PhysicalBioAssayImporter
instead@Deprecated public class HybridizationImporter extends AbstractItemImporter<PhysicalBioAssay>
Plugin.MainType
Modifier and Type | Field and Description |
---|---|
protected static PluginParameter<String> |
arrayIndexColumnMapping
Deprecated.
|
private Mapper |
arrayIndexMapper
Deprecated.
|
protected static PluginParameter<String> |
arraySlideColumnMapping
Deprecated.
|
private Mapper |
arraySlideMapper
Deprecated.
|
private Mapper |
createdMapper
Deprecated.
|
private Mapper |
descriptionMapper
Deprecated.
|
private boolean |
failIfMultipleArrayIndex
Deprecated.
|
private static Set<GuiContext> |
guiContexts
Deprecated.
|
protected static PluginParameter<String> |
hardwareColumnMapping
Deprecated.
|
private Mapper |
hardwareMapper
Deprecated.
|
private static PluginParameter<String> |
multipleArrayIndexErrorParameter
Deprecated.
|
private Mapper |
nameMapper
Deprecated.
|
protected static PluginParameter<String> |
numArraysColumnMapping
Deprecated.
|
private Mapper |
numArraysMapper
Deprecated.
|
private Mapper |
parentMapper
Deprecated.
|
private Mapper |
protocolMapper
Deprecated.
|
private Mapper |
usedQuantityMapper
Deprecated.
|
defaultsSection, descriptionColumnMapping, externalIdColumnMapping, identificationSection, internalIdColumnMapping, 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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HybridizationImporter()
Deprecated.
|
Modifier and Type | Method and Description |
---|---|
protected void |
addMoreColumnMappingParameters(List<PluginParameter<?>> parameters)
Deprecated.
Adds column mappings for name, externalId, description,
protocol, creation date, original quantity, pooled, parent
and used quantity from parent.
|
protected void |
addMoreErrorParameters(List<PluginParameter<?>> parameters)
Deprecated.
Add extra parameters to the "Error handling" section that the subclass
needs.
|
protected void |
createColumnMappers(FlatFileParser ffp,
boolean cropStrings)
Deprecated.
Create mappers that can be used to extract data values from the file
that is currently being parsed by the
ffp FlatFileParser . |
protected PhysicalBioAssay |
createItem(DbControl dc,
FlatFileParser.Data data)
Deprecated.
Create a new item and populate it with data from the current line.
|
protected ItemQuery<PhysicalBioAssay> |
createItemQuery()
Deprecated.
Calls
PhysicalBioAssay.getQuery() . |
Set<GuiContext> |
getGuiContexts()
Deprecated.
Get a set containing all items that the plugin handles.
|
protected IdMethod[] |
getIdMethods()
Deprecated.
|
protected void |
updateItem(DbControl dc,
PhysicalBioAssay hyb,
FlatFileParser.Data data)
Deprecated.
Update an item with data from the current line.
|
protected void |
updateMultiLineItem(DbControl dc,
PhysicalBioAssay hyb,
FlatFileParser.Data data,
int multiLineNum)
Deprecated.
Add parent labeled extracts and the used quantities
|
addMoreJobParameters, addMoreParsingParameters, begin, beginData, configure, doneWithItem, end, findArrayBatch, findArrayDesign, findArraySlide, findBioPlate, findBioPlateType, findBioSource, findBioSource, findBioWell, findDataFileType, findDerivedBioAssay, findExtract, findExtract, findFileServer, findHardware, findHardware, findHybridization, findItemSubtype, findItemSubtype, findLabeledExtract, findPermissionTemplate, findPhysicalBioAssay, findPlateGeometry, findPlatform, findProtocol, findProtocol, findRawDataType, findReferencedItem, findReferencedItemWithSubtype, findSample, findSample, findSoftware, findSoftware, findTag, findTag, findVariant, getConfigureOptionsParameters, getConfigureParserParameters, getDefaultItemFunction, getIdMethod, getInitializedFlatFileParser, getInitializedFlatFileParser, getItemForSubtypes, 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, 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> hardwareColumnMapping
protected static final PluginParameter<String> arraySlideColumnMapping
protected static final PluginParameter<String> numArraysColumnMapping
protected static final PluginParameter<String> arrayIndexColumnMapping
private static final PluginParameter<String> multipleArrayIndexErrorParameter
private Mapper nameMapper
private Mapper descriptionMapper
private Mapper numArraysMapper
private Mapper createdMapper
private Mapper protocolMapper
private Mapper hardwareMapper
private Mapper parentMapper
private Mapper usedQuantityMapper
private Mapper arrayIndexMapper
private Mapper arraySlideMapper
private boolean failIfMultipleArrayIndex
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<PhysicalBioAssay>
protected void addMoreColumnMappingParameters(List<PluginParameter<?>> parameters)
addMoreColumnMappingParameters
in class AbstractItemImporter<PhysicalBioAssay>
parameters
- The list of parameters to add the column
mapping parameters toprotected void addMoreErrorParameters(List<PluginParameter<?>> parameters)
AbstractItemImporter
addMoreErrorParameters
in class AbstractItemImporter<PhysicalBioAssay>
parameters
- The list of parameters to add the column
mapping parameters toprotected ItemQuery<PhysicalBioAssay> createItemQuery()
PhysicalBioAssay.getQuery()
.createItemQuery
in class AbstractItemImporter<PhysicalBioAssay>
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<PhysicalBioAssay>
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 PhysicalBioAssay 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<PhysicalBioAssay>
dc
- The DbControl to use for database accessdata
- The current data lineprotected void updateItem(DbControl dc, PhysicalBioAssay hyb, 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<PhysicalBioAssay>
dc
- The DbControl to use for database accesshyb
- The item to updatedata
- The current data lineprotected void updateMultiLineItem(DbControl dc, PhysicalBioAssay hyb, FlatFileParser.Data data, int multiLineNum)
updateMultiLineItem
in class AbstractItemImporter<PhysicalBioAssay>
dc
- The DbControl to use for database accesshyb
- The item to updatedata
- The current data linemultiLineNum
- The number of the multi-line entry, starting with 1
for the first multi-line