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/** |
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nicklas |
$Id$ |
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3 |
|
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jari |
Copyright (C) 2006, 2007 Nicklas Nordborg |
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5 |
|
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This file is part of BASE - BioArray Software Environment. |
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Available at http://base.thep.lu.se/ |
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8 |
|
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BASE 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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05 Sep 08 |
jari |
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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13 |
|
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BASE 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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18 |
|
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You should have received a copy of the GNU General Public License |
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11 Sep 08 |
jari |
along with BASE. If not, see <http://www.gnu.org/licenses/>. |
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*/ |
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22 |
package net.sf.basedb.util.zip; |
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|
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24 |
import java.io.InputStream; |
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25 |
import java.util.ArrayList; |
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import java.util.Arrays; |
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import java.util.Collection; |
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import java.util.Collections; |
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import java.util.EnumSet; |
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import java.util.HashSet; |
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import java.util.List; |
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32 |
import java.util.Set; |
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33 |
|
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34 |
import net.sf.basedb.core.AbsoluteProgressReporter; |
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35 |
import net.sf.basedb.core.BaseException; |
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36 |
import net.sf.basedb.core.BooleanParameterType; |
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37 |
import net.sf.basedb.core.DbControl; |
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38 |
import net.sf.basedb.core.Directory; |
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39 |
import net.sf.basedb.core.File; |
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40 |
import net.sf.basedb.core.Item; |
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41 |
import net.sf.basedb.core.ItemParameterType; |
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42 |
import net.sf.basedb.core.Path; |
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import net.sf.basedb.core.PathParameterType; |
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import net.sf.basedb.core.Permission; |
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import net.sf.basedb.core.PluginParameter; |
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46 |
import net.sf.basedb.core.ProgressReporter; |
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47 |
import net.sf.basedb.core.RequestInformation; |
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48 |
import net.sf.basedb.core.SimpleAbsoluteProgressReporter; |
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49 |
import net.sf.basedb.core.plugin.AbstractPlugin; |
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50 |
import net.sf.basedb.core.plugin.GuiContext; |
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import net.sf.basedb.core.plugin.InteractivePlugin; |
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import net.sf.basedb.core.plugin.Permissions; |
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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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/** |
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This is a base class for all plugins that wants to implement the {@link FileUnpacker} |
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interface. This class takes care of all the hard work that is required by a plugin. |
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Ie. the creating and saving the parameters that are needed, context checking, etc. |
