Changeset 2568

Timestamp:

Aug 22, 2006, 2:22:13 PM (16 years ago)

Author:

Nicklas Nordborg

Message:

Fixes #221: Create enhanced test procedure.
References #222: Automated test program suite for enhanced test procedure.

Location:

trunk

Files:

• doc/styles.css (modified) (4 diffs)
• doc/test/permissions (deleted)
• doc/test/roles (added)
• doc/test/roles/correction.dyeswap.png (added)
• doc/test/roles/correction.png (added)
• doc/test/roles/histogram.png (added)
• doc/test/roles/index.html (added)
• doc/test/roles/overview.dyeswap.png (added)
• doc/test/roles/overview.png (added)
• doc/test/roles/scatter.png (added)
• src/test/net/sf/basedb/test/TestUtil.java (modified) (6 diffs)
• src/test/net/sf/basedb/test/roles/AnalysisTest.java (modified) (1 diff)
• src/test/net/sf/basedb/test/roles/PowerUserTest.java (modified) (3 diffs)
• src/test/net/sf/basedb/test/roles/Run.java (modified) (7 diffs)
• src/test/net/sf/basedb/test/roles/UserTest.java (modified) (5 diffs)

trunk/doc/styles.css

@@ -30 +30 @@
 }
 
-td {
+td, th {
   font-family: verdana, arial, sans-serif;
   font-size: 10pt;
@@ -165 +165 @@
 .red {
   background: #FF0000;
-  xborder: 1px solid #000000;
   width: 20px;
   text-align: center;
@@ -172 +171 @@
 .yellow {
   background: #FFFF00;
-  xborder: 1px solid #000000;
   width: 20px;
   text-align: center;
@@ -179 +177 @@
 .green {
   background: #00FF00;
-  xborder: 1px solid #000000;
   width: 20px;
   text-align: center;
   font-weight: bold;
 }
+
+table.listing {
+  border: 1px solid #999999;
+  width: 100%;
+}
+table.listing tr {
+  vertical-align: top;
+}
+table.listing th {
+  text-align: left;
+  background: #E0E0E0;
+  border-bottom: 1px solid #999999;
+}
+table.listing tr.oddrow {
+}
+table.listing tr.evenrow, .shaded {
+  background: #E0E0E0;
+}
+
+
+

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

@@ -24 +24 @@
 package net.sf.basedb.test;
 
+import java.io.FileWriter;
+import java.io.Writer;
 import java.net.InetAddress;
 
@@ -50 +52 @@
   private static String client = "net.sf.basedb.clients.test";
   private static SessionControl sc = null;
+  private static Writer memoryLog = null;
+  private static long startTime = 0;
+  private static Runtime runtime = Runtime.getRuntime();
 
   /**
     Start the testing. Starts BASE and creates a SessionControl.
   */
-  public static void begin()
+  public static void begin(boolean logMemoryUsage)
   {
     if (Application.isRunning()) return;
@@ -60 +65 @@
     {
       write("++Starting BASE...");
-      Application.start();
+      if (logMemoryUsage)
+      {
+        memoryLog = new FileWriter("memory.log");
+        memoryLog.write("Time (ms)\tTotal\tFree\tUsed\n");
+        startTime = System.currentTimeMillis();
+      }
+      Application.start(false);
       sc = Application.newSessionControl(client, getLocalIp(), null);
       write("done.\n");
@@ -83 +94 @@
       if (sc != null && sc.isLoggedIn()) sc.logout();
       Application.stop();
+      if (memoryLog != null) memoryLog.close();
       write("done.\n");
     }
@@ -96 +108 @@
   public static SessionControl getSessionControl()
   {
-    if (sc == null) begin();
+    if (sc == null) begin(false);
     return sc;
   }
@@ -105 +117 @@
   public static DbControl getDbControl()
   {
+    if (memoryLog != null)
+    {
+      try
+      {
+        long time = System.currentTimeMillis() - startTime;
+        long total = runtime.totalMemory();
+        long free = runtime.freeMemory();
+        long used = total - free;
+        memoryLog.write(time + "\t" + total +"\t"+free+"\t"+used+"\n");
+        memoryLog.flush();
+      }
+      catch (Throwable t)
+      {}
+    }
     return getSessionControl().newDbControl();
   }

