Changeset 12495 for branches/GBT/HeuristicLab.Persistence/3.3

Timestamp:

06/23/15 12:50:05 (9 years ago)

Author:

gkronber

Message:

#2261: merged trunk changes to branch
r12494
#2403: added a null check in the MatlabParameterVectorEvaluator to prevent exceptions when clearstate is called

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r12493
#2369: added support for squared errors and relative errors to error-characteristic-curve view

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r12492
#2392: implemented PearsonsRCalculator to fix incorrect correlation values in the correlation matrix.

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r12491
#2402 don't set task state to waiting when it fails

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r12490
#2401 added missing Mono.Cecil plugin dependency

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r12488
#2400 - Interfaces for Capaciated-, PickupAndDelivery- and TimeWindowed-ProblemInstances now specify an additional penalty parameter to set the current penalty factor for the constraint relaxation. - The setter of the penalty-property in ...

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r12485
#2374 made RegressionSolution and ClassificationSolution non-abstract

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r12482
#2320: Fixed warnings in unit test solutions introduced in r12420 by marking methods as obsolete.

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r12481
#2320: Fixed AfterDeserialization of GEArtifialAntEvaluator.

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r12480
#2320: Fixed error in symbolicexpressiontree crossover regarding the wiring of lookup parameters if persisted file is loaded.

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r12479
#2397 moved GeoIP project into ExtLibs

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r12478
#2329 fixed bug in simple code editor

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r12476
#2331 removed outdated plugins

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r12475
#2368 fixed compile warnings

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r12474
#2399 worked on Mono project prepare script

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r12473
#2329 added a simple code editor for Linux

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r12472
#2399 - fixed MathJax.js file name - worked on Mono project prepare script

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r12471
#2399 worked on Mono project prepare script

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r12470
#2399 fixed pre-build events in project files

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r12465
#2399 worked on mono project prepare script

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r12464
#2399 added patch to project

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r12463
#2399 fixed EPPlus so that it compiles on Linux

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r12461
#2398: Skip root and start symbols when calculating impacts and replacement values in the pruning operators.

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r12458
#2354 show label when no data is displayed and don't show the legend

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r12457
#2353 removed duplicated call to Any() in Hive Status page

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r12456
#2368 fixed modifier

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r12455
#2368 added support in persistence for typecaches in streams

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r12445
#2394: Changed Web.config compilation from debug to release to force script bundling. Changed history loading type from lazy to eager loading to increase performance. Fixed "getCoreStatus" typo in statusCtrl.js

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r12443
#2394: Fixed UserTaskQuery and GetStatusHistory in the WebApp.Status plugin

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r12442
#2394 added nuget folders to svn ignore list

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r12435
#2394: Improved PluginManager and updated hive status monitor.

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r12434
#2396 added symbolic expression tree formatter for C#

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r12433
#2395: Minor change in DoubleValue.GetValue.

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r12432
#2395 Use simple round-trip format for doubles because G17 prints some strange numbers (20.22 to 20.219999999999999999). Some accuracy can still be lost on 64bit machines, but should be very rare and minimal. double.MaxValue can still be pa...

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r12431
#2395 Fixed parsing issues by using the G17 format.

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r12430
#2394 added missing package config

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r12429
#2394 added missing package config

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r12428
#2394 added web app and status page to trunk

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r12424
#2320: Adapted plugin file and updated project file of SymbolicExpressionTreeEncoding.

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r12422
#2320: Merged the encoding class and all accompanying changes in the trunk.

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r12401
#2387 Fixed a bug where the automatic selection of the first element behaved differently for the NewItemDialog.

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r12400
#2387 Forgot to commit a file.

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r12399
#2387 - Added context-menu for expanding and collapsing tree-nodes. - Improve response time when expanding/collapsing all nodes for TypeSelector and NewItemDialog.

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r12398
#2387 - Added clearSearch-button in TypeSelector. - Adapted behavior of TypeSelector and NewItemDialog that a selected node stays selected as long as it matches the search criteria.

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r12397
#2387 - Adapted behavior of the matching in the TypeSelector that it behave the same as the NewItemDialog. The search string is tokenized by space and matches if all tokens are contained, (eg. "Sym Reg" matches "SymbolicRegression...")...

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r12393
#2025 - Removed Expand/CollapseAll buttons. - Removed cycling of items.

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r12392
#2386: Updated GetHashCode method in the EnumerableBoolEqualityComparer.

