Merge pull request #5099 from mvdbeek/toolshed_install_stability

[17.09] Toolshed install stability improvements

lib/galaxy/model/tool_shed_install/__init__.py

@@ -143,7 +143,7 @@ class ToolShedRepository(object):
                             if tool_id in tool_ids:
                                 self.shed_config_filename = name
                                 return shed_tool_conf_dict
-        if self.includes_datatypes:
+        if self.includes_datatypes or self.includes_data_managers:
             # We need to search by file paths here, which is less desirable.
             tool_shed = common_util.remove_protocol_and_port_from_tool_shed_url(self.tool_shed)
             for shed_tool_conf_dict in app.toolbox.dynamic_confs(include_migrated_tool_conf=True):

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))

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