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/* |
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Copyright (C) 2006, 2007, 2011 Nicklas Nordborg |
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3 |
|
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This file is part of the Example Code Package for BASE. |
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Available at http://baseplugins.thep.lu.se/ |
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BASE main site: http://base.thep.lu.se/ |
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7 |
|
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This is free software; you can redistribute it and/or |
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modify it under the terms of the GNU General Public License |
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as published by the Free Software Foundation; either version 3 |
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of the License, or (at your option) any later version. |
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12 |
|
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The software is distributed in the hope that it will be useful, |
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but WITHOUT ANY WARRANTY; without even the implied warranty of |
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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GNU General Public License for more details. |
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17 |
|
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You should have received a copy of the GNU General Public License |
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along with BASE. If not, see <http://www.gnu.org/licenses/>. |
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*/ |
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package net.sf.basedb.examples.plugins; |
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|
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import net.sf.basedb.core.BooleanParameterType; |
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import net.sf.basedb.core.BaseException; |
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import net.sf.basedb.core.DbControl; |
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import net.sf.basedb.core.Item; |
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import net.sf.basedb.core.Job; |
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import net.sf.basedb.core.File; |
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import net.sf.basedb.core.FileParameterType; |
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import net.sf.basedb.core.PluginParameter; |
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import net.sf.basedb.core.ProgressReporter; |
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import net.sf.basedb.core.RequestInformation; |
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|
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import net.sf.basedb.core.plugin.About; |
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import net.sf.basedb.core.plugin.AboutImpl; |
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36 |
import net.sf.basedb.core.plugin.AbstractPlugin; |
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37 |
import net.sf.basedb.core.plugin.AutoDetectingImporter; |
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import net.sf.basedb.core.plugin.InteractivePlugin; |
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import net.sf.basedb.core.plugin.GuiContext; |
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import net.sf.basedb.core.plugin.Plugin; |
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import net.sf.basedb.core.plugin.Request; |
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import net.sf.basedb.core.plugin.Response; |
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import net.sf.basedb.core.signal.SignalHandler; |
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import net.sf.basedb.core.signal.SignalTarget; |
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import net.sf.basedb.core.signal.ThreadSignalHandler; |
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|
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import java.io.InputStream; |
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import java.util.ArrayList; |
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import java.util.Arrays; |
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import java.util.Collections; |
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import java.util.List; |
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import java.util.Set; |
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|
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|
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/** |
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An example plugin that pretends to import samples. It can't be configured, |
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but will ask for a file to import from and if existing samples should be updated |
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or not. It won't actually import any samples, but will report that a few samples |
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has been imported. |
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60 |
|
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@base.modified $Date$ |
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@author Nicklas |
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@version 2.0 |
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*/ |
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public class ExampleImporter |
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extends AbstractPlugin |
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implements InteractivePlugin, AutoDetectingImporter, SignalTarget |
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{ |
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|
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private static final About about = |
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new AboutImpl |
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( |
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"Example importer", |
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"An example plugin that pretends to import samples. It can't be configured, " + |
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"but will ask for a file to import from and if existing samples should be updated " + |
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"or not. It won't actually import any samples, but will report that a few samples " + |
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"has been imported.", |
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"2.17", |
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"2006, Base 2 development team", |
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null, |
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null, |
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"http://base.thep.lu.se" |
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); |
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|
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private static final Set<GuiContext> guiContexts = Collections.singleton( |
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new GuiContext(Item.SAMPLE, GuiContext.Type.LIST) |
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); |
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|
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// Plugin configuration is created by getConfigurePlugin() |
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private RequestInformation configurePlugin; |
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|
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// Job configuration is created by getConfigureJob() |
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private RequestInformation configureJob; |
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|
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// Parameter that asks for the file to import from |
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private PluginParameter<File> fileParameter; |
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|
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// Parameter that asks if existing items should be updated or not |
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private PluginParameter<Boolean> updateExistingParameter; |
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|
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// |
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private DbControl dc; |
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|
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// So we can react to ABORT requests |
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private ThreadSignalHandler signalHandler; |
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|
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/** |
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Create a new example importer. |
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*/ |
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public ExampleImporter() |
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{} |
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|
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/* |
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From the Plugin interface |
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------------------------------------------- |
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116 |
*/ |
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@Override |
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public Plugin.MainType getMainType() |
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{ |
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return Plugin.MainType.IMPORT; |
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} |
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@Override |
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public boolean supportsConfigurations() |
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{ |
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return true; |
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} |
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@Override |
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public boolean requiresConfiguration() |
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{ |
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return false; |
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} |
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@Override |
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public void run(Request request, Response response, ProgressReporter progress) |
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{ |
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// Ensure that the ABORT signal gets sent to this thread |
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if (signalHandler != null) signalHandler.setWorkerThread(null); |
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|
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// Open a connection to the database |
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// sc is set by init() method |
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DbControl dc = sc.newDbControl(); |
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try |
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{ |
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// Get the parameters from the job configuration |
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boolean updateExisting = (Boolean)job.getValue("updateExisting"); |
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File f = (File)job.getValue("file"); |
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|
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// Open the file an import it |
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f = File.getById(dc, f.getId()); |
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InputStream in = f.getDownloadStream(0); |
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doImport(in, progress); |
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in.close(); |
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|
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// Commit the work |
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dc.commit(); |
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response.setDone("Plugin ended successfully"); |
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} |
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catch (Throwable t) |
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{ |
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// All exceptions must be catched and sent back |
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// using the response object |
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response.setError(t.getMessage(), Arrays.asList(t)); |
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} |
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finally |
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{ |
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// IMPORTANT!!! Make sure opened connections are closed |
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if (dc != null) dc.close(); |
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} |
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} |
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// ------------------------------------------- |
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|
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/* |
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From the InteractivePlugin interface |
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------------------------------------------- |
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174 |
*/ |
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175 |
/** |
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Return a set containing the context [SAMPLE, LIST]. |
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177 |
*/ |
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@Override |
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179 |
public Set<GuiContext> getGuiContexts() |
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{ |
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181 |
return guiContexts; |
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} |
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183 |
/** |
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Always null, we are not dealing with individual items. |
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185 |
*/ |
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@Override |
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public String isInContext(GuiContext context, Object item) |
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188 |
{ |
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189 |
return null; |
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} |
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191 |
/** |
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The {@link Request#COMMAND_CONFIGURE_PLUGIN} command will not ask |
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for any parameters. |
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<p> |
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The {@link Request#COMMAND_CONFIGURE_JOB} command will ask for |
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a file and if existing samples should be updated or ignored. |
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197 |
*/ |
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198 |
@Override |
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199 |
public RequestInformation getRequestInformation(GuiContext context, String command) |
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200 |
throws BaseException |
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201 |
{ |
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202 |
RequestInformation requestInformation = null; |
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203 |
if (command.equals(Request.COMMAND_CONFIGURE_PLUGIN)) |
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204 |
{ |
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205 |
requestInformation = getConfigurePlugin(); |
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28 Apr 11 |
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206 |
} |
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207 |
else if (command.equals(Request.COMMAND_CONFIGURE_JOB)) |
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{ |
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209 |
requestInformation = getConfigureJob(context); |
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210 |
} |
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211 |
return requestInformation; |
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212 |
} |
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213 |
/** |
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Store configuration settings for {@link Request#COMMAND_CONFIGURE_PLUGIN} and |
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11 Apr 08 |
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{@link Request#COMMAND_CONFIGURE_JOB}. |
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216 |
*/ |
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217 |
@Override |
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218 |
public void configure(GuiContext context, Request request, Response response) |
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11 Apr 08 |
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219 |
{ |
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11 Apr 08 |
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220 |
String command = request.getCommand(); |
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11 Apr 08 |
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221 |
try |
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11 Apr 08 |
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222 |
{ |
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223 |
if (command.equals(Request.COMMAND_CONFIGURE_PLUGIN)) |
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11 Apr 08 |
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224 |
{ |
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11 Apr 08 |
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225 |
List<Throwable> errors = |
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28 Apr 11 |
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226 |
validateRequestParameters(getConfigurePlugin().getParameters(), request); |
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28 Apr 11 |
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227 |
if (errors != null) |
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28 Apr 11 |
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228 |
{ |
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28 Apr 11 |
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229 |
response.setError(errors.size()+" invalid parameter(s) were found in the request", errors); |
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28 Apr 11 |
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230 |
return; |
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28 Apr 11 |
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231 |
} |
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28 Apr 11 |
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232 |
|
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28 Apr 11 |
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233 |
storeValue(configuration, request, updateExistingParameter); |
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28 Apr 11 |
