force update after a loooong time

... to 1.8.4

bycon/__init__.py

@@ -30,16 +30,13 @@
     from service_utils import *
     from variant_mapping import *
 
-    byc: object = {
-        "parsed_config_paths": []
-    }
-
-    read_service_definition_files(byc)
-    # updates `entity_defaults`, `dataset_definitions` and `local_paths`
-    update_rootpars_from_local(LOC_PATH, byc)
-    set_entity_mappings()
-    set_beacon_defaults(byc)
-    parse_arguments(byc)
+    read_service_definition_files()
+    update_rootpars_from_local()
+    rest_path_elements()
+    set_beacon_defaults()
+    parse_arguments()
+    set_entities()
+    initialize_bycon_service()
 
 except Exception:
     if not "local" in ENV:

bycon/beaconServer/beacon.py

@@ -25,9 +25,8 @@ def main():
 
 def beacon():
     """
-    The type of execution depends on the requested entity defined in the 
-    `path_entry_type_mappings` generated from `request_entity_path_id` (or aliases)
-    in `entity_defaults`.
+    The type of execution depends on the requested entity defined in the
+    `request_entity_path_id` (or aliases) in `entity_defaults`.
     The entity is determined from different potential inputs and overwritten
     by the next one in the order, if existing:
 
@@ -39,49 +38,34 @@ def beacon():
     Fallback is `/info`.
     """
 
-    p_e_m = BYC.get("path_entry_type_mappings", {})
-    e_p_m = BYC.get("entry_type_path_mappings", {})
     d_p_e = BYC.get("data_pipeline_entities", [])
-    byc.update({"request_path_root": "beacon"})
-    rest_path_elements(byc)
-
-    e_p_id = BYC_PARS.get("request_entity_path_id", "___none___")
-    if e_p_id in p_e_m:
-        byc.update({"request_entity_path_id": e_p_id})
-    rq_p_id = byc.get("request_entity_path_id", "info")
-    update_entity_ids_from_path(byc)
-    rp_p_id = byc.get("response_entity_path_id", rq_p_id)
-    prdbug(f'beacon.py - request_entity_path_id: {rq_p_id}')
-    prdbug(f'beacon.py - response_entity_path_id: {rp_p_id}')
-
-    # e = p_e_m.get(rq_p_id)
-    e = p_e_m.get(rp_p_id)
-    f = e_p_m.get(e)
-
-    if not f:
+    rq_id = BYC.get("request_entity_id", "info")
+    rq_p_id = BYC.get("request_entity_path_id", "info")
+    rp_id = BYC.get("response_entity_id")
+
+    if not rp_id:
         pass
-    elif e in d_p_e:
-        initialize_bycon_service(byc, f)
-        r = BeaconDataResponse(byc).resultsetResponse()
+    elif rq_id in d_p_e:
+        r = BeaconDataResponse().resultsetResponse()
         print_json_response(r)
-    elif f:
+    elif rq_p_id:
         # dynamic package/function loading; e.g. `filtering_terms` loads
         # `filtering_terms` from `filtering_terms.py`...
         try:
-            mod = import_module(f)
-            serv = getattr(mod, f)
+            mod = import_module(rq_p_id)
+            serv = getattr(mod, rq_p_id)
             serv()
             exit()
         except Exception as e:
             print('Content-Type: text')
             print('status:422')
             print()
-            print('Service {} WTF error: {}'.format(f, e))
+            print(f'Service {rq_id} WTF error: {e}')
 
             exit()
 
     BYC["ERRORS"].append("No correct service path provided. Please refer to the documentation at http://docs.progenetix.org")
-    BeaconErrorResponse(byc).response(422)
+    BeaconErrorResponse().response(422)
 
 
 ################################################################################

bycon/beaconServer/cohorts.py

@@ -24,9 +24,9 @@ def main():
 ################################################################################
 
 def cohorts():
-    initialize_bycon_service(byc, "cohorts")
-    r = BeaconDataResponse(byc).collectionsResponse()
-    print_json_response(r)
+    # initialize_bycon_service()
+    r = BeaconDataResponse()
+    print_json_response(r.collectionsResponse())
 
 
 ################################################################################

bycon/beaconServer/configuration.py

@@ -15,8 +15,8 @@ def main():
 ################################################################################
 
 def configuration():
-    initialize_bycon_service(byc, "configuration")
-    r = BeaconInfoResponse(byc)
+    # initialize_bycon_service()
+    r = BeaconInfoResponse()
     c_f = get_schema_file_path("beaconConfiguration")
     c = load_yaml_empty_fallback(c_f)
     print_json_response(r.populatedInfoResponse(c))

bycon/beaconServer/datasets.py

@@ -21,12 +21,11 @@ def main():
     except Exception:
         print_text_response(traceback.format_exc(), 302)
 
-
 ################################################################################
 
 def datasets():
-    initialize_bycon_service(byc, "datasets")
-    r = BeaconDataResponse(byc)
+    # initialize_bycon_service()
+    r = BeaconDataResponse()
     print_json_response(r.collectionsResponse())
 
 

bycon/beaconServer/entry_types.py

@@ -21,11 +21,10 @@ def main():
 ################################################################################
 
 def entry_types():
-
-    initialize_bycon_service(byc, "entry_types")
-    r = BeaconInfoResponse(byc)
+    # initialize_bycon_service()
+    r = BeaconInfoResponse()
     e_f = get_schema_file_path("beaconConfiguration")
-    e_t_s = load_yaml_empty_fallback( e_f )
+    e_t_s = load_yaml_empty_fallback(e_f)
     print_json_response(r.populatedInfoResponse({"entry_types": e_t_s["entryTypes"] }))
 
