Package net.sf.basedb.plugins
Class PlateMappingImporter
java.lang.Object
net.sf.basedb.core.plugin.AbstractPlugin
net.sf.basedb.plugins.AbstractFlatFileImporter
net.sf.basedb.plugins.PlateMappingImporter
- All Implemented Interfaces:
AutoDetectingImporter
,InteractivePlugin
,Plugin
,SignalTarget
Importer for plate mappings. It has a fixed file format:
Source plates=1 Source rows=3 Source columns=3 Destination plates=1 Destination rows=3 Destination columns=3 Source plate Source row Source column Destination plate Destination row Destination column 0 0 0 0 0 0 0 0 1 0 1 0 0 0 2 0 2 0 0 1 0 0 0 1 0 1 1 0 1 1 0 1 2 0 2 1 0 2 0 0 0 2 0 2 1 0 1 2 0 2 2 0 2 2
- Version:
- 2.0
- Author:
- nicklas
- Last modified
- $Date: 2012-09-14 09:28:35 +0200 (fr, 14 sep 2012) $
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Nested Class Summary
Nested classes/interfaces inherited from interface net.sf.basedb.core.plugin.Plugin
Plugin.MainType
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Field Summary
Modifier and TypeFieldDescriptionprivate RequestInformation
private DbControl
private static final PluginParameter<String>
private Mapper
private Mapper
private Mapper
private FlatFileParser
private static final Set<GuiContext>
private static final PluginParameter<String>
private static final Set<Permissions>
private PlateMapping
private static final StringParameterType
private Mapper
private Mapper
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
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Constructor Summary
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Method Summary
Modifier and TypeMethodDescriptionprotected void
begin
(FlatFileParser ffp) Save reference to parser.protected void
Create aDbControl
and a newPlateMapping
.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 DbControl.private PlateGeometry
findGeometry
(DbControl dc, int rows, int columns) private RequestInformation
getConfigureJobParameters
(GuiContext context) Return a set containing the context:s [PLATEMAPPING, LIST].protected FlatFileParser
Get an initialized parser that is configured by job or configuration values.Request create and write access to PlateMapping:s, create and use access to PlateGeometries and read access to File:s.getRequestInformation
(GuiContext context, String command) This method will return theRequestInformation
for a given command, i.e.protected String
getSuccessMessage
(int skippedLines) ReturnPlatemapping 'name' created.
.protected void
Add a mapping detail.isInContext
(GuiContext context, Object item) Always null.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, 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
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Field Details
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guiContexts
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permissions
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requiredStringParameter
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configureJob
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nameParameter
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descriptionParameter
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dc
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pm
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sourcePlateMapper
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sourceRowMapper
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sourceColumnMapper
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destPlateMapper
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destRowMapper
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destColumnMapper
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ffp
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Constructor Details
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PlateMappingImporter
public PlateMappingImporter()Create a new importer.
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Method Details
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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
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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
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getPermissions
Request create and write access to PlateMapping:s, create and use access to PlateGeometries and read access to File:s.- Specified by:
getPermissions
in interfacePlugin
- Overrides:
getPermissions
in classAbstractPlugin
- Returns:
- A collection of permissions or null to not use permissions
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getGuiContexts
Return a set containing the context:s [PLATEMAPPING, LIST].- Specified by:
getGuiContexts
in interfaceInteractivePlugin
- Returns:
- A
Set
containingItem
:s, or null if the plugin is not concerned about items
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isInContext
Always null.- 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
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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
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getRequestInformation
public RequestInformation getRequestInformation(GuiContext context, String command) throws BaseException Description copied from interface:InteractivePlugin
This method will return theRequestInformation
for a given command, i.e. the list of parameters and some nice help text.- 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
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begin
Save reference to parser.- Overrides:
begin
in classAbstractFlatFileImporter
- Throws:
BaseException
- See Also:
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beginData
protected void beginData()- Overrides:
beginData
in classAbstractFlatFileImporter
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handleData
Add a mapping detail.- Specified by:
handleData
in classAbstractFlatFileImporter
- Throws:
BaseException
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end
Close and commit/rollback the DbControl.- Overrides:
end
in classAbstractFlatFileImporter
- Parameters:
success
- TRUE if the file was parsed successfully, FALSE otherwise- Throws:
BaseException
- See Also:
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getSuccessMessage
ReturnPlatemapping 'name' created.
.- Overrides:
getSuccessMessage
in classAbstractFlatFileImporter
- Parameters:
skippedLines
- The number of data lines that were skipped due to errors
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getInitializedFlatFileParser
Description copied from class:AbstractFlatFileImporter
Get an initialized parser that is configured by job or configuration values.- Overrides:
getInitializedFlatFileParser
in classAbstractFlatFileImporter
- Throws:
BaseException
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getConfigureJobParameters
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findGeometry
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