Changeset 3659

Timestamp:

Aug 13, 2007, 12:55:26 PM (16 years ago)

Author:

Nicklas Nordborg

Message:

References #294: Performance testing

Added framework for testing BASE 2 plug-ins.

Location:

trunk

Files:

• config/test (added)
• config/test/performance.properties (added)
• doc/test/performance (added)
• doc/test/performance/index.html (added)
• src/test/net/sf/basedb/test/FileUtil.java (modified) (2 diffs)
• src/test/net/sf/basedb/test/PluginUtil.java (modified) (3 diffs)
• src/test/net/sf/basedb/test/performance/Config.java (added)
• src/test/net/sf/basedb/test/performance/FilterTest.java (added)
• src/test/net/sf/basedb/test/performance/LowessTest.java (added)
• src/test/net/sf/basedb/test/performance/PrepareTest.java (added)
• src/test/net/sf/basedb/test/performance/RawDataTest.java (modified) (6 diffs)
• src/test/net/sf/basedb/test/performance/RootTest.java (added)
• src/test/net/sf/basedb/test/performance/Run.java (modified) (2 diffs)
• src/test/net/sf/basedb/test/performance/Util.java (added)
• src/test/net/sf/basedb/test/roles/PowerUserTest.java (modified) (1 diff)
• src/test/set_classpath.bat (modified) (1 diff)
• src/test/set_classpath.sh (modified) (1 diff)

trunk/src/test/net/sf/basedb/test/FileUtil.java

@@ -41 +41 @@
 
   /**
-    Upload a file to the logged in user's home directory.
+    Upload a file to the logged in user's home directory, or into the root
+    directory if the user has no home directory.
   */
   public static File uploadFile(DbControl dc, String filename, String fileTypeId)
@@ -56 +57 @@
       file.setFileType(FileType.getById(dc, SystemItems.getId(fileTypeId)));
     }
-    if (!file.isInDatabase()) dc.saveItem(file);
-    
-    file.upload(TestUtil.class.getResourceAsStream(path), false);
+    if (!file.isInDatabase()) 
+    {
+      dc.saveItem(file);
+      file.upload(TestUtil.class.getResourceAsStream(path), false);
+    }
     return file;
   }

trunk/src/test/net/sf/basedb/test/PluginUtil.java

@@ -57 +57 @@
 {
 
+  /**
+    Create a new or load the existing plug-in configuration with a given name. Note!
+    If the configuration already exists, the parameters are not updated.
+  */
   public static PluginConfiguration createPluginConfiguration(DbControl dc, String name, String className, Map<String, Object> parameters)
   {
     TestUtil.write("--Creating/loading plugin configuration: " + name + "\n");
     
-    ItemQuery<PluginConfiguration> query = PluginConfiguration.getQuery();
+    PluginDefinition definition = PluginDefinition.getByClassName(dc, className);
+    ItemQuery<PluginConfiguration> query = definition.getPluginConfigurations();
     query.restrict(Restrictions.eq(Hql.property("name"), Expressions.string(name)));
     List<PluginConfiguration> result = query.list(dc);
     if (result.size() > 0) return result.get(0);
     
-    PluginDefinition definition = PluginDefinition.getByClassName(dc, className);
     PluginConfiguration config = PluginConfiguration.getNew(dc, definition);
     config.setName(name);
@@ -98 +102 @@
   /**
     Import reporters.
+    @param jobName The name of the job
   */
-  public static void importReporters(PluginConfiguration config, File file)
+  public static void importReporters(PluginConfiguration config, File file, String jobName)
     throws Exception
   {
@@ -109 +114 @@
       config = PluginConfiguration.getById(dc, config.getId());
       Job job = Job.getNew(dc, config.getPluginDefinition(), config);
-      job.setName("Importing reporters for project A");
+      job.setName(jobName);
       job.setParameterValue("file", new FileParameterType(), file);
       job.setParameterValue("updateExisting", new BooleanParameterType(), true);

trunk/src/test/net/sf/basedb/test/performance/RawDataTest.java

@@ -24 +24 @@
 package net.sf.basedb.test.performance;
 
-
-import java.util.List;
-
 import net.sf.basedb.core.ArrayDesign;
 import net.sf.basedb.core.DbControl;
+import net.sf.basedb.core.Experiment;
 import net.sf.basedb.core.File;
 import net.sf.basedb.core.FileParameterType;
-import net.sf.basedb.core.FileType;
 import net.sf.basedb.core.ItemParameterType;
-import net.sf.basedb.core.ItemQuery;
 import net.sf.basedb.core.Job;
 import net.sf.basedb.core.PluginConfiguration;
@@ -39 +35 @@
 import net.sf.basedb.core.RawDataTypes;
 import net.sf.basedb.core.StringParameterType;
-import net.sf.basedb.core.query.Expressions;
-import net.sf.basedb.core.query.Hql;
-import net.sf.basedb.core.query.Restrictions;
-import net.sf.basedb.test.FileUtil;
-import net.sf.basedb.test.MouseData;
 import net.sf.basedb.test.PluginUtil;
 import net.sf.basedb.test.TestUtil;
+import net.sf.basedb.util.Values;
 
 /**
-
+  Import raw data.
 
