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-rw-r--r--gn3/api/gemma.py140
1 files changed, 59 insertions, 81 deletions
diff --git a/gn3/api/gemma.py b/gn3/api/gemma.py
index 1751530..a69b73e 100644
--- a/gn3/api/gemma.py
+++ b/gn3/api/gemma.py
@@ -7,12 +7,10 @@ from flask import current_app
from flask import jsonify
from flask import request
-from gn3.commands import compose_gemma_cmd
from gn3.commands import queue_cmd
from gn3.commands import run_cmd
-from gn3.file_utils import get_hash_of_files
from gn3.file_utils import jsonfile_to_dict
-from gn3.computations.gemma import compute_k_values
+from gn3.computations.gemma import generate_gemma_cmd
from gn3.computations.gemma import do_paths_exist
from gn3.computations.gemma import generate_hash_of_string
from gn3.computations.gemma import generate_pheno_txt_file
@@ -116,12 +114,12 @@ traitfile, and snpsfile are extracted from a metadata.json file.
if not do_paths_exist([genofile, phenofile, snpsfile]):
raise FileNotFoundError
gemma_kwargs = {"g": genofile, "p": phenofile, "a": snpsfile}
- results = compute_k_values(gemma_cmd=current_app.config.get(
- "GEMMA_"
- "WRAPPER_CMD"),
- output_dir=current_app.config.get('TMPDIR'),
- token=token,
- gemma_kwargs=gemma_kwargs)
+ results = generate_gemma_cmd(
+ gemma_cmd=current_app.config.get("GEMMA_"
+ "WRAPPER_CMD"),
+ output_dir=current_app.config.get('TMPDIR'),
+ token=token,
+ gemma_kwargs=gemma_kwargs)
return jsonify(unique_id=queue_cmd(
conn=redis.Redis(),
email=(request.get_json() or {}).get('email'),
@@ -153,13 +151,13 @@ values.
if not do_paths_exist([genofile, phenofile, snpsfile]):
raise FileNotFoundError
gemma_kwargs = {"g": genofile, "p": phenofile, "a": snpsfile}
- results = compute_k_values(gemma_cmd=current_app.config.get(
- "GEMMA_"
- "WRAPPER_CMD"),
- output_dir=current_app.config.get('TMPDIR'),
- token=token,
- gemma_kwargs=gemma_kwargs,
- chromosomes=chromosomes)
+ results = generate_gemma_cmd(
+ gemma_cmd=current_app.config.get("GEMMA_"
+ "WRAPPER_CMD"),
+ output_dir=current_app.config.get('TMPDIR'),
+ token=token,
+ gemma_kwargs=gemma_kwargs,
+ chromosomes=chromosomes)
return jsonify(unique_id=queue_cmd(
conn=redis.Redis(),
email=(request.get_json() or {}).get('email'),
@@ -193,27 +191,22 @@ def compute_gwa(k_filename, token):
"a": snpsfile,
"lmm": _dict.get("lmm", 9)
}
- _hash = get_hash_of_files([genofile, phenofile, snpsfile])
- _output_filename = f"{_hash}-gwa-output.json"
+ results = generate_gemma_cmd(
+ gemma_cmd=current_app.config.get("GEMMA_"
+ "WRAPPER_CMD"),
+ output_dir=current_app.config.get('TMPDIR'),
+ token=token,
+ gemma_kwargs=gemma_kwargs,
+ gemma_wrapper_kwargs={
+ "input": os.path.join(working_dir, k_filename)
+ })
return jsonify(unique_id=queue_cmd(
conn=redis.Redis(),
email=(request.get_json() or {}).get('email'),
job_queue=current_app.config.get("REDIS_JOB_QUEUE"),
- cmd=compose_gemma_cmd(gemma_wrapper_cmd=current_app.config.get(
- "GEMMA_"
- "WRAPPER_CMD"),
- gemma_wrapper_kwargs={
- "input":
- os.path.join(working_dir, k_filename)
- },
- gemma_kwargs=gemma_kwargs,
- gemma_args=[
- "gk", ">",
- (f"{current_app.config.get('TMPDIR')}/"
- f"{token}/{_output_filename}")
- ])),
+ cmd=results.get("gemma_cmd")),
status="queued",
- output_file=_output_filename)
+ output_file=results.get("output_file"))
# pylint: disable=W0703
except Exception:
return jsonify(
@@ -224,7 +217,7 @@ def compute_gwa(k_filename, token):
@gemma.route("/gwa-compute/covars/<k_filename>/<token>", methods=["POST"])
def compute_gwa_with_covar(k_filename, token):
- """Compute GWA values. Covariates provided.
+ """Compute GWA values. No Loco; Covariates provided.
