Update CLI.

Author: hyletic

src/lovd/__init__.py

@@ -1,4 +1,3 @@
-
 """
 LOVD Querying Interfaces
 ========================
@@ -7,14 +6,15 @@
 Variants Database (LOVD).
 
 """
-from . import client, config, constants
+
+from . import cli, client, config, constants
 
 from .client import (
     LOVD_RATE_LIMIT,
     LOVDClient,
-    get_lovd_variants,
+    get_variants,
     get_variants_from_config,
-    variants_to_dataframe
+    variants_to_dataframe,
 )
 from .config import load_acquisition_config, options
 from .constants import (
@@ -25,18 +25,18 @@
     LOVDTOOLS_DATA_PATH,
     LOVDTOOLS_ROOT_PATH,
     LOVDTOOLS_STATE_PATH,
+    LOVDTOOLS_VERSION,
     LOVD_EMAIL,
     NCBI_EMAIL,
     TARGET_GENE_SYMBOLS,
-    USER_AGENT_STRING
-
+    USER_AGENT_STRING,
 )
 
 
 # : package metadata
-__author__ = "Caleb Rice"
+__author__ = "Caleb R."
 __email__ = "hyletic@proton.me"
-__version__ = "0.1.0-dev8"
+__version__ = "0.1.0-dev28"
 
 
 __all__ = [
@@ -48,26 +48,24 @@
     "LOVDTOOLS_DATA_PATH",
     "LOVDTOOLS_ROOT_PATH",
     "LOVDTOOLS_STATE_PATH",
+    "LOVDTOOLS_VERSION",
     "LOVD_EMAIL",
     "LOVD_RATE_LIMIT",
     "NCBI_EMAIL",
     "TARGET_GENE_SYMBOLS",
     "USER_AGENT_STRING",
-
     # : modules
+    "cli",
     "client",
     "config",
     "constants",
-
     # : classes
     "LOVDClient",
-
     # : functions
     "get_variants_from_config",
-    "get_lovd_variants",
+    "get_variants",
     "load_acquisition_config",
     "variants_to_dataframe",
-
     # : objects
-    "options"
+    "options",
 ]

