JAL-2843 toStableString, fromString for Jalview features file format

[jalview.git] / test / jalview / datamodel / features / FeatureMatcherSetTest.java

diff --git a/test/jalview/datamodel/features/FeatureMatcherSetTest.java b/test/jalview/datamodel/features/FeatureMatcherSetTest.java
index 56644fd..34bc8fe 100644 (file)
--- a/test/jalview/datamodel/features/FeatureMatcherSetTest.java
+++ b/test/jalview/datamodel/features/FeatureMatcherSetTest.java
@@ -2,6 +2,7 @@ package jalview.datamodel.features;
 
 import static org.testng.Assert.assertEquals;
 import static org.testng.Assert.assertFalse;
+import static org.testng.Assert.assertNull;
 import static org.testng.Assert.assertSame;
 import static org.testng.Assert.assertTrue;
 import static org.testng.Assert.fail;
@@ -127,7 +128,7 @@ public class FeatureMatcherSetTest
     FeatureMatcherSetI fms = new FeatureMatcherSet();
     assertEquals(fms.toString(), "");
     fms.and(fm1);
-    assertEquals(fms.toString(), "(AF < 1.2)");
+    assertEquals(fms.toString(), "AF < 1.2");
     fms.and(fm2);
     assertEquals(fms.toString(),
             "(AF < 1.2) and (CLIN_SIG does not contain 'path')");
@@ -138,7 +139,7 @@ public class FeatureMatcherSetTest
     fms = new FeatureMatcherSet();
     assertEquals(fms.toString(), "");
     fms.or(fm1);
-    assertEquals(fms.toString(), "(AF < 1.2)");
+    assertEquals(fms.toString(), "AF < 1.2");
     fms.or(fm2);
     assertEquals(fms.toString(),
             "(AF < 1.2) or (CLIN_SIG does not contain 'path')");
@@ -282,4 +283,136 @@ public class FeatureMatcherSetTest
     csq.put("Consequence", "Catastrophic");
     assertTrue(fms.matches(sf));
   }
+
+  /**
+   * Tests for toStableString which (unlike toString) does not i18n the
+   * conditions
+   * 
+   * @see FeatureMatcherTest#testToStableString()
+   */
+  @Test(groups = "Functional")
+  public void testToStableString()
+  {
+    FeatureMatcherI fm1 = FeatureMatcher.byAttribute(Condition.LT, "1.2",
+            "AF");
+    assertEquals(fm1.toStableString(), "AF LT 1.2");
+  
+    FeatureMatcher fm2 = FeatureMatcher.byAttribute(Condition.NotContains,
+            "path", "CLIN_SIG");
+    assertEquals(fm2.toStableString(), "CLIN_SIG NotContains path");
+  
+    /*
+     * AND them
+     */
+    FeatureMatcherSetI fms = new FeatureMatcherSet();
+    assertEquals(fms.toStableString(), "");
+    fms.and(fm1);
+    // no brackets needed if a single condition
+    assertEquals(fms.toStableString(), "AF LT 1.2");
+    // brackets if more than one condition
+    fms.and(fm2);
+    assertEquals(fms.toStableString(),
+            "(AF LT 1.2) AND (CLIN_SIG NotContains path)");
+  
+    /*
+     * OR them
+     */
+    fms = new FeatureMatcherSet();
+    assertEquals(fms.toStableString(), "");
+    fms.or(fm1);
+    assertEquals(fms.toStableString(), "AF LT 1.2");
+    fms.or(fm2);
+    assertEquals(fms.toStableString(),
+            "(AF LT 1.2) OR (CLIN_SIG NotContains path)");
+  
+    /*
+     * attribute or value including space is quoted
+     */
+    FeatureMatcher fm3 = FeatureMatcher.byAttribute(Condition.NotMatches,
+            "foo bar", "CSQ", "Poly Phen");
+    assertEquals(fm3.toStableString(),
+            "'CSQ:Poly Phen' NotMatches 'foo bar'");
+    fms.or(fm3);
+    assertEquals(fms.toStableString(),
+            "(AF LT 1.2) OR (CLIN_SIG NotContains path) OR ('CSQ:Poly Phen' NotMatches 'foo bar')");
+
+    try
+    {
+      fms.and(fm1);
+      fail("Expected exception");
+    } catch (IllegalStateException e)
+    {
+      // expected
+    }
+  }
+
+  /**
+   * Tests for parsing a string representation of a FeatureMatcherSet
+   * 
+   * @see FeatureMatcherSetTest#testToStableString()
+   */
+  @Test(groups = "Functional")
+  public void testFromString()
+  {
+    String descriptor = "AF LT 1.2";
+    FeatureMatcherSetI fms = FeatureMatcherSet.fromString(descriptor);
+
+    /*
+     * shortcut asserts by verifying a 'roundtrip', 
+     * which we trust if other tests pass :-)
+     */
+    assertEquals(fms.toStableString(), descriptor);
+
+    // brackets optional, quotes optional, condition case insensitive
+    fms = FeatureMatcherSet.fromString("('AF' lt '1.2')");
+    assertEquals(fms.toStableString(), descriptor);
+
+    descriptor = "(AF LT 1.2) AND (CLIN_SIG NotContains path)";
+    fms = FeatureMatcherSet.fromString(descriptor);
+    assertEquals(fms.toStableString(), descriptor);
+
+    // AND is not case-sensitive
+    fms = FeatureMatcherSet
+            .fromString("(AF LT 1.2) and (CLIN_SIG NotContains path)");
+    assertEquals(fms.toStableString(), descriptor);
+  
+    descriptor = "(AF LT 1.2) OR (CLIN_SIG NotContains path)";
+    fms = FeatureMatcherSet.fromString(descriptor);
+    assertEquals(fms.toStableString(), descriptor);
+
+    // OR is not case-sensitive
+    fms = FeatureMatcherSet
+            .fromString("(AF LT 1.2) or (CLIN_SIG NotContains path)");
+    assertEquals(fms.toStableString(), descriptor);
+
+    // can get away without brackets on last match condition
+    fms = FeatureMatcherSet
+            .fromString("(AF LT 1.2) or CLIN_SIG NotContains path");
+    assertEquals(fms.toStableString(), descriptor);
+  
+    descriptor = "(AF LT 1.2) OR (CLIN_SIG NotContains path) OR ('CSQ:Poly Phen' NotMatches 'foo bar')";
+    fms = FeatureMatcherSet.fromString(descriptor);
+    assertEquals(fms.toStableString(), descriptor);
+
+    // can't mix OR and AND
+    descriptor = "(AF LT 1.2) OR (CLIN_SIG NotContains path) AND ('CSQ:Poly Phen' NotMatches 'foo bar')";
+    assertNull(FeatureMatcherSet.fromString(descriptor));
+
+    // can't mix AND and OR
+    descriptor = "(AF LT 1.2) and (CLIN_SIG NotContains path) or ('CSQ:Poly Phen' NotMatches 'foo bar')";
+    assertNull(FeatureMatcherSet.fromString(descriptor));
+
+    // brackets missing
+    assertNull(FeatureMatcherSet
+            .fromString("AF LT 1.2 or CLIN_SIG NotContains path"));
+
+    // invalid conjunction
+    assertNull(FeatureMatcherSet.fromString("(AF LT 1.2) but (AF GT -2)"));
+
+    // unbalanced quote (1)
+    assertNull(FeatureMatcherSet.fromString("('AF lt '1.2')"));
+
+    // unbalanced quote (2)
+    assertNull(FeatureMatcherSet.fromString("('AF' lt '1.2)"));
+  }
 }