Package net.sf.basedb.plugins
Class BfsExporterPlugin
- java.lang.Object
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- net.sf.basedb.core.plugin.AbstractPlugin
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- net.sf.basedb.plugins.BfsExporterPlugin
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- All Implemented Interfaces:
InteractivePlugin
,Plugin
,SignalTarget
public class BfsExporterPlugin extends AbstractPlugin implements InteractivePlugin, SignalTarget
Exports bioassay set data to BFS format.- Since:
- 2.15
- Author:
- Nicklas
- Last modified
- $Date: 2019-02-26 11:10:15 +0100 (tis, 26 feb. 2019) $
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Nested Class Summary
Nested Classes Modifier and Type Class Description static class
BfsExporterPlugin.ExtendedExportableField
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Nested classes/interfaces inherited from interface net.sf.basedb.core.plugin.Plugin
Plugin.MainType
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Field Summary
Fields Modifier and Type Field Description private BioAssaySet
bas
private RequestInformation
configureJob
private DbControl
dc
private Map<String,BfsExporterPlugin.ExtendedExportableField>
exportableFields
private static Set<GuiContext>
guiContexts
static String
PARAMETER_FILEFORMAT
static String
PARAMETER_FILENAMEGENERATOR
private ThreadSignalHandler
signalHandler
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Fields inherited from class net.sf.basedb.core.plugin.AbstractPlugin
annotationSection, configuration, COPY_ANNOTATIONS, job, OVERWRITE_ANNOTATIONS, sc
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Constructor Summary
Constructors Constructor Description BfsExporterPlugin()
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Method Summary
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Methods inherited from class net.sf.basedb.core.plugin.AbstractPlugin
cloneParameterWithDefaultValue, closeLogFile, createLogFile, done, getCopyAnnotationsParmeter, getCurrentConfiguration, getCurrentJob, getJobOrConfigurationValue, getOverwriteAnnotationsParameters, getPermissions, init, log, log, storeValue, storeValue, storeValues, validateRequestParameters
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Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
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Methods inherited from interface net.sf.basedb.core.plugin.Plugin
done, getPermissions, init
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Field Detail
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guiContexts
private static final Set<GuiContext> guiContexts
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signalHandler
private ThreadSignalHandler signalHandler
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configureJob
private RequestInformation configureJob
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dc
private DbControl dc
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bas
private BioAssaySet bas
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exportableFields
private Map<String,BfsExporterPlugin.ExtendedExportableField> exportableFields
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PARAMETER_FILEFORMAT
public static final String PARAMETER_FILEFORMAT
- See Also:
- Constant Field Values
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PARAMETER_FILENAMEGENERATOR
public static final String PARAMETER_FILENAMEGENERATOR
- See Also:
- Constant Field Values
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Method Detail
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getMainType
public Plugin.MainType getMainType()
Description copied from interface:Plugin
Get the type of the plugin. This method must always return the same value.- Specified by:
getMainType
in interfacePlugin
- Returns:
- MainType.EXPORT
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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:AbstractPlugin
Returns FALSE, since that is how the plugins used to work before this method was introduced.- Specified by:
requiresConfiguration
in interfacePlugin
- Overrides:
requiresConfiguration
in classAbstractPlugin
- Returns:
- TRUE or FALSE
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getGuiContexts
public Set<GuiContext> 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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isInContext
public String isInContext(GuiContext context, Object item)
Description copied from interface:InteractivePlugin
Check if the plugin can be used on the specified object. The item is either aBasicItem
orBasicData
object, or null if called from a list context. A client application should only call this method for contexts matching one of the contexts in the set returned by theInteractivePlugin.getGuiContexts()
method. ForGuiContext.Type.ITEM
contexts an item of the correct type should be passed as a parameter.The plug-in can response with a null value indicating success, a warning-level message or throw an exception to indicate an error-level message. Client application should normally only show error-level messages to users, unless the user has requested to see warning messages.
NOTE! Before BASE 2.4 all messages were treated as error-level messages.
- 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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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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configure
public void configure(GuiContext context, Request request, Response response)
Description copied from interface:InteractivePlugin
Configure the plugin. Hopefully the client is supplying values for the parameters specified byInteractivePlugin.getRequestInformation(GuiContext, String)
.- 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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run
public void run(Request request, Response response, ProgressReporter progress)
Description copied from interface:Plugin
Run the plugin. If a progress reporter object is passed it is recommended that the plugin makes use of it.- Specified by:
run
in interfacePlugin
- Parameters:
request
- Request object with the command and parametersresponse
- Response object in for the plugin to response throughprogress
- AProgressReporter
where the plugin can report its progess, can be null
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getSignalHandler
public SignalHandler getSignalHandler()
Description copied from interface:SignalTarget
Get the signal handler that is handling signals on behalf of this object. Multiple invokations of this method may receive the same or different objects. Null may be returned if, for some reason, the current object instance doesn't want to receive signals. Returning null is the same as not implementing this interface.- Specified by:
getSignalHandler
in interfaceSignalTarget
- Returns:
- A SignalHandler object, or null if the current instance doesn't support signals
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begin
protected void begin(DbControl dc)
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performExport
protected void performExport(ProgressReporter progress) throws IOException
- Throws:
IOException
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end
protected void end(boolean success)
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getSuccessMessage
protected String getSuccessMessage()
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getConfigureJobParameters
private RequestInformation getConfigureJobParameters(GuiContext context)
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getExportableFields
public Map<String,BfsExporterPlugin.ExtendedExportableField> getExportableFields(DbControl dc, BioAssaySet source)
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getFormulaFields
private List<BfsExporterPlugin.ExtendedExportableField> getFormulaFields(DbControl dc, BioAssaySet source)
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getRawdataFields
private List<BfsExporterPlugin.ExtendedExportableField> getRawdataFields(BioAssaySet source)
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rawField
private BfsExporterPlugin.ExtendedExportableField rawField(String property, String title, Type type, Formula.AverageMethod averageMethod)
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getReporterFields
public static Collection<BfsExporterPlugin.ExtendedExportableField> getReporterFields()
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reporterField
private static BfsExporterPlugin.ExtendedExportableField reporterField(String property, String guiTitle, Type type, Formula.AverageMethod averageMethod)
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getExtraValueFields
private Collection<BfsExporterPlugin.ExtendedExportableField> getExtraValueFields(DbControl dc, BioAssaySet source)
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getSpotFields
private Collection<BfsExporterPlugin.ExtendedExportableField> getSpotFields(BioAssaySet source)
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getAssayFields
private List<BfsExporterPlugin.ExtendedExportableField> getAssayFields(DbControl dc, BioAssaySet source)
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assayField
private BfsExporterPlugin.ExtendedExportableField assayField(String property, String guiTitle, Type type)
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createFile
private File createFile(File dir, String name) throws IOException
- Throws:
IOException
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getFileFormatParameter
public static PluginParameter<String> getFileFormatParameter()
Create a plug-in parameter that asks for the BFS subtype to use in the export.
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getFileNameGeneratorParameter
public static PluginParameter<String> getFileNameGeneratorParameter()
Create a plug-in parameter that asks for the file name generation strategy.
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