Merge pull request #168 from pbashyal-nmdp/add_validate_endpoint

mmaiers-nmdp · web-flow · commit a7efff83bb0a · 2022-06-01T09:24:26.000-05:00
Add `validate` endpoint
diff --git a/.dockerignore b/.dockerignore
@@ -0,0 +1,23 @@
+.github
+.git
+.direnv
+.idea
+.eggs/
+build
+dist
+*.egg
+*.egg-info
+tests
+venv
+
+__pycache__
+*.pyo
+*.pyd
+*.output
+.coverage
+.coverage.*
+.cache
+htmlcov/
+.pytest_cache
+allure_report
+CHANGELOG.md
diff --git a/CHANGELOG.md b/CHANGELOG.md
diff --git a/Dockerfile b/Dockerfile
@@ -0,0 +1,19 @@
+FROM python:3.10-slim-buster
+
+LABEL MAINTAINER="Pradeep Bashyal"
+
+WORKDIR /app
+
+COPY requirements.txt /app
+RUN pip install --no-cache-dir --upgrade pip && \
+    pip install --no-cache-dir -r requirements.txt
+
+COPY requirements-deploy.txt /app
+RUN pip install --no-cache-dir -r requirements-deploy.txt
+
+COPY app.py /app/
+COPY api.py /app/
+COPY api-spec.yaml /app/
+COPY pyard /app/pyard
+
+CMD ["gunicorn", "--bind", "0.0.0.0:8080", "--worker-tmp-dir", "/dev/shm",  "--timeout", "30", "app:app"]
diff --git a/Makefile b/Makefile
@@ -95,18 +95,18 @@ dist: clean ## builds source and wheel package
 	ls -l dist
 
 docker-build: ## build a docker image for the service
-	docker build -t my-project-template-service:0.0.1 .
+	docker build -t pyard-service:latest .
 
 docker: docker-build ## build a docker image and run the service
-	docker run --name my-project-template -p 8080:8080 my-project-template-service:0.0.1
+	docker run --name pyard-service -p 8080:8080 pyard-service:latest
 
 install: clean ## install the package to the active Python's site-packages
 	pip install --upgrade pip
-	python setup.py install
 	pip install -r requirements.txt
 	pip install -r requirements-tests.txt
 	pip install -r requirements-dev.txt
 	pip install -r requirements-deploy.txt
+	python setup.py install
 	pre-commit install
 
 venv: ## creates a Python3 virtualenv environment in venv
diff --git a/README.md b/README.md
@@ -119,6 +119,7 @@ ard.redux_gl('B14', 'lg')
 | `lgx`          | Reduce to 2 field ARD level                     |
 | `W`            | Reduce/Expand to 3 field WHO nomenclature level |
 | `exon`         | Reduce/Expand to exon level                     |
+| `U2`           | Reduce to 2 field unambiguous level             |
 
 # Command Line Tools
 
@@ -186,3 +187,19 @@ A*01:01/A*01:02/A*01:03/A*01:06/A*01:07/A*01:08/A*01:09/A*01:10/A*01:12/ ...
 ### Batch Reduce a CSV file
 
