Class SampleImporter
java.lang.Object
net.sf.basedb.core.plugin.AbstractPlugin
net.sf.basedb.plugins.AbstractFlatFileImporter
net.sf.basedb.plugins.batchimport.AbstractItemImporter<Sample>
net.sf.basedb.plugins.batchimport.SampleImporter
- All Implemented Interfaces:
AutoDetectingImporter
,InteractivePlugin
,Plugin
,SignalTarget
,ConfigureByExample
Plug-in for importing sample items in a batch. The plug-in can create new
items and updated existing items.
- Version:
- 2.8
- Author:
- nicklas
- Last modified
- $Date: 2021-12-09 13:52:23 +0100 (Thu, 09 Dec 2021) $
-
Nested Class Summary
Nested classes/interfaces inherited from interface net.sf.basedb.core.plugin.Plugin
Plugin.MainType
-
Field Summary
Modifier and TypeFieldDescriptionprotected static final PluginParameter<String>
Column mapping parameter for the bioplateprivate Mapper
protected static final PluginParameter<String>
Column mapping parameter for the biowell's columnprivate Mapper
protected static final PluginParameter<String>
Column mapping parameter for the biowell's rowprivate Mapper
protected static final PluginParameter<String>
Column mapping parameter for the sample creation date.private Mapper
private DefaultItemFunction<Protocol>
private Mapper
private Mapper
private static final Set<GuiContext>
private Mapper
private Mapper
protected static final PluginParameter<String>
Column mapping parameter for the original quantity.private Mapper
protected static final PluginParameter<String>
Column mapping parameter for the parent (biosource OR sample)private Mapper
protected static final PluginParameter<String>
Column mapping parameter for the parent type.private Mapper
private Mapper
private Mapper
protected static final PluginParameter<String>
Column mapping parameter for the used quantity from the parent.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
-
Constructor Summary
-
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
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 Sample
createItem
(DbControl dc, FlatFileParser.Data data) Create a new item and populate it with data from the current line.CallsSample.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, Sample sample, FlatFileParser.Data data) Update an item with data from the current line.protected void
updateMultiLineItem
(DbControl dc, Sample sample, FlatFileParser.Data data, int multiLineNum) If the sample is pooled, add the parent sample.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, 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
-
Field Details
-
guiContexts
-
createdColumnMapping
Column mapping parameter for the sample creation date. -
originalQuantityColumnMapping
Column mapping parameter for the original quantity. -
parentTypeColumnMapping
Column mapping parameter for the parent type. -
parentColumnMapping
Column mapping parameter for the parent (biosource OR sample) -
usedQuantityColumnMapping
Column mapping parameter for the used quantity from the parent. -
bioPlateColumnMapping
Column mapping parameter for the bioplate -
bioWellRowColumnMapping
Column mapping parameter for the biowell's row -
bioWellColColumnMapping
Column mapping parameter for the biowell's column -
nameMapper
-
descriptionMapper
-
externalIdMapper
-
originalQuantityMapper
-
createdMapper
-
registeredMapper
-
protocolMapper
-
kitMapper
-
defaultPrototolFunction
-
parentTypeMapper
-
parentMapper
-
usedQuantityMapper
-
bioPlateMapper
-
bioWellRowMapper
-
bioWellColMapper
-
-
Constructor Details
-
SampleImporter
public SampleImporter()
-
-
Method Details
-
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
-
getIdMethods
Useable methods are:- Overrides:
getIdMethods
in classAbstractItemImporter<Sample>
-
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<Sample>
- Returns:
- An Item or null
-
getItemForAnnotationTypes
Enable annotations as item identifier.- Overrides:
getItemForAnnotationTypes
in classAbstractItemImporter<Sample>
- Returns:
- An Item or null
-
addMoreColumnMappingParameters
Adds column mappings for name, externalId, description, protocol, creation date, original quantity, pooled, parent and used quantity from parent.- Overrides:
addMoreColumnMappingParameters
in classAbstractItemImporter<Sample>
- Parameters:
parameters
- The list of parameters to add the column mapping parameters to
-
createItemQuery
CallsSample.getQuery()
.- Specified by:
createItemQuery
in classAbstractItemImporter<Sample>
- Returns:
- A query
-
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<Sample>
- 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)
-
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<Sample>
- Parameters:
dc
- The DbControl to use for database accessdata
- The current data line- Returns:
- A new item
-
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<Sample>
- Parameters:
dc
- The DbControl to use for database accesssample
- The item to updatedata
- The current data line
-
updateMultiLineItem
protected void updateMultiLineItem(DbControl dc, Sample sample, FlatFileParser.Data data, int multiLineNum) If the sample is pooled, add the parent sample.- Overrides:
updateMultiLineItem
in classAbstractItemImporter<Sample>
- Parameters:
dc
- The DbControl to use for database accesssample
- The item to updatedata
- The current data linemultiLineNum
- The number of the multi-line entry, starting with 1 for the first multi-line
-