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/** |
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$Id$ |
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3 |
|
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Copyright (C) 2008 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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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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along with BASE. If not, see <http://www.gnu.org/licenses/>. |
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*/ |
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package net.sf.basedb.util.overview.validator; |
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|
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import java.util.Collections; |
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import java.util.List; |
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26 |
|
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27 |
import net.sf.basedb.core.BasicItem; |
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28 |
import net.sf.basedb.core.DataFileType; |
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29 |
import net.sf.basedb.core.DbControl; |
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30 |
import net.sf.basedb.core.File; |
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31 |
import net.sf.basedb.core.FileSet; |
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32 |
import net.sf.basedb.core.FileSetMember; |
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33 |
import net.sf.basedb.core.FileStoreEnabled; |
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34 |
import net.sf.basedb.core.ItemQuery; |
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35 |
import net.sf.basedb.core.ItemSubtype; |
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36 |
import net.sf.basedb.core.ItemSubtypeFileType; |
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37 |
import net.sf.basedb.core.PermissionDeniedException; |
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38 |
import net.sf.basedb.core.Platform; |
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39 |
import net.sf.basedb.core.PlatformFileType; |
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import net.sf.basedb.core.PlatformVariant; |
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import net.sf.basedb.core.RootRawBioAssay; |
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import net.sf.basedb.core.Subtypable; |
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import net.sf.basedb.core.UsableDataFileType; |
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44 |
import net.sf.basedb.core.query.Expressions; |
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45 |
import net.sf.basedb.core.query.Hql; |
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46 |
import net.sf.basedb.core.query.Restrictions; |
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47 |
import net.sf.basedb.util.overview.Fix; |
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48 |
import net.sf.basedb.util.overview.OverviewContext; |
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49 |
import net.sf.basedb.util.overview.Validator; |
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import net.sf.basedb.util.overview.Node; |
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|
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52 |
/** |
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Validator implementation for data files. The node containing |
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the data files is expected to live in a folder-type node that |
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has a {@link FileStoreEnabled} item as it's parent (if there |
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are more than one file) or as an immediate child node to |
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it's parent item (if there is only one file). |
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Validation rules: |
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<ul> |
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<li>Denied access to file: {@link Validator#DENIED_FILE} |
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<li>Denied access to file type: {@link Validator#DENIED_DATAFILETYPE} |
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<li>File is not a valid file: {@link Validator#DATAFILE_INVALID} |
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<li>File has not been validated: {@link Validator#DATAFILE_NOTVALIDATED} |
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<li>File type doesn't match parent item type: {@link Validator#DATAFILE_INVALID_ITEM} |
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<li>File type is not part of used platform: {@link Validator#DATAFILE_NOTPLATFORM} |
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<li>Too many files of a single-file file type: {@link Validator#DATAFILE_TOOMANYFILES} |
