Merge pull request #38 from genenetwork/feature/wgcna_analysis

script for wgcna analysis

4 files changed, 80 insertions, 0 deletions

diff --git a/gn3/api/wgcna.py b/gn3/api/wgcna.py
new file mode 100644
index 0000000..fa044cf
--- /dev/null
+++ b/gn3/api/wgcna.py
@@ -0,0 +1,25 @@
+"""endpoint to run wgcna analysis"""
+from flask import Blueprint
+from flask import request
+from flask import current_app
+from flask import jsonify
+
+from gn3.computations.wgcna import call_wgcna_script
+
+wgcna = Blueprint("wgcna", __name__)
+
+
+@wgcna.route("/run_wgcna", methods=["POST"])
+def run_wgcna():
+    """run wgcna:output should be a json with a the data"""
+
+    wgcna_data = request.json
+
+    wgcna_script = current_app.config["WGCNA_RSCRIPT"]
+
+    results = call_wgcna_script(wgcna_script, wgcna_data)
+
+    if results.get("data") is None:
+        return jsonify(results), 401
+
+    return jsonify(results), 200
diff --git a/gn3/app.py b/gn3/app.py
index 5e852e1..a25332c 100644
--- a/gn3/app.py
+++ b/gn3/app.py
@@ -13,6 +13,7 @@ from gn3.api.general import general
 from gn3.api.heatmaps import heatmaps
 from gn3.api.correlation import correlation
 from gn3.api.data_entry import data_entry
+from gn3.api.wgcna import wgcna
 
 def create_app(config: Union[Dict, str, None] = None) -> Flask:
     """Create a new flask object"""
@@ -42,4 +43,5 @@ def create_app(config: Union[Dict, str, None] = None) -> Flask:
     app.register_blueprint(heatmaps, url_prefix="/api/heatmaps")
     app.register_blueprint(correlation, url_prefix="/api/correlation")
     app.register_blueprint(data_entry, url_prefix="/api/dataentry")
+    app.register_blueprint(wgcna, url_prefix="/api/wgcna")
     return app
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"
+        }
diff --git a/gn3/settings.py b/gn3/settings.py
index 9d7bba3..150d96d 100644
--- a/gn3/settings.py
+++ b/gn3/settings.py
@@ -25,6 +25,8 @@ GN2_BASE_URL = "http://www.genenetwork.org/"
 # biweight script
 BIWEIGHT_RSCRIPT = "~/genenetwork3/scripts/calculate_biweight.R"
 
+# wgcna script
+WGCNA_RSCRIPT = "wgcna_analysis.R"
 # qtlreaper command
 REAPER_COMMAND = "{}/bin/qtlreaper".format(os.environ.get("GUIX_ENVIRONMENT"))