From e5bcb0faccf67f213538cad3670a8d1378c56ce7 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Mon, 8 Mar 2021 15:22:26 +0300 Subject: Remove "/k-gwa-computation" --- gn3/api/gemma.py | 58 -------------------------------------------------------- 1 file changed, 58 deletions(-) (limited to 'gn3/api') diff --git a/gn3/api/gemma.py b/gn3/api/gemma.py index ed698d3..21c4cf5 100644 --- a/gn3/api/gemma.py +++ b/gn3/api/gemma.py @@ -26,64 +26,6 @@ def get_version(): return jsonify(run_cmd(f"{gemma_cmd} -v | head -n 1")) -# This is basically extracted from genenetwork2 -# wqflask/wqflask/marker_regression/gemma_ampping.py -@gemma.route("/k-gwa-computation", methods=["POST"]) -def run_gemma(): - """Generates a command for generating K-Values and then later, generate a GWA -command that contains markers. These commands are queued; and the expected -file output is returned. - - """ - data = request.get_json() - app_defaults = current_app.config - __hash = generate_hash_of_string(f"{data.get('genofile_name')}_" - ''.join(data.get("values", ""))) - gemma_kwargs = { - "geno_filename": - os.path.join(app_defaults.get("GENODIR"), "bimbam", - f"{data.get('geno_filename')}"), - "trait_filename": - generate_pheno_txt_file( - tmpdir=app_defaults.get("TMPDIR"), - values=data.get("values"), - # Generate this file on the fly! - trait_filename=(f"{data.get('dataset_groupname')}_" - f"{data.get('trait_name')}_" - f"{__hash}.txt")) - } - gemma_wrapper_kwargs = {} - if data.get("loco"): - gemma_wrapper_kwargs["loco"] = f"--input {data.get('loco')}" - k_computation_cmd = generate_gemma_computation_cmd( - gemma_cmd=app_defaults.get("GEMMA_WRAPPER_CMD"), - gemma_wrapper_kwargs={"loco": f"--input {data.get('loco')}"}, - gemma_kwargs=gemma_kwargs, - output_file=(f"{app_defaults.get('TMPDIR')}/gn2/" - f"{data.get('dataset_name')}_K_" - f"{__hash}.json")) - gemma_kwargs["lmm"] = data.get("lmm", 9) - gemma_wrapper_kwargs["input"] = (f"{data.get('dataset_name')}_K_" - f"{__hash}.json") - gwa_cmd = generate_gemma_computation_cmd( - gemma_wrapper_kwargs=gemma_wrapper_kwargs, - gemma_cmd=app_defaults.get("GEMMA_WRAPPER_CMD"), - gemma_kwargs=gemma_kwargs, - output_file=(f"{data.get('dataset_name')}_GWA_" - f"{__hash}.txt")) - if not all([k_computation_cmd, gwa_cmd]): - return jsonify(status=128, - error="Unable to generate cmds for computation!"), 500 - return jsonify(unique_id=queue_cmd( - conn=redis.Redis(), - email=data.get("email"), - job_queue=app_defaults.get("REDIS_JOB_QUEUE"), - cmd=f"{k_computation_cmd} && {gwa_cmd}"), - status="queued", - output_file=(f"{data.get('dataset_name')}_GWA_" - f"{__hash}.txt")) - - @gemma.route("/status/", methods=["GET"]) def check_cmd_status(unique_id): """Given a (url-encoded) UNIQUE-ID which is returned when hitting any of the -- cgit v1.2.3