Merge pull request #7331 from mvdbeek/test_data_managers

[19.01] Discriminate data managers and allow managed testing

lib/galaxy/tools/data_manager/manager.py

@@ -57,11 +57,19 @@ class DataManagers(object):
                 tool_path = '.'
             self.tool_path = tool_path
         for data_manager_elem in root.findall('data_manager'):
-            self.load_manager_from_elem(data_manager_elem, tool_path=self.tool_path)
+            if not self.load_manager_from_elem(data_manager_elem, tool_path=self.tool_path):
+                # Wasn't able to load manager, could happen when galaxy is managed by planemo.
+                # Fall back to loading relative to the data_manager_conf.xml file
+                tool_path = os.path.dirname(xml_filename)
+                self.load_manager_from_elem(data_manager_elem, tool_path=tool_path)
 
     def load_manager_from_elem(self, data_manager_elem, tool_path=None, add_manager=True):
         try:
             data_manager = DataManager(self, data_manager_elem, tool_path=tool_path)
+        except IOError as e:
+            if e.errno == errno.ENOENT:
+                # File does not exist
+                return None
         except Exception as e:
             log.error("Error loading data_manager '%s':\n%s" % (e, util.xml_to_string(data_manager_elem)))
             return None

lib/galaxy/tools/loader_directory.py

@@ -19,6 +19,7 @@ PATH_AND_RECURSIVE_ERROR = "Cannot specify a single file and recursive."
 LOAD_FAILURE_ERROR = "Failed to load tool with path %s."
 TOOL_LOAD_ERROR = object()
 TOOL_REGEX = re.compile(r"<tool\s")
+DATA_MANAGER_REGEX = re.compile(r"\stool_type=\"manage_data\"")
 
 YAML_EXTENSIONS = [".yaml", ".yml", ".json"]
 CWL_EXTENSIONS = YAML_EXTENSIONS + [".cwl"]
@@ -153,8 +154,7 @@ def looks_like_a_tool(path_or_uri_like, invalid_names=[], enable_beta_formats=Fa
     return looks
 
 
-def looks_like_a_tool_xml(path):
-    """Quick check to see if a file looks like it may be a Galaxy XML tool file."""
+def looks_like_xml(path, regex=TOOL_REGEX):
     full_path = os.path.abspath(path)
 
     if not full_path.endswith(".xml"):
@@ -172,12 +172,22 @@ def looks_like_a_tool_xml(path):
 
     with open(path, "r") as f:
         start_contents = f.read(5 * 1024)
-        if TOOL_REGEX.search(start_contents):
+        if regex.search(start_contents):
             return True
 
     return False
 
 
+def looks_like_a_tool_xml(path):
+    """Quick check to see if a file looks like it may be a Galaxy XML tool file."""
+    return looks_like_xml(path=path, regex=TOOL_REGEX)
+
+
+def looks_like_a_data_manager_xml(path):
+    """Quick check to see if a file looks like it may be a Galaxy data manager XML file."""
+    return looks_like_xml(path=path, regex=DATA_MANAGER_REGEX)
+
+
 def is_a_yaml_with_class(path, classes):
     """Determine if a file is a valid YAML with a supplied ``class`` entry."""
     if not _has_extension(path, YAML_EXTENSIONS):