From f42fa6f865bcb3aec681759c6217af36794fcc18 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Daniel=20G=C3=B3mez-S=C3=A1nchez?=
 <daniel.gomez.sanchez@hotmail.es>
Date: Wed, 11 Oct 2017 11:06:00 +0200
Subject: [PATCH] Throw CommandLineParserInternalException for immutable
 collections

---
 .../argparser/CommandLineArgumentParser.java     | 16 +++++++++++-----
 .../argparser/CollectionArgumentUnitTests.java   | 11 +++++++++++
 2 files changed, 22 insertions(+), 5 deletions(-)

diff --git a/src/main/java/org/broadinstitute/barclay/argparser/CommandLineArgumentParser.java b/src/main/java/org/broadinstitute/barclay/argparser/CommandLineArgumentParser.java
index 1c32f2db..c83386b9 100644
--- a/src/main/java/org/broadinstitute/barclay/argparser/CommandLineArgumentParser.java
+++ b/src/main/java/org/broadinstitute/barclay/argparser/CommandLineArgumentParser.java
@@ -684,11 +684,17 @@ private void setArgument(ArgumentDefinition argumentDefinition, List<String> val
             if (argumentDefinition.isCollection) {
                 @SuppressWarnings("rawtypes")
                 final Collection c = (Collection) argumentDefinition.getFieldValue();
-                if (value == null) {
-                    //user specified this arg=null which is interpreted as empty list
-                    c.clear();
-                } else {
-                    c.add(value);
+                try {
+                    if (value == null) {
+                        //user specified this arg=null which is interpreted as empty list
+                        c.clear();
+                    } else {
+                        c.add(value);
+                    }
+                } catch (UnsupportedOperationException e) {
+                    throw new CommandLineException.CommandLineParserInternalException(String.format("Collection arguments seems immutable: \"%s\". Initialized collection should support the clear and add methods, but %s does not.",
+                            argumentDefinition.getLongName(),
+                            c.getClass().getName()));
                 }
                 argumentDefinition.hasBeenSet = true;
             } else {
diff --git a/src/test/java/org/broadinstitute/barclay/argparser/CollectionArgumentUnitTests.java b/src/test/java/org/broadinstitute/barclay/argparser/CollectionArgumentUnitTests.java
index 9b21bae5..16252abd 100644
--- a/src/test/java/org/broadinstitute/barclay/argparser/CollectionArgumentUnitTests.java
+++ b/src/test/java/org/broadinstitute/barclay/argparser/CollectionArgumentUnitTests.java
@@ -277,6 +277,17 @@ public void testCollectionThatCannotBeAutoInitialized() {
         new CommandLineArgumentParser(o);
     }
 
+    class ImmutableCollectionArguments {
+        @Argument
+        public List<String> LIST = Collections.emptyList();
+    }
+
+    @Test(expectedExceptions = CommandLineException.CommandLineParserInternalException.class)
+    public void testCollectionThatIsImmmutable() {
+        final ImmutableCollectionArguments o = new ImmutableCollectionArguments();
+        new CommandLineArgumentParser(o).parseArguments(System.err, new String[]{"--LIST", "A"});
+    }
+
     //////////////////////////////////////////////////////////////////
     // Helper methods