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The subclass only has to implement the remaingin methods in the {@link FileUnpacker} |
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interface which basically boils down to implementing the actual unpacking of the |
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compressed file. |
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<p> |
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The implementation in this class asks for three parameters: |
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<ul> |
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<li>The file to unpack |
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<li>The directory where the files should be placed |
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<li>If existing files should be overwritten or not |
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</ul> |
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A subclass may override any of the methods in this class if it has different |
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needs. |
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76 |
|
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@author nicklas |
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@version 2.0 |
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@base.modified $Date$ |
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80 |
*/ |
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public abstract class AbstractFileUnpacker |
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extends AbstractPlugin |
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implements FileUnpacker, InteractivePlugin, SignalTarget |
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{ |
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85 |
|
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86 |
/** |
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The context is always [ FILE, ITEM]. |
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88 |
*/ |
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private static final Set<GuiContext> guiContexts = |
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Collections.singleton(new GuiContext(Item.FILE, GuiContext.Type.ITEM)); |
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|
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private static final Set<Permissions> permissions = new HashSet<Permissions>(); |
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93 |
|
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94 |
/** |
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The parameter type for file to unpack. |
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96 |
*/ |
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97 |
private static final ItemParameterType<File> zipFileType = |
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new ItemParameterType<File>(File.class, null, true, 1, null); |
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99 |
|
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100 |
/** |
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The parameter type for unpack directory. |
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102 |
*/ |
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103 |
private static final PathParameterType unpackType = |
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104 |
new PathParameterType(Path.Type.DIRECTORY, null, true); |
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105 |
|
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106 |
private RequestInformation configureJob; |
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107 |
|
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private ThreadSignalHandler signalHandler; |
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109 |
|
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110 |
/* |
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02 Oct 06 |
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From the Plugin interface |
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02 Oct 06 |
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112 |
------------------------------------------- |
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113 |
*/ |
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@Override |
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public MainType getMainType() |
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{ |
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return Plugin.MainType.OTHER; |
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} |
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/** |
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Returns FALSE. |
