refactor config to support different config options for datasets in different dataroots. (#1596)

This will give us the ability to specify different config options for
different dataroots.

the key of the dataroot dictionary is no longer the same as the dataroot_url.
Previously key==dataroot_url, and now those are separated.

Added an "is_multi_dataset" function to simplify logic where it branched on single vs multi.

Simplified the rest.py interface by no longer passing in the user annotations object, since
that can be retrieved from the dataset.

server/data_common/data_adaptor.py

@@ -14,12 +14,17 @@ from server.common.app_config import AppFeature, AppConfig
 class DataAdaptor(metaclass=ABCMeta):
     """Base class for loading and accessing matrix data"""
 
-    def __init__(self, config):
-        if type(config) != AppConfig:
+    def __init__(self, data_locator, app_config, dataset_config=None):
+        if type(app_config) != AppConfig:
             raise TypeError("config expected to be of type AppConfig")
 
+        # location to the dataset
+        self.data_locator = data_locator
+
         # config is the application configuration
-        self.config = config
+        self.app_config = app_config
+        self.server_config = self.app_config.server_config
+        self.dataset_config = dataset_config or app_config.default_dataset_config
 
         # parameters set by this data adaptor based on the data.
         self.parameters = {}
@@ -31,7 +36,7 @@ class DataAdaptor(metaclass=ABCMeta):
 
     @staticmethod
     @abstractmethod
-    def open(data_locator, config):
+    def open(data_locator, app_config, dataset_config):
         pass
 
     @staticmethod
@@ -109,13 +114,11 @@ class DataAdaptor(metaclass=ABCMeta):
     def cleanup(self):
         pass
 
-    @abstractmethod
-    def get_location(self):
-        pass
-
-    @abstractmethod
     def get_data_locator(self):
-        pass
+        return self.data_locator
+
+    def get_location(self):
+        return self.data_locator.uri_or_path
 
     def get_about(self):
         return None
@@ -149,8 +152,8 @@ class DataAdaptor(metaclass=ABCMeta):
         features = [
             AppFeature("/cluster/", method="POST", available=False),
             AppFeature("/layout/obs", method="GET", available=self.get_embedding_names() is not None),
-            AppFeature("/layout/obs", method="PUT", available=self.config.embeddings__enable_reembedding),
-            AppFeature("/diffexp/", method="POST", available=self.config.diffexp__enable),
+            AppFeature("/layout/obs", method="PUT", available=self.dataset_config.embeddings__enable_reembedding),
+            AppFeature("/diffexp/", method="POST", available=self.dataset_config.diffexp__enable),
             AppFeature("/annotations/obs", method="PUT", available=annotations is not None),
         ]
         return features
@@ -260,7 +263,6 @@ class DataAdaptor(metaclass=ABCMeta):
         * currently only supports access on VAR axis
         * currently only supports filtering on VAR axis
         """
-
         if axis != Axis.VAR:
             raise ValueError("Only VAR dimension access is supported")
 
@@ -273,7 +275,7 @@ class DataAdaptor(metaclass=ABCMeta):
             raise FilterError("filtering on obs unsupported")
 
         num_columns = self.get_shape()[1] if var_selector is None else np.count_nonzero(var_selector)
-        if self.config.exceeds_limit("column_request_max", num_columns):
+        if self.server_config.exceeds_limit("column_request_max", num_columns):
             raise ExceedsLimitError("Requested dataframe columns exceed column request limit")
 
         X = self.get_X_array(obs_selector, var_selector)
@@ -301,14 +303,14 @@ class DataAdaptor(metaclass=ABCMeta):
         except (KeyError, IndexError):
             raise FilterError("Error parsing filter")
         if top_n is None:
-            top_n = self.config.diffexp__top_n
+            top_n = self.dataset_config.diffexp__top_n
 
-        if self.config.exceeds_limit(
+        if self.server_config.exceeds_limit(
             "diffexp_cellcount_max", np.count_nonzero(obs_mask_A) + np.count_nonzero(obs_mask_B)
         ):
             raise ExceedsLimitError("Diffexp request exceeds max cell count limit")
 
-        result = self.compute_diffexp_ttest(obs_mask_A, obs_mask_B, top_n, self.config.diffexp__lfc_cutoff)
+        result = self.compute_diffexp_ttest(obs_mask_A, obs_mask_B, top_n, self.dataset_config.diffexp__lfc_cutoff)
 
         try:
             return jsonify_numpy(result)