Package net.sf.basedb.plugins.batchimport

Class AnnotationTypeImporter

java.lang.Object

net.sf.basedb.core.plugin.AbstractPlugin

net.sf.basedb.plugins.AbstractFlatFileImporter

net.sf.basedb.plugins.batchimport.AbstractItemImporter<AnnotationType>

net.sf.basedb.plugins.batchimport.AnnotationTypeImporter

All Implemented Interfaces:

AutoDetectingImporter, InteractivePlugin, Plugin, SignalTarget, ConfigureByExample

public class AnnotationTypeImporter
extends AbstractItemImporter<AnnotationType>

Plug-in for importing annotation type items in a batch. The plug-in can create new items and updated existing items.

Since:

3.8

Author:

nicklas

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
private static PluginParameter<String>	categoryColumnMapping	Column mapping parameter for assigning annotation types to categories.
private Mapper	categoryMapper
private static PluginParameter<String>	defaultUnitColumnMapping	Column mapping parameter for "Default unit".
private Mapper	defaultUnitMapper
private static PluginParameter<String>	defaultValueColumnMapping	Column mapping parameter for "Default value".
private Mapper	defaultValueMapper
private Mapper	descriptionMapper
private static PluginParameter<String>	disableChangeLogColumnMapping	Column mapping parameter for "Disabled history log" flag.
private Mapper	disableChangeLogMapper
private static PluginParameter<String>	disableInheritanceColumnMapping	Column mapping parameter for "Disable inheritance" flag.
private Mapper	disableInheritanceMapper
private static PluginParameter<String>	enumerationColumnMapping	Column mapping parameter for "Enumeration".
private Mapper	enumerationMapper
private Pattern	enumerationSplitter
private static PluginParameter<String>	enumerationSplitterRegexpParameter	Regular expression splitter parameter for enumerations.
private Mapper	externalIdMapper
private static Set<GuiContext>	guiContexts
private static PluginParameter<String>	isIdentifierColumnMapping	Column mapping parameter for "Is identifier" flag.
private Mapper	isIdentifierMapper
private static PluginParameter<String>	itemTypesColumnMapping	Column mapping parameter for "Item types".
private Mapper	itemTypesMapper
private static PluginParameter<String>	maxValueColumnMapping	Column mapping parameter for "Max value".
private Mapper	maxValueMapper
private static PluginParameter<String>	miameColumnMapping	Column mapping parameter for "Required for MIAME" flag.
private Mapper	miameMapper
private static PluginParameter<String>	minValueColumnMapping	Column mapping parameter for "Min value".
private Mapper	minValueMapper
private static PluginParameter<String>	multiplicityColumnMapping	Column mapping parameter for annotation multiplicty.
private Mapper	multiplicityMapper
private Mapper	nameMapper
private NumberFormat	numberFormat
private static PluginParameter<String>	protocolParameterColumnMapping	Column mapping parameter for "Protocol parameter" flag.
private Mapper	protocolParameterMapper
private Mapper	registeredMapper
private static PluginParameter<String>	usableUnitColumnMapping	Column mapping parameter for "Usable unit".
private Mapper	usableUnitMapper
private static PluginParameter<String>	valueTypeColumnMapping	Column mapping parameter for the annotation value type
private Mapper	valueTypeMapper

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
AnnotationTypeImporter()

Method Summary

Modifier and Type	Method	Description
protected void	addMoreColumnMappingParameters(List<PluginParameter<?>> parameters)	Adds column mappings for name and description.
protected void	addMoreParsingParameters(List<PluginParameter<?>> parameters)	Add extra parameters to the "Parser settings" section that the subclass needs.
void	configure(GuiContext context, Request request, Response response)	Override this method so that we can make some extra parameter checks: A mapping for 'Value type' must be specified when 'create' or 'create+update' mode is used
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 AnnotationType	createItem(DbControl dc, FlatFileParser.Data data)	Create a new item and populate it with data from the current line.
protected ItemQuery<AnnotationType>	createItemQuery()	Calls AnnotationType.getQuery(Item).
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 void	updateItem(DbControl dc, AnnotationType at, FlatFileParser.Data data)	Update an item with data from the current line.
protected void	updateMultiLineItem(DbControl dc, AnnotationType at, FlatFileParser.Data data, int multiLineNum)	Update an item with data from a multi-line entry.

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

addMoreErrorParameters, addMoreJobParameters, begin, beginData, 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, getItemForAnnotationTypes, getItemForSubtypes, 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

valueTypeColumnMapping

private static final PluginParameter<String> valueTypeColumnMapping

Column mapping parameter for the annotation value type

categoryColumnMapping

private static final PluginParameter<String> categoryColumnMapping

Column mapping parameter for assigning annotation types to categories.

multiplicityColumnMapping

private static final PluginParameter<String> multiplicityColumnMapping

Column mapping parameter for annotation multiplicty.

defaultValueColumnMapping

private static final PluginParameter<String> defaultValueColumnMapping

Column mapping parameter for "Default value".

isIdentifierColumnMapping

private static final PluginParameter<String> isIdentifierColumnMapping

Column mapping parameter for "Is identifier" flag.

miameColumnMapping

private static final PluginParameter<String> miameColumnMapping

Column mapping parameter for "Required for MIAME" flag.

