diff options
Diffstat (limited to 'gn3')
| -rw-r--r-- | gn3/commands.py | 27 |
1 files changed, 6 insertions, 21 deletions
diff --git a/gn3/commands.py b/gn3/commands.py index 7201a68..51c1582 100644 --- a/gn3/commands.py +++ b/gn3/commands.py @@ -10,14 +10,9 @@ from uuid import uuid4 from redis.client import Redis # Used only in type hinting from gn3.exceptions import RedisConnectionError -from gn3.file_utils import lookup_file -from gn3.file_utils import jsonfile_to_dict -# pylint: disable=locally-disabled, too-many-arguments def compose_gemma_cmd( - token: str, - metadata_filename: str, gemma_wrapper_cmd: str = "gemma-wrapper", gemma_wrapper_kwargs: Optional[Dict] = None, gemma_kwargs: Optional[Dict] = None, @@ -26,25 +21,15 @@ def compose_gemma_cmd( cmd = f"{gemma_wrapper_cmd} --json" if gemma_wrapper_kwargs: cmd += (" " # Add extra space between commands - " ".join([f" --{key} {val}" for key, val + " ".join([f"--{key} {val}" for key, val in gemma_wrapper_kwargs.items()])) - data = jsonfile_to_dict(lookup_file("TMPDIR", - token, - metadata_filename)) - geno_file = lookup_file(environ_var="TMPDIR", - root_dir="genotype", - file_name=data.get("geno", "")) - pheno_file = lookup_file(environ_var="TMPDIR", - root_dir=token, - file_name=data.get("geno", "")) - cmd += f" -- -g {geno_file} -p {pheno_file}" + cmd += " -- " if gemma_kwargs: - cmd += (" " - " ".join([f" -{key} {val}" - for key, val in gemma_kwargs.items()])) + cmd += " ".join([f"-{key} {val}" + for key, val in gemma_kwargs.items()]) if gemma_args: - cmd += (" " - " ".join([f" {arg}" for arg in gemma_args])) + cmd += " " + cmd += " ".join([f"{arg}" for arg in gemma_args]) return cmd |