diff options
Diffstat (limited to 'gn3/api')
| -rw-r--r-- | gn3/api/gemma.py | 52 |
1 files changed, 30 insertions, 22 deletions
diff --git a/gn3/api/gemma.py b/gn3/api/gemma.py index 7fcf2a2..e5a38e4 100644 --- a/gn3/api/gemma.py +++ b/gn3/api/gemma.py @@ -113,21 +113,24 @@ traitfile, and snpsfile are extracted from a metadata.json file. genofile, phenofile, snpsfile = [os.path.join(working_dir, _dict.get(x)) for x in ["geno", "pheno", "snps"]] + if not do_paths_exist([genofile, phenofile, snpsfile]): + raise FileNotFoundError gemma_kwargs = {"g": genofile, "p": phenofile, "a": snpsfile} _hash = get_hash_of_files([genofile, phenofile, snpsfile]) k_output_filename = f"{_hash}-k-output.json" - k_computation_cmd = generate_gemma_computation_cmd( - gemma_cmd=current_app.config.get("GEMMA_WRAPPER_CMD"), - gemma_wrapper_kwargs=None, - gemma_kwargs=gemma_kwargs, - output_file=(f"{current_app.config.get('TMPDIR')}/" - f"{token}/{k_output_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=f"{k_computation_cmd}"), + cmd=compose_gemma_cmd( + gemma_wrapper_cmd=current_app.config.get("GEMMA_" + "WRAPPER_CMD"), + gemma_wrapper_kwargs=None, + gemma_kwargs=gemma_kwargs, + gemma_args=["-gk", ">", + (f"{current_app.config.get('TMPDIR')}/" + f"{token}/{k_output_filename}")])), status="queued", output_file=k_output_filename) # pylint: disable=W0703 @@ -154,18 +157,19 @@ values. gemma_kwargs = {"g": genofile, "p": phenofile, "a": snpsfile} _hash = get_hash_of_files([genofile, phenofile, snpsfile]) k_output_filename = f"{_hash}-k-output.json" - k_computation_cmd = generate_gemma_computation_cmd( - gemma_cmd=current_app.config.get("GEMMA_WRAPPER_CMD"), - gemma_wrapper_kwargs={"loco": f"--input {chromosomes}"}, - gemma_kwargs=gemma_kwargs, - output_file=(f"{current_app.config.get('TMPDIR')}/" - f"{token}/{k_output_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=f"{k_computation_cmd}"), + cmd=compose_gemma_cmd( + gemma_wrapper_cmd=current_app.config.get("GEMMA_" + "WRAPPER_CMD"), + gemma_wrapper_kwargs={"loco": f"--input {chromosomes}"}, + gemma_kwargs=gemma_kwargs, + gemma_args=["-gk", ">", + (f"{current_app.config.get('TMPDIR')}/" + f"{token}/{k_output_filename}")])), status="queued", output_file=k_output_filename) # pylint: disable=W0703 @@ -198,14 +202,16 @@ def compute_gwa(k_filename, token): conn=redis.Redis(), email=(request.get_json() or {}).get('email'), job_queue=current_app.config.get("REDIS_JOB_QUEUE"), - cmd=generate_gemma_computation_cmd( - gemma_cmd=current_app.config.get("GEMMA_WRAPPER_CMD"), + 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, - output_file=(f"{current_app.config.get('TMPDIR')}/" - f"{token}/{_output_filename}"))), + gemma_args=["gk", ">", + (f"{current_app.config.get('TMPDIR')}/" + f"{token}/{_output_filename}")])), status="queued", output_file=_output_filename) # pylint: disable=W0703 @@ -239,14 +245,16 @@ def compute_gwa_with_covar(k_filename, token): conn=redis.Redis(), email=(request.get_json() or {}).get('email'), job_queue=current_app.config.get("REDIS_JOB_QUEUE"), - cmd=generate_gemma_computation_cmd( - gemma_cmd=current_app.config.get("GEMMA_WRAPPER_CMD"), + 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, - output_file=(f"{current_app.config.get('TMPDIR')}/" - f"{token}/{_output_filename}"))), + gemma_args=["-gk", ">", + (f"{current_app.config.get('TMPDIR')}/" + f"{token}/{_output_filename}")])), status="queued", output_file=_output_filename) # pylint: disable=W0703 |