImporter
extends AbstractItemImporter<Scan>

Plug-in for importing scan 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
private Mapper	descriptionMapper
private static Set<GuiContext>	guiContexts
protected static PluginParameter<String>	hardwareColumnMapping
private Mapper	hardwareMapper
protected static PluginParameter<String>	hybridizationColumnMapping
private Mapper	hybridizationMapper
protected static PluginParameter<String>	imageDescriptionColumnMapping
private Mapper	imageDescriptionMapper
protected static PluginParameter<String>	imageFileColumnMapping
private Mapper	imageFileMapper
protected static PluginParameter<String>	imageFormatColumnMapping
private Mapper	imageFormatMapper
protected static PluginParameter<String>	imageNameColumnMapping
private Mapper	imageNameMapper
protected static PluginParameter<String>	imagePreviewColumnMapping
private Mapper	imagePreviewMapper
private String	imagesDirectory
private Mapper	nameMapper
private Mapper	protocolMapper

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

ScanImporter()

Method Summary

protected void	addMoreColumnMappingParameters(List<PluginParameter<?>> parameters) Adds column mappings for name, internalId, description, hybridization, protocol, hardware, image-file, image-name, image-format and image-description.
protected void	addMoreJobParameters(List<PluginParameter<?>> parameters) Add parameter for "Image directory" directory where image 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 Scan	createItem(DbControl dc, FlatFileParser.Data data) Create a new item and populate it with data from the current line.
protected ItemQuery<Scan>	createItemQuery() Calls Scan.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, Scan scan, FlatFileParser.Data data) Update an item with data from the current line.
protected void	updateMultiLineItem(DbControl dc, Scan scan, FlatFileParser.Data data, int multiLineNum) Update an item with data from a multi-line entry.

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

addMoreErrorParameters, 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

hybridizationColumnMapping

protected static final PluginParameter<String> hybridizationColumnMapping

imageFileColumnMapping

protected static final PluginParameter<String> imageFileColumnMapping

imageNameColumnMapping

protected static final PluginParameter<String> imageNameColumnMapping

imageFormatColumnMapping

protected static final PluginParameter<String> imageFormatColumnMapping

imagePreviewColumnMapping

protected static final PluginParameter<String> imagePreviewColumnMapping

imageDescriptionColumnMapping

protected static final PluginParameter<String> imageDescriptionColumnMapping

nameMapper

private Mapper nameMapper

descriptionMapper

private Mapper descriptionMapper

protocolMapper

private Mapper protocolMapper

hardwareMapper

private Mapper hardwareMapper

hybridizationMapper

private Mapper hybridizationMapper

imageFileMapper

private Mapper imageFileMapper

imageNameMapper

private Mapper imageNameMapper

imageFormatMapper

private Mapper imageFormatMapper

imagePreviewMapper

private Mapper imagePreviewMapper

imageDescriptionMapper

private Mapper imageDescriptionMapper

imagesDirectory

private String imagesDirectory

Constructor Detail

ScanImporter

public ScanImporter()

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<Scan>

addMoreColumnMappingParameters

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

Adds column mappings for name, internalId, description, hybridization, protocol, hardware, image-file, image-name, image-format and image-description.

Overrides:

addMoreColumnMappingParameters in class AbstractItemImporter<Scan>

Parameters:

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

addMoreJobParameters

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

Add parameter for "Image directory" directory where image files may be located.

Overrides:

addMoreJobParameters in class AbstractItemImporter<Scan>

Parameters:

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

createItemQuery

protected ItemQuery<Scan> createItemQuery()

Calls Scan.getQuery().

Specified by:

createItemQuery in class AbstractItemImporter<Scan>

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<Scan>

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 Scan 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<Scan>

Parameters:

dc - The DbControl to use for database access

data - The current data line

Returns:

A new item

updateItem

protected void updateItem(DbControl dc,
                          Scan scan,
                          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<Scan>

Parameters:

dc - The DbControl to use for database access

scan - The item to update

data - The current data line

updateMultiLineItem

protected void updateMultiLineItem(DbControl dc,
                                   Scan scan,
                                   FlatFileParser.Data data,
                                   int multiLineNum)

Description copied from class: AbstractItemImporter

Update an item with data from a multi-line entry. Items which can have multiple parents should have data for the other parents on lines following the first line.

Overrides:

updateMultiLineItem in class AbstractItemImporter<Scan>

Parameters:

dc - The DbControl to use for database access

scan - 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