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121 |
*/ |
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122 |
@Override |
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123 |
public boolean supportsConfigurations() |
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124 |
{ |
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125 |
return false; |
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126 |
} |
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127 |
/** |
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03 Oct 06 |
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Returns FALSE. |
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129 |
*/ |
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@Override |
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131 |
public boolean requiresConfiguration() |
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132 |
{ |
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133 |
return false; |
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134 |
} |
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135 |
/** |
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11 Oct 06 |
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Request create and write access to File:s and Directory:s. |
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137 |
*/ |
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@Override |
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public Collection<Permissions> getPermissions() |
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{ |
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11 Oct 06 |
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141 |
if (permissions.size() == 0) |
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11 Oct 06 |
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142 |
{ |
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permissions.add(new Permissions(Item.FILE, null, EnumSet.of(Permission.CREATE, Permission.WRITE))); |
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permissions.add(new Permissions(Item.DIRECTORY, null, EnumSet.of(Permission.CREATE, Permission.WRITE))); |
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23 Sep 11 |
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permissions.add(new Permissions(Item.ITEMSUBTYPE, EnumSet.of(Permission.USE), null)); |
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146 |
} |
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147 |
return permissions; |
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148 |
} |
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149 |
|
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@Override |
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151 |
public void run(Request request, Response response, ProgressReporter progress) |
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02 Oct 06 |
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152 |
{ |
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02 Oct 06 |
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153 |
DbControl dc = sc.newDbControl(); |
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154 |
InputStream in = null; |
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02 Oct 06 |
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155 |
try |
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156 |
{ |
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02 Oct 06 |
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// Get all parameters |
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02 Oct 06 |
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158 |
File zipFile = getZipFile(dc); |
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02 Oct 06 |
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159 |
Directory dir = getUnpackDirectory(dc); |
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02 Oct 06 |
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160 |
boolean overwrite = getOverwrite(); |
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02 Oct 06 |
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161 |
|
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02 Oct 06 |
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162 |
in = zipFile.getDownloadStream(0); |
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02 Oct 06 |
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163 |
AbsoluteProgressReporter absoluteProgress = progress == null ? |
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02 Oct 06 |
nicklas |
164 |
null : new SimpleAbsoluteProgressReporter(progress, zipFile.getSize()); |
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02 Oct 06 |
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165 |