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<li>Missing a required file: {@link Validator#MISSING_DATAFILE} |
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</ul> |
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69 |
|
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@author Nicklas |
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@version 2.10 |
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@base.modified $Date$ |
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73 |
*/ |
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74 |
public class DataFileValidator |
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extends BasicNodeValidator<FileSetMember> |
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{ |
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|
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public DataFileValidator() |
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{ |
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super(null, null); |
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} |
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82 |
|
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83 |
/* |
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05 Feb 09 |
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From BasicNodeValidator class |
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85 |
----------------------------- |
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86 |
*/ |
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87 |
@Override |
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88 |
public void postValidate(DbControl dc, OverviewContext context, Node node, Node parentNode) |
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89 |
{ |
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super.postValidate(dc, context, node, parentNode); |
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FileSetMember member = (FileSetMember)node.getItem(dc); |
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// The parent node is either a folder (if we have more than one file) |
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05 Feb 09 |
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// or the actual parent (for a single file) |
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01 Oct 15 |
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BasicItem parentItem = parentNode.getNodeType() == Node.Type.FOLDER ? |
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01 Oct 15 |
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95 |
parentNode.getParent().getItem(dc) : parentNode.getItem(dc); |
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01 Oct 15 |
nicklas |
96 |
if (parentItem instanceof RootRawBioAssay) |
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01 Oct 15 |
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97 |
{ |
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// The parent may be a root raw bioasay if the overview starts at the |
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01 Oct 15 |
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// experiment level |
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01 Oct 15 |
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100 |
parentItem = ((RootRawBioAssay)parentItem).getRawBioAssay(); |
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01 Oct 15 |
nicklas |
101 |
} |
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102 |
FileStoreEnabled fileStoreItem = (FileStoreEnabled)parentItem; |
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103 |
|
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// Check that we have access to the file and it's file type |
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105 |
DataFileType fileType = null; |
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05 Feb 09 |
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106 |
File file = null; |
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05 Feb 09 |
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107 |
try |
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108 |
{ |
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109 |
fileType = member.getDataFileType(); |
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05 Feb 09 |
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110 |
} |
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111 |
catch (PermissionDeniedException ex) |
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112 |
{} |
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113 |
try |
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114 |
{ |
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05 Feb 09 |
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115 |
file = member.getFile(); |
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05 Feb 09 |
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116 |
} |
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117 |
catch (PermissionDeniedException ex) |
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05 Feb 09 |
nicklas |
118 |
{} |
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05 Feb 09 |
nicklas |
119 |
if (fileType == null) |
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05 Feb 09 |
nicklas |
120 |
{ |
4740 |
05 Feb 09 |
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121 |
context.createFailure(Validator.DENIED_DATAFILETYPE, node, null); |
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05 Feb 09 |
nicklas |
122 |
} |
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05 Feb 09 |
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123 |
if (file == null) |
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05 Feb 09 |
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124 |
{ |
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05 Feb 09 |
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125 |
context.createFailure(Validator.DENIED_FILE, node, null); |
4740 |
05 Feb 09 |
nicklas |
126 |
} |
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05 Feb 09 |
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127 |
|
4740 |
05 Feb 09 |
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// Check if a validator has determined that the file IS invalid |
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05 Feb 09 |
nicklas |
129 |
if (Boolean.FALSE.equals(member.isValid())) |
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05 Feb 09 |
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130 |
{ |
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05 Feb 09 |
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131 |
String errorMsg = fileType == null ? "Data file " : fileType.getName(); |
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05 Feb 09 |
nicklas |
132 |
errorMsg += " is not valid: " + member.getErrorMessage(); |
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05 Feb 09 |
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133 |
context.createFailure(Validator.DATAFILE_INVALID, node, errorMsg, |
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01 Oct 15 |
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134 |
new Fix("Select another file", parentItem, member) |
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05 Feb 09 |
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135 |
); |
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05 Feb 09 |
nicklas |
136 |
} |
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05 Feb 09 |
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137 |
|
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05 Feb 09 |
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138 |
if (fileType != null) |
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05 Feb 09 |
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139 |
{ |
4740 |
05 Feb 09 |
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// Check if the file hasn't been validated even if a validator exists |
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06 May 11 |
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141 |
if (fileType.hasActiveValidator(dc) && member.isValid() == null) |
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05 Feb 09 |
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142 |
{ |
4740 |
05 Feb 09 |
nicklas |
143 |
context.createFailure(Validator.DATAFILE_NOTVALIDATED, node, |
4740 |
05 Feb 09 |
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144 |
fileType.getName() + " has not been validated", |
6959 |
01 Oct 15 |
nicklas |
145 |
new Fix("Validate the file / Select another file", parentItem, member)); |
4740 |
05 Feb 09 |
nicklas |
146 |
} |
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05 Feb 09 |
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147 |
|
4740 |
05 Feb 09 |
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// Check that the file type is matching the parent item's type |
4740 |
05 Feb 09 |
nicklas |
149 |
if (fileType.getItemType() != parentItem.getType()) |
4740 |
05 Feb 09 |
nicklas |
150 |
{ |
4740 |
05 Feb 09 |
nicklas |
151 |
context.createFailure(Validator.DATAFILE_INVALID_ITEM, node, |
4740 |
05 Feb 09 |
nicklas |
152 |
"Data file '" + fileType.getName() + "' can't be used on item type: " + parentItem.getType(), |
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01 Oct 15 |
nicklas |
153 |
new Fix("Remove file", parentItem, member) |
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05 Feb 09 |
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154 |
); |
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05 Feb 09 |
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155 |
} |
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156 |
|
5721 |
06 Sep 11 |
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// Check that the file type is part of the used platform/variant/subtype |
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11 Feb 09 |
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158 |
try |
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11 Feb 09 |
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159 |
{ |
