diff options
Diffstat (limited to 'gn3/api')
| -rw-r--r-- | gn3/api/gemma.py | 140 |
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( |