Merge pull request #238 from CSCfi/dev

release 1.9.0

Author: blankdots

.github/workflows/docs.yml

@@ -12,10 +12,9 @@ jobs:
     runs-on: ${{ matrix.os }}
 
     steps:
-    - name: Spell check install
-      run: curl -L https://git.io/misspell | bash
-    - name: Spell check docs
-      run: bin/misspell -error docs/*
+    - uses: actions/checkout@master
+    - uses: rojopolis/spellcheck-github-actions@0.20.0
+      name: Spellcheck
 
   code_docs:
     strategy:

.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

.github/workflows/style.yml

@@ -26,9 +26,11 @@ jobs:
       run: tox -e flake8
     - name: Do bandit static check with tox
       run: tox -e bandit
+    - name: Black formatting check
+      run: tox -e black
     - name: Install libcurl-devel
       run: |
         sudo apt-get update
         sudo apt-get install libcurl4-openssl-dev
-    - name: Do typing check with tox
+    - name: Type hints check
       run: tox -e mypy

.spellcheck.yml

@@ -0,0 +1,27 @@
+matrix:
+- name: Markdown
+  aspell:
+    lang: en
+  dictionary:
+    wordlists:
+    - .wordlist.txt
+    encoding: utf-8
+  pipeline:
+  - pyspelling.filters.markdown:
+  - pyspelling.filters.context:
+      context_visible_first: true
+      escapes: '\\[\\`~]'
+      delimiters:
+      # Ignore text between inline back ticks as this is code or hightlight words
+      - open: '(?P<open>`+)'
+        close: '(?P=open)'
+      # Ignore surrounded in <> as in RST it is link
+      - open: '<([A-Za-z0-9-_:.]+)|(https?://[^\\s/$.?#].[^\\s]+|[A-Za-z0-9-_:.]+)'
+        close: '>'
+      # Ignore code in RST starting with $
+      - open: '\$.+'
+        close: ''
+  sources:
+  - 'docs/*.rst'
+  - '**/*.md'
+  default_encoding: utf-8

.wordlist.txt

@@ -0,0 +1,144 @@
+AAI
+accessType
+aiohttp
+alleleCount
+alleleRequest
+alternateBases
+alternativeUrl
+api
+APIBehavior
+APITest
+apiVersion
+assemblyId
+automodule
+autosummary
+beacondb
+beaconId
+beaconpy
+BND
+BONA
+btree
+callCount
+cd
+chr
+CHR
+claimName
+conf
+config
+contactUrl
+containerPort
+createdAt
+createDateTime
+csc
+CSC
+cscfi
+CSCfi
+datafile
+datafiles
+dataloader
+dataset
+DATASET
+datasetAlleleResponses
+datasetHandover
+datasetId
+datasetIds
+datasets
+dedent
+documentationUrl
+ebi
+ega
+EGA
+endMax
+endMin
+env
+ENV
+Espoo
+examplebrowser
+exampleid
+externalUrl
+fi
+FIDE
+finland
+ga
+genomic
+gh
+GH
+GHBeacon
+github
+GRCh
+Gunicorn
+GunicornUVLoopWebWorker
+handoverType
+hg
+hostPath
+html
+http
+HttpLocust
+https
+ICT
+ietf
+imagePullPolicy
+includeDatasetResponses
+ini
+init
+io
+javascript
+jpg
+json
+JSON
+JWK
+jwt
+JWT
+Keilaranta
+literalinclude
+localhost
+logoUrl
+matchLabels
+mateID
+mateName
+mateStart
+mountPath
+namespace
+NodePort
+OAuth
+orgInfo
+persistentVolumeClaim
+pgtune
+postgres
+POSTGRES
+py
+readthedocs
+referenceBases
+referenceID
+referenceName
+restartPolicy
+rfc
+RGB
+sampleAlleleRequests
+sampleCount
+schemas
+secretKeyRef
+SNP
+sql
+startMax
+startMin
+targetPort
+TaskSet
+TCP
+toctree
+txt
+ua
+uk
+updatedAt
+updateDateTime
+uri
+url
+utils
+valueFrom
+variantCount
+varianttype
+variantType
+vcf
+volumeMounts
+welcomeUrl
+www

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/__init__.py

@@ -24,7 +24,7 @@
 __url__ = CONFIG_INFO.url
 __alturl__ = CONFIG_INFO.alturl
 __createtime__ = CONFIG_INFO.createtime
-__updatetime__ = datetime.datetime.now().strftime('%Y-%m-%dT%H:%M:%SZ')  # Every restart of the application means an update to it
+__updatetime__ = datetime.datetime.now().strftime("%Y-%m-%dT%H:%M:%SZ")  # Every restart of the application means an update to it
 
 __org_id__ = CONFIG_INFO.org_id
 __org_name__ = CONFIG_INFO.org_name
@@ -33,12 +33,10 @@
 __org_welcomeUrl__ = CONFIG_INFO.org_welcomeUrl
 __org_contactUrl__ = CONFIG_INFO.org_contactUrl
 __org_logoUrl__ = CONFIG_INFO.org_logoUrl
-__org_info__ = {'orgInfo': CONFIG_INFO.org_info}
+__org_info__ = {"orgInfo": CONFIG_INFO.org_info}
 
 __sample_queries__ = SAMPLE_QUERIES
 
 # GA4GH Discovery
-__service_type__ = {'group': f'{CONFIG_INFO.service_group}',
-                    'artifact': f'{CONFIG_INFO.service_artifact}',
-                    'version': f'{__apiVersion__}'}
+__service_type__ = {"group": f"{CONFIG_INFO.service_group}", "artifact": f"{CONFIG_INFO.service_artifact}", "version": f"{__apiVersion__}"}
 __service_env__ = CONFIG_INFO.environment

beacon_api/api/exceptions.py

@@ -3,7 +3,7 @@
 API specification requires custom messages upon error.
 """
 
-import json
+import ujson
 from typing import Dict
 from aiohttp import web
 from .. import __apiVersion__
@@ -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
@@ -51,7 +61,7 @@ class BeaconBadRequest(web.HTTPBadRequest):
     def __init__(self, request: Dict, host: str, error: str) -> None:
         """Return custom bad request exception."""
         data = process_exception_data(request, host, 400, error)
-        super().__init__(text=json.dumps(data), content_type="application/json")
+        super().__init__(text=ujson.dumps(data, escape_forward_slashes=False), content_type="application/json")
         LOG.error(f"401 ERROR MESSAGE: {error}")
 
 
@@ -65,14 +75,10 @@ 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=json.dumps(data),
+            text=ujson.dumps(data, escape_forward_slashes=False),
             # we use auth scheme Bearer by default
             headers=headers_401,
         )
@@ -90,7 +96,7 @@ class BeaconForbidden(web.HTTPForbidden):
     def __init__(self, request: Dict, host: str, error: str) -> None:
         """Return custom forbidden exception."""
         data = process_exception_data(request, host, 403, error)
-        super().__init__(content_type="application/json", text=json.dumps(data))
+        super().__init__(content_type="application/json", text=ujson.dumps(data, escape_forward_slashes=False))
         LOG.error(f"403 ERROR MESSAGE: {error}")
 
 
@@ -103,5 +109,5 @@ class BeaconServerError(web.HTTPInternalServerError):
     def __init__(self, error: str) -> None:
         """Return custom forbidden exception."""
         data = {"errorCode": 500, "errorMessage": error}
-        super().__init__(content_type="application/json", text=json.dumps(data))
+        super().__init__(content_type="application/json", text=ujson.dumps(data, escape_forward_slashes=False))
         LOG.error(f"500 ERROR MESSAGE: {error}")