JAL-2835 update test for CSQ data held as a Map

diff --git a/test/jalview/io/vcf/VCFLoaderTest.java b/test/jalview/io/vcf/VCFLoaderTest.java
index 5607b4b..246337d 100644 (file)
--- a/test/jalview/io/vcf/VCFLoaderTest.java
+++ b/test/jalview/io/vcf/VCFLoaderTest.java
@@ -1,8 +1,8 @@
 package jalview.io.vcf;
 
 import static org.testng.Assert.assertEquals;
-import static org.testng.Assert.assertTrue;
 
+import jalview.bin.Cache;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.Mapping;
@@ -21,7 +21,9 @@ import java.io.File;
 import java.io.IOException;
 import java.io.PrintWriter;
 import java.util.List;
+import java.util.Map;
 
+import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
 public class VCFLoaderTest
@@ -64,6 +66,17 @@ public class VCFLoaderTest
       // insertion G/GA is transferred to nucleotide but not to peptide
       "17\t45051613\t.\tG\tGA,C\t1666.64\tRF\tAC=15;AF=3.0e-03,2.0e-03" };
 
+  @BeforeClass
+  public void setUp()
+  {
+    /*
+     * configure to capture all available VCF and VEP (CSQ) fields
+     */
+    Cache.loadProperties("test/jalview/io/testProps.jvprops");
+    Cache.setProperty("VCF_FIELDS", ".*");
+    Cache.setProperty("VEP_FIELDS", ".*");
+  }
+
   @Test(groups = "Functional")
   public void testDoLoad() throws IOException
   {
@@ -432,49 +445,56 @@ public class VCFLoaderTest
     assertEquals(sf.getScore(), 0.1f, DELTA);
     assertEquals(sf.getValue("alleles"), "C,A");
     // gene features include Consequence for all transcripts
-    assertEquals(((String) sf.getValue("CSQ")).split(",").length, 2);
+    Map map = (Map) sf.getValue("CSQ");
+    assertEquals(map.size(), 9);
 
     sf = geneFeatures.get(1);
     assertEquals(sf.getBegin(), 5);
     assertEquals(sf.getEnd(), 5);
     assertEquals(sf.getScore(), 0.2f, DELTA);
     assertEquals(sf.getValue("alleles"), "C,T");
-    assertEquals(((String) sf.getValue("CSQ")).split(",").length, 2);
+    map = (Map) sf.getValue("CSQ");
+    assertEquals(map.size(), 9);
 
     sf = geneFeatures.get(2);
     assertEquals(sf.getBegin(), 9);
     assertEquals(sf.getEnd(), 11); // deletion over 3 positions
     assertEquals(sf.getScore(), 0.3f, DELTA);
     assertEquals(sf.getValue("alleles"), "CGG,C");
-    assertEquals(((String) sf.getValue("CSQ")).split(",").length, 2);
+    map = (Map) sf.getValue("CSQ");
+    assertEquals(map.size(), 9);
 
     sf = geneFeatures.get(3);
     assertEquals(sf.getBegin(), 13);
     assertEquals(sf.getEnd(), 13);
     assertEquals(sf.getScore(), 0.5f, DELTA);
     assertEquals(sf.getValue("alleles"), "C,T");
-    assertEquals(((String) sf.getValue("CSQ")).split(",").length, 2);
+    map = (Map) sf.getValue("CSQ");
+    assertEquals(map.size(), 9);
 
     sf = geneFeatures.get(4);
     assertEquals(sf.getBegin(), 13);
     assertEquals(sf.getEnd(), 13);
     assertEquals(sf.getScore(), 0.4f, DELTA);
     assertEquals(sf.getValue("alleles"), "C,G");
-    assertEquals(((String) sf.getValue("CSQ")).split(",").length, 2);
+    map = (Map) sf.getValue("CSQ");
+    assertEquals(map.size(), 9);
 
     sf = geneFeatures.get(5);
     assertEquals(sf.getBegin(), 17);
     assertEquals(sf.getEnd(), 17);
     assertEquals(sf.getScore(), 0.7f, DELTA);
     assertEquals(sf.getValue("alleles"), "A,G");
-    assertEquals(((String) sf.getValue("CSQ")).split(",").length, 2);
+    map = (Map) sf.getValue("CSQ");
+    assertEquals(map.size(), 9);
 
     sf = geneFeatures.get(6);
     assertEquals(sf.getBegin(), 17);
     assertEquals(sf.getEnd(), 17); // insertion
     assertEquals(sf.getScore(), 0.6f, DELTA);
     assertEquals(sf.getValue("alleles"), "A,AC");
-    assertEquals(((String) sf.getValue("CSQ")).split(",").length, 2);
+    map = (Map) sf.getValue("CSQ");
+    assertEquals(map.size(), 9);
 
