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authorBonfaceKilz2021-02-17 17:47:27 +0300
committerBonfaceKilz2021-02-24 14:20:29 +0300
commitbe43fb87bd9ce6b6a37b3e12d7c553e4531ea322 (patch)
treebd57d164cf8fade32391a5acf920188823020644 /gn3/api/gemma.py
parentea7cacc0104c5a0493d3f9bd80a37bd57a5539ce (diff)
downloadgenenetwork3-be43fb87bd9ce6b6a37b3e12d7c553e4531ea322.tar.gz
Add endpoint for running GEMMA
Diffstat (limited to 'gn3/api/gemma.py')
-rw-r--r--gn3/api/gemma.py62
1 files changed, 59 insertions, 3 deletions
diff --git a/gn3/api/gemma.py b/gn3/api/gemma.py
index 1a7232d..95e71e2 100644
--- a/gn3/api/gemma.py
+++ b/gn3/api/gemma.py
@@ -1,9 +1,16 @@
"""Endpoints for running the gemma cmd"""
+import os
+import redis
+
from flask import Blueprint
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
gemma = Blueprint("gemma", __name__)
@@ -16,8 +23,57 @@ def get_version():
run_cmd(f"{gemma_cmd} -v | head -n 1"))
+# This is basically extracted from genenetwork2
+# wqflask/wqflask/marker_regression/gemma_ampping.py
+@gemma.route("/run", methods=["POST"])
+def run_gemma():
+ """Generates a command for generating K-Values and then later, generate a GWA
+command that contains markers. These commands are queued; and the expected
+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)
+ 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"),
+ 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"):
+ 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"),
+ 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")