public class ExtractImporter extends AbstractItemImporter<Extract>
Plugin.MainType
Modifier and Type | Field and Description |
---|---|
private Mapper |
bioPlateMapper |
private Mapper |
bioWellColMapper |
private Mapper |
bioWellRowMapper |
private Mapper |
createdMapper |
private DefaultItemFunction<Protocol> |
defaultPrototolFunction |
private Mapper |
descriptionMapper |
private Mapper |
externalIdMapper |
private static Set<GuiContext> |
guiContexts |
private Mapper |
kitMapper |
private Mapper |
nameMapper |
private Mapper |
originalQuantityMapper |
private Mapper |
parentMapper |
private Mapper |
parentTypeMapper |
private Mapper |
protocolMapper |
protected static PluginParameter<String> |
tagColumnMapping |
private Mapper |
tagMapper |
private Mapper |
usedQuantityMapper |
defaultsSection, descriptionColumnMapping, externalIdColumnMapping, identificationSection, internalIdColumnMapping, kitColumnMapping, nameColumnMapping, optionalColumnMapping, permissionTemplateColumnMapping, protocolColumnMapping, requiredColumnMapping, subtypeColumnMapping
complexMappings, dataFooterRegexpParameter, dataHeaderRegexpParameter, dataSplitterRegexpParameter, defaultErrorParameter, errorSection, fileParameter, fileType, headerRegexpParameter, ignoreRegexpParameter, invalidUseOfNullErrorParameter, mappingSection, maxDataColumnsParameter, minDataColumnsParameter, numberFormatErrorParameter, numberOutOfRangeErrorParameter, numDataColumnsType, optionalRegexpType, parserSection, requiredRegexpType, sectionRegexpParameter, stringTooLongErrorParameter, trimQuotesParameter
annotationSection, configuration, COPY_ANNOTATIONS, job, OVERWRITE_ANNOTATIONS, sc
Constructor and Description |
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ExtractImporter() |
Modifier and Type | Method and 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 Extract |
createItem(DbControl dc,
FlatFileParser.Data data)
Create a new item and populate it with data from the current line.
|
protected ItemQuery<Extract> |
createItemQuery()
Calls
Extract.getQuery() . |
Set<GuiContext> |
getGuiContexts()
Get a set containing all items that the plugin handles.
|
protected IdMethod[] |
getIdMethods()
|
protected Item |
getItemForSubtypes()
Does the importer want to use item subtypes when importing?
|
protected void |
updateItem(DbControl dc,
Extract extract,
FlatFileParser.Data data)
Update an item with data from the current line.
|
protected void |
updateMultiLineItem(DbControl dc,
Extract extract,
FlatFileParser.Data data,
int multiLineNum)
If the sample is pooled, add the parent sample.
|
addMoreErrorParameters, addMoreJobParameters, addMoreParsingParameters, begin, beginData, configure, 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, getConfigureOptionsParameters, getConfigureParserParameters, getDefaultItemFunction, getIdMethod, getInitializedFlatFileParser, getInitializedFlatFileParser, getProjectDefaultPlatform, getProjectDefaultRawDataType, getProjectDefaultVariant, getRequestInformation, getSuccessMessage, handleData, initReferenceQuery, isInContext, parseDate, requiresConfiguration, setOrAddFile, setUpErrorHandling, supportsConfigurations, updateItemSubtype, updatePermissions
addErrorHandler, checkColumnMapping, checkColumnMapping, continueWithNextFileAfterError, doImport, finish, getCharset, getCharset, getDecimalSeparator, getErrorHandler, getErrorOption, getFileIterator, getMainType, getMapper, getMapper, getNumberFormat, getNumBytes, getPattern, getProgress, getSignalHandler, getTotalFileSize, handleHeader, handleSection, isImportable, isImportable, log, log, log, log, run, start, wrapInputStream
cloneParameterWithDefaultValue, closeLogFile, createLogFile, done, getCopyAnnotationsParmeter, getCurrentConfiguration, getCurrentJob, getJobOrConfigurationValue, getOverwriteAnnotationsParameters, getPermissions, init, log, log, storeValue, storeValue, storeValues, validateRequestParameters
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
done, getMainType, getPermissions, init, run
private static final Set<GuiContext> guiContexts
protected static final PluginParameter<String> tagColumnMapping
private Mapper nameMapper
private Mapper descriptionMapper
private Mapper externalIdMapper
private Mapper tagMapper
private Mapper originalQuantityMapper
private Mapper createdMapper
private Mapper protocolMapper
private Mapper kitMapper
private DefaultItemFunction<Protocol> defaultPrototolFunction
private Mapper parentTypeMapper
private Mapper parentMapper
private Mapper usedQuantityMapper
private Mapper bioPlateMapper
private Mapper bioWellRowMapper
private Mapper bioWellColMapper
public Set<GuiContext> getGuiContexts()
InteractivePlugin
Item.REPORTER
.
This information is used by client applications to put the plugin
in the proper place in the user interface.Set
containing Item
:s, or null
if the plugin is not concerned about itemsprotected IdMethod[] getIdMethods()
getIdMethods
in class AbstractItemImporter<Extract>
protected Item getItemForSubtypes()
AbstractItemImporter
getItemForSubtypes
in class AbstractItemImporter<Extract>
protected void addMoreColumnMappingParameters(List<PluginParameter<?>> parameters)
addMoreColumnMappingParameters
in class AbstractItemImporter<Extract>
parameters
- The list of parameters to add the column
mapping parameters toprotected ItemQuery<Extract> createItemQuery()
Extract.getQuery()
.createItemQuery
in class AbstractItemImporter<Extract>
protected void createColumnMappers(FlatFileParser ffp, boolean cropStrings)
AbstractItemImporter
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);
createColumnMappers
in class AbstractItemImporter<Extract>
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)protected Extract createItem(DbControl dc, FlatFileParser.Data data)
AbstractItemImporter
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.
createItem
in class AbstractItemImporter<Extract>
dc
- The DbControl to use for database accessdata
- The current data lineprotected void updateItem(DbControl dc, Extract extract, FlatFileParser.Data data)
AbstractItemImporter
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.
updateItem
in class AbstractItemImporter<Extract>
dc
- The DbControl to use for database accessextract
- The item to updatedata
- The current data lineprotected void updateMultiLineItem(DbControl dc, Extract extract, FlatFileParser.Data data, int multiLineNum)
updateMultiLineItem
in class AbstractItemImporter<Extract>
dc
- The DbControl to use for database accessextract
- The item to updatedata
- The current data linemultiLineNum
- The number of the multi-line entry, starting with 1
for the first multi-line