Changeset 8107

Timestamp:

Jan 23, 2023, 8:27:43 AM (8 months ago)

Author:

Nicklas Nordborg

Message:

Merge BASE 3.19.6 to the trunk

Location:

trunk

Files:

• . (modified) (1 prop)
• .classpath (modified) (2 diffs)
• doc/3rd-party-components.txt (modified) (1 diff)
• lib/dist/postgresql-42.2.20.jar (deleted)
• lib/dist/postgresql-42.5.1.jar (copied) (copied from tags/3.19.6/lib/dist/postgresql-42.5.1.jar)
• src/clients/web/net/sf/basedb/clients/web/taglib/table/ColumnDef.java (modified) (1 diff)
• src/clients/web/net/sf/basedb/clients/web/taglib/table/PresetSelector.java (modified) (1 diff)
• src/clients/web/net/sf/basedb/clients/web/taglib/table/Table.java (modified) (1 diff)
• src/core/common-queries.xml (modified) (1 diff)
• src/core/net/sf/basedb/core/Install.java (modified) (1 diff)
• src/core/net/sf/basedb/core/Job.java (modified) (1 diff)
• src/core/net/sf/basedb/core/PluginConfiguration.java (modified) (1 diff)
• src/core/net/sf/basedb/core/PluginDefinition.java (modified) (1 diff)
• src/core/net/sf/basedb/core/PropertyFilter.java (modified) (1 diff)
• src/core/net/sf/basedb/core/Update.java (modified) (2 diffs)
• src/core/net/sf/basedb/core/data/PluginConfigurationData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/hibernate-properties-PluginConfigurationData.xml (copied) (copied from tags/3.19.6/src/core/net/sf/basedb/core/data/hibernate-properties-PluginConfigurationData.xml)
• src/core/net/sf/basedb/core/dtd/raw-data-types.dtd (modified) (1 diff)
• src/core/net/sf/basedb/util/AutoDetectFileFormat.java (modified) (1 diff)
• src/core/net/sf/basedb/util/extensions/manager/Settings.java (modified) (12 diffs)
• www/admin/pluginconfigurations/edit_configuration.jsp (modified) (4 diffs)
• www/admin/pluginconfigurations/index.jsp (modified) (1 diff)
• www/admin/pluginconfigurations/list_configurations.jsp (modified) (2 diffs)
• www/admin/pluginconfigurations/view_configuration.jsp (modified) (1 diff)
• www/common/import/index.jsp (modified) (1 diff)
• www/common/plugin/index.jsp (modified) (1 diff)

trunk/.classpath

@@ -26 +26 @@
   <classpathentry kind="lib" path="lib/dist/json-simple-1.1.1-1.jar"/>
   <classpathentry kind="lib" path="lib/dist/utf8-with-fallback-1.1.0.jar"/>
-  <classpathentry kind="lib" path="lib/dist/postgresql-42.2.20.jar"/>
   <classpathentry kind="lib" path="lib/dist/httpclient-4.5.13.jar"/>
   <classpathentry kind="lib" path="lib/dist/httpcore-4.4.14.jar"/>
@@ -35 +34 @@
   <classpathentry kind="lib" path="lib/dist/poi-ooxml-5.0.0.jar"/>
   <classpathentry kind="lib" path="lib/dist/hibernate-core-5.5.6.Final.jar"/>
+  <classpathentry kind="lib" path="lib/dist/postgresql-42.5.1.jar"/>
   <classpathentry kind="lib" path="lib/dist/zip4j-2.11.2.jar"/>
   <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-11">

trunk/doc/3rd-party-components.txt

@@ -118 +118 @@
 
 More info : http://jdbc.postgresql.org/
-Version   : 42.2.20
+Version   : 42.5.1
 License   : BSD License (postgres.license.txt)
-Jar files : postgresql-42.2.20.jar
+Jar files : postgresql-42.5.1.jar
 
