cleaning old files

pephub/helpers.py

@@ -2,115 +2,14 @@
 from typing import List, Union, Tuple
 from fastapi import Response, UploadFile
 from fastapi.exceptions import HTTPException
-from ubiquerg import VersionInHelpParser
 
-from os.path import exists, basename
-from yaml import safe_load
+from os.path import basename
 import zipfile
 import io
 import yaml
 
 import peppy
 from peppy.const import SAMPLE_DF_KEY
-from pephub.exceptions import PepHubException
-
-from ._version import __version__ as v
-from .const import DEFAULT_PORT, PKG_NAME
-
-
-def build_parser():
-    """
-    Building argument parser
-    :return argparse.ArgumentParser
-    """
-    banner = "%(prog)s - PEP web server"
-    additional_description = (
-        "For subcommand-specific options, type: '%(prog)s <subcommand> -h'"
-    )
-    additional_description += "\nhttps://github.com/pepkit/pepserver"
-
-    parser = VersionInHelpParser(
-        prog=PKG_NAME, description=banner, epilog=additional_description
-    )
-
-    parser.add_argument(
-        "-V", "--version", action="version", version="%(prog)s {v}".format(v=v)
-    )
-
-    msg_by_cmd = {"serve": "run the server"}
-
-    subparsers = parser.add_subparsers(dest="command")
-
-    def add_subparser(cmd, description):
-        return subparsers.add_parser(cmd, description=description, help=description)
-
-    sps = {}
-    # add arguments that are common for both subparsers
-    for cmd, desc in msg_by_cmd.items():
-        sps[cmd] = add_subparser(cmd, desc)
-        sps[cmd].add_argument(
-            "-c",
-            "--config",
-            required=False,
-            dest="config",
-            help="A path to the pepserver config file",
-        )
-
-    sps["serve"].add_argument(
-        "-p",
-        "--port",
-        dest="port",
-        type=int,
-        help="The port the webserver should be run on.",
-        default=DEFAULT_PORT,
-    )
-
-    sps["serve"].add_argument(
-        "-r",
-        "--reload",
-        dest="reload",
-        type=bool,
-        help="Run the server in reload configuration",
-        default=False,
-    )
-
-    sps["serve"].add_argument(
-        "--log-level",
-        dest="log_level",
-        type=str,
-        help="The level of logging to use",
-        default="INFO",
-    )
-
-    sps["serve"].add_argument(
-        "--uvicorn-log-level",
-        dest="uvicorn_log_level",
-        type=str,
-        help="The level of logging to use for uvicorn",
-        default="info",
-    )
-
-    return parser
-
-
-def read_server_configuration(path: str) -> dict:
-    """Read in a server configuration file at a specified path"""
-    if not exists(path):
-        raise FileNotFoundError(f"Configuration file at {path} could not be found.")
-    with open(path, "r") as f:
-        cfg = safe_load(f)
-        if cfg.get("data") is None:
-            raise PepHubException(
-                "'data' section is required in the configuration file."
-            )
-        if cfg["data"].get("path") is None:
-            raise PepHubException(
-                "No path to PEPs was specified in the configuration file."
-            )
-
-        return {
-            "data": {"path": cfg["data"]["path"], "index": cfg["data"].get("index")}
-        }
 
 
 def get_project_sample_names(proj: peppy.Project) -> List[str]: