clean up config handling

bedhost/cli.py

@@ -1,5 +1,5 @@
-from bedhost import PKG_NAME
-from bedhost._version import __version__
+from . import PKG_NAME
+from ._version import __version__
 from ubiquerg import VersionInHelpParser
 from yacman import select_config
 
@@ -47,11 +47,4 @@ def add_subparser(cmd, description):
             f"the first available environment variable among: {', '.join(CFG_ENV_VARS)} will be used if set."
             f" Currently: {env_var_val}",
         )
-        sps[cmd].add_argument(
-            "-d",
-            "--dbg",
-            action="store_true",
-            dest="debug",
-            help="Set logger verbosity to debug",
-        )
     return parser

bedhost/const.py

@@ -12,7 +12,7 @@
     CFG_SERVER_PORT_KEY,
 )
 
-from bedhost._version import __version__ as SERVER_VERSION
+from ._version import __version__ as SERVER_VERSION
 
 PKG_NAME = "bedhost"
 LOG_FORMAT = "%(levelname)s in %(funcName)s: %(message)s"

bedhost/data_models.py

@@ -3,13 +3,14 @@
 from pydantic import BaseModel
 from enum import Enum
 
-from bedhost.const import CFG_REMOTE_KEY
+from .const import CFG_REMOTE_KEY
 
 # from bedhost.main import bbc
-from bedhost.dependencies import get_bbconf
+# from bedhost.dependencies import get_bbconf
 
-bbc = get_bbconf()
+# bbc = get_bbconf()
 
+# from .main import bbc
 
 class DBResponse(BaseModel):
     """
@@ -20,9 +21,14 @@ class DBResponse(BaseModel):
     data: Union[List[List], List[Dict], Tuple, Dict]
 
 
+# RemoteClassEnum = Enum(
+#     "RemoteClassEnum",
+#     {r: r for r in bbc.config[CFG_REMOTE_KEY]} if bbc.is_remote else {"http": "http"},
+# )
+
 RemoteClassEnum = Enum(
     "RemoteClassEnum",
-    {r: r for r in bbc.config[CFG_REMOTE_KEY]} if bbc.is_remote else {"http": "http"},
+    {"http": "http"},
 )
 
 BedsetDigest = Path(

bedhost/dependencies.py

@@ -1,14 +0,0 @@
-from bedhost.helpers import BedHostConf
-import os
-from bedhost.exceptions import BedHostException
-
-bb_conf_file_path = os.environ.get("BEDBASE_CONFIG") or None
-
-try:
-    bedbase_conf = BedHostConf(bb_conf_file_path)
-except Exception as e:
-    raise BedHostException(f"Bedbase config was not provided or is incorrect: {e}")
-
-
-def get_bbconf() -> BedHostConf:
-    return bedbase_conf

bedhost/helpers.py

@@ -1,19 +1,20 @@
 import os
-from urllib import parse
-from typing import List, Union
 
 from bbconf import BedBaseConf
 from starlette.responses import FileResponse, RedirectResponse
+from typing import List, Union
+from urllib import parse
 
-from bedhost import _LOGGER
-
-from bedhost.const import (
+from . import _LOGGER
+from .const import (
+    CFG_PATH_KEY,
+    CFG_PATH_PIPELINE_OUTPUT_KEY,
+    CFG_REMOTE_KEY,
     TYPES_MAPPING,
     VALIDATIONS_MAPPING,
     OPERATORS_MAPPING,
 )
-from bedhost.exceptions import IncorrectSchemaException
-
+from .exceptions import BedHostException
 
 class BedHostConf(BedBaseConf):
     """
@@ -194,6 +195,46 @@ def get_openapi_version(app):
         return "3.0.2"
 