     /*
      * verify variant feature(s) added to transcript3
@@ -492,24 +512,25 @@ public class VCFLoaderTest
     assertEquals(sf.getScore(), 0.2f, DELTA);
     assertEquals(sf.getValue("alleles"), "C,T");
     // transcript features only have Consequence for that transcripts
-    assertEquals(((String) sf.getValue("CSQ")).split(",").length, 1);
-    assertTrue(sf.getValue("CSQ").toString().contains("transcript3"));
+    map = (Map) sf.getValue("CSQ");
+    assertEquals(map.size(), 9);
+    assertEquals(sf.getValueAsString("CSQ", "Feature"), "transcript3");
 
     sf = transcriptFeatures.get(1);
     assertEquals(sf.getBegin(), 11);
     assertEquals(sf.getEnd(), 11);
     assertEquals(sf.getScore(), 0.7f, DELTA);
     assertEquals(sf.getValue("alleles"), "A,G");
-    assertEquals(((String) sf.getValue("CSQ")).split(",").length, 1);
-    assertTrue(sf.getValue("CSQ").toString().contains("transcript3"));
+    assertEquals(map.size(), 9);
+    assertEquals(sf.getValueAsString("CSQ", "Feature"), "transcript3");
 
     sf = transcriptFeatures.get(2);
     assertEquals(sf.getBegin(), 11);
     assertEquals(sf.getEnd(), 11);
     assertEquals(sf.getScore(), 0.6f, DELTA);
     assertEquals(sf.getValue("alleles"), "A,AC");
-    assertEquals(((String) sf.getValue("CSQ")).split(",").length, 1);
-    assertTrue(sf.getValue("CSQ").toString().contains("transcript3"));
+    assertEquals(map.size(), 9);
+    assertEquals(sf.getValueAsString("CSQ", "Feature"), "transcript3");
 
     /*
      * verify variants computed on protein product for transcript3
@@ -548,31 +569,31 @@ public class VCFLoaderTest
     assertEquals(sf.getEnd(), 7);
     assertEquals(sf.getScore(), 0.5f, DELTA);
     assertEquals(sf.getValue("alleles"), "C,T");
-    assertEquals(((String) sf.getValue("CSQ")).split(",").length, 1);
-    assertTrue(sf.getValue("CSQ").toString().contains("transcript4"));
+    assertEquals(map.size(), 9);
+    assertEquals(sf.getValueAsString("CSQ", "Feature"), "transcript4");
 
     sf = transcriptFeatures.get(1);
     assertEquals(sf.getBegin(), 7);
     assertEquals(sf.getEnd(), 7);
     assertEquals(sf.getScore(), 0.4f, DELTA);
     assertEquals(sf.getValue("alleles"), "C,G");
-    assertEquals(((String) sf.getValue("CSQ")).split(",").length, 1);
-    assertTrue(sf.getValue("CSQ").toString().contains("transcript4"));
+    assertEquals(map.size(), 9);
+    assertEquals(sf.getValueAsString("CSQ", "Feature"), "transcript4");
 
     sf = transcriptFeatures.get(2);
     assertEquals(sf.getBegin(), 11);
     assertEquals(sf.getEnd(), 11);
     assertEquals(sf.getScore(), 0.7f, DELTA);
     assertEquals(sf.getValue("alleles"), "A,G");
-    assertEquals(((String) sf.getValue("CSQ")).split(",").length, 1);
-    assertTrue(sf.getValue("CSQ").toString().contains("transcript4"));
+    assertEquals(map.size(), 9);
+    assertEquals(sf.getValueAsString("CSQ", "Feature"), "transcript4");
 
     sf = transcriptFeatures.get(3);
     assertEquals(sf.getBegin(), 11);
     assertEquals(sf.getEnd(), 11);
     assertEquals(sf.getScore(), 0.6f, DELTA);
     assertEquals(sf.getValue("alleles"), "A,AC");
-    assertEquals(((String) sf.getValue("CSQ")).split(",").length, 1);
-    assertTrue(sf.getValue("CSQ").toString().contains("transcript4"));
+    assertEquals(map.size(), 9);
+    assertEquals(sf.getValueAsString("CSQ", "Feature"), "transcript4");
   }
 }