Changeset 5732

Timestamp:

Sep 12, 2011, 12:57:44 PM (10 years ago)

Author:

Nicklas Nordborg

Message:

References #1615: Add test program in BASE 2.17 that create data that need special handling when updating to BASE 3

• Added some images to scans.
• Simulate context related to filtering and sorting on fileType, softwareType, etc.

File:

• branches/2.17-stable/src/test/net/sf/basedb/test/roles/ExtraTest.java (modified) (12 diffs)

branches/2.17-stable/src/test/net/sf/basedb/test/roles/ExtraTest.java

@@ -29 +29 @@
 import net.sf.basedb.core.BioMaterial;
 import net.sf.basedb.core.BioWell.LockMode;
+import net.sf.basedb.core.Application;
 import net.sf.basedb.core.BioMaterialEvent;
 import net.sf.basedb.core.BioMaterialList;
 import net.sf.basedb.core.DbControl;
 import net.sf.basedb.core.Extract;
+import net.sf.basedb.core.File;
+import net.sf.basedb.core.FileType;
+import net.sf.basedb.core.HardwareType;
 import net.sf.basedb.core.Hybridization;
+import net.sf.basedb.core.Image;
 import net.sf.basedb.core.Include;
 import net.sf.basedb.core.Item;
+import net.sf.basedb.core.ItemContext;
 import net.sf.basedb.core.ItemParameterType;
 import net.sf.basedb.core.ItemQuery;
@@ -42 +48 @@
 import net.sf.basedb.core.LabeledExtract;
 import net.sf.basedb.core.MeasuredBioMaterial;
+import net.sf.basedb.core.Operator;
 import net.sf.basedb.core.Platform;
 import net.sf.basedb.core.PluginConfiguration;
 import net.sf.basedb.core.PluginDefinition;
 import net.sf.basedb.core.Project;
+import net.sf.basedb.core.PropertyFilter;
+import net.sf.basedb.core.ProtocolType;
 import net.sf.basedb.core.RawBioAssay;
 import net.sf.basedb.core.RawDataType;
@@ -51 +60 @@
 import net.sf.basedb.core.Sample;
 import net.sf.basedb.core.Scan;
+import net.sf.basedb.core.SessionControl;
+import net.sf.basedb.core.SoftwareType;
+import net.sf.basedb.core.SystemItems;
 import net.sf.basedb.core.Type;
 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.TestUtil;
 import net.sf.basedb.util.ArrayIterator;
@@ -74 +87 @@
   {
     DbControl dc = null;
+    SessionControl sc = null;
     TestUtil.write("++Entering extra tests\n");
     try
     {
+      // Fake that we are using the web client since we want to
+      // create context settings for the list pages
+      sc = Application.newSessionControl("net.sf.basedb.clients.web", TestUtil.getLocalIp(), null);
+      sc.login("extra", "extra", "Running extra test program", false);
+      dc = sc.newDbControl();
+      
       // Activate project
-      TestUtil.login("extra", "extra", false);
-      dc = TestUtil.getDbControl();
       Project p = Util.findProject(dc, "Project A");
-      TestUtil.getSessionControl().setActiveProject(p);
+      sc.setActiveProject(p);
 
       // Create annotation types, for Labeled extract, Hybridization and
@@ -98 +116 @@
       Platform affymetrix = Platform.getByExternalId(dc, Platform.AFFYMETRIX);
       RawDataType genepix = RawDataTypes.getSafeRawDataType("genepix");
+      File redFile = FileUtil.uploadFile(dc, "/data", "spots.tif", FileType.IMAGE);
+      File greenFile = FileUtil.uploadFile(dc, "/data", "test.upload.png", FileType.IMAGE);
       
       // Create biomaterials with no parent items
@@ -111 +131 @@
       poolBioMaterial(dc, ple, "Labeled extract A.%h");
       
-      // Create hyb, scan and raw bioassays
+      // Create hybs, scans, images and raw bioassays
       Hybridization hyb = UserTest.createHybridization(dc, "Hyb2Channel-3.0", null, false, le, ple);
       Hybridization hyb2 = UserTest.createHybridization(dc, "HybMultiArray-3.0", null, true, le, ple);
       Scan scan = UserTest.createScan(dc, "Scan2Channel-3.0", hyb, null, null);
       Scan scan2 = UserTest.createScan(dc, "ScanMultiArray-3.0", hyb2, null, null);
+      createImage(dc, "RedImage-3.0", scan, redFile);
+      createImage(dc, "GreenImage-3.0", scan, greenFile);
       RawBioAssay rba1 = UserTest.createRawBioAssay(dc, generic, genepix, "RawBioAssay-3.0", scan, null);
       RawBioAssay rba2 = UserTest.createRawBioAssay(dc, affymetrix, null, "RawBioAssay[1]-3.0", scan2, null);
@@ -143 +165 @@
       createBioMaterialList(dc, "Labeled extracts", le);
       
