Merge pull request #141 from CSCfi/dev

blankdots · web-flow · commit 89de6dc8fa9a · 2020-01-17T10:42:28.000+02:00
Release 1.6.0
diff --git a/.travis.yml b/.travis.yml
@@ -61,8 +61,8 @@ jobs:
       name: "Integration Tests"
       python: 3.6
       before_script:
-        - wget https://github.com/openshift/source-to-image/releases/download/v1.1.12/source-to-image-v1.1.12-2a783420-linux-amd64.tar.gz
-        - tar -xvf source-to-image-v1.1.12-2a783420-linux-amd64.tar.gz
+        - 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
         - sudo cp s2i /usr/local/bin
         - s2i build . centos/python-36-centos7 cscfi/beacon-python
         - cd deploy/test
diff --git a/README.md b/README.md
@@ -11,7 +11,7 @@ Documentation: https://beacon-python.readthedocs.io
 
 `beacon-python` Web Server requires:
 * Python 3.6+;
-* running DB [PostgreSQL Server](https://www.postgresql.org/) 9.6+.
+* running DB [PostgreSQL Server](https://www.postgresql.org/) 9.6+ (recommended 11.6).
 
 ```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:9.6
+           -p 5432:5432 postgres:11.6
 ```
 
 #### Run beacon-python
diff --git a/beacon_api/__init__.py b/beacon_api/__init__.py
@@ -38,5 +38,7 @@
 __sample_queries__ = SAMPLE_QUERIES
 
 # GA4GH Discovery
-__service_type__ = f'{CONFIG_INFO.service_type}:{__apiVersion__}'
+__service_type__ = {'group': f'{CONFIG_INFO.service_group}',
+                    'artifact': f'{CONFIG_INFO.service_artifact}',
+                    'version': f'{__apiVersion__}'}
 __service_env__ = CONFIG_INFO.environment
diff --git a/beacon_api/app.py b/beacon_api/app.py
@@ -94,6 +94,8 @@ def set_cors(server):
             allow_credentials=True,
             expose_headers="*",
             allow_headers="*",
+            allow_methods=["GET", "POST", "OPTIONS"],
+            max_age=86400,
         )
     })
     # Apply CORS to endpoints
diff --git a/beacon_api/conf/__init__.py b/beacon_api/conf/__init__.py
@@ -33,7 +33,8 @@ def parse_config_file(path):
         'url': config.get('beacon_api_info', 'url'),
         'alturl': config.get('beacon_api_info', 'alturl'),
         'createtime': config.get('beacon_api_info', 'createtime'),
-        'service_type': config.get('beacon_api_info', 'service_type'),
+        'service_group': config.get('beacon_api_info', 'service_group'),
+        'service_artifact': config.get('beacon_api_info', 'service_artifact'),
         'environment': config.get('beacon_api_info', 'environment'),
         'org_id': config.get('organisation_info', 'org_id'),
         'org_name': config.get('organisation_info', 'org_name'),
diff --git a/beacon_api/conf/config.ini b/beacon_api/conf/config.ini
@@ -7,7 +7,7 @@
 title=GA4GHBeacon at CSC
 
 # Version of the Beacon implementation
-version=1.5.0
+version=1.6.0
 
 # Author of this software
 author=CSC developers
@@ -42,8 +42,9 @@ alturl=
 createtime=2018-07-25T00:00:00Z
 
 # GA4GH Discovery type `groupId` and `artifactId`, joined in /service-info with apiVersion
-# See https://github.com/ga4gh-discovery/ga4gh-service-registry for more information and possible values
-service_type=org.ga4gh:beacon
+# See https://github.com/ga4gh-discovery/ga4gh-service-info for more information and possible values
+service_group=org.ga4gh
+service_artifact=beacon
 
 # GA4GH Discovery server environment, possible values: prod, dev, test
 environment=prod
diff --git a/beacon_api/schemas/service-info.json b/beacon_api/schemas/service-info.json
@@ -0,0 +1,91 @@
+{
+    "definitions": {},
+    "type": "object",
+    "additionalProperties": false,
+    "required": [
+      "id",
+      "name",
+      "type",
+      "description",
+      "organization",
+      "version"
+    ],
+    "properties": {
+      "id": {
+        "type": "string",
+        "pattern": "^(.*)$"
+      },
+      "name": {
+        "type": "string",
+        "pattern": "^(.*)$"
+      },
+      "type": {
+        "type": "object",
+        "required": [
+          "group",
+          "artifact",
+          "version"
+        ],
+        "properties": {
+          "group": {
+            "type": "string",
+            "pattern": "^(.*)$"
+          },
+          "artifact": {
+            "type": "string",
+            "pattern": "^(.*)$"
+          },
+          "version": {
+            "type": "string",
+            "pattern": "^(.*)$"
+          }
+        }
+      },
+      "description": {
+        "type": "string",
+        "pattern": "^(.*)$"
+      },
+      "organization": {
+        "type": "object",
+        "required": [
+          "name",
+          "url"
+        ],
+        "properties": {
+          "name": {
+            "type": "string",
+            "pattern": "^(.*)$"
+          },
+          "url": {
+            "type": "string",
+            "pattern": "^(.*)$"
+          }
+        }
+      },
+      "contactUrl": {
+        "type": "string",
+        "pattern": "^(.*)$"
+      },
+      "documentationUrl": {
+        "type": "string",
+        "pattern": "^(.*)$"
+      },
+      "createdAt": {
+        "type": "string",
+        "pattern": "^(.*)$"
+      },
+      "updatedAt": {
+        "type": "string",
+        "pattern": "^(.*)$"
+      },
+      "environment": {
+        "type": "string",
+        "pattern": "^(.*)$"
+      },
+      "version": {
+        "type": "string",
+        "pattern": "^(.*)$"
+      }
+    }
+  }
+  
diff --git a/deploy/docker-compose.yml b/deploy/docker-compose.yml
@@ -3,7 +3,7 @@ version: '3.2'
 services:
   postgres:
     hostname: postgres
-    image: postgres:11.2
+    image: postgres:11.6
     environment:
       POSTGRES_USER: beacon
       POSTGRES_DB: beacondb
diff --git a/deploy/test/auth_test.ini b/deploy/test/auth_test.ini
@@ -7,7 +7,7 @@
 title=GA4GHBeacon at CSC
 
 # Version of the Beacon implementation
-version=1.5.0
+version=1.6.0
 
 # Author of this software
 author=CSC developers
@@ -41,8 +41,9 @@ alturl=https://ega-archive.org/
 createtime=2018-07-25T00:00:00Z
 
 # GA4GH Discovery type `groupId` and `artifactId`, joined in /service-info with apiVersion
-# See https://github.com/ga4gh-discovery/ga4gh-service-registry for more information and possible values
-service_type=org.ga4gh:beacon
+# See https://github.com/ga4gh-discovery/ga4gh-service-info for more information and possible values
+service_group=org.ga4gh
+service_artifact=beacon
 
 # GA4GH Discovery server environment, possible values: prod, dev, test
 environment=prod
diff --git a/deploy/test/docker-compose.yml b/deploy/test/docker-compose.yml
@@ -3,7 +3,7 @@ version: '3.2'
 services:
   postgres:
     hostname: postgres
-    image: postgres:11.2
+    image: postgres:11.6
     environment:
       POSTGRES_USER: beacon
       POSTGRES_DB: beacondb
diff --git a/deploy/test/integ_test.py b/deploy/test/integ_test.py
@@ -704,5 +704,6 @@ async def test_32():
             # GA4GH Discovery Service-Info is small and its length should be at least 5 (required keys), when the Beacon info is very long
             # https://github.com/ga4gh-discovery/service-info/blob/develop/service-info.yaml
             assert len(data) >= 5, 'Service info size error'  # ga4gh service-info has 5 required keys, and option to add custom keys
-            assert data['type'].startswith('org.ga4gh:beacon'), 'Service type error'  # a new key used in beacon network
+            assert data['type'].get('group'), 'Service type error'  # a new key used in beacon network
+            assert data['type']['group'].startswith('org.ga4gh'), 'Service type error'  # a new key used in beacon network
             assert resp.status == 200, 'HTTP Status code error'
diff --git a/docs/db.rst b/docs/db.rst
@@ -3,7 +3,7 @@
 Database
 ========
 
