1 files changed, 135 insertions, 0 deletions
diff --git a/uploader/__init__.py b/uploader/__init__.py
new file mode 100644
index 0000000..98e8141
--- /dev/null
+++ b/uploader/__init__.py
@@ -0,0 +1,135 @@
+"""The Quality-Control Web Application entry point"""
+import os
+import sys
+import logging
+from pathlib import Path
+from typing import Optional
+
+from flask import Flask, request
+
+from cachelib import FileSystemCache
+
+from gn_libs import jobs as gnlibs_jobs
+
+from flask_session import Session
+
+
+from uploader.oauth2.client import user_logged_in, authserver_authorise_uri
+
+from . import session
+from .base_routes import base
+from .files.views import files
+from .species import speciesbp
+from .publications import pubbp
+from .oauth2.views import oauth2
+from .expression_data import exprdatabp
+from .errors import register_error_handlers
+from .background_jobs import background_jobs_bp
+
+logging.basicConfig(
+    format=("%(asctime)s — %(filename)s:%(lineno)s — %(levelname)s "
+            "(%(thread)d:%(threadName)s): %(message)s")
+)
+
+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 setup_modules_logging(app_logger, modules):
+    """Setup module-level loggers to the same log-level as the application."""
+    loglevel = logging.getLevelName(app_logger.getEffectiveLevel())
+    for module in modules:
+        _logger = logging.getLogger(module)
+        _logger.setLevel(loglevel)
+
+
+def create_app(config: Optional[dict] = None):
+    """The application factory.
+
+    config: dict
+      Useful to override settings in the settings files and environment
+      especially in environments such as testing."""
+    if config is None:
+        config = {}
+
+    app = Flask(__name__)
+
+    ### BEGIN: Application configuration
+    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)
+    app.config.update(config) # Override everything with passed in config
+    ### END: Application configuration
+
+    app.config["SESSION_CACHELIB"] = FileSystemCache(
+        cache_dir=Path(app.config["SESSION_FILESYSTEM_CACHE_PATH"]).absolute(),
+        threshold=int(app.config["SESSION_FILESYSTEM_CACHE_THRESHOLD"]),
+        default_timeout=int(app.config["SESSION_FILESYSTEM_CACHE_TIMEOUT"]))
+
+    setup_logging(app)
+    setup_modules_logging(app.logger, (
+        "uploader.publications.models",
+        "uploader.publications.datatables",
+        "uploader.phenotypes.models"))
+
+    # 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)
+    app.add_template_global(lambda : session.user_details()["email"], name="user_email")
+
+    Session(app)
+
+    # setup blueprints
+    app.register_blueprint(base, url_prefix="/")
+    app.register_blueprint(files, url_prefix="/files")
+    app.register_blueprint(oauth2, url_prefix="/oauth2")
+    app.register_blueprint(speciesbp, url_prefix="/species")
+    app.register_blueprint(pubbp, url_prefix="/publications")
+    app.register_blueprint(background_jobs_bp, url_prefix="/background-jobs/")
+
+    register_error_handlers(app)
+    gnlibs_jobs.init_app(app)
+    return app