JAL-724 JAL-715 refactor and create new test for RSBS framework and Multi-harmony...

[jalview.git] / test / jalview / ws / rest / ShmmrRSBSService.java

diff --git a/test/jalview/ws/rest/ShmmrRSBSService.java b/test/jalview/ws/rest/ShmmrRSBSService.java
new file mode 100644 (file)
index 0000000..05f7cd0
--- /dev/null
+++ b/test/jalview/ws/rest/ShmmrRSBSService.java
@@ -0,0 +1,132 @@
+/**
+ * 
+ */
+package jalview.ws.rest;
+
+import static org.junit.Assert.*;
+
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Map;
+
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AlignmentView;
+import jalview.gui.AlignFrame;
+import jalview.io.FileParse;
+import jalview.ws.rest.InputType;
+import jalview.ws.rest.params.SeqGroupIndexVector;
+
+import org.junit.AfterClass;
+import org.junit.BeforeClass;
+import org.junit.Test;
+
+/**
+ * @author jimp
+ * 
+ */
+public class ShmmrRSBSService
+{
+
+  @Test
+  public void testSeparatorListToArrayForRestServiceDescriptions()
+  {
+    assertTrue(
+            "separatorListToArray is faulty.",
+            RestServiceDescription.separatorListToArray(
+                    "foo=',',min='foo',max='1,2,3',fa=','", ",").length == 4);
+    assertTrue("separatorListToArray is faulty.",
+            RestServiceDescription.separatorListToArray(
+                    "minsize='2', sep=','", ",").length != 2); // probably should come as 2
+  }
+
+  @Test
+  public void testShmmrService()
+  {
+
+    assertTrue(
+            "Test Rsd Exchange using using default Shmmr service failed.",
+            testRsdExchange("Test using default Shmmr service",
+                    RestClient.makeShmmrRestClient().service));
+  }
+  @Test
+  public void testShmmrServiceDataprep() throws Exception
+  {
+    RestClient _rc = RestClient.makeShmmrRestClient();
+    assertNotNull(_rc);
+    AlignFrame alf = new jalview.io.FileLoader(false).LoadFileWaitTillLoaded("examples/testdata/smad.fa", jalview.io.FormatAdapter.FILE);
+    assertNotNull("Couldn't find test data.",alf);
+    alf.loadJalviewDataFile("examples/testdata/smad_groups.jva",
+            jalview.io.FormatAdapter.FILE, null, null);
+    assertTrue("Couldn't load the test data's annotation file (should be 5 groups but found "+alf.getViewport().getAlignment().getGroups().size()+").", alf.getViewport().getAlignment().getGroups().size()==5);
+    
+    RestClient rc = new RestClient(_rc.service, alf, true);
+    
+    
+    
+    assertNotNull("Couldn't creat RestClient job.",rc);
+    jalview.bin.Cache.initLogger();
+    RestJob rjb = new RestJob(0, new RestJobThread(rc),rc.av.getAlignment(),null);
+    rjb.setAlignmentForInputs(rc.service.getInputParams().values(), rc.av.getAlignment());
+    for (Map.Entry<String,InputType> e:rc.service.getInputParams().entrySet()) {
+      System.out.println("For Input '"+e.getKey()+":\n"+e.getValue().formatForInput(rjb).getContentLength());
+    }
+  }
+
+  private static boolean testRsdExchange(String desc, String servicestring)
+  {
+    try
+    {
+      RestServiceDescription newService = new RestServiceDescription(
+              servicestring);
+      if (!newService.isValid())
+      {
+        throw new Error("Failed to create service from '" + servicestring
+                + "'.\n" + newService.getInvalidMessage());
+      }
+      return testRsdExchange(desc, newService);
+    } catch (Throwable x)
+    {
+      System.err.println("Failed for service (" + desc + "): "
+              + servicestring);
+      x.printStackTrace();
+      return false;
+    }
+  }
+
+  private static boolean testRsdExchange(String desc,
+          RestServiceDescription service)
+  {
+    try
+    {
+      String fromservicetostring = service.toString();
+      RestServiceDescription newService = new RestServiceDescription(
+              fromservicetostring);
+      if (!newService.isValid())
+      {
+        throw new Error("Failed to create service from '"
+                + fromservicetostring + "'.\n"
+                + newService.getInvalidMessage());
+      }
+
+      if (!service.equals(newService))
+      {
+        System.err.println("Failed for service (" + desc + ").");
+        System.err.println("Original service and parsed service differ.");
+        System.err.println("Original: " + fromservicetostring);
+        System.err.println("Parsed  : " + newService.toString());
+        return false;
+      }
+    } catch (Throwable x)
+    {
+      System.err.println("Failed for service (" + desc + "): "
+              + service.toString());
+      x.printStackTrace();
+      return false;
+    }
+    return true;
+  }
+
+}