diff options
| -rw-r--r-- | gn3/api/gemma.py | 75 |
1 files changed, 35 insertions, 40 deletions
diff --git a/gn3/api/gemma.py b/gn3/api/gemma.py index 95e71e2..e5fe499 100644 --- a/gn3/api/gemma.py +++ b/gn3/api/gemma.py @@ -7,10 +7,11 @@ 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 jsonfile_to_dict +from gn3.computations.gemma import generate_hash_of_string +from gn3.computations.gemma import generate_pheno_txt_file +from gn3.computations.gemma import generate_gemma_computation_cmd gemma = Blueprint("gemma", __name__) @@ -33,47 +34,41 @@ file output is returned. """ data = request.get_json() - if not data.get("token"): - return jsonify(status=128, error="Please provide a token"), 400 app_defaults = current_app.config.get('APP_DEFAULTS') - metadata = os.path.join(app_defaults.get("TMPDIR"), - data.get("token"), - data.get("metadata", "metadata.json")) - if not os.path.isfile(metadata): - return jsonify(status=128, - error=f"{metadata}: file does not exist"), 500 - metadata = jsonfile_to_dict(metadata) + __hash = generate_hash_of_string("".join(data.get("values"))) gemma_kwargs = { - "g": os.path.join(app_defaults.get("GENODIR"), "bimbam", - metadata.get("genotype_file")), - "p": os.path.join(app_defaults.get("GENODIR"), "bimbam", - metadata.get("phenotype_file")), - "a": os.path.join(app_defaults.get("GENODIR"), "bimbam", - metadata.get("snp_file"))} - generate_k_cmd = compose_gemma_cmd( - gemma_wrapper_cmd=app_defaults.get("GEMMA_WRAPPER_CMD"), + "geno_filename": os.path.join(app_defaults.get("GENODIR"), "bimbam", + f"{data.get('genofile_name')}.txt"), + "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"))} + k_computation_cmd = generate_gemma_computation_cmd( + gemma_cmd=app_defaults.get("GEMMA_WRAPPER_CMD"), gemma_kwargs=gemma_kwargs, - gemma_args=["-gk", ">", - os.path.join(app_defaults.get("TMPDIR"), "gn2", - f"k_output_{data.get('token')}.txt")]) - if metadata.get("covariates"): + output_file=(f"{app_defaults.get('TMPDIR')}/gn2/" + f"{data.get('dataset_name')}_K_" + f"{__hash}.json")) + if data.get("covariates"): gemma_kwargs["c"] = os.path.join(app_defaults.get("GENODIR"), "bimbam", - metadata.get("covariates")) - # Prevents command injection! - for _, value in gemma_kwargs.items(): - if not os.path.isfile(value): - return jsonify(status=128, error=f"{value}: Does not exist!"), 500 - - gemma_kwargs["lmm"] = 9 - gwa_cmd = compose_gemma_cmd( - gemma_wrapper_cmd=app_defaults.get("GEMMA_WRAPPER_CMD"), + data.get("covariates")) + gemma_kwargs["lmm"] = data.get("lmm", 9) + gwa_cmd = generate_gemma_computation_cmd( + gemma_cmd=app_defaults.get("GEMMA_WRAPPER_CMD"), gemma_kwargs=gemma_kwargs, - gemma_args=[">", - os.path.join(app_defaults.get("TMPDIR"), - "gn2", - f"gemma_output_{data.get('token')}.txt")]) - unique_id = queue_cmd(conn=redis.Redis(), email=metadata.get("email"), - cmd=f"{generate_k_cmd} && {gwa_cmd}") - return jsonify(unique_id=unique_id, status="queued", - output_file=f"gemma_output_{data.get('token')}.txt") + 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"), + cmd=f"{k_computation_cmd} && {gwa_cmd}"), + status="queued", + output_file=(f"{data.get('dataset_name')}_GWA_" + f"{__hash}.txt")) |