Merge pull request #202 from BioAnalyticResource/dev

Update Main branch

Author: asherpasha

api/resources/efp_image.py

@@ -136,6 +136,37 @@ def get(self, efp="", view="", mode="", gene_1="", gene_2=""):
         return send_from_directory(directory="../output/", path=path, mimetype="image/png")
 
 
+@efp_image.route("/get_efp_data_source/<species>")
+class eFPDataSource(Resource):
+    @efp_image.param("species", _in="path", default="sorghum")
+    def get(self, species=""):
+        """
+        Returns Data sources using eFP Directory
+        Supported species: Sorghum
+        """
+
+        species = escape(species)
+        species = species.lower()
+        results = []
+
+        # This will only work on the BAR
+        if os.environ.get("BAR"):
+            if species in ["arabidopsis", "arachis", "cannabis", "maize", "sorghum", "soybean"]:
+                efp_base_path = "/var/www/html/efp_" + species + "/data"
+            else:
+                return BARUtils.error_exit("Invalid species.")
+
+            data_files = os.listdir(efp_base_path)
+
+            for file in data_files:
+                if file.endswith(".xml") and file != "efp_info.xml":
+                    results.append(file.replace(".xml", ""))
+
+            return BARUtils.success_exit(results)
+        else:
+            return BARUtils.error_exit("Only available on the BAR.")
+
+
 @efp_image.route("/get_efp_dir/<species>")
 class eFPXMLSVGList(Resource):
     @efp_image.param("species", _in="path", default="arabidopsis")
@@ -145,6 +176,7 @@ def get(self, species=""):
         Supported species: Arabidopsis, Poplar
         """
 
+        species = escape(species)
         species = species.lower()
 
         if species == "arabidopsis":
@@ -159,6 +191,8 @@ def get(self, species=""):
             XML_name = "Populus_trichocarpa.xml"
             SVG_name = "Populus_trichocarpa.svg"
             base_url = "//bar.utoronto.ca/eplant_poplar/data/"
+        else:
+            return BARUtils.error_exit("Invalid species.")
 
         efp_folders = os.listdir(efp_base_path)
 

requirements.txt

@@ -1,11 +1,11 @@
 aniso8601==9.0.1
 async-timeout==4.0.3
 attrs==23.1.0
-black==23.10.0
-blinker==1.6.3
+black==23.10.1
+blinker==1.7.0
 cachelib==0.9.0
 certifi==2023.7.22
-charset-normalizer==3.3.0
+charset-normalizer==3.3.2
 click==8.1.7
 coverage==7.3.2
 Deprecated==1.2.14
@@ -17,13 +17,13 @@ Flask-Limiter==3.5.0
 flask-marshmallow==0.15.0
 flask-restx==1.1.0
 Flask-SQLAlchemy==3.1.1
-greenlet==3.0.0
+greenlet==3.0.1
 idna==3.4
 importlib-resources==6.1.0
 iniconfig==2.0.0
 itsdangerous==2.1.2
 Jinja2==3.1.2
-jsonschema==4.19.1
+jsonschema==4.19.2
 jsonschema-specifications==2023.7.1
 limits==3.6.0
 markdown-it-py==3.0.0
@@ -41,8 +41,8 @@ pluggy==1.3.0
 pycodestyle==2.11.1
 pyflakes==3.1.0
 Pygments==2.16.1
-pyrsistent==0.19.3
-pytest==7.4.2
+pyrsistent==0.20.0
+pytest==7.4.3
 python-dateutil==2.8.2
 pytz==2023.3.post1
 redis==5.0.1
@@ -51,7 +51,7 @@ requests==2.31.0
 rich==13.6.0
 rpds-py==0.10.6
 six==1.16.0
-SQLAlchemy==2.0.22
+SQLAlchemy==2.0.23
 typing_extensions==4.8.0
 urllib3==2.0.7
 Werkzeug==2.3.7

tests/resources/test_efp_image.py

@@ -24,6 +24,14 @@ def test_get_efp_image_list(self):
         }
         self.assertEqual(response.json, expected)
 
+    def test_get_efp_data_source(self):
+        """This function tests eFP data source error return
+        :return:
+        """
+        response = self.app_client.get("/efp_image/get_efp_data_source/soybean")
+        expected = {"wasSuccessful": False, "error": "Only available on the BAR."}
+        self.assertEqual(response.json, expected)
+
     def test_get_efp_image(self):
         """This function test eFP image endpoint get request
         :return: