POST gene annotations (eplant rice)

api/__init__.py

@@ -88,6 +88,7 @@ def create_app():
     annotations_lookup_db.init_app(bar_app)
     eplant2_db.init_app(bar_app)
     eplant_poplar_db.init_app(bar_app)
+    eplant_rice_db.init_app(bar_app)
     eplant_tomato_db.init_app(bar_app)
     poplar_nssnp_db.init_app(bar_app)
     tomato_nssnp_db.init_app(bar_app)
@@ -147,6 +148,7 @@ def create_app():
 annotations_lookup_db = SQLAlchemy(metadata=MetaData())
 eplant2_db = SQLAlchemy(metadata=MetaData())
 eplant_poplar_db = SQLAlchemy(metadata=MetaData())
+eplant_rice_db = SQLAlchemy(metadata=MetaData())
 eplant_tomato_db = SQLAlchemy(metadata=MetaData())
 poplar_nssnp_db = SQLAlchemy(metadata=MetaData())
 tomato_nssnp_db = SQLAlchemy(metadata=MetaData())

api/models/eplant_rice.py

@@ -0,0 +1,9 @@
+from api import eplant_rice_db as db
+
+
+class GeneAnnotation(db.Model):
+    __bind_key__ = "eplant_rice"
+    __tablename__ = "gene_annotation"
+
+    gene = db.Column(db.String(20), nullable=False, primary_key=True)
+    annotation = db.Column(db.String(64000), nullable=False, primary_key=False)

api/resources/gene_annotation.py

@@ -1,10 +1,13 @@
-from flask_restx import Namespace, Resource
+from flask_restx import Namespace, Resource, fields
+from flask import request
 from markupsafe import escape
 from sqlalchemy.exc import OperationalError
+from api.models.eplant_rice import GeneAnnotation as EplantRiceAnnotation
 from api.models.eplant_poplar import GeneAnnotation as EplantPoplarAnnotation
 from api.models.eplant_tomato import GeneAnnotation as EplantTomatoAnnotation
 from api.models.eplant2 import AgiAnnotation, TAIR10, GeneRIFs
 from api.utils.bar_utils import BARUtils
+from marshmallow import Schema, ValidationError, fields as marshmallow_fields
 
 
 gene_annotation = Namespace(
@@ -22,6 +25,7 @@ def get(self, query=""):
         annotation_db_list = {
             "tomato": EplantTomatoAnnotation,
             "poplar": EplantPoplarAnnotation,
+            "rice": EplantRiceAnnotation,
             "arabidopsis": [AgiAnnotation, TAIR10, GeneRIFs],
         }
 
@@ -105,3 +109,73 @@ def get(self, query=""):
         else:
             # return first 10 matches
             return {"status": "success", "query": query, "result": res[:10]}
+
+
+anntn_post_ex = gene_annotation.model(
+    "AntnRiceGenes",
+    {
+        "species": fields.String(required=True, example="rice"),
+        "genes": fields.List(
+            required=True,
+            example=["LOC_Os01g01010", "LOC_Os01g01050"],
+            cls_or_instance=fields.String,
+        ),
+    },
+)
+
+
+class GeneIntrnsSchema(Schema):
+    species = marshmallow_fields.String(required=True)
+    genes = marshmallow_fields.List(cls_or_instance=marshmallow_fields.String)
+
+
+@gene_annotation.route("/")
+class GeneAnnotationPost(Resource):
+    @gene_annotation.expect(anntn_post_ex)
+    def post(self, query=""):
+        """
+        Returns gene annotation(s) give a set of gene(s) for a species
+        Supported species: 'rice'
+        """
+
+        json_data = request.get_json()
+
+        try:
+            json_data = GeneIntrnsSchema().load(json_data)
+        except ValidationError as err:
+            return BARUtils.error_exit(err.messages), 400
+
+        species = json_data["species"].lower()
+        genes = json_data["genes"]
+
+        if species == "rice":
+            for gene in genes:
+                if not BARUtils.is_rice_gene_valid(gene):
+                    return BARUtils.error_exit("Invalid gene id"), 400
+
+            try:
+                rows = EplantRiceAnnotation.query.filter(
+                        EplantRiceAnnotation.gene.in_(genes)
+                ).all()
+                if len(rows) == 0:
+                    return (
+                        BARUtils.error_exit(
+                            "No data for the given species/genes"
+                        ),
+                        400,
+                    )
+                else:
+                    print(rows)
+                    res = [
+                        {
+                            "gene": i.gene,
+                            "annotation": i.annotation,
+                        }
+                        for i in rows
+                    ]
+                    return BARUtils.success_exit(res)
+            except OperationalError:
+                return BARUtils.error_exit("An internal error has occurred."), 500
+
+        else:
+            return BARUtils.error_exit("Invalid species"), 400

