fix(ENGKNOW-2803): Fix case insensitivity in calcifmissing

gortools/src/main/scala/gorsat/Commands/CalcIfMissing.scala

@@ -39,11 +39,11 @@ class CalcIfMissing extends CommandInfo("CALCIFMISSING",
     val columnNames = Calc.getColumnsFromArgs(args)
     val exprSrc = Calc.getExpressionsFromArgs(args, columnNames)
 
-    val existingColumns = forcedInputHeader.split('\t')
+    val existingColumns = forcedInputHeader.toLowerCase.split('\t')
     val newColumns = ArrayBuffer[String]()
     val expressions = ArrayBuffer[String]()
     for (i <- columnNames.indices) {
-      if (!existingColumns.contains(columnNames(i))) {
+      if (!existingColumns.contains(columnNames(i).toLowerCase)) {
         newColumns += columnNames(i)
         expressions += exprSrc(i)
       }

gortools/src/main/scala/gorsat/Utilities/IteratorUtilities.scala

@@ -92,8 +92,11 @@ object IteratorUtilities {
         if (ALLOW_DUPLICATE_COLUMNS || allowDuplicates) {
           column = column + "x"
           colToUp = column.toUpperCase
+          if (!allowDuplicates) {
+            logger.warn(s"Duplicate column name '$col' detected in header: $header. Renaming to '$column'")
+          }
         } else {
-          throw new GorDataException(f"Error: Duplicate column name '$column%s' detected in header: $header%s")
+          throw new GorDataException(f"Error: Duplicate column name '$column' detected in header: $header")
         }
       }
       usedCols.add(colToUp)

gortools/src/test/java/gorsat/UTestHeaderFlags.java

@@ -25,7 +25,11 @@
 import gorsat.Utilities.IteratorUtilities;
 import org.gorpipe.exceptions.GorDataException;
 import org.junit.Assert;
+import org.junit.Ignore;
+import org.junit.Rule;
 import org.junit.Test;
+import org.junit.contrib.java.lang.system.RestoreSystemProperties;
+import org.junit.contrib.java.lang.system.SystemErrRule;
 import org.slf4j.LoggerFactory;
 
 import java.io.File;
@@ -35,6 +39,13 @@
 public class UTestHeaderFlags {
 
     private static final org.slf4j.Logger log = LoggerFactory.getLogger(UTestHeaderFlags.class);
+
+    @Rule
+    public final RestoreSystemProperties restoreSystemProperties = new RestoreSystemProperties();
+
+    @Rule
+    public final SystemErrRule systemErrRule = new SystemErrRule().enableLog();
+
     /**
      * If an excluded char becomes included after the initial state in gorsat.Utilities.IteratorUtilities#validHeader
      * this test will throw an exception.
@@ -68,6 +79,8 @@ public void testValidHeaderUsedKeywordsWithDupAllowingDup() {
         String testHeader = "#abc\tstart\tfrom\tselect\tmax\tmin\tfrom\tgroup\trange\torder\trank\torder";
         String resultingHeader = IteratorUtilities.validHeader(testHeader, true);
         Assert.assertEquals("#abc\tstart\tfrom\tselect\tmax\tmin\tfromx\tgroup\trange\torder\trank\torderx", resultingHeader);
+        Assert.assertFalse(systemErrRule.getLog().contains("Duplicate column name 'from'"));
+        Assert.assertFalse(systemErrRule.getLog().contains("Duplicate column name 'order'"));
     }
 
     @Test
@@ -76,6 +89,17 @@ public void testValidHeaderUsedKeywordsWithDupNotAllowingDup() {
         Assert.assertThrows(GorDataException.class, () -> IteratorUtilities.validHeader(testHeader, false));
     }
 
+    @Ignore("Only works if run alone, as the property is read only on class load")
+    @Test
+    public void testValidHeaderUsedKeywordsWithDupAllowingDupOnlyGlobal() {
+        System.setProperty("gor.iterators.allowDuplicateColumns", "true");
+        String testHeader = "#abc\tstart\tfrom\tselect\tmax\tmin\tfrom\tgroup\trange\torder\trank\torder";
+        String resultingHeader = IteratorUtilities.validHeader(testHeader, false);
+        Assert.assertEquals("#abc\tstart\tfrom\tselect\tmax\tmin\tfromx\tgroup\trange\torder\trank\torderx", resultingHeader);
+        Assert.assertTrue(systemErrRule.getLog().contains("Duplicate column name 'from'"));
+        Assert.assertTrue(systemErrRule.getLog().contains("Duplicate column name 'order'"));
+    }
+
     @Test
     public void testHeaderParsing() {
         String testStr = "test$He*aDer";

gortools/src/test/java/gorsat/parser/UTestCalcIfMissing.java

@@ -58,4 +58,12 @@ public void addsOnlyMissingColumns() {
                 "chr1\t1\t64\t3.14\tbingo\n";
         Assert.assertEquals(expected, result);
     }
+
+    @Test
+    public void ignoresColumnWhenItExistsWithCaseDiff() {
+        final String result = TestUtils.runGorPipe("gorrow 1,1 | calc data1 64 | calcifmissing DATA1,data2,data3 42,3.14,'bingo'");
+        final String expected = "chrom\tpos\tdata1\tdata2\tdata3\n" +
+                "chr1\t1\t64\t3.14\tbingo\n";
+        Assert.assertEquals(expected, result);
+    }
 }