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

@@ -176 +176 @@
       job.setParameterValue("delta", new FloatParameterType(), 0.1f);
       job.setParameterValue("iter", new IntegerParameterType(), 4);
-      job.setParameterValue("blockGroup", new IntegerParameterType(), 100);
+      job.setParameterValue("blockGroup", new IntegerParameterType(), 1);
       
       dc.saveItem(job);

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

@@ -120 +120 @@
       Protocol printing = createProtocol(dc, "Printing A", ProtocolType.PRINTING);
       
+      Hardware hybStation = createHardware(dc, "Hybridization station A", HardwareType.HYBRIDIZATION_STATION);
       Hardware robot = createHardware(dc, "Print robot A", HardwareType.PRINT_ROBOT);
       Hardware scanner = createHardware(dc, "Scanner A", HardwareType.SCANNER);
@@ -167 +168 @@
       dc = TestUtil.getDbControl();
       ArrayDesign design = createArrayDesign(dc, "Array design A");
+      dc.commit();
+
+      importFeatures(printMapImporter, printMap, design);
+      
+      dc = TestUtil.getDbControl();
       ArrayBatch batch = createArrayBatch(dc, "Array batch A", design, robot, printing);
       ArraySlide slide1 = createArraySlide(dc, "Array slide A.1", batch, 1);
       ArraySlide slide2 = createArraySlide(dc, "Array slide A.2", batch, 2);
-      dc.commit();
-
-      importFeatures(printMapImporter, printMap, design);
+      ArraySlide slide3 = createArraySlide(dc, "Array slide A.3", batch, 3);
+      ArraySlide slide4 = createArraySlide(dc, "Array slide A.4", batch, 4);
+      dc.commit();
+
       TestUtil.logout();
     }
@@ -450 +457 @@
     parameters.put("dataSplitterRegexp", "\\t");
     parameters.put("ignoreRegexp", ".*(NoOligoInfo|no clone).*");
-    parameters.put("dataHeaderRegexp", "\"Block\"\\t\"Column\"\\t\"Row\"\\t\"Name\"\\t\"ID\".*");
+    if (dyeSwap)
+    {
+      parameters.put("dataHeaderRegexp", "\"Block\"\\t\"Column\"\\t\"Row\"\\t\"Name\"\\t\"ID\".*\"Ratio of Medians \\(635\\/532\\)\".*");   
+    }
+    else
+    {
+      parameters.put("dataHeaderRegexp", "\"Block\"\\t\"Column\"\\t\"Row\"\\t\"Name\"\\t\"ID\".*\"Ratio of Medians \\(532\\/635\\)\".*");
+    }
     parameters.put("minDataColumns", 48);
     parameters.put("maxDataColumns", 48);     

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

@@ -44 +44 @@
     Set<String> cmds = new HashSet<String>(Arrays.asList(args));
     boolean all = cmds.contains("all");
+    boolean logMemoryUsage = cmds.contains("-m");
     
     int tests = 0;
@@ -49 +50 @@
     if (ok && (all || cmds.contains("root")))
     {
-      TestUtil.begin();
+      TestUtil.begin(logMemoryUsage);
       ok = RootTest.run();
       tests++;
@@ -55 +56 @@
     if (ok && (all || cmds.contains("admin")))
     {
-      TestUtil.begin();
+      TestUtil.begin(logMemoryUsage);
       ok = AdminTest.run();
       tests++;
@@ -61 +62 @@
     if (ok && (all || cmds.contains("power")))
     {
-      TestUtil.begin();
+      TestUtil.begin(logMemoryUsage);
       ok = PowerUserTest.run();
       tests++;
@@ -67 +68 @@
     if (ok && (all || cmds.contains("user")))
     {
-      TestUtil.begin();
+      TestUtil.begin(logMemoryUsage);
       ok = UserTest.run();
       tests++;
@@ -73 +74 @@
     if (ok && (all || cmds.contains("guest")))
     {
-      TestUtil.begin();
+      TestUtil.begin(logMemoryUsage);
       ok = GuestTest.run();
       tests++;
@@ -89 +90 @@
   {
     TestUtil.write(
-      "test.sh roles <cmds>\n" + 
+      "test.sh roles [-m] <cmds>\n" + 
+      "     -m = log memory usage to file memory.log\n" +
       "     cmds = list of tests to run; all, root, admin, power, user, guest\n\n");
     

