eFP Image end point

api/resources/api_manager.py

@@ -40,14 +40,14 @@ def check_admin_pass(password):
     @staticmethod
     def validate_captcha(value):
         """Validates a reCaptcha value using our secret token"""
-        if(os.environ.get("BAR")):
+        if os.environ.get("BAR"):
             with open(CAPTCHA_KEY_FILE, "rb") as f:
                 for line in f:
                     key = line
             if key:
                 ret = requests.post(
                     "https://www.google.com/recaptcha/api/siteverify",
-                    data={"secret": key, "response": value}
+                    data={"secret": key, "response": value},
                 )
                 return ret.json()["success"]
             else:
@@ -128,7 +128,7 @@ class ApiManagerRequest(Resource):
     def post(self):
         if request.method == "POST":
             captchaVal = request.headers.get("captchaVal")
-            if(ApiManagerUtils.validate_captcha(captchaVal)):
+            if ApiManagerUtils.validate_captcha(captchaVal):
                 response_json = request.get_json()
                 df = pandas.DataFrame.from_records([response_json])
                 con = db.get_engine(bind="summarization")

api/resources/efp_image.py

@@ -2,11 +2,14 @@
 import re
 import requests
 import random
-import redis.connection
+import os
+import time
+import redis.exceptions
 from flask_restx import Namespace, Resource
 from markupsafe import escape
 from flask import send_from_directory
 from api.utils.bar_utils import BARUtils
+from api.utils.efp_utils import eFPUtils
 
 efp_image = Namespace(
     "eFP Image", description="eFP Image generation service", path="/efp_image"
@@ -18,8 +21,14 @@ class eFPImageList(Resource):
     def get(self):
         """This end point returns the list of species available"""
         # This are the only species available so far
-        # If this is updated, update get request and test as well
-        species = ["efp_arabidopsis"]
+        # If this is updated, update efp_utils.py and unit tests as well
+        species = [
+            "efp_arabidopsis",
+            "efp_cannabis",
+            "efp_arachis",
+            "efp_soybean",
+            "efp_maize",
+        ]
         return BARUtils.success_exit(species)
 
 
@@ -29,63 +38,43 @@ def get(self):
     doc=False,
 )
 class eFPImage(Resource):
-    @staticmethod
-    def is_efp_mode(efp_mode):
-        """This function checks if the eFP mode is valid
-        :param efp_mode: string eFP Mode
-        :return: True or False
-        """
-        # This are case sensitive
-        valid_modes = ["Absolute", "Relative", "Compare"]
-        if efp_mode in valid_modes:
-            return True
-        else:
-            return False
-
     @efp_image.param("efp", _in="path", default="efp_arabidopsis")
     @efp_image.param("view", _in="path", default="Developmental_Map")
     @efp_image.param("mode", _in="path", default="Absolute")
     @efp_image.param("gene_1", _in="path", default="At1g01010")
     @efp_image.param("gene_2", _in="path", default="At3g27340")
     def get(self, efp="", view="", mode="", gene_1="", gene_2=""):
         """This end point returns eFP images."""
-        # list of allowed eFPs
-        # See endpoint able
-        species = ["efp_arabidopsis"]
-
         # Escape input data
         efp = escape(efp)
         view = escape(view)
         mode = escape(mode)
         gene_1 = escape(gene_1)
         gene_2 = escape(gene_2)
 
-        # Validate values
-        if efp not in species:
-            return BARUtils.error_exit("Invalid eFP."), 400
-
-        # Validate view
-        if not BARUtils.is_efp_view_name(view):
-            return BARUtils.error_exit("Invalid eFP View name."), 400
-
-        # Validate mode
-        if not self.is_efp_mode(mode):
-            return BARUtils.error_exit("Invalid eFP mode."), 400
+        validation = eFPUtils.is_efp_input_valid(efp, view, mode, gene_1, gene_2)
+        if validation[0] is False:
+            return BARUtils.error_exit(validation[1]), 400
 
-        # Validate gene ids
-        if not BARUtils.is_arabidopsis_gene_valid(gene_1):
-            return BARUtils.error_exit("Gene 1 is invalid."), 400
+        # Data are valid. Clear directory before running
+        for file in os.listdir("output"):
+            # Full file name is required at this point
+            file = os.path.join("output", file)
 
