superficial fixes

server/common/config/app_config.py

@@ -5,7 +5,7 @@
 from flatten_dict import unflatten as _unflatten, flatten as _flatten
 
 from server.common.errors import ConfigurationError
-from server.common.config.config_model import Config
+from server.common.config.config_model import AppConfigModel
 from server.default_config import get_default_config
 
 

server/common/config/client_config.py

@@ -9,9 +9,6 @@ def get_client_config(app_config: AppConfig, data_adaptor: Dataset, current_app)
     """
     dataset_config = data_adaptor.app_config
 
-    # FIXME The current set of config is not consistently presented:
-    # we have camalCase, hyphen-text, and underscore_text
-
     # make sure the configuration has been checked.
     app_config.complete_config()
 

server/common/config/config_model.py

@@ -1,7 +1,15 @@
+"""
+This module contains the configuration model used to validate the cellxgene configuration.
+
+Note: `root_validator`s and class variables are executed in the order they are defined in the class definition.
+"""
+
 from __future__ import annotations
 
 import os
+import sys
 import warnings
+from enum import Enum
 from typing import List, Optional, Union, Dict
 from urllib.parse import quote_plus
 
@@ -67,8 +75,7 @@ def check_web_base_url(cls, values):
     @validator("verbose")
     def check_verbose(cls, value):
         if not value:
-            pass
-            # sys.tracebacklimit = 0  # TODO undo
+            sys.tracebacklimit = 0
         return value
 
 
@@ -111,6 +118,7 @@ def check_dataroot(cls, values):
         base_urls = [d.base_url for d in values["dataroots"].values()]
         if len(base_urls) > len(set(base_urls)):
             raise ValueError("error in multi_dataset__dataroot:  base_urls must be unique")
+        # TODO check that at least one dataroot is set. Then we can remove AppConfig.handle_data_source.
         return values
 
 
@@ -150,7 +158,7 @@ class Server(BaseModel):
     adaptor: Adaptor
     limits: Limits
 
-    @root_validator(skip_on_failure=True)  # TODO try skip_on_failure=True
+    @root_validator(skip_on_failure=True)
     def check_data_locator(cls, values):
         if values["data_locator"].s3_region_name is True:
             path = values["multi_dataset"].dataroots or values["multi_dataset"].dataroot
@@ -181,13 +189,11 @@ def check_cxg_adaptor(cls, values):
         return values
 
 
-class ScriptsItem(BaseModel, extra=Extra.allow):
+class ScriptsItem(BaseModel):
     src: str
 
-    # class Config:
-    #     extra = Extra.ignore
-    # integrity: Optional[str] = None
-    # crossorigin: Optional[str] = None
+    class Config:
+        extra = Extra.allow
 
 
 class DatasetApp(BaseModel):
@@ -237,6 +243,6 @@ def check_x_approximate_distribution(cls, value):
         return value
 
 
-class Config(BaseModel):
+class AppConfigModel(BaseModel):
     server: Optional[Server]
     default_dataset: Optional[DefaultDataset]

server/default_config.py

@@ -24,15 +24,15 @@
     web_base_url: null
 
   multi_dataset:
-    # Dataroot must be set, then cellxgene may serve multiple datasets.
-    # dataroot may be a string, representing the path to a directory or S3 prefix.  In this
+    # dataroot or dataroots must be set, then cellxgene may serve multiple datasets.
+    # dataroot must be a string, representing the path to a directory or S3 prefix.  In this
     # case the datasets in that location are accessed from <server>/d/<datasetname>.
     # example:
     #     dataroot:  /path/to/datasets/
     # or
     #     dataroot:  s3://bucket/prefix/
     #
-    # As an alternative, dataroot can be a dictionary, where a dataset key is associated with a base_url
+    # dataroots can be a dictionary, where a dataset key is associated with a base_url
     # and a dataroot.
     # example:
     #     dataroots:
@@ -105,12 +105,6 @@
     count: 15
 
   X_approximate_distribution: normal # currently fixed config
-
-  # You can retrieve configuration parameters from this config file, the environment,
-  # the AWS secrets manager, or from the "cellxgene launch" command line arguments.
-  # They are applied in that order, meaning that if a parameter is defined in more
-  # than one location, the last one applied takes effect.
-
 """