Package net.sf.basedb.plugins
Class PrintMapFlatFileImporter
java.lang.Object
net.sf.basedb.core.plugin.AbstractPlugin
net.sf.basedb.plugins.AbstractFlatFileImporter
net.sf.basedb.plugins.PrintMapFlatFileImporter
- All Implemented Interfaces:
AutoDetectingImporter
,InteractivePlugin
,Plugin
,SignalTarget
A plugin that imports an
ArrayDesign
from a printmap. The
formats supported are TAM and MwBr- Version:
- 2.0
- Author:
- Enell
- Last modified
- $Date: 2019-03-20 14:31:03 +0100 (ons, 20 mars 2019) $
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Nested Class Summary
Modifier and TypeClassDescriptionprivate static enum
private static class
private static enum
Nested classes/interfaces inherited from interface net.sf.basedb.core.plugin.Plugin
Plugin.MainType
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Field Summary
Modifier and TypeFieldDescriptionprivate ArrayDesign
private PluginParameter<ArrayDesign>
private ItemParameterType<ArrayDesign>
private FeatureBatcher
private Map<BlockInfo,
ArrayDesignBlock> private RequestInformation
private DbControl
private int
private static final Set<GuiContext>
private Map<Integer,
PrintMapFlatFileImporter.MetaBlock> protected static final PluginParameter<String>
private int
private int
private static final Set<Permissions>
private FileSetMember
private PrintMapFlatFileImporter.Section
private int
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) Create aDbControl
and aFeatureBatcher
.void
configure
(GuiContext context, Request request, Response response) Store configuration settings forRequest.COMMAND_CONFIGURE_PLUGIN
andRequest.COMMAND_CONFIGURE_JOB
.protected void
end
(boolean success) Called just after the last line of the file has been parsed, or immediately after an error has ocurred.private Well
findWell
(int platePosition, int row, int column) private RequestInformation
getConfigureJobParameters
(GuiContext context) Get a set containing all items that the plugin handles.protected FlatFileParser
Get an initialized parser that is configured by job or configuration values.Request write access to ArrayDesign:s, read access to Plate:s, 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) Called if the parsing was successful to let the subclass generate a simple message that is sent back to the core and user interface.protected void
Called by the parser for every line in the file that is a data line.protected void
Called by the parser for every line in the file that is a header line.protected void
Called by the parser for every line in the file that is a section line.protected boolean
Check that the file is a TAM or MwBr file.isInContext
(GuiContext context, Object item) Returns null if the item is aArrayDesign
that doesn't already have any features and isn't an affy design.boolean
Return TRUE, since the implementation requires it for finding the regular expressions used by theFlatFileParser
.private void
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, beginData, checkColumnMapping, checkColumnMapping, continueWithNextFileAfterError, doImport, finish, getCharset, getCharset, getDateFormatter, getDecimalSeparator, getErrorHandler, getErrorOption, getFileIterator, getInitializedFlatFileParser, getMainType, getMapper, getMapper, getNumberFormat, getNumBytes, getPattern, getPattern, getProgress, getSignalHandler, getTimestampFormatter, getTotalFileSize, 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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missingWellErrorParameter
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configureJob
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dc
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batcher
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blocks
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metaBlocks
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arrayDesign
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printMapMember
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arrayDesignType
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arrayDesignParameter
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numFeatures
private int numFeatures -
numBlocks
private int numBlocks -
section
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formatType
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expectedNumBlocks
private int expectedNumBlocks -
spotSize
private int spotSize
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Constructor Details
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PrintMapFlatFileImporter
public PrintMapFlatFileImporter()
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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 write access to ArrayDesign:s, read access to Plate:s, 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
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isInContext
Returns null if the item is aArrayDesign
that doesn't already have any features and isn't an affy design.- 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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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 containingItem.REPORTER
. This information is used by client applications to put the plugin in the proper place in the user interface.- Specified by:
getGuiContexts
in interfaceInteractivePlugin
- Returns:
- A
Set
containingItem
:s, or null if the plugin is not concerned about items
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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:
command
- the command for the requestcontext
- The current context of the client application, it is one of the values found in set returned byInteractivePlugin.getGuiContexts()
- Returns:
- The
RequestInformation
for the command - Throws:
BaseException
- if there is an error
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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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isImportable
Check that the file is a TAM or MwBr file.- Overrides:
isImportable
in classAbstractFlatFileImporter
- Parameters:
ffp
- The FlatFileParser object used to parse the file- Returns:
- TRUE if a FormatName header is present and contains "TAM" or "MwBr", FALSE otherwise
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begin
- Overrides:
begin
in classAbstractFlatFileImporter
- Throws:
BaseException
- See Also:
-
handleHeader
Description copied from class:AbstractFlatFileImporter
Called by the parser for every line in the file that is a header line.- Overrides:
handleHeader
in classAbstractFlatFileImporter
- Throws:
BaseException
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handleSection
Description copied from class:AbstractFlatFileImporter
Called by the parser for every line in the file that is a section line.- Overrides:
handleSection
in classAbstractFlatFileImporter
- Throws:
BaseException
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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
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end
Description copied from class:AbstractFlatFileImporter
Called just after the last line of the file has been parsed, or immediately after an error has ocurred. A subclass should clean up any resources aquired in theAbstractFlatFileImporter.begin(FlatFileParser)
method here. Note that this metod is called once for every file returned by theAbstractFlatFileImporter.getFileIterator()
iterator.- Overrides:
end
in classAbstractFlatFileImporter
- Parameters:
success
- TRUE if the file was parsed successfully, FALSE otherwise- Throws:
BaseException
- See Also:
-
getSuccessMessage
Description copied from class:AbstractFlatFileImporter
Called if the parsing was successful to let the subclass generate a simple message that is sent back to the core and user interface. An example message might by:178 reporters imported successfully
. The default implementation always return null. Note that this method is called once for every file returned byAbstractFlatFileImporter.getFileIterator()
.- 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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findWell
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setBlockValue
private void setBlockValue(PrintMapFlatFileImporter.MetaBlock block, FlatFileParser.Line line) throws BaseException - Throws:
BaseException
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