   @author nicklas
@@ -70 +62 @@
       TestUtil.login(user, password, false);
 
-      // Create importers
-      dc = TestUtil.getDbControl();
-      // Importer for reporters
-      PluginConfiguration reporterImporter = PluginUtil.createPluginConfiguration(dc, 
-        "Reporters for performance test", 
-        "net.sf.basedb.plugins.ReporterFlatFileImporter", MouseData.getReporterParameters());
-      
-      // Importer for raw data
-      PluginConfiguration rawDataImporter = PluginUtil.createPluginConfiguration(dc, 
-        "Raw data for performance test", 
-        "net.sf.basedb.plugins.RawDataFlatFileImporter", MouseData.getGenePixRawDataParameters(false));
-      
-      // Importer for features
-      PluginConfiguration genePixFeatureImporter = PluginUtil.createPluginConfiguration(dc, 
-        "Features from GenePix file",
-        "net.sf.basedb.plugins.ReporterMapFlatFileImporter", MouseData.getGenePixReporterMapParameters());
-      dc.commit();
-      
-      // Upload files
-      dc = TestUtil.getDbControl();
-      File reporters = FileUtil.uploadFile(dc, "plates_and_reporters.mouse.v4.37k.txt", FileType.REPORTER);
-      File rawData1 = FileUtil.uploadFile(dc, "genepix.mouse.v4.37k.00h.gpr", FileType.RAW_DATA);
-      File rawData2 = FileUtil.uploadFile(dc, "genepix.mouse.v4.37k.24h.gpr", FileType.RAW_DATA);
-      dc.commit();
-      
-      // Import reporters
-      PluginUtil.importReporters(reporterImporter, reporters);
-      
-      // Create array design
-      dc = TestUtil.getDbControl();
-      ArrayDesign design = createArrayDesign(dc, "Array design for performance test");
-      dc.commit();
-      
-      // Import features
-      if (!design.hasFeatures()) 
-      {
-        importFeatures(genePixFeatureImporter, rawData1, design);
-      }
-      
       // Create raw bioassays
       dc = TestUtil.getDbControl();
+      
+      // Load prepared items
+      ArrayDesign design = PrepareTest.getArrayDesign(dc);
+      Experiment experiment = PrepareTest.getExperiment(dc);
+      PluginConfiguration rawDataImporter = PrepareTest.getRawDataImporter(dc);
+      File rawData1 = PrepareTest.getRawDataFile1(dc);
+      File rawData2 = PrepareTest.getRawDataFile2(dc);
+      
+      long startNum = experiment.getRawBioAssays().count(dc);
       RawBioAssay[] rba = new RawBioAssay[numIterations];
       for (int i = 0; i < numIterations; ++i)
       {
-        rba[i] = createRawBioAssay(dc, "Performance test #" + i, design);
+        rba[i] = createRawBioAssay(dc, "PerformanceTest #" + (startNum + i), design);
       }
       dc.commit();
       
       // Import raw data
+      long minTime = Long.MAX_VALUE;
+      long maxTime = 0;
+      long totalTime = 0;
       for (int i = 0; i < numIterations; i += 2)
       {
         TestUtil.gc();
         long time = importRawData(rawDataImporter, rawData1, rba[i]) / 1000;
-        TestUtil.write("Import #" + i + "\t" + time + " s\n");
+        totalTime += time;
+        if (time < minTime) minTime = time;
+        if (time > maxTime) maxTime = time;
+        TestUtil.write("Import #" + i + "\t" + Values.formatTime(time) + "\n");
+
         time = importRawData(rawDataImporter, rawData2, rba[i+1]) / 1000;
-        TestUtil.write("Import #" + (i + 1) + "\t" + time + " s\n");
+        totalTime += time;
+        if (time < minTime) minTime = time;
+        if (time > maxTime) maxTime = time;
+        TestUtil.write("Import #" + (i + 1) + "\t" + Values.formatTime(time) + " s\n");
       }
+      TestUtil.write("---------------------------------------------\n");
+      TestUtil.write("Imported " + numIterations + " raw data sets\n");
+      TestUtil.write("Max time: " + Values.formatTime(maxTime) + "\n");
+      TestUtil.write("Min time: " + Values.formatTime(minTime) + "\n");
+      TestUtil.write("Mean time: " + Values.formatTime(totalTime / numIterations) + "\n");
+      TestUtil.write("---------------------------------------------\n");
+      
+      // Add raw bioassays to experiment
+      dc = TestUtil.getDbControl();
+      dc.reattachItem(experiment);
+      for (int i = 0; i < numIterations; i++)
+      {
+        dc.refreshItem(rba[i]);
+        experiment.addRawBioAssay(rba[i]);
+      }
+      dc.commit();
       
       TestUtil.logout();
@@ -141 +129 @@
     TestUtil.write("++Leaving raw data test (" + (ok ? "OK" : "FAILED") + ")\n");
     return ok;
-  }
-
-  /**
-    Create an array design or load the existing one.
-  */
-  public static ArrayDesign createArrayDesign(DbControl dc, String name)
-  {
-    TestUtil.write("--Creating/loading array design: " + name + "\n");
-
-    ItemQuery<ArrayDesign> query = ArrayDesign.getQuery();
-    query.restrict(Restrictions.eq(Hql.property("name"), Expressions.string(name)));
-    List<ArrayDesign> result = query.list(dc);
-    if (result.size() > 0) return result.get(0);
-    ArrayDesign design = ArrayDesign.getNew(dc, false);
-    design.setName(name); 
-    dc.saveItem(design);
-    return design;
-  }
-
-  /**
-    Import features.
-  */
-  public static void importFeatures(PluginConfiguration plugin, File file, ArrayDesign design)
-    throws Exception
-  {
-    TestUtil.write("--Importing features from file: " + file.getName() + "\n");
-    DbControl dc = TestUtil.getDbControl();
-    try
-    {
-      plugin = PluginConfiguration.getById(dc, plugin.getId());
-      Job job = Job.getNew(dc, plugin.getPluginDefinition(), plugin);
-      job.setName("Importing features to array design: " + design.getName());
-      job.setParameterValue("file", new FileParameterType(), file);
-      job.setParameterValue("arrayDesign", 
-        new ItemParameterType<ArrayDesign>(ArrayDesign.class, null), design);
-      job.setParameterValue("missingReporterError", new StringParameterType(), "skip");
-      dc.saveItem(job);
-      dc.commit();
-      PluginUtil.executeJob(job);
-    }
-    finally
-    {
-      if (dc != null) dc.close();
-    }
   }
 
@@ -212 +156 @@
       config = PluginConfiguration.getById(dc, config.getId());
       Job job = Job.getNew(dc, config.getPluginDefinition(), config);
-      job.setName("Importing data to raw bioassay: " + rba.getName());
+      job.setName("PerformanceTest: Import data to raw bioassay: " + rba.getName());
+      job.setSendMessage(false);
+      job.setRemoveJobWhenFinished(true);
       job.setParameterValue("file", new FileParameterType(), file);
       job.setParameterValue("rawBioAssay", 
@@ -222 +168 @@
       long time = System.currentTimeMillis();
       PluginUtil.executeJob(job);
-      return System.currentTimeMillis() - time;
+      return  System.currentTimeMillis() - time;
     }
     finally

trunk/src/test/net/sf/basedb/test/performance/Run.java

@@ -24 +24 @@
 package net.sf.basedb.test.performance;
 
+import java.util.Arrays;
+import java.util.HashSet;
+import java.util.Set;
+
 import net.sf.basedb.test.CmdLine;
 import net.sf.basedb.test.TestUtil;
@@ -42 +46 @@
     CmdLine cmdLine = new CmdLine(args);
 
-    String cmd = cmdLine.getCmd();
-    boolean all = "all".equals(cmd);
+    Set<String> cmds = new HashSet<String>(Arrays.asList(args));
+    boolean all = cmds.contains("all");
     
     String user = cmdLine.getOption("-u", "root");
     String password = cmdLine.getOption("-p", "root");
-    int numIterations = Values.getInt(cmdLine.getOption("-n"), 100);
+    int numItems = Values.getInt(cmdLine.getOption("-n"), 4);
 
     int tests = 0;
-    boolean ok = true;
-    if (ok && (all || "raw".equals(cmd)))
+    TestUtil.begin(false);
+    boolean ok = PrepareTest.run(user, password);
+    if (ok && (all || cmds.contains("raw")))
     {
-      TestUtil.begin(false);
-      ok = RawDataTest.run(user, password, numIterations);
+      ok = RawDataTest.run(user, password, numItems);
+      tests++;
+    }
+    if (ok && (all || cmds.contains("root")))
+    {
+      ok = RootTest.run(user, password, numItems);
+      tests++;
+    }
+    if (ok && (all || cmds.contains("filter")))
+    {
+      ok = FilterTest.run(user, password);
+      tests++;
+    }
+    if (ok && (all || cmds.contains("lowess")))
+    {
+      ok = LowessTest.run(user, password);
+      tests++;
+    }
+    if (ok && cmds.contains("clean"))
+    {
+      ok = PrepareTest.cleanUp(user, password);
       tests++;
     }

trunk/src/test/net/sf/basedb/test/roles/PowerUserTest.java

@@ -160 +160 @@
       dc.commit();
       
-      PluginUtil.importReporters(reporterImporter, reporters);
+      PluginUtil.importReporters(reporterImporter, reporters, "Importing reporters for project A");
       importPlates(platesImporter, plates, "Plate A", plateType);
       

trunk/src/test/set_classpath.bat

@@ -27 +27 @@
 SET CP=%CP%;../../config/local
 SET CP=%CP%;../../config/dist
+SET CP=%CP%;../../config/test
 
 REM Testdata

trunk/src/test/set_classpath.sh

@@ -27 +27 @@
 CP=$CP:../../config/local
 CP=$CP:../../config/dist
+CP=$CP:../../config/test
 
 # Testdata