|
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02 Oct 06 |
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// Unpack the file |
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23 Sep 11 |
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167 |
int numFiles = unpack(dc, dir, in, zipFile, overwrite, absoluteProgress); |
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02 Oct 06 |
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168 |
dc.commit(); |
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02 Oct 06 |
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169 |
|
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02 Oct 06 |
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170 |
response.setDone(numFiles + " file(s) unpacked successfully"); |
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02 Oct 06 |
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171 |
} |
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172 |
catch (Throwable t) |
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173 |
{ |
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02 Oct 06 |
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174 |
response.setError(t.getMessage(), Arrays.asList(t)); |
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02 Oct 06 |
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175 |
} |
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02 Oct 06 |
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finally |
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02 Oct 06 |
nicklas |
177 |
{ |
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02 Oct 06 |
nicklas |
178 |
if (dc != null) dc.close(); |
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02 Oct 06 |
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179 |
} |
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180 |
} |
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02 Oct 06 |
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181 |
// ------------------------------------------- |
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02 Oct 06 |
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182 |
|
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02 Oct 06 |
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183 |
/* |
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02 Oct 06 |
nicklas |
From the InteractivePlugin interface |
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02 Oct 06 |
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185 |
------------------------------------------- |
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02 Oct 06 |
nicklas |
186 |
*/ |
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187 |
@Override |
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02 Oct 06 |
nicklas |
188 |
public Set<GuiContext> getGuiContexts() |
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02 Oct 06 |
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189 |
{ |
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02 Oct 06 |
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190 |
return guiContexts; |
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02 Oct 06 |
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191 |
} |
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14 Sep 12 |
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192 |
@Override |
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02 Oct 06 |
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193 |
public String isInContext(GuiContext context, Object item) |
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02 Oct 06 |
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194 |
{ |
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02 Oct 06 |
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195 |
String message = null; |
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02 Oct 06 |
nicklas |
196 |
if (item == null) |
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02 Oct 06 |
nicklas |
197 |
{ |
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02 Oct 06 |
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198 |
message = "The object is null"; |
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02 Oct 06 |
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199 |
} |
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02 Oct 06 |
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200 |
else if (!(item instanceof File)) |
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02 Oct 06 |
nicklas |
201 |
{ |
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02 Oct 06 |
nicklas |
202 |
message = "The object is not a File: " + item; |
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02 Oct 06 |
nicklas |
203 |
} |
