Minor changes

.github/workflows/bar-api.yml

@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-24.04
     strategy:
       matrix:
-        python-version: [3.9, 3.10.15, 3.11, 3.12, 3.13]
+        python-version: [3.10.16, 3.11, 3.12, 3.13]
 
     services:
       redis:

api/models/canola_nssnp.py

@@ -1,6 +1,5 @@
 from typing import Optional
 from api import db
-# from sqlalchemy.ext.declarative import declarative_base
 
 
 # CanolaBase = declarative_base()

api/models/homologs_db.py

@@ -3,7 +3,7 @@
 
 class homologs(db.Model):
     __bind_key__ = "homologs_db"
-    __tablename__ = 'homologs'
+    __tablename__ = "homologs"
 
     homologs_id: db.Mapped[int] = db.mapped_column(db.Integer(), primary_key=True, autoincrement=True)
     search_protein_name: db.Mapped[str] = db.mapped_column(db.String(45), nullable=False)

api/resources/snps.py

@@ -19,7 +19,7 @@
 )
 from api.models.canola_nssnp import (
     CanolaProteinReference as CanolaProteinReference,
-    CanolaSnpsToProtein as CanolaSnpsToProtein
+    CanolaSnpsToProtein as CanolaSnpsToProtein,
 )
 from api.models.homologs_db import homologs as HomologsDB
 from api.utils.bar_utils import BARUtils
@@ -557,13 +557,14 @@ def get(self, search_species="", search_gene="", target_species=""):
         gene_id = escape(search_gene)
         target_species = escape(target_species)
         supported = ["arabidopsis", "canola"]
+
         if (search_species not in supported) or (target_species not in supported):
             return BARUtils.error_exit("Species not supported"), 400
-        elif (search_species == "arabidopsis" and BARUtils.is_arabidopsis_gene_valid(gene_id)) or (search_species == "canola" and BARUtils.is_canola_gene_valid(gene_id)):
+        elif (search_species == "arabidopsis" and BARUtils.is_arabidopsis_gene_valid(gene_id)) or (
+            search_species == "canola" and BARUtils.is_canola_gene_valid(gene_id)
+        ):
             results = HomologsDB.query.filter_by(
-                search_protein_name=gene_id,
-                search_species_name=search_species,
-                result_species_name=target_species
+                search_protein_name=gene_id, search_species_name=search_species, result_species_name=target_species
             ).all()
             if not results:
                 return BARUtils.error_exit("No homologs found for the given query"), 400
@@ -575,7 +576,7 @@ def get(self, search_species="", search_gene="", target_species=""):
                     "result_species_name": target_species,
                     "result_protein_name": homolog.result_protein_name,
                     "Percent_id": float(homolog.Percent_id),
-                    "e_score": float(homolog.e_score)
+                    "e_score": float(homolog.e_score),
                 }
                 for homolog in results
             ]

api/utils/bar_utils.py

@@ -86,9 +86,9 @@ def is_cannabis_gene_valid(gene):
     @staticmethod
     def is_canola_gene_valid(gene):
         """This function verifies if canola gene (BnaC07g42830D) is valid
-                :param gene:
-                :return:
-                """
+        :param gene:
+        :return:
+        """
         if re.search(r"^Bna[AC]\d{2}g\d{5}[A-D]?$", gene, re.I):
             return True
         else:

config/BAR_API.cfg

@@ -15,6 +15,7 @@ SQLALCHEMY_BINDS = {
     'arachis': 'mysql://root:root@localhost/arachis',
     'brassica_rapa': 'mysql://root:root@localhost/brassica_rapa',
     'cannabis': 'mysql://root:root@localhost/cannabis',
+    'canola_nssnp' : 'mysql://root:root@localhost/canola_nssnp',
     'dna_damage': 'mysql://root:root@localhost/dna_damage',
     'embryo': 'mysql://root:root@localhost/embryo',
     'eplant2': 'mysql://root:root@localhost/eplant2',
@@ -24,6 +25,7 @@ SQLALCHEMY_BINDS = {
     'eplant_tomato' : 'mysql://root:root@localhost/eplant_tomato',
     'fastpheno' :  'mysql://root:root@localhost/fastpheno',
     'germination': 'mysql://root:root@localhost/germination',
+    'homologs_db' : 'mysql://root:root@localhost/homologs_db',
     'kalanchoe': 'mysql://root:root@localhost/kalanchoe',
     'klepikova': 'mysql://root:root@localhost/klepikova',
     'llama3': 'mysql://root:root@localhost/llama3',
@@ -40,8 +42,5 @@ SQLALCHEMY_BINDS = {
     'striga' : 'mysql://root:root@localhost/striga',
     'tomato_nssnp' : 'mysql://root:root@localhost/tomato_nssnp',
     'tomato_sequence' :  'mysql://root:root@localhost/tomato_sequence',
-    'triphysaria' :  'mysql://root:root@localhost/triphysaria',
-    'canola_nssnp' : 'mysql://root:root@localhost/canola_nssnp',
-    'homologs_db' : 'mysql://root:root@localhost/homologs_db'
-
+    'triphysaria' :  'mysql://root:root@localhost/triphysaria'
 }