config/BAR_API.cfg

@@ -17,6 +17,7 @@ SQLALCHEMY_BINDS = {
     'poplar_nssnp' : 'mysql://root:root@localhost/poplar_nssnp',
     'tomato_nssnp' : 'mysql://root:root@localhost/tomato_nssnp',
     'eplant_poplar' : 'mysql://root:root@localhost/eplant_poplar',
+    'eplant_rice' : 'mysql://root:root@localhost/eplant_rice',
     'eplant_tomato' : 'mysql://root:root@localhost/eplant_tomato',
     'tomato_sequence' :  'mysql://root:root@localhost/tomato_sequence',
     'rice_interactions': 'mysql://root:root@localhost/rice_interactions'

config/databases/eplant_rice.sql

@@ -0,0 +1,60 @@
+-- MySQL dump 10.13  Distrib 8.0.23, for Linux (x86_64)
+--
+-- Host: localhost    Database: eplant_rice
+-- ------------------------------------------------------
+-- Server version	8.0.23-3
+
+/*!40101 SET @OLD_CHARACTER_SET_CLIENT=@@CHARACTER_SET_CLIENT */;
+/*!40101 SET @OLD_CHARACTER_SET_RESULTS=@@CHARACTER_SET_RESULTS */;
+/*!40101 SET @OLD_COLLATION_CONNECTION=@@COLLATION_CONNECTION */;
+/*!50503 SET NAMES utf8mb4 */;
+/*!40103 SET @OLD_TIME_ZONE=@@TIME_ZONE */;
+/*!40103 SET TIME_ZONE='+00:00' */;
+/*!40014 SET @OLD_UNIQUE_CHECKS=@@UNIQUE_CHECKS, UNIQUE_CHECKS=0 */;
+/*!40014 SET @OLD_FOREIGN_KEY_CHECKS=@@FOREIGN_KEY_CHECKS, FOREIGN_KEY_CHECKS=0 */;
+/*!40101 SET @OLD_SQL_MODE=@@SQL_MODE, SQL_MODE='NO_AUTO_VALUE_ON_ZERO' */;
+/*!40111 SET @OLD_SQL_NOTES=@@SQL_NOTES, SQL_NOTES=0 */;
+
+--
+-- Current Database: `eplant_rice`
+--
+
+CREATE DATABASE /*!32312 IF NOT EXISTS*/ `eplant_rice` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */;
+
+USE `eplant_rice`;
+
+--
+-- Table structure for table `gene_annotation`
+--
+
+DROP TABLE IF EXISTS `gene_annotation`;
+/*!40101 SET @saved_cs_client     = @@character_set_client */;
+/*!50503 SET character_set_client = utf8mb4 */;
+CREATE TABLE `gene_annotation` (
+  `gene` varchar(20) NOT NULL,
+  `annotation` mediumtext NOT NULL,
+  PRIMARY KEY (`gene`)
+) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+/*!40101 SET character_set_client = @saved_cs_client */;
+
+--
+-- Dumping data for table `gene_annotation`
+--
+-- WHERE:  1 limit 5
+
+LOCK TABLES `gene_annotation` WRITE;
+/*!40000 ALTER TABLE `gene_annotation` DISABLE KEYS */;
+INSERT INTO `gene_annotation` VALUES ('LOC_Os01g01010','protein TBC domain containing protein, expressed'),('LOC_Os01g01030','protein monocopper oxidase, putative, expressed'),('LOC_Os01g01050', 'protein R3H domain containing protein, expressed');
+/*!40000 ALTER TABLE `gene_annotation` ENABLE KEYS */;
+UNLOCK TABLES;
+/*!40103 SET TIME_ZONE=@OLD_TIME_ZONE */;
+
+/*!40101 SET SQL_MODE=@OLD_SQL_MODE */;
+/*!40014 SET FOREIGN_KEY_CHECKS=@OLD_FOREIGN_KEY_CHECKS */;
+/*!40014 SET UNIQUE_CHECKS=@OLD_UNIQUE_CHECKS */;
+/*!40101 SET CHARACTER_SET_CLIENT=@OLD_CHARACTER_SET_CLIENT */;
+/*!40101 SET CHARACTER_SET_RESULTS=@OLD_CHARACTER_SET_RESULTS */;
+/*!40101 SET COLLATION_CONNECTION=@OLD_COLLATION_CONNECTION */;
+/*!40111 SET SQL_NOTES=@OLD_SQL_NOTES */;
+
+-- Dump completed on 2021-06-26 19:08:20

