From 562ea1d5e2f5662c7cce0ca954541c3c5833b839 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Mon, 27 Nov 2017 09:54:36 +0100
Subject: [PATCH] Do not write shed_tool_data_table_config in place

This should prevent errors such as:
```
galaxy.util ERROR 2017-11-17 09:20:12,842 Error parsing file /data/users/mvandenb/gx/config/shed_tool_data_table_conf.xml
Traceback (most recent call last):
  File "lib/galaxy/util/__init__.py", line 217, in parse_xml
    root = tree.parse(fname, parser=ElementTree.XMLParser(target=DoctypeSafeCallbackTarget()))
  File "/usr/lib/python2.7/xml/etree/ElementTree.py", line 657, in parse
    self._root = parser.close()
  File "/usr/lib/python2.7/xml/etree/ElementTree.py", line 1654, in close
    self._raiseerror(v)
  File "/usr/lib/python2.7/xml/etree/ElementTree.py", line 1506, in _raiseerror
    raise err
ParseError: no element found: line 1, column 0
```
reported in https://github.com/galaxyproject/galaxy/issues/5031.
---
 lib/galaxy/tools/data/__init__.py         |  3 +-
 lib/galaxy/util/renamed_temporary_file.py | 42 +++++++++++++++++++++++
 2 files changed, 44 insertions(+), 1 deletion(-)
 create mode 100644 lib/galaxy/util/renamed_temporary_file.py

diff --git a/lib/galaxy/tools/data/__init__.py b/lib/galaxy/tools/data/__init__.py
index d3ec66072b7..95ea5c0470d 100644
--- a/lib/galaxy/tools/data/__init__.py
+++ b/lib/galaxy/tools/data/__init__.py
@@ -21,6 +21,7 @@ import requests
 from galaxy import util
 from galaxy.util.dictifiable import Dictifiable
 from galaxy.util.odict import odict
+from galaxy.util.renamed_temporary_file import RenamedTemporaryFile
 
 log = logging.getLogger(__name__)
 
@@ -186,7 +187,7 @@ class ToolDataTableManager(object):
         # add new elems
         out_elems.extend(new_elems)
         out_path_is_new = not os.path.exists(full_path)
-        with open(full_path, 'wb') as out:
+        with RenamedTemporaryFile(full_path) as out:
             out.write('<?xml version="1.0"?>\n<tables>\n')
             for elem in out_elems:
                 out.write(util.xml_to_string(elem, pretty=True))
diff --git a/lib/galaxy/util/renamed_temporary_file.py b/lib/galaxy/util/renamed_temporary_file.py
new file mode 100644
index 00000000000..ecbfb7a38c3
--- /dev/null
+++ b/lib/galaxy/util/renamed_temporary_file.py
@@ -0,0 +1,42 @@
+"""Safely write file to temporary file and then move file into place."""
+# Copied from https://stackoverflow.com/a/12007885.
+import os
+import tempfile
+
+
+class RenamedTemporaryFile(object):
+    """
+    A temporary file object which will be renamed to the specified
+    path on exit.
+    """
+    def __init__(self, final_path, **kwargs):
+        tmpfile_dir = kwargs.pop('dir', None)
+
+        # Put temporary file in the same directory as the location for the
+        # final file so that an atomic move into place can occur.
+
+        if tmpfile_dir is None:
+            tmpfile_dir = os.path.dirname(final_path)
+
+        self.tmpfile = tempfile.NamedTemporaryFile(dir=tmpfile_dir, **kwargs)
+        self.final_path = final_path
+
+    def __getattr__(self, attr):
+        """
+        Delegate attribute access to the underlying temporary file object.
+        """
+        return getattr(self.tmpfile, attr)
+
+    def __enter__(self):
+        self.tmpfile.__enter__()
+        return self
+
+    def __exit__(self, exc_type, exc_val, exc_tb):
+        if exc_type is None:
+            self.tmpfile.delete = False
+            result = self.tmpfile.__exit__(exc_type, exc_val, exc_tb)
+            os.rename(self.tmpfile.name, self.final_path)
+        else:
+            result = self.tmpfile.__exit__(exc_type, exc_val, exc_tb)
+
+        return result