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authorBonfaceKilz2021-03-08 10:52:44 +0300
committerBonfaceKilz2021-03-08 21:09:58 +0300
commit79f931b0fbe0712954201a15278f9088fd7cdb8a (patch)
tree170c7aedb13e32ea6b29aa78dbe23eb537aa007c /gn3
parent13428f9d9496dc2af44065f03fc7fc747a5a0ea9 (diff)
downloadgenenetwork3-79f931b0fbe0712954201a15278f9088fd7cdb8a.tar.gz
Add "/gemma/k-gwa-compute/<token>"
Diffstat (limited to 'gn3')
-rw-r--r--gn3/api/gemma.py70
1 files changed, 70 insertions, 0 deletions
diff --git a/gn3/api/gemma.py b/gn3/api/gemma.py
index a69b73e..2d1fedf 100644
--- a/gn3/api/gemma.py
+++ b/gn3/api/gemma.py
@@ -349,3 +349,73 @@ def compute_gwa_with_loco_covar(k_filename, maf, token):
status=128,
# use better message
message="Metadata file non-existent!")
+
+
+@gemma.route("/k-gwa-compute/<token>", methods=["POST"])
+def compute_k_gwa(token):
+ """Given a genofile, traitfile, snpsfile, and the token, compute the k-values
+and return <hash-of-inputs>.json with a UNIQUE-ID of the job. The genofile,
+traitfile, and snpsfile are extracted from a metadata.json file. No Loco no
+covars; lmm defaults to 9!
+
+ """
+ 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 = [
+ 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}
+ gemma_k_cmd = generate_gemma_cmd(
+ gemma_cmd=current_app.config.get("GEMMA_"
+ "WRAPPER_CMD"),
+ output_dir=current_app.config.get('TMPDIR'),
+ token=token,
+ gemma_kwargs=gemma_kwargs)
+ gemma_kwargs["lmm"] = _dict.get("lmm", 9)
+ gemma_gwa_cmd = generate_gemma_cmd(
+ gemma_cmd=current_app.config.get("GEMMA_"
+ "WRAPPER_CMD"),
+ output_dir=current_app.config.get('TMPDIR'),
+ token=token,
+ gemma_kwargs=gemma_kwargs,
+ gemma_wrapper_kwargs={
+ "input": os.path.join(working_dir,
+ gemma_k_cmd.get("output_file"))
+ })
+ 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"{gemma_k_cmd.get('gemma_cmd')} && "
+ f"{gemma_gwa_cmd.get('gemma_cmd')}")),
+ status="queued",
+ output_file=gemma_gwa_cmd.get("output_file"))
+ # pylint: disable=W0703
+ except Exception:
+ return jsonify(
+ status=128,
+ # use better message
+ message="Metadata file non-existent!")
+ gemma_cmd=current_app.config.get("GEMMA_"
+ "WRAPPER_CMD"),
+ output_dir=current_app.config.get('TMPDIR'),
+ token=token,
+ gemma_kwargs=gemma_kwargs)
+ 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"{gemma_k_cmd.get('gemma_cmd')} && "
+ f"{gemma_gwa_cmd.get('gemma_cmd')}")),
+ status="queued",
+ output_file=gemma_gwa_cmd.get("output_file"))
+ # pylint: disable=W0703
+ except Exception:
+ return jsonify(
+ status=128,
+ # use better message
+ message="Metadata file non-existent!")