Restructure tool external file logic in load_tool_from_tmp_config in ToolValidator...

... so internals of tool XML description are only utilized in the galaxy.tools module (and submodules). Add some unit tests for this new method for finding externally referenced files.

lib/galaxy/tools/__init__.py

@@ -69,7 +69,7 @@ from galaxy.model.item_attrs import Dictifiable
 from galaxy.model import Workflow
 from tool_shed.util import common_util
 from tool_shed.util import shed_util_common as suc
-from .loader import load_tool, template_macro_params
+from .loader import load_tool, template_macro_params, raw_tool_xml_tree
 from .execute import execute as execute_job
 from .wrappers import (
     ToolParameterValueWrapper,
@@ -2989,6 +2989,21 @@ class Tool( object, Dictifiable ):
     def get_default_history_by_trans( self, trans, create=False ):
         return trans.get_history( create=create )
 
+    @classmethod
+    def get_externally_referenced_paths( self, path ):
+        """ Return relative paths to externally referenced files by the tool
+        described by file at `path`. External components should not assume things
+        about the structure of tool xml files (this is the tool's responsibility).
+        """
+        tree = raw_tool_xml_tree(path)
+        root = tree.getroot()
+        external_paths = []
+        for code_elem in root.findall( 'code' ):
+            external_path = code_elem.get( 'file' )
+            if external_path:
+                external_paths.append( external_path )
+        return external_paths
+
 
 class OutputParameterJSONTool( Tool ):
     """

lib/galaxy/tools/loader.py

@@ -10,7 +10,7 @@ def load_tool(path):
     """
     Loads tool from file system and preprocesses tool macros.
     """
-    tree = parse_xml(path)
+    tree = raw_tool_xml_tree(path)
     root = tree.getroot()
 
     _import_macros(root, path)
@@ -38,6 +38,14 @@ def template_macro_params(root):
     return param_dict
 
 
+def raw_tool_xml_tree(path):
+    """ Load raw (no macro expansion) tree representation of tool represented
+    at the specified path.
+    """
+    tree = parse_xml(path)
+    return tree
+
+
 def _import_macros(root, path):
     tool_dir = os.path.dirname(path)
     macros_el = root.find('macros')

lib/tool_shed/tools/tool_validator.py

@@ -3,6 +3,7 @@ import logging
 import os
 import tempfile
 
+from galaxy.tools import Tool
 from galaxy.tools import parameters
 from galaxy.tools.parameters import dynamic_options
 
@@ -311,15 +312,14 @@ class ToolValidator( object ):
         message = ''
         tmp_tool_config = hg_util.get_named_tmpfile_from_ctx( ctx, ctx_file, work_dir )
         if tmp_tool_config:
-            element_tree, error_message = xml_util.parse_xml( tmp_tool_config )
-            if element_tree is None:
+            tool_element, error_message = xml_util.parse_xml( tmp_tool_config )
+            if tool_element is None:
                 return tool, message
-            element_tree_root = element_tree.getroot()
-            # Look for code files required by the tool config.
+            # Look for external files required by the tool config.
             tmp_code_files = []
-            for code_elem in element_tree_root.findall( 'code' ):
-                code_file_name = code_elem.get( 'file' )
-                tmp_code_file_name = hg_util.copy_file_from_manifest( repo, ctx, code_file_name, work_dir )
+            external_paths = Tool.get_externally_referenced_paths( tmp_tool_config )
+            for path in external_paths:
+                tmp_code_file_name = hg_util.copy_file_from_manifest( repo, ctx, path, work_dir )
                 if tmp_code_file_name:
                     tmp_code_files.append( tmp_code_file_name )
             tool, valid, message = self.load_tool_from_config( repository_id, tmp_tool_config )

test/unit/tools/test_tool_external_files.py

@@ -0,0 +1,26 @@
+""" Unit test logic related to finding externally referenced files in tool
+descriptions.
+"""
+import tempfile
+import os
+import shutil
+from galaxy.tools import Tool
+
+
+def test_finds_external_code_file():
+    assert __external_files("""<tool><code file="foo.py" /></tool>""") == ["foo.py"]
+
+
+def test_finds_skips_empty_code_file_attribute():
+    assert __external_files("""<tool><code /></tool>""") == []
+
+
+def __external_files(contents):
+    base_path = tempfile.mkdtemp()
+    try:
+        tool_path = os.path.join(base_path, "tool.xml")
+        with open(tool_path, "w") as f:
+            f.write(contents)
+        return Tool.get_externally_referenced_paths(tool_path)
+    finally:
+        shutil.rmtree(base_path)