 

trunk/src/clients/web/net/sf/basedb/clients/web/taglib/table/ColumnDef.java

@@ -935 +935 @@
       if (isFilterable && hasFilter) 
       {
-        table.addFilteredColumn(getFilterproperty(), isVisible);
+        table.addFilteredColumn(getId(), getFilterproperty(), isVisible);
       }
     }

trunk/src/clients/web/net/sf/basedb/clients/web/taglib/table/PresetSelector.java

@@ -319 +319 @@
               if (value.startsWith("/"))
               {
-                if (value.endsWith("/name") || value.endsWith(".name"))
+                if (value.endsWith("/name"))
                 {
                   value = value.replace("/name", "/.");

trunk/src/clients/web/net/sf/basedb/clients/web/taglib/table/Table.java

@@ -565 +565 @@
     columnFilter.put(columnId+"@"+row, filterHtml);
   }
-  void addFilteredColumn(String columnId, boolean visible)
+  void addFilteredColumn(String columnId, String filterProperty, boolean visible)
   {
     numFilteredColumns++;
-    if (visible) hiddenFilteredColumns.remove(columnId);
+    // Swap the filter property with column id if needed
+    hiddenFilteredColumns.remove(filterProperty);
+    if (!visible) hiddenFilteredColumns.add(columnId);
   }
   Set<String> getHiddenFilteredColumns()

trunk/src/core/common-queries.xml

@@ -1856 +1856 @@
       )
       AND plg.disabled = false
+      AND (cfg.id IS NULL OR cfg.disabled = false)
       GROUP BY plg.mainType
     </sql>

trunk/src/core/net/sf/basedb/core/Install.java

@@ -119 +119 @@
     method.
   */
-  public static final int NEW_SCHEMA_VERSION = Integer.valueOf(151).intValue();
+  public static final int NEW_SCHEMA_VERSION = Integer.valueOf(152).intValue();
   
   public static synchronized int createTables(SchemaGenerator.Mode mode, ProgressReporter progress,

trunk/src/core/net/sf/basedb/core/Job.java

@@ -128 +128 @@
       {
         throw new InvalidDataException("Plugin " + plugin.getName() + " requires a configuration");
+      }
+      
+      if (plugin.isDisabled())
+      {
+        throw new PermissionDeniedException("The plugin is disabled: " + plugin.getName());
+      }
+      if (config != null && config.isDisabled())
+      {
+        throw new PermissionDeniedException("The plugin configuration is disabled: " + config.getName());
       }
       

trunk/src/core/net/sf/basedb/core/PluginConfiguration.java

@@ -364 +364 @@
     getData().setPluginDefinition(pd.getData());
   }
+  
+  /**
+    Checks if this plugin configuration is disabled or not. A disabled configuration
+    can't be used.
+    @since 3.19.6
+  */
+  public boolean isDisabled()
+  {
+    return getData().isDisabled();
+  }
+  
+  /**
+    Disabled or enable this plugin configuration.
+    @since 3.19.6
+  */
+  public void setDisabled(boolean disabled)
+  {
+    checkPermission(Permission.WRITE);
+    getData().setDisabled(disabled);
+  }
 
   /**

trunk/src/core/net/sf/basedb/core/PluginDefinition.java

@@ -303 +303 @@
       )
       AND plg.disabled = false
+      AND (cfg.id IS NULL OR cfg.disabled = false)
       GROUP BY plg.mainType
     */

trunk/src/core/net/sf/basedb/core/PropertyFilter.java

@@ -907 +907 @@
       ItemContext targetItemContext = new ItemContext(targetType, pp);
       targetItemContext.configureQuery(dc, subquery, subContext, true);
+      subquery.setIncludes(Include.ALL);
       if (context != null && targetItemContext.getException() != null)
       {

trunk/src/core/net/sf/basedb/core/Update.java

@@ -467 +467 @@
     </td>
   </tr>
+  <tr>
+    <td>152</td>
+    <td>
+      Added {@link PluginConfiguration#isDisabled()}. The update will set the value to FALSE 
+      for all existing configurations.
+    </td>
+  </tr>
   </table>
 
