1.5.0

bycon/__init__.py

@@ -1,15 +1,17 @@
 # __init__.py
-import sys
+import sys, traceback
 from os import environ, path
 from pathlib import Path
-import traceback
 
 pkg_path = path.dirname( path.abspath(__file__) )
 bycon_lib_path = path.join( pkg_path, "lib" )
+sys.path.append( pkg_path )
 sys.path.append( bycon_lib_path )
 
 try:
 
+    from config import *
+
     from args_parsing import *
     from beacon_auth import *
     from beacon_response_generation import *
@@ -31,19 +33,16 @@
     byc: object = {
         "args": {},
         "form_data": {},
-        "pkg_path": pkg_path,
         "bycon_lib_path": bycon_lib_path,
-        "parsed_config_paths": [],
-        "env": "server"
+        "parsed_config_paths": []
     }
-    if not environ.get('HTTP_HOST'):
-        byc.update({"env": "local"})
 
     read_service_definition_files(byc)
-    set_byc_config_pars(byc)
+    # updates `beacon_defaults`, `dataset_definitions` and `local_paths`
+    update_rootpars_from_local(LOC_PATH, byc)
     set_beacon_defaults(byc)
-    parse_query(byc)
-    
+    parse_arguments(byc)
+
 except Exception:
 
     if environ.get('HTTP_HOST'):

bycon/beaconServer/beacon.py

@@ -6,7 +6,6 @@
 from importlib import import_module
 
 from bycon import *
-pkg_path = path.dirname( path.abspath(__file__) )
 
 """
 """
@@ -20,22 +19,19 @@ def main():
     try:
         beacon()
     except Exception:
-        print_text_response(traceback.format_exc(), byc["env"], 302)
+        print_text_response(traceback.format_exc(), 302)
 
 ################################################################################
 
 def beacon():
-
-    set_debug_state(debug=0)
-
-    loc_dir = path.join( pkg_path, "local" )
     # updates `beacon_defaults`, `dataset_definitions` and `local_paths`
-    update_rootpars_from_local(loc_dir, byc)
-    set_beacon_defaults(byc)
+    # update_rootpars_from_local(LOC_PATH, byc)
+    # set_beacon_defaults(byc)
 
-    s_a_s = byc["beacon_defaults"].get("service_path_aliases", {})
-    r_w = byc["beacon_defaults"].get("rewrites", {})
-    d_p_s = byc["beacon_defaults"].get("data_pipeline_path_ids", [])
+    defs = byc.get("beacon_defaults", {})
+    s_a_s = defs.get("service_path_aliases", {})
+    r_w = defs.get("rewrites", {})
+    d_p_s = defs.get("data_pipeline_path_ids", [])
 
     """
     The type of execution depends on the requested entity defined in `beacon_defaults`
@@ -53,18 +49,17 @@ def beacon():
     Fallback is `/info`.
     """
     byc.update({"request_path_root": "beacon"})
-
     rest_path_elements(byc)
-    args_update_form(byc)
-    prdbug(f'beacon.py - request_entity_path_id: {byc.get("request_entity_path_id")}', byc.get("debug_mode"))
+    # args_update_form(byc)
+    prdbug(f'beacon.py - request_entity_path_id: {byc.get("request_entity_path_id")}')
 
     e_p_id = byc["form_data"].get("request_entity_path_id", "___none___")
-    prdbug(f'beacon.py - form e_p_id: {e_p_id}', byc.get("debug_mode"))
+    prdbug(f'beacon.py - form e_p_id: {e_p_id}')
     if e_p_id in s_a_s or e_p_id in r_w:
         byc.update({"request_entity_path_id": e_p_id})
     r_p_id = byc.get("request_entity_path_id", "info")
 
-    prdbug(f'beacon.py - request_entity_path_id: {r_p_id}', byc.get("debug_mode"))
+    prdbug(f'beacon.py - request_entity_path_id: {r_p_id}')
 
     # check for rewrites
     if r_p_id in r_w:
@@ -81,7 +76,7 @@ def beacon():
         initialize_bycon_service(byc, f)
         run_beacon_init_stack(byc)
         r = BeaconDataResponse(byc).resultsetResponse()
-        print_json_response(r, byc["env"])
+        print_json_response(r)
     elif f:
         # dynamic package/function loading; e.g. `filtering_terms` loads
         # `filtering_terms` from `filtering_terms.py`...
@@ -98,9 +93,8 @@ def beacon():
 
             exit()
 
