Merge pull request #221 from CSCfi/dependabot/pip/aiohttp-3.8.1

Bump aiohttp from 3.7.4.post0 to 3.8.1

Author: blankdots

.github/workflows/s2i-build.yml

@@ -18,9 +18,9 @@ jobs:
 
     - name: Install requirements
       run: |
-        wget https://github.com/openshift/source-to-image/releases/download/v1.2.0/source-to-image-v1.2.0-2a579ecd-linux-amd64.tar.gz
-        tar -xvf source-to-image-v1.2.0-2a579ecd-linux-amd64.tar.gz
+        wget https://github.com/openshift/source-to-image/releases/download/v1.3.1/source-to-image-v1.3.1-a5a77147-linux-amd64.tar.gz
+        tar -xvf source-to-image-v1.3.1-a5a77147-linux-amd64.tar.gz
         sudo cp s2i /usr/local/bin
     - name: Build image
       run:  |
-        s2i build . centos/python-36-centos7 cscfi/beacon-python
+        s2i build . centos/python-38-centos7 cscfi/beacon-python

Dockerfile

@@ -1,22 +1,24 @@
-FROM python:3.8-alpine3.13 as BUILD
+FROM python:3.8-alpine3.15 as BUILD
 
 RUN apk add --update \
     && apk add --no-cache build-base curl-dev linux-headers bash git musl-dev\
-    && apk add --no-cache libressl-dev libffi-dev autoconf bzip2-dev xz-dev\
+    && apk add --no-cache openssl-dev libffi-dev autoconf bzip2-dev xz-dev\
     && apk add --no-cache python3-dev rust cargo \
     && rm -rf /var/cache/apk/*
 
 COPY requirements.txt /root/beacon/requirements.txt
-COPY setup.py /root/beacon/setup.py
-COPY beacon_api /root/beacon/beacon_api
 
 ENV CYTHONIZE=1
 
 RUN pip install --upgrade pip && \
-    pip install -r /root/beacon/requirements.txt && \
-    pip install /root/beacon
+    pip install Cython==0.29.26 && \
+    pip install -r /root/beacon/requirements.txt
+
+COPY setup.py /root/beacon/setup.py
+COPY beacon_api /root/beacon/beacon_api
+RUN pip install /root/beacon
 
-FROM python:3.8-alpine3.13
+FROM python:3.8-alpine3.15
 
 RUN apk add --no-cache --update bash
 

README.md

@@ -10,8 +10,8 @@ Documentation: https://beacon-python.readthedocs.io
 ### Quick start
 
 `beacon-python` Web Server requires:
-* Python 3.6+;
-* running DB [PostgreSQL Server](https://www.postgresql.org/) 9.6+ (recommended 11.6).
+* Python 3.8+;
+* running DB [PostgreSQL Server](https://www.postgresql.org/) 9.6+ (recommended 13).
 
 ```shell
 git clone https://github.com/CSCfi/beacon-python
@@ -30,7 +30,7 @@ docker run -e POSTGRES_USER=beacon \
            -e POSTGRES_PASSWORD=beacon \
            -v "$PWD/data":/docker-entrypoint-initdb.d \
            -e POSTGRES_DB=beacondb \
-           -p 5432:5432 postgres:11.6
+           -p 5432:5432 postgres:13
 ```
 
 #### Run beacon-python

beacon_api/api/exceptions.py

@@ -35,7 +35,17 @@ def process_exception_data(request: Dict, host: str, error_code: int, error: str
     # include datasetIds only if they are specified
     # as per specification if they don't exist all datatsets will be queried
     # Only one of `alternateBases` or `variantType` is required, validated by schema
-    oneof_fields = ["alternateBases", "variantType", "start", "end", "startMin", "startMax", "endMin", "endMax", "datasetIds"]
+    oneof_fields = [
+        "alternateBases",
+        "variantType",
+        "start",
+        "end",
+        "startMin",
+        "startMax",
+        "endMin",
+        "endMax",
+        "datasetIds",
+    ]
     data["alleleRequest"].update({k: request.get(k) for k in oneof_fields if k in request})
 
     return data
@@ -65,11 +75,7 @@ class BeaconUnauthorised(web.HTTPUnauthorized):
     def __init__(self, request: Dict, host: str, error: str, error_message: str) -> None:
         """Return custom unauthorized exception."""
         data = process_exception_data(request, host, 401, error)
-        headers_401 = {
-            "WWW-Authenticate": f'Bearer realm="{CONFIG_INFO.url}"\n\
-                         error="{error}"\n\
-                         error_description="{error_message}"'
-        }
+        headers_401 = {"WWW-Authenticate": f"""Bearer realm=\"{CONFIG_INFO.url}\",error=\"{error},\" error_description=\"{error_message}\""""}
         super().__init__(
             content_type="application/json",
             text=ujson.dumps(data, escape_forward_slashes=False),

beacon_api/app.py

@@ -125,11 +125,17 @@ def main():
     # sslcontext.load_cert_chain(ssl_certfile, ssl_keyfile)
     # sslcontext = ssl.create_default_context(ssl.Purpose.CLIENT_AUTH)
     # sslcontext.check_hostname = False
-    web.run_app(init(), host=os.environ.get("HOST", "0.0.0.0"), port=os.environ.get("PORT", "5050"), shutdown_timeout=0, ssl_context=None)  # nosec  # nosec
+    web.run_app(
+        init(),
+        host=os.environ.get("HOST", "0.0.0.0"),  # nosec
+        port=os.environ.get("PORT", "5050"),
+        shutdown_timeout=0,
+        ssl_context=None,
+    )
 
