Merge pull request #277 from BioAnalyticResource/dev

Added eFP Grape

Author: asherpasha

api/resources/efp_image.py

@@ -24,6 +24,7 @@ def get(self):
             "efp_arabidopsis",
             "efp_arachis",
             "efp_cannabis",
+            "efp_grape",
             "efp_maize",
             "efp_rice",
             "efp_sorghum",

api/utils/bar_utils.py

@@ -33,6 +33,17 @@ def is_arabidopsis_gene_valid(gene):
         else:
             return False
 
+    @staticmethod
+    def is_grape_gene_valid(gene):
+        """This function verifies if grape gene is valid: VIT_00s0120g00060
+        :param gene:
+        :return:
+        """
+        if re.search(r"^VIT_\d{0,3}\D\d{0,5}g\d{0,6}$", gene, re.I):
+            return True
+        else:
+            return False
+
     @staticmethod
     def is_poplar_gene_valid(gene):
         """This function verifies if Poplar v3 gene is valid

api/utils/efp_utils.py

@@ -36,6 +36,7 @@ def is_efp_input_valid(efp, view, mode, gene_1, gene_2=None):
             "efp_arabidopsis",
             "efp_arachis",
             "efp_cannabis",
+            "efp_grape",
             "efp_maize",
             "efp_rice",
             "efp_sorghum",
@@ -82,6 +83,15 @@ def is_efp_input_valid(efp, view, mode, gene_1, gene_2=None):
                 if not BARUtils.is_cannabis_gene_valid(gene_2):
                     return False, "Gene 2 is invalid."
 
+        if efp == "efp_grape":
+            # Validate gene Ids
+            if not BARUtils.is_grape_gene_valid(gene_1):
+                return False, "Gene 1 is invalid."
+
+            if mode == "Compare":
+                if not BARUtils.is_grape_gene_valid(gene_2):
+                    return False, "Gene 2 is invalid."
+
         if efp == "efp_maize":
             # Validate gene ids
             if not BARUtils.is_maize_gene_valid(gene_1):

requirements.txt

@@ -4,10 +4,10 @@ attrs==25.3.0
 black==25.1.0
 blinker==1.9.0
 cachelib==0.13.0
-certifi==2025.7.14
+certifi==2025.8.3
 charset-normalizer==3.4.2
 click==8.2.1
-coverage==7.10.0
+coverage==7.10.2
 Deprecated==1.2.18
 flake8==7.3.0
 Flask==3.1.1
@@ -17,15 +17,15 @@ Flask-Limiter==3.12
 flask-marshmallow==1.3.0
 flask-restx==1.3.0
 Flask-SQLAlchemy==3.1.1
-greenlet==3.2.3
+greenlet==3.2.4
 idna==3.10
 importlib_resources==6.5.2
 iniconfig==2.1.0
 itsdangerous==2.2.0
 Jinja2==3.1.6
 jsonschema==4.25.0
 jsonschema-specifications==2025.4.1
-limits==5.4.0
+limits==5.5.0
 markdown-it-py==3.0.0
 MarkupSafe==3.0.2
 marshmallow==4.0.0
@@ -45,14 +45,14 @@ pyrsistent==0.20.0
 pytest==8.4.1
 python-dateutil==2.9.0.post0
 pytz==2025.2
-redis==6.2.0
+redis==6.4.0
 referencing==0.36.2
 requests==2.32.4
 rich==13.9.4
-rpds-py==0.26.0
+rpds-py==0.27.0
 setuptools==80.9.0
 six==1.17.0
-SQLAlchemy==2.0.41
+SQLAlchemy==2.0.42
 typing_extensions==4.14.1
 urllib3==2.5.0
 Werkzeug==3.1.3

tests/resources/test_efp_image.py

@@ -17,6 +17,7 @@ def test_get_efp_image_list(self):
                 "efp_arabidopsis",
                 "efp_arachis",
                 "efp_cannabis",
+                "efp_grape",
                 "efp_maize",
                 "efp_rice",
                 "efp_sorghum",

tests/utils/test_bar_utils.py

@@ -37,6 +37,14 @@ def test_is_brassica_rapa_gene_valid(self):
         result = BARUtils.is_brassica_rapa_gene_valid("abc")
         self.assertFalse(result)
 
+    def test_is_grape_gene_valid(self):
+        result = BARUtils.is_grape_gene_valid("VIT_00s0120g00060")
+        self.assertTrue(result)
+
+        # Invalid gene
+        result = BARUtils.is_grape_gene_valid("abc")
+        self.assertFalse(result)
+
     def test_is_kalanchoe_gene_valid(self):
         # Valid gene
         result = BARUtils.is_kalanchoe_gene_valid("Kaladp0001s0001")

tests/utils/test_efp_utils.py

@@ -130,6 +130,16 @@ def test_is_efp_input_valid(self):
         self.assertFalse(result[0])
         self.assertEqual(result[1], expected)
 
+        # eFP Grape Absolute
+        result = eFPUtils.is_efp_input_valid("efp_grape", "grape_developmental", "Absolute", "VIT_00s0120g00060")
+        self.assertTrue(result[0])
+        self.assertIsNone(result[1])
+
+        result = eFPUtils.is_efp_input_valid("efp_grape", "grape_developmental", "Absolute", "Abc")
+        expected = "Gene 1 is invalid."
+        self.assertFalse(result[0])
+        self.assertEqual(result[1], expected)
+
         # eFP Sorghum Absolute
         result = eFPUtils.is_efp_input_valid("efp_sorghum", "Stress_Atlas", "Absolute", "Sobic.001G000100")
         self.assertTrue(result[0])