Add commands for adding / removing hub-parsers paths from sys.path

Author: ctrl-schaff

biothings/cli/commands/pathing.py

@@ -2,17 +2,16 @@
 Module for creating the cli interface for the path interface
 """
 
-import asyncio
+import logging
 import pathlib
 import sys
-from typing import Optional
 
 import typer
-from typing_extensions import Annotated
 from rich.console import Console
 from rich.table import Table
 
-from biothings.cli.commands import operations
+from biothings.cli.commands.decorators import cli_system_path, operation_mode
+
 
 SHORT_HELP = "[green]CLI tool for viewing the python system path and adding external parsers to the system path[/green]"
 FULL_HELP = (
@@ -26,13 +25,51 @@
     rich_markup_mode="rich",
 )
 
+logger = logging.getLogger(name="biothings-cli")
+
 
 @path_application.command(name="view")
 def view_system_path() -> None:
     """
     View the system paths current discovered by python, along with potential hub parsers of interest
     that the user may wish to add to the system path for usage in data plugin testing
     """
+    display_system_paths()
+
+
+@path_application.command(name="add-hub-parsers")
+def add_parser_to_system_path() -> None:
+    """
+    Add discovered file parsers paths to the python system path for aiding in testing various data plugins
+
+    Creates the file "bt_custom.pth", in the same file extension used by the `site` module
+    provided by python. It will create this file in the biothings_hub, and if found when running any
+    command, it will add the files to the system path
+    """
+    update_system_paths()
+    display_system_paths()
+
+
+@path_application.command(name="remove-hub-parsers")
+def remove_parser_from_system_path() -> None:
+    """
+    Remove the hub parsers discovered from the python system path
+
+    Simply removes the bt_custom.pth file from the biothings-cli directory
+    """
+    remove_system_paths()
+    display_system_paths()
+
+
+@cli_system_path
+@operation_mode
+def display_system_paths() -> None:
+    """
+    Method for displaying the system path information used for the
+    biothing-cli application
+
+    External method so we can call it from multiple typer commands
+    """
     path_table = Table(title="Python System Path(s)")
 
     path_table.add_column("Index", style="cyan")
@@ -50,27 +87,53 @@ def view_system_path() -> None:
 
     hub_parser_paths = find_hub_parsers()
     for index, parser_path in enumerate(hub_parser_paths):
-        parser_table.add_row(str(index), str(parser_path), str(parser_path in system_paths))
+        parser_table.add_row(str(index), str(parser_path), str(str(parser_path) in system_paths))
 
     console = Console()
     console.print(path_table)
     console.print(parser_table)
 
 
-@path_application.command(name="add")
-def add_to_system_path() -> None:
-    """
-    Add file paths to the python system path for aiding in testing various data plugins
-    """
-    pass
+@cli_system_path
+@operation_mode
+def update_system_paths() -> None:
+    from biothings import config
+
+    discovery_path = pathlib.Path(config.BIOTHINGS_CLI_PATH).resolve().absolute()
+    discovery_path.mkdir(parents=True, exist_ok=True)
+
+    hub_parser_paths = find_hub_parsers()
+
+    path_file = discovery_path.joinpath(".biothings_cli.pth")
+    with open(path_file, "w", encoding="utf-8") as path_handle:
+        for parser_path in hub_parser_paths:
+            logger.info("Adding %s -> %s", parser_path, path_file)
+            path_handle.write(f"{parser_path}\n")
+
+
+@cli_system_path
+@operation_mode
+def remove_system_paths() -> None:
+    from biothings import config
+
+    discovery_path = pathlib.Path(config.BIOTHINGS_CLI_PATH).resolve().absolute()
+    path_file = discovery_path.joinpath(".biothings_cli.pth")
+    path_file.unlink(missing_ok=True)
+
+    hub_parser_paths = find_hub_parsers()
+    for parser_path in hub_parser_paths:
+        try:
+            sys.path.remove(str(parser_path))
+        except ValueError:
+            pass
 
 
-def find_hub_parsers() -> list[pathlib.Path]:
+def find_hub_parsers(upward_depth: int = 2) -> list[pathlib.Path]:
     """
     Attempts to locate any potential hub-based parsers that are use across different plugins
     within a shared hub instance
 
-    Will attempt to traverse recursively at most 3 levels above the present working directory
+    Will attempt to traverse recursively by <upward_depth> levels (defaults to 2 levels) above the present working directory
     The typical hub structure has the plugins directory at the same level as the hub directory
 
     pending.api structure:
@@ -86,7 +149,7 @@ def find_hub_parsers() -> list[pathlib.Path]:
 
     In either structure, the user is expected to be operating within the directory of a specific
     plugin (root/plugin/plugin_directory/) or acting as a HUB within the (root/plugin) directory
-    Either case we should be able to find the shared parsers within 3 upper levels
+    Either case we should be able to find the shared parsers within 2 upper levels
     """
     directory_pointer = pathlib.Path.cwd()
 
@@ -96,11 +159,11 @@ def find_hub_parsers() -> list[pathlib.Path]:
     # Match any path ending explicitly in hub. The bracket "[a]" matches the character literal
     # enclosed in the bracket, so [h][u][b] matches the literal hub
     match_expr = "**/[h][u][b]"
-    while traversal_counter < 2:
+    while traversal_counter < upward_depth:
         directory_pointer = directory_pointer.parent
         for hub_path in directory_pointer.glob(match_expr):
             hub_dataload = hub_path.joinpath("dataload")
             if hub_dataload.exists():
-                external_parser_paths.append(hub_dataload.resolve().absolute())
+                external_parser_paths.append(hub_path.resolve().absolute())
         traversal_counter += 1
     return external_parser_paths