From bed5ae1d4ea091129d9dd09047b06d17b369eddb Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Mon, 6 Oct 2014 09:24:53 -0400
Subject: [PATCH] Eliminate Galaxy dependencies from
 lib/galaxy/tools/loader.py. Should allow for reuse in command-line tools that
 operate on Galaxy tools. Updates for targetting Python 2.6+.

---
 lib/galaxy/tools/loader.py | 35 ++++++++++++++++++++---------------
 1 file changed, 20 insertions(+), 15 deletions(-)

diff --git a/lib/galaxy/tools/loader.py b/lib/galaxy/tools/loader.py
index 52a1d6d20f7..a17a3a5fc6e 100644
--- a/lib/galaxy/tools/loader.py
+++ b/lib/galaxy/tools/loader.py
@@ -1,10 +1,8 @@
-from __future__ import with_statement
+from xml.etree import ElementTree, ElementInclude
 
 from copy import deepcopy
 import os
 
-from galaxy.util import parse_xml
-
 
 def load_tool(path):
     """
@@ -16,7 +14,7 @@ def load_tool(path):
     _import_macros(root, path)
 
     # Expand xml macros
-    macro_dict = _macros_of_type(root, 'xml', lambda el: list(el.getchildren()))
+    macro_dict = _macros_of_type(root, 'xml', lambda el: list(el))
     _expand_macros([root], macro_dict)
 
     # Expand tokens
@@ -42,7 +40,7 @@ def raw_tool_xml_tree(path):
     """ Load raw (no macro expansion) tree representation of tool represented
     at the specified path.
     """
-    tree = parse_xml(path)
+    tree = _parse_xml(path)
     return tree
 
 
@@ -54,7 +52,7 @@ def imported_macro_paths(root):
 def _import_macros(root, path):
     tool_dir = os.path.dirname(path)
     macros_el = _macros_el(root)
-    if macros_el:
+    if macros_el is not None:
         macro_els = _load_macros(macros_el, tool_dir)
         _xml_set_children(macros_el, macro_els)
 
@@ -66,7 +64,7 @@ def _macros_el(root):
 def _macros_of_type(root, type, el_func):
     macros_el = root.find('macros')
     macro_dict = {}
-    if macros_el:
+    if macros_el is not None:
         macro_els = macros_el.findall('macro')
         macro_dict = dict([(macro_el.get("name"), el_func(macro_el)) \
             for macro_el in macro_els \
@@ -88,7 +86,7 @@ def _expand_tokens(elements, tokens):
             new_value = _expand_tokens_str(value, tokens)
             if not (new_value is value):
                 element.attrib[key] = new_value
-        _expand_tokens(list(element.getchildren()), tokens)
+        _expand_tokens(list(element), tokens)
 
 
 def _expand_tokens_str(str, tokens):
@@ -129,7 +127,7 @@ def _expand_macro(element, expand_el, macros):
 def _expand_yield_statements(macro_def, expand_el):
     yield_els = [yield_el for macro_def_el in macro_def for yield_el in macro_def_el.findall('.//yield')]
 
-    expand_el_children = expand_el.getchildren()
+    expand_el_children = list(expand_el)
     macro_def_parent_map = \
         dict((c, p) for macro_def_el in macro_def for p in macro_def_el.getiterator() for c in p)
 
@@ -151,7 +149,7 @@ def _load_embedded_macros(macros_el, tool_dir):
 
     macro_els = []
     # attribute typed macro
-    if macros_el:
+    if macros_el is not None:
         macro_els = macros_el.findall("macro")
     for macro in macro_els:
         if 'type' not in macro.attrib:
@@ -163,7 +161,7 @@ def _load_embedded_macros(macros_el, tool_dir):
     typed_tag = ['template', 'xml', 'token']
     for tag in typed_tag:
         macro_els = []
-        if macros_el:
+        if macros_el is not None:
             macro_els = macros_el.findall(tag)
         for macro_el in macro_els:
             macro_el.attrib['type'] = tag
@@ -188,7 +186,7 @@ def _load_imported_macros(macros_el, tool_dir):
 def _imported_macro_paths_from_el(macros_el):
     imported_macro_paths = []
     macro_import_els = []
-    if macros_el:
+    if macros_el is not None:
         macro_import_els = macros_el.findall("import")
     for macro_import_el in macro_import_els:
         raw_import_path = macro_import_el.text
@@ -199,13 +197,13 @@ def _imported_macro_paths_from_el(macros_el):
 
 
 def _load_macro_file(path, tool_dir):
-    tree = parse_xml(path)
+    tree = _parse_xml(path)
     root = tree.getroot()
     return _load_macros(root, tool_dir)
 
 
 def _xml_set_children(element, new_children):
-    for old_child in element.getchildren():
+    for old_child in element:
         element.remove(old_child)
     for i, new_child in enumerate(new_children):
         element.insert(i, new_child)
@@ -216,7 +214,7 @@ def _xml_replace(query, targets, parent_map):
     parent_el = parent_map[query]
     matching_index = -1
     #for index, el in enumerate(parent_el.iter('.')):  ## Something like this for newer implementation
-    for index, el in enumerate(parent_el.getchildren()):
+    for index, el in enumerate(list(parent_el)):
         if el == query:
             matching_index = index
             break
@@ -226,3 +224,10 @@ def _xml_replace(query, targets, parent_map):
         current_index += 1
         parent_el.insert(current_index, deepcopy(target))
     parent_el.remove(query)
+
+
+def _parse_xml(fname):
+    tree = ElementTree.parse(fname)
+    root = tree.getroot()
+    ElementInclude.include(root)
+    return tree