protocolParameterColumnMapping

private static final PluginParameter<String> protocolParameterColumnMapping

Column mapping parameter for "Protocol parameter" flag.

disableChangeLogColumnMapping

private static final PluginParameter<String> disableChangeLogColumnMapping

Column mapping parameter for "Disabled history log" flag.

disableInheritanceColumnMapping

private static final PluginParameter<String> disableInheritanceColumnMapping

Column mapping parameter for "Disable inheritance" flag.

itemTypesColumnMapping

private static final PluginParameter<String> itemTypesColumnMapping

Column mapping parameter for "Item types".

defaultUnitColumnMapping

private static final PluginParameter<String> defaultUnitColumnMapping

Column mapping parameter for "Default unit".

usableUnitColumnMapping

private static final PluginParameter<String> usableUnitColumnMapping

Column mapping parameter for "Usable unit".

enumerationColumnMapping

private static final PluginParameter<String> enumerationColumnMapping

Column mapping parameter for "Enumeration".

enumerationSplitterRegexpParameter

private static final PluginParameter<String> enumerationSplitterRegexpParameter

Regular expression splitter parameter for enumerations.

minValueColumnMapping

private static final PluginParameter<String> minValueColumnMapping

Column mapping parameter for "Min value".

maxValueColumnMapping

private static final PluginParameter<String> maxValueColumnMapping

Column mapping parameter for "Max value".

nameMapper

private Mapper nameMapper

externalIdMapper

private Mapper externalIdMapper

descriptionMapper

private Mapper descriptionMapper

valueTypeMapper

private Mapper valueTypeMapper

categoryMapper

private Mapper categoryMapper

registeredMapper

private Mapper registeredMapper

multiplicityMapper

private Mapper multiplicityMapper

defaultValueMapper

private Mapper defaultValueMapper

isIdentifierMapper

private Mapper isIdentifierMapper

miameMapper

private Mapper miameMapper

protocolParameterMapper

private Mapper protocolParameterMapper

disableChangeLogMapper

private Mapper disableChangeLogMapper

disableInheritanceMapper

private Mapper disableInheritanceMapper

itemTypesMapper

private Mapper itemTypesMapper

defaultUnitMapper

private Mapper defaultUnitMapper

usableUnitMapper

private Mapper usableUnitMapper

enumerationMapper

private Mapper enumerationMapper

minValueMapper

private Mapper minValueMapper

maxValueMapper

private Mapper maxValueMapper

numberFormat

private NumberFormat numberFormat

enumerationSplitter

private Pattern enumerationSplitter

Constructor Details

AnnotationTypeImporter

public AnnotationTypeImporter()

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

configure

public void configure(GuiContext context,
Request request,
Response response)

Override this method so that we can make some extra parameter checks: A mapping for 'Value type' must be specified when 'create' or 'create+update' mode is used

Specified by:

configure in interface InteractivePlugin

Overrides:

configure in class AbstractItemImporter<AnnotationType>

Parameters:

context - The current context of the client application, it is one of the values found in set returned by InteractivePlugin.getGuiContexts()

request - Request object with the command and parameters

response - Response object in for the plugin to response through

getIdMethods

protected IdMethod[] getIdMethods()

Useable methods are:

• PropertyIdMethod.NAME
• PropertyIdMethod.EXTERNAL_ID
• InternalIdMethod.INTERNAL_ID
• FallbackIdMethod.NAME_OR_ID

Overrides:

getIdMethods in class AbstractItemImporter<AnnotationType>

addMoreParsingParameters

protected void addMoreParsingParameters(List<PluginParameter<?>> parameters)

Description copied from class: AbstractItemImporter

Add extra parameters to the "Parser settings" section that the subclass needs. This method is called during configuration of the plug-in and the default implementation does nothing.

Overrides:

addMoreParsingParameters in class AbstractItemImporter<AnnotationType>

Parameters:

parameters - The list of parameters to add the column mapping parameters to

addMoreColumnMappingParameters

protected void addMoreColumnMappingParameters(List<PluginParameter<?>> parameters)

Adds column mappings for name and description.

Overrides:

addMoreColumnMappingParameters in class AbstractItemImporter<AnnotationType>

Parameters:

parameters - The list of parameters to add the column mapping parameters to

createItemQuery

protected ItemQuery<AnnotationType> createItemQuery()

Calls AnnotationType.getQuery(Item).

Specified by:

createItemQuery in class AbstractItemImporter<AnnotationType>

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<AnnotationType>

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 AnnotationType 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<AnnotationType>

Parameters:

dc - The DbControl to use for database access

data - The current data line

Returns:

A new item

updateItem

protected void updateItem(DbControl dc,
AnnotationType at,
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<AnnotationType>

Parameters:

dc - The DbControl to use for database access

at - The item to update

data - The current data line

updateMultiLineItem

protected void updateMultiLineItem(DbControl dc,
AnnotationType at,
FlatFileParser.Data data,
int multiLineNum)

Description copied from class: AbstractItemImporter

Update an item with data from a multi-line entry. Items which can have multiple parents should have data for the other parents on lines following the first line.

Overrides:

updateMultiLineItem in class AbstractItemImporter<AnnotationType>

Parameters:

dc - The DbControl to use for database access

at - 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