Added unit tests for eFP Image service.

.github/workflows/bar-api.yml

@@ -58,4 +58,4 @@ jobs:
     - name: "Upload coverage to Codecov"
       uses: codecov/codecov-action@v2
       with:
-        fail_ci_if_error: true
+        fail_ci_if_error: false

api/resources/api_manager.py

@@ -44,22 +44,22 @@ def send_email_notification():
                 for line in f:
                     recipient = line
             port = 465
-            key = os.environ.get('EMAIL_PASS_KEY')
+            key = os.environ.get("EMAIL_PASS_KEY")
             cipher_suite = Fernet(key)
-            with open(os.environ.get('EMAIL_PASS_FILE'), "rb") as f:
+            with open(os.environ.get("EMAIL_PASS_FILE"), "rb") as f:
                 for line in f:
                     encrypted_key = line
             uncipher_text = cipher_suite.decrypt(encrypted_key)
             password = bytes(uncipher_text).decode("utf-8")
             context = create_default_context()
-            smtp_server = 'smtp.gmail.com'
-            sender_email = 'bar.summarization@gmail.com'
+            smtp_server = "smtp.gmail.com"
+            sender_email = "bar.summarization@gmail.com"
             subject = "[Bio-Analytic Resource] New API key request"
             text = """\
                 There is a new API key request.
                 You can approve or reject it at http://bar.utoronto.ca/~bpereira/webservices/bar-request-manager/build/index.html
             """
-            m_text = MIMEText(text, _subtype='plain', _charset='UTF-8')
+            m_text = MIMEText(text, _subtype="plain", _charset="UTF-8")
             msg = MIMEMultipart()
             msg["From"] = sender_email
             msg["To"] = recipient

api/resources/efp_image.py

@@ -1,5 +1,8 @@
+import base64
 import re
 import requests
+import random
+import redis.connection
 from flask_restx import Namespace, Resource
 from markupsafe import escape
 from flask import send_from_directory
@@ -14,7 +17,9 @@
 class eFPImageList(Resource):
     def get(self):
         """This end point returns the list of species available"""
-        species = ["efp_arabidopsis"]  # This are the only species available so far
+        # This are the only species available so far
+        # If this is updated, update get request and test as well
+        species = ["efp_arabidopsis"]
         return BARUtils.success_exit(species)
 
 
@@ -46,7 +51,7 @@ def get(self, efp="", view="", mode="", gene_1="", gene_2=""):
         """This end point returns eFP images."""
         # list of allowed eFPs
         # See endpoint able
-        efp_list = ["efp_arabidopsis"]
+        species = ["efp_arabidopsis"]
 
         # Escape input data
         efp = escape(efp)
@@ -56,7 +61,7 @@ def get(self, efp="", view="", mode="", gene_1="", gene_2=""):
         gene_2 = escape(gene_2)
 
         # Validate values
-        if efp not in efp_list:
+        if efp not in species:
             return BARUtils.error_exit("Invalid eFP."), 400
 
         # Validate view
@@ -76,41 +81,72 @@ def get(self, efp="", view="", mode="", gene_1="", gene_2=""):
                 return BARUtils.error_exit("Gene 2 is invalid."), 400
 
         # Check if request is cached
+        try:
+            r = BARUtils.connect_redis()
+            key = "BAR_API_efp_image_" + "_".join([efp, view, mode, gene_1, gene_2])
+            efp_image_base64 = r.get(key)
+        except redis.connection.ConnectionError:
+            # Failed redis connection
+            r = None
+            key = None
+            efp_image_base64 = None
+
+        if efp_image_base64 is None:
+            # Request is not cached
+            # Run eFP. Note, this is currently running from home directory!
+            efp_url = (
+                "https://bar.utoronto.ca/~asher/python3/"
+                + efp
+                + "/cgi-bin/efpWeb.cgi?dataSource="
+                + view
+                + "&mode="
+                + mode
+                + "&primaryGene="
+                + gene_1
+                + "&secondaryGene="
+                + gene_2
+                + "&grey_low=None&grey_stddev=None"
+            )
+            efp_html = requests.get(efp_url)
+
+            # Now search for something like <img src=\"../output/efp-2nBNhe.png\"
+            # This is the eFP output image
+            match = re.search(r'"\.\./output/(efp-.{1,10}\.png)', efp_html.text)
+
+            # File is not found
+            if match is None:
+                return (
+                    BARUtils.error_exit(
+                        "Failed to retrieve image. Data for the given gene may not exist."
+                    ),
+                    500,
+                )
+
+            # Save this path for later use
+            path = match[1]
+            efp_file_link = (
+                "https://bar.utoronto.ca/~asher/python3/" + efp + "/output/" + path
+            )
+
+            # Download and serve that image
+            img_data = requests.get(efp_file_link).content
+            with open("output/" + path, "wb") as file:
+                file.write(img_data)
+
+            # Cache the request if redis is alive
+            if r:
+                efp_image_base64 = base64.b64encode(img_data)
+                r.set(key, efp_image_base64)
+                r.close()
 