+      // Set filter, sort order, etc. on some contexts
+      TestUtil.write("--Creating context for: PROTOCOL\n");
+      ItemContext cc = sc.getCurrentContext(Item.PROTOCOL);
+      cc.setSortProperty("protocolType.name");
+      cc.setPropertyFilter(new PropertyFilter("protocolType", Operator.IN, 
+        SystemItems.getId(ProtocolType.EXTRACTION) + "|"+SystemItems.getId(ProtocolType.SAMPLING), Type.INT));
+      TestUtil.write("--Creating context for: PROTOCOLTYPE\n");
+      cc = sc.getCurrentContext(Item.PROTOCOLTYPE);
+      cc.setSortProperty("name");
+      cc.setSetting("base-3.0", "should be gone after update");
+      
+      TestUtil.write("--Creating context for: SOFTWARE\n");
+      cc = sc.getCurrentContext(Item.SOFTWARE);
+      cc.setSortProperty("softwareType.name");
+      cc.setPropertyFilter(new PropertyFilter("softwareType", Operator.EQ, 
+          SystemItems.getId(SoftwareType.FEATURE_EXTRACTION) + "", Type.INT));
+      TestUtil.write("--Creating context for: SOFTWARETYPE\n");
+      cc = sc.getCurrentContext(Item.SOFTWARETYPE);
+      cc.setSortProperty("name");
+      cc.setSetting("base-3.0", "should be gone after update");
+
+      TestUtil.write("--Creating context for: HARDWARE\n");
+      cc = sc.getCurrentContext(Item.HARDWARE);
+      cc.setSortProperty("hardwareType.name");
+      cc.setPropertyFilter(new PropertyFilter("hardwareType", Operator.IN, 
+          SystemItems.getId(HardwareType.SCANNER) + "|" + SystemItems.getId(HardwareType.FREEZER), Type.INT));
+      TestUtil.write("--Creating context for: HARDWARETYPE\n");
+      cc = sc.getCurrentContext(Item.HARDWARETYPE);
+      cc.setSortProperty("name");
+      cc.setSetting("base-3.0", "should be gone after update");
+
+      TestUtil.write("--Creating context for: FILE\n");
+      cc = sc.getCurrentContext(Item.FILE);
+      cc.setSortProperty("fileType.name");
+      cc.setPropertyFilter(new PropertyFilter("fileType", Operator.IN, 
+          SystemItems.getId(FileType.IMAGE) + "|" + SystemItems.getId(FileType.RAW_DATA), Type.INT));
+      TestUtil.write("--Creating context for: FILETYPE\n");
+      cc = sc.getCurrentContext(Item.FILETYPE);
+      cc.setSortProperty("name");
+      cc.setSetting("base-3.0", "should be gone after update");
+
+      TestUtil.write("--Creating context for: MIMETYPE\n");
+      cc = sc.getCurrentContext(Item.MIMETYPE);
+      cc.setSortProperty("fileType.name");
+      cc.setPropertyFilter(new PropertyFilter("fileType", Operator.IN, 
+          SystemItems.getId(FileType.IMAGE) + "|" + SystemItems.getId(FileType.RAW_DATA), Type.INT));
+
+      TestUtil.write("--Creating context for: DATAFILETYPE\n");
+      cc = sc.getCurrentContext(Item.DATAFILETYPE);
+      cc.setSortProperty("genericType.name");
+      cc.setPropertyFilter(new PropertyFilter("genericType", Operator.IN, 
+          SystemItems.getId(FileType.IMAGE) + "|" + SystemItems.getId(FileType.RAW_DATA), Type.INT));
+
       dc.commit();
-      TestUtil.logout();
+      TestUtil.write("--Logging out\n");
+      sc.logout();
     }
     catch (Throwable t)
@@ -171 +247 @@
       String name, PluginDefinition plugin, BasicItem... parameters)
   {
+    TestUtil.write("--Creating fake plug-in configuration: " + name + " for plug-in " + plugin.getName() + "\n");
     PluginConfiguration config = plugin.newPluginConfiguration();
     config.setName(name);
@@ -186 +263 @@
   public static Job createJob(DbControl dc, String name, BasicItem... parameters)
   {
+    TestUtil.write("--Creating fake job: " + name + "\n");
     Job job = Job.getNew(dc, null, null, null);
     job.setName(name);
@@ -201 +279 @@
     BioMaterial... items)
   {
+    TestUtil.write("--Creating biomaterial list: " + name + "\n");
     BioMaterialList list = BioMaterialList.getNew(dc, items[0].getType());
     list.setName(name);
@@ -211 +290 @@
       String parentNamePattern)
   {
+    TestUtil.write("--Creating pooled biomaterial: " + bioMaterial.getName() + "\n");
     bioMaterial.setPooled(true);
     BioMaterialEvent event = bioMaterial.getCreationEvent();
@@ -237 +317 @@
     }
   }
+  
+  /**
+    Create an image.
+  */
+  public static Image createImage(DbControl dc, String name, Scan scan, File file)
+  {
+    TestUtil.write("--Creating image: " + name + "\n");
+    Image img = Image.getNew(dc, scan);
+    img.setFile(file);
+    dc.saveItem(img);
+    return img;
+  }
+  
 }