config/init.sh

@@ -14,6 +14,7 @@ mysql -u $DB_USER -p$DB_PASS < ./config/databases/arabidopsis_ecotypes.sql
 mysql -u $DB_USER -p$DB_PASS < ./config/databases/arachis.sql
 mysql -u $DB_USER -p$DB_PASS < ./config/databases/brassica_rapa.sql
 mysql -u $DB_USER -p$DB_PASS < ./config/databases/cannabis.sql
+mysql -u $DB_USER -p$DB_PASS < ./config/databases/canola_nssnp.sql
 mysql -u $DB_USER -p$DB_PASS < ./config/databases/dna_damage.sql
 mysql -u $DB_USER -p$DB_PASS < ./config/databases/embryo.sql
 mysql -u $DB_USER -p$DB_PASS < ./config/databases/eplant2.sql
@@ -23,6 +24,7 @@ mysql -u $DB_USER -p$DB_PASS < ./config/databases/eplant_soybean.sql
 mysql -u $DB_USER -p$DB_PASS < ./config/databases/eplant_tomato.sql
 mysql -u $DB_USER -p$DB_PASS < ./config/databases/fastpheno.sql
 mysql -u $DB_USER -p$DB_PASS < ./config/databases/germination.sql
+mysql -u $DB_USER -p$DB_PASS < ./config/databases/homologs_db.sql
 mysql -u $DB_USER -p$DB_PASS < ./config/databases/kalanchoe.sql
 mysql -u $DB_USER -p$DB_PASS < ./config/databases/klepikova.sql
 mysql -u $DB_USER -p$DB_PASS < ./config/databases/llama3.sql
@@ -40,9 +42,6 @@ mysql -u $DB_USER -p$DB_PASS < ./config/databases/striga.sql
 mysql -u $DB_USER -p$DB_PASS < ./config/databases/tomato_nssnp.sql
 mysql -u $DB_USER -p$DB_PASS < ./config/databases/tomato_sequence.sql
 mysql -u $DB_USER -p$DB_PASS < ./config/databases/triphysaria.sql
-mysql -u $DB_USER -p$DB_PASS < ./config/databases/canola_nssnp.sql
-mysql -u $DB_USER -p$DB_PASS < ./config/databases/homologs_db.sql
-
 
 echo "Data are now loaded. Preparing API config"
 echo "Please manually edit config file!"

requirements.txt

@@ -1,31 +1,31 @@
 aniso8601==10.0.0
 async-timeout==5.0.1
-attrs==25.1.0
+attrs==25.3.0
 black==25.1.0
 blinker==1.9.0
 cachelib==0.9.0
 certifi==2025.1.31
 charset-normalizer==3.4.1
 click==8.1.8
-coverage==7.6.10
+coverage==7.7.1
 Deprecated==1.2.18
-flake8==7.1.1
+flake8==7.2.0
 Flask==3.1.0
-Flask-Caching==2.3.0
-Flask-Cors==5.0.0
-Flask-Limiter==3.10.1
+Flask-Caching==2.3.1
+flask-cors==5.0.1
+Flask-Limiter==3.12
 flask-marshmallow==1.3.0
 flask-restx==1.3.0
 Flask-SQLAlchemy==3.1.1
 greenlet==3.1.1
 idna==3.10
 importlib_resources==6.5.2
-iniconfig==2.0.0
+iniconfig==2.1.0
 itsdangerous==2.2.0
-Jinja2==3.1.5
+Jinja2==3.1.6
 jsonschema==4.23.0
 jsonschema-specifications==2024.10.1
-limits==4.0.1
+limits==4.4.1
 markdown-it-py==3.0.0
 MarkupSafe==3.0.2
 marshmallow==3.26.1
@@ -36,24 +36,24 @@ mysqlclient==2.2.7
 ordered-set==4.1.0
 packaging==24.2
 pathspec==0.12.1
-platformdirs==4.3.6
+platformdirs==4.3.7
 pluggy==1.5.0
-pycodestyle==2.12.1
-pyflakes==3.2.0
+pycodestyle==2.13.0
+pyflakes==3.3.0
 Pygments==2.19.1
 pyrsistent==0.20.0
-pytest==8.3.4
+pytest==8.3.5
 python-dateutil==2.9.0.post0
-pytz==2025.1
+pytz==2025.2
 redis==5.2.1
 referencing==0.36.2
 requests==2.32.3
 rich==13.9.4
-rpds-py==0.22.3
-setuptools==75.8.0
+rpds-py==0.24.0
+setuptools==78.1.0
 six==1.17.0
-SQLAlchemy==2.0.38
-typing_extensions==4.12.2
+SQLAlchemy==2.0.40
+typing_extensions==4.13.0
 urllib3==2.3.0
 Werkzeug==3.1.3
 wheel==0.45.1

tests/resources/test_snps.py

@@ -115,9 +115,9 @@ def test_get_snps(self):
                     "protein_coding",
                     "CODING",
                     "GSBRNA2T00000007001",
-                    0.0066
+                    0.0066,
                 ]
-            ]
+            ],
         }
         self.assertEqual(response.json, expected)