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authorBonfaceKilz2021-03-04 21:06:09 +0300
committerBonfaceKilz2021-03-08 21:09:58 +0300
commitd072471bc353663149203d29a82fa9b7b2b95a1d (patch)
tree430c1c64826077818bd530c20f734d2393db305e /gn3/api
parent13b66fddd5c905e1a7b320051cedeb9ea234e1c3 (diff)
downloadgenenetwork3-d072471bc353663149203d29a82fa9b7b2b95a1d.tar.gz
Add new endpoint: "/gwa-compute/covars/<k_filename>/<token>"
Diffstat (limited to 'gn3/api')
-rw-r--r--gn3/api/gemma.py41
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!")