1.6.3

bycon/__init__.py

@@ -35,8 +35,9 @@
     }
 
     read_service_definition_files(byc)
-    # updates `beacon_defaults`, `dataset_definitions` and `local_paths`
+    # 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)
 

bycon/beaconServer/beacon.py

@@ -24,22 +24,12 @@ def main():
 ################################################################################
 
 def beacon():
-    # updates `beacon_defaults`, `dataset_definitions` and `local_paths`
-    # update_rootpars_from_local(LOC_PATH, byc)
-    # set_beacon_defaults(byc)
-
-    defs = BYC["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`
-    which can either be one of the Beacon entities (also recognizing aliases)
-    in `beacon_defaults.service_path_aliases` or targets of a rewrite from
-    `beacon_defaults.rewrites`.
+    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 entity is determined from different potential inputs and overwritten
-    by the next one in the oreder, if existing:
+    by the next one in the order, if existing:
 
     1. from the path (element after "beacon", e.g. `biosamples` from
        `/beacon/biosamples/...`)
@@ -48,31 +38,25 @@ 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)
-    # args_update_form(byc)
-    prdbug(f'beacon.py - request_entity_path_id: {byc.get("request_entity_path_id")}')
 
     e_p_id = BYC_PARS.get("request_entity_path_id", "___none___")
-    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:
+    if e_p_id in p_e_m:
         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}')
 
-    # check for rewrites
-    if r_p_id in r_w:
-        uri = environ.get('REQUEST_URI')
-        pat = re.compile( rf"^.+\/{r_p_id}\/?(.*?)$" )
-        if pat.match(uri):
-            stuff = pat.match(uri).group(1)
-            print_uri_rewrite_response(r_w[r_p_id], stuff)
+    e = p_e_m.get(r_p_id)
+    f = e_p_m.get(e)
 
-    f = s_a_s.get(r_p_id)
     if not f:
         pass
-    elif f in d_p_s:
+    elif e in d_p_e:
         initialize_bycon_service(byc, f)
         r = BeaconDataResponse(byc).resultsetResponse()
         print_json_response(r)

bycon/beaconServer/info.py

@@ -25,8 +25,7 @@ def info():
     initialize_bycon_service(byc, "info")
     r = BeaconInfoResponse(byc)
 
-    defs = BYC["beacon_defaults"]
-    b_e_d = defs.get("entity_defaults", {})
+    b_e_d = BYC.get("entity_defaults", {})
     info = b_e_d.get("info", {})
     pgx_info = info.get("content", {})
     beacon_info = object_instance_from_schema_name("beaconInfoResults", "")
@@ -38,9 +37,11 @@ def info():
 
     # TODO: All the schemas really only here?
     beacon_schemas = []
+    entry_type_responses = ["beaconCollectionsResponse", "beaconResultsetsResponse"]
     for e_t, e_d in b_e_d.items():
         b_s = e_d.get("beacon_schema", {})
-        if e_d.get("is_entry_type", True) is True:
+        r_s = e_d.get("response_schema", "___none___")
+        if r_s in entry_type_responses:
             beacon_schemas.append(b_s)
 
     response.update( { "returned_schemas": beacon_schemas } )

bycon/beaconServer/service_info.py

@@ -22,7 +22,7 @@ def main():
 
 def service_info():
     initialize_bycon_service(byc, "service_info")
-    b_e_d = BYC["beacon_defaults"].get("entity_defaults", {})
+    b_e_d = BYC.get("entity_defaults", {})
     pgx_info = b_e_d.get("info", {})
     c = pgx_info.get("content", {})
     info = object_instance_from_schema_name("ga4gh-service-info-1-0-0-schema", "")

bycon/config.py

@@ -44,7 +44,16 @@
   "ERRORS": [],
   "WARNINGS": [],
   "USER": "anonymous",
-  "beacon_defaults": {},
+  "beacon_defaults": {
+    "defaults": {
+      "default_dataset_id": "examplez",
+      "test_domains": ["localhost"]
+    },
+  },
+  "entity_defaults": {"info":{}},
+  "path_entry_type_mappings": {},
+  "entry_type_path_mappings": {},
+  "data_pipeline_entities": [],
   "datatable_mappings": {}
 }
 

bycon/definitions/argument_definitions.yaml

@@ -57,7 +57,8 @@ request_entity_path_id:
   type: string
   cmdFlags:
     - --requestEntityPathId
-  description: required data entry point, equal to the first REST path element in Beacon
+  description: >-
+    data entry point, equal to the first REST path element in Beacon
 
 requested_schema:
   type: string
@@ -455,12 +456,12 @@ source:
     - --source
   description: some source label, e.g. `analyses`
 
-query:
-  type: string
-  cmdFlags:
-    - -q
-    - --query
-  description: complete query string, e.g. `{"biosamples":{"external_references.id":"geo:GSE7428"}}`
+# query:
+#   type: string
+#   cmdFlags:
+#     - -q
+#     - --query
+#   description: complete query string, e.g. `{"biosamples":{"external_references.id":"geo:GSE7428"}}`
 
 delivery_keys:
   type: array