Refactor czi_hosted and server into backend directory, pull common code into backend/common, refactor tests (#2102)

* move local_server -> backend/server server-> backend/czi_hosted, pull common code into backend/common update imports, tests and make commands

backend/server/app/app.py

@@ -0,0 +1,244 @@
+import datetime
+import logging
+from functools import wraps
+from http import HTTPStatus
+
+from flask import (
+    Flask,
+    current_app,
+    make_response,
+    render_template,
+    Blueprint,
+    request,
+    send_from_directory,
+)
+from flask_restful import Api, Resource
+
+import backend.server.common.rest as common_rest
+from backend.common.errors import DatasetAccessError, RequestException
+from backend.server.common.health import health_check
+from backend.common.utils.utils import Float32JSONEncoder
+
+webbp = Blueprint("webapp", "backend.server.common.web", template_folder="templates")
+
+
+@webbp.route("/", methods=["GET"])
+def dataset_index():
+    app_config = current_app.app_config
+
+    dataset_config = app_config.get_dataset_config()
+    scripts = dataset_config.app__scripts
+    inline_scripts = dataset_config.app__inline_scripts
+
+    try:
+        args = {"SCRIPTS": scripts, "INLINE_SCRIPTS": inline_scripts}
+        return render_template("index.html", **args)
+
+    except DatasetAccessError as e:
+        return common_rest.abort_and_log(
+            e.status_code, f"Invalid dataset: {e.message}", loglevel=logging.INFO, include_exc_info=True
+        )
+
+
+@webbp.errorhandler(RequestException)
+def handle_request_exception(error):
+    return common_rest.abort_and_log(error.status_code, error.message, loglevel=logging.INFO, include_exc_info=True)
+
+
+def requires_authentication(func):
+    @wraps(func)
+    def wrapped_function(self, *args, **kwargs):
+        auth = current_app.auth
+        if auth.is_user_authenticated():
+            return func(self, *args, **kwargs)
+        else:
+            return make_response("not authenticated", HTTPStatus.UNAUTHORIZED)
+
+    return wrapped_function
+
+
+def rest_get_data_adaptor(func):
+    @wraps(func)
+    def wrapped_function(self):
+        try:
+            return func(self, current_app.data_adaptor)
+        except DatasetAccessError as e:
+            return common_rest.abort_and_log(
+                e.status_code, f"Invalid dataset: {e.message}", loglevel=logging.INFO, include_exc_info=True
+            )
+
+    return wrapped_function
+
+
+class HealthAPI(Resource):
+    def get(self):
+        config = current_app.app_config
+        return health_check(config)
+
+
+class SchemaAPI(Resource):
+    # TODO @mdunitz separate dataset schema and user schema
+    @rest_get_data_adaptor
+    def get(self, data_adaptor):
+        return common_rest.schema_get(data_adaptor)
+
+
+class ConfigAPI(Resource):
+    @rest_get_data_adaptor
+    def get(self, data_adaptor):
+        return common_rest.config_get(current_app.app_config, data_adaptor)
+
+
+class UserInfoAPI(Resource):
+    @rest_get_data_adaptor
+    def get(self, data_adaptor):
+        return common_rest.userinfo_get(current_app.app_config, data_adaptor)
+
+
+class AnnotationsObsAPI(Resource):
+    @rest_get_data_adaptor
+    def get(self, data_adaptor):
+        return common_rest.annotations_obs_get(request, data_adaptor)
+
+    @requires_authentication
+    @rest_get_data_adaptor
+    def put(self, data_adaptor):
+        return common_rest.annotations_obs_put(request, data_adaptor)
+
+
+class AnnotationsVarAPI(Resource):
+    @rest_get_data_adaptor
+    def get(self, data_adaptor):
+        return common_rest.annotations_var_get(request, data_adaptor)
+
+
+class DataVarAPI(Resource):
+    @rest_get_data_adaptor
+    def put(self, data_adaptor):
+        return common_rest.data_var_put(request, data_adaptor)
+
+    @rest_get_data_adaptor
+    def get(self, data_adaptor):
+        return common_rest.data_var_get(request, data_adaptor)