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Location:

branches/GBT

Files:

• . (modified) (2 props)
• HeuristicLab.Persistence (modified) (1 prop)
• HeuristicLab.Persistence/3.3/Default/Xml/EasyXmlGenerator.cs (modified) (2 diffs)
• HeuristicLab.Persistence/3.3/Default/Xml/XmlGenerator.cs (modified) (6 diffs)
• HeuristicLab.Persistence/3.3/Default/Xml/XmlParser.cs (modified) (2 diffs)

branches/GBT/HeuristicLab.Persistence/3.3/Default/Xml/EasyXmlGenerator.cs

@@ -167 +167 @@
     /// <param name="obj">The object.</param>
     /// <param name="stream">The stream.</param>
-    public new static void Serialize(object obj, Stream stream) {
+    public static void Serialize(object obj, Stream stream) {
       Serialize(obj, stream, ConfigurationService.Instance.GetConfiguration(new XmlFormat()));
     }
@@ -178 +178 @@
     /// <param name="stream">The stream.</param>
     /// <param name="config">The configuration.</param>
-    public new static void Serialize(object obj, Stream stream, Configuration config) {
+    public static void Serialize(object obj, Stream stream, Configuration config) {
       try {
         using (StreamWriter writer = new StreamWriter(stream)) {

branches/GBT/HeuristicLab.Persistence/3.3/Default/Xml/XmlGenerator.cs

@@ -311 +311 @@
     }
 
+    private static void Serialize(object obj, Stream stream, Configuration config, bool includeAssemblies
+   , CompressionLevel compression) {
+      Serializer serializer = new Serializer(obj, config);
+      Serialize(stream, includeAssemblies, compression, serializer);
+    }
+
+    private static void Serialize(Stream stream, bool includeAssemblies, CompressionLevel compression, Serializer serializer) {
+      try {
+        DateTime start = DateTime.Now;
+        serializer.InterleaveTypeInformation = false;
+        XmlGenerator generator = new XmlGenerator();
+        using (ZipArchive zipArchive = new ZipArchive(stream, ZipArchiveMode.Create)) {
+          ZipArchiveEntry entry = zipArchive.CreateEntry("data.xml", compression);
+          using (StreamWriter writer = new StreamWriter(entry.Open())) {
+            foreach (ISerializationToken token in serializer) {
+              string line = generator.Format(token);
+              writer.Write(line);
+            }
+          }
+          entry = zipArchive.CreateEntry("typecache.xml", compression);
+          using (StreamWriter writer = new StreamWriter(entry.Open())) {
+            foreach (string line in generator.Format(serializer.TypeCache)) {
+              writer.Write(line);
+            }
+          }
+          if (includeAssemblies) {
+            foreach (string name in serializer.RequiredFiles) {
+              Uri uri = new Uri(name);
+              if (!uri.IsFile) {
+                Logger.Warn("cannot read non-local files");
+                continue;
+              }
+              entry = zipArchive.CreateEntry(Path.GetFileName(uri.PathAndQuery), compression);
+              using (BinaryWriter bw = new BinaryWriter(entry.Open())) {
+                using (FileStream reader = File.OpenRead(uri.PathAndQuery)) {
+                  byte[] buffer = new byte[1024 * 1024];
+                  while (true) {
+                    int bytesRead = reader.Read(buffer, 0, 1024 * 1024);
+                    if (bytesRead == 0)
+                      break;
+                    bw.Write(buffer, 0, bytesRead);
+                  }
+                }
+              }
+            }
+          }
+        }
+        Logger.Info(String.Format("serialization took {0} seconds with compression level {1}",
+          (DateTime.Now - start).TotalSeconds, compression));
+      }
+      catch (Exception) {
+        Logger.Warn("Exception caught, no data has been serialized.");
+        throw;
+      }
+    }
+
     /// <summary>
     /// Serializes the specified object into a file.
@@ -322 +378 @@
       try {
         string tempfile = Path.GetTempFileName();
-        DateTime start = DateTime.Now;
+
         using (FileStream stream = File.Create(tempfile)) {
-          Serializer serializer = new Serializer(obj, config);
-          serializer.InterleaveTypeInformation = false;
-          XmlGenerator generator = new XmlGenerator();
-          using (ZipArchive zipArchive = new ZipArchive(stream, ZipArchiveMode.Create)) {
-            ZipArchiveEntry entry = zipArchive.CreateEntry("data.xml", compression);
-            using (StreamWriter writer = new StreamWriter(entry.Open())) {
-              foreach (ISerializationToken token in serializer) {
-                string line = generator.Format(token);
-                writer.Write(line);
-              }
-            }
-            entry = zipArchive.CreateEntry("typecache.xml", compression);
-            using (StreamWriter writer = new StreamWriter(entry.Open())) {
-              foreach (string line in generator.Format(serializer.TypeCache)) {
-                writer.Write(line);
-              }
-            }
-            if (includeAssemblies) {
-              foreach (string name in serializer.RequiredFiles) {
-                Uri uri = new Uri(name);
-                if (!uri.IsFile) {
-                  Logger.Warn("cannot read non-local files");
-                  continue;
-                }
-                entry = zipArchive.CreateEntry(Path.GetFileName(uri.PathAndQuery), compression);
-                using (BinaryWriter bw = new BinaryWriter(entry.Open())) {
-                  using (FileStream reader = File.OpenRead(uri.PathAndQuery)) {
-                    byte[] buffer = new byte[1024 * 1024];
-                    while (true) {
-                      int bytesRead = reader.Read(buffer, 0, 1024 * 1024);
-                      if (bytesRead == 0)
-                        break;
-                      bw.Write(buffer, 0, bytesRead);
-                    }
-                  }
-                }
-              }
-            }
-          }
-        }
-        Logger.Info(String.Format("serialization took {0} seconds with compression level {1}",
-          (DateTime.Now - start).TotalSeconds, compression));
+          Serialize(obj, stream, config, includeAssemblies, compression);
+        }
+
         File.Copy(tempfile, filename, true);
         File.Delete(tempfile);
@@ -381 +398 @@
     /// <param name="obj">The object.</param>
     /// <param name="stream">The stream.</param>
-    public static void Serialize(object obj, Stream stream) {
-      Serialize(obj, stream, ConfigurationService.Instance.GetConfiguration(new XmlFormat()));
+    /// <param name="useZip">If true, uses zip for compression, otherwise gzip.</param>
+    public static void Serialize(object obj, Stream stream, bool useZip = false) {
+      Serialize(obj, stream, ConfigurationService.Instance.GetConfiguration(new XmlFormat()), useZip);
     }
 
