Changeset 5136
- Timestamp:
- Oct 15, 2009, 8:33:07 AM (13 years ago)
- Location:
- trunk
- Files:
-
- 11 edited
Legend:
- Unmodified
- Added
- Removed
-
trunk/doc/src/docbook/admindoc/installation_upgrade.xml
r5031 r5136 7 7 8 8 Copyright (C) 2007 Jari Häkkinen, Peter Johansson, Nicklas Nordborg, Martin Svensson 9 Copyright (C) 2008 Jari Häkkinen, Nicklas Nordborg, Martin Svensson 10 Copyright (C) 2009 Jari Häkkinen, Nicklas Nordborg 9 11 10 12 This file is part of BASE - BioArray Software Environment. … … 670 672 <listitem> 671 673 <para> 672 Download and install Apache Tomcat 6.0. 14or later, available674 Download and install Apache Tomcat 6.0.20 or later, available 673 675 from <ulink 674 676 url="http://tomcat.apache.org" />. … … 1338 1340 <listitem> 1339 1341 <para> 1340 The title of the message. It should be a short and con sice to1342 The title of the message. It should be a short and concise to 1341 1343 avoid confusion. The title will be displayed on a lot of places 1342 1344 and a user may have to click on it to read the more detailed … … 1349 1351 <listitem> 1350 1352 <para> 1351 Mark this check box to try to prevent new users from logging in. To1353 Mark this check-box to try to prevent new users from logging in. To 1352 1354 avoid problems that can be caused by blocking the server admin out, 1353 1355 the login is not completely, disabled. Any user can still login but -
trunk/src/clients/web/net/sf/basedb/clients/web/formatter/FormatterFactory.java
r4544 r5136 26 26 import net.sf.basedb.clients.web.Base; 27 27 import net.sf.basedb.core.Annotation; 28 import net.sf.basedb.core.AnnotationType;29 28 import net.sf.basedb.core.Coloring; 30 29 import net.sf.basedb.core.ExtendedProperty; … … 330 329 public static Formatter<?> getAnnotationFormatter(SessionControl sc, Annotation a, Unit unit) 331 330 { 332 AnnotationType at = a.getAnnotationType();333 331 Formatter<?> f = getTypeFormatter(sc, a.getValueType()); 334 332 return a.getUnitFormatter(f, unit); -
trunk/src/core/net/sf/basedb/core/ArrayDesign.java
r4889 r5136 131 131 ad.setNumArrays(1); 132 132 ad.getData().setFeatureIdentificationMethod(FeatureIdentificationMethod.NONE.getValue()); 133 ad.getData().setEntryDate(new Date()); 133 134 return ad; 134 135 } -
trunk/src/core/net/sf/basedb/core/HibernateUtil.java
r5038 r5136 1236 1236 most useful with <code>lockMode</code> = {@link LockMode#NONE} if 1237 1237 the logged in user only has read permission to the object. 1238 @see DbControl#reattachItem(BasicItem )1238 @see DbControl#reattachItem(BasicItem, boolean) 1239 1239 */ 1240 1240 static void lockData(Session session, BasicData data, LockMode lockMode) -
trunk/src/core/net/sf/basedb/core/ItemContext.java
r5061 r5136 1293 1293 <li>%: The rest of the string is the channel number. We use the 1294 1294 {@link Dynamic#column(VirtualColumn)} to create the expression 1295 for {@link VirtualColumn#channel (int)}1295 for {@link VirtualColumn#channelRaw(int)} 1296 1296 1297 1297 <li>$: The rest of the string is a raw data property name. We use -
trunk/src/core/net/sf/basedb/util/overview/validator/PlatformValidator.java
r4764 r5136 24 24 import net.sf.basedb.core.BasicItem; 25 25 import net.sf.basedb.core.DbControl; 26 import net.sf.basedb.core.FileStoreEnabled; 26 27 import net.sf.basedb.core.Item; 27 28 import net.sf.basedb.core.Platform; … … 71 72 BasicItem defaultVariant = OverviewUtil.getProjectDefaultItem(dc, project, Project.Default.PLATFORM_VARIANT); 72 73 Platform platform = (Platform)node.getItem(); 73 Node variantNode = node.getChild("variant");74 PlatformVariant variant = variantNode == null ? null : (PlatformVariant)node.getItem();74 PlatformVariant variant = null; 75 