1 files changed, 90 insertions, 0 deletions
diff --git a/uploader/__init__.py b/uploader/__init__.py
new file mode 100644
index 0000000..347f170
--- /dev/null
+++ b/uploader/__init__.py
@@ -0,0 +1,90 @@
+"""The Quality-Control Web Application entry point"""
+import os
+import sys
+import logging
+from pathlib import Path
+
+from flask import Flask, request
+from flask_session import Session
+
+from uploader.oauth2.client import user_logged_in, authserver_authorise_uri
+
+from .base_routes import base
+from .species import speciesbp
+from .dbinsert import dbinsertbp
+from .oauth2.views import oauth2
+from .expression_data import exprdatabp
+from .errors import register_error_handlers
+
+def override_settings_with_envvars(
+        app: Flask, ignore: tuple[str, ...]=tuple()) -> None:
+    """Override settings in `app` with those in ENVVARS"""
+    for setting in (key for key in app.config if key not in ignore):
+        app.config[setting] = os.environ.get(setting) or app.config[setting]
+
+
+def __log_gunicorn__(app: Flask) -> Flask:
+    """Set up logging for the WSGI environment with GUnicorn"""
+    logger = logging.getLogger("gunicorn.error")
+    app.logger.handlers = logger.handlers
+    app.logger.setLevel(logger.level)
+    return app
+
+
+def __log_dev__(app: Flask) -> Flask:
+    """Set up logging for the development environment."""
+    stderr_handler = logging.StreamHandler(stream=sys.stderr)
+    app.logger.addHandler(stderr_handler)
+
+    root_logger = logging.getLogger()
+    root_logger.addHandler(stderr_handler)
+    root_logger.setLevel(app.config["LOG_LEVEL"])
+
+    return app
+
+
+def setup_logging(app: Flask) -> Flask:
+    """Set up logging for the application."""
+    software, *_version_and_comments = os.environ.get(
+        "SERVER_SOFTWARE", "").split('/')
+    return __log_gunicorn__(app) if bool(software) else __log_dev__(app)
+
+
+def create_app():
+    """The application factory"""
+    app = Flask(__name__)
+    app.config.from_pyfile(
+        Path(__file__).parent.joinpath("default_settings.py"))
+    if "UPLOADER_CONF" in os.environ:
+        app.config.from_envvar("UPLOADER_CONF") # Override defaults with instance path
+
+    override_settings_with_envvars(app, ignore=tuple())
+
+    secretsfile = app.config.get("UPLOADER_SECRETS", "").strip()
+    if bool(secretsfile):
+        secretsfile = Path(secretsfile).absolute()
+        app.config["UPLOADER_SECRETS"] = secretsfile
+        if secretsfile.exists():
+            # Silently ignore secrets if the file does not exist.
+            app.config.from_pyfile(secretsfile)
+
+    setup_logging(app)
+
+    # setup jinja2 symbols
+    app.add_template_global(lambda : request.url, name="request_url")
+    app.add_template_global(authserver_authorise_uri)
+    app.add_template_global(lambda: app.config["GN2_SERVER_URL"],
+                            name="gn2server_uri")
+    app.add_template_global(user_logged_in)
+
+    Session(app)
+
+    # setup blueprints
+    app.register_blueprint(base, url_prefix="/")
+    app.register_blueprint(oauth2, url_prefix="/oauth2")
+    app.register_blueprint(speciesbp, url_prefix="/species")
+    app.register_blueprint(dbinsertbp, url_prefix="/dbinsert")
+    app.register_blueprint(exprdatabp, url_prefix="/expression-data")
+
+    register_error_handlers(app)
+    return app