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authorBonfaceKilz2021-02-17 16:39:24 +0300
committerBonfaceKilz2021-02-24 14:20:29 +0300
commit64c648a2595cc3ff48e244d91cbd9a6891e01224 (patch)
tree20b7c683b91a2bb061853f4627da3ebe7925788f /gn3
parent571548f1fa5ceaf79d62d809462b77933d5cff90 (diff)
downloadgenenetwork3-64c648a2595cc3ff48e244d91cbd9a6891e01224.tar.gz
gn3: commands: Remove token and metadata_filename args
Diffstat (limited to 'gn3')
-rw-r--r--gn3/commands.py27
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