"""
working_dir = os.path.join(current_app.config.get("TMPDIR"), token)
@@ -241,27 +234,22 @@ def compute_gwa_with_covar(k_filename, token):
"c": covarfile,
"lmm": _dict.get("lmm", 9)
}
- _hash = get_hash_of_files([genofile, phenofile, snpsfile, covarfile])
- _output_filename = f"{_hash}-gwa-output.json"
+ results = generate_gemma_cmd(
+ gemma_cmd=current_app.config.get("GEMMA_"
+ "WRAPPER_CMD"),
+ output_dir=current_app.config.get('TMPDIR'),
+ token=token,
+ gemma_kwargs=gemma_kwargs,
+ gemma_wrapper_kwargs={
+ "input": os.path.join(working_dir, k_filename)
+ })
return jsonify(unique_id=queue_cmd(
conn=redis.Redis(),
email=(request.get_json() or {}).get('email'),
job_queue=current_app.config.get("REDIS_JOB_QUEUE"),
- cmd=compose_gemma_cmd(gemma_wrapper_cmd=current_app.config.get(
- "GEMMA_"
- "WRAPPER_CMD"),
- gemma_wrapper_kwargs={
- "input":
- os.path.join(working_dir, k_filename)
- },
- gemma_kwargs=gemma_kwargs,
- gemma_args=[
- "-gk", ">",
- (f"{current_app.config.get('TMPDIR')}/"
- f"{token}/{_output_filename}")
- ])),
+ cmd=results.get("gemma_cmd")),
status="queued",
- output_file=_output_filename)
+ output_file=results.get("output_file"))
# pylint: disable=W0703
except Exception:
return jsonify(
@@ -292,27 +280,22 @@ def compute_gwa_with_loco_maf(k_filename, maf, token):
"lmm": _dict.get("lmm", 9),
'maf': float(maf)
}
- _hash = get_hash_of_files([genofile, phenofile, snpsfile])
- _output_filename = f"{_hash}-gwa-output.json"
+ results = generate_gemma_cmd(
+ gemma_cmd=current_app.config.get("GEMMA_"
+ "WRAPPER_CMD"),
+ output_dir=current_app.config.get('TMPDIR'),
+ token=token,
+ gemma_kwargs=gemma_kwargs,
+ gemma_wrapper_kwargs={
+ "loco": f"--input {os.path.join(working_dir, k_filename)}"
+ })
return jsonify(unique_id=queue_cmd(
conn=redis.Redis(),
email=(request.get_json() or {}).get('email'),
job_queue=current_app.config.get("REDIS_JOB_QUEUE"),
- cmd=compose_gemma_cmd(
- gemma_wrapper_cmd=current_app.config.get("GEMMA_"
- "WRAPPER_CMD"),
- gemma_wrapper_kwargs={
- "loco": ("--input "
- f"{os.path.join(working_dir, k_filename)}")
- },
- gemma_kwargs=gemma_kwargs,
- gemma_args=[
- "-gk", ">",
- (f"{current_app.config.get('TMPDIR')}/"
- f"{token}/{_output_filename}")
- ])),
+ cmd=results.get("gemma_cmd")),
status="queued",
- output_file=_output_filename)
+ output_file=results.get("output_file"))
# pylint: disable=W0703
except Exception:
return jsonify(
@@ -344,27 +327,22 @@ def compute_gwa_with_loco_covar(k_filename, maf, token):
"lmm": _dict.get("lmm", 9),
"maf": float(maf)
}
- _hash = get_hash_of_files([genofile, phenofile, snpsfile, covarfile])
- _output_filename = f"{_hash}-gwa-output.json"
+ results = generate_gemma_cmd(
+ gemma_cmd=current_app.config.get("GEMMA_"
+ "WRAPPER_CMD"),
+ output_dir=current_app.config.get('TMPDIR'),
+ token=token,
+ gemma_kwargs=gemma_kwargs,
+ gemma_wrapper_kwargs={
+ "loco": f"--input {os.path.join(working_dir, k_filename)}"
+ })
return jsonify(unique_id=queue_cmd(
conn=redis.Redis(),
email=(request.get_json() or {}).get('email'),
job_queue=current_app.config.get("REDIS_JOB_QUEUE"),
- cmd=compose_gemma_cmd(
- gemma_wrapper_cmd=current_app.config.get("GEMMA_"
- "WRAPPER_CMD"),
- gemma_wrapper_kwargs={
- "loco": ("--input "
- f"{os.path.join(working_dir, k_filename)}")
- },
- gemma_kwargs=gemma_kwargs,
- gemma_args=[
- "-gk", ">",
- (f"{current_app.config.get('TMPDIR')}/"
- f"{token}/{_output_filename}")
- ])),
+ cmd=results.get("gemma_cmd")),
status="queued",
- output_file=_output_filename)
+ output_file=results.get("output_file"))
# pylint: disable=W0703
except Exception:
return jsonify(
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-23 12:04:21 +0000