Merge branch 'main' of https://github.com/genenetwork/genenetwork3 into bug/fix_rqtl_covariates

1 files changed, 51 insertions, 0 deletions

diff --git a/gn3/computations/wgcna.py b/gn3/computations/wgcna.py
new file mode 100644
index 0000000..fd508fa
--- /dev/null
+++ b/gn3/computations/wgcna.py
@@ -0,0 +1,51 @@
+"""module contains code to preprocess and call wgcna script"""
+
+import os
+import json
+import uuid
+from gn3.settings import TMPDIR
+
+from gn3.commands import run_cmd
+
+
+def dump_wgcna_data(request_data: dict):
+    """function to dump request data to json file"""
+    filename = f"{str(uuid.uuid4())}.json"
+
+    temp_file_path = os.path.join(TMPDIR, filename)
+
+    with open(temp_file_path, "w") as output_file:
+        json.dump(request_data, output_file)
+
+    return temp_file_path
+
+
+def compose_wgcna_cmd(rscript_path: str, temp_file_path: str):
+    """function to componse wgcna cmd"""
+    # (todo):issue relative paths to abs paths
+    cmd = f"Rscript ./scripts/{rscript_path}  {temp_file_path}"
+    return cmd
+
+
+def call_wgcna_script(rscript_path: str, request_data: dict):
+    """function to call wgcna script"""
+    generated_file = dump_wgcna_data(request_data)
+    cmd = compose_wgcna_cmd(rscript_path, generated_file)
+
+    try:
+
+        run_cmd_results = run_cmd(cmd)
+
+        with open(generated_file, "r") as outputfile:
+
+            if run_cmd_results["code"] != 0:
+                return run_cmd_results
+            return {
+                "data": json.load(outputfile),
+                **run_cmd_results
+            }
+    except FileNotFoundError:
+        # relook  at handling errors gn3
+        return {
+            "output": "output file not found"
+        }