Dockerize

.dockerignore

@@ -0,0 +1,9 @@
+.git
+.github
+.gitignore
+.travis.yml
+mkdocs.yml
+docs
+tests
+Dockerfile
+docker-compose.yml

CHANGELOG.md

@@ -1,7 +1,7 @@
-## [] -
+## [1.3] - 2020.10.25
 ### Added
 - Created deployment WSGI file
-- Cython requirement
+- Dockerfiles for backend and frontend
 
 
 ## [1.2] - 2020.10.19

README.md

@@ -34,6 +34,7 @@ git clone https://github.com/Clinical-Genomics/cgbeacon2.git
 
 Change directory to the cloned folder and from there, install the software using the following command:
 ```
+pip install -r requirements.txt
 pip install -e .
 ```
 

cgbeacon2/__version__.py

@@ -1 +1 @@
-__version__ = "1.2"
+__version__ = "1.3"

cgbeacon2/server/__init__.py

@@ -41,7 +41,12 @@ def create_app():
         LOG.warning("Please add database settings param in your config file.")
         quit()
 
-    client = MongoClient(app.config["DB_URI"])
+    # If app is runned from inside a container, override host port
+    db_uri = app.config["DB_URI"]
+    if os.getenv("MONGODB_HOST"):
+        db_uri=f"mongodb://{os.getenv('MONGODB_HOST')}:{'27017'}/{'cgbeacon2'}"
+
+    client = MongoClient(db_uri)
     app.db = client[app.config["DB_NAME"]]
     LOG.info("database connection info:{}".format(app.db))
 

containers/base/Dockerfile

@@ -0,0 +1,18 @@
+FROM python:3.8-alpine3.12
+
+MAINTAINER Chiara Rasi
+
+RUN apk update
+RUN apk add make automake gcc g++ linux-headers curl libcurl curl-dev \
+  zlib-dev bzip2-dev xz-dev libffi-dev curl libressl-dev bash \
+  && rm -rf /var/cache/apk/*s
+
+WORKDIR /home/worker/app
+COPY . /home/worker/app
+
+RUN pip install -r requirements.txt
+RUN pip install -e .
+
+RUN adduser -D worker
+RUN chown worker:worker -R /home/worker
+USER worker

containers/frontend/Dockerfile

@@ -0,0 +1,7 @@
+FROM northwestwitch/cgbeacon2:latest
+
+MAINTAINER Chiara Rasi
+
+EXPOSE 5000
+
+CMD cgbeacon2 run --host 0.0.0.0

docker-compose.yml

@@ -0,0 +1,34 @@
+version: '3'
+# usage:
+# sudo docker-compose build
+# sudo docker-compose up
+services:
+  mongodb:
+    image: mvertes/alpine-mongo
+    container_name: mongodb
+    ports:
+      - '27017:27017'
+    expose:
+      - '27017'
+
+  beacon-cli:
+    environment:
+      MONGODB_HOST: mongodb
+    image: northwestwitch/cgbeacon2
+    container_name: beacon-cli
+    links:
+      - mongodb
+    command: bash -c 'cgbeacon2 add demo'
+
+  beacon-web:
+    environment:
+      MONGODB_HOST: mongodb
+    image: northwestwitch/cgbeacon2
+    container_name: beacon-web
+    links:
+      - mongodb
+    expose:
+      - '5000'
+    ports:
+      - '5000:5000'
+    command: bash -c 'cgbeacon2 run --host 0.0.0.0'

requirements.txt

@@ -18,6 +18,4 @@ PyJWT
 # utils
 cyvcf2
 pybedtools
-pysam<0.16 #Avoid ImportError: libchtslib.cpython-35m-x86_64-linux-gnu.so
 jsonschema
-cython

setup.py

@@ -22,29 +22,6 @@
 
 here = os.path.abspath(os.path.dirname(__file__))
 
-def parse_reqs(req_path='./requirements.txt'):
-    """Recursively parse requirements from nested pip files."""
-    install_requires = []
-    with io.open(os.path.join(here, 'requirements.txt'), encoding='utf-8') as handle:
-        # remove comments and empty lines
-        lines = (line.strip() for line in handle
-                 if line.strip() and not line.startswith('#'))
-
-        for line in lines:
-            # check for nested requirements files
-            if line.startswith('-r'):
-                # recursively call this function
-                install_requires += parse_reqs(req_path=line[3:])
-
-            else:
-                # add the line as a new requirement
-                install_requires.append(line)
-
-    return install_requires
-
-# What packages are required for this module to be executed?
-REQUIRED = parse_reqs()
-
 # The rest you shouldn't have to touch too much :)
 # ------------------------------------------------
 # Except, perhaps the License and Trove Classifiers!
@@ -106,7 +83,6 @@ def run(self):
     download_url = '/'.join([URL,'tarball',version]),
     keywords = KEYWORDS,
     packages=find_packages(),
-    install_requires=REQUIRED,
     include_package_data=True,
     license=LICENSE,
     classifiers=[

tests/server/test_init.py

@@ -6,5 +6,22 @@
 def test_create_app_from_envar(monkeypatch):
     """Test option to create app from a file specified by an environment variable"""
 
+    # GIVEN a a config file defined in the environment
     monkeypatch.setenv("CGBEACON2_CONFIG", config_file_path, prepend=False)
-    assert create_app()
+    # THEN the app should connect to a database on localhost, port 27017 as defined on config file
+    app = create_app()
+    assert app
+    db_attrs = str(vars(app.db))  # convert database attributes to string
+    assert "host=['127.0.0.1:27017']" in db_attrs
+
+
+def test_create_app_in_container(monkeypatch):
+    """Test creating app from inside a container, when an env varianble named 'MONGODB_HOST' is present to modify the hosr provided in config file"""
+
+    # GIVEN an env var named MONGODB_HOST
+    monkeypatch.setenv("MONGODB_HOST", "mongodb")
+    # THEN the app should connect to a mongo host named mongodb on port 27017
+    app = create_app()
+    assert app
+    db_attrs = str(vars(app.db))  # convert database attributes to string
+    assert "host=['mongodb:27017']" in db_attrs