Class PhysicalBioAssayImporter
java.lang.Object
net.sf.basedb.core.plugin.AbstractPlugin
net.sf.basedb.plugins.AbstractFlatFileImporter
net.sf.basedb.plugins.batchimport.AbstractItemImporter<PhysicalBioAssay>
net.sf.basedb.plugins.batchimport.PhysicalBioAssayImporter
- All Implemented Interfaces:
AutoDetectingImporter
,InteractivePlugin
,Plugin
,SignalTarget
,ConfigureByExample
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: 2021-12-09 13:52:23 +0100 (Thu, 09 Dec 2021) $
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Nested Class Summary
Nested classes/interfaces inherited from interface net.sf.basedb.core.plugin.Plugin
Plugin.MainType
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Field Summary
Modifier and TypeFieldDescriptionprotected static final PluginParameter<String>
private Mapper
private Mapper
private DefaultItemFunction<Hardware>
private DefaultItemFunction<Protocol>
private Mapper
protected static final PluginParameter<String>
private Mapper
private boolean
private static final Set<GuiContext>
protected static final PluginParameter<String>
private Mapper
private Mapper
private static final PluginParameter<String>
private Mapper
private Mapper
private Mapper
private Mapper
protected static final PluginParameter<String>
private Mapper
private 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
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Constructor Summary
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Method Summary
Modifier and TypeMethodDescriptionprotected 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 theffp
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>
CallsPhysicalBioAssay.getQuery()
.Get a set containing all items that the plugin handles.protected IdMethod[]
protected Item
Enable annotations as item identifier.protected Item
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 quantitiesMethods inherited from class net.sf.basedb.plugins.batchimport.AbstractItemImporter
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
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Field Details
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guiContexts
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hardwareColumnMapping
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arraySlideColumnMapping
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sizeColumnMapping
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extractPositionColumnMapping
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multiplePositionsError
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nameMapper
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descriptionMapper
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sizeMapper
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createdMapper
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registeredMapper
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protocolMapper
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defaultProtocolFunction
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hardwareMapper
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defaultHardwareFunction
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kitMapper
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parentMapper
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usedQuantityMapper
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extractPositionMapper
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arraySlideMapper
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failIfMultiplePositions
private boolean failIfMultiplePositions
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Constructor Details
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PhysicalBioAssayImporter
public PhysicalBioAssayImporter()
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Method Details
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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
Useable methods are:- Overrides:
getIdMethods
in classAbstractItemImporter<PhysicalBioAssay>
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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 classAbstractItemImporter<PhysicalBioAssay>
- Returns:
- An Item or null
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getItemForAnnotationTypes
Enable annotations as item identifier.- Overrides:
getItemForAnnotationTypes
in classAbstractItemImporter<PhysicalBioAssay>
- Returns:
- An Item or null
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addMoreColumnMappingParameters
Adds column mappings for name, externalId, description, protocol, creation date, original quantity, pooled, parent and used quantity from parent.- Overrides:
addMoreColumnMappingParameters
in classAbstractItemImporter<PhysicalBioAssay>
- Parameters:
parameters
- The list of parameters to add the column mapping parameters to
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addMoreErrorParameters
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 classAbstractItemImporter<PhysicalBioAssay>
- Parameters:
parameters
- The list of parameters to add the column mapping parameters to
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createItemQuery
CallsPhysicalBioAssay.getQuery()
.- Specified by:
createItemQuery
in classAbstractItemImporter<PhysicalBioAssay>
- Returns:
- A query
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createColumnMappers
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<PhysicalBioAssay>
- 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
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<PhysicalBioAssay>
- Parameters:
dc
- The DbControl to use for database accessdata
- The current data line- Returns:
- A new item
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updateItem
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<PhysicalBioAssay>
- Parameters:
dc
- The DbControl to use for database accesspba
- The item to updatedata
- The current data line
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updateMultiLineItem
protected void updateMultiLineItem(DbControl dc, PhysicalBioAssay pba, FlatFileParser.Data data, int multiLineNum) Add parent extracts and the used quantities- Overrides:
updateMultiLineItem
in classAbstractItemImporter<PhysicalBioAssay>
- Parameters:
dc
- The DbControl to use for database accesspba
- The item to updatedata
- The current data linemultiLineNum
- The number of the multi-line entry, starting with 1 for the first multi-line
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