Class RawBioAssayImporter
- 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<RawBioAssay>
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- net.sf.basedb.plugins.batchimport.RawBioAssayImporter
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- All Implemented Interfaces:
AutoDetectingImporter
,InteractivePlugin
,Plugin
,SignalTarget
,ConfigureByExample
public class RawBioAssayImporter extends AbstractItemImporter<RawBioAssay>
Plug-in for importing raw bioassay items in a batch. The plug-in can create new items and updated existing items.- Version:
- 2.8
- 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
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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 RawBioAssayImporter()
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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, externalId, description, protocol, creation date, original quantity, pooled, parent and used quantity from parent.protected void
addMoreJobParameters(List<PluginParameter<?>> parameters)
Add parameter for "Data directory" directory where data 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 theffp
FlatFileParser
.protected RawBioAssay
createItem(DbControl dc, FlatFileParser.Data data)
Create a new item and populate it with data from the current line.protected ItemQuery<RawBioAssay>
createItemQuery()
CallsRawBioAssay.getQuery()
.protected void
doneWithItem(DbControl dc, RawBioAssay rba, int numMultiLines)
Validate data files if they have been set.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, RawBioAssay rba, FlatFileParser.Data data)
Update an item with data from the current line.protected void
updateMultiLineItem(DbControl dc, RawBioAssay rba, FlatFileParser.Data data, int multiLineNum)
Add data files-
Methods inherited from class net.sf.basedb.plugins.batchimport.AbstractItemImporter
addMoreErrorParameters, addMoreParsingParameters, begin, beginData, configure, createItemQuery, 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, 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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platformColumnMapping
protected static final PluginParameter<String> platformColumnMapping
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variantColumnMapping
protected static final PluginParameter<String> variantColumnMapping
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rawDataTypeColumnMapping
protected static final PluginParameter<String> rawDataTypeColumnMapping
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softwareColumnMapping
protected static final PluginParameter<String> softwareColumnMapping
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bioAssayColumnMapping
protected static final PluginParameter<String> bioAssayColumnMapping
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extractColumnMapping
protected static final PluginParameter<String> extractColumnMapping
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arrayDesignColumnMapping
protected static final PluginParameter<String> arrayDesignColumnMapping
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fileTypeColumnMapping
protected static final PluginParameter<String> fileTypeColumnMapping
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fileColumnMapping
protected static final PluginParameter<String> fileColumnMapping
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nameMapper
private Mapper nameMapper
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descriptionMapper
private Mapper descriptionMapper
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registeredMapper
private Mapper registeredMapper
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protocolMapper
private Mapper protocolMapper
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defaultProtocolFunction
private DefaultItemFunction<Protocol> defaultProtocolFunction
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softwareMapper
private Mapper softwareMapper
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defaultSoftwareFunction
private DefaultItemFunction<Software> defaultSoftwareFunction
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bioAssayMapper
private Mapper bioAssayMapper
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extractMapper
private Mapper extractMapper
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arrayDesignMapper
private Mapper arrayDesignMapper
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defaultArrayDesignFunction
private DefaultItemFunction<ArrayDesign> defaultArrayDesignFunction
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platformMapper
private Mapper platformMapper
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variantMapper
private Mapper variantMapper
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rawDataTypeMapper
private Mapper rawDataTypeMapper
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fileTypeMapper
private Mapper fileTypeMapper
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fileMapper
private Mapper fileMapper
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dataDirectory
private String dataDirectory
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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<RawBioAssay>
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getItemForAnnotationTypes
protected Item getItemForAnnotationTypes()
Enable annotations as item identifier.- Overrides:
getItemForAnnotationTypes
in classAbstractItemImporter<RawBioAssay>
- Returns:
- An Item or null
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addMoreJobParameters
protected void addMoreJobParameters(List<PluginParameter<?>> parameters)
Add parameter for "Data directory" directory where data files may be located.- Overrides:
addMoreJobParameters
in classAbstractItemImporter<RawBioAssay>
- Parameters:
parameters
- The list of parameters to add the column mapping parameters to
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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 classAbstractItemImporter<RawBioAssay>
- Parameters:
parameters
- The list of parameters to add the column mapping parameters to
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createItemQuery
protected ItemQuery<RawBioAssay> createItemQuery()
CallsRawBioAssay.getQuery()
.- Specified by:
createItemQuery
in classAbstractItemImporter<RawBioAssay>
- 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<RawBioAssay>
- 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 RawBioAssay 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<RawBioAssay>
- 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, RawBioAssay rba, 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<RawBioAssay>
- Parameters:
dc
- The DbControl to use for database accessrba
- The item to updatedata
- The current data line
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updateMultiLineItem
protected void updateMultiLineItem(DbControl dc, RawBioAssay rba, FlatFileParser.Data data, int multiLineNum)
Add data files- Overrides:
updateMultiLineItem
in classAbstractItemImporter<RawBioAssay>
- Parameters:
dc
- The DbControl to use for database accessrba
- 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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doneWithItem
protected void doneWithItem(DbControl dc, RawBioAssay rba, int numMultiLines)
Validate data files if they have been set.- Overrides:
doneWithItem
in classAbstractItemImporter<RawBioAssay>
- Parameters:
dc
- The DbControl to use for database accessrba
- The item to updatenumMultiLines
- The number of the multi-line entries, starting with 1 for the first multi-line (0 for single-line entries)
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