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01 Oct 15 |
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160 |
Platform platform = fileStoreItem.getPlatform(); |
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01 Oct 15 |
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161 |
PlatformVariant variant = fileStoreItem.getVariant(); |
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11 Feb 09 |
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162 |
if (platform != null) |
4750 |
11 Feb 09 |
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163 |
{ |
4750 |
11 Feb 09 |
nicklas |
// The item to apply fixes on, variant or platform |
4750 |
11 Feb 09 |
nicklas |
165 |
String pvName = null; |
4750 |
11 Feb 09 |
nicklas |
166 |
BasicItem pvItem = null; |
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11 Feb 09 |
nicklas |
167 |
if (variant != null) |
4750 |
11 Feb 09 |
nicklas |
168 |
{ |
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11 Feb 09 |
nicklas |
169 |
pvItem = variant; |
4750 |
11 Feb 09 |
nicklas |
170 |
pvName = variant.getName(); |
4750 |
11 Feb 09 |
nicklas |
171 |
} |
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11 Feb 09 |
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172 |
else |
4750 |
11 Feb 09 |
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173 |
{ |
4750 |
11 Feb 09 |
nicklas |
174 |
pvItem = platform; |
4750 |
11 Feb 09 |
nicklas |
175 |
pvName = platform.getName(); |
4750 |
11 Feb 09 |
nicklas |
176 |
} |
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06 Sep 11 |
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177 |
if (platform.getFileType(fileType, variant, false) == null) |
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11 Feb 09 |
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178 |
{ |
4750 |
11 Feb 09 |
nicklas |
179 |
context.createFailure(Validator.DATAFILE_NOTPLATFORM, node, |
4750 |
11 Feb 09 |
nicklas |
180 |
fileType.getName() + " can't be used with '" + pvName + "' platform", |
4750 |
11 Feb 09 |
nicklas |
181 |
new Fix("Remove '" + fileType.getName() + "' from " + parentItem.getType().toString().toLowerCase(), |
6960 |
01 Oct 15 |
nicklas |
182 |
parentItem, fileType), |
4750 |
11 Feb 09 |
nicklas |
183 |
new Fix("Add '" + fileType.getName() +"' to '" + pvName + "' platform", pvItem, fileType) |
4750 |
11 Feb 09 |
nicklas |
184 |
); |
4750 |
11 Feb 09 |
nicklas |
185 |
} |
4750 |
11 Feb 09 |
nicklas |
186 |
} |
5721 |
06 Sep 11 |
nicklas |
187 |
else if (parentItem instanceof Subtypable) |
5721 |
06 Sep 11 |
nicklas |
188 |
{ |
5721 |
06 Sep 11 |
nicklas |
189 |
ItemSubtype subtype = ((Subtypable)parentItem).getItemSubtype(); |
5721 |
06 Sep 11 |
nicklas |
190 |
if (subtype != null) |
5721 |
06 Sep 11 |
nicklas |
191 |
{ |
5721 |
06 Sep 11 |
nicklas |
192 |
if (subtype.getAssociatedDataFileType(fileType, false) == null) |
5721 |
06 Sep 11 |
nicklas |
193 |
{ |
5721 |
06 Sep 11 |
nicklas |
194 |
context.createFailure(Validator.DATAFILE_NOTPLATFORM, node, |
5721 |
06 Sep 11 |
nicklas |
195 |
fileType.getName() + " can't be used with '" + subtype.getName() + "' subtype", |
5721 |
06 Sep 11 |
nicklas |
196 |
new Fix("Remove '" + fileType.getName() + "' from " + parentItem.getType().toString().toLowerCase(), |
6960 |
01 Oct 15 |
nicklas |
197 |
parentItem, fileType), |
5721 |
06 Sep 11 |
nicklas |
198 |
new Fix("Add '" + fileType.getName() +"' to '" + subtype.getName() + "' subtype", subtype, fileType) |
5721 |
06 Sep 11 |
nicklas |
199 |
); |
5721 |
06 Sep 11 |
nicklas |
200 |
} |
5721 |
06 Sep 11 |
nicklas |
201 |
} |
5721 |
06 Sep 11 |
nicklas |
202 |
} |
4750 |
11 Feb 09 |
nicklas |
203 |
} |
4750 |
11 Feb 09 |
nicklas |
204 |
catch (PermissionDeniedException ex) |
4750 |
11 Feb 09 |
nicklas |
205 |
{} |
4740 |
05 Feb 09 |
nicklas |
206 |
} |
4740 |
05 Feb 09 |
nicklas |
207 |
} |
4740 |
05 Feb 09 |
nicklas |
208 |
|
4740 |
05 Feb 09 |
nicklas |
209 |
/** |
4740 |
05 Feb 09 |
nicklas |
@return Always "null" |
4740 |
05 Feb 09 |
nicklas |
211 |
*/ |
4740 |
05 Feb 09 |
nicklas |
212 |
@Override |
5651 |
08 Jun 11 |
nicklas |
213 |
protected Fix getMissingItemFix(DbControl dc, Node parentNode) |
4740 |
05 Feb 09 |
nicklas |
214 |
{ |
4740 |
05 Feb 09 |
nicklas |
215 |
return null; |
4740 |
05 Feb 09 |
nicklas |
216 |
} |
4750 |
11 Feb 09 |
nicklas |
217 |
|
4750 |
11 Feb 09 |
nicklas |
218 |
@Override |
4750 |
11 Feb 09 |
nicklas |
219 |
public void postValidateFolder(DbControl dc, OverviewContext context, |
4750 |
11 Feb 09 |
nicklas |
220 |
Node folderNode, Node parentNode) |
4740 |
05 Feb 09 |
nicklas |
221 |
{ |
4750 |
11 Feb 09 |
nicklas |
222 |
super.postValidateFolder(dc, context, folderNode, parentNode); |
6959 |
01 Oct 15 |
nicklas |
223 |
BasicItem parentItem = parentNode.getItem(dc); |
6959 |
01 Oct 15 |
nicklas |
224 |
if (parentItem instanceof RootRawBioAssay) |
6959 |
01 Oct 15 |
nicklas |
225 |
{ |
6959 |
01 Oct 15 |
nicklas |
// The parent may be a root raw bioasay if the overview starts at the |
6959 |
01 Oct 15 |
nicklas |
// experiment level |
6959 |
01 Oct 15 |
nicklas |
228 |
parentItem = ((RootRawBioAssay)parentItem).getRawBioAssay(); |
