3.2.4: 2013-12-06

net.sf.basedb.plugins.batchimport
Class PhysicalBioAssayImporter

java.lang.Object
  extended by net.sf.basedb.core.plugin.AbstractPlugin
      extended by net.sf.basedb.plugins.AbstractFlatFileImporter
          extended by net.sf.basedb.plugins.batchimport.AbstractItemImporter<PhysicalBioAssay>
              extended by 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: 2011-12-06 09:17:37 +0100 (Tue, 06 Dec 2011) $

Nested Class Summary
 
Nested classes/interfaces inherited from interface net.sf.basedb.core.plugin.Plugin
Plugin.MainType
 
Field Summary
protected static PluginParameter<String> arraySlideColumnMapping
           
private  Mapper arraySlideMapper
           
private  Mapper createdMapper
           
private  DefaultItemFunction<Hardware> defaultHardwareFunction
           
private  DefaultItemFunction<Protocol> defaultProtocolFunction
           
private  Mapper descriptionMapper
           
protected static PluginParameter<String> extractPositionColumnMapping
           
private  Mapper extractPositionMapper
           
private  boolean failIfMultiplePositions
           
private static Set<GuiContext> guiContexts
           
protected static PluginParameter<String> hardwareColumnMapping
           
private  Mapper hardwareMapper
           
private static PluginParameter<String> multiplePositionsError
           
private  Mapper nameMapper
           
private  Mapper parentMapper
           
private  Mapper protocolMapper
           
protected static PluginParameter<String> sizeColumnMapping
           
private  Mapper sizeMapper
           
private  Mapper usedQuantityMapper
           
 
Fields inherited from class net.sf.basedb.plugins.batchimport.AbstractItemImporter
defaultsSection, descriptionColumnMapping, externalIdColumnMapping, identificationSection, internalIdColumnMapping, nameColumnMapping, optionalColumnMapping, permissionTemplateColumnMapping, protocolColumnMapping, requiredColumnMapping, subtypeColumnMapping
 
Fields inherited from class net.sf.basedb.plugins.AbstractFlatFileImporter
complexMappings, dataFooterRegexpParameter, dataHeaderRegexpParameter, dataSplitterRegexpParameter, 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
PhysicalBioAssayImporter()
           
 
Method Summary
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 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, doneWithItem, end, findArrayBatch, findArrayDesign, findArraySlide, findBioPlate, findBioPlateType, findBioSource, findBioSource, findBioWell, findDataFileType, findDerivedBioAssay, findExtract, findExtract, findHardware, findHardware, findHybridization, findItemSubtype, findItemSubtype, findLabeledExtract, findPermissionTemplate, findPhysicalBioAssay, findPlateGeometry, findPlatform, findProtocol, findProtocol, findRawDataType, findReferencedItem, findReferencedItemWithSubtype, findSample, findSample, findSoftware, findSoftware, findTag, findTag, findVariant, getConfigureOptionsParameters, getConfigureParserParameters, getDefaultItemFunction, getIdMethod, getInitializedFlatFileParser, getInitializedFlatFileParser, 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, getDecimalSeparator, getErrorHandler, getErrorOption, getFileIterator, getMainType, getMapper, getMapper, getNumberFormat, getNumBytes, getProgress, getSignalHandler, 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, 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

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

protocolMapper

private Mapper protocolMapper

defaultProtocolFunction

private DefaultItemFunction<Protocol> defaultProtocolFunction

hardwareMapper

private Mapper hardwareMapper

defaultHardwareFunction

private DefaultItemFunction<Hardware> defaultHardwareFunction

parentMapper

private Mapper parentMapper

usedQuantityMapper

private Mapper usedQuantityMapper

extractPositionMapper

private Mapper extractPositionMapper

arraySlideMapper

private Mapper arraySlideMapper

failIfMultiplePositions

private boolean failIfMultiplePositions
Constructor Detail

PhysicalBioAssayImporter

public PhysicalBioAssayImporter()
Method Detail

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:

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

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

3.2.4: 2013-12-06