@@ -767 +774 @@
         if (progress != null) progress.display((int)(progress_current), "--Updating schema version: " + schemaVersion + " -> 151...");
         schemaVersion = updateToSchemaVersion151(session, schemaVersion, progress);
+        progress_current += progress_step;
+      }
+      
+      if (schemaVersion < 152)
+      {
+        if (progress != null) progress.display((int)(progress_current), "--Updating schema version: " + schemaVersion + " -> 150...");
+        schemaVersion = setSchemaVersionInTransaction(session, 152);
         progress_current += progress_step;
       }

trunk/src/core/net/sf/basedb/core/data/PluginConfigurationData.java

@@ -58 +58 @@
   }
 // -------------------------------------------
+  private boolean disabled;
+  /**
+    If the plugin is enabled or disabled.
+    // Mapped in hibernate-properties-PluginConfigurationData.xml since annotation doesn't support a default value
+    @since 3.19.6
+  */
+  public boolean isDisabled()
+  {
+    return disabled;
+  }
+  public void setDisabled(boolean disabled)
+  {
+    this.disabled = disabled;
+  }
 
   private PluginDefinitionData pluginDefinition;

trunk/src/core/net/sf/basedb/core/dtd/raw-data-types.dtd

@@ -20 +20 @@
   along with BASE. If not, see <http://www.gnu.org/licenses/>.
 -->
-<!ELEMENT raw-data-types (raw-data-type+) >
+<!ELEMENT raw-data-types (raw-data-type*) >
 
 <!ELEMENT raw-data-type (property*,intensity-formula*) >

trunk/src/core/net/sf/basedb/util/AutoDetectFileFormat.java

@@ -130 +130 @@
         ItemQuery<PluginConfiguration> configQuery = plugin.getPluginConfigurations();
         configQuery.restrict(Restrictions.gt(Hql.property("parameterVersion"), Expressions.integer(0)));
+        configQuery.restrict(Restrictions.eq(Hql.property("disabled"), Expressions.parameter("isDisabled", false)));
         configQuery.order(Orders.asc(Hql.property("name")));
         configQuery.include(Include.MINE, Include.SHARED, Include.IN_PROJECT, Include.OTHERS);

trunk/src/core/net/sf/basedb/util/extensions/manager/Settings.java

@@ -32 +32 @@
 import java.util.List;
 
+import net.sf.basedb.core.Config;
 import net.sf.basedb.core.Presets;
 import net.sf.basedb.core.Presets.Preset;
@@ -70 +71 @@
   private final File file;
   private final ExtensionsManager manager;
+  private final String pluginsDir;
+  private final String userFilesDir;
   private boolean hasChanged;
   private Presets presets;
@@ -89 +92 @@
     this.manager = manager;
     this.file = file;
+    this.pluginsDir = new File(Config.getString("plugins.dir")).getAbsolutePath();
+    this.userFilesDir = new File(Config.getString("userfiles")).getAbsolutePath();
     this.presets = new Presets();
     if (file != null && file.isFile())
@@ -104 +109 @@
     }
     this.settings = presets.getDefault();
-    this.installedFiles = presets.getPreset("installed-files");
-    this.ignoredFiles = presets.getPreset("ignored-files");
+    this.installedFiles = fixPaths(presets.getPreset("installed-files"));
+    this.ignoredFiles = fixPaths(presets.getPreset("ignored-files"));
     this.disabledExtensionPoints = presets.getPreset("disabled-extension-points");
     this.disabledExtensions = presets.getPreset("disabled-extensions");
@@ -200 +205 @@
   
