Add cli configuration application (#418)

* Add a configuration typer application ...

Creates a commands module to store the command logic in one location.
Moves settings configuration into the config submodule in commands
Attempts to create a clear logically distinction between cli logic and
hub logic

* Update the docstrings for both config commands

* Add proper handling for local configuration file

Author: ctrl-schaff

biothings/cli/__init__.py

@@ -2,34 +2,40 @@
 Entrypoint for the biothings-cli tool
 """
 
+from typing import Literal
 import importlib.util
 import logging
 import os
 import sys
 
+import typer
+from rich.logging import RichHandler
 
-from biothings.cli.settings import (
-    setup_biothings_configuration,
-    setup_commandline_configuration,
-    setup_logging_configuration,
-)
+from biothings.cli.commands.admin import build_admin_application
+from biothings.cli.commands.config import config_application, load_configuration
+from biothings.cli.commands.dataplugin import dataplugin_application
 
 
-def check_module_import_status(module: str) -> bool:
+def setup_logging_configuration(logging_level: Literal[10, 20, 30, 40, 50]) -> None:
     """
-    Verify that we can import a module prior to proceeding with creating our commandline
-    tooling that depends on those modules
+    Configures the logging based off our environment configuration
     """
-    module_specification = importlib.util.find_spec(module)
-    status = module_specification is not None
-    return status
+    rich_handler = RichHandler(
+        level=logging_level,
+        markup=True,
+        rich_tracebacks=False,  # typer creates it already
+        show_path=False,
+        tracebacks_suppress=[typer],
+    )
+    logging.basicConfig(level=logging_level, format="%(message)s", datefmt="[%X]", handlers=[rich_handler])
 
 
 def main():
     """
-    The entrypoint for running the BioThings CLI to test your local data plugin
+    The entrypoint for running the BioThings CLI
     """
-    typer_status = check_module_import_status("typer")
+    module_specification = importlib.util.find_spec("typer")
+    typer_status = module_specification is not None
     if not typer_status:
         logging.error(
             (
@@ -48,14 +54,13 @@ def main():
     cli_debug_flag = os.environ.get("BTCLI_DEBUG", False)
     cli_rich_traceback_flag = os.environ.get("BTCLI_RICH_TRACEBACK", False)
 
-    cli = setup_commandline_configuration(debug=cli_debug_flag, rich_traceback=cli_rich_traceback_flag)
+    admin_application = build_admin_application(debug=cli_debug_flag, rich_traceback=cli_rich_traceback_flag)
     logging_level = logging.WARNING
     if cli_debug_flag:
         logging_level = logging.DEBUG
     setup_logging_configuration(logging_level)
-    setup_biothings_configuration()
+    load_configuration()
 
-    from biothings.cli.dataplugin import dataplugin_application
-
-    cli.add_typer(dataplugin_application, name="dataplugin")
-    return cli()
+    admin_application.add_typer(dataplugin_application, name="dataplugin")
+    admin_application.add_typer(config_application, name="config")
+    return admin_application()

biothings/cli/assistant.py

@@ -38,7 +38,7 @@ class CLIAssistant(BaseAssistant):
 
     plugin_type = "CLI"
 
-    def __init__(self, plugin_name: Optional[str] = None, job_manager: "JobManager" = None):
+    def __init__(self, plugin_name: Optional[str] = None, job_manager: CLIJobManager = None):
         from biothings import config
         from biothings.hub.databuild.builder import BuilderManager
         from biothings.hub.dataindex.indexer import IndexManager

biothings/cli/commands/__init__.py

@@ -0,0 +1,47 @@
+"""
+Configuration settings for the biothings-cli tool
+
+> Logging
+> Tool Configuration
+    > Creates a mock config used in the biothings.api backend
+"""
+
+import sys
+
+import typer
+
+
+def build_admin_application(debug: bool, rich_traceback: bool) -> typer.Typer:
+    """
+    Builds the main administrative command line application for the
+    biothings-cli application
+    """
+    pretty_exceptions_show_locals = False
+    pretty_exceptions_enable = False
+    sys.tracebacklimit = 1
+
+    if rich_traceback:
+        pretty_exceptions_enable = True
+        sys.tracebacklimit = 1000
+
+    if debug:
+        pretty_exceptions_enable = True
+        pretty_exceptions_show_locals = True
+        sys.tracebacklimit = 1000
+
+    # prevent dimming the help text from the 2nd line
+    # see: https://github.com/tiangolo/typer/issues/437#issuecomment-1224149402
+    typer.rich_utils.STYLE_HELPTEXT = ""
+
+    context_settings = {"help_option_names": ["-h", "--help"]}
+    typer_instance = typer.Typer(
+        help="[green]BioThings Admin CLI to test your local data plugins. See helps for each command for specific usage.[/green]",
+        rich_help_panel="Help and Others",
+        rich_markup_mode="rich",
+        context_settings=context_settings,
+        no_args_is_help=True,
+        pretty_exceptions_show_locals=pretty_exceptions_show_locals,
+        pretty_exceptions_enable=pretty_exceptions_enable,
+    )
+
+    return typer_instance