+
+
+class ColorsAPI(Resource):
+    @rest_get_data_adaptor
+    def get(self, data_adaptor):
+        return common_rest.colors_get(data_adaptor)
+
+
+class DiffExpObsAPI(Resource):
+    @rest_get_data_adaptor
+    def post(self, data_adaptor):
+        return common_rest.diffexp_obs_post(request, data_adaptor)
+
+
+class LayoutObsAPI(Resource):
+    @rest_get_data_adaptor
+    def get(self, data_adaptor):
+        return common_rest.layout_obs_get(request, data_adaptor)
+
+    @rest_get_data_adaptor
+    def put(self, data_adaptor):
+        return common_rest.layout_obs_put(request, data_adaptor)
+
+
+class GenesetsAPI(Resource):
+    @rest_get_data_adaptor
+    def get(self, data_adaptor):
+        return common_rest.genesets_get(request, data_adaptor)
+
+    @requires_authentication
+    @rest_get_data_adaptor
+    def put(self, data_adaptor):
+        return common_rest.genesets_put(request, data_adaptor)
+
+
+class GenesetSummaryAPI(Resource):
+    @rest_get_data_adaptor
+    def get(self, data_adaptor):
+        return common_rest.geneset_summary_get(request, data_adaptor)
+
+
+def get_api_base_resources(bp_base):
+    """Add resources that are accessed from the api url"""
+    api = Api(bp_base)
+
+    # Diagnostics routes
+    api.add_resource(HealthAPI, "/health")
+    return api
+
+
+def get_api_dataroot_resources(bp_dataroot):
+    """Add resources that refer to a dataset"""
+    api = Api(bp_dataroot)
+
+    def add_resource(resource, url):
+        """convenience function to make the outer function less verbose"""
+        api.add_resource(resource, url)
+
+    # Initialization routes
+    add_resource(SchemaAPI, "/schema")
+    add_resource(ConfigAPI, "/config")
+    add_resource(UserInfoAPI, "/userinfo")
+    # Data routes
+    add_resource(AnnotationsObsAPI, "/annotations/obs")
+    add_resource(AnnotationsVarAPI, "/annotations/var")
+    add_resource(DataVarAPI, "/data/var")
+    add_resource(GenesetsAPI, "/genesets")
+    add_resource(GenesetSummaryAPI, "/geneset_summary")
+    # Display routes
+    add_resource(ColorsAPI, "/colors")
+    # Computation routes
+    add_resource(DiffExpObsAPI, "/diffexp/obs")
+    add_resource(LayoutObsAPI, "/layout/obs")
+    return api
+
+
+class Server:
+    @staticmethod
+    def _before_adding_routes(app, app_config):
+        """ will be called before routes are added, during __init__.  Subclass protocol """
+        pass
+
+    def __init__(self, app_config):
+        self.app = Flask(__name__, static_folder=None)
+        self._before_adding_routes(self.app, app_config)
+        self.app.json_encoder = Float32JSONEncoder
+        server_config = app_config.server_config
+
+        # enable session data
+        self.app.permanent_session_lifetime = datetime.timedelta(days=50 * 365)
+
+        # Config
+        secret_key = server_config.app__flask_secret_key
+        self.app.config.update(SECRET_KEY=secret_key)
+
+        self.app.register_blueprint(webbp)
+
+        api_version = "/api/v0.2"
+        api_path = "/"
+
+        bp_base = Blueprint("bp_base", __name__, url_prefix=api_path)
+        base_resources = get_api_base_resources(bp_base)
+        self.app.register_blueprint(base_resources.blueprint)
+
+        bp_api = Blueprint("api", __name__, url_prefix=f"{api_path}{api_version}")
+        resources = get_api_dataroot_resources(bp_api)
+        self.app.register_blueprint(resources.blueprint)
+        self.app.add_url_rule(
+            "/static/<path:filename>",
+            "static_assets",
+            view_func=lambda filename: send_from_directory("../common/web/static", filename),
+            methods=["GET"],
+        )
+
+        self.app.data_adaptor = server_config.data_adaptor
+        self.app.app_config = app_config
+
+        auth = server_config.auth
+        self.app.auth = auth
+        if auth.requires_client_login():
+            auth.add_url_rules(self.app)
+        auth.complete_setup(self.app)