fix(ENGKNOW-3340): gor turn on the duplicate column check

VERSION

@@ -1 +1 @@
-5.9.0
+5.9.1

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

@@ -43,7 +43,7 @@ object IteratorUtilities {
 
   private val logger = LoggerFactory.getLogger(this.getClass)
 
-  private val ALLOW_DUPLICATE_COLUMNS = System.getProperty("gor.iterators.allowDuplicateColumns", "true").toBoolean
+  val ALLOW_DUPLICATE_COLUMNS_KEY = "gor.iterators.allowDuplicateColumns"
 
   def getHeader(filename: String, gorRoot: String, context: GorContext): String = {
     val gm: GorMonitor = null
@@ -89,7 +89,7 @@ object IteratorUtilities {
       //just appending x to used columns
       var colToUp = column.toUpperCase
       while (usedCols.contains(colToUp)) {
-        if (ALLOW_DUPLICATE_COLUMNS || allowDuplicates) {
+        if (System.getProperty(ALLOW_DUPLICATE_COLUMNS_KEY, "false").toBoolean || allowDuplicates) {
           column = column + "x"
           colToUp = column.toUpperCase
           if (!allowDuplicates) {

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

@@ -83,7 +83,6 @@ public void testValidHeaderUsedKeywordsWithDupAllowingDup() {
         Assert.assertFalse(systemErrRule.getLog().contains("Duplicate column name 'order'"));
     }
 
-    @Ignore("Only works if run alone, as the property is read only on class load")
     @Test
     public void testValidHeaderUsedKeywordsWithDupNotAllowingDup() {
         System.setProperty("gor.iterators.allowDuplicateColumns", "false");
@@ -94,6 +93,7 @@ public void testValidHeaderUsedKeywordsWithDupNotAllowingDup() {
 
     @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);

gortools/src/test/java/gorsat/UTestRename.java

@@ -25,13 +25,18 @@
 import org.gorpipe.exceptions.GorDataException;
 import org.gorpipe.exceptions.GorParsingException;
 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 java.io.IOException;
 import java.nio.file.Files;
 
 public class UTestRename {
+
+    @Rule
+    public final RestoreSystemProperties restoreSystemProperties = new RestoreSystemProperties();
+
     @Test
     public void testSimpleRename() {
         String query = "gorrow chr1,1,1 | calc Foo_0001 0 | rename Foo_0001 Bar_CAR | top 0";
@@ -141,12 +146,12 @@ public void renameStrictWithNoMatch() {
 
     @Test
     public void renameToExistingAllowDup() {
+        System.setProperty("gor.iterators.allowDuplicateColumns", "true");
         String query = "gorrow chr1,1 | calc Foo 0 | calc Bar 1 | rename Foo Bar | top 0";
         String result = TestUtils.runGorPipe(query);
         Assert.assertEquals("chrom\tpos\tBar\tBarx\n", result);
     }
 
-    @Ignore("Only works if run alone, as the property is read only on class load")
     @Test
     public void renameToExistingNotAllowDup() {
         System.setProperty("gor.iterators.allowDuplicateColumns", "false");

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

@@ -39,14 +39,12 @@ public void addsNewColumn() {
         Assert.assertEquals(expected, result);
     }
 
-    @Ignore("Only works if run alone, as the property is read only on class load")
     @Test
     public void addsNewExistingColumn() {
         System.setProperty("gor.iterators.allowDuplicateColumns", "false");
         Assert.assertThrows(GorDataException.class, () -> TestUtils.runGorPipe("gorrow 1,1 | calc pos 42"));
     }
 
-    @Ignore("Only works if run alone, as the property is read only on class load")
     @Test
     public void addsNewColumnWithSuffixWhenItExists() {
         System.setProperty("gor.iterators.allowDuplicateColumns", "false");