boolean failedVariant = false; 75 76 BasicItem parentItem = parentNode.getItem(); 77 try 78 { 79 variant = ((FileStoreEnabled)parentItem).getVariant(); 80 } 81 catch (Throwable t) 82 { 83 // Failure to load the variant is detected by other validators 84 failedVariant = true; 85 } 76 86 String parentTypeName = parentNode.getItemType().toString().toLowerCase(); 77 87 boolean canChangePlatform = false; … … 83 93 84 94 if ((defaultPlatform != null && !defaultPlatform.equals(platform)) || 85 (defaultVariant != null && !defaultVariant.equals(variant) ))95 (defaultVariant != null && !defaultVariant.equals(variant) && !failedVariant)) 86 96 { 87 97 context.createFailure(Validator.NONDEFAULT_PLATFORM, parentNode, null, -
trunk/www/common/share/submit_share.jsp
r4889 r5136 107 107 } 108 108 mp.updateKeys(dc, recursive); 109 sc.reloadPermissions(); 109 110 dc.commit(); 110 111 cc.removeObject("MultiPermissions"); -
trunk/www/filemanager/files/ajax.jsp
r4867 r5136 27 27 import="net.sf.basedb.core.Config" 28 28 import="net.sf.basedb.core.File" 29 import="net.sf.basedb.core.InvalidDataException" 29 30 import="net.sf.basedb.util.Values" 30 31 import="net.sf.basedb.util.FileUtil" … … 57 58 try 58 59 { 60 int size = Values.getInt(request.getParameter("size"), -1); 59 61 dc = sc.newDbControl(); 60 62 File f = File.getById(dc, itemId); … … 68 70 Writer toFile = new OutputStreamWriter( 69 71 f.getUploadStream(false, f.isCompressed()), charset); 70 FileUtil.copy(in, toFile); 72 int copied = (int)FileUtil.copy(in, toFile); 73 if (size >= 0 && copied != size) 74 { 75 throw new InvalidDataException("Incomplete file; expected " + size + 76 " bytes; got " + copied + "."); 77 } 71 78 toFile.flush(); 72 79 toFile.close(); … … 76 83 catch (Exception ex) 77 84 { 78 out.println(" Failed: " + ex.getMessage());85 out.println("Save failed: " + ex.getMessage()); 79 86 ex.printStackTrace(); 80 87 } -
trunk/www/filemanager/files/edit_file_data.jsp
r4889 r5136 127 127 var frm = document.forms['file']; 128 128 var url = 'ajax.jsp?ID=<%=ID%>&cmd=StoreFile&item_id=<%=itemId%>'; 129 url += '&size='+frm.filedata.value.length; 129 130 var request = Main.getAjaxRequest(); 130 131 request.closeIfSuccess = closeIfSuccess; … … 136 137 { 137 138 var response = request.responseText; 138 var failed = response.indexOf(' Failed') == 0;139 var failed = response.indexOf('Save failed') == 0; 139 140 if (!failed) 140 141 { -
trunk/www/lims/arrayslides/create_wizard.jsp
r4511 r5136 315 315 <input type="hidden" name="arraybatch_id" value="<%=arrayBatchId%>"> 316 316 <input type="hidden" name="quantity" value="<%=quantity%>"> 317 317 <input type="hidden" name="start_at" value="<%=startAt%>"> 318 318 319 <h3 class="docked"><%=title%> <base:help tabcontrol="settings" /></h3> 319 320 <t:tabcontrol id="settings" contentstyle="<%="height: "+(int)(scale*370)+"px;"%>" -
trunk/www/lims/arrayslides/index.jsp
r5060 r5136 183 183 dc = sc.newDbControl(); 184 184 int quantity = Values.getInt(request.getParameter("quantity")); 185 int batchId = Values.getInt(request.getParameter("arraybatch_id")); 185 int batchId = Values.getInt(request.getParameter("arraybatch_id")); 186 int startAt = Values.getInt(request.getParameter("start_at"), 1); 186 187 String description = Values.getStringOrNull(request.getParameter("description")); 187 188 ArrayBatch batch = ArrayBatch.getById(dc, batchId); … … 195 196 dc.saveItem(slide); 196 197 slide.setName(Values.getStringOrNull(request.getParameter("name"+i))); 197 slide.setBatchIndex( batchId);198 slide.setBatchIndex(startAt + i); 198 199 199 200 String newBarcode = Values.getStringOrNull(request.getParameter("barcode" + i));
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