Merge pull request BioAnalyticResource#199 from asherpasha/dev

eFP Data Source.

Author: asherpasha

api/resources/efp_image.py

@@ -136,6 +136,36 @@ 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 = species.lower()
+        results = []
+
+        # This will only work on the BAR
+        if os.environ.get("BAR"):
+            if species == "sorghum":
+                efp_base_path = "/var/www/html/efp_sorghum/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.rstrip(".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")

requirements.txt

@@ -1,11 +1,11 @@
 aniso8601==9.0.1
 async-timeout==4.0.3
 attrs==23.1.0
-black==23.10.0
+black==23.10.1
 blinker==1.6.3
 cachelib==0.9.0
 certifi==2023.7.22
-charset-normalizer==3.3.0
+charset-normalizer==3.3.1
 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