src/lovd/cli.py

@@ -0,0 +1,203 @@
+"""
+LOVDTools CLI
+=============
+
+This module provides a command-line interface for the LOVDTools API client.
+
+"""
+
+from __future__ import annotations
+
+import logging
+
+import click
+
+from .client import LOVDClient
+from .config import options
+from .constants import ACQUISITION_CONFIG_PATH, LOVDTOOLS_VERSION
+
+
+# : API client initialization
+#
+client = LOVDClient()
+
+
+# : command-line interface
+#
+@click.group(invoke_without_command=True)
+@click.option(
+    "--version",
+    "-V",
+    is_flag=True,
+    help="Show `lovdtools`'s version string and exit."
+)
+@click.pass_context
+def cli(ctx, version):
+    """LOVDTools – An API client for the global–shared LOVD instance.
+
+    This is a command-line interface for the LOVD API client, which
+    provides various utilities for querying the global–shared instance
+    of the Leiden Open Variants Database (LOVD).
+
+    """
+    logging.basicConfig(level="INFO", format="%(name)s – %(levelname)s: %(message)s")
+    ctx.logger = logging.getLogger(__name__)
+
+    ctx.logger.debug("Logger setup complete.")
+
+    if version:
+        click.echo(f"lovdtools, v{LOVDTOOLS_VERSION}")
+
+    if not ctx.invoked_subcommand and not version:
+        click.echo(ctx.get_help())
+
+
+@cli.group()
+def config():
+    pass
+
+
+@config.command(name="show")
+def show_config():
+    """List all configuration options, along with their current values."""
+    print()
+    print("LOVDTools Configuration")
+    print("─" * 70)
+
+    for k, v in options.items():
+        print(f"o    {k}: {v}")
+
+    print("─" * 70 + "\n")
+
+
+@config.command(name="get")
+@click.argument("key", metavar="KEY", required=True)
+def get_config_option(key: str):
+    """Get the current value of a specific configuration option."""
+    print(f"\n{key.lower()}: {options[key]}\n")
+
+
+@config.command(name="set")
+@click.argument("key", metavar="KEY", required=True)
+@click.argument("value", nargs=-1, metavar="VALUE", required=True)
+def set_config_option(key: str, value: tuple[str]):
+    """Set the current value of a specific configuration option."""
+    try:
+        # Join the tuple elements into a single string
+        value_str = " ".join(value)
+        
+        # Determine if this key should be a list or string
+        # target_gene_symbols and search_terms should be lists
+        # email and user_agent should be strings
+        if key in ["target_gene_symbols", "search_terms"]:
+            # Split by spaces to create a list
+            values = value_str.split()
+            options[key] = values
+        else:
+            # Keep as a single string (don't split)
+            options[key] = value_str
+        
+        with open(ACQUISITION_CONFIG_PATH, "w") as f:
+            import yaml
+            yaml.safe_dump(options, f)
+            
+        click.echo(f"Set configuration option `{key}` to `{value_str}`.")
+    except Exception as e:
+        raise e
+
+
+@cli.command(name="query")
+@click.argument("symbols", nargs=-1, metavar="SYMBOLS")
+@click.option(
+    "--search-terms",
+    "-S",
+    multiple=True,
+    help="A search term or array of search terms by which to filter results."
+)
+@click.option(
+    "--filters",
+    "-F",
+    multiple=True,
+    help="An array of [KEY]:[VALUE] pairs to pass as parameters to the LOVD API call."
+)
+@click.option(
+    "--out",
+    "-o",
+    help="The directory to which results are output."
+)
+@click.option(
+    "--include-effect",
+    "-E",
+    is_flag=True,
+    help="Includes variants' reported effects in results."
+)
+@click.option(
+    "--verbose",
+    "-v",
+    is_flag=True,
+    help="Enables verbose output."
+)
+@click.option(
+    "--progressive",
+    "-p",
+    is_flag=True,
+    help="Enables a progress bar indicator for the query."
+)
+def query(
+    symbols: tuple[str],
+    search_terms: tuple[str] | None,
+    filters: tuple[str] | None,
+    out: str | None,
+    include_effect: bool | None,
+    verbose: bool | None,
+    progressive: bool | None
+):
+    """Query LOVD for the given gene symbol(s).
+
+    Retrieves records for variants reported on the given gene symbols,
+    according to the provided filters.
+
+    """
+    if progressive:
+        client.with_progress()
+    
+    symbols = symbols or options["target_gene_symbols"]
+
+    if verbose:
+        click.echo("Getting variants reported on the following gene(s):")
+
+    for s in symbols:
+        if s in "email target_gene_symbols user_agent":
+            raise click.BadArgumentUsage(
+                "It looks like you're trying to get the current value of a\n"
+                "configuration option, but you used `lovdtools get [KEY]`, which is\n"
+                "for querying LOVD for variants on one or more gene symbols.\n"
+                "\nInstead, you should use `lovdtools config get [KEY]`."
+            )
+
+        else:
+            if verbose:
+                click.echo(f"    o  {s}")
+
+    try:
+        variants = client.get_variants_for_genes(
+            symbols,
+            out or "./output",
+            search_terms,
+            include_effect or True,
+            list({k:v for k, v in [f.split(sep=":") for f in filters]}),
+        )
+    except click.BadArgumentUsage as e:
+        e("Improper argument usage.")
+    except click.BadOptionUsage as e:
+        e("Improper option usage.")
+    except click.BadParameter as e:
+        e("Bad parameter usage.")
+    except Exception as e:
+        e("LOVDTools encountered an unhandled exception. Double-check your inputs.")
+
+    if verbose:
+        click.echo("Requisition complete.")
+
+    return variants
+