-    e_m = "No correct service path provided. Please refer to the documentation at http://docs.progenetix.org"
-    e_r = BeaconErrorResponse(byc).error(e_m, 422)
-    print_json_response(e_r, byc["env"])
+    BYC["ERRORS"].append("No correct service path provided. Please refer to the documentation at http://docs.progenetix.org")
+    BeaconErrorResponse(byc).response(422)
 
 
 ################################################################################

bycon/beaconServer/cohorts.py

@@ -19,15 +19,15 @@ def main():
     try:
         cohorts()
     except Exception:
-        print_text_response(traceback.format_exc(), byc["env"], 302)
+        print_text_response(traceback.format_exc(), 302)
 
 ################################################################################
 
 def cohorts():
     initialize_bycon_service(byc, "cohorts")
     run_beacon_init_stack(byc)
     r = BeaconDataResponse(byc).collectionsResponse()
-    print_json_response(r, byc["env"])
+    print_json_response(r)
 
 
 ################################################################################

bycon/beaconServer/configuration.py

@@ -7,21 +7,19 @@
 ################################################################################
 
 def main():
-
     try:
         configuration()
     except Exception:
-        print_text_response(traceback.format_exc(), byc["env"], 302)    
+        print_text_response(traceback.format_exc(), 302)    
 
 ################################################################################
 
 def configuration():
-
     initialize_bycon_service(byc, "configuration")
     r = BeaconInfoResponse(byc)
     c_f = get_schema_file_path(byc, "beaconConfiguration")
     c = load_yaml_empty_fallback(c_f)
-    print_json_response(r.populatedInfoResponse(c), byc["env"])
+    print_json_response(r.populatedInfoResponse(c))
 
 
 ################################################################################

bycon/beaconServer/datasets.py

@@ -19,7 +19,7 @@ def main():
     try:
         datasets()
     except Exception:
-        print_text_response(traceback.format_exc(), byc["env"], 302)
+        print_text_response(traceback.format_exc(), 302)
 
 
 ################################################################################
@@ -28,7 +28,7 @@ def datasets():
     initialize_bycon_service(byc, "datasets")
     run_beacon_init_stack(byc)
     r = BeaconDataResponse(byc)
-    print_json_response(r.collectionsResponse(), byc["env"])
+    print_json_response(r.collectionsResponse())
 
 
 ################################################################################

bycon/beaconServer/entry_types.py

@@ -15,7 +15,7 @@ def main():
     try:
         entry_types()
     except Exception:
-        print_text_response(traceback.format_exc(), byc["env"], 302)
+        print_text_response(traceback.format_exc(), 302)
 
 
 ################################################################################
@@ -26,7 +26,7 @@ def entry_types():
     r = BeaconInfoResponse(byc)
     e_f = get_schema_file_path(byc, "beaconConfiguration")
     e_t_s = load_yaml_empty_fallback( e_f )
-    print_json_response(r.populatedInfoResponse({"entry_types": e_t_s["entryTypes"] }), byc["env"])
+    print_json_response(r.populatedInfoResponse({"entry_types": e_t_s["entryTypes"] }))
 
 
 ################################################################################

bycon/beaconServer/filtering_terms.py

@@ -18,7 +18,7 @@ def main():
     try:
         filtering_terms()
     except Exception:
-        print_text_response(traceback.format_exc(), byc["env"], 302)
+        print_text_response(traceback.format_exc(), 302)
 
 
 ################################################################################
@@ -27,7 +27,7 @@ def filtering_terms():
     initialize_bycon_service(byc, "filtering_terms")
     run_beacon_init_stack(byc)
     r = BeaconDataResponse(byc)
-    print_json_response(r.filteringTermsResponse(), byc["env"])
+    print_json_response(r.filteringTermsResponse())
 
 
 ################################################################################

bycon/beaconServer/info.py

@@ -17,16 +17,17 @@ def main():
     try:
         info()
     except Exception:
-        print_text_response(traceback.format_exc(), byc["env"], 302)
+        print_text_response(traceback.format_exc(), 302)
 
