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authorBonfaceKilz2021-03-03 11:51:29 +0300
committerBonfaceKilz2021-03-08 21:09:58 +0300
commit87a3e2254bdd837e9647c42b9c4ab98e986c5e1d (patch)
tree4f4622d2b3b679b48f22fb31c112edba0d2c637e /gn3/api
parent3b2b49ba367cf33adc294809feeb917b10f340a0 (diff)
downloadgenenetwork3-87a3e2254bdd837e9647c42b9c4ab98e986c5e1d.tar.gz
Add new endpoint: "/gemma/k-compute/<token>"
* gn3/api/gemma.py (compute_k): New function. * tests/integration/test_gemma.py (tesk_k_compute): New test case.
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 a351ab1..ec5f3f0 100644
--- a/gn3/api/gemma.py
+++ b/gn3/api/gemma.py
@@ -9,6 +9,8 @@ from flask import request
from gn3.commands import queue_cmd
from gn3.commands import run_cmd
+from gn3.file_utils import get_hash_of_files
+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
@@ -92,3 +94,42 @@ gemma endpoints, return the status of the command
return jsonify(status=128,
error="The unique id you used does not exist!"), 500
return jsonify(status=status.decode("utf-8"))
+
+
+@gemma.route("/k-compute/<token>", methods=["POST"])
+def compute_k(token):
+ """Given a genofile, traitfile, snpsfile, and the token, compute the k-valuen
+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.
+
+ """
+ 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=None,
+ 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!")