From 1a474851973c8306ad4c7de7b00a4fc236ea3cb4 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Mon, 13 Jun 2016 15:03:11 -0400
Subject: [PATCH] Update against latest galaxy-lib.

In return it needed to be updated for recent changes to cwltool and Galaxy.
---
 lib/galaxy/tools/cwl/parser.py | 2 +-
 lib/galaxy/tools/cwl/schema.py | 1 -
 lib/galaxy/tools/parser/cwl.py | 6 ++++++
 3 files changed, 7 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/tools/cwl/parser.py b/lib/galaxy/tools/cwl/parser.py
index bbcc4d9f680..d262b29e51e 100644
--- a/lib/galaxy/tools/cwl/parser.py
+++ b/lib/galaxy/tools/cwl/parser.py
@@ -237,8 +237,8 @@ class JobProxy(object):
         if self._cwl_job is None:
             self._cwl_job = self._tool_proxy._tool.job(
                 self._input_dict,
-                self._job_directory,
                 self._output_callback,
+                basedir=self._job_directory,
                 use_container=False
             ).next()
             self._is_command_line_job = hasattr(self._cwl_job, "command_line")
diff --git a/lib/galaxy/tools/cwl/schema.py b/lib/galaxy/tools/cwl/schema.py
index 4ecbd0f7a2a..a879bdbd76e 100644
--- a/lib/galaxy/tools/cwl/schema.py
+++ b/lib/galaxy/tools/cwl/schema.py
@@ -61,7 +61,6 @@ class SchemaLoader(object):
         tool = load_tool.make_tool(
             process_definition.document_loader,
             process_definition.avsc_names,
-            process_definition.process_object,
             process_definition.metadata,
             process_definition.raw_process_reference.uri,
             make_tool,
diff --git a/lib/galaxy/tools/parser/cwl.py b/lib/galaxy/tools/parser/cwl.py
index b9a4731e712..19e74e0c749 100644
--- a/lib/galaxy/tools/parser/cwl.py
+++ b/lib/galaxy/tools/parser/cwl.py
@@ -60,6 +60,12 @@ class CwlToolSource(ToolSource):
 
         return environment_variables
 
+    def parse_edam_operations(self):
+        return []
+
+    def parse_edam_topics(self):
+        return []
+
     def parse_help(self):
         return self.tool_proxy.description() or ""