1 files changed, 55 insertions, 0 deletions
diff --git a/gn3/api/rqtl2.py b/gn3/api/rqtl2.py
new file mode 100644
index 0000000..dc06d1d
--- /dev/null
+++ b/gn3/api/rqtl2.py
@@ -0,0 +1,55 @@
+""" File contains endpoints for rqlt2"""
+import shutil
+from pathlib import Path
+from flask import current_app
+from flask import jsonify
+from flask import Blueprint
+from flask import request
+from gn3.computations.rqtl2 import (compose_rqtl2_cmd,
+                                    prepare_files,
+                                    validate_required_keys,
+                                    write_input_file,
+                                    process_qtl2_results
+                                    )
+from gn3.computations.streaming import run_process
+from gn3.computations.streaming import enable_streaming
+
+rqtl2 = Blueprint("rqtl2", __name__)
+
+
+@rqtl2.route("/compute", methods=["POST"])
+@enable_streaming
+def compute(log_file):
+    """Endpoint for computing QTL analysis using R/QTL2"""
+    data = request.json
+    required_keys = ["crosstype", "geno_data","pheno_data", "geno_codes"]
+    valid, error = validate_required_keys(required_keys,data)
+    if not valid:
+        return jsonify(error=error), 400
+    # Provide atleast one  of this data entries.
+    if "physical_map_data" not in data and "geno_map_data" not in data:
+        return jsonify(error="You need to Provide\
+        Either the Physical map or Geno Map data of markers"), 400
+    run_id = request.args.get("id", "output")
+    # prepare necessary files and dir for computation
+    (workspace_dir, input_file,
+     output_file, _log2_file) = prepare_files(current_app.config.get("TMPDIR"))
+    # write the input file with data required for creating the cross
+    write_input_file(input_file, workspace_dir, data)
+    # TODO : Implement a better way for fetching the file Path.
+    rqtl_path =Path(__file__).absolute().parent.parent.parent.joinpath("scripts/rqtl2_wrapper.R")
+    if not rqtl_path.is_file():
+        return jsonify({"error" : f"The script {rqtl_path} does not exists"}), 400
+    rqtl2_cmd = compose_rqtl2_cmd(rqtl_path, input_file,
+                                  output_file, workspace_dir,
+                                  data, current_app.config)
+    process_output = run_process(rqtl2_cmd.split(),log_file, run_id)
+    if process_output["code"] != 0:
+        # Err out for any non-zero status code
+        return jsonify(process_output), 400
+    results = process_qtl2_results(output_file)
+    shutil.rmtree(workspace_dir, ignore_errors=True, onerror=None)
+    # append this at end of computation to the log file to mark end of gn3 computation
+    with open(log_file, "ab+") as file_handler:
+        file_handler.write("Done with GN3 Computation".encode("utf-8"))
+    return jsonify(results)