Merge pull request #42 from PennChopMicrobiomeProgram/38-allow-explic…

…it-sqlalchemy-uri-via-env

Switch to single spec for db URI

Dockerfile

@@ -7,5 +7,7 @@ COPY . .
 RUN pip install -r requirements.txt
 RUN pip install /app/app/sample_registry/
 
+# Define env vars for debug and connection info
+
 ENTRYPOINT [ "python" ]
 CMD [ "app/app.py" ]

README.md

@@ -27,11 +27,11 @@ export FLASK_DEBUG=1 && flask --app app/app run
 
 How you want to deploy this will depend on your needs, facilities, and ability. We have it deployed by a Kubernetes cluster but you could also 1) just run it in development mode from a lab computer or 2) setup Nginx/Apache on a dedicated server or 3) run it serverlessly in the cloud (e.g. with [Zappa](https://github.com/zappa/Zappa) on AWS) or 4) do something else. There are lots of well documented examples of deploying Flask sites out there, look around and find what works best for you.
 
-When running, it will default to using a SQLite3 database located in the root of this repository (automatically created if it doesn't already exist). You can change to a PostgreSQL backend by providing the environment variables SAMPLE_REGISTRY_DB_HOST, SAMPLE_REGISTRY_DB_NAME, SAMPLE_REGISTRY_DB_USER, and SAMPLE_REGISTRY_DB_PSWD. If you want to use a different backend, you'll have to do a bit of modification to ``app/sample_registry/src/sample_registry/__init__.py`` and be somewhat familiar with SQLAlchemy URI strings.
+When running, it will default to using a SQLite3 database located in the root of this repository (automatically created if it doesn't already exist). You can change to use a different backend by setting the `SAMPLE_REGISTRY_DB_URI` environment variable before running the app. For example, another sqlite database could be specified with a URI like this: `export SAMPLE_REGISTRY_DB_URI=sqlite:////path/to/db.sqlite3`.
 
 ## Using the library
 
-The `sample_registry` library can be installed and run anywhere by following the instructions in Development (you don't need to do the `create_test_db` and running the site (bottom two commands)). To connect it to a Postgres backend, you'll need to also set the environment variables `SAMPLE_REGISTRY_DB_HOST`, `SAMPLE_REGISTRY_DB_USER`, `SAMPLE_REGISTRY_DB_NAME`, and `SAMPLE_REGISTRY_DB_PSWD`.
+The `sample_registry` library can be installed and run anywhere by following the instructions in Development (you don't need to do the `create_test_db` and running the site (bottom two commands)). To connect to a non-dev backend, see the above on SQLAlchemy URIs.
 
 ## Manually build Docker image
 

app/app.py

@@ -346,5 +346,4 @@ def index():
 
 
 if __name__ == "__main__":
-    # port = int(os.environ.get("PORT", 80))
     app.run(host="0.0.0.0", port=80)

app/sample_registry/src/sample_registry/__init__.py

@@ -4,36 +4,25 @@
 from sqlalchemy import create_engine
 from sqlalchemy.orm import sessionmaker
 
-__version__ = "1.0.5"
+__version__ = "1.1.0"
 
 
 def sample_registry_version():
     sys.stderr.write(__version__)
 
 
+try:
+    SQLALCHEMY_DATABASE_URI = os.environ["SAMPLE_REGISTRY_DB_URI"]
+except KeyError:
+    sys.stdout.write(
+        "Missing database connection information in environment, using test SQLite database\n"
+    )
+    SQLALCHEMY_DATABASE_URI = f"sqlite:///{Path(__file__).parent.parent.parent.parent.parent.resolve()}/sample_registry.sqlite3"
+
+
 if "PYTEST_VERSION" in os.environ:
     # Set SQLALCHEMY_DATABASE_URI to an in-memory SQLite database for testing
     SQLALCHEMY_DATABASE_URI = "sqlite:///:memory:"
-else:
-    try:
-        db_host = os.environ["SAMPLE_REGISTRY_DB_HOST"]
-        db_user = os.environ["SAMPLE_REGISTRY_DB_USER"]
-        db_name = os.environ["SAMPLE_REGISTRY_DB_NAME"]
-        db_pswd = os.environ["SAMPLE_REGISTRY_DB_PSWD"]
-        SQLALCHEMY_DATABASE_URI = (
-            f"postgresql://{db_user}:{db_pswd}@{db_host}/{db_name}"
-        )
-    except KeyError:
-        # For development purposes, use a SQLite db prefilled with some demo data
-        sys.stdout.write(
-            "Missing database connection information in environment, using test SQLite database\n"
-        )
-        sys.stdout.write(
-            f"SAMPLE_REGISTRY_DB_HOST: {os.environ.get('SAMPLE_REGISTRY_DB_HOST')}\nSAMPLE_REGISTRY_DB_USER: {os.environ.get('SAMPLE_REGISTRY_DB_USER')}\nSAMPLE_REGISTRY_DB_NAME: {os.environ.get('SAMPLE_REGISTRY_DB_NAME')}\nSAMPLE_REGISTRY_DB_PSWD: {os.environ.get('SAMPLE_REGISTRY_DB_PSWD')}\n"
-        )
-        SQLALCHEMY_DATABASE_URI = f"sqlite:///{Path(__file__).parent.parent.parent.parent.parent.resolve()}/sample_registry.sqlite3"
-
-print(SQLALCHEMY_DATABASE_URI)
 
 # Create database engine
 engine = create_engine(SQLALCHEMY_DATABASE_URI, echo=False)