Class BioPlateImporter
- java.lang.Object
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- net.sf.basedb.core.plugin.AbstractPlugin
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- net.sf.basedb.plugins.AbstractFlatFileImporter
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- net.sf.basedb.plugins.batchimport.AbstractItemImporter<BioPlate>
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- net.sf.basedb.plugins.batchimport.BioPlateImporter
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- All Implemented Interfaces:
AutoDetectingImporter
,InteractivePlugin
,Plugin
,SignalTarget
,ConfigureByExample
public class BioPlateImporter extends AbstractItemImporter<BioPlate>
Plug-in for importing bioplate items in a batch. The plug-in can create new items and updated existing items.- Since:
- 2.16
- Author:
- nicklas
- Last modified
- $Date: 2019-03-21 08:45:42 +0100 (tors, 21 mars 2019) $
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Nested Class Summary
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Nested classes/interfaces inherited from interface net.sf.basedb.core.plugin.Plugin
Plugin.MainType
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Field Summary
Fields Modifier and Type Field Description protected static PluginParameter<String>
barcodeColumnMapping
private Mapper
barcodeMapper
protected static PluginParameter<String>
bioPlateTypeColumnMapping
private Mapper
bioPlateTypeMapper
private Mapper
createdMapper
private DefaultItemFunction<Hardware>
defaultHardwareFunction
private Mapper
descriptionMapper
private static Set<GuiContext>
guiContexts
protected static PluginParameter<String>
hardwareColumnMapping
private Mapper
hardwareMapper
private Mapper
nameMapper
protected static PluginParameter<String>
plateGeometryColumnMapping
private Mapper
plateGeometryMapper
protected static PluginParameter<String>
positionColumnMapping
private Mapper
positionMapper
private Mapper
registeredMapper
protected static PluginParameter<String>
sectionColumnMapping
private Mapper
sectionMapper
protected static PluginParameter<String>
trayColumnMapping
private Mapper
trayMapper
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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
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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
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Fields inherited from class net.sf.basedb.core.plugin.AbstractPlugin
annotationSection, configuration, COPY_ANNOTATIONS, job, OVERWRITE_ANNOTATIONS, sc
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Constructor Summary
Constructors Constructor Description BioPlateImporter()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description protected void
addMoreColumnMappingParameters(List<PluginParameter<?>> parameters)
Adds column mappings for name, description, plate type, plate geometry, barcode and freezer.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 theffp
FlatFileParser
.protected BioPlate
createItem(DbControl dc, FlatFileParser.Data data)
Create a new item and populate it with data from the current line.protected ItemQuery<BioPlate>
createItemQuery()
CallsBioPlate.getQuery()
.Set<GuiContext>
getGuiContexts()
Get a set containing all items that the plugin handles.protected IdMethod[]
getIdMethods()
protected Item
getItemForAnnotationTypes()
Enable annotations as item identifier.protected void
updateItem(DbControl dc, BioPlate plate, FlatFileParser.Data data)
Update an item with data from the current line.-
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, getInitializedFlatFileParser, getItemForSubtypes, getProjectDefaultPlatform, getProjectDefaultRawDataType, getProjectDefaultVariant, getRequestInformation, getSuccessMessage, handleData, initReferenceQuery, isInContext, parseDate, requiresConfiguration, setOrAddFile, setUpErrorHandling, supportsConfigurations, updateItemSubtype, updateMultiLineItem, updatePermissions
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Methods inherited from class net.sf.basedb.plugins.AbstractFlatFileImporter
addErrorHandler, checkColumnMapping, checkColumnMapping, continueWithNextFileAfterError, doImport, finish, getCharset, getCharset, getDateFormatter, getDecimalSeparator, getErrorHandler, getErrorOption, getFileIterator, getInitializedFlatFileParser, getMainType, getMapper, getMapper, getNumberFormat, getNumBytes, getPattern, getProgress, getSignalHandler, getTimestampFormatter, getTotalFileSize, handleHeader, handleSection, isImportable, isImportable, log, log, log, log, run, start, wrapInputStream
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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
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Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
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Methods inherited from interface net.sf.basedb.core.plugin.Plugin
done, getMainType, getPermissions, init, run
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Field Detail
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guiContexts
private static final Set<GuiContext> guiContexts
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bioPlateTypeColumnMapping
protected static final PluginParameter<String> bioPlateTypeColumnMapping
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plateGeometryColumnMapping
protected static final PluginParameter<String> plateGeometryColumnMapping
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hardwareColumnMapping
protected static final PluginParameter<String> hardwareColumnMapping
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sectionColumnMapping
protected static final PluginParameter<String> sectionColumnMapping
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trayColumnMapping
protected static final PluginParameter<String> trayColumnMapping
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positionColumnMapping
protected static final PluginParameter<String> positionColumnMapping
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barcodeColumnMapping
protected static final PluginParameter<String> barcodeColumnMapping
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nameMapper
private Mapper nameMapper
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descriptionMapper
private Mapper descriptionMapper
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bioPlateTypeMapper
private Mapper bioPlateTypeMapper
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plateGeometryMapper
private Mapper plateGeometryMapper
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createdMapper
private Mapper createdMapper
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registeredMapper
private Mapper registeredMapper
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hardwareMapper
private Mapper hardwareMapper
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defaultHardwareFunction
private DefaultItemFunction<Hardware> defaultHardwareFunction
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sectionMapper
private Mapper sectionMapper
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trayMapper
private Mapper trayMapper
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positionMapper
private Mapper positionMapper
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barcodeMapper
private Mapper barcodeMapper
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Method Detail
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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 containingItem.REPORTER
. This information is used by client applications to put the plugin in the proper place in the user interface.- Returns:
- A
Set
containingItem
:s, or null if the plugin is not concerned about items
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getIdMethods
protected IdMethod[] getIdMethods()
Useable methods are:- Overrides:
getIdMethods
in classAbstractItemImporter<BioPlate>
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getItemForAnnotationTypes
protected Item getItemForAnnotationTypes()
Enable annotations as item identifier.- Overrides:
getItemForAnnotationTypes
in classAbstractItemImporter<BioPlate>
- Returns:
- An Item or null
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addMoreColumnMappingParameters
protected void addMoreColumnMappingParameters(List<PluginParameter<?>> parameters)
Adds column mappings for name, description, plate type, plate geometry, barcode and freezer.- Overrides:
addMoreColumnMappingParameters
in classAbstractItemImporter<BioPlate>
- Parameters:
parameters
- The list of parameters to add the column mapping parameters to
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createItemQuery
protected ItemQuery<BioPlate> createItemQuery()
CallsBioPlate.getQuery()
.- Specified by:
createItemQuery
in classAbstractItemImporter<BioPlate>
- Returns:
- A query
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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 theffp
FlatFileParser
. This method is called during initialisation of the plug-in when theFlatFileParser.parseHeaders()
has successfully found the start of data. Use theAbstractFlatFileImporter.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 classAbstractItemImporter<BioPlate>
- Parameters:
ffp
- The parser that is parsing the data filecropStrings
- If strings that are too long to fit in the database should be cropped or not (=generate an error)
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createItem
protected BioPlate 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 callDbControl.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 classAbstractItemImporter<BioPlate>
- Parameters:
dc
- The DbControl to use for database accessdata
- The current data line- Returns:
- A new item
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updateItem
protected void updateItem(DbControl dc, BioPlate plate, 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 classAbstractItemImporter<BioPlate>
- Parameters:
dc
- The DbControl to use for database accessplate
- The item to updatedata
- The current data line
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