   /**
+    A file is typically stored under the absolute path, but
+    if it matches the plug-ins directory we replace it with {plugins.dir}.
+    @since 3.19.6
+  */
+  private String toKey(File file)
+  {
+    String key = file.getAbsolutePath();
+    if (pluginsDir != null) key = key.replace(pluginsDir, "{plugins.dir}");
+    if (userFilesDir != null) key = key.replace(userFilesDir, "{userfiles.dir}");
+    return key;
+  }
+  
+  /**
+    A file is typically stored under the absolute path, but
+    if it matches the plug-ins directory we replace it with {plugins.dir}.
+    @since 3.19.6
+  */
+  private File toFile(String key)
+  {
+    if (pluginsDir != null) key = key.replace("{plugins.dir}", pluginsDir);
+    if (userFilesDir != null) key = key.replace("{userfiles.dir}", userFilesDir);
+    return new File(key);
+  }
+  
+  /**
+    Fix paths in older config files. This code can be removed some time in the future when
+    we are sure that everyone has upgraded. Eg. in BASE 3.21 since we must allow upgrades 
+    between BASE 3.19.x and BASE 3.20.x.
+  */
+  private Preset fixPaths(Preset preset)
+  {
+    for (String key : preset.getKeys())
+    {
+      if (key.contains(pluginsDir))
+      {
+        preset.setSetting(key.replace(pluginsDir, "{plugins.dir}"), preset.getSetting(key));
+        preset.setSetting(key, null);
+        hasChanged = true;
+      }
+      else if (key.contains(userFilesDir))
+      {
+        preset.setSetting(key.replace(userFilesDir, "{userfiles.dir}"), preset.getSetting(key));
+        preset.setSetting(key, null);
+        hasChanged = true;
+      }
+    }
+    return preset;
+  }
+  
+  /**
     Check if the given file is marked as installed.
     @since 3.0
@@ -205 +260 @@
   public boolean isInstalledFile(File file)
   {
-    return Values.getBoolean(installedFiles.getSetting(file.getAbsolutePath()));
+    String key = toKey(file);
+    return Values.getBoolean(installedFiles.getSetting(key));
   }
   
@@ -216 +272 @@
     if (file == null) return;
     hasChanged = true;
-    installedFiles.setSetting(file.getAbsolutePath(), "1");
+    installedFiles.setSetting(toKey(file), "1");
   }
   
@@ -227 +283 @@
     if (file == null) return;
     hasChanged = true;
-    installedFiles.setSetting(file.getAbsolutePath(), null);
+    installedFiles.setSetting(toKey(file), null);
   }
   
@@ -236 +292 @@
   public List<File> getInstalledFiles()
   {
-    List<String> paths = installedFiles.getKeys();
-    List<File> files = new ArrayList<File>(paths.size());
-    for (String path : paths)
-    {
-      files.add(new File(path));
+    List<String> keys = installedFiles.getKeys();
+    List<File> files = new ArrayList<File>(keys.size());
+    for (String key : keys)
+    {
+      files.add(toFile(key));
     }
     return files;
@@ -252 +308 @@
   public boolean isIgnoredFile(File file)
   {
-    return Values.getBoolean(ignoredFiles.getSetting(file.getAbsolutePath()));
+    return Values.getBoolean(ignoredFiles.getSetting(toKey(file)));
   }
   
@@ -263 +319 @@
     if (file == null) return;
     hasChanged = true;
-    ignoredFiles.setSetting(file.getAbsolutePath(), ignore ? "1" :  null);
+    ignoredFiles.setSetting(toKey(file), ignore ? "1" :  null);
   }
   
@@ -272 +328 @@
   public List<File> getIgnoredFiles()
   {
-    List<String> paths = ignoredFiles.getKeys();
-    List<File> files = new ArrayList<File>(paths.size());
-    for (String path : paths)
-    {
-      files.add(new File(path));
+    List<String> keys = ignoredFiles.getKeys();
+    List<File> files = new ArrayList<File>(keys.size());
+    for (String key : keys)
+    {
+      files.add(toFile(key));
     }
     return files;

trunk/www/admin/pluginconfigurations/edit_configuration.jsp

@@ -71 +71 @@
   String name = null;
   String description = null;
+  boolean isDisabled = false;
   
   // Load recently used items
@@ -105 +106 @@
     name = "Copy of " + originalConfiguration.getName();
     description = originalConfiguration.getDescription();
+    isDisabled = originalConfiguration.isDisabled();
     try
     {
@@ -122 +124 @@
     name = configuration.getName();
     description = configuration.getDescription();
+    isDisabled = configuration.isDisabled();
     try
     {
@@ -193 +196 @@
         <td></td>
       </tr>
+      <tr>
+        <th>Disabled</th>
+        <td>
+          <input type="radio" name="disabled" id="disabledNo" value="0" 
+            <%=!isDisabled ? "checked" : ""%>><label for="disabledNo">no</label>
+          <input type="radio" name="disabled" id="disabledYes" value="1" 
+            <%=isDisabled ? "checked" : ""%>><label for="disabledYes">yes</label>
+        </td>
+        <td></td>
+      </tr> 
       <tr class="dynamic">
         <th>Description</th>

trunk/www/admin/pluginconfigurations/index.jsp

@@ -174 +174 @@
       configuration.setName(Values.getStringOrNull(request.getParameter("name")));
       configuration.setDescription(Values.getStringOrNull(request.getParameter("description")));
+      configuration.setDisabled(Values.getBoolean(request.getParameter("disabled")));
       // Annotations tab
       Base.updateAnnotations(dc, configuration, configuration, request);

trunk/www/admin/pluginconfigurations/list_configurations.jsp

@@ -211 +211 @@
         datatype="string"
         title="Plugin definition"
+        sortable="true" 
+        filterable="true"
+        exportable="true"
+      />
+      <tbl:columndef 
+        id="disabled"
+        property="disabled"
+        datatype="boolean"
+        title="Disabled"
         sortable="true" 
         filterable="true"
@@ -472 +481 @@
                 <tbl:cell column="contexts"><%=plugin == null ? "<i>- denied -</i>" : (contexts.isEmpty() ? "<i>- none -</i>" : Values.getString(contexts, ", ", true))%></tbl:cell>
                 <tbl:cell column="pluginDefinition"><%=mode.hasPropertyLink() ? Base.getLinkedName(ID, plugin, plugin == null, mode.hasEditLink()): Base.getEncodedName(nameableProxy, plugin == null)%></tbl:cell>
+                <tbl:cell column="disabled"><%=item.isDisabled()%></tbl:cell>
                 <tbl:cell column="owner"
                   ><base:propertyvalue 

trunk/www/admin/pluginconfigurations/view_configuration.jsp

@@ -260 +260 @@
         <th>Registered</th>
         <td><%=dateFormatter.format(configuration.getEntryDate())%></td>
+      </tr>
+      <tr>
+        <th>Disabled</th>
+        <td><%=configuration.isDisabled() ? "Yes" : "No"%></td>
       </tr>
       <tr>

trunk/www/common/import/index.jsp

@@ -107 +107 @@
         )
       );
+    configQuery.restrict(Restrictions.eq(Hql.property("disabled"), Expressions.parameter("isDisabled", false)));
     configQuery.order(Orders.asc(Hql.property("name")));
     configQuery.include(Include.MINE, Include.SHARED, Include.IN_PROJECT, Include.OTHERS);

trunk/www/common/plugin/index.jsp

@@ -180 +180 @@
       );
     configQuery.restrict(Restrictions.gt(Hql.property("parameterVersion"), Expressions.integer(0)));
+    configQuery.restrict(Restrictions.eq(Hql.property("disabled"), Expressions.parameter("isDisabled", false)));
     configQuery.order(Orders.asc(Hql.property("name")));
     configQuery.include(Include.MINE, Include.SHARED, Include.IN_PROJECT, Include.OTHERS);