Changeset 4625

Timestamp:

Nov 4, 2008, 4:45:36 PM (15 years ago)

Author:

Martin Svensson

Message:

References #1151 Created new classes which do the power user-role test and user-role test with batch importers. The new functionallity is not tested yet.

Location:

trunk/src/test/net/sf/basedb/test/roles

Files:

• AdminTest.java (modified) (2 diffs)
• PowerUserBatchImporterTest.java (added)
• Run.java (modified) (4 diffs)
• UserBatchImporterTest.java (added)
• Util.java (modified) (3 diffs)

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

@@ -47 +47 @@
 import net.sf.basedb.plugins.PrintMapFlatFileImporter;
 import net.sf.basedb.plugins.ReporterMapFlatFileImporter;
+import net.sf.basedb.plugins.batchimport.ArrayBatchImporter;
+import net.sf.basedb.plugins.batchimport.ArrayDesignImporter;
+import net.sf.basedb.plugins.batchimport.ArraySlideImporter;
+import net.sf.basedb.plugins.batchimport.BioSourceImporter;
+import net.sf.basedb.plugins.batchimport.ExtractImporter;
+import net.sf.basedb.plugins.batchimport.HybridizationImporter;
+import net.sf.basedb.plugins.batchimport.LabeledExtractImporter;
+import net.sf.basedb.plugins.batchimport.RawBioAssayImporter;
+import net.sf.basedb.plugins.batchimport.SampleImporter;
+import net.sf.basedb.plugins.batchimport.ScanImporter;
 import net.sf.basedb.test.AffymetrixData;
 import net.sf.basedb.test.FileUtil;
@@ -98 +108 @@
       plugins.add(PluginDefinition.getByClassName(dc, ReporterMapFlatFileImporter.class.getName()));
       plugins.add(PluginDefinition.getByClassName(dc, PrintMapFlatFileImporter.class.getName()));
+      
+      plugins.add(PluginDefinition.getByClassName(dc, ArrayDesignImporter.class.getName()));
+      plugins.add(PluginDefinition.getByClassName(dc, ArrayBatchImporter.class.getName()));
+      plugins.add(PluginDefinition.getByClassName(dc, ArraySlideImporter.class.getName()));           
       addPermissions(dc, powerUser, plugins, USE);
+      
+      plugins.clear();
+      plugins.add(PluginDefinition.getByClassName(dc, BioSourceImporter.class.getName()));
+      plugins.add(PluginDefinition.getByClassName(dc, SampleImporter.class.getName()));
+      plugins.add(PluginDefinition.getByClassName(dc, ExtractImporter.class.getName()));
+      plugins.add(PluginDefinition.getByClassName(dc, LabeledExtractImporter.class.getName()));
+      plugins.add(PluginDefinition.getByClassName(dc, HybridizationImporter.class.getName()));
+      plugins.add(PluginDefinition.getByClassName(dc, ScanImporter.class.getName()));
+      plugins.add(PluginDefinition.getByClassName(dc, RawBioAssayImporter.class.getName()));
+      addPermissions(dc, user, plugins, USE);
       dc.commit();
       

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

@@ -43 +43 @@
     boolean all = cmds.contains("all");
     boolean logMemoryUsage = cmds.contains("-m");
+    boolean useBatchImporters = cmds.contains("-b");
     
     int tests = 0;
@@ -61 +62 @@
     {
       TestUtil.begin(logMemoryUsage, true);
-      ok = PowerUserTest.run();
+      ok = useBatchImporters ? PowerUserBatchImporterTest.run() : PowerUserTest.run();
       tests++;
     }
@@ -67 +68 @@
     {
       TestUtil.begin(logMemoryUsage, true);
-      ok = UserTest.run();
+      ok = useBatchImporters ? UserBatchImporterTest.run() : UserTest.run();
       tests++;
     }
@@ -88 +89 @@
   {
     TestUtil.write(
-      "test.sh roles [-m] <cmds>\n" + 
+      "test.sh roles [OPTION] <cmds>\n" + 
       "     -m = log memory usage to file memory.log\n" +
+      "   -b = use the batch importers to insert items into BASE.\n" +  
       "     cmds = list of tests to run; all, root, admin, power, user, guest\n\n");
     

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

@@ -32 +32 @@
 import net.sf.basedb.core.ArraySlide;
 import net.sf.basedb.core.BioAssaySet;
+import net.sf.basedb.core.BioSource;
 import net.sf.basedb.core.DbControl;
 import net.sf.basedb.core.Experiment;
@@ -47 +48 @@
 import net.sf.basedb.core.Protocol;
 import net.sf.basedb.core.Quota;
+import net.sf.basedb.core.RawBioAssay;
 import net.sf.basedb.core.RawDataType;
 import net.sf.basedb.core.Role;
+import net.sf.basedb.core.Sample;
 import net.sf.basedb.core.Software;
 import net.sf.basedb.core.Unit;
@@ -270 +273 @@
     return query.list(dc).get(0);
   }
-  
+
+  /**
+    Returns the first raw bioassay that was found with a certain name
+   */
+  public static RawBioAssay findRawBioAssay(DbControl dc, String name)
+  {
+    ItemQuery<RawBioAssay> query = RawBioAssay.getQuery();
+    query.restrict(Restrictions.eq(Hql.property("name"), Expressions.string(name)));
+    return query.list(dc).get(0);
+  }
+  
+  /**
+    Returns the first sample that was found with a certain name
+   */
+  public static Sample findSample(DbControl dc, String name)
+  {
+    ItemQuery<Sample> query = Sample.getQuery();
+    query.restrict(Restrictions.eq(Hql.property("name"), Expressions.string(name)));
+    return query.list(dc).get(0);
+  }
+  
+  /**
+    Returns the first biosource that was found with a certain name
+   */
+  public static BioSource findBioSource(DbControl dc, String name)
+  {
+    ItemQuery<BioSource> query = BioSource.getQuery();
+    query.restrict(Restrictions.eq(Hql.property("name"), Expressions.string(name)));
+    return query.list(dc).get(0);
+  }
 }