diff options
Diffstat (limited to 'gn3')
| -rw-r--r-- | gn3/api/gemma.py | 41 |
1 files changed, 41 insertions, 0 deletions
diff --git a/gn3/api/gemma.py b/gn3/api/gemma.py index 709643d..acaec68 100644 --- a/gn3/api/gemma.py +++ b/gn3/api/gemma.py @@ -211,3 +211,44 @@ def compute_gwa(k_filename, token): return jsonify(status=128, # use better message message="Metadata file non-existent!") + + +@gemma.route("/gwa-compute/covars/<k_filename>/<token>", methods=["POST"]) +def compute_gwa_with_covar(k_filename, token): + """Compute GWA values. Covariates provided. + + """ + working_dir = os.path.join(current_app.config.get("TMPDIR"), + token) + _dict = jsonfile_to_dict(os.path.join(working_dir, + "metadata.json")) + try: + genofile, phenofile, snpsfile, covarfile = [ + os.path.join(working_dir, + _dict.get(x)) + for x in ["geno", "pheno", "snps", "covar"]] + gemma_kwargs = {"g": genofile, "p": phenofile, + "a": snpsfile, "c": covarfile, + "lmm": _dict.get("lmm", 9)} + _hash = get_hash_of_files([genofile, phenofile, snpsfile, covarfile]) + _output_filename = f"{_hash}-gwa-output.json" + 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=generate_gemma_computation_cmd( + gemma_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}"))), + status="queued", + output_file=_output_filename) + # pylint: disable=W0703 + except Exception: + return jsonify(status=128, + # use better message + message="Metadata file non-existent!") |