diff options
Diffstat (limited to 'gn3')
| -rw-r--r-- | gn3/api/gemma.py | 62 |
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") |