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-rw-r--r--gn3/api/gemma.py38
1 files changed, 38 insertions, 0 deletions
diff --git a/gn3/api/gemma.py b/gn3/api/gemma.py
index ec5f3f0..e5a1a72 100644
--- a/gn3/api/gemma.py
+++ b/gn3/api/gemma.py
@@ -133,3 +133,41 @@ traitfile, and snpsfile are extracted from a metadata.json file.
return jsonify(status=128,
# use better message
message="Metadata file non-existent!")
+
+
+@gemma.route("/k-compute/loco/<chromosomes>/<token>", methods=["POST"])
+def compute_k_loco(chromosomes, token):
+ """Similar to 'compute_k' with the extra option of using loco given chromosome
+values.
+
+ """
+ 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"]]
+ gemma_kwargs = {"g": genofile, "p": phenofile, "a": snpsfile}
+ _hash = get_hash_of_files([genofile, phenofile, snpsfile])
+ k_output_filename = f"{_hash}-k-output.json"
+ k_computation_cmd = generate_gemma_computation_cmd(
+ gemma_cmd=current_app.config.get("GEMMA_WRAPPER_CMD"),
+ gemma_wrapper_kwargs={"loco": f"--input {chromosomes}"},
+ gemma_kwargs=gemma_kwargs,
+ output_file=(f"{current_app.config.get('TMPDIR')}/"
+ f"{token}/{k_output_filename}"))
+ 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"{k_computation_cmd}"),
+ status="queued",
+ output_file=k_output_filename)
+ # pylint: disable=W0703
+ except Exception:
+ return jsonify(status=128,
+ # use better message
+ message="Metadata file non-existent!")