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

2 files changed, 61 insertions, 0 deletions

diff --git a/gn3/api/heatmaps.py b/gn3/api/heatmaps.py
new file mode 100644
index 0000000..62ca2ad
--- /dev/null
+++ b/gn3/api/heatmaps.py
@@ -0,0 +1,36 @@
+"""
+Module to hold the entrypoint functions that generate heatmaps
+"""
+
+import io
+from flask import jsonify
+from flask import request
+from flask import Blueprint
+from gn3.heatmaps import build_heatmap
+from gn3.db_utils import database_connector
+
+heatmaps = Blueprint("heatmaps", __name__)
+
+@heatmaps.route("/clustered", methods=("POST",))
+def clustered_heatmaps():
+    """
+    Parses the incoming data and responds with the JSON-serialized plotly figure
+    representing the clustered heatmap.
+    """
+    traits_names = request.get_json().get("traits_names", tuple())
+    if len(traits_names) < 2:
+        return jsonify({
+            "message": "You need to provide at least two trait names."
+        }), 400
+    conn, _cursor = database_connector()
+    def parse_trait_fullname(trait):
+        name_parts = trait.split(":")
+        return "{dataset_name}::{trait_name}".format(
+            dataset_name=name_parts[1], trait_name=name_parts[0])
+    traits_fullnames = [parse_trait_fullname(trait) for trait in traits_names]
+
+    with io.StringIO() as io_str:
+        _filename, figure = build_heatmap(traits_fullnames, conn)
+        figure.write_json(io_str)
+        fig_json = io_str.getvalue()
+    return fig_json, 200
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