-We use a PostgreSQL database (version 9.6+) for working with beacon data.
+We use a PostgreSQL database (recomended version 11.6) 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
diff --git a/docs/example.rst b/docs/example.rst
@@ -126,7 +126,7 @@ Example Response:
     "createdAt": "2019-09-04T12:00:00Z",
     "updatedAt": "2019-09-05T05:55:18Z",
     "environment": "prod",
-    "version": "1.5.0"
+    "version": "1.6.0"
   }
 
 Query Endpoint
diff --git a/docs/instructions.rst b/docs/instructions.rst
@@ -4,7 +4,7 @@ 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+.
+  * running DB `PostgreSQL Server <https://www.postgresql.org/>`_  9.6+ (recommended 11.6).
 
 .. _env-setup:
 
@@ -69,7 +69,7 @@ pointing to the location of the file using `CONFIG_FILE` environment variable.
 
 .. literalinclude:: /../beacon_api/conf/config.ini
    :language: python
-   :lines: 1-75
+   :lines: 1-76
 
 .. _oauth2:
 
@@ -81,23 +81,23 @@ The configuration variables reside in the same `CONFIG_FILE` as described above
 
 .. literalinclude:: /../beacon_api/conf/config.ini
    :language: python
-   :lines: 97-123
+   :lines: 98-124
 
 * ``server`` should point to an API that returns a public key, which can be used to validate the received JWTBearer token.
 * ``issuers`` is a string of comma separated values, e.g. `one,two,three` without spaces. The issuers string should contain
   a list of entities that are viewed as trusted organisations.
 * ``bona_fide`` should point to an API that returns the `bona_fide_status` this is
   `ELIXIR AAI <https://www.elixir-europe.org/services/compute/aai>`_ specific.
 * ``audience`` is a string of comma separated values, e.g. ``aud1,aud2,aud3`` of intended audiences. Audience is a value
-  in JWT that describes what service(s) the token is intended for. 
+  in JWT that describes what service(s) the token is intended for.
 
-The audience `hash` or `URI` from the AAI service can be used, or if the service is part of a `Beacon Network`, 
+The audience `hash` or `URI` from the AAI service can be used, or if the service is part of a `Beacon Network`,
 use the key provided by the Beacon Network administrator.
 
 **Leave empty if the service doesn't care about the intended audience.**
 
 ``verify_aud`` can be set to either ``True`` or ``False``. If enabled, this option forces Beacon to verify the audience(s)
-in the supplied token. If disabled, the audience(s) of a token will not be validated. 
+in the supplied token. If disabled, the audience(s) of a token will not be validated.
 
 Disabling this can be a good solution for standalone
 Beacons, that want to be able to use tokens generated by any authority. If ``verify_aud=True`` is set
@@ -164,7 +164,7 @@ Starting PostgreSQL using Docker:
                -e POSTGRES_PASSWORD=beacon \
                -e POSTGRES_DB=beacondb \
                -v "$PWD/data":/docker-entrypoint-initdb.d
-               -p 5432:5432 postgres:9.6
+               -p 5432:5432 postgres:11.6
 
 .. hint:: If one has their own database the ``beacon_init`` utility can be skipped,
           and make use of their own database by:
diff --git a/docs/optionals.rst b/docs/optionals.rst
@@ -17,7 +17,7 @@ The handover protocol can be configured in ``config.ini`` as follows:
 
 .. literalinclude:: /../beacon_api/conf/config.ini
    :language: python
-   :lines: 78-94
+   :lines: 79-95
 
 .. note:: Handover protocol is disabled by default, as shown by the commented out ``drs`` variable. This variable should point
           to the server, which serves the additional data. To enable the handover protocol, uncomment the ``drs`` variable.
@@ -106,7 +106,7 @@ Currently querying for a ``BND`` using ``startMin``, ``startMax`` and ``endMin``
 with ``variantType=BND`` has the response illustrated below.
 Fixed ``start`` and ``end`` can be utilised, as well as ``mateName`` as depicted above.
 