-        # If request is not cached, run the search
-        # Run eFP. Note, this is currently running from home directory
-        efp_url = (
-            "https://bar.utoronto.ca/~asher/python3/"
-            + efp
-            + "/cgi-bin/efpWeb.cgi?dataSource="
-            + view
-            + "&mode="
-            + mode
-            + "&primaryGene="
-            + gene_1
-            + "&secondaryGene="
-            + gene_2
-            + "&grey_low=None&grey_stddev=None"
-        )
-        efp_html = requests.get(efp_url)
-
-        # Now search for something like <img src=\"../output/efp-2nBNhe.png\"
-        # This is the eFP output image
-        match = re.search(r'"\.\./output/(efp-.{1,10}\.png)', efp_html.text)
-
-        # File is not found
-        if match is None:
-            return BARUtils.error_exit("Failed to retrieve image. Data for the given gene may not exist."), 500
-
-        efp_file_link = (
-            "https://bar.utoronto.ca/~asher/python3/" + efp + "/output/" + match[1]
-        )
-
-        # Download and serve that image
-        img_data = requests.get(efp_file_link).content
-        with open("output/" + match[1], "wb") as file:
-            file.write(img_data)
+        else:
+            # Request is cached
+            img_data = base64.b64decode(efp_image_base64)
+            path = key + str(random.randrange(0, 1000000)) + ".png"
+            with open("output/" + path, "wb") as file:
+                file.write(img_data)
+            r.close()
 
         return send_from_directory(
-            directory="../output/", path=match[1], mimetype="image/png"
+            directory="../output/", path=path, mimetype="image/png"
         )

api/utils/bar_utils.py

@@ -1,4 +1,6 @@
 import re
+import redis
+import os
 
 
 class BARUtils:
@@ -95,7 +97,18 @@ def is_efp_view_name(efp_view):
         :param efp_view: string view name
         :return: True if valid
         """
-        if efp_view and re.search(r"[a-z1-9_]{1,20}", efp_view, re.I):
+        if efp_view and re.search(r"^[a-z1-9_]{1,20}$", efp_view, re.I):
             return True
         else:
             return False
+
+    @staticmethod
+    def connect_redis():
+        """This function connects to redis
+        :returns: redis connection
+        """
+        r = redis.Redis(
+            host="localhost", port=6379, password=os.environ.get("BAR_REDIS_PASSWORD")
+        )
+
+        return r

docs/requirements.txt

@@ -3,7 +3,7 @@ Babel==2.9.1
 beautifulsoup4==4.10.0
 certifi==2021.10.8
 charset-normalizer==2.0.9
-docutils==0.17.1
+docutils==0.18.1
 furo==2021.11.23
 idna==3.3
 imagesize==1.3.0

requirements.txt

@@ -51,7 +51,7 @@ regex==2021.11.10
 requests==2.26.0
 scour==0.38.2
 six==1.16.0
-SQLAlchemy==1.4.27
+SQLAlchemy==1.4.28
 toml==0.10.2
 typed-ast==1.5.1
 typing_extensions==4.0.1

