fixed conflict in changelog

.github/workflows/black.yml

@@ -14,7 +14,7 @@ jobs:
           python-version: 3.8
       - name: install black
         run: |
-          pip install black==20.8b1
+          pip install black==19.10b0
       - name: run black
         run: |
           black . --check --line-length 100

CHANGELOG.md

@@ -4,6 +4,14 @@
 ### Fixed
 - removed unused docker folder
 
+## [2.3.1] - 2020-12-04
+### Added
+### Changed
+- Install requirements in setup
+- Improved Dockerfile and docker-compose files
+### Fixed
+- Connection string to database when creating the app
+
 ## [2.3] - 2020-12-01
 ### Changed
 - Pulling Docker images in docker-compose from clinicalgenomics Docker Hub

docker-compose.yml

@@ -10,6 +10,8 @@ services:
     # when the container is first launched.
     image: vepo/mongo
     container_name: mongo
+    networks:
+      - pmatcher-net
     environment:
       - AUTH=y
       - ADMIN_USER=root
@@ -23,23 +25,42 @@ services:
       - '27017'
 
   pmatcher-cli:
+    container_name: pmatcher-cli
+    build:
+      context: .
+      dockerfile: Dockerfile
     image: clinicalgenomics/patientmatcher
     environment:
       MONGODB_HOST: mongodb
-    container_name: pmatcher-cli
-    links:
+      PMATCHER_CONFIG: '/home/worker/app/patientMatcher/patientMatcher/instance/config.py'
+    depends_on:
       - mongodb
-    command: bash -c 'pmatcher add demodata --ensembl_genes'
+    networks:
+      - pmatcher-net
+    command: bash -c "pmatcher add client -id test_client -token custom_token -url custom_url && pmatcher add demodata --ensembl_genes"
 
   pmatcher-web:
-    image: clinicalgenomics/patientmatcher
+    container_name: pmatcher-web
+    build:
+      context: .
+      dockerfile: Dockerfile
     environment:
       MONGODB_HOST: mongodb
-    container_name: pmatcher-web
-    links:
+      PMATCHER_CONFIG: '/home/worker/app/patientMatcher/patientMatcher/instance/config.py'
+    depends_on:
       - mongodb
+    networks:
+      - pmatcher-net
     expose:
       - '5000'
     ports:
       - '5000:5000'
     command: bash -c 'pmatcher run --host 0.0.0.0'
+
+networks:
+  pmatcher-net:
+    driver: bridge
+    ipam:
+      driver: default
+      config:
+        - subnet: 172.21.0.0/24

patientMatcher/__version__.py

@@ -1 +1 @@
-__version__ = "2.3"
+__version__ = "2.3.1"

patientMatcher/instance/config.py

@@ -1,3 +1,5 @@
+import os
+
 # Turns on debugging features in Flask
 DEBUG = True
 
@@ -8,8 +10,11 @@
 DB_USERNAME = "pmUser"
 DB_PASSWORD = "pmPassword"
 DB_NAME = "pmatcher"
-DB_HOST = "127.0.0.1"
+DB_HOST = (
+    os.getenv("MONGODB_HOST") or "127.0.0.1"
+)  # simply substitute with 'mongodb' if connecting to MongoDB running in a container
 DB_PORT = 27017
+DB_URI = "mongodb://{}:{}@{}:{}/{}".format(DB_USERNAME, DB_PASSWORD, DB_HOST, DB_PORT, DB_NAME)
 
 # Matching Algorithms scores
 # sum of MAX_GT_SCORE and MAX_PHENO_SCORE should be 1

patientMatcher/server/__init__.py

@@ -28,15 +28,7 @@ def create_app():
         app = Flask(__name__, instance_path=instance_path, instance_relative_config=True)
         app.config.from_pyfile("config.py")
 
-    db_username = app.config["DB_USERNAME"]
-    db_password = app.config["DB_PASSWORD"]
-    # If app is runned from inside a container, override host port
-    db_host = os.getenv("MONGODB_HOST") or app.config["DB_HOST"]
-    db_port = app.config["DB_PORT"]
-    db_name = app.config["DB_NAME"]
-    db_uri = f"mongodb://{db_username}:{db_password}@{db_host}:{db_port}/{db_name}"
-
-    client = MongoClient(db_uri)
+    client = MongoClient(app.config["DB_URI"])
     app.client = client
     app.db = client[app.config["DB_NAME"]]
     LOG.info("database connection info:{}".format(app.db))

setup.py

@@ -33,6 +33,34 @@
 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!
+# If you do change the License, remember to change the Trove Classifier for that!
+
 # Import the README and use it as the long-description.
 # Note: this will only work if 'README.rst' is present in your MANIFEST.in file!
 with io.open(os.path.join(here, "README.md"), encoding="utf-8") as f:
@@ -89,6 +117,7 @@ def run(self):
     download_url="/".join([URL, "tarball", version]),
     keywords=KEYWORDS,
     packages=find_packages(),
+    install_requires=REQUIRED,
     include_package_data=True,
     license=LICENSE,
     classifiers=[
@@ -103,11 +132,7 @@ def run(self):
         "Operating System :: MacOS",
         "Operating System :: Unix",
     ],
-    entry_points={
-        "console_scripts": ["pmatcher = patientMatcher.cli.commands:cli"],
-    },
+    entry_points={"console_scripts": ["pmatcher = patientMatcher.cli.commands:cli"],},
     # $ setup.py publish support.
-    cmdclass={
-        "upload": UploadCommand,
-    },
+    cmdclass={"upload": UploadCommand,},
 )

tests/server/test_server_responses.py

@@ -33,14 +33,7 @@ def test_match_async_request(mock_app, database, async_response_obj, json_patien
     data = {
         "query_id": async_response_obj["query_id"],
         "source": "fakey node",
-        "response": {
-            "results": [
-                {
-                    "score": {"patient": 0.8},
-                    "patient": json_patients[1],
-                }
-            ]
-        },
+        "response": {"results": [{"score": {"patient": 0.8}, "patient": json_patients[1],}]},
     }
 
     response = mock_app.test_client().post(