-.. note:: By default when using ``mateName``, ``variantType`` is implicit ``BND``, 
+.. note:: By default when using ``mateName``, ``variantType`` is implicit ``BND``,
           but it can also be set in an explicit manner using both ``mateName`` and
           ``variantType=BND`` in a query.
 
diff --git a/requirements.txt b/requirements.txt
@@ -12,4 +12,4 @@ aiocache
 ujson
 aiomcache
 authlib
-gunicorn==19.9.0
+gunicorn>=20.0.1
diff --git a/setup.py b/setup.py
@@ -45,10 +45,10 @@
           'Programming Language :: Python :: 3.6',
           'Programming Language :: Python :: 3.7',
       ],
-      install_requires=['aiohttp', 'asyncpg', 'authlib',
-                        'jsonschema', 'gunicorn==19.9.0'],
+      install_requires=['aiohttp', 'asyncpg', 'authlib', 'aiohttp_cors',
+                        'jsonschema', 'gunicorn>=20.0.1'],
       extras_require={
-          'test': ['coverage', 'pytest', 'pytest-cov',
+          'test': ['coverage==4.5.4', 'pytest', 'pytest-cov',
                    'coveralls', 'testfixtures', 'tox',
                    'flake8', 'flake8-docstrings', 'asynctest', 'aioresponses'],
           'docs': [
diff --git a/tests/test.ini b/tests/test.ini
@@ -7,7 +7,7 @@
 title=GA4GHBeacon at CSC
 
 # Version of the Beacon implementation
-version=1.5.0
+version=1.6.0
 
 # Author of this software
 author=CSC developers
@@ -41,8 +41,9 @@ alturl=https://ega-archive.org/
 createtime=2018-07-25T00:00:00Z
 
 # GA4GH Discovery type `groupId` and `artifactId`, joined in /service-info with apiVersion
-# See https://github.com/ga4gh-discovery/ga4gh-service-registry for more information and possible values
-service_type=org.ga4gh:beacon
+# See https://github.com/ga4gh-discovery/ga4gh-service-info for more information and possible values
+service_group=org.ga4gh
+service_artifact=beacon
 
 # GA4GH Discovery server environment, possible values: prod, dev, test
 environment=test
diff --git a/tests/test_app.py b/tests/test_app.py
@@ -102,12 +102,12 @@ async def tearDown(self):
         await caches.get('default').delete("jwk_key")
 
     @unittest_run_loop
-    async def test_info(self):
-        """Test the info endpoint.
+    async def test_beacon_info(self):
+        """Test the Beacon info endpoint.
 
         The status should always be 200.
         """
-        with asynctest.mock.patch('beacon_api.app.beacon_info', side_effect={"smth": "value"}):
+        with asynctest.mock.patch('beacon_api.app.beacon_info', return_value={"id": "value"}):
             resp = await self.client.request("GET", "/")
         assert 200 == resp.status
 
@@ -117,7 +117,7 @@ async def test_ga4gh_info(self):
 
         The status should always be 200.
         """
-        with asynctest.mock.patch('beacon_api.app.beacon_info', side_effect={"smth": "value"}):
+        with asynctest.mock.patch('beacon_api.app.ga4gh_info', return_value={"id": "value"}):
             resp = await self.client.request("GET", "/service-info")
         assert 200 == resp.status
 
@@ -130,6 +130,15 @@ async def test_post_info(self):
         resp = await self.client.request("POST", "/")
         assert 405 == resp.status
 
+    @unittest_run_loop
+    async def test_post_service_info(self):
+        """Test the service-info endpoint with POST.
+
+        The status should always be 405.
+        """
+        resp = await self.client.request("POST", "/service-info")
+        assert 405 == resp.status
+
     @unittest_run_loop
     async def test_empty_get_query(self):
         """Test empty GET query endpoint."""
diff --git a/tests/test_response.py b/tests/test_response.py

Original file line number	Diff line number	Diff line change
`@@ -94,6 +94,8 @@ def set_cors(server):`
`94`	`94`	`allow_credentials=True,`
`95`	`95`	`expose_headers="*",`
`96`	`96`	`allow_headers="*",`
	`97`	`+ allow_methods=["GET", "POST", "OPTIONS"],`
	`98`	`+ max_age=86400,`
`97`	`99`	`)`
`98`	`100`	`})`
`99`	`101`	`# Apply CORS to endpoints`