Improve hosted cellxgene (#1234)

* Improve hosted cellxgene

 - option to turn off the test index page, or supply a page for redirect.
   For EB, The default is to return 404.  For cli launch, the default is the test page.

 - option to select which matrix types are allowed for multi dataset servers.
   For EB, The default is CXG only.  For cli launch, the default is any matrix type.

 - Return early with an error response if diffexp is requested when not configured

 - Verified that reembedings and user annotations also return with an error response
   if used when not enabled.

TODO:  The new options cannot currently be set by the user.
I plan to add a configuration file where these and all other settings can be set.

 Fixes #1210 
 Fixes #1228  
 Fixes #1229

server/common/app_config.py

@@ -35,6 +35,15 @@ class AppConfig(object):
         self.enable_reembedding = False
         self.anndata_backed = False
 
+        # The index page when in multi-dataset mode:
+        #   False or None:  this returns a 404 code
+        #   True:  loads a test index page, which links to the datasets that are available in the dataroot
+        #   string/URL:  redirect to this URL:  flask.redirect(config.multi_dataset_index)
+        self.multi_dataset_index = False
+
+        # A list of allowed matrix types.  If an empty list, then all matrix types are allowed
+        self.multi_dataset_allowed_matrix_type = []
+
         # TODO these options may not apply to all datasets in the multi dataset.
         # may need to invent a way to associate these config parameters with
         # specific datasets.
@@ -58,12 +67,13 @@ class AppConfig(object):
             "anndata_backed",
             "disable_diffexp",
             "enable_reembedding",
+            "multi_dataset_index",
+            "multi_dataset_allowed_matrix_type",
         ]
 
         self.update(inputs, kw)
 
     def update(self, inputs, kw):
-
         for k, v in kw.items():
             if k in inputs:
                 setattr(self, k, v)

server/common/rest.py

@@ -68,11 +68,12 @@ def annotations_put_fbs_helper(data_adaptor, annotations, fbs):
 
 
 def annotations_obs_put(request, data_adaptor, annotations):
-    anno_collection = request.args.get("annotation-collection-name", default=None)
-    fbs = request.get_data()
     if annotations is None:
         return make_response("Error, annotations are not configured", HTTPStatus.BAD_REQUEST)
 
+    anno_collection = request.args.get("annotation-collection-name", default=None)
+    fbs = request.get_data()
+
     if anno_collection is not None:
         if not annotations.is_safe_collection_name(anno_collection):
             return make_response(f"Error, bad annotation collection name", HTTPStatus.BAD_REQUEST)
@@ -130,11 +131,14 @@ def data_var_put(request, data_adaptor):
 
 
 def diffexp_obs_post(request, data_adaptor):
+    if data_adaptor.config.disable_diffexp:
+        return make_response(f"diffexp not supported.", HTTPStatus.BAD_REQUEST)
+
     args = request.get_json()
     # confirm mode is present and legal
     try:
         mode = DiffExpMode(args["mode"])
-    except KeyError:
+    except (KeyError, TypeError):
         return make_response("Error: mode is required", HTTPStatus.BAD_REQUEST)
     except ValueError:
         return make_response(f"Error: invalid mode option {args['mode']}", HTTPStatus.BAD_REQUEST)