-        if mode == "Compare":
-            if not BARUtils.is_arabidopsis_gene_valid(gene_2):
-                return BARUtils.error_exit("Gene 2 is invalid."), 400
+            # Check if it is a png file and is greater than 5 minutes old
+            if (
+                os.path.isfile(file)
+                and (os.path.splitext(file)[1] == ".png")
+                and (os.stat(file).st_mtime < (time.time() - 5 * 60))
+            ):
+                os.remove(file)
 
         # 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:
+        except redis.exceptions.ConnectionError:
             # Failed redis connection
             r = None
             key = None

api/utils/bar_utils.py

@@ -72,6 +72,58 @@ def is_tomato_gene_valid(gene, isoform_id=False):
         else:
             return False
 
+    @staticmethod
+    def is_cannabis_gene_valid(gene):
+        """This function verifies if cannabis gene is valid: AGQN03000001
+        :param gene:
+        :return: True if valid
+        """
+        if gene and re.search(r"^AGQN\d{0,10}$", gene, re.I):
+            return True
+        else:
+            return False
+
+    @staticmethod
+    def is_arachis_gene_valid(gene):
+        """This function verifies if arachis gene is valid: Adur10000_comp0_c0_seq1
+        :param gene:
+        :return: True if valid
+        """
+        if gene and re.search(
+            r"Adur\d{1,10}_comp\d{1,3}_\D{1,3}\d{1,3}_seq\d{1,5}", gene, re.I
+        ):
+            return True
+        else:
+            return False
+
+    @staticmethod
+    def is_soybean_gene_valid(gene):
+        """This function verifies if soybean gene is valid: Glyma06g47400
+        :param gene:
+        :return: True if valid
+        """
+        if gene and re.search(
+            r"^((Glyma\d{1,3}g\d{1,6}\.?\d?)|(Glyma\.\d{1,3}g\d{1,8}))$", gene, re.I
+        ):
+            return True
+        else:
+            return False
+
+    @staticmethod
+    def is_maize_gene_valid(gene):
+        """This function verifies if maize gene is valid: Zm00001d046170
+        :param gene:
+        :return: True if valid
+        """
+        if gene and re.search(
+            r"^(AC[0-9]{6}\.[0-9]{1}_FG[0-9]{3})|(AC[0-9]{6}\.[0-9]{1}_FGT[0-9]{3})|(GRMZM(2|5)G[0-9]{6})|(GRMZM(2|5)G[0-9]{6}_T[0-9]{2})|(Zm\d+d\d+)$",
+            gene,
+            re.I,
+        ):
+            return True
+        else:
+            return False
+
     @staticmethod
     def is_integer(data):
         """Check if the input is at max ten figure number.
@@ -91,17 +143,6 @@ def format_poplar(poplar_gene):
         """
         return poplar_gene.translate(str.maketrans("pOTRIg", "PotriG"))
 
-    @staticmethod
-    def is_efp_view_name(efp_view):
-        """This function is used for validated eFP View names for eFP service
-        :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):
-            return True
-        else:
-            return False
-
     @staticmethod
     def connect_redis():
         """This function connects to redis