 `pyard-csv-reduce` can be used to batch process a CSV file with HLA typings. See [documentation](extras/README.md) for instructions on how to configure and run.
+
+## py-ard REST Service
+
+Run `py-ard` as a service so that it can be accessed as a REST service endpoint.
+
+Build the docker image:
+```shell
+make docker-build
+```
+
+Build the docker and run it with:
+```shell
+make docker
+```
+
+The endpoint should then be available at [localhost:8080](http://0.0.0.0:8080)
diff --git a/api-spec.yaml b/api-spec.yaml
@@ -0,0 +1,121 @@
+openapi: 3.0.3
+info:
+  title: ARD Reduction
+  description: Reduce to ARD Level
+  version: "0.8.0"
+servers:
+  - url: 'http://localhost:8080'
+tags:
+  - name: ARD Reduction
+    description: Reduce GL String to ARD
+paths:
+  /redux:
+    post:
+      tags:
+        - ARD Reduction
+      operationId: api.redux_controller
+      summary: Reduce to ARD
+      description: |
+        Given a GL String and a reduction method perform ARD Reduction
+      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"
+                reduction_method:
+                  description: Reduction Method
+                  type: string
+                  enum:
+                    - G
+                    - lg
+                    - lgx
+                    - W
+                    - exon
+                    - U2
+                  example: "lgx"
+      responses:
+        200:
+          description: Reduction Result
+          content:
+            application/json:
+              schema:
+                type: object
+                properties:
+                  ard:
+                    description: ARD reduced version of GL String
+                    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 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:
+                type: object
+                properties:
+                  message:
+                    description: Describes what went wrong
+                    type: string
+                    example: "Invalid HLA locus"
diff --git a/api.py b/api.py
@@ -0,0 +1,47 @@
+from flask import request
+
+from pyard import ARD
+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"}, 404
+        # Perform redux
+        try:
+            redux_gl_string = ard.redux_gl(gl_string, reduction_method)
+            return {"ard": redux_gl_string}, 200
+        except PyArdError as e:
+            return {"message": e.message}, 400
+
+    # if no data is sent
+    return {"message": "No input data provided"}, 404
diff --git a/app.py b/app.py
@@ -0,0 +1,17 @@
+#!/usr/bin/env python3
+import connexion
+
+from flask import redirect
+
+app = connexion.App(__name__)
+application = app.app
+api = app.add_api("api-spec.yaml")
+
+
+@app.route("/")
+def index():
+    return redirect(api.base_path + "/ui")
+
+
+if __name__ == "__main__":
+    app.run(port=8080, debug=True)
diff --git a/pyard/db.py b/pyard/db.py
@@ -57,10 +57,11 @@ def create_db_connection(data_dir, imgt_version, ro=False):
     if ro:
         # Open the database in read-only mode
         file_uri = f"file:{db_filename}?mode=ro"
-    else:
-        # Open the database in read-only mode
-        file_uri = f"file:{db_filename}"
+        # Multiple threads can access the same connection since it's only ro
+        return sqlite3.connect(file_uri, check_same_thread=False, uri=True)
 
+    # Open the database for read/write
+    file_uri = f"file:{db_filename}"
     return sqlite3.connect(file_uri, uri=True)
 
 
diff --git a/pyard/exceptions.py b/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}"
diff --git a/pyard/pyard.py b/pyard/pyard.py
@@ -276,8 +276,7 @@ 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.")
+        self.validate(glstring)
 
         if re.search(r"\^", glstring):
             return self.sorted_unique_gl(
@@ -359,6 +358,21 @@ def redux_gl(self, glstring: str, redux_type: VALID_REDUCTION_TYPES) -> str:
 
         return self.redux(glstring, redux_type)
 
+    def validate(self, glstring):
+        """
+        Validates GL String
+        Raise an exception if not valid.
+
+        :param glstring: GL String to validate
+        :return: boolean indicating success
+        """
+        try:
+            return self.isvalid_gl(glstring)
+        except InvalidAlleleError as e:
+            raise InvalidTypingError(
+                f"{glstring} is not valid GL String. \n {e.message}", e
+            )
+
     def is_XX(self, glstring: str, loc_antigen: str = None, code: str = None) -> bool:
         if loc_antigen is None or code is None:
             if ":" in glstring:
@@ -603,7 +617,10 @@ 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:
         """
diff --git a/requirements-tests.txt b/requirements-tests.txt
@@ -1,2 +1,3 @@
 behave==1.2.6
 PyHamcrest==2.0.2
+pytest==7.1.2
diff --git a/setup.cfg b/setup.cfg
@@ -11,6 +11,10 @@ replace = version="{new_version}"
 search = __version__ = "{current_version}"
 replace = __version__ = "{new_version}"
 
+[bumpversion:file:api-spec.yaml]
+search = version: "{current_version}"
+replace = version: "{new_version}"
+
 [bdist_wheel]
 universal = 1
 