 
 if __name__ == "__main__":
-    if sys.version_info < (3, 6):
-        LOG.error("beacon-python requires python 3.6")
+    if sys.version_info < (3, 8):
+        LOG.error("beacon-python requires python 3.8")
         sys.exit(1)
     main()

deploy/docker-compose.yml

@@ -3,7 +3,7 @@ version: '3.2'
 services:
   postgres:
     hostname: postgres
-    image: postgres:11.6
+    image: postgres:13
     environment:
       POSTGRES_USER: beacon
       POSTGRES_DB: beacondb
@@ -20,7 +20,7 @@ services:
     environment:
       DATABASE_URL: postgres
     links:
-    - postgres:postgres
+      - postgres:postgres
     ports:
       - 5050:5050
     restart: on-failure

deploy/test/docker-compose.yml

@@ -3,7 +3,7 @@ version: '3.2'
 services:
   postgres:
     hostname: postgres
-    image: postgres:11.6
+    image: postgres:13
     environment:
       POSTGRES_USER: beacon
       POSTGRES_DB: beacondb
@@ -42,4 +42,4 @@ services:
       - 8000:8000
     volumes:
       - ./mock_auth.py:/mock_auth.py
-    entrypoint: ["python", "/mock_auth.py", "0.0.0.0", "8000"]
+    entrypoint: [ "python", "/mock_auth.py", "0.0.0.0", "8000" ]

docs/db.rst

@@ -3,7 +3,7 @@
 Database
 ========
 
-We use a PostgreSQL database (recommended version 11.6) for working with beacon data.
+We use a PostgreSQL database (recommended version 13) for working with beacon data.
 For more information on setting up the database consult :ref:`database-setup`.
 
 .. attention:: We recommend https://pgtune.leopard.in.ua/ for establishing PostgreSQL

docs/instructions.rst

@@ -3,8 +3,8 @@ Instructions
 
 .. note:: In order to run ``beacon-python`` Web Server requirements are as specified below:
 
-  * Python 3.6+;
-  * running DB `PostgreSQL Server <https://www.postgresql.org/>`_  9.6+ (recommended 11.6).
+  * Python 3.8+;
+  * running DB `PostgreSQL Server <https://www.postgresql.org/>`_  9.6+ (recommended 13).
 
 .. _env-setup:
 
@@ -165,7 +165,7 @@ Starting PostgreSQL using Docker:
                -e POSTGRES_PASSWORD=beacon \
                -e POSTGRES_DB=beacondb \
                -v "$PWD/data":/docker-entrypoint-initdb.d \
-               -p 5432:5432 postgres:11.6
+               -p 5432:5432 postgres:13
 
 .. hint:: If one has their own database the ``beacon_init`` utility can be skipped,
           and make use of their own database by:

requirements.txt

@@ -1,16 +1,11 @@
-aiohttp==3.7.4.post0
+aiohttp==3.8.1
 aiohttp-cors==0.7.0
 asyncpg==0.25.0
-jsonschema==3.2.0; python_version < '3.7'
-jsonschema==4.3.2; python_version >= '3.7'
+jsonschema==4.3.2
 Cython==0.29.26
-cyvcf2==0.10.1; python_version < '3.7'
-cyvcf2; python_version >= '3.7'
-uvloop==0.14.0; python_version < '3.7'
-uvloop==0.16.0; python_version >= '3.7'
+cyvcf2==0.30.14
+uvloop==0.16.0
 aiocache==0.11.1
-ujson==4.3.0; python_version < '3.7'
-ujson==5.1.0; python_version >= '3.7'
-aiomcache==0.6.0
+ujson==5.1.0
 Authlib==0.15.5
 gunicorn==20.1.0

setup.py

@@ -33,31 +33,25 @@
         "Topic :: Internet :: WWW/HTTP :: HTTP Servers",
         "Topic :: Scientific/Engineering :: Bio-Informatics",
         "License :: OSI Approved :: Apache Software License",
-        "Programming Language :: Python :: 3.6",
         "Programming Language :: Python :: 3.7",
+        "Programming Language :: Python :: 3.8",
     ],
     install_requires=[
         "asyncpg==0.25.0",
-        "aiohttp==3.7.4.post0",
+        "aiohttp==3.8.1",
         "Authlib==0.15.5",
         "aiohttp-cors==0.7.0",
-        "jsonschema==3.2.0; python_version < '3.7'",
-        "jsonschema==4.3.2; python_version >= '3.7'",
+        "jsonschema==4.3.2",
         "gunicorn==20.1.0",
-        "uvloop==0.14.0; python_version < '3.7'",
-        "uvloop==0.16.0; python_version >= '3.7'",
-        "cyvcf2==0.10.1; python_version < '3.7'",
-        "cyvcf2; python_version >= '3.7'",
+        "uvloop==0.16.0",
+        "cyvcf2==0.30.14",
         "aiocache==0.11.1",
-        "aiomcache==0.6.0",
-        "ujson==4.3.0; python_version < '3.7'",
-        "ujson==5.1.0; python_version >= '3.7'",
+        "ujson==5.1.0",
     ],
     extras_require={
         "vcf": [
-            "cyvcf2==0.10.1; python_version < '3.7'",
             "numpy==1.21.5",
-            "cyvcf2; python_version >= '3.7'",
+            "cyvcf2==0.30.14",
             "Cython==0.29.26",
         ],
         "test": [
@@ -68,7 +62,6 @@
             "tox==3.24.4",
             "flake8==4.0.1",
             "flake8-docstrings==1.6.0",
-            "asynctest==0.13.0",
             "aioresponses==0.7.2",
             "black==21.12b0",
         ],