From 3f2fc320fb7fb03eb7bf42e9ce3c1cb3e44a1028 Mon Sep 17 00:00:00 2001
From: jreback <jeff@reback.net>
Date: Tue, 4 Mar 2014 13:32:23 -0500
Subject: [PATCH] BUG: Bug in setitem with a duplicate index and an alignable
 rhs (GH6541)

---
 doc/source/release.rst        |  1 +
 pandas/core/index.py          |  9 +++++++--
 pandas/core/indexing.py       |  4 +++-
 pandas/tests/test_indexing.py | 23 +++++++++++++++++++++++
 4 files changed, 34 insertions(+), 3 deletions(-)

diff --git a/doc/source/release.rst b/doc/source/release.rst
index 29fd5bad16986..f5e2c80289c5c 100644
--- a/doc/source/release.rst
+++ b/doc/source/release.rst
@@ -199,6 +199,7 @@ Bug Fixes
 - Bug that caused _ref_locs corruption when slice indexing across columns axis of a DataFrame (:issue:`6525`)
 - Regression from 0.13 in the treatmenet of numpy ``datetime64`` non-ns dtypes in Series creation (:issue:`6529`)
 - ``.names`` attribute of MultiIndexes passed to ``set_index`` are now preserved (:issue:`6459`).
+- Bug in setitem with a duplicate index and an alignable rhs (:issue:`6541`)
 
 pandas 0.13.1
 -------------
diff --git a/pandas/core/index.py b/pandas/core/index.py
index c16e2eff06904..f67270530c3f8 100644
--- a/pandas/core/index.py
+++ b/pandas/core/index.py
@@ -987,8 +987,13 @@ def intersection(self, other):
             except TypeError:
                 pass
 
-        indexer = self.get_indexer(other.values)
-        indexer = indexer.take((indexer != -1).nonzero()[0])
+        try:
+            indexer = self.get_indexer(other.values)
+            indexer = indexer.take((indexer != -1).nonzero()[0])
+        except:
+            # duplicates
+            indexer = self.get_indexer_non_unique(other.values)[0].unique()
+
         return self.take(indexer)
 
     def diff(self, other):
diff --git a/pandas/core/indexing.py b/pandas/core/indexing.py
index 6691db5f35bb4..288934dbd27f4 100644
--- a/pandas/core/indexing.py
+++ b/pandas/core/indexing.py
@@ -441,7 +441,9 @@ def can_do_equal_len():
                         # align to
                         if item in value:
                             v = value[item]
-                            v = v.reindex(self.obj[item].index & v.index)
+                            i = self.obj[item].index
+                            v = v.reindex(i & v.index)
+
                             setter(item, v.values)
                         else:
                             setter(item, np.nan)
diff --git a/pandas/tests/test_indexing.py b/pandas/tests/test_indexing.py
index d373f2f43ad3e..f466ea302ee1c 100644
--- a/pandas/tests/test_indexing.py
+++ b/pandas/tests/test_indexing.py
@@ -564,6 +564,29 @@ def test_loc_setitem(self):
         expected = DataFrame({'a' : [0.5,-0.5,-1.5], 'b' : [0,1,2] })
         assert_frame_equal(df,expected)
 
+    def test_loc_setitem_dups(self):
+
+        # GH 6541
+        df_orig = DataFrame({'me' : list('rttti'),
+                             'foo': list('aaade'),
+                             'bar': np.arange(5,dtype='float64')*1.34+2,
+                             'bar2': np.arange(5,dtype='float64')*-.34+2}).set_index('me')
+
+        indexer = tuple(['r',['bar','bar2']])
+        df = df_orig.copy()
+        df.loc[indexer]*=2.0
+        assert_series_equal(df.loc[indexer],2.0*df_orig.loc[indexer])
+
+        indexer = tuple(['r','bar'])
+        df = df_orig.copy()
+        df.loc[indexer]*=2.0
+        self.assertEqual(df.loc[indexer],2.0*df_orig.loc[indexer])
+
+        indexer = tuple(['t',['bar','bar2']])
+        df = df_orig.copy()
+        df.loc[indexer]*=2.0
+        assert_frame_equal(df.loc[indexer],2.0*df_orig.loc[indexer])
+
     def test_chained_getitem_with_lists(self):
 
         # GH6394