Package net.sf.basedb.plugins
Class ReporterMapFlatFileImporter
java.lang.Object
net.sf.basedb.core.plugin.AbstractPlugin
net.sf.basedb.plugins.AbstractFlatFileImporter
net.sf.basedb.plugins.ReporterMapFlatFileImporter
- All Implemented Interfaces:
AutoDetectingImporter
,InteractivePlugin
,Plugin
,SignalTarget
,ConfigureByExample
- Direct Known Subclasses:
GtfReporterMapImporter
public class ReporterMapFlatFileImporter
extends AbstractFlatFileImporter
implements InteractivePlugin, ConfigureByExample
A plugin that imports features to an ArrayDesign from a flat file. The ArrayDesign
will not have any connections to plates.
- Version:
- 2.0
- Author:
- Enell
- Last modified
- $Date: 2019-03-20 16:21:26 +0100 (ons, 20 mars 2019) $
-
Nested Class Summary
Nested classes/interfaces inherited from interface net.sf.basedb.core.plugin.Plugin
Plugin.MainType
-
Field Summary
Modifier and TypeFieldDescriptionprivate List<PluginParameter<String>>
private ArrayDesign
private PluginParameter<ArrayDesign>
private ItemParameterType<ArrayDesign>
private FeatureBatcher
protected static final PluginParameter<String>
private Mapper
private Map<BlockInfo,
ArrayDesignBlock> protected static final PluginParameter<String>
private Mapper
private RequestInformation
private RequestInformation
private DbControl
protected static final PluginParameter<String>
private boolean
protected static final PluginParameter<String>
protected static final PluginParameter<String>
private Mapper
private FlatFileParser
private static final Set<GuiContext>
protected static final PluginParameter<String>
private Mapper
protected static final PluginParameter<String>
private Mapper
protected static final PluginParameter<String>
private int
private int
private static final StringParameterType
private static final Set<Permissions>
protected static final PluginParameter<String>
private Mapper
private ReporterBatcher
protected static final PluginParameter<String>
private FileSetMember
private Mapper
private static final StringParameterType
protected static final PluginParameter<String>
private Mapper
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
begin
(FlatFileParser ffp) Create aDbControl
and aFeatureBatcher
.protected void
Initialise columnMapper
:s.void
configure
(GuiContext context, Request request, Response response) Store configuration settings forRequest.COMMAND_CONFIGURE_PLUGIN
andRequest.COMMAND_CONFIGURE_JOB
.protected void
end
(boolean success) Close and commit/rollback the FeatureBatcher and DbControl.private List<PluginParameter<String>>
private RequestInformation
getConfigureJobParameters
(GuiContext context) private RequestInformation
getConfigurePluginParameters
(GuiContext context) Return a set containing the element [ARRAYDESIGN, ITEM].Request write access to ArrayDesign:s, read access to Reporter:s, DataFileType:s, Platform:s and File:s.getRequestInformation
(GuiContext context, String command) TheRequest.COMMAND_CONFIGURE_PLUGIN
command will ask for parser regular expressions and column mappings.protected String
getSuccessMessage
(int skippedLines) Returnx features inserted; y blocks inserted
.protected void
Called by the parser for every line in the file that is a data line.isInContext
(GuiContext context, Object item) Returns null if the item is aArrayDesign
that doesn't already have any features and is using a supported platform/variant.boolean
Return TRUE, since the implementation requires it for finding the regular expressions used by theFlatFileParser
.boolean
Returns TRUE, since that is how the plugins used to work before this method was introduced.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, setUpErrorHandling, start, wrapInputStream
Methods inherited from class net.sf.basedb.core.plugin.AbstractPlugin
cloneParameterWithDefaultValue, closeLogFile, createLogFile, done, getCopyAnnotationsParmeter, getCurrentConfiguration, getCurrentJob, getJobOrConfigurationValue, getOverwriteAnnotationsParameters, 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, init, run
-
Field Details
-
guiContexts
-
permissions
-
requiredColumnMapping
-
optionalColumnMapping
-
featureIdentificationParameter
-
reporterIdColumnMapping
-
featureIdColumnMapping
-
positionColumnMapping
-
blockColumnMapping
-
metaGridXColumnMapping
-
metaGridYColumnMapping
-
columnColumnMapping
-
rowColumnMapping
-
missingReporterErrorParameter
-
duplicateFeatureErrorParameter
-
configurePlugin
-
configureJob
-
dc
-
batcher
-
reporterBatcher
-
reporterMapMember
-
arrayDesign
-
blocks
-
ffp
-
arrayDesignType
-
arrayDesignParameter
-
allColumnMappings
-
errorIfNotFound
private boolean errorIfNotFound -
reporterMapper
-
featureIdMapper
-
positionMapper
-
blockMapper
-
columnMapper
-
rowMapper
-
metaGridXMapper
-
metaGridYMapper
-
numFeatures
private int numFeatures -
numBlocks
private int numBlocks
-
-
Constructor Details
-
ReporterMapFlatFileImporter
public ReporterMapFlatFileImporter()Create a new importer.
