Allow setting file_actions in client via dict objects instead of paths.

This should just work with new Galaxy YAML job configs, embedding paths to YAML files in XML config files was awkard.

pulsar/client/action_mapper.py

@@ -196,7 +196,7 @@ class FileActionMapper(object):
         if action_config_path:
             config = read_file(action_config_path)
         else:
-            config = dict()
+            config = getattr(client, "file_actions", {})
         config["default_action"] = client.default_file_action
         config["files_endpoint"] = client.files_endpoint
         for attr in ['ssh_key', 'ssh_user', 'ssh_port', 'ssh_host']:

test/client_staging_test.py

@@ -93,6 +93,22 @@ class TestStager(TempDirectoryTestCase):
         assert uploaded_file1[1] == "unstructured"
         self.assertEqual(uploaded_file1[0], local_unstructured_file)
 
+    def test_file_actions_by_dict(self):
+        self.client_job_description.rewrite_paths = True
+        self.client.set_action_map_config(dict(paths=[
+            dict(path=self.temp_directory, path_types="*any*"),
+        ]), by_path=False)
+        local_unstructured_file = os.path.join(self.temp_directory, "A_RANDOM_FILE")
+        open(local_unstructured_file, "wb").write(b"Hello World!")
+        command_line = "foo.exe %s" % local_unstructured_file
+        self.client_job_description.command_line = command_line
+        self.client.expect_put_paths(["/pulsar/staging/1/other/A_RANDOM_FILE"])
+        self.client.expect_command_line("foo.exe /pulsar/staging/1/other/A_RANDOM_FILE")
+        self._submit()
+        uploaded_file1 = self.client.put_files[0]
+        assert uploaded_file1[1] == "unstructured"
+        self.assertEqual(uploaded_file1[0], local_unstructured_file)
+
     def test_submit_no_rewrite(self):
         # Expect no rewrite of paths
         command_line_template = "run_test.exe --input1=%s --input2=%s"
@@ -144,8 +160,11 @@ class MockClient(object):
         ])
         self.put_files = []
 
-    def set_action_map_config(self, config):
-        self.action_config_path = write_config(self, config, name="actions.yaml")
+    def set_action_map_config(self, config, by_path=True):
+        if by_path:
+            self.action_config_path = write_config(self, config, name="actions.yaml")
+        else:
+            self.file_actions = config
 
     def expect_put_paths(self, paths):
         self.put_paths = deque(paths)