experimental re-embedding (#1186)

* first cut at re-embedding route and back-end support

* update and expand config route tests

* add scanpy_umap

* add reembedding to config route parameters

* front-end support for reembedding fetch and UI

* remove unused imports

* add loading state

* save reembedding in reducer state

* improve withColsFrom

* transmit reembed schema to client; pick unique embedding names

* display embeddings

* format

* lint

* spaces, tab size 2

* lint

* test hack for smoke-test race

* back out hack sleep

* add check for backed mode

* add unit test for reembedding

* lint

* hide re-embedding CLI param from help

server/common/app_config.py

@@ -32,6 +32,7 @@ class AppConfig(object):
         self.max_category_items = 100
         self.diffexp_lfc_cutoff = 0.01
         self.disable_diffexp = False
+        self.enable_reembedding = False
         self.anndata_backed = False
 
         # TODO these options may not apply to all datasets in the multi dataset.
@@ -56,6 +57,7 @@ class AppConfig(object):
             "var_names",
             "anndata_backed",
             "disable_diffexp",
+            "enable_reembedding",
         ]
 
         self.update(inputs, kw)
@@ -80,7 +82,7 @@ class AppConfig(object):
         # we have camalCase, hyphen-text, and underscore_text
 
         # features
-        features = [f.todict() for f in data_adaptor.get_features().values()]
+        features = [f.todict() for f in data_adaptor.get_features(annotation)]
 
         # display_names
         title = self.get_title(data_adaptor)
@@ -105,6 +107,7 @@ class AppConfig(object):
             "diffexp_lfc_cutoff": self.diffexp_lfc_cutoff,
             "backed": self.anndata_backed,
             "disable-diffexp": self.disable_diffexp,
+            "enable-reembedding": self.enable_reembedding,
             "annotations": False,
             "annotations_file": None,
             "annotations_output_dir": None,

server/common/rest.py

@@ -165,7 +165,7 @@ def diffexp_obs_post(request, data_adaptor):
     try:
         diffexp = data_adaptor.diffexp_topN(set1_filter, set2_filter, count)
         return make_response(diffexp, HTTPStatus.OK, {"Content-Type": "application/json"})
-    except (ValueError, FilterError) as e:
+    except (ValueError, DisabledFeatureError, FilterError) as e:
         return make_response(str(e), HTTPStatus.BAD_REQUEST)
     except JSONEncodingValueError as e:
         # JSON encoding failure, usually due to bad data
@@ -188,3 +188,33 @@ def layout_obs_get(request, data_adaptor):
         return make_response(str(e), HTTPStatus.INTERNAL_SERVER_ERROR)
     except ValueError as e:
         return make_response(str(e), HTTPStatus.INTERNAL_SERVER_ERROR)
+
+
+def layout_obs_put(request, data_adaptor):
+    preferred_mimetype = request.accept_mimetypes.best_match(["application/octet-stream"])
+    if preferred_mimetype != "application/octet-stream":
+        return make_response(f"Unsupported MIME type '{request.accept_mimetypes}'", HTTPStatus.NOT_ACCEPTABLE)
+    if not data_adaptor.config.enable_reembedding:
+        return make_response(f"Computed embedding not supported.", HTTPStatus.BAD_REQUEST)
+
+    args = request.get_json()
+    filter = args["filter"] if args else None
+    if not filter:
+        return make_response("Error: obs filter is required", HTTPStatus.BAD_REQUEST)
+    method = args["method"] if args else "umap"
+
+    try:
+        schema, fbs = data_adaptor.compute_embedding(method, filter)
+        return make_response(
+            fbs,
+            HTTPStatus.OK,
+            {
+                "Content-Type": "application/octet-stream",
+                "CxG-Schema": json.dumps(schema),
+                "Access-Control-Expose-Headers": "CxG-Schema",
+            },
+        )
+    except NotImplementedError as e:
+        return make_response(str(e), HTTPStatus.NOT_IMPLEMENTED)
+    except (ValueError, DisabledFeatureError, FilterError) as e:
+        return make_response(str(e), HTTPStatus.BAD_REQUEST)