start refactor:

- remove graphql stuff
- start to adopt new bbconf
- start new way to run with uvicorn for dev

bedhost/const.py

@@ -4,6 +4,7 @@
 
 from bbconf._version import __version__ as bbconf_v
 from bbconf.const import *
+from bbconf.const import CFG_REMOTE_KEY  # nice to have this explicit, rather than *
 
 from bedhost._version import __version__ as server_v
 

bedhost/helpers.py

@@ -225,7 +225,7 @@ def assert_table_columns_match(bbc, table_name, columns):
         msg = f"Could not determine columns for table: {table_name}"
         _LOGGER.warning(msg)
         raise HTTPException(status_code=404, detail=msg)
-    diff = set(columns).difference(list(schema.keys()))
+    diff = set(columns).difference(list(schema.sample_level_data.keys()))
     if diff:
         msg = f"Columns not found in '{table_name}' table: {', '.join(diff)}"
         _LOGGER.warning(msg)
@@ -357,7 +357,7 @@ def get_id_map(bbc, table_name, file_type):
     id_map = {}
 
     schema = serve_schema_for_table(bbc=bbc, table_name=table_name)
-    for key, value in schema.items():
+    for key, value in schema.sample_level_data.items():
         if value["type"] == file_type:
             id_map[value["label"]] = key
 
@@ -374,9 +374,8 @@ def get_enum_map(bbc, table_name, file_type):
     """
 
     enum_map = {}
-
     schema = serve_schema_for_table(bbc=bbc, table_name=table_name)
-    for key, value in schema.items():
+    for key, value in schema.sample_level_data.items():
         if value["type"] == file_type:
             enum_map[value["label"]] = value["label"]
 

bedhost/main.py

@@ -1,24 +1,21 @@
-import sys
-from logging import DEBUG, INFO
-from typing import Dict, List, Optional
-
 import bbconf
 import logmuse
+import logging
+import sys
 import uvicorn
+
 from bbconf import BedBaseConf
+from logging import DEBUG, INFO
+from typing import Dict, List, Optional
 from fastapi import FastAPI, HTTPException, Path, Query
-from pipestat_reader import PipestatReader
-from starlette_graphene3 import GraphQLApp, make_graphiql_handler
-from starlette.middleware.cors import CORSMiddleware
-from starlette.responses import FileResponse, RedirectResponse
-from starlette.staticfiles import StaticFiles
+from fastapi.middleware.cors import CORSMiddleware
 
 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",
@@ -50,7 +47,7 @@ async def index():
     """
     Display the index UI page
     """
-    return FileResponse(os.path.join(UI_PATH, "index.html"))
+    return FileResponse(os.path.join(STATIC_PATH, "index.html"))
 
 
 def main():
@@ -98,18 +95,31 @@ def main():
         else:
             raise FileNotFoundError(f"React UI path to mount not found: {UI_PATH}")
 
-        app.mount("/ui", StaticFiles(directory=UI_PATH))
+        # app.mount("/ui", StaticFiles(directory=UI_PATH))
+
 
-        psr = PipestatReader(pipestat_managers=[bbc.bed, bbc.bedset, bbc.dist])
-        _LOGGER.info("Generating GraphQL schema")
-        graphql_schema = psr.generate_graphql_schema()
-        app.mount(
-            "/graphql", GraphQLApp(graphql_schema, on_get=make_graphiql_handler())
-        )
 
         _LOGGER.info(f"running {PKG_NAME} app")
         uvicorn.run(
             app,
             host=bbc.config[CFG_SERVER_KEY][CFG_HOST_KEY],
             port=bbc.config[CFG_SERVER_KEY][CFG_PORT_KEY],
         )
+
+
+def register_globals(cfg):
+    global bbc
+    bbc = BedBaseConf(bbconf.get_bedbase_cfg(cfg))
+
+if __name__ != "__main__":
+    if os.environ.get("BEDBASE_CONFIG"):
+        # Establish global config when running through uvicorn CLI
+        register_globals(os.environ.get("BEDBASE_CONFIG"))
+        from .routers import api, private_api
+
+        app.include_router(api.router, prefix="/api")
+        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

@@ -46,13 +46,13 @@
 
 img_map_bed = get_id_map(bbc, BED_TABLE, "image")
 
-ex_bed_digest = serve_columns_for_table(
-    bbc=bbc, table_name=BED_TABLE, columns=["md5sum"], limit=1
-).get("data")[0][0]
+# ex_bed_digest = serve_columns_for_table(
+#     bbc=bbc, table_name=BED_TABLE, columns=["md5sum"], limit=1
+# ).get("data")[0][0]
 
-ex_bedset_digest = serve_columns_for_table(
-    bbc=bbc, table_name=BEDSET_TABLE, columns=["md5sum"], limit=1
-).get("data")[0][0]
+# ex_bedset_digest = serve_columns_for_table(
+#     bbc=bbc, table_name=BEDSET_TABLE, columns=["md5sum"], limit=1
+# ).get("data")[0][0]
 
 ex_chr = "chr1"
 
@@ -63,7 +63,7 @@
     regex=r"^\w+$",
     max_length=32,
     min_length=32,
-    example=ex_bed_digest,
+    # example=ex_bed_digest,
 )
 
 bsd = Path(
@@ -72,7 +72,7 @@
     regex=r"^\w+$",
     max_length=32,
     min_length=32,
-    example=ex_bedset_digest,
+    # example=ex_bedset_digest,
 )
 
 c = Path(

bedhost/static/index.html

@@ -0,0 +1 @@
+test.