Introduce a config file to cellxgene (#1264)

* Introduce a config file to cellxgene

The config file format is in yaml.  The default config is located
in server/common/default_config.py.  A user may create a yaml file
that contains a subset of these fields.  It can be used during cellxgene
launch, or for hosted cellxgene.

The code has also been refactored.  Much of the logic to check arguments
has moved from launch to app config.

It is now possible to set the tiledb context parameters using the config
file.  Other feature will soon be handled in a similar way.

server/data_anndata/anndata_adaptor.py

@@ -95,7 +95,9 @@ class AnndataAdaptor(DataAdaptor):
         """
         self.original_obs_index = self.data.obs.index
 
-        for (ax_name, config_name) in ((Axis.OBS, "obs_names"), (Axis.VAR, "var_names")):
+        for (ax_name, var_name) in ((Axis.OBS, "obs"), (Axis.VAR, "var")):
+            config_name = f"single_dataset__{var_name}_names"
+            parameter_name = f"{var_name}_names"
             name = getattr(self.config, config_name)
             df_axis = getattr(self.data, str(ax_name))
             if name is None:
@@ -107,7 +109,7 @@ class AnndataAdaptor(DataAdaptor):
                         "alternative with --{ax_name}-name."
                     )
                 name = self._create_unique_column_name(df_axis.columns, "name_")
-                self.parameters[config_name] = name
+                self.parameters[parameter_name] = name
                 # reset index to simple range; alias name to point at the
                 # previously specified index.
                 df_axis.rename_axis(name, inplace=True)
@@ -119,7 +121,7 @@ class AnndataAdaptor(DataAdaptor):
                         f"Values in {ax_name}.{name} must be unique. " "Please prepare data to contain unique values."
                     )
                 df_axis.reset_index(drop=True, inplace=True)
-                self.parameters[config_name] = name
+                self.parameters[parameter_name] = name
             else:
                 # user specified a non-existent column name
                 raise KeyError(f"Annotation name {name}, specified in --{ax_name}-name does not exist.")
@@ -157,7 +159,7 @@ class AnndataAdaptor(DataAdaptor):
             with data_locator.local_handle() as lh:
                 # as of AnnData 0.6.19, backed mode performs initial load fast, but at the
                 # cost of significantly slower access to X data.
-                backed = "r" if self.config.anndata_backed else None
+                backed = "r" if self.config.adaptor__anndata_adaptor__backed else None
                 self.data = anndata.read_h5ad(lh, backed=backed)
 
         except ValueError:
@@ -177,7 +179,7 @@ class AnndataAdaptor(DataAdaptor):
             )
 
     def _validate_and_initialize(self):
-        if anndata_version_is_pre_070() and self.config.anndata_backed:
+        if anndata_version_is_pre_070() and self.config.adaptor__anndata_adaptor__backed:
             warnings.warn(
                 f"Use of --backed mode with anndata versions older than 0.7 will have serious "
                 "performance issues. Please update to at least anndata 0.7 or later."
@@ -195,7 +197,7 @@ class AnndataAdaptor(DataAdaptor):
 
         # heuristic
         n_values = self.data.shape[0] * self.data.shape[1]
-        if (n_values > 1e8 and self.config.anndata_backed is True) or (n_values > 5e8):
+        if (n_values > 1e8 and self.config.adaptor__anndata_adaptor__backed is True) or (n_values > 5e8):
             self.parameters.update({"diffexp_may_be_slow": True})
 
     def _is_valid_layout(self, arr):
@@ -242,7 +244,7 @@ class AnndataAdaptor(DataAdaptor):
                     )
                 if isinstance(datatype, CategoricalDtype):
                     category_num = len(curr_axis[ann].dtype.categories)
-                    if category_num > 500 and category_num > self.config.max_category_items:
+                    if category_num > 500 and category_num > self.config.presentation__max_categories:
                         warnings.warn(
                             f"{str(ax).title()} annotation '{ann}' has {category_num} categories, this may be "
                             f"cumbersome or slow to display. We recommend setting the "
@@ -273,7 +275,7 @@ class AnndataAdaptor(DataAdaptor):
             c) cap total list of layouts at global const MAX_LAYOUTS
         """
         # load default layouts from the data.
-        layouts = self.config.layout
+        layouts = self.config.embeddings__names
 
         if layouts is None or len(layouts) == 0:
             layouts = [key[2:] for key in self.data.obsm_keys() if type(key) == str and key.startswith("X_")]
@@ -342,7 +344,7 @@ class AnndataAdaptor(DataAdaptor):
         return getattr(self.data.obs, term_name)
 
     def get_obs_index(self):
-        name = getattr(self.config, "obs_names")
+        name = self.config.single_dataset__obs_names
         if name is None:
             return self.original_obs_index
         else: