net.sf.basedb.plugins.batchimport.SampleImporter

All Implemented Interfaces:: AutoDetectingImporter, InteractivePlugin, Plugin, SignalTarget, ConfigureByExample

public class SampleImporter
extends AbstractItemImporter<Sample>

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

Fields
Modifier and Type	Field	Description
`protected static PluginParameter<String>`	`bioPlateColumnMapping`	Column mapping parameter for the bioplate
`private Mapper`	`bioPlateMapper`
`protected static PluginParameter<String>`	`bioWellColColumnMapping`	Column mapping parameter for the biowell's column
`private Mapper`	`bioWellColMapper`
`protected static PluginParameter<String>`	`bioWellRowColumnMapping`	Column mapping parameter for the biowell's row
`private Mapper`	`bioWellRowMapper`
`protected static PluginParameter<String>`	`createdColumnMapping`	Column mapping parameter for the sample creation date.
`private Mapper`	`createdMapper`
`private DefaultItemFunction<Protocol>`	`defaultPrototolFunction`
`private Mapper`	`descriptionMapper`
`private Mapper`	`externalIdMapper`
`private static Set<GuiContext>`	`guiContexts`
`private Mapper`	`kitMapper`
`private Mapper`	`nameMapper`
`protected static PluginParameter<String>`	`originalQuantityColumnMapping`	Column mapping parameter for the original quantity.
`private Mapper`	`originalQuantityMapper`
`protected static PluginParameter<String>`	`parentColumnMapping`	Column mapping parameter for the parent (biosource OR sample)
`private Mapper`	`parentMapper`
`protected static PluginParameter<String>`	`parentTypeColumnMapping`	Column mapping parameter for the parent type.
`private Mapper`	`parentTypeMapper`
`private Mapper`	`protocolMapper`
`private Mapper`	`registeredMapper`
`protected static PluginParameter<String>`	`usedQuantityColumnMapping`	Column mapping parameter for the used quantity from the parent.
`private UsedQuantityMapper`	`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

Constructors

Constructor Description

SampleImporter()

Method Summary

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`	`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 Sample`	`createItem(DbControl dc, FlatFileParser.Data data)`	Create a new item and populate it with data from the current line.
`protected ItemQuery<Sample>`	`createItemQuery()`	Calls `Sample.getQuery()`.
`Set<GuiContext>`	`getGuiContexts()`	Get a set containing all items that the plugin handles.
`protected IdMethod[]`	`getIdMethods()`	Useable methods are: `PropertyIdMethod.NAME` `PropertyIdMethod.EXTERNAL_ID` `InternalIdMethod.INTERNAL_ID` `FallbackIdMethod.NAME_OR_ID`
`protected Item`	`getItemForAnnotationTypes()`	Enable annotations as item identifier.
`protected Item`	`getItemForSubtypes()`	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
  
  private static final Set<GuiContext> guiContexts
- createdColumnMapping
  
  protected static final PluginParameter<String> createdColumnMapping
  
  Column mapping parameter for the sample creation date.
- originalQuantityColumnMapping
  
  protected static final PluginParameter<String> originalQuantityColumnMapping
  
  Column mapping parameter for the original quantity.
- parentTypeColumnMapping
  
  protected static final PluginParameter<String> parentTypeColumnMapping
  
  Column mapping parameter for the parent type.
- parentColumnMapping
  
  protected static final PluginParameter<String> parentColumnMapping
  
  Column mapping parameter for the parent (biosource OR sample)
- usedQuantityColumnMapping
  
  protected static final PluginParameter<String> usedQuantityColumnMapping
  
  Column mapping parameter for the used quantity from the parent.
- bioPlateColumnMapping
  
