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java.lang.Object net.sf.basedb.core.plugin.AbstractPlugin net.sf.basedb.plugins.BfsExporterPlugin
public class BfsExporterPlugin
Exports bioassay set data to BFS format.
Nested Class Summary | |
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static class |
BfsExporterPlugin.ExtendedExportableField
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Nested classes/interfaces inherited from interface net.sf.basedb.core.plugin.Plugin |
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Plugin.MainType |
Field Summary | |
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private static About |
about
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private BioAssaySet |
bas
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private RequestInformation |
configureJob
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private DbControl |
dc
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private Map<String,BfsExporterPlugin.ExtendedExportableField> |
exportableFields
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private static Set<GuiContext> |
guiContexts
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static String |
PARAMETER_FILEFORMAT
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static String |
PARAMETER_FILENAMEGENERATOR
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private ThreadSignalHandler |
signalHandler
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Fields inherited from class net.sf.basedb.core.plugin.AbstractPlugin |
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annotationSection, configuration, COPY_ANNOTATIONS, job, OVERWRITE_ANNOTATIONS, sc |
Constructor Summary | |
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BfsExporterPlugin()
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Methods inherited from class net.sf.basedb.core.plugin.AbstractPlugin |
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checkInterrupted, cloneParameterWithDefaultValue, closeLogFile, createLogFile, done, getCopyAnnotationsParmeter, getCurrentConfiguration, getCurrentJob, getJobOrConfigurationValue, getOverwriteAnnotationsParameters, getPermissions, init, log, log, storeValue, storeValue, storeValues, validateRequestParameters |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Methods inherited from interface net.sf.basedb.core.plugin.Plugin |
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done, getPermissions, init |
Field Detail |
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private static final About about
private static final Set<GuiContext> guiContexts
private ThreadSignalHandler signalHandler
private RequestInformation configureJob
private DbControl dc
private BioAssaySet bas
private Map<String,BfsExporterPlugin.ExtendedExportableField> exportableFields
public static final String PARAMETER_FILEFORMAT
public static final String PARAMETER_FILENAMEGENERATOR
Constructor Detail |
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public BfsExporterPlugin()
Method Detail |
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public Plugin.MainType getMainType()
Plugin
getMainType
in interface Plugin
public About getAbout()
Plugin
getAbout
in interface Plugin
About
objectpublic boolean supportsConfigurations()
AbstractPlugin
supportsConfigurations
in interface Plugin
supportsConfigurations
in class AbstractPlugin
public boolean requiresConfiguration()
AbstractPlugin
requiresConfiguration
in interface Plugin
requiresConfiguration
in class AbstractPlugin
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.
getGuiContexts
in interface InteractivePlugin
Set
containing Item
:s, or null
if the plugin is not concerned about itemspublic String isInContext(GuiContext context, Object item)
InteractivePlugin
BasicItem
or BasicData
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 the InteractivePlugin.getGuiContexts()
method. For GuiContext.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.
isInContext
in interface InteractivePlugin
context
- The current context of the client application,
it is one of the values found in set returned by InteractivePlugin.getGuiContexts()
item
- The currently active item, it's type should match the
GuiContext.getItem()
type, or null if the context is a list
context
Null
if the plugin can use that item, or
a warning-level message explaining why the plugin can't be usedpublic RequestInformation getRequestInformation(GuiContext context, String command) throws BaseException
InteractivePlugin
RequestInformation
for a given command, i.e.
the list of parameters and some nice help text.
getRequestInformation
in interface InteractivePlugin
context
- The current context of the client application,
it is one of the values found in set returned by InteractivePlugin.getGuiContexts()
command
- The command
RequestInformation
for the command
BaseException
- if there is an errorpublic void configure(GuiContext context, Request request, Response response)
InteractivePlugin
InteractivePlugin.getRequestInformation(GuiContext, String)
.
configure
in interface InteractivePlugin
context
- The current context of the client application,
it is one of the values found in set returned by InteractivePlugin.getGuiContexts()
request
- Request object with the command and parametersresponse
- Response object in for the plugin to response
throughpublic void run(Request request, Response response, ProgressReporter progress)
Plugin
run
in interface Plugin
request
- Request object with the command and parametersresponse
- Response object in for the plugin to response
throughprogress
- A ProgressReporter
where the plugin can report
its progess, can be nullpublic SignalHandler getSignalHandler()
SignalTarget
getSignalHandler
in interface SignalTarget
protected void begin(DbControl dc)
protected void performExport(ProgressReporter progress) throws IOException
IOException
protected void end(boolean success)
protected String getSuccessMessage()
private RequestInformation getConfigureJobParameters(GuiContext context)
public Map<String,BfsExporterPlugin.ExtendedExportableField> getExportableFields(DbControl dc, BioAssaySet source)
private List<BfsExporterPlugin.ExtendedExportableField> getFormulaFields(DbControl dc, BioAssaySet source)
private List<BfsExporterPlugin.ExtendedExportableField> getRawdataFields(BioAssaySet source)
private BfsExporterPlugin.ExtendedExportableField rawField(String property, String title, Type type, Formula.AverageMethod averageMethod)
public static Collection<BfsExporterPlugin.ExtendedExportableField> getReporterFields()
private static BfsExporterPlugin.ExtendedExportableField reporterField(String property, String guiTitle, Type type, Formula.AverageMethod averageMethod)
private Collection<BfsExporterPlugin.ExtendedExportableField> getExtraValueFields(DbControl dc, BioAssaySet source)
private Collection<BfsExporterPlugin.ExtendedExportableField> getSpotFields(BioAssaySet source)
private List<BfsExporterPlugin.ExtendedExportableField> getAssayFields(DbControl dc, BioAssaySet source)
private BfsExporterPlugin.ExtendedExportableField assayField(String property, String guiTitle, Type type)
private File createFile(File dir, String name) throws IOException
IOException
private File createFile(DbControl dc, Directory dir, String name)
public static PluginParameter<String> getFileFormatParameter()
public static PluginParameter<String> getFileNameGeneratorParameter()
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