6959 |
01 Oct 15 |
nicklas |
229 |
} |
6959 |
01 Oct 15 |
nicklas |
230 |
FileStoreEnabled fileStoreItem = (FileStoreEnabled)parentItem; |
4740 |
05 Feb 09 |
nicklas |
231 |
|
4750 |
11 Feb 09 |
nicklas |
// Check that we have linked a file for all file types that |
5721 |
06 Sep 11 |
nicklas |
// are required by the platform and that the multiplicity setting |
5721 |
06 Sep 11 |
nicklas |
// is ok |
4750 |
11 Feb 09 |
nicklas |
235 |
try |
4740 |
05 Feb 09 |
nicklas |
236 |
{ |
6959 |
01 Oct 15 |
nicklas |
237 |
Platform platform = fileStoreItem.getPlatform(); |
6959 |
01 Oct 15 |
nicklas |
238 |
PlatformVariant variant = fileStoreItem.getVariant(); |
5721 |
06 Sep 11 |
nicklas |
239 |
BasicItem pvItem = null; |
5721 |
06 Sep 11 |
nicklas |
240 |
ItemSubtype subtype = parentItem instanceof Subtypable ? |
5721 |
06 Sep 11 |
nicklas |
241 |
((Subtypable)parentItem).getItemSubtype() : null; |
5721 |
06 Sep 11 |
nicklas |
// List for holding all file types defined by the platform or subtype |
6089 |
22 Aug 12 |
nicklas |
243 |
List<? extends UsableDataFileType> fileTypes = Collections.emptyList(); |
5721 |
06 Sep 11 |
nicklas |
244 |
if (platform != null) |
4740 |
05 Feb 09 |
nicklas |
245 |
{ |
5721 |
06 Sep 11 |
nicklas |
246 |
pvItem = variant != null ? variant : platform; |
5721 |
06 Sep 11 |
nicklas |
// Create a query that returns all required platform file types |
5721 |
06 Sep 11 |
nicklas |
248 |
ItemQuery<PlatformFileType> query = platform.getFileTypes(variant, variant == null); |
5721 |
06 Sep 11 |
nicklas |
249 |
query.join(Hql.innerJoin("dataFileType", "dft")); |
5721 |
06 Sep 11 |
nicklas |
250 |
query.restrict( |
5721 |
06 Sep 11 |
nicklas |
251 |
Restrictions.eq( |
5721 |
06 Sep 11 |
nicklas |
252 |
Hql.property("dft", "itemType"), |
6959 |
01 Oct 15 |
nicklas |
253 |
Expressions.integer(parentItem.getType().getValue()) |
5721 |
06 Sep 11 |
nicklas |
254 |
) |
5721 |
06 Sep 11 |
nicklas |
255 |
); |
5721 |
06 Sep 11 |
nicklas |
256 |
fileTypes = query.list(dc); |
4740 |
05 Feb 09 |
nicklas |
257 |
} |
5721 |
06 Sep 11 |
nicklas |
258 |
if (subtype != null) |
4740 |
05 Feb 09 |
nicklas |
259 |
{ |
5721 |
06 Sep 11 |
nicklas |
260 |
pvItem = subtype; |
5721 |
06 Sep 11 |
nicklas |
// Create a query that returns all required subtype file types |
5721 |
06 Sep 11 |
nicklas |
262 |
ItemQuery<ItemSubtypeFileType> query = subtype.getDataFileTypes(); |
5721 |
06 Sep 11 |
nicklas |
263 |
query.join(Hql.innerJoin("dataFileType", "dft")); |
5721 |
06 Sep 11 |
nicklas |
264 |
query.restrict( |
5721 |
06 Sep 11 |
nicklas |
265 |
Restrictions.eq( |
5721 |
06 Sep 11 |
nicklas |
266 |
Hql.property("dft", "itemType"), |
6959 |
01 Oct 15 |
nicklas |
267 |
Expressions.integer(parentItem.getType().getValue()) |
5721 |
06 Sep 11 |
nicklas |
268 |
) |
5721 |
06 Sep 11 |
nicklas |
269 |
); |
5721 |
06 Sep 11 |
nicklas |
270 |
fileTypes = query.list(dc); |
4740 |
05 Feb 09 |
nicklas |
271 |
} |
6959 |
01 Oct 15 |
nicklas |
272 |
FileSet fs = fileStoreItem.hasFileSet() ? fileStoreItem.getFileSet() : null; |
5721 |
06 Sep 11 |
nicklas |
273 |
for (UsableDataFileType fileType : fileTypes) |
5721 |
06 Sep 11 |
nicklas |
274 |
{ |
5721 |
06 Sep 11 |
nicklas |
275 |
DataFileType dft = fileType.getDataFileType(); |
5721 |
06 Sep 11 |
nicklas |
276 |
int numMembers = fs == null ? 0 : fs.getNumMembers(dft); |
5721 |
06 Sep 11 |
nicklas |
277 |
if (fileType.isRequired() && numMembers == 0) |
5721 |
06 Sep 11 |
nicklas |
278 |
{ |
5721 |
06 Sep 11 |
nicklas |
279 |
context.createFailure(Validator.MISSING_DATAFILE, parentNode, |
5721 |
06 Sep 11 |
nicklas |
280 |
"Missing '" + dft.getName() + "'", |
5721 |
06 Sep 11 |
nicklas |
281 |
new Fix("Add '" + dft.getName() + "' to " + parentItem.getType().toString().toLowerCase(), |
6960 |
01 Oct 15 |
nicklas |
282 |
parentItem, dft), |
5721 |
06 Sep 11 |
nicklas |
283 |
new Fix("Remove 'Required' flag from '" + dft.getName() + "'", pvItem, dft) |
5721 |
06 Sep 11 |
nicklas |
284 |
); |
5721 |
06 Sep 11 |
nicklas |
285 |
} |
5721 |
06 Sep 11 |
nicklas |
286 |
if (!fileType.getAllowMultiple() && numMembers > 1) |
5721 |
06 Sep 11 |
nicklas |
287 |
{ |
5721 |
06 Sep 11 |
nicklas |
288 |
context.createFailure(Validator.DATAFILE_TOOMANYFILES, parentNode, |
5721 |
06 Sep 11 |
nicklas |
289 |
"Too many files: '" + dft.getName() + "'", |
5721 |
06 Sep 11 |
nicklas |
290 |
new Fix("Remove '" + dft.getName() + "' from " + parentItem.getType().toString().toLowerCase(), |
6960 |
01 Oct 15 |
nicklas |
291 |
parentItem, dft), |
5721 |
06 Sep 11 |
nicklas |
292 |
new Fix("Check 'Allow multiple files' on '" + dft.getName() + "'", pvItem, dft) |
5721 |
06 Sep 11 |
nicklas |
293 |
); |
5721 |
06 Sep 11 |
nicklas |
294 |
} |
5721 |
06 Sep 11 |
nicklas |
295 |
} |
4740 |
05 Feb 09 |
nicklas |
296 |
} |
4750 |
11 Feb 09 |
nicklas |
297 |
catch (PermissionDeniedException ex) |
4750 |
11 Feb 09 |
nicklas |
298 |
{} |
4740 |
05 Feb 09 |
nicklas |
299 |
} |
4750 |
11 Feb 09 |
nicklas |
300 |
// ---------------------------- |
4750 |
11 Feb 09 |
nicklas |
301 |
|
4740 |
05 Feb 09 |
nicklas |
302 |
} |