tests/resources/test_efp_image.py

@@ -13,3 +13,81 @@ def test_get_efp_image_list(self):
         response = self.app_client.get("/efp_image/")
         expected = {"wasSuccessful": True, "data": ["efp_arabidopsis"]}
         self.assertEqual(response.json, expected)
+
+    def test_get_efp_image(self):
+        """This function test eFP image endpoint get request
+        :return:
+        """
+        # Test absolute modes in the beginning
+        # A very basic test for Arabidopsis requests
+        # https://bar.utoronto.ca/api/efp_image/efp_arabidopsis/Developmental_Map/Absolute/At1g01010
+        response = self.app_client.get(
+            "/efp_image/efp_arabidopsis/Developmental_Map/Absolute/At1g01010"
+        )
+        self.assertEqual(response.status_code, 200)
+        self.assertEqual(response.content_type, "image/png")
+
+        # Now rerun for Cached requests. A image should be return from the cache
+        response = self.app_client.get(
+            "/efp_image/efp_arabidopsis/Developmental_Map/Absolute/At1g01010"
+        )
+        self.assertEqual(response.status_code, 200)
+        self.assertEqual(response.content_type, "image/png")
+
+        # Test for invalid species:
+        response = self.app_client.get(
+            "/efp_image/abc/Developmental_Map/Absolute/At1g01010"
+        )
+        expected = {"wasSuccessful": False, "error": "Invalid eFP."}
+        self.assertEqual(response.json, expected)
+
+        # Test for eFP view name
+        response = self.app_client.get(
+            "/efp_image/efp_arabidopsis/ab.!c/Absolute/At1g01010"
+        )
+        expected = {"wasSuccessful": False, "error": "Invalid eFP View name."}
+        self.assertEqual(response.json, expected)
+
+        # Test for eFP mode
+        response = self.app_client.get("/efp_image/efp_arabidopsis/Root/abc/At1g01010")
+        expected = {"wasSuccessful": False, "error": "Invalid eFP mode."}
+        self.assertEqual(response.json, expected)
+
+        # Test for gene 1 using Arabidopsis
+        response = self.app_client.get(
+            "/efp_image/efp_arabidopsis/Root/Absolute/At1g0101X"
+        )
+        expected = {"wasSuccessful": False, "error": "Gene 1 is invalid."}
+        self.assertEqual(response.json, expected)
+
+        response = self.app_client.get(
+            "/efp_image/efp_arabidopsis/Developmental_Map/Absolute/At1g01011"
+        )
+        expected = {
+            "wasSuccessful": False,
+            "error": "Failed to retrieve image. Data for the given gene may not exist.",
+        }
+        self.assertEqual(response.json, expected)
+
+        # Test for gene 2 using Arabidopsis
+        response = self.app_client.get(
+            "/efp_image/efp_arabidopsis/Root/Compare/At1g01010/Abc"
+        )
+        expected = {"wasSuccessful": False, "error": "Gene 2 is invalid."}
+        self.assertEqual(response.json, expected)
+
+        # Test compare modes in the end
+        # A very basic test for Arabidopsis requests
+        # https://bar.utoronto.ca/api/efp_image/efp_arabidopsis/Developmental_Map/Compare/At1g01010/At1g01030
+        response = self.app_client.get(
+            "/efp_image/efp_arabidopsis/Developmental_Map/Compare/At1g01010/At1g01030"
+        )
+        self.assertEqual(response.status_code, 200)
+        self.assertEqual(response.content_type, "image/png")
+
+        # Rerun for cached request. An image should be returned
+        response = self.app_client.get(
+            "/efp_image/efp_arabidopsis/Developmental_Map/Compare/At1g01010/At1g01030"
+        )
+        self.assertEqual(response.status_code, 200)
+        self.assertEqual(response.content_type, "image/png")

tests/utils/test_bar_utils.py

@@ -28,6 +28,11 @@ def test_is_arabidopsis_gene_valid(self):
         result = BARUtils.is_arabidopsis_gene_valid("At1g01010.11")
         self.assertFalse(result)
 
+    def test_is_tomato_gene_valid(self):
+        # For some reason, coverage is saying that we need this test
+        result = BARUtils.is_tomato_gene_valid("Solyc04g014530")
+        self.assertTrue(result)
+
     def test_is_integer(self):
         # Valid result
         result = BARUtils.is_integer("5")