From 44e3b611c39cf39aed53ba2983f055127a9e3caa Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Wed, 1 May 2019 16:33:27 -0400
Subject: [PATCH] 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 | 2 +-
test/client_staging_test.py | 23 +++++++++++++++++++++--
2 files changed, 22 insertions(+), 3 deletions(-)
diff --git a/pulsar/client/action_mapper.py b/pulsar/client/action_mapper.py
index 96a70d97..4bbc6fb6 100644
--- a/pulsar/client/action_mapper.py
+++ b/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']:
diff --git a/test/client_staging_test.py b/test/client_staging_test.py
index 8eaab8e6..d6ae5155 100644
--- a/test/client_staging_test.py
+++ b/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)
--
GitLab