api/utils/efp_utils.py

@@ -0,0 +1,106 @@
+import re
+from api.utils.bar_utils import BARUtils
+
+
+class eFPUtils:
+    @staticmethod
+    def is_efp_view_name(efp_view):
+        """This function is used for validated eFP View names for eFP service
+        :param efp_view: string view name
+        :return: True if valid
+        """
+        if efp_view and re.search(r"^[a-z1-9_]{1,50}$", efp_view, re.I):
+            return True
+        else:
+            return False
+
+    @staticmethod
+    def is_efp_mode(efp_mode):
+        """This function checks if the eFP mode is valid
+        :param efp_mode: string eFP Mode
+        :return: True or False
+        """
+        # These are case-sensitive
+        valid_modes = ["Absolute", "Relative", "Compare"]
+        if efp_mode in valid_modes:
+            return True
+        else:
+            return False
+
+    @staticmethod
+    def is_efp_input_valid(efp, view, mode, gene_1, gene_2=None):
+        """Test if eFP input is valid
+        :return: List with boolean and string
+        """
+        species = [
+            "efp_arabidopsis",
+            "efp_cannabis",
+            "efp_arachis",
+            "efp_soybean",
+            "efp_maize",
+        ]
+
+        # Validate values
+        if efp not in species:
+            return False, "Invalid eFP."
+
+        # Validate view
+        if not eFPUtils.is_efp_view_name(view):
+            return False, "Invalid eFP View name."
+
+        # Validate mode
+        if not eFPUtils.is_efp_mode(mode):
+            return False, "Invalid eFP mode."
+
+        # Maybe this part could be improved
+        if efp == "efp_arabidopsis":
+            # Validate gene ids
+            if not BARUtils.is_arabidopsis_gene_valid(gene_1):
+                return False, "Gene 1 is invalid."
+
+            if mode == "Compare":
+                if not BARUtils.is_arabidopsis_gene_valid(gene_2):
+                    return False, "Gene 2 is invalid."
+
+        if efp == "efp_cannabis":
+            # Validate gene ids
+            if not BARUtils.is_cannabis_gene_valid(gene_1):
+                return False, "Gene 1 is invalid."
+
+            if mode == "Compare":
+                if not BARUtils.is_cannabis_gene_valid(gene_2):
+                    return False, "Gene 2 is invalid."
+
+        if efp == "efp_arachis":
+            # Validate gene ids
+            if not BARUtils.is_arachis_gene_valid(gene_1):
+                return False, "Gene 1 is invalid."
+
+            if mode == "Compare":
+                if not BARUtils.is_arachis_gene_valid(gene_2):
+                    return False, "Gene 2 is invalid."
+
+        if efp == "efp_soybean":
+            # Validate gene ids
+            if not BARUtils.is_soybean_gene_valid(gene_1):
+                return False, "Gene 1 is invalid."
+
+            if mode == "Compare":
+                if not BARUtils.is_soybean_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):
+                return False, "Gene 1 is invalid."
+
+            if mode == "Compare":
+                if not BARUtils.is_maize_gene_valid(gene_2):
+                    return False, "Gene 2 is invalid."
+
+        # In compare mode gene1 != gene2
+        if mode == "Compare" and gene_1 == gene_2:
+            return False, "In compare mode, both genes should be different."
+
+        # Assuming all check have passed
+        return True, None

requirements.txt

@@ -1,21 +1,21 @@
 aniso8601==9.0.1
 appdirs==1.4.4
-attrs==21.2.0
+attrs==21.4.0
 black==20.8b1
 certifi==2021.10.8
 cffi==1.15.0
 chardet==4.0.0
 charset-normalizer==2.0.9
 click==8.0.3
 coverage==6.2
-cryptography==36.0.0
+cryptography==36.0.1
 Deprecated==1.2.13
 docopt==0.6.2
 flake8==4.0.1
 Flask==2.0.2
 Flask-Caching==1.10.1
 Flask-Cors==3.0.10
-Flask-Limiter==2.0.2
+Flask-Limiter==2.0.4
 flask-marshmallow==0.14.0
 flask-restx==0.5.1
 Flask-SQLAlchemy==2.5.1
@@ -24,17 +24,17 @@ idna==3.3
 iniconfig==1.1.1
 itsdangerous==2.0.1
 Jinja2==3.0.3
-jsonschema==4.2.1
-limits==2.0.3
+jsonschema==4.3.2
+limits==2.1.0
 MarkupSafe==2.0.1
 marshmallow==3.14.1
 mccabe==0.6.1
 more-itertools==8.12.0
 mypy-extensions==0.4.3
 mysqlclient==2.1.0
-numpy==1.21.4
+numpy==1.21.5
 packaging==21.3
-pandas==1.3.4
+pandas==1.3.5
 pathspec==0.9.0
 pluggy==1.0.0
 py==1.11.0
@@ -46,12 +46,12 @@ pyrsistent==0.18.0
 pytest==6.2.5
 python-dateutil==2.8.2
 pytz==2021.3
-redis==4.0.2
+redis==4.1.0
 regex==2021.11.10
 requests==2.26.0
 scour==0.38.2
 six==1.16.0
-SQLAlchemy==1.4.28
+SQLAlchemy==1.4.29
 toml==0.10.2
 typed-ast==1.5.1
 typing_extensions==4.0.1