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234 |
response.setDone("Configuration completed"); |
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28 Apr 11 |
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235 |
} |
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28 Apr 11 |
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236 |
else if (command.equals(Request.COMMAND_CONFIGURE_JOB)) |
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28 Apr 11 |
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237 |
{ |
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28 Apr 11 |
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238 |
List<Throwable> errors = |
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11 Apr 08 |
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239 |
validateRequestParameters(getConfigureJob(context).getParameters(), request); |
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11 Apr 08 |
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240 |
if (errors != null) |
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11 Apr 08 |
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241 |
{ |
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11 Apr 08 |
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242 |
response.setError(errors.size()+" invalid parameter(s) were found in the request", errors); |
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11 Apr 08 |
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243 |
return; |
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11 Apr 08 |
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244 |
} |
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11 Apr 08 |
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245 |
|
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11 Apr 08 |
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246 |
storeValue(job, request, fileParameter); |
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11 Apr 08 |
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247 |
storeValue(job, request, updateExistingParameter); |
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248 |
File importFile = (File)job.getValue(fileParameter.getName()); |
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24 Feb 11 |
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249 |
response.setSuggestedJobName("Import samples from '" + importFile.getName() + "'"); |
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11 Apr 08 |
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250 |
response.setDone("Job configuration complete", Job.ExecutionTime.SHORT); |
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11 Apr 08 |
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// TODO - maybe check file size to make a better estimate |
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11 Apr 08 |
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252 |
} |
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11 Apr 08 |
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253 |
} |
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11 Apr 08 |
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254 |
catch (Throwable ex) |
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11 Apr 08 |
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255 |
{ |
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11 Apr 08 |
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256 |
response.setError(ex.getMessage(), Arrays.asList(ex)); |
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11 Apr 08 |
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257 |
} |
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11 Apr 08 |
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258 |
} |
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11 Apr 08 |
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259 |
// ------------------------------------------- |
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11 Apr 08 |
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260 |
|
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11 Apr 08 |
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261 |
|
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11 Apr 08 |
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262 |
/* |
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11 Apr 08 |
nicklas |
From the AutoDetectingImporter interface |
647 |
11 Apr 08 |
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264 |
------------------------------------------- |
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11 Apr 08 |
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265 |
*/ |
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11 Apr 08 |
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266 |
/** |
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11 Apr 08 |
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Always true, since we accept all files. |
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11 Apr 08 |
nicklas |
268 |
*/ |
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24 Feb 11 |
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269 |
@Override |
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11 Apr 08 |
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270 |
public boolean isImportable(InputStream in) |
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11 Apr 08 |
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271 |
throws BaseException |
647 |
11 Apr 08 |
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272 |
{ |
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11 Apr 08 |
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273 |
return true; |
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11 Apr 08 |
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274 |
} |
647 |
11 Apr 08 |
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275 |
/** |
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11 Apr 08 |
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We don't do anything in this method. |
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11 Apr 08 |
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277 |
*/ |
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278 |
@Override |
647 |
11 Apr 08 |
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279 |
public void doImport(InputStream in, ProgressReporter progress) |
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11 Apr 08 |
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280 |
throws BaseException |
647 |
11 Apr 08 |
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281 |
{ |
647 |
11 Apr 08 |
nicklas |
// Check if the ABORT signal has been sent |