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02 Oct 06 |
nicklas |
204 |
else |
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02 Oct 06 |
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205 |
{ |
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02 Oct 06 |
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206 |
File f = (File)item; |
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02 Oct 06 |
nicklas |
207 |
String name = f.getName(); |
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02 Oct 06 |
nicklas |
208 |
String mimeType = f.getMimeType(); |
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02 Oct 06 |
nicklas |
209 |
if (!getMimeTypes().contains(mimeType)) |
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02 Oct 06 |
nicklas |
210 |
{ |
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19 Jun 07 |
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211 |
for (String extension : getExtensions()) |
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02 Oct 06 |
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212 |
{ |
3510 |
19 Jun 07 |
nicklas |
213 |
if (name.endsWith(extension)) return null; |
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02 Oct 06 |
nicklas |
214 |
} |
3510 |
19 Jun 07 |
nicklas |
215 |
message = "Unsupported file: " + f.getPath().toString(); |
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02 Oct 06 |
nicklas |
216 |
} |
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02 Oct 06 |
nicklas |
217 |
} |
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02 Oct 06 |
nicklas |
218 |
return message; |
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02 Oct 06 |
nicklas |
219 |
} |
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02 Oct 06 |
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220 |
|
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14 Sep 12 |
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221 |
@Override |
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02 Oct 06 |
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222 |
public RequestInformation getRequestInformation(GuiContext context, String command) |
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02 Oct 06 |
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223 |
throws BaseException |
2689 |
02 Oct 06 |
nicklas |
224 |
{ |
2689 |
02 Oct 06 |
nicklas |
225 |
RequestInformation requestInformation = null; |
2689 |
02 Oct 06 |
nicklas |
226 |
if (command.equals(Request.COMMAND_CONFIGURE_JOB)) |
2689 |
02 Oct 06 |
nicklas |
227 |
{ |
2689 |
02 Oct 06 |
nicklas |
228 |
requestInformation = getConfigureJobParameters(context); |
2689 |
02 Oct 06 |
nicklas |
229 |
} |
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02 Oct 06 |
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230 |
return requestInformation; |
2689 |
02 Oct 06 |
nicklas |
231 |
} |
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232 |
@Override |
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02 Oct 06 |
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233 |
public void configure(GuiContext context, Request request, Response response) |
2689 |
02 Oct 06 |
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234 |
{ |
2689 |
02 Oct 06 |
nicklas |
235 |
String command = request.getCommand(); |
2689 |
02 Oct 06 |
nicklas |
236 |
try |
2689 |
02 Oct 06 |
nicklas |
237 |
{ |
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02 Oct 06 |
nicklas |
238 |
if (command.equals(Request.COMMAND_CONFIGURE_JOB)) |
2689 |
02 Oct 06 |
nicklas |
239 |
{ |
2689 |
02 Oct 06 |
nicklas |
240 |
RequestInformation ri = getConfigureJobParameters(context); |
2689 |
02 Oct 06 |
nicklas |
241 |
List<Throwable> errors = validateRequestParameters (ri.getParameters(), request); |
2689 |
02 Oct 06 |
nicklas |
242 |
if (errors != null) |
2689 |
02 Oct 06 |
nicklas |
243 |
{ |
2689 |
02 Oct 06 |
nicklas |
244 |
response.setError(errors.size() + " invalid parameters were found in the request",errors); |
2689 |
02 Oct 06 |
nicklas |
245 |
return; |
2689 |
02 Oct 06 |
nicklas |
246 |
} |
2689 |
02 Oct 06 |
nicklas |
247 |
|
2689 |
02 Oct 06 |
nicklas |
248 |
storeValue(job, request, ri.getParameter(ZIP_FILE)); |
2689 |
02 Oct 06 |
nicklas |
249 |
storeValue(job, request, ri.getParameter(UNPACK_DIRECTORY)); |
2689 |
02 Oct 06 |
nicklas |
250 |
storeValue(job, request, ri.getParameter(OVERWRITE)); |
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02 Oct 06 |
nicklas |
251 |
|
5481 |
08 Nov 10 |
nicklas |
252 |
File file = (File)job.getValue(ZIP_FILE); |
5481 |
08 Nov 10 |
nicklas |
253 |
response.setSuggestedJobName("Unpack file '" + file.getName() + |
5481 |
08 Nov 10 |
nicklas |
254 |
"' to " + job.getValue(UNPACK_DIRECTORY)); |
5481 |
08 Nov 10 |
nicklas |
255 |
|
2689 |
02 Oct 06 |
nicklas |
256 |