-
-
Method Details
-
supportsConfigurations
public boolean supportsConfigurations()Description copied from class:AbstractPlugin
Returns TRUE, since that is how the plugins used to work before this method was introduced.- Specified by:
supportsConfigurations
in interfacePlugin
- Overrides:
supportsConfigurations
in classAbstractPlugin
- Returns:
- TRUE or FALSE
-
requiresConfiguration
public boolean requiresConfiguration()Description copied from class:AbstractFlatFileImporter
Return TRUE, since the implementation requires it for finding the regular expressions used by theFlatFileParser
. If this method is overridden and returns FALSE, the subclass must also override theAbstractFlatFileImporter.getInitializedFlatFileParser()
method and provide a parser with all regular expressions and other options set.- Specified by:
requiresConfiguration
in interfacePlugin
- Overrides:
requiresConfiguration
in classAbstractFlatFileImporter
- Returns:
- TRUE or FALSE
-
getPermissions
Request write access to ArrayDesign:s, read access to Reporter:s, DataFileType:s, Platform:s and File:s.- Specified by:
getPermissions
in interfacePlugin
- Overrides:
getPermissions
in classAbstractPlugin
- Returns:
- A collection of permissions or null to not use permissions
-
getGuiContexts
Return a set containing the element [ARRAYDESIGN, ITEM].- Specified by:
getGuiContexts
in interfaceInteractivePlugin
- Returns:
- A
Set
containingItem
:s, or null if the plugin is not concerned about items
-
isInContext
Returns null if the item is aArrayDesign
that doesn't already have any features and is using a supported platform/variant.- Specified by:
isInContext
in interfaceInteractivePlugin
- Parameters:
context
- The current context of the client application, it is one of the values found in set returned byInteractivePlugin.getGuiContexts()
item
- The currently active item, it's type should match theGuiContext.getItem()
type, or null if the context is a list context- Returns:
Null
if the plugin can use that item, or a warning-level message explaining why the plugin can't be used- Throws:
PermissionDeniedException
- If the array design already has features or if the logged in user doesn't have write permission
-
getRequestInformation
public RequestInformation getRequestInformation(GuiContext context, String command) throws BaseException TheRequest.COMMAND_CONFIGURE_PLUGIN
command will ask for parser regular expressions and column mappings. TheRequest.COMMAND_CONFIGURE_JOB
command will ask for a file and the array design that features should be added to.- Specified by:
getRequestInformation
in interfaceInteractivePlugin
- Parameters:
context
- The current context of the client application, it is one of the values found in set returned byInteractivePlugin.getGuiContexts()
command
- The command- Returns:
- The
RequestInformation
for the command - Throws:
BaseException
- if there is an error
-
configure
Store configuration settings forRequest.COMMAND_CONFIGURE_PLUGIN
andRequest.COMMAND_CONFIGURE_JOB
.- Specified by:
configure
in interfaceInteractivePlugin
- Parameters:
context
- The current context of the client application, it is one of the values found in set returned byInteractivePlugin.getGuiContexts()
request
- Request object with the command and parametersresponse
- Response object in for the plugin to response through
-
begin
- Overrides:
begin
in classAbstractFlatFileImporter
- Throws:
BaseException
- See Also:
-
beginData
protected void beginData()Initialise columnMapper
:s.- Overrides:
beginData
in classAbstractFlatFileImporter
-
handleData
Description copied from class:AbstractFlatFileImporter
Called by the parser for every line in the file that is a data line.- Specified by:
handleData
in classAbstractFlatFileImporter
- Throws:
BaseException
-
end
Close and commit/rollback the FeatureBatcher and DbControl.- Overrides:
end
in classAbstractFlatFileImporter
- Parameters:
success
- TRUE if the file was parsed successfully, FALSE otherwise- Throws:
BaseException
- See Also:
-
getSuccessMessage
Returnx features inserted; y blocks inserted
.- Overrides:
getSuccessMessage
in classAbstractFlatFileImporter
- Parameters:
skippedLines
- The number of data lines that were skipped due to errors
-
getAllColumnMappings
-
getConfigureJobParameters
-
getConfigurePluginParameters
-