1.3.6

see docs/changes.md (or the website)
progenetix · Nov 27, 2023 · be19a12 · be19a12
1 parent 48c337d
commit be19a12
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Showing 18 changed files with 106 additions and 428 deletions.
diff --git a/bycon/beaconServer/beacon.py b/bycon/beaconServer/beacon.py
@@ -79,12 +79,6 @@ def beacon():
         run_beacon_init_stack(byc)
         r = BeaconDataResponse(byc).resultsetResponse()
         print_json_response(r, byc["env"])
-        # byc.update({
-        #     "service_response": r.resultsetResponse(),
-        #     "error_response": r.errorResponse()
-        # })
-        # cgi_print_response(byc, 200)
-
     elif f:
         # dynamic package/function loading; e.g. `filtering_terms` loads
         # `filtering_terms` from `filtering_terms.py`...

diff --git a/bycon/config/datatable_mappings.yaml b/bycon/config/datatable_mappings.yaml
@@ -450,12 +450,12 @@ definitions:
         type: string
         db_key: variant_state.label
         compact: True
-      reference_bases:
+      reference_sequence:
         type: string
         db_key: reference_sequence
         indexed: True
         compact: True
-      alternate_bases:
+      sequence:
         type: string
         db_key: sequence
         indexed: True

diff --git a/bycon/lib/beacon_response_generation.py b/bycon/lib/beacon_response_generation.py
@@ -70,6 +70,7 @@ def __init__(self, byc: dict):
         self.service_config = self.byc.get("service_config", {})
         self.response_schema = byc["response_schema"]
         self.requested_granularity = self.form_data.get("requested_granularity", "record")
+        self.include_handovers = self.form_data.get("include_handovers", False)
         self.beacon_schema = self.byc["response_entity"].get("beacon_schema", "___none___")
         self.record_queries = {}
         self.data_response = object_instance_from_schema_name(byc, self.response_schema, "")
@@ -94,7 +95,13 @@ def resultsetResponse(self):
         self.data_response["response"].update({"result_sets": self.result_sets})
         self.__resultset_response_update_summaries()
         if not "record" in self.requested_granularity:
-            self.data_response.pop("response", None)
+            # TODO /CUSTOM: This non-standard modification removes the results
+            # but keeps the resultSets nstructure (handovers ...)
+            if self.include_handovers is True:
+                for rs in self.data_response["response"]["result_sets"]:
+                    rs.pop("results", None)
+            else:
+                self.data_response.pop("response", None)
         if "boolean" in self.requested_granularity:
             self.data_response["response_summary"].pop("num_total_results", None)
 
@@ -585,14 +592,14 @@ def __init__(self, byc: dict):
     # -------------------------------------------------------------------------#
 
     def populatedResultSets(self):
-
         self.__retrieve_datasets_data()
         self.__retrieve_variants_data()
         self.__populate_result_sets()
         self.__result_sets_save_handovers()
 
         return self.result_sets, self.record_queries
 
+
     # -------------------------------------------------------------------------#
 
     def datasetsData(self):

diff --git a/bycon/lib/cgi_parsing.py b/bycon/lib/cgi_parsing.py
@@ -164,12 +164,12 @@ def parse_GET(byc):
     if not "filters" in form:
         form.update({"filters": []})
 
-    form.update({
-        "requested_granularity": get.getvalue("requestedGranularity", b_defs.get("requested_granularity", "record")),
-        "include_resultset_responses": get.getvalue("includeResultsetResponses",
-                                                    b_defs.get("include_resultset_responses", "HIT")),
-        "include_handovers": get.getvalue("includeHandovers", b_defs.get("include_handovers", False))
-    })
+    # form.update({
+    #     "requested_granularity": get.getvalue("requestedGranularity", b_defs.get("requested_granularity", "record")),
+    #     "include_resultset_responses": get.getvalue("includeResultsetResponses",
+    #                                                 b_defs.get("include_resultset_responses", "HIT")),
+    #     "include_handovers": get.getvalue("includeHandovers", b_defs.get("include_handovers", False))
+    # })
 
     if "requested_schema" in form:
         try:

diff --git a/bycon/lib/dataset_parsing.py b/bycon/lib/dataset_parsing.py
@@ -1,10 +1,9 @@
-import pymongo
 import re
+from pymongo import MongoClient
 from os import environ
 
 from bycon.lib.cgi_parsing import rest_path_value
 
-
 ################################################################################
 
 def select_dataset_ids(byc):
@@ -24,17 +23,6 @@ def select_dataset_ids(byc):
 
 ################################################################################
 
-def ds_id_from_default(byc):
-    ds_id = byc.get("default_dataset_id", "___undefined___")
-
-    if ds_id not in byc["dataset_definitions"].keys():
-        return False
-
-    byc.update({"dataset_ids": [ ds_id ]})
-    return True
-
-################################################################################
-
 def ds_id_from_rest_path_value(byc):
     ds_id = rest_path_value("datasets")
     if ds_id is None:
@@ -60,7 +48,7 @@ def ds_id_from_accessid(byc):
     if any(x is False for x in [accessid, ho_db, ho_collname]):
         return False
 
-    ho_client = pymongo.MongoClient(host=environ.get("BYCON_MONGO_HOST", "localhost"))
+    ho_client = MongoClient(host=environ.get("BYCON_MONGO_HOST", "localhost"))
     h_o = ho_client[ho_db][ho_collname].find_one({"id": accessid})
     if not h_o:
         return False
@@ -107,3 +95,17 @@ def ds_ids_from_args(byc):
         return True
 
     return False
+
+
+################################################################################
+
+def ds_id_from_default(byc):
+    ds_id = byc.get("default_dataset_id", "___undefined___")
+
+    if ds_id not in byc["dataset_definitions"].keys():
+        return False
+
+    byc.update({"dataset_ids": [ ds_id ]})
+    return True
+
+