response.setDone("The job configuration is complete"); |
2689 |
02 Oct 06 |
nicklas |
257 |
} |
2689 |
02 Oct 06 |
nicklas |
258 |
} |
2689 |
02 Oct 06 |
nicklas |
259 |
catch(Throwable ex) |
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02 Oct 06 |
nicklas |
260 |
{ |
2689 |
02 Oct 06 |
nicklas |
261 |
response.setError(ex.getMessage(), Arrays.asList(ex)); |
2689 |
02 Oct 06 |
nicklas |
262 |
} |
2689 |
02 Oct 06 |
nicklas |
263 |
} |
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02 Oct 06 |
nicklas |
264 |
// ------------------------------------------- |
4118 |
01 Feb 08 |
nicklas |
265 |
/* |
4118 |
01 Feb 08 |
nicklas |
From the SignalTarget interface |
4118 |
01 Feb 08 |
nicklas |
267 |
------------------------------------------- |
4118 |
01 Feb 08 |
nicklas |
268 |
*/ |
6127 |
14 Sep 12 |
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269 |
@Override |
4118 |
01 Feb 08 |
nicklas |
270 |
public SignalHandler getSignalHandler() |
4118 |
01 Feb 08 |
nicklas |
271 |
{ |
4118 |
01 Feb 08 |
nicklas |
272 |
signalHandler = new ThreadSignalHandler(); |
4118 |
01 Feb 08 |
nicklas |
273 |
return signalHandler; |
4118 |
01 Feb 08 |
nicklas |
274 |
} |
4118 |
01 Feb 08 |
nicklas |
275 |
// ------------------------------------------- |
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02 Oct 06 |
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276 |
|
2689 |
02 Oct 06 |
nicklas |
277 |
/** |
2689 |
02 Oct 06 |
nicklas |
The name of the parameter that asks for the file that is going to |
2689 |
02 Oct 06 |
nicklas |
be unpacked. |
2689 |
02 Oct 06 |
nicklas |
@see #getZipFileParameter(String, String) |
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02 Oct 06 |
nicklas |
281 |
*/ |
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02 Oct 06 |
nicklas |
282 |
protected static final String ZIP_FILE = "zipFile"; |
2689 |
02 Oct 06 |
nicklas |
283 |
|
2689 |
02 Oct 06 |
nicklas |
284 |
/** |
2689 |
02 Oct 06 |
nicklas |
Get a plugin parameter that asks for the file that is going to |
2689 |
02 Oct 06 |
nicklas |
be unpacked. |
2689 |
02 Oct 06 |
nicklas |
287 |
|
2689 |
02 Oct 06 |
nicklas |
@param label The parameter label, or null to use the default (File) |
2689 |
02 Oct 06 |
nicklas |
@param description The parameter description, or null to use the default |
2689 |
02 Oct 06 |
nicklas |
(The file to unpack.) |
2689 |
02 Oct 06 |
nicklas |
291 |
*/ |
2689 |
02 Oct 06 |
nicklas |
292 |
protected PluginParameter<File> getZipFileParameter(String label, String description) |
2689 |
02 Oct 06 |
nicklas |
293 |
{ |
2689 |
02 Oct 06 |
nicklas |
294 |
if (label == null) label = "File"; |
2689 |
02 Oct 06 |
nicklas |
295 |
if (description == null) description = "The file to unpack."; |
2689 |
02 Oct 06 |
nicklas |
296 |
return new PluginParameter<File>(ZIP_FILE, label, description, zipFileType); |
2689 |
02 Oct 06 |
nicklas |
297 |
} |
2689 |
02 Oct 06 |
nicklas |
298 |
|
2689 |
02 Oct 06 |
nicklas |
299 |
/** |
2689 |
02 Oct 06 |
nicklas |
Get the file that is going to be unpacked by the plugin. |
2689 |
02 Oct 06 |
nicklas |
The file is only available in the execution phase if the plugin has saved |
2689 |
02 Oct 06 |
nicklas |
it as a job parameter during the configuration of a job (this is the default) |
2689 |
02 Oct 06 |
nicklas |
303 |
|
2689 |
02 Oct 06 |
nicklas |
@return The packed file or null |
2689 |
02 Oct 06 |
nicklas |
@see #getZipFileParameter(String, String) |
3510 |
19 Jun 07 |
nicklas |
@see #getCurrentFile(DbControl) |
2689 |
02 Oct 06 |
nicklas |
307 |
*/ |
2689 |
02 Oct 06 |
nicklas |
308 |
protected File getZipFile(DbControl dc) |
2689 |
02 Oct 06 |
nicklas |
309 |
{ |
2689 |
02 Oct 06 |
nicklas |
310 |
File zipFile = (File)job.getValue(ZIP_FILE); |
2689 |
02 Oct 06 |
nicklas |
311 |
if (zipFile != null) zipFile = File.getById(dc, zipFile.getId()); |
2689 |
02 Oct 06 |
nicklas |
312 |
return zipFile; |
2689 |
02 Oct 06 |
nicklas |
313 |
} |
2689 |
02 Oct 06 |
nicklas |
314 |
|
2689 |
02 Oct 06 |
nicklas |
315 |
/** |
2689 |
02 Oct 06 |
nicklas |
The name of the parameter that asks for the directory where the |
2689 |
02 Oct 06 |
nicklas |
unpacked files are stored. |
2981 |
30 Nov 06 |
nicklas |
@see #getZipFileParameter(String, String) |
2689 |
02 Oct 06 |
nicklas |
319 |
*/ |
2689 |
02 Oct 06 |
nicklas |
320 |
protected static final String UNPACK_DIRECTORY = "unpackDirectory"; |
2689 |
02 Oct 06 |
nicklas |
321 |
|
2689 |
02 Oct 06 |
nicklas |
322 |
/** |
2689 |
02 Oct 06 |
nicklas |
Get a plugin parameter that asks for the directory where the |
2689 |
02 Oct 06 |
nicklas |
unpacked files are stored. |
2689 |
02 Oct 06 |
nicklas |
325 |
|
2689 |
02 Oct 06 |
nicklas |
@param label The parameter label, or null to use the default (Save in) |
2689 |
02 Oct 06 |
nicklas |
@param description The parameter description, or null to use the default |