@@ -392 +410 @@
     /// <param name="stream">The stream.</param>
     /// <param name="config">The configuration.</param>
-    public static void Serialize(object obj, Stream stream, Configuration config) {
-      Serialize(obj, stream, config, false);
+    /// <param name="useZip">If true, uses zip for compression, otherwise gzip.</param>
+    public static void Serialize(object obj, Stream stream, Configuration config, bool useZip = false) {
+      Serialize(obj, stream, config, false, useZip);
     }
 
@@ -403 +422 @@
     /// <param name="config">The configuration.</param>
     /// <param name="includeAssemblies">if set to <c>true</c> include need assemblies.</param>
-    public static void Serialize(object obj, Stream stream, Configuration config, bool includeAssemblies) {
+    /// <param name="useZip">If true, uses zip for compression, otherwise gzip.</param>
+    public static void Serialize(object obj, Stream stream, Configuration config, bool includeAssemblies, bool useZip = false) {
       try {
         Serializer serializer = new Serializer(obj, config);
-        Serialize(stream, serializer);
+        if (useZip) {
+          Serialize(obj, stream, config, includeAssemblies, CompressionLevel.Optimal);
+        } else {
+          Serialize(stream, serializer);
+        }
       }
       catch (PersistenceException) {
@@ -424 +448 @@
     /// <param name="includeAssemblies">if set to <c>true</c> include need assemblies.</param>
     /// <param name="types">The list of all serialized types.</param>
-    public static void Serialize(object obj, Stream stream, Configuration config, bool includeAssemblies, out IEnumerable<Type> types) {
+    /// <param name="useZip">If true, uses zip for compression, otherwise gzip.</param>
+    public static void Serialize(object obj, Stream stream, Configuration config, bool includeAssemblies, out IEnumerable<Type> types, bool useZip = false) {
       try {
         Serializer serializer = new Serializer(obj, config);
-        Serialize(stream, serializer);
+        if (useZip) {
+          Serialize(stream, includeAssemblies, CompressionLevel.Optimal, serializer);
+        } else {
+          Serialize(stream, serializer);
+        }
         types = serializer.SerializedTypes;
       }

branches/GBT/HeuristicLab.Persistence/3.3/Default/Xml/XmlParser.cs

@@ -218 +218 @@
 
     /// <summary>
-    /// Deserializes an object from the specified stream.
+    /// Deserializes an object from the specified stream using GZip compression.
     /// </summary>
     /// <param name="stream">The stream.</param>
     /// <returns>A fresh object instance.</returns>
-    public static object Deserialize(Stream stream) {
+    private static object DeserializeWithGZip(Stream stream) {
       try {
         using (StreamReader reader = new StreamReader(new GZipStream(stream, CompressionMode.Decompress))) {
@@ -239 +239 @@
 
     /// <summary>
+    /// Deserializes an object from the specified stream using Zip compression.
+    /// </summary>
+    /// <param name="stream">The stream.</param>
+    /// <returns>A fresh object instance.</returns>
+    private static object DeserializeWithZip(Stream stream) {
+      ZipArchive zipFile = new ZipArchive(stream);
+      return Deserialize(zipFile);
+    }
+
+    /// <summary>
     /// Deserializes an object from the specified stream.
     /// </summary>
     /// <typeparam name="T">object type expected from the serialized stream</typeparam>
     /// <param name="stream">The stream.</param>
+    /// <param name="useZip">If true, uses zip for decompression, otherwise gzip.</param>
     /// <returns>A fresh object instance.</returns>
-    public static T Deserialize<T>(Stream stream) {
-      return (T)Deserialize(stream);
+    public static T Deserialize<T>(Stream stream, bool useZip = false) {
+      return (T)Deserialize(stream, useZip);
+    }
+
+    /// <summary>
+    /// Deserializes an object from the specified stream.
+    /// </summary>
+    /// <param name="stream">The stream.</param>
+    /// <param name="useZip">If true, uses zip for decompression, otherwise gzip.</param>
+    /// <returns>A fresh object instance.</returns>
+    public static object Deserialize(Stream stream, bool useZip = false) {
+      if (useZip) {
+        return DeserializeWithZip(stream);
+      } else {
+        return DeserializeWithGZip(stream);
+      }
     }