 ################################################################################
 
 def info():
 
-    initialize_bycon_service(byc)
+    initialize_bycon_service(byc, "info")
     r = BeaconInfoResponse(byc)
 
-    b_e_d = byc["beacon_defaults"].get("entity_defaults", {})
+    defs = byc.get("beacon_defaults", {})
+    b_e_d = defs.get("entity_defaults", {})
     info = b_e_d.get("info", {})
     pgx_info = info.get("content", {})
     beacon_info = object_instance_from_schema_name(byc, "beaconInfoResults", "")
@@ -44,7 +45,7 @@ def info():
             beacon_schemas.append(b_s)
 
     response.update( { "returned_schemas": beacon_schemas } )
-    print_json_response(response, byc["env"])
+    print_json_response(response)
 
 
 ################################################################################

bycon/beaconServer/map.py

@@ -15,7 +15,7 @@ def main():
     try:
         map()
     except Exception:
-        print_text_response(traceback.format_exc(), byc["env"], 302)
+        print_text_response(traceback.format_exc(), 302)
 
 ################################################################################
 
@@ -25,7 +25,7 @@ def map():
     r = BeaconInfoResponse(byc)
     m_f = get_schema_file_path(byc, "beaconMap")
     beaconMap = load_yaml_empty_fallback( m_f )
-    print_json_response(r.populatedInfoResponse(beaconMap), byc["env"])
+    print_json_response(r.populatedInfoResponse(beaconMap))
 
 
 ################################################################################

bycon/beaconServer/service_info.py

@@ -13,18 +13,15 @@
 ################################################################################
 
 def main():
-
     try:
         service_info()
     except Exception:
-        print_text_response(traceback.format_exc(), byc["env"], 302)
+        print_text_response(traceback.format_exc(), 302)
 
 ################################################################################
 
 def service_info():
-
-    initialize_bycon_service(byc)
-
+    initialize_bycon_service(byc, "service_info")
     defs = byc.get("beacon_defaults", {})
     b_e_d = defs.get("entity_defaults", {})
     pgx_info = b_e_d.get("info", {})
@@ -33,7 +30,7 @@ def service_info():
     for k in info.keys():
         if k in c:
             info.update({k:c[k]})
-    print_json_response(info, byc["env"])
+    print_json_response(info)
 
 ################################################################################
 ################################################################################

bycon/beaconServer/tests/PUT-individuals-from-NCIT-filters.json

@@ -12,7 +12,7 @@
                 "datasetIds": ["progenetix"]
             }
         },
-        "filters": [{ "id": "NCIT:C4536" }]
+        "filters": [{"id": "NCIT:C4536"}]
     },
     "debugMode": 0
 }

bycon/config.py

@@ -0,0 +1,54 @@
+import inspect
+from os import environ, path, pardir
+
+pkg_path = path.dirname( path.abspath(__file__) )
+
+"""
+Global variables
+"""
+
+ENV = environ.get('HTTP_HOST', "local")
+
+PKG_PATH = pkg_path
+CONF_PATH = path.join( pkg_path, "definitions")
+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")
+
+# Database settings
+# TODO: wrap them into object to make them mutable for local changes
+DB_MONGOHOST = environ.get("BYCON_MONGO_HOST", "localhost")
+HOUSEKEEPING_DB = "_byconHousekeepingDB"
+HOUSEKEEPING_INFO_COLL = "beaconinfo"
+HOUSEKEEPING_HO_COLL = "querybuffer"
+
+SERVICES_DB = "_byconServicesDB"
+GENES_COLL = "genes"
+GEOLOCS_COLL = "geolocs"
+
+#------------------------------------------------------------------------------#
+
+# not really to be modified...
+
+GRANULARITY_LEVELS = {
+  "none": 0,
+  "boolean": 1,
+  "count": 2,
+  "record": 3
+}
+
+################################################################################
+
+# to be modified during execution
+
+BYC = {
+  "DEBUG_MODE": False,
+  "TEST_MODE": False,
+  "ERRORS": [],
+  "WARNINGS": []
+}
+
+################################################################################
+