Merge pull request #8 from PsychoinformaticsLab/enh/test

Move to Python 3.8, add tests

.travis.yml

@@ -2,15 +2,15 @@ matrix:
   include:
     - language: python
       python:
-        - "3.6"
+        - "3.8"
       install:
         - pip install -U setuptools==45
         - pip install -r neurostuff/requirements.txt
         - pip install pytest-cov
       script:
         - python -m pytest neurostuff/ --cov=./
       env:
-      - APP_SETTINGS=neurostuff.config.app.TravisConfig PYTHONHASHSEED=0
+      - APP_SETTINGS=neurostuff.config.TravisConfig PYTHONHASHSEED=0
       addons:
         postgresql: "9.4"
       before_script:

README.md

@@ -1,6 +1,6 @@
 # neurostuff
 
-[Add badges]
+[![Build Status](https://travis-ci.com/PsychoinformaticsLab/neurostuff.svg?branch=master)](https://travis-ci.com/PsychoinformaticsLab/neurostuff)
 
 Requirements: Docker and docker-compose.
 
@@ -47,3 +47,13 @@ If you need to upgrade the db after changing any models:
 
     docker-compose exec neurostuff python manage.py db migrate
     docker-compose exec neurostuff python manage.py db upgrade
+
+
+## Running tests
+To run tests, after starting services, create a test database:
+
+    docker-compose exec postgres psql -h postgres -U postgres -c "create database test_db"
+
+and execute:
+
+    docker-compose run -e "APP_SETTINGS=neurostuff.config.DockerTestConfig" --rm -w /neurostuff neurostuff python -m pytest neurostuff/tests

neurostuff/Dockerfile

@@ -1,4 +1,4 @@
-FROM python:3.6-stretch
+FROM python:3.8-buster
 ARG DEBIAN_FRONTEND=noninteractive
 
 RUN mkdir -p /usr/src/app

neurostuff/example_config.py

@@ -11,7 +11,7 @@ class Config(object):
     SQLALCHEMY_TRACK_MODIFICATIONS = False
     WTF_CSRF_ENABLED = False
 
-    POSTGRES_PASSWORD = os.environ['POSTGRES_PASSWORD']
+    POSTGRES_PASSWORD = os.environ.get('POSTGRES_PASSWORD', '')
     DB_NAME = 'neurostuff'
     SQLALCHEMY_DATABASE_URI = "postgres://postgres:" \
         f"{POSTGRES_PASSWORD}@postgres:5432/{DB_NAME}"
@@ -21,6 +21,9 @@ class Config(object):
     GITHUB_CLIENT_SECRET = "github-secret"
     DANCE_SECRET_KEY = "temporary"
 
+    SECURITY_PASSWORD_HASH = 'pbkdf2_sha512'
+    SECURITY_PASSWORD_SALT = 'A_SECRET'
+
 
 class ProductionConfig(Config):
     ENV = 'production'
@@ -37,7 +40,7 @@ class TestingConfig(Config):
 
 
 class DockerTestConfig(TestingConfig):
-    SQLALCHEMY_DATABASE_URI = 'postgres://postgres@postgres:5432/scout_test'
+    SQLALCHEMY_DATABASE_URI = 'postgres://postgres@postgres:5432/test_db'
 
 
 class TravisConfig(TestingConfig):

neurostuff/ingest/__init__.py

@@ -84,7 +84,7 @@ def ingest_neurosynth(max_rows=None):
     #    tf.write(response.raw.read())
     #   tf.seek(0)
 
-    path = Path(__file__).parent / '..' / 'data' / 'data_0.7.July_2018.tar.gz'
+    path = Path(__file__).parent.parent / 'data' / 'data_0.7.July_2018.tar.gz'
     with open(path, 'rb') as tf:
         tar = tarfile.open(fileobj=tf)
         f = tar.extractfile('database.txt')

neurostuff/requirements.txt

@@ -41,6 +41,7 @@ psycopg2==2.8.3
 PyLD==2.0.3
 python-dateutil==2.8.1
 pytz==2020.1
+pytest==6.0.1
 requests==2.24.0
 requests-oauthlib==1.3.0
 Rx==1.6.1