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24 Feb 11 |
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283 |
ThreadSignalHandler.checkInterrupted(); |
647 |
11 Apr 08 |
nicklas |
284 |
/* |
647 |
11 Apr 08 |
nicklas |
Pseudo code: |
647 |
11 Apr 08 |
nicklas |
Parse input stream, for each found sample: |
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24 Feb 11 |
nicklas |
ThreadSignalHandler.checkInterrupted(); // Do this as the first thing in a loop |
647 |
11 Apr 08 |
nicklas |
String name = ... |
647 |
11 Apr 08 |
nicklas |
String externalId = ... |
647 |
11 Apr 08 |
nicklas |
boolean isNew = false; |
647 |
11 Apr 08 |
nicklas |
Sample s = getByExternalId(externalId); |
647 |
11 Apr 08 |
nicklas |
if (s == null) |
647 |
11 Apr 08 |
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293 |
{ |
647 |
11 Apr 08 |
nicklas |
s = Sample.getNew(dc); |
1292 |
24 Feb 11 |
nicklas |
s.setName(name) // and other properites |
647 |
11 Apr 08 |
nicklas |
dc.saveItem(s); |
647 |
11 Apr 08 |
nicklas |
isNew = true; |
647 |
11 Apr 08 |
nicklas |
298 |
} |
647 |
11 Apr 08 |
nicklas |
if (updateExisting || isNew) |
647 |
11 Apr 08 |
nicklas |
300 |
{ |
647 |
11 Apr 08 |
nicklas |
s.setName(name); |
647 |
11 Apr 08 |
nicklas |
s.setExternalId(externalId); |
647 |
11 Apr 08 |
nicklas |
303 |
... |
647 |
11 Apr 08 |
nicklas |
304 |
} |
647 |
11 Apr 08 |
nicklas |
305 |
*/ |
647 |
11 Apr 08 |
nicklas |
306 |
} |
647 |
11 Apr 08 |
nicklas |
307 |
// ------------------------------------------- |
647 |
11 Apr 08 |
nicklas |
308 |
/* |
647 |
11 Apr 08 |
nicklas |
From the SignalTarget interface |
647 |
11 Apr 08 |
nicklas |
310 |
------------------------------------------- |
647 |
11 Apr 08 |
nicklas |
311 |
*/ |
1292 |
24 Feb 11 |
nicklas |
312 |
@Override |
647 |
11 Apr 08 |
nicklas |
313 |
public SignalHandler getSignalHandler() |
647 |
11 Apr 08 |
nicklas |
314 |
{ |
647 |
11 Apr 08 |
nicklas |
315 |
signalHandler = new ThreadSignalHandler(); |
647 |
11 Apr 08 |
nicklas |
316 |
return signalHandler; |
647 |
11 Apr 08 |
nicklas |
317 |
} |
647 |
11 Apr 08 |
nicklas |
318 |
// ------------------------------------------- |
647 |
11 Apr 08 |
nicklas |
319 |
|
647 |
11 Apr 08 |
nicklas |
320 |
private RequestInformation getConfigureJob(GuiContext context) |
647 |
11 Apr 08 |
nicklas |
321 |
{ |
647 |
11 Apr 08 |
nicklas |
322 |
if (configureJob == null) |
647 |
11 Apr 08 |
nicklas |
323 |
{ |
647 |
11 Apr 08 |
nicklas |
// Create file parameter |
647 |
11 Apr 08 |
nicklas |
325 |
fileParameter = new PluginParameter<File>( |
647 |
11 Apr 08 |
nicklas |
326 |
"file", |
647 |
11 Apr 08 |
nicklas |
327 |
"File", |
647 |
11 Apr 08 |
nicklas |
328 |
"The file to import the data from", |
647 |
11 Apr 08 |
nicklas |
329 |
new FileParameterType(null, true, 1) |
647 |
11 Apr 08 |
nicklas |
330 |
); |
647 |
11 Apr 08 |
nicklas |
331 |
|
1351 |
28 Apr 11 |
nicklas |
332 |
boolean defaultUpdateExisting = false; |
1351 |
28 Apr 11 |
nicklas |
333 |
if (configuration != null) |
1351 |
28 Apr 11 |
nicklas |
334 |
{ |
1351 |
28 Apr 11 |
nicklas |
335 |
defaultUpdateExisting = Boolean.TRUE.equals(configuration.getValue("updateExisting")); |
1351 |
28 Apr 11 |
nicklas |
336 |
} |
647 |
11 Apr 08 |
nicklas |
// Create update existing parameter |
647 |
11 Apr 08 |
nicklas |
338 |
updateExistingParameter = new PluginParameter<Boolean>( |
647 |
11 Apr 08 |
nicklas |
339 |
"updateExisting", |
647 |
11 Apr 08 |
nicklas |
340 |
"Update existing samples", |
647 |
11 Apr 08 |
nicklas |
341 |
"If this option is selected, already existing samples will be updated with the information "+ |
647 |
11 Apr 08 |
nicklas |
342 |
"in the file. If this option isn't selected existing samples are left untouched.", |
1351 |
28 Apr 11 |
nicklas |
343 |
new BooleanParameterType(defaultUpdateExisting, true) |
647 |
11 Apr 08 |
nicklas |
344 |
); |
647 |
11 Apr 08 |
nicklas |
345 |
|
647 |
11 Apr 08 |
nicklas |
// Create parameter list and request informaion |
647 |
11 Apr 08 |
nicklas |
347 |
List<PluginParameter<?>> parameters = new ArrayList<PluginParameter<?>>(); |
647 |
11 Apr 08 |
nicklas |
348 |
parameters.add(fileParameter); |
647 |
11 Apr 08 |
nicklas |
349 |
parameters.add(updateExistingParameter); |
647 |
11 Apr 08 |
nicklas |
350 |
|
647 |
11 Apr 08 |
nicklas |
351 |
configureJob = new RequestInformation |
647 |
11 Apr 08 |
nicklas |
352 |
( |
647 |
11 Apr 08 |
nicklas |
353 |
Request.COMMAND_CONFIGURE_JOB, |
647 |
11 Apr 08 |
nicklas |
354 |
"Select a file to import samples from", |
647 |
11 Apr 08 |
nicklas |
355 |
"This is an example plugin, it will accept any file but won't import any samples.", |
647 |
11 Apr 08 |
nicklas |
356 |
parameters |
647 |
11 Apr 08 |
nicklas |
357 |
); |
647 |
11 Apr 08 |
nicklas |
358 |
} |
647 |
11 Apr 08 |
nicklas |
359 |
return configureJob; |
647 |
11 Apr 08 |
nicklas |
360 |
} |
647 |
11 Apr 08 |
nicklas |
361 |
|
1351 |
28 Apr 11 |
nicklas |
362 |
private RequestInformation getConfigurePlugin() |
1351 |
28 Apr 11 |
nicklas |
363 |
{ |
1351 |
28 Apr 11 |
nicklas |
364 |
if (configurePlugin == null) |
1351 |
28 Apr 11 |
nicklas |
365 |
{ |
1351 |
28 Apr 11 |
nicklas |
366 |
|
1351 |
28 Apr 11 |
nicklas |
// Create update existing parameter |
1351 |
28 Apr 11 |
nicklas |
368 |
updateExistingParameter = new PluginParameter<Boolean>( |
1351 |
28 Apr 11 |
nicklas |
369 |
"updateExisting", |
1351 |
28 Apr 11 |
nicklas |
370 |
"Update existing samples", |
1351 |
28 Apr 11 |
nicklas |
371 |
"If this option is selected, already existing samples will be updated with the information "+ |
1351 |
28 Apr 11 |
nicklas |
372 |
"in the file. If this option isn't selected existing samples are left untouched.", |
1351 |
28 Apr 11 |
nicklas |
373 |
new BooleanParameterType(false, true) |
1351 |
28 Apr 11 |
nicklas |
374 |
); |
1351 |
28 Apr 11 |
nicklas |
375 |
|
1351 |
28 Apr 11 |
nicklas |
// Create parameter list and request informaion |
1351 |
28 Apr 11 |
nicklas |
377 |
List<PluginParameter<?>> parameters = new ArrayList<PluginParameter<?>>(); |
1351 |
28 Apr 11 |
nicklas |
378 |
parameters.add(updateExistingParameter); |
1351 |
28 Apr 11 |
nicklas |
379 |
|
1351 |
28 Apr 11 |
nicklas |
380 |
configurePlugin = new RequestInformation |
1351 |
28 Apr 11 |
nicklas |
381 |
( |
1351 |
28 Apr 11 |
nicklas |
382 |
Request.COMMAND_CONFIGURE_PLUGIN, |
1351 |
28 Apr 11 |
nicklas |
383 |
"Default settings", |
1351 |
28 Apr 11 |
nicklas |
384 |
"This is an example plugin, it will accept any file but won't import any samples.", |
1351 |
28 Apr 11 |
nicklas |
385 |
parameters |
1351 |
28 Apr 11 |
nicklas |
386 |
); |
1351 |
28 Apr 11 |
nicklas |
387 |
} |
1351 |
28 Apr 11 |
nicklas |
388 |
return configurePlugin; |
1351 |
28 Apr 11 |
nicklas |
389 |
} |
1351 |
28 Apr 11 |
nicklas |
390 |
|
1351 |
28 Apr 11 |
nicklas |
391 |
|
647 |
11 Apr 08 |
nicklas |
392 |
} |