config/init.sh

@@ -17,6 +17,7 @@ mysql -u $DB_USER -p$DB_PASS < ./config/databases/poplar_nssnp.sql
 mysql -u $DB_USER -p$DB_PASS < ./config/databases/tomato_nssnp.sql
 mysql -u $DB_USER -p$DB_PASS < ./config/databases/eplant_poplar.sql
 mysql -u $DB_USER -p$DB_PASS < ./config/databases/eplant_tomato.sql
+mysql -u $DB_USER -p$DB_PASS < ./config/databases/eplant_rice.sql
 mysql -u $DB_USER -p$DB_PASS < ./config/databases/tomato_sequence.sql
 mysql -u $DB_USER -p$DB_PASS < ./config/databases/rice_interactions.sql
 

tests/resources/test_gene_annotation.py

@@ -1,5 +1,6 @@
 from api import app
 from unittest import TestCase
+import json
 
 
 class TestIntegrations(TestCase):
@@ -36,3 +37,58 @@ def test_keyword_search(self):
             "error": "There are no data found for the given query",
         }
         self.assertEqual(response.json, expected)
+
+    def test_post_anntns(self):
+        """
+        This function test retrieving gene annotations for various species' genes via POST.
+        """
+
+        # Valid request
+        response = self.app_client.post(
+            "/gene_annotation/",
+            json={"species": "rice", "genes": ["LOC_Os01g01010", "LOC_Os01g01050"]},
+        )
+        data = json.loads(response.get_data(as_text=True))
+        expected = {
+            "wasSuccessful": True,
+            "data": [
+                {
+                    "gene": "LOC_Os01g01010",
+                    "annotation": "protein TBC domain containing protein, expressed"
+                },
+                {
+                    "gene": "LOC_Os01g01050",
+                    "annotation": "protein R3H domain containing protein, expressed"
+                }
+            ]
+        }
+        self.assertEqual(data, expected)
+
+        # Invalid species
+        response = self.app_client.post(
+            "/interactions/",
+            json={"species": "poplar", "genes": ["LOC_Os01g01080", "LOC_Os01g73310"]},
+        )
+        data = json.loads(response.get_data(as_text=True))
+        expected = {"wasSuccessful": False, "error": "Invalid species"}
+        self.assertEqual(data, expected)
+
+        # Invalid gene ID
+        response = self.app_client.post(
+            "/interactions/", json={"species": "rice", "genes": ["abc", "xyz"]}
+        )
+        data = json.loads(response.get_data(as_text=True))
+        expected = {"wasSuccessful": False, "error": "Invalid gene id"}
+        self.assertEqual(data, expected)
+
+        # No data for valid gene IDs
+        response = self.app_client.post(
+            "/interactions/",
+            json={"species": "rice", "genes": ["LOC_Os01g01085", "LOC_Os01g52565"]},
+        )
+        data = json.loads(response.get_data(as_text=True))
+        expected = {
+            "wasSuccessful": False,
+            "error": "No data for the given species/genes",
+        }
+        self.assertEqual(data, expected)