 
+def attach_routers(app):
+    _LOGGER.info("Mounting routers...")
+    from .routers import bed_api, bedset_api, base, search_api
+    app.include_router(base.router)
+    app.include_router(bed_api.router)
+    app.include_router(bedset_api.router)
+    app.include_router(search_api.search_router)
+    return app
+
+
+def configure(bbconf_file_path):
+    try:
+        # bbconf_file_path = os.environ.get("BEDBASE_CONFIG") or None
+        _LOGGER.info(f"Loading config...{bbconf_file_path}")
+        bbc = BedHostConf(bbconf_file_path)
+    except Exception as e:
+        raise BedHostException(f"Bedbase config was not provided or is incorrect: {e}")
+
+    if not CFG_REMOTE_KEY in bbc.config:
+        _LOGGER.debug(
+            f"Using local files for serving: "
+            f"{bbc.config[CFG_PATH_KEY][CFG_PATH_PIPELINE_OUTPUT_KEY]}"
+        )
+        app.mount(
+            bbc.get_bedstat_output_path(),
+            StaticFiles(directory=bbc.get_bedstat_output_path()),
+            name="bedfile",
+        )
+        app.mount(
+            bbc.get_bedbuncher_output_path(),
+            StaticFiles(directory=bbc.get_bedbuncher_output_path()),
+            name="bedset",
+        )
+    else:
+        _LOGGER.debug(
+            f"Using remote files for serving. Prefix: {bbc.config[CFG_REMOTE_KEY]['http']['prefix']}"
+        )
+    return bbc
+
+
 # def get_id_map(bbc, table_name, file_type):
 #     """
 #     Get a dict for avalible file/figure ids

bedhost/main.py

@@ -1,16 +1,15 @@
+import coloredlogs
 import logging
-import sys
 import os
-
-import coloredlogs
+import sys
 import uvicorn
-from fastapi import FastAPI
-from fastapi.middleware.cors import CORSMiddleware
-from fastapi.staticfiles import StaticFiles
 
-from bedhost import _LOGGER
-from bedhost.cli import build_parser
-from bedhost.const import (
+from . import _LOGGER
+import bedhost.dependencies as dependencies
+from .helpers import FileResponse, configure, attach_routers
+
+from .cli import build_parser
+from .const import (
     CFG_PATH_KEY,
     CFG_PATH_PIPELINE_OUTPUT_KEY,
     CFG_REMOTE_KEY,
@@ -21,30 +20,9 @@
     STATIC_PATH,
     SERVER_VERSION,
 )
-
-from bedhost.helpers import FileResponse
-
-from bedhost.dependencies import get_bbconf
-from bedhost.routers import bed_api, bedset_api, base, search_api
-
-
-_LOGGER_UVICORN = logging.getLogger("uvicorn.access")
-coloredlogs.install(
-    logger=_LOGGER_UVICORN,
-    level=logging.INFO,
-    datefmt="%b %d %Y %H:%M:%S",
-    fmt="[%(levelname)s] [%(asctime)s] [BEDHOST] %(message)s",
-)
-
-
-_LOGGER_BEDHOST = logging.getLogger("bedhost")
-coloredlogs.install(
-    logger=_LOGGER_BEDHOST,
-    level=logging.INFO,
-    datefmt="%b %d %Y %H:%M:%S",
-    fmt="[%(levelname)s] [%(asctime)s] [BEDHOST] %(message)s",
-)
-
+from fastapi import FastAPI
+from fastapi.middleware.cors import CORSMiddleware
+from fastapi.staticfiles import StaticFiles
 
 app = FastAPI(
     title=PKG_NAME,
@@ -58,10 +36,9 @@
     "http://localhost:8000",
     "http://localhost:5173",
     "https://bedbase.org",
-    "*",
+    "*", # allow cross origin resource sharing, since this is a public API
 ]
 
-# uncomment below for development, to allow cross origin resource sharing
 app.add_middleware(
     CORSMiddleware,
     allow_origins=origins,
@@ -78,37 +55,12 @@ async def index():
     """
     return FileResponse(os.path.join(STATIC_PATH, "index.html"))
 
-
-def attach_routers(app):
-    _LOGGER.debug("Mounting routers")
-
-    app.include_router(base.router)
-    app.include_router(bed_api.router)
-    app.include_router(bedset_api.router)
-    app.include_router(search_api.search_router)
-
-    bbc = get_bbconf()
-
-    if not CFG_REMOTE_KEY in bbc.config:
-        _LOGGER.debug(
-            f"Using local files for serving: "
-            f"{bbc.config[CFG_PATH_KEY][CFG_PATH_PIPELINE_OUTPUT_KEY]}"
-        )
-        app.mount(
-            bbc.get_bedstat_output_path(),
-            StaticFiles(directory=bbc.get_bedstat_output_path()),
-            name="bedfile",
-        )
-        app.mount(
-            bbc.get_bedbuncher_output_path(),
-            StaticFiles(directory=bbc.get_bedbuncher_output_path()),
-            name="bedset",
-        )
-    else:
-        _LOGGER.debug(
-            f"Using remote files for serving. Prefix: {bbc.config[CFG_REMOTE_KEY]['http']['prefix']}"
-        )
-
+@app.get("/test", response_model=int)
+async def get_bedfile_count():
+    """
+    Returns the number of bedfiles available in the database
+    """
+    return int(bbc['conf'].bed.record_count)
 
