Merge branch 'main' into feature/minor-fixes

2 files changed, 17 insertions, 3 deletions

diff --git a/gn3/api/gemma.py b/gn3/api/gemma.py
index 81e185d..6b0b20e 100644
--- a/gn3/api/gemma.py
+++ b/gn3/api/gemma.py
@@ -9,8 +9,8 @@ from flask import request
 
 from gn3.commands import queue_cmd
 from gn3.commands import run_cmd
-from gn3.file_utils import cache_ipfs_file
-from gn3.file_utils import jsonfile_to_dict
+from gn3.fs_helpers import cache_ipfs_file
+from gn3.fs_helpers import jsonfile_to_dict
 from gn3.computations.gemma import generate_gemma_cmd
 from gn3.computations.gemma import do_paths_exist
 
diff --git a/gn3/api/general.py b/gn3/api/general.py
index 38e6154..cebb2e3 100644
--- a/gn3/api/general.py
+++ b/gn3/api/general.py
@@ -5,7 +5,8 @@ from flask import current_app
 from flask import jsonify
 from flask import request
 
-from gn3.file_utils import extract_uploaded_file
+from gn3.fs_helpers import extract_uploaded_file
+from gn3.commands import run_cmd
 
 
 general = Blueprint("general", __name__)
@@ -50,3 +51,16 @@ TTL is set in the metadata file. If none is provided, the default is 1 week.
     if results.get("status") > 0:
         status = 500
     return jsonify(results), status
+
+
+@general.route("/qtl/run/<geno_filestr>/<pheno_filestr>",
+               methods=["POST"],
+               strict_slashes=False)
+def run_r_qtl(geno_filestr, pheno_filestr):
+    """Run r_qtl command using the written rqtl_wrapper program
+
+    """
+    rqtl_wrapper = current_app.config["RQTL_WRAPPER"]
+    cmd = (f"Rscript {rqtl_wrapper} "
+           f"{geno_filestr} {pheno_filestr}")
+    return jsonify(run_cmd(cmd)), 201