2689 |
02 Oct 06 |
nicklas |
(The directory where the unpacked files should be saved.) |
2689 |
02 Oct 06 |
nicklas |
329 |
*/ |
2689 |
02 Oct 06 |
nicklas |
330 |
protected PluginParameter<String> getDirectoryParameter(String label, String description) |
2689 |
02 Oct 06 |
nicklas |
331 |
{ |
2689 |
02 Oct 06 |
nicklas |
332 |
if (label == null) label = "Save in"; |
2689 |
02 Oct 06 |
nicklas |
333 |
if (description == null) description = "The directory where the unpacked files should be saved."; |
3510 |
19 Jun 07 |
nicklas |
334 |
DbControl dc = sc.newDbControl(); |
3510 |
19 Jun 07 |
nicklas |
335 |
String defaultDir = null; |
3510 |
19 Jun 07 |
nicklas |
336 |
try |
3510 |
19 Jun 07 |
nicklas |
337 |
{ |
3510 |
19 Jun 07 |
nicklas |
338 |
Directory dir = getCurrentDirectory(dc); |
3510 |
19 Jun 07 |
nicklas |
339 |
if (dir != null) defaultDir = dir.getPath().toString(); |
3510 |
19 Jun 07 |
nicklas |
340 |
} |
3510 |
19 Jun 07 |
nicklas |
341 |
finally |
3510 |
19 Jun 07 |
nicklas |
342 |
{ |
3510 |
19 Jun 07 |
nicklas |
343 |
if (dc != null) dc.close(); |
3510 |
19 Jun 07 |
nicklas |
344 |
} |
3510 |
19 Jun 07 |
nicklas |
345 |
return new PluginParameter<String>(UNPACK_DIRECTORY, label, description , defaultDir, unpackType); |
2689 |
02 Oct 06 |
nicklas |
346 |
} |
2689 |
02 Oct 06 |
nicklas |
347 |
|
2689 |
02 Oct 06 |
nicklas |
348 |
/** |
3510 |
19 Jun 07 |
nicklas |
Get the current directory or null there is no current or it can't be loaded. |
3510 |
19 Jun 07 |
nicklas |
This method will first try to load the current file and use the file's |
3510 |
19 Jun 07 |
nicklas |
directory as the current. If there is no current file, the current directory |
3510 |
19 Jun 07 |
nicklas |
is loaded from the session context. |
3510 |
19 Jun 07 |
nicklas |
The current directory is only available in the configuration phase. |
3510 |
19 Jun 07 |
nicklas |
354 |
|
3510 |
19 Jun 07 |
nicklas |
@param dc A DbControl to use for database access |
3510 |
19 Jun 07 |
nicklas |
@return A directory or null |
3510 |
19 Jun 07 |
nicklas |
@since 2.4 |
3510 |
19 Jun 07 |
nicklas |
@see #getUnpackDirectory(DbControl) |
3510 |
19 Jun 07 |
nicklas |
359 |
*/ |
3510 |
19 Jun 07 |
nicklas |
360 |
protected Directory getCurrentDirectory(DbControl dc) |
3510 |
19 Jun 07 |
nicklas |
361 |
{ |
3510 |
19 Jun 07 |
nicklas |
362 |
File currentFile = getCurrentFile(dc); |
3510 |
19 Jun 07 |
nicklas |
363 |
if (currentFile != null) return currentFile.getDirectory(); |
3510 |
19 Jun 07 |
nicklas |
364 |
int directoryId = sc.getCurrentContext(Item.DIRECTORY).getId(); |
3510 |
19 Jun 07 |
nicklas |
365 |
if (directoryId != 0) |
3510 |
19 Jun 07 |
nicklas |
366 |
{ |
3510 |
19 Jun 07 |
nicklas |
367 |
try |
3510 |
19 Jun 07 |
nicklas |
368 |
{ |
3510 |
19 Jun 07 |
nicklas |
369 |
return Directory.getById(dc, directoryId); |
3510 |
19 Jun 07 |
nicklas |
370 |
} |
3510 |
19 Jun 07 |
nicklas |
371 |
catch (Throwable t) |
3510 |
19 Jun 07 |
nicklas |
372 |
{} |
3510 |
19 Jun 07 |
nicklas |
373 |
} |
3510 |
19 Jun 07 |
nicklas |
374 |
return null; |
3510 |
19 Jun 07 |
nicklas |
375 |
} |
3510 |
19 Jun 07 |
nicklas |
376 |
|
3510 |
19 Jun 07 |
nicklas |
377 |
/** |
3510 |
19 Jun 07 |
nicklas |
Get the current file or null there is no current or it can't be loaded. |
3510 |
19 Jun 07 |
nicklas |
The current file is only available in the configuration phase. |
3510 |
19 Jun 07 |
nicklas |
@param dc A DbControl to use for database access |
3510 |
19 Jun 07 |
nicklas |
@return A file or null |
3510 |
19 Jun 07 |
nicklas |
@since 2.4 |
3510 |
19 Jun 07 |
nicklas |
@see #getZipFile(DbControl) |
3510 |
19 Jun 07 |
nicklas |
384 |
*/ |
3510 |
19 Jun 07 |
nicklas |
385 |
protected File getCurrentFile(DbControl dc) |
3510 |
19 Jun 07 |
nicklas |
386 |
{ |
3510 |
19 Jun 07 |
nicklas |
387 |
int fileId = sc.getCurrentContext(Item.FILE).getId(); |
3510 |
19 Jun 07 |
nicklas |
388 |
if (fileId != 0) |
3510 |
19 Jun 07 |
nicklas |
389 |
{ |
3510 |
19 Jun 07 |
nicklas |
390 |
try |
3510 |
19 Jun 07 |
nicklas |
391 |
{ |
3510 |
19 Jun 07 |
nicklas |
392 |
return File.getById(dc, fileId); |
3510 |
19 Jun 07 |
nicklas |
393 |
} |
3510 |
19 Jun 07 |
nicklas |
394 |
catch (Throwable t) |
3510 |
19 Jun 07 |
nicklas |
395 |
{} |
3510 |
19 Jun 07 |
nicklas |
396 |
} |
3510 |
19 Jun 07 |
nicklas |
397 |
return null; |
3510 |
19 Jun 07 |
nicklas |
398 |
} |
3510 |
19 Jun 07 |
nicklas |
399 |
|
3510 |
19 Jun 07 |
nicklas |
400 |
/** |
2689 |
02 Oct 06 |
nicklas |
Get the directory where the unpacked files are placed by the plugin. |
2689 |
02 Oct 06 |
nicklas |
The directory is only available in the execution phase if the plugin has saved |
2689 |
02 Oct 06 |
nicklas |
it as a job parameter during the configuration of a job. |
2689 |
02 Oct 06 |
nicklas |
404 |
|
2689 |
02 Oct 06 |
nicklas |
@return The directory or null |