 def main():
     parser = build_parser()
@@ -119,9 +71,11 @@ def main():
         sys.exit(1)
 
     if args.command == "serve":
-        attach_routers(app)
         _LOGGER.info(f"Running {PKG_NAME} app...")
-        bbc = get_bbconf()
+        bbconf_file_path = args.config or os.environ.get("BEDBASE_CONFIG") or None
+        global bbc
+        bbc = configure(bbconf_file_path)
+        attach_routers(app)
         uvicorn.run(
             app,
             host=bbc.config[CFG_SERVER_KEY][CFG_SERVER_HOST_KEY],
@@ -131,6 +85,9 @@ def main():
 
 if __name__ != "__main__":
     if os.environ.get("BEDBASE_CONFIG"):
+        bbconf_file_path = os.environ.get("BEDBASE_CONFIG") or None
+        global bbc
+        bbc = configure(bbconf_file_path)
         attach_routers(app)
     else:
         raise EnvironmentError(

bedhost/routers/base.py

@@ -1,18 +1,17 @@
 import os
 
+from fastapi import APIRouter
+from fastapi.responses import FileResponse
 from typing import Dict
 
-from bedhost.const import (
+
+from ..const import (
     STATIC_PATH,
     ALL_VERSIONS,
 )
-from fastapi import APIRouter
-from fastapi.responses import FileResponse
-from bedhost.main import _LOGGER
-from bedhost.helpers import get_openapi_version
-from bedhost.dependencies import get_bbconf
-
-bbc = get_bbconf()
+from ..helpers import get_openapi_version
+from .. import _LOGGER
+from ..main import bbc
 
 router = APIRouter(prefix="/api", tags=["base"])
 

bedhost/routers/bed_api.py

@@ -1,31 +1,34 @@
 import subprocess
 import os
-from typing import Annotated, Dict, Optional, List
+try:
+    from typing import Annotated, Dict, Optional, List
+except:
+    from typing_extensions import Annotated
+    from typing import  Dict, Optional, List
+
 import tempfile
 
 from fastapi import APIRouter, HTTPException, Query, Response, Path, Depends
 from fastapi.responses import PlainTextResponse, StreamingResponse
 from pipestat.exceptions import RecordNotFoundError
 
-from bedhost.main import _LOGGER
-
-from bedhost.data_models import (
-    DBResponse,
-    RemoteClassEnum,
-    BedDigest,
-    chromosome_number,
-)
-from bedhost.const import (
+from .. import _LOGGER
+from ..main import bbc
+from ..const import (
     CFG_PATH_PIPELINE_OUTPUT_KEY,
     CFG_REMOTE_KEY,
     CFG_PATH_KEY,
     FIG_FORMAT,
 )
-from bedhost.dependencies import get_bbconf
+from ..data_models import (
+    DBResponse,
+    RemoteClassEnum,
+    BedDigest,
+    chromosome_number,
+)
 
 
 router = APIRouter(prefix="/api/bed", tags=["bed"])
-bbc = get_bbconf()
 
 
 @router.get("/genomes")

bedhost/routers/bedset_api.py

@@ -5,19 +5,15 @@
 import os
 
 
-from bedhost import _LOGGER
-from bedhost.const import (
+from .. import _LOGGER
+from ..const import (
     CFG_REMOTE_KEY,
     CFG_PATH_KEY,
     CFG_PATH_PIPELINE_OUTPUT_KEY,
     FIG_FORMAT,
 )
-
-# from bedhost.helpers import
-from bedhost.data_models import DBResponse, RemoteClassEnum, BedsetDigest, BedList
-from bedhost.dependencies import get_bbconf
-
-bbc = get_bbconf()
+from ..data_models import DBResponse, RemoteClassEnum, BedsetDigest, BedList
+from ..main import bbc
 
 router = APIRouter(prefix="/api/bedset", tags=["bedset"])