move common code into server, update tests and makefile (#2425)

* move common code into server, update tests and makefile

remove backend directory, refactor

update smoke tests

server/app/app.py

@@ -0,0 +1,267 @@
+import datetime
+import logging
+from functools import wraps
+
+from flask import (
+    Flask,
+    current_app,
+    make_response,
+    render_template,
+    Blueprint,
+    request,
+    send_from_directory,
+)
+from flask_restful import Api, Resource
+
+import server.common.rest as common_rest
+from server.common.errors import DatasetAccessError, RequestException
+from server.common.health import health_check
+from server.common.utils.utils import StrictJSONEncoder
+
+webbp = Blueprint("webapp", "server.common.web", template_folder="templates")
+
+ONE_WEEK = 7 * 24 * 60 * 60
+
+
+def _cache_control(always, **cache_kwargs):
+    """
+    Used to easily manage cache control headers on responses.
+    See Werkzeug for attributes that can be set, eg, no_cache, private, max_age, etc.
+    https://werkzeug.palletsprojects.com/en/1.0.x/datastructures/#werkzeug.datastructures.ResponseCacheControl
+    """
+
+    def inner_cache_control(f):
+        @wraps(f)
+        def wrapper(*args, **kwargs):
+            response = make_response(f(*args, **kwargs))
+            if not always and not current_app.app_config.server_config.app__generate_cache_control_headers:
+                return response
+            if response.status_code >= 400:
+                return response
+            for k, v in cache_kwargs.items():
+                setattr(response.cache_control, k, v)
+            return response
+
+        return wrapper
+
+    return inner_cache_control
+
+
+def cache_control(**cache_kwargs):
+    """ config driven """
+    return _cache_control(False, **cache_kwargs)
+
+
+def cache_control_always(**cache_kwargs):
+    """ always generate headers, regardless of the config """
+    return _cache_control(True, **cache_kwargs)
+
+
+@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 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):
+    @cache_control_always(no_store=True)
+    def get(self):
+        config = current_app.app_config
+        return health_check(config)
+
+
+class SchemaAPI(Resource):
+    # TODO @mdunitz separate dataset schema and user schema
+    @cache_control(public=True, max_age=ONE_WEEK)
+    @rest_get_data_adaptor
+    def get(self, data_adaptor):
+        return common_rest.schema_get(data_adaptor)
+
+
+class ConfigAPI(Resource):
+    @cache_control(public=True, max_age=ONE_WEEK)
+    @rest_get_data_adaptor
+    def get(self, data_adaptor):
+        return common_rest.config_get(current_app.app_config, data_adaptor)
+
+
+class AnnotationsObsAPI(Resource):
+    @cache_control(public=True, max_age=ONE_WEEK)
+    @rest_get_data_adaptor
+    def get(self, data_adaptor):
+        return common_rest.annotations_obs_get(request, data_adaptor)
+
+    @cache_control(no_store=True)
+    @rest_get_data_adaptor
+    def put(self, data_adaptor):
+        return common_rest.annotations_obs_put(request, data_adaptor)
+
+
+class AnnotationsVarAPI(Resource):
+    @cache_control(public=True, max_age=ONE_WEEK)
+    @rest_get_data_adaptor
+    def get(self, data_adaptor):
+        return common_rest.annotations_var_get(request, data_adaptor)
+
+
+class DataVarAPI(Resource):
+    @cache_control(no_store=True)
+    @rest_get_data_adaptor
+    def put(self, data_adaptor):
+        return common_rest.data_var_put(request, data_adaptor)
+
+    @cache_control(public=True, max_age=ONE_WEEK)
+    @rest_get_data_adaptor
+    def get(self, data_adaptor):
+        return common_rest.data_var_get(request, data_adaptor)
+
+
+class ColorsAPI(Resource):
+    @cache_control(public=True, max_age=ONE_WEEK)
+    @rest_get_data_adaptor
+    def get(self, data_adaptor):
+        return common_rest.colors_get(data_adaptor)
+
+
+class DiffExpObsAPI(Resource):
+    @cache_control(no_store=True)
+    @rest_get_data_adaptor
+    def post(self, data_adaptor):
+        return common_rest.diffexp_obs_post(request, data_adaptor)
+
+
+class LayoutObsAPI(Resource):
+    @cache_control(public=True, max_age=ONE_WEEK)
+    @rest_get_data_adaptor
+    def get(self, data_adaptor):
+        return common_rest.layout_obs_get(request, data_adaptor)
+
+
+class GenesetsAPI(Resource):
+    @cache_control(public=True, max_age=ONE_WEEK)
+    @rest_get_data_adaptor
+    def get(self, data_adaptor):
+        return common_rest.genesets_get(request, data_adaptor)
+
+    @cache_control(no_store=True)
+    @rest_get_data_adaptor
+    def put(self, data_adaptor):
+        return common_rest.genesets_put(request, data_adaptor)
+
+
+class SummarizeVarAPI(Resource):
+    @rest_get_data_adaptor
+    @cache_control(public=True, max_age=ONE_WEEK)
+    def get(self, data_adaptor):
+        return common_rest.summarize_var_get(request, data_adaptor)
+
+    @rest_get_data_adaptor
+    @cache_control(no_store=True)
+    def post(self, data_adaptor):
+        return common_rest.summarize_var_post(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")
+    # Data routes
+    add_resource(AnnotationsObsAPI, "/annotations/obs")
+    add_resource(AnnotationsVarAPI, "/annotations/var")
+    add_resource(DataVarAPI, "/data/var")
+    add_resource(GenesetsAPI, "/genesets")
+    add_resource(SummarizeVarAPI, "/summarize/var")
+    # 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 = StrictJSONEncoder
+        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

server/app/session.py

@@ -0,0 +1,13 @@
+from uuid import uuid4
+
+from flask.sessions import SessionMixin
+
+CXGUID = "cxguid"
+
+
+def get_user_id(session: SessionMixin) -> str:
+    """ Gets a session-persistent user id. Creates one in the Flask session if non-extant """
+    if CXGUID not in session:
+        session[CXGUID] = uuid4().hex
+        session.permanent = True
+    return session[CXGUID]