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/test/test_anndata_adaptor.py

@@ -13,6 +13,7 @@ import pandas as pd
 from server.data_anndata.anndata_adaptor import AnndataAdaptor
 from server.common.errors import FilterError
 from server.common.data_locator import DataLocator
+from server.common.app_config import AppConfig
 
 """
 Test the anndata adaptor using the pbmc3k data set.
@@ -33,14 +34,18 @@ Test the anndata adaptor using the pbmc3k data set.
 class AdaptorTest(unittest.TestCase):
     def setUp(self):
         args = {
-            "layout": ["umap"],
-            "max_category_items": 100,
-            "obs_names": None,
-            "var_names": None,
-            "diffexp_lfc_cutoff": 0.01,
-            "anndata_backed": self.backed,
+            "embeddings__names": ["umap"],
+            "presentation__max_categories": 100,
+            "single_dataset__obs_names": None,
+            "single_dataset__var_names": None,
+            "diffexp__lfc_cutoff": 0.01,
+            "adaptor__anndata_adaptor__backed": self.backed,
+            "single_dataset__datapath" : self.data_locator
         }
-        self.data = AnndataAdaptor(DataLocator(self.data_locator), args)
+        config = AppConfig()
+        config.update(**args)
+        config.complete_config()
+        self.data = AnndataAdaptor(DataLocator(self.data_locator), config)
 
     def test_init(self):
         self.assertEqual(self.data.cell_count, 2638)
@@ -88,7 +93,7 @@ class AdaptorTest(unittest.TestCase):
     def test_get_schema(self):
         with open(path.join(path.dirname(__file__), "schema.json")) as fh:
             schema = json.load(fh)
-            self.assertEqual(self.data.get_schema(), schema)
+            self.assertDictEqual(self.data.get_schema(), schema)
 
     def test_schema_produces_error(self):
         self.data.data.obs["time"] = pd.Series(
@@ -109,9 +114,9 @@ class AdaptorTest(unittest.TestCase):
             self.assertEqual(len(feature), 1)
 
         check_feature("POST", "/cluster/", False)
-        check_feature("POST", "/diffexp/", not self.data.config.disable_diffexp)
+        check_feature("POST", "/diffexp/", self.data.config.diffexp__enable)
         check_feature("GET", "/layout/obs", True)
-        check_feature("PUT", "/layout/obs", self.data.config.enable_reembedding)
+        check_feature("PUT", "/layout/obs", self.data.config.embeddings__enable_reembedding)
         check_feature("PUT", "/annotations/obs", False)
 
     def test_layout(self):