Describe the bug
When launching cellxgene single cell explorer from the CLI and specifying a config.yaml file, several of the keys present in the default_config.yaml raise an error where they are unrecognized. Specifically, server__app__server_timing_headers, server__app__csp_directives, and both server__app__api_base_url and server__app__web_ base_url all raise an error like Error: Unknown key from config file: server__app__server_timing_headers. This happens regardless of the values provided to these keys; leaving the default values in all of them is sufficient to trigger the error. Other keys work normally; for example, setting the host and port with this config.yaml works as expected, so long as the offending keys are commented out.
To Reproduce
Steps to reproduce the behavior:
Create a config.yaml based on the default_config.yaml (i.e.):
server:
app:
verbose: false
debug: false
# if debug mode is enabled, then the server will not open a browser, and verbose mode will be enabled.
host: localhost
port : null
open_browser: false
force_https: false
flask_secret_key: null
generate_cache_control_headers: false
server_timing_headers: false
csp_directives: null
# By default, cellxgene will serve api requests from the same base url as the webpage.
# In general api_base_url and web_base_url will not need to be set.
# Reasons to set these parameters:
# 1. The cellxgene deploymnent is in an environment where the webpage and api have
# different base urls. In this case both api_base_url and web_base_url must be set.
# It is up to the server admin to ensure that the networking is setup correctly for this environment.
api_base_url: null
web_base_url: null
Run cellxgene from the CLI including this file as the config: `cellxgene launch pbmc3k.h5ad -c path/to/config.yaml
The error (Error: Unknown key from config file: serverappserver_timing_headers) is returned and the app is not launched
(to confirm the config is read at all) - delete/comment out everything after port: null, change the port to another open port, and then note that launching the app with this config does successfully use the port defined in this config.yaml
Expected behavior
All keys in default_config.yaml should be successfully parsed by the app
Version (please complete the following information):
Describe the bug When launching cellxgene single cell explorer from the CLI and specifying a config.yaml file, several of the keys present in the default_config.yaml raise an error where they are unrecognized. Specifically,
server__app__server_timing_headers,server__app__csp_directives, and bothserver__app__api_base_urlandserver__app__web_ base_urlall raise an error likeError: Unknown key from config file: server__app__server_timing_headers. This happens regardless of the values provided to these keys; leaving the default values in all of them is sufficient to trigger the error. Other keys work normally; for example, setting the host and port with this config.yaml works as expected, so long as the offending keys are commented out.To Reproduce Steps to reproduce the behavior:
Create a config.yaml based on the default_config.yaml (i.e.):
Run cellxgene from the CLI including this file as the config: `cellxgene launch pbmc3k.h5ad -c path/to/config.yaml
The error (Error: Unknown key from config file: serverappserver_timing_headers) is returned and the app is not launched
(to confirm the config is read at all) - delete/comment out everything after port: null, change the port to another open port, and then note that launching the app with this config does successfully use the port defined in this config.yaml
Expected behavior All keys in default_config.yaml should be successfully parsed by the app
Version (please complete the following information):
Additional context Thanks for any help with this!