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

@@ -92 +92 @@
       Extract eRef = createExtract(dc, "Extract A.ref", sRef);
       
-      LabeledExtract le1 = createLabeledExtract(dc, "Labeled extract A.00h", e1, "cy3");
-      LabeledExtract le2 = createLabeledExtract(dc, "Labeled extract A.24h", e2, "cy3");
-      LabeledExtract leRef = createLabeledExtract(dc, "Labeled extract A.ref", eRef, "cy5");
+      Label cy3 = Util.findLabel(dc, "cy3");      
+      Label cy5 = Util.findLabel(dc, "cy5");      
+      LabeledExtract le1 = createLabeledExtract(dc, "Labeled extract A.00h", e1, cy3);
+      LabeledExtract le2 = createLabeledExtract(dc, "Labeled extract A.24h", e2, cy3);
+      LabeledExtract leRef = createLabeledExtract(dc, "Labeled extract A.ref", eRef, cy5);
+      LabeledExtract le1DyeSwap = createLabeledExtract(dc, "Labeled extract A.00h (dye-swap)", e1, cy5);
+      LabeledExtract le2DyeSwap = createLabeledExtract(dc, "Labeled extract A.24h (dye-swap)", e2, cy5);
+      LabeledExtract leRefDyeSwap = createLabeledExtract(dc, "Labeled extract A.ref (dye-swap)", eRef, cy3);
       dc.commit();
       
@@ -101 +106 @@
       Hybridization h1 = createHybridization(dc, "Hybridization A.00h", "Array slide A.1", le1, leRef);
       Hybridization h2 = createHybridization(dc, "Hybridization A.24h", "Array slide A.2", le2, leRef);
+      Hybridization h1DyeSwap = createHybridization(dc, "Hybridization A.00h (dye-swap)", "Array slide A.3", le1, leRef);
+      Hybridization h2DyeSwap = createHybridization(dc, "Hybridization A.24h (dye-swap)", "Array slide A.4", le2, leRef);
 
       Scan sc1 = createScan(dc, "Scan A.00h", h1);
       Scan sc2 = createScan(dc, "Scan A.24h", h2);
+      Scan sc1DyeSwap = createScan(dc, "Scan A.00h (dye-swap)", h1DyeSwap);
+      Scan sc2DyeSwap = createScan(dc, "Scan A.24h (dye-swap)", h2DyeSwap);
       
       // Images
@@ -111 +120 @@
       RawBioAssay rba1 = createRawBioAssay(dc, "Raw bioassay A.00h", sc1);
       RawBioAssay rba2 = createRawBioAssay(dc, "Raw bioassay A.24h", sc2);
-      RawBioAssay rba1DyeSwap = createRawBioAssay(dc, "Raw bioassay A.00h (dye-swap)", sc1);
-      RawBioAssay rba2DyeSwap = createRawBioAssay(dc, "Raw bioassay A.24h (dye-swap)", sc2);
+      RawBioAssay rba1DyeSwap = createRawBioAssay(dc, "Raw bioassay A.00h (dye-swap)", sc1DyeSwap);
+      RawBioAssay rba2DyeSwap = createRawBioAssay(dc, "Raw bioassay A.24h (dye-swap)", sc2DyeSwap);
       inheritAnnotations(dc, rba1, s1, bioSource);
       inheritAnnotations(dc, rba2, s2, bioSource);
@@ -219 +228 @@
     Create a labeled extract.
   */
-  public static LabeledExtract createLabeledExtract(DbControl dc, String name, Extract extract, String labelName)
+  public static LabeledExtract createLabeledExtract(DbControl dc, String name, Extract extract, Label label)
   {
     TestUtil.write("--Creating labeled extract: " + name + "\n");
-    
-    Label label = Util.findLabel(dc, labelName);
     
     LabeledExtract labeledExtract = LabeledExtract.getNew(dc, label);
@@ -245 +252 @@
     BioMaterialEvent creationEvent = hyb.getCreationEvent();
     creationEvent.setProtocol(Util.findProtocol(dc, "Hybridization A"));
+    creationEvent.setHardware(Util.findHardware(dc, "Hybridization station A"));
     for (LabeledExtract le : extracts)
     {