Update py-ard REST Service

 - add `validate` endpoint to validate a GL String

Author: pbashyal-nmdp

api-spec.yaml

@@ -50,7 +50,66 @@ paths:
                     type: string
                     example: "A*01:01+A*01:01^B*07:02+B*08:01^C*02:02/C*02:10+C*07:01/C*07:150Q^DPB1*28:01+DPB1*28:01"
         400:
-          description: Invalid GL String
+          description: Invalid GL String Form
+          content:
+            application/json:
+              schema:
+                type: object
+                properties:
+                  message:
+                    description: Describes what went wrong
+                    type: string
+                    example: "Invalid HLA locus"
+  /validate:
+    post:
+      tags:
+        - ARD Reduction
+      operationId: api.validate_controller
+      summary: Validate GL String
+      description: |
+        Given a GL String report whether it is valid or not
+      requestBody:
+        content:
+          application/json:
+            schema:
+              properties:
+                gl_string:
+                  description: GL String
+                  type: string
+                  example: "A*01:01+A*01:01^B*08:ASXJP+B*07:02^C*02:02+C*07:HTGM^DPB1*28:01:01G+DPB1*296:01"
+      responses:
+        200:
+          description: Validation Result
+          content:
+            application/json:
+              schema:
+                type: object
+                properties:
+                  valid:
+                    description: Is GL String valid
+                    type: boolean
+                    example: true
+        404:
+          description: GL String didn't validate
+          content:
+            application/json:
+              schema:
+                type: object
+                properties:
+                  valid:
+                    description: Is GL String valid
+                    type: boolean
+                    example: false
+                  message:
+                    description: Describes what went wrong
+                    type: string
+                    example: "Provided GL String is invalid: HLA-A*01:BLAH"
+                  cause:
+                    description: Explanation of why the GL String is not valid
+                    type: string
+                    example: "HLA-A*01:BLAH is not a valid GL Allele"
+        400:
+          description: Invalid GL String Form
           content:
             application/json:
               schema:

api.py

@@ -1,20 +1,41 @@
 from flask import request
 
 from pyard import ARD
-from pyard.exceptions import PyArdError
+from pyard.exceptions import PyArdError, InvalidAlleleError
 
 # Globally accessible for all endpoints
 ard = ARD()
 
 
+def validate_controller():
+    if request.json:
+        # Check the request has required inputs
+        try:
+            gl_string = request.json["gl_string"]
+        except KeyError:
+            return {"message": "gl_string not provided"}, 404
+        # Validate
+        try:
+            ard.isvalid_gl(gl_string)
+            return {"valid": True}, 200
+        except InvalidAlleleError as e:
+            return {
+                "valid": False,
+                "message": f"Provided GL String is invalid: {gl_string}",
+                "cause": e.message,
+            }, 404
+        except PyArdError as e:
+            return {"message": e.message}, 400
+
+
 def redux_controller():
     if request.json:
         # Check the request has required inputs
         try:
             gl_string = request.json["gl_string"]
             reduction_method = request.json["reduction_method"]
         except KeyError:
-            return {"message": "gl_string and reduction_method not provided"}, 400
+            return {"message": "gl_string and reduction_method not provided"}, 404
         # Perform redux
         try:
             redux_gl_string = ard.redux_gl(gl_string, reduction_method)

pyard/exceptions.py

@@ -23,8 +23,9 @@ def __str__(self) -> str:
 
 
 class InvalidTypingError(PyArdError):
-    def __init__(self, message: str) -> None:
+    def __init__(self, message: str, cause=None) -> None:
         self.message = message
+        self.cause = cause
 
     def __str__(self) -> str:
         return f"Invalid HLA Typing: {self.message}"

pyard/pyard.py

@@ -276,8 +276,12 @@ def redux_gl(self, glstring: str, redux_type: VALID_REDUCTION_TYPES) -> str:
 
         validate_reduction_type(redux_type)
 
-        if not self.isvalid_gl(glstring):
-            raise InvalidTypingError(f"{glstring} is not a valid typing.")
+        try:
+            self.isvalid_gl(glstring)
+        except InvalidAlleleError as e:
+            raise InvalidTypingError(
+                f"{glstring} is not valid GL String. \n {e.message}", e
+            )
 
         if re.search(r"\^", glstring):
             return self.sorted_unique_gl(
@@ -603,7 +607,10 @@ def isvalid_gl(self, glstring: str) -> bool:
             return all(map(self.isvalid_gl, glstring.split("/")))
 
         # what falls through here is an allele
-        return self.isvalid(glstring)
+        is_valid_allele = self.isvalid(glstring)
+        if not is_valid_allele:
+            raise InvalidAlleleError(f"{glstring} is not a valid Allele")
+        return is_valid_allele
 
     def mac_toG(self, allele: str) -> str:
         """