X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fws%2Fsifts%2FSiftsClientTest.java;h=28113d6d13d0d5d3cba3d3f7aff82f4a69579f90;hb=cbf0b72e90f4c719dff345e467b5c9b9873247ed;hp=7443f4a9953238cecdf955ee381b696400bec8ab;hpb=de0e24ab7826daa950257b9659c7e0937f15fb2f;p=jalview.git

diff --git a/test/jalview/ws/sifts/SiftsClientTest.java b/test/jalview/ws/sifts/SiftsClientTest.java
index 7443f4a..28113d6 100644
--- a/test/jalview/ws/sifts/SiftsClientTest.java
+++ b/test/jalview/ws/sifts/SiftsClientTest.java
@@ -26,7 +26,9 @@ import jalview.datamodel.SequenceI;
 
 import java.io.ByteArrayOutputStream;
 import java.io.File;
+import java.io.IOException;
 import java.io.PrintStream;
+import java.util.HashMap;
 
 import org.testng.Assert;
 import org.testng.FileAssert;
@@ -40,6 +42,11 @@ public class SiftsClientTest
 {
   private final ByteArrayOutputStream outContent = new ByteArrayOutputStream();
 
+  public static final String DEFAULT_SIFTS_DOWNLOAD_DIR = System
+          .getProperty("user.home")
+          + File.separatorChar
+          + ".sifts_downloads" + File.separatorChar;
+
   private String testPDBId = "1a70";
 
   private SiftsClient siftsClient = null;
@@ -52,39 +59,29 @@ public class SiftsClientTest
 
   int u = SiftsClient.UNASSIGNED;
 
-  int[][] expectedMapping = { { u, u }, { u, u }, { u, u }, { u, u },
-      { u, u }, { u, u }, { u, u }, { u, u }, { u, u }, { u, u }, { u, u },
-      { u, u }, { u, u }, { u, u }, { u, u }, { u, u }, { u, u }, { u, u },
-      { u, u }, { u, u }, { u, u }, { u, u }, { u, u }, { u, u }, { u, u },
-      { u, u }, { u, u }, { u, u }, { u, u }, { u, u }, { u, u }, { u, u },
-      { u, u }, { u, u }, { u, u }, { u, u }, { u, u }, { u, u }, { u, u },
-      { u, u }, { u, u }, { u, u }, { u, u }, { u, u }, { u, u }, { u, u },
-      { u, u }, { u, u }, { u, u }, { u, u }, { u, u }, { 1, u }, { 2, u },
-      { 3, u }, { 4, u }, { 5, u }, { 6, u }, { 7, u }, { 8, u }, { 9, u },
-      { 10, u }, { 11, u }, { 12, u }, { 13, u }, { 14, u }, { 15, u },
-      { 16, u }, { 17, u }, { 18, u }, { 19, u }, { 20, u }, { 21, u },
-      { 22, u }, { 23, u }, { 24, u }, { 25, u }, { 26, u }, { 27, u },
-      { 28, u }, { 29, u }, { 30, u }, { 31, u }, { 32, u }, { 33, u },
-      { 34, u }, { 35, u }, { 36, u }, { 37, u }, { 38, u }, { 39, u },
-      { 40, u }, { 41, u }, { 42, u }, { 43, u }, { 44, u }, { 45, u },
-      { 46, u }, { 47, u }, { 48, u }, { 49, u }, { 50, u }, { 51, u },
-      { 52, u }, { 53, u }, { 54, u }, { 55, u }, { 56, u }, { 57, u },
-      { 58, u }, { 59, u }, { 60, u }, { 61, u }, { 62, u }, { 63, u },
-      { 64, u }, { 65, u }, { 66, u }, { 67, u }, { 68, u }, { 69, u },
-      { 70, u }, { 71, u }, { 72, u }, { 73, u }, { 74, u }, { 75, u },
-      { 76, u }, { 77, u }, { 78, u }, { 79, u }, { 80, u }, { 81, u },
-      { 82, u }, { 83, u }, { 84, u }, { 85, u }, { 86, u }, { 87, u },
-      { 88, u }, { 89, u }, { 90, u }, { 91, u }, { 92, u }, { 93, u },
-      { 94, u }, { 95, u }, { 96, u }, { 97, u } };
+  HashMap<Integer, int[]> expectedMapping = new HashMap<Integer, int[]>();
 
   @BeforeTest(alwaysRun = true)
-  public void setUpSiftsClient()
+  public void populateExpectedMapping() throws SiftsException
+   {
+    for (int x = 1; x <= 97; x++)
+    {
+      expectedMapping.put(50 + x, new int[] { x, u });
+    }
+   }
+   
+  @BeforeTest(alwaysRun = true)
+  public void setUpSiftsClient() throws SiftsException
   {
     // SIFTs entries are updated weekly - so use saved SIFTs file to enforce
     // test reproducibility
+    SiftsSettings.setSiftDownloadDirectory(jalview.bin.Cache.getDefault(
+            "sifts_download_dir", DEFAULT_SIFTS_DOWNLOAD_DIR));
+
     File testSiftsFile = new File("test/jalview/io/" + testPDBId
             + ".xml.gz");
     PDBfile pdbFile = new PDBfile(false, false, false);
+    pdbFile.setId(testPDBId);
     siftsClient = new SiftsClient(pdbFile, testSiftsFile);
   }
 
@@ -107,7 +104,7 @@ public class SiftsClientTest
   }
 
   @Test(groups = { "Functional" })
-  public void getSIFTsFileTest()
+  public void getSIFTsFileTest() throws SiftsException
   {
     Assert.assertTrue(SiftsClient.deleteSiftsFileByPDBId(testPDBId));
     SiftsClient.getSiftsFile(testPDBId);
@@ -121,14 +118,21 @@ public class SiftsClientTest
   }
 
   @Test(groups = { "Functional" })
-  public void downloadSiftsFileTest()
+  public void downloadSiftsFileTest() throws SiftsException
   {
     // Assert that file isn't yet downloaded - if already downloaded, assert it
     // is deleted
     Assert.assertTrue(SiftsClient.deleteSiftsFileByPDBId(testPDBId));
-    File siftsFile = SiftsClient.downloadSiftsFile(testPDBId);
-    FileAssert.assertFile(siftsFile);
-    SiftsClient.downloadSiftsFile(testPDBId);
+    File siftsFile;
+    try
+    {
+      siftsFile = SiftsClient.downloadSiftsFile(testPDBId);
+      FileAssert.assertFile(siftsFile);
+      SiftsClient.downloadSiftsFile(testPDBId);
+    } catch (IOException e)
+    {
+      e.printStackTrace();
+    }
   }
 
   @Test(groups = { "Functional" })
@@ -155,7 +159,8 @@ public class SiftsClientTest
 
     try
     {
-      int[][] actualMapping = siftsClient.getGreedyMapping("A", testSeq,
+      HashMap<Integer, int[]> actualMapping = siftsClient.getGreedyMapping(
+              "A", testSeq,
               null);
       Assert.assertEquals(actualMapping, expectedMapping);
       Assert.assertEquals(testSeq.getStart(), 1);