 

bycon/beaconServer/filtering_terms.py

@@ -24,8 +24,8 @@ def main():
 ################################################################################
 
 def filtering_terms():
-    initialize_bycon_service(byc, "filtering_terms")
-    r = BeaconDataResponse(byc)
+    # initialize_bycon_service()
+    r = BeaconDataResponse()
     print_json_response(r.filteringTermsResponse())
 
 

bycon/beaconServer/info.py

@@ -22,8 +22,8 @@ def main():
 ################################################################################
 
 def info():
-    initialize_bycon_service(byc, "info")
-    r = BeaconInfoResponse(byc)
+    # initialize_bycon_service()
+    r = BeaconInfoResponse()
 
     b_e_d = BYC.get("entity_defaults", {})
     info = b_e_d.get("info", {})

bycon/beaconServer/map.py

@@ -19,8 +19,8 @@ def main():
 ################################################################################
 
 def map():
-    initialize_bycon_service(byc, "map")
-    r = BeaconInfoResponse(byc)
+    # initialize_bycon_service()
+    r = BeaconInfoResponse()
     m_f = get_schema_file_path("beaconMap")
     beaconMap = load_yaml_empty_fallback( m_f )
     print_json_response(r.populatedInfoResponse(beaconMap))

bycon/beaconServer/service_info.py

@@ -21,7 +21,7 @@ def main():
 ################################################################################
 
 def service_info():
-    initialize_bycon_service(byc, "service_info")
+    # initialize_bycon_service()
     b_e_d = BYC.get("entity_defaults", {})
     pgx_info = b_e_d.get("info", {})
     c = pgx_info.get("content", {})

bycon/config.py

@@ -1,5 +1,7 @@
 import inspect
 from os import environ, path, pardir
+from pymongo import MongoClient
+import sys
 
 pkg_path = path.dirname( path.abspath(__file__) )
 
@@ -14,8 +16,14 @@
 LIB_PATH = path.join( pkg_path, "lib")
 
 # path of the calling script is used to point to a local config directory
-__caller_path = path.dirname(path.abspath((inspect.stack()[1])[1]))
-LOC_PATH = path.join(__caller_path, "local")
+# __caller_path = path.dirname(path.abspath((inspect.stack()[1])[1]))
+__caller_path = path.dirname( path.abspath(sys.argv[0]))
+LOC_PATH = path.join(__caller_path, pardir, "local")
+
+REQUEST_PATH_ROOT = "beacon"
+
+if "services" in LOC_PATH or "byconaut" in LOC_PATH:
+    REQUEST_PATH_ROOT = "services"
 
 #------------------------------------------------------------------------------#
 # Database settings
@@ -38,31 +46,74 @@
 # to be modified during execution ##############################################
 ################################################################################
 
+mongo_client = MongoClient(host=DB_MONGOHOST)
+db_names = list(mongo_client.list_database_names())
+
 BYC = {
   "DEBUG_MODE": False,
   "TEST_MODE": False,
   "ERRORS": [],
   "WARNINGS": [],
   "USER": "anonymous",
+
+  "BYC_DATASET_IDS": [],
+  "DATABASE_NAMES": [x for x in db_names if x not in [HOUSEKEEPING_DB, SERVICES_DB, "admin", "config", "local"]],
+  "BYC_FILTERS": [],
+
   "beacon_defaults": {
     "defaults": {
       "default_dataset_id": "examplez",
       "test_domains": ["localhost"]
     },
   },
+
+  # ..._mappings / ..._definitions are generated from YAML files & should stay static
+
   "argument_definitions": {},
-  "data_pipeline_entities": [],
+  "dataset_definitions": {},
   "datatable_mappings": {},
   "entity_defaults": {"info":{}},
-  "entry_type_path_mappings": {},
+  "filter_definitions": {},
+  "geoloc_definitions": {},
+  "handover_definitions": {},
   "interval_definitions": {},
-  "path_entry_type_mappings": {},
   "variant_request_definitions": {},
   "variant_type_definitions": {},
 
+  "loc_mod_pars": [
+    "authorizations",
+    "dataset_definitions",
+    "local_paths",
+    "datatable_mappings",
+    "plot_defaults"
+  ],
+
+  "authorizations": {},
+  "local_paths": {},
+  "plot_defaults": {},
+  "map_defaults": {},
+  "query_meta": {},
+  "service_config": {},
+
+  # -------------------------------------------------------------------------- #
+
+  "authorized_granularities": {},
+  "data_pipeline_entities": [],
+  "parsed_config_paths": [],
+  "request_entity_path_id": None,
+  "request_entity_id": None,
+  "response_entity_path_id": None,
+  "response_entity_id": None,
+  "response_entity": {},
+  "response_schema": "beaconInfoResponse",
+  "returned_granularity": "boolean",
+
   "cytobands": [],
   "cytolimits": {},
-  "genome_size": 0
+  "genome_size": 0,
+  "cytoband_intervals": {},
+  "genomic_intervals": {},
+  "genomic_interval_count": 0
 
 }
 
@@ -71,7 +122,7 @@
 # provifding default values
 BYC_PARS = {}
 
-# an object to make global, pre-processed variant parameters accessible
+# objects to make global, pre-processed variant parameters accessible
 BYC_VARGS = {}
 
 # default authorization levels; a local `authorizations.yaml` file can add to