diff options
Diffstat (limited to 'gn3/api/rqtl.py')
| -rw-r--r-- | gn3/api/rqtl.py | 19 |
1 files changed, 3 insertions, 16 deletions
diff --git a/gn3/api/rqtl.py b/gn3/api/rqtl.py index 9fd7017..7b29cef 100644 --- a/gn3/api/rqtl.py +++ b/gn3/api/rqtl.py @@ -15,14 +15,15 @@ from gn3.computations.rqtl import ( process_rqtl_pairscan, process_perm_output, ) -from gn3.computations.streaming import run_process +from gn3.computations.streaming import run_process, enable_streaming from gn3.fs_helpers import assert_path_exists, get_tmpdir rqtl = Blueprint("rqtl", __name__) @rqtl.route("/compute", methods=["POST"]) -def compute(): +@enable_streaming +def compute(stream_ouput_file): """Given at least a geno_file and pheno_file, generate and run the rqtl_wrapper script and return the results as JSON @@ -31,17 +32,6 @@ def compute(): phenofile = request.form["pheno_file"] assert_path_exists(genofile) assert_path_exists(phenofile) - - run_id = request.args.get("id") - with open( - os.path.join(current_app.config.get("TMPDIR"), f"{run_id}.txt"), - "w+", - encoding="utf-8", - ): - # TODO thos should be refactored - pass - # Split kwargs by those with values and boolean ones - # that just convert to True/False kwargs = ["covarstruct", "model", "method", "nperm", "scale", "control"] boolean_kwargs = ["addcovar", "interval", "pstrata", "pairscan"] all_kwargs = kwargs + boolean_kwargs @@ -75,7 +65,6 @@ def compute(): ) rqtl_output = {} - # get the stdout file run_id = request.args.get("id", str(uuid.uuid4())) if not os.path.isfile( os.path.join( @@ -83,8 +72,6 @@ def compute(): ) ): pass - stream_ouput_file = os.path.join(current_app.config.get("TMPDIR"), f"{run_id}.txt") - run_process(rqtl_cmd.get("rqtl_cmd").split(), stream_ouput_file, run_id) if "pairscan" in rqtl_bool_kwargs: |