Merge pull request #215 from BioAnalyticResource/dev

Update main branch

Author: asherpasha

.github/workflows/bar-api.yml

@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-22.04
     strategy:
       matrix:
-        python-version: [3.8, 3.9, 3.10.13, 3.11, 3.12]
+        python-version: [3.8, 3.9, 3.10.14, 3.11, 3.12]
 
     services:
       redis:

.readthedocs.yaml

@@ -0,0 +1,31 @@
+# Read the Docs configuration file for Sphinx projects
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the OS, Python version and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.12"
+
+# Build documentation in the "docs/" directory with Sphinx
+sphinx:
+  configuration: docs/source/conf.py
+  # You can configure Sphinx to use a different builder, for instance use the dirhtml builder for simpler URLs
+  # builder: "dirhtml"
+  # Fail on all warnings to avoid broken references
+  # fail_on_warning: true
+
+# Optionally build your docs in additional formats such as PDF and ePub
+formats:
+  - pdf
+  - epub
+
+# Optional but recommended, declare the Python requirements required
+# to build your documentation
+# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
+python:
+  install:
+    - requirements: docs/requirements.txt

api/resources/fastpheno.py

@@ -3,6 +3,7 @@
 Author: Vince L
 Fastpheno endpoint for retrieving tree data
 """
+
 from flask_restx import Namespace, Resource
 from api import db
 from api.models.fastpheno import Sites, Trees, Band, Height

api/resources/sequence.py

@@ -4,6 +4,7 @@
 Sequence endpoint that returns the amino acid sequence of a given protein, with additional options
 for predicted sequences (Phyre2) that we host
 """
+
 from flask_restx import Namespace, Resource
 from api.utils.bar_utils import BARUtils
 from markupsafe import escape

api/resources/snps.py

@@ -26,6 +26,7 @@
 from api.utils.hotspot_utils import HotspotUtils
 import sys
 from api import db, cache, limiter
+from api.utils.docking_utils import Docker
 
 
 snps = Namespace("SNPs", description="Information about SNPs", path="/snps")
@@ -47,6 +48,35 @@
 )
 
 
+@snps.route("/docking/<receptor>/<ligand>")
+class Docking(Resource):
+    decorators = [limiter.limit("2/minute")]
+
+    @snps.param("receptor", _in="path", default="bri1")
+    @snps.param("ligand", _in="path", default="brass")
+    def get(self, receptor, ligand):
+        receptor = escape(receptor)
+        ligand = escape(ligand)
+        docking_pdb_path = "/DATA/HEX_API/RESULTS/"
+
+        if not BARUtils.is_arabidopsis_gene_valid(receptor):
+            return BARUtils.error_exit("Invalid arapbidopsis pdb gene id"), 400
+
+        matched = re.search("[a-z]", ligand)
+        if matched is None:
+            return BARUtils.error_exit("Invalid ligand name"), 400
+
+        # start function to initiate docking_utils file
+
+        final_json = Docker.start(receptor, ligand, docking_pdb_path)
+        if final_json == "Receptor file not found":
+            return BARUtils.error_exit("There are no data found for the given gene"), 400
+        elif final_json == "Ligand file not found":
+            return BARUtils.error_exit("There are no data found for the given ligand"), 400
+        else:
+            return BARUtils.success_exit(final_json)
+
+
 @snps.route("/phenix/<fixed_pdb>/<moving_pdb>")
 class Phenix(Resource):
     @snps.param("fixed_pdb", _in="path", default="Potri.016G107900.1")