neurostuff/tests/api/test_analyses.py

@@ -0,0 +1,30 @@
+from ..request_utils import decode_json
+
+
+def test_get_analyses(auth_client, ingest_neurosynth):
+    # List of analyses
+    resp = auth_client.get('/api/analyses/')
+    assert resp.status_code == 200
+    analysis_list = decode_json(resp)
+    assert type(analysis_list) == list
+
+    assert len(analysis_list) == 1
+
+    # Check analysis keys
+    analysis = analysis_list[0]
+    keys = ['@context', '@id', '@type', 'condition', 'created_at', 'image',
+            'name', 'point', 'study', 'weight']
+    for k in keys:
+        assert k in analysis
+
+    assert analysis['@context'] == {'@vocab': 'http://neurostuff.org/nimads/'}
+    assert analysis['@type'] == 'Analysis'
+    a_id = analysis['@id'].split('/')[-1]
+
+    # Query specify analysis ID
+    resp = auth_client.get(f"/api/analyses/{a_id}")
+    assert resp.status_code == 200
+    assert decode_json(resp) == analysis
+
+    assert decode_json(resp)['@id'] == \
+        f'http://neurostuff.org/api/analyses/{a_id}'

neurostuff/tests/api/test_conditions.py

@@ -0,0 +1,4 @@
+
+def test_get_conditions(auth_client, ingest_neurosynth):
+    # Currently no conditions in db
+    assert 1

neurostuff/tests/api/test_datasets.py

@@ -0,0 +1,5 @@
+
+
+def test_get_datasets(auth_client, ingest_neurosynth):
+    # Currently no datasets in db
+    assert 1

neurostuff/tests/api/test_images.py

@@ -0,0 +1,14 @@
+from ..request_utils import decode_json
+
+
+def test_get_images(auth_client, ingest_neurosynth):
+    # List of datasets
+    resp = auth_client.get('/api/images/')
+    assert resp.status_code == 200
+    images_list = decode_json(resp)
+
+    assert type(images_list) == list
+
+    assert len(images_list) == 0
+
+    # Add more tests for images with ingest_neurovault

neurostuff/tests/api/test_points.py

@@ -0,0 +1,19 @@
+from ..request_utils import decode_json
+
+
+def test_get_points(auth_client, ingest_neurosynth):
+    # Get an analysis
+    resp = auth_client.get('/api/analyses/')
+    analysis = decode_json(resp)[0]
+
+    point_id = analysis['point'][0].split('/')[-1]
+
+    # Get a point
+    resp = auth_client.get(f'/api/points/{point_id}')
+    point = decode_json(resp)
+
+    # Test a few fields
+    assert point['@id'] == f'http://neurostuff.org/api/points/{point_id}'
+    assert point['coordinates'] == [-34.0, -68.0, -15.0]
+    assert point['space'] == 'TAL'
+    assert point['@type'] == 'Point'

neurostuff/tests/api/test_studies.py

@@ -0,0 +1,33 @@
+from ..request_utils import decode_json
+
+
+def test_get_studies(auth_client, ingest_neurosynth):
+    # List of studies
+    resp = auth_client.get('/api/studies/')
+    assert resp.status_code == 200
+    studies_list = decode_json(resp)
+
+    assert type(studies_list) == list
+
+    assert len(studies_list) == 1
+
+    # Check study keys
+    study = studies_list[0]
+
+    assert study['@context'] == {'@vocab': 'http://neurostuff.org/nimads/'}
+    assert study['@type'] == 'Study'
+    s_id = study['@id'].split('/')[-1]
+
+    # Query specify analysis ID
+    resp = auth_client.get(f"/api/studies/{s_id}")
+    assert resp.status_code == 200
+    full_study = decode_json(resp)
+
+    # Check extra keys
+    for k in ['analysis', 'created_at', 'doi', 'name']:
+        assert k in full_study
+
+    assert full_study['doi'] == '10.1016/S0896-6273(00)80456-0'
+
+    assert full_study['@id'] == \
+        f'http://neurostuff.org/api/studies/{s_id}'

neurostuff/tests/conftest.py

@@ -75,7 +75,7 @@ def auth_client(add_users):
     """ Return authorized client wrapper """
     from .request_utils import Client
 
-    _, ((email, password), _) = add_users
+    _, email, password = add_users
     client = Client(email=email, password=password)
     return client
 
@@ -96,7 +96,6 @@ def add_users(app, db, session):
     pass1 = 'test1'
 
     user_datastore.create_user(email=user1, password=encrypt_password(pass1),
-                               user_name='testuser',
                                confirmed_at=datetime.datetime.now())
     session.commit()
     id_1 = user_datastore.find_user(email=user1).id
@@ -107,4 +106,4 @@ def add_users(app, db, session):
 @pytest.fixture(scope="function")
 def ingest_neurosynth(session):
     """ Add a dataset with two subjects """
-    return ingest.ingest_neurosynth()
+    return ingest.ingest_neurosynth(800)

nginx/nginx.dev.conf

@@ -48,9 +48,6 @@ http {
         gzip_types text/plain text/css application/json application/x-javascript text/xml application/xml application/xml+rss text/javascript;
 
         server {
-            server_name _;
-            root /neurostuff/neurostuff/frontend/build;
-
             location /static/ {
             }