2689 |
02 Oct 06 |
nicklas |
@see #getDirectoryParameter(String, String) |
3510 |
19 Jun 07 |
nicklas |
@see #getCurrentDirectory(DbControl) |
2689 |
02 Oct 06 |
nicklas |
408 |
*/ |
2689 |
02 Oct 06 |
nicklas |
409 |
protected Directory getUnpackDirectory(DbControl dc) |
2689 |
02 Oct 06 |
nicklas |
410 |
{ |
2689 |
02 Oct 06 |
nicklas |
411 |
String path = (String)job.getValue(UNPACK_DIRECTORY); |
2689 |
02 Oct 06 |
nicklas |
412 |
Directory unpackDirectory = null; |
2689 |
02 Oct 06 |
nicklas |
413 |
if (path != null) |
2689 |
02 Oct 06 |
nicklas |
414 |
{ |
2689 |
02 Oct 06 |
nicklas |
415 |
unpackDirectory = Directory.getNew(dc, new Path(path, Path.Type.DIRECTORY)); |
2689 |
02 Oct 06 |
nicklas |
416 |
if (!unpackDirectory.isInDatabase()) dc.saveItem(unpackDirectory); |
2689 |
02 Oct 06 |
nicklas |
417 |
} |
2689 |
02 Oct 06 |
nicklas |
418 |
return unpackDirectory; |
2689 |
02 Oct 06 |
nicklas |
419 |
} |
2689 |
02 Oct 06 |
nicklas |
420 |
|
2689 |
02 Oct 06 |
nicklas |
421 |
/** |
2689 |
02 Oct 06 |
nicklas |
The name of the parameter that asks if existing files should be |
2689 |
02 Oct 06 |
nicklas |
overwritten or not. |
2981 |
30 Nov 06 |
nicklas |
@see #getOverwriteParameter(String, String) |
2689 |
02 Oct 06 |
nicklas |
425 |
*/ |
2689 |
02 Oct 06 |
nicklas |
426 |
protected static final String OVERWRITE = "overwrite"; |
2689 |
02 Oct 06 |
nicklas |
427 |
|
2689 |
02 Oct 06 |
nicklas |
428 |
/** |
2689 |
02 Oct 06 |
nicklas |
Get a plugin parameter that asks if existing files should be overwritten |
2689 |
02 Oct 06 |
nicklas |
or not. |
2689 |
02 Oct 06 |
nicklas |
431 |
|
2689 |
02 Oct 06 |
nicklas |
@param label The parameter label, or null to use the default (Overwrite) |
2689 |
02 Oct 06 |
nicklas |
@param description The parameter description, or null to use the default |
2689 |
02 Oct 06 |
nicklas |
(Specify if existing files should be overwritten or not.) |
2689 |
02 Oct 06 |
nicklas |
435 |
*/ |
2689 |
02 Oct 06 |
nicklas |
436 |
protected PluginParameter<Boolean> getOverwriteParameter(String label, String description) |
2689 |
02 Oct 06 |
nicklas |
437 |
{ |
2689 |
02 Oct 06 |
nicklas |
438 |
if (label == null) label = "Overwrite"; |
2689 |
02 Oct 06 |
nicklas |
439 |
if (description == null) description = "Specify if existing files should be overwritten or not."; |
2689 |
02 Oct 06 |
nicklas |
440 |
return new PluginParameter<Boolean>(OVERWRITE, label, description, |
2689 |
02 Oct 06 |
nicklas |
441 |
new BooleanParameterType(false, false)); |
2689 |
02 Oct 06 |
nicklas |
442 |
} |
2689 |
02 Oct 06 |
nicklas |
443 |
|
2689 |
02 Oct 06 |
nicklas |
444 |
/** |
2689 |
02 Oct 06 |
nicklas |
If existing file should be overwritten or not. |
2689 |
02 Oct 06 |
nicklas |
446 |
|
2689 |
02 Oct 06 |
nicklas |
@return TRUE if files should be overwritten, FALSE otherwise |
2689 |
02 Oct 06 |
nicklas |
@see #getOverwriteParameter(String, String) |
2689 |
02 Oct 06 |
nicklas |
449 |
*/ |
2689 |
02 Oct 06 |
nicklas |
450 |
protected boolean getOverwrite() |
2689 |
02 Oct 06 |
nicklas |
451 |
{ |
2689 |
02 Oct 06 |
nicklas |
452 |
Boolean overwrite = (Boolean)job.getValue(OVERWRITE); |
2689 |
02 Oct 06 |
nicklas |
453 |
if (overwrite == null) overwrite = Boolean.FALSE; |
2689 |
02 Oct 06 |
nicklas |
454 |
return overwrite; |
2689 |
02 Oct 06 |
nicklas |
455 |
} |
2689 |
02 Oct 06 |
nicklas |
456 |
|
2689 |
02 Oct 06 |
nicklas |
457 |
private RequestInformation getConfigureJobParameters(GuiContext context) |
2689 |
02 Oct 06 |
nicklas |
458 |
{ |
5384 |
13 Aug 10 |
nicklas |
459 |
if (configureJob == null) |
2689 |
02 Oct 06 |
nicklas |
460 |
{ |
5384 |
13 Aug 10 |
nicklas |
// Parameters for CONFIGURE_JOB |
5384 |
13 Aug 10 |
nicklas |
462 |
List<PluginParameter<?>> parameters = new ArrayList<PluginParameter<?>>(); |
2689 |
02 Oct 06 |
nicklas |
463 |
|
5384 |
13 Aug 10 |
nicklas |
// Source and child bioassay set parameters |
5384 |
13 Aug 10 |
nicklas |
465 |
parameters.add(getZipFileParameter(null, null)); |
5384 |
13 Aug 10 |
nicklas |
466 |
parameters.add(getDirectoryParameter(null, null)); |
5384 |
13 Aug 10 |
nicklas |
467 |
parameters.add(getOverwriteParameter(null, null)); |
5384 |
13 Aug 10 |
nicklas |
468 |
|
5384 |
13 Aug 10 |
nicklas |
469 |
configureJob = new RequestInformation |
5384 |
13 Aug 10 |
nicklas |
470 |
( |
5384 |
13 Aug 10 |
nicklas |
471 |
Request.COMMAND_CONFIGURE_JOB, |
5384 |
13 Aug 10 |
nicklas |
472 |
"Unpack file", |
5384 |
13 Aug 10 |
nicklas |
473 |
"Select a file to unpack and where to put the unpacked files", |
5384 |
13 Aug 10 |
nicklas |
474 |
parameters |
5384 |
13 Aug 10 |
nicklas |
475 |
); |
2689 |
02 Oct 06 |
nicklas |
476 |
} |
2689 |
02 Oct 06 |
nicklas |
477 |
return configureJob; |
2689 |
02 Oct 06 |
nicklas |
478 |
} |
2689 |
02 Oct 06 |
nicklas |
479 |
|
2689 |
02 Oct 06 |
nicklas |
480 |
} |