start to work toward using new bbconf

bedhost/__init__.py

@@ -0,0 +1,5 @@
+import logging
+from .const import PKG_NAME
+
+global _LOGGER
+_LOGGER = logging.getLogger(PKG_NAME)

bedhost/helpers.py

@@ -1,17 +1,15 @@
 import enum
-from logging import getLogger
 from urllib import parse
 
 from starlette.exceptions import HTTPException
 from starlette.responses import FileResponse, RedirectResponse
 from ubiquerg import VersionInHelpParser
 from yacman import get_first_env_var
 
+from . import _LOGGER
 from ._version import __version__ as v
 from .const import *
 
-_LOGGER = getLogger(PKG_NAME)
-
 
 def build_parser():
     """
@@ -374,7 +372,11 @@ def get_enum_map(bbc, table_name, file_type):
     """
 
     enum_map = {}
+    _LOGGER.debug(f"Getting enum map for {file_type} in {table_name}")
+
+    # TO FIX: I think we need a different way to get the schema
     schema = serve_schema_for_table(bbc=bbc, table_name=table_name)
+
     for key, value in schema.sample_level_data.items():
         if value["type"] == file_type:
             enum_map[value["label"]] = value["label"]

bedhost/main.py

@@ -1,6 +1,6 @@
 import bbconf
 import logmuse
-import logging
+
 import sys
 import uvicorn
 
@@ -10,12 +10,11 @@
 from logging import DEBUG, INFO
 from typing import Dict, List, Optional
 
+from . import _LOGGER
 from .const import *
 from .data_models import DBResponse
 from .helpers import *
 
-global _LOGGER
-_LOGGER = logging.getLogger(__name__)
 app = FastAPI(
     title=PKG_NAME,
     description="BED file/sets statistics and image server API",
@@ -96,11 +95,17 @@ def main():
             port=bbc.config[CFG_SERVER_KEY][CFG_PORT_KEY],
         )
 
-
 def register_globals(cfg):
+    import logging
+    _LOGGER.setLevel(logging.DEBUG)
+    stream = logging.StreamHandler(sys.stdout)
+    stream.setLevel(logging.DEBUG)
+    _LOGGER.addHandler(stream)
     global bbc
     bbc = BedBaseConf(bbconf.get_bedbase_cfg(cfg))
 
+    _LOGGER.debug("Registering uvicorn globals")
+
 if __name__ != "__main__":
     # TODO: streamline this to make it work easily with either CLI or uvicorn
 
@@ -109,9 +114,13 @@ def register_globals(cfg):
         register_globals(os.environ.get("BEDBASE_CONFIG"))
         from .routers import api, private_api
 
+        _LOGGER.debug("Mounting routers")
         app.include_router(api.router)
         app.include_router(private_api.router, prefix="/_private_api")
 
+
+
+
     else:
         # Warn
         _LOGGER.warning("No BEDBASE_CONFIG found. Can't configure server.")

bedhost/routers/api.py

@@ -28,8 +28,18 @@
     else {"http": "http"},
 )
 
+# This is using Python's Functional API to create enumerations without the typical
+# class syntax. This is useful for creating enumerations dynamically, which is
+# what we're doing here. We're creating a new enumeration for each table in the
+# database, and then creating a new enumeration for each column in each table.
+# This is done by calling the `get_enum_map` function, which returns a dictionary
+# of column names and values. The `enum.Enum` function then creates a new
+# enumeration class with the given name and values.
+
+
 FileColumnBedset = enum.Enum(
-    "FileColumnBedset", get_enum_map(bbc, BEDSET_TABLE, "file")
+    value="FileColumnBedset",  # name of the enumeration
+    names=get_enum_map(bbc, BEDSET_TABLE, "file")  # dictionary of names and values
 )
 
 FileColumnBed = enum.Enum("FileColumnBed", get_enum_map(bbc, BED_TABLE, "file"))
@@ -105,7 +115,7 @@ async def get_bed_genome_assemblies():
     Returns available genome assemblies in the database
     """
 
-    return bbc.bed.select_distinct(table_name=BED_TABLE, columns=["genome"])
+    return bbc.bed.backend.select_distinct(table_name=BED_TABLE, columns=["genome"])
 
 
 @router.get("/bed/count", response_model=int)
@@ -127,7 +137,7 @@ async def get_all_bed_metadata(
     if ids:
         assert_table_columns_match(bbc=bbc, table_name=BED_TABLE, columns=ids)
 
-    res = bbc.bed.select(columns=ids, limit=limit)
+    res = bbc.bed.backend.select(columns=ids, limit=limit)
 
     if res:
         if ids: