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fix: type parsing for ces,actions,credentials #118

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Feb 28, 2024
Merged

fix: type parsing for ces,actions,credentials #118

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51 changes: 19 additions & 32 deletions seqerakit/helper.py
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Original file line number Diff line number Diff line change
Expand Up @@ -113,10 +113,10 @@ def parse_all_yaml(file_paths, destroy=False):
def parse_block(block_name, item):
# Define the mapping from block names to functions.
block_to_function = {
"credentials": parse_credentials_block,
"compute-envs": parse_compute_envs_block,
"credentials": parse_type_block,
"compute-envs": parse_type_block,
"actions": parse_type_block,
"teams": parse_teams_block,
"actions": parse_actions_block,
"datasets": parse_datasets_block,
"pipelines": parse_pipelines_block,
"launch": parse_launch_block,
Expand All @@ -141,27 +141,28 @@ def parse_generic_block(item):
return cmd_args


def parse_credentials_block(item):
def parse_type_block(item, priority_keys=["type", "config-mode", "file-path"]):
cmd_args = []
for key, value in item.items():
if key == "type":
cmd_args.append(str(value))
elif isinstance(value, bool):
if value:
cmd_args.append(f"--{key}")
else:
cmd_args.extend([f"--{key}", str(value)])
return cmd_args

# Ensure at least one of 'type' or 'file-path' is present
if not any(key in item for key in ["type", "file-path"]):
raise ValueError(
"Please specify at least 'type' or 'file-path' for creating the resource."
)

# Process priority keys first
for key in priority_keys:
if key in item:
cmd_args.append(str(item[key]))
del item[key] # Remove the key to avoid repeating in args

def parse_compute_envs_block(item):
cmd_args = []
for key, value in item.items():
if key == "file-path" or key == "type" or key == "config-mode":
cmd_args.append(str(value))
elif isinstance(value, bool):
if isinstance(value, bool):
if value:
cmd_args.append(f"--{key}")
elif key == "params":
temp_file_name = utils.create_temp_yaml(value)
cmd_args.extend(["--params-file", temp_file_name])
else:
cmd_args.extend([f"--{key}", str(value)])
return cmd_args
Expand Down Expand Up @@ -194,20 +195,6 @@ def parse_teams_block(item):
return (cmd_args, members_cmd_args)


def parse_actions_block(item):
cmd_args = []
temp_file_name = None
for key, value in item.items():
if key == "type":
cmd_args.append(str(value))
elif key == "params":
temp_file_name = utils.create_temp_yaml(value)
cmd_args.extend(["--params-file", temp_file_name])
else:
cmd_args.extend([f"--{key}", str(value)])
return cmd_args


def parse_datasets_block(item):
cmd_args = []
for key, value in item.items():
Expand Down
65 changes: 61 additions & 4 deletions tests/unit/test_helper.py
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Original file line number Diff line number Diff line change
Expand Up @@ -130,14 +130,14 @@ def test_create_mock_dataset_yaml(mock_yaml_file):
assert result["datasets"] == expected_block_output


def test_create_mock_computeevs_yaml(mock_yaml_file):
def test_create_mock_computeevs_source_yaml(mock_yaml_file):
test_data = {
"compute-envs": [
{
"name": "test_computeenv",
"workspace": "my_organization/my_workspace",
"credentials": "my_credentials",
"file-path": "./examples/yaml/computeenvs/computeenvs.yaml",
"file-path": "./computeenvs/computeenv.json",
"wait": "AVAILABLE",
"fusion-v2": True,
"fargate": False,
Expand All @@ -149,9 +149,9 @@ def test_create_mock_computeevs_yaml(mock_yaml_file):
expected_block_output = [
{
"cmd_args": [
"./computeenvs/computeenv.json",
"--credentials",
"my_credentials",
"./examples/yaml/computeenvs/computeenvs.yaml",
"--fusion-v2",
"--name",
"test_computeenv",
Expand All @@ -171,6 +171,43 @@ def test_create_mock_computeevs_yaml(mock_yaml_file):
assert result["compute-envs"] == expected_block_output


def test_create_mock_computeevs_cli_yaml(mock_yaml_file):
test_data = {
"compute-envs": [
{
"name": "test_computeenv",
"workspace": "my_organization/my_workspace",
"credentials": "my_credentials",
"type": "aws-batch",
"config-mode": "forge",
"wait": "AVAILABLE",
}
],
}

expected_block_output = [
{
"cmd_args": [
"aws-batch",
"forge",
"--credentials",
"my_credentials",
"--name",
"test_computeenv",
"--wait",
"AVAILABLE",
"--workspace",
"my_organization/my_workspace",
],
"overwrite": False,
}
]
file_path = mock_yaml_file(test_data)
result = helper.parse_all_yaml([file_path])
assert "compute-envs" in result
assert result["compute-envs"] == expected_block_output


def test_create_mock_pipeline_add_yaml(mock_yaml_file):
test_data = {
"pipelines": [
Expand All @@ -191,7 +228,6 @@ def test_create_mock_pipeline_add_yaml(mock_yaml_file):
}
]
}

# params file cmds parsed separately
expected_block_output = [
{
Expand Down Expand Up @@ -239,3 +275,24 @@ def test_empty_yaml_file(mock_yaml_file):
assert f"The file '{file_path}' is empty or does not contain valid data." in str(
e.value
)


def test_error_type_yaml_file(mock_yaml_file):
test_data = {
"compute-envs": [
{
"name": "test_computeenv",
"workspace": "my_organization/my_workspace",
"credentials": "my_credentials",
"wait": "AVAILABLE",
}
],
}
file_path = mock_yaml_file(test_data)

with pytest.raises(ValueError) as e:
helper.parse_all_yaml([file_path])
assert (
"Please specify at least 'type' or 'file-path' for creating the resource."
in str(e.value)
)
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