  protected static final PluginParameter<String> bioPlateColumnMapping
  
  Column mapping parameter for the bioplate
- bioWellRowColumnMapping
  
  protected static final PluginParameter<String> bioWellRowColumnMapping
  
  Column mapping parameter for the biowell's row
- bioWellColColumnMapping
  
  protected static final PluginParameter<String> bioWellColColumnMapping
  
  Column mapping parameter for the biowell's column
- nameMapper
  
  private Mapper nameMapper
- descriptionMapper
  
  private Mapper descriptionMapper
- externalIdMapper
  
  private Mapper externalIdMapper
- originalQuantityMapper
  
  private Mapper originalQuantityMapper
- createdMapper
  
  private Mapper createdMapper
- registeredMapper
  
  private Mapper registeredMapper
- protocolMapper
  
  private Mapper protocolMapper
- kitMapper
  
  private Mapper kitMapper
- defaultPrototolFunction
  
  private DefaultItemFunction<Protocol> defaultPrototolFunction
- parentTypeMapper
  
  private Mapper parentTypeMapper
- parentMapper
  
  private Mapper parentMapper
- usedQuantityMapper
  
  private UsedQuantityMapper usedQuantityMapper
- bioPlateMapper
  
  private Mapper bioPlateMapper
- bioWellRowMapper
  
  private Mapper bioWellRowMapper
- bioWellColMapper
  
  private Mapper bioWellColMapper
Constructor Details
- SampleImporter
  
  public SampleImporter()
Method Details
- 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:
  
  PropertyIdMethod.NAME
  PropertyIdMethod.EXTERNAL_ID
  InternalIdMethod.INTERNAL_ID
  FallbackIdMethod.NAME_OR_ID
  Overrides:
  
  getIdMethods in class AbstractItemImporter<Sample>
- 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<Sample>
  
  Returns:
  
  An Item or null
- getItemForAnnotationTypes
  
  protected Item getItemForAnnotationTypes()
  
  Enable annotations as item identifier.
  
  Overrides:
  
  getItemForAnnotationTypes in class AbstractItemImporter<Sample>
  
  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<Sample>
  
  Parameters:
  
  parameters - The list of parameters to add the column mapping parameters to
- createItemQuery
  
  protected ItemQuery<Sample> createItemQuery()
  
  Calls Sample.getQuery().
  
  Specified by:
  
  createItemQuery in class AbstractItemImporter<Sample>
  
  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<Sample>
  
  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 Sample 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<Sample>
  
  Parameters:
  
  dc - The DbControl to use for database access
  
  data - The current data line
  
  Returns:
  
  A new item
- updateItem
  
  protected void updateItem(DbControl dc, Sample sample, 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<Sample>
  
  Parameters:
  
  dc - The DbControl to use for database access
  
  sample - The item to update
  
  data - 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 class AbstractItemImporter<Sample>
  
  Parameters:
  
  dc - The DbControl to use for database access
  
  sample - 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

Class SampleImporter

Nested Class Summary

Nested classes/interfaces inherited from interface net.sf.basedb.core.plugin.Plugin

Field Summary

Fields inherited from class net.sf.basedb.plugins.batchimport.AbstractItemImporter

Fields inherited from class net.sf.basedb.plugins.AbstractFlatFileImporter

Fields inherited from class net.sf.basedb.core.plugin.AbstractPlugin

Constructor Summary

Method Summary

Methods inherited from class net.sf.basedb.plugins.batchimport.AbstractItemImporter

Methods inherited from class net.sf.basedb.plugins.AbstractFlatFileImporter

Methods inherited from class net.sf.basedb.core.plugin.AbstractPlugin

Methods inherited from class java.lang.Object

Methods inherited from interface net.sf.basedb.core.plugin.Plugin

Field Details

guiContexts

createdColumnMapping

originalQuantityColumnMapping

parentTypeColumnMapping

parentColumnMapping

usedQuantityColumnMapping

bioPlateColumnMapping

bioWellRowColumnMapping

bioWellColColumnMapping

nameMapper

descriptionMapper

externalIdMapper

originalQuantityMapper

createdMapper

registeredMapper

protocolMapper

kitMapper

defaultPrototolFunction

parentTypeMapper

parentMapper

usedQuantityMapper

bioPlateMapper

bioWellRowMapper

bioWellColMapper

Constructor Details

SampleImporter

Method Details

getGuiContexts

getIdMethods

getItemForSubtypes

getItemForAnnotationTypes

addMoreColumnMappingParameters

createItemQuery

createColumnMappers

createItem

updateItem

updateMultiLineItem