Handle both EOL cases (\n and \r\n).

aalhossary · aalhossary · commit 77694bbbd747 · 2021-09-25T10:13:58.000+08:00
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixTest.java b/biojava-core/src/test/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixTest.java
@@ -55,7 +55,7 @@ void matrixToString(){
         String asString = sm.toString();
         // description + 5*2 for ATCGNatcgn + 1 header + 1  for '-'
         assertEquals(13, asString.split("\n").length);
-        String header = asString.split("\n")[1];
+        String header = asString.split("\r?\n")[1];
         assertTrue(header.replaceAll(" ","").matches("[ATCGatcgNn-]+"));
     }
 
@@ -65,7 +65,7 @@ void matrixAsString(){
 
         // 5*2 for ATCGNatcgn + 1 header + 1  for '-'
         assertEquals(12, asString.split("\n").length);
-        String header = asString.split("\n")[0];
+        String header = asString.split("\r?\n")[0];
         assertTrue(header.replaceAll(" ","").matches("[ATCGatcgNn-]+"));
     }
 }
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/util/PrettyXMLWriterTest.java b/biojava-core/src/test/java/org/biojava/nbio/core/util/PrettyXMLWriterTest.java
@@ -1,6 +1,6 @@
 package org.biojava.nbio.core.util;
 
-import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.Assert.fail;
 
 import java.io.IOException;
 import java.io.PrintWriter;
@@ -57,8 +57,8 @@ void simpleOutput() throws IOException {
 
         xw.closeTag("to");
         System.out.println(sw.toString());
-        assertEquals(EXPECTED, sw.toString());
-
+        if(! StringManipulationHelper.equalsToIgnoreEndline(EXPECTED, sw.toString()))
+        	fail(String.format("Strings are not equal (ignoring endline differences. expected: [%s], but it was:[%s]", EXPECTED, sw.toString()));
     }
 
     @Test
@@ -68,7 +68,8 @@ void specialCharsAreEscaped() throws IOException {
         xw.print("<code>some literal xml </code>");
         xw.closeTag("dt");
 
-        assertEquals(EXPECTED, sw.toString());
+        if(! StringManipulationHelper.equalsToIgnoreEndline(EXPECTED, sw.toString()))
+        	fail(String.format("Strings are not equal (ignoring endline differences. expected: [%s], but it was:[%s]", EXPECTED, sw.toString()));
     }
 
     @Test
@@ -82,6 +83,7 @@ void namespacesAreAddedToElements() throws IOException {
         xw.print("<code>some literal xml </code>");
         xw.closeTag(HTTP_TEST_NAMESPACE, "dt");
 
-        assertEquals(EXPECTED, sw.toString());
+        if(! StringManipulationHelper.equalsToIgnoreEndline(EXPECTED, sw.toString()))
+        	fail(String.format("Strings are not equal (ignoring endline differences. expected: [%s], but it was:[%s]", EXPECTED, sw.toString()));
     }
 }

Original file line number	Diff line number	Diff line change
`@@ -55,7 +55,7 @@ void matrixToString(){`
`55`	`55`	`String asString = sm.toString();`
`56`	`56`	`// description + 5*2 for ATCGNatcgn + 1 header + 1 for '-'`
`57`	`57`	`assertEquals(13, asString.split("\n").length);`
`58`		`- String header = asString.split("\n")[1];`
	`58`	`+ String header = asString.split("\r?\n")[1];`
`59`	`59`	`assertTrue(header.replaceAll(" ","").matches("[ATCGatcgNn-]+"));`
`60`	`60`	`}`
`61`	`61`
`@@ -65,7 +65,7 @@ void matrixAsString(){`
`65`	`65`
`66`	`66`	`// 5*2 for ATCGNatcgn + 1 header + 1 for '-'`
`67`	`67`	`assertEquals(12, asString.split("\n").length);`
`68`		`- String header = asString.split("\n")[0];`
	`68`	`+ String header = asString.split("\r?\n")[0];`
`69`	`69`	`assertTrue(header.replaceAll(" ","").matches("[ATCGatcgNn-]+"));`
`70`	`70`	`}`
`71`	`71`	`}`