1.8.5

progenetix · Jul 1, 2024 · 9681a5b · 9681a5b
1 parent c7065aa
commit 9681a5b
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Showing 20 changed files with 44 additions and 17 deletions.
diff --git a/bycon/beaconServer/__init__.py b/bycon/beaconServer/__init__.py
diff --git a/bycon/beaconServer/beacon.py b/bycon/beaconServer/beacon.py
diff --git a/bycon/beaconServer/cohorts.py b/bycon/beaconServer/cohorts.py
diff --git a/bycon/beaconServer/configuration.py b/bycon/beaconServer/configuration.py
diff --git a/bycon/beaconServer/datasets.py b/bycon/beaconServer/datasets.py
diff --git a/bycon/beaconServer/entry_types.py b/bycon/beaconServer/entry_types.py
diff --git a/bycon/beaconServer/filtering_terms.py b/bycon/beaconServer/filtering_terms.py
diff --git a/bycon/beaconServer/info.py b/bycon/beaconServer/info.py
diff --git a/bycon/beaconServer/map.py b/bycon/beaconServer/map.py
diff --git a/bycon/beaconServer/service_info.py b/bycon/beaconServer/service_info.py
diff --git a/bycon/definitions/variant_request_definitions.yaml b/bycon/definitions/variant_request_definitions.yaml
@@ -138,7 +138,6 @@ request_types:
       * `mateName` can be the same or different to `referenceName`
       * `mateName` is the higher numbered/named chromosome
     all_of:
-      # - assembly_id
       - reference_name
       - mate_name
       - start

diff --git a/bycon/lib/args_parsing.py b/bycon/lib/args_parsing.py
@@ -11,7 +11,7 @@ def args_update_form():
     parameter collection (in "local" context).
     """
     a_defs = BYC.get("argument_definitions", {})
-    cmd_args = create_args_parser(a_defs)
+    cmd_args = __create_args_parser(a_defs)
     arg_vars = vars(cmd_args)
     for p in arg_vars.keys():
         if not (v := arg_vars.get(p)):
@@ -29,16 +29,15 @@ def args_update_form():
 
 ################################################################################
 
-def create_args_parser(a_defs):
+def __create_args_parser(a_defs):
     parser = argparse.ArgumentParser()
     for a_n, a_d in a_defs.items():
         if "cmdFlags" in a_d:
             argDef = {
                 "flags": a_d.get("cmdFlags"),
                 "help": a_d.get("description", "TBD"),
             }
-            default = a_d.get("default")
-            if default:
+            if (default := a_d.get("default")):
                 argDef.update({"default": default})
             parser.add_argument(*argDef.pop("flags"), **argDef)
     cmd_args = parser.parse_args()

diff --git a/bycon/lib/beacon_response_generation.py b/bycon/lib/beacon_response_generation.py
@@ -667,7 +667,7 @@ def __get_handover_access_key(self):
 
     def __result_sets_save_handovers(self):
         ho_client = MongoClient(host=DB_MONGOHOST)
-        ho_coll = ho_client[HOUSEKEEPING_DB].ho_db[HOUSEKEEPING_HO_COLL]
+        ho_coll = ho_client[HOUSEKEEPING_DB][HOUSEKEEPING_HO_COLL]
         for ds_id, d_s in self.datasets_results.items():
             if not d_s:
                 continue

diff --git a/bycon/lib/dataset_parsing.py b/bycon/lib/dataset_parsing.py
@@ -75,7 +75,7 @@ def ds_id_from_accessid():
         return False
     if ds_id not in BYC["DATABASE_NAMES"]:
         return False
-    BYC.update({"BYC_DATASET_IDS":  ds_ids})
+    BYC.update({"BYC_DATASET_IDS":  [ds_id]})
     return True
 
 

diff --git a/bycon/lib/query_generation.py b/bycon/lib/query_generation.py
@@ -543,12 +543,8 @@ def __create_variantRangeRequest_query(self, v_pars):
             v_p_defs["end"]["db_key"]: { "$gt": int(vp[ "start" ][0]) }
         }
 
-        p_n = "variant_min_length"
-        if p_n in vp:
-            v_q.update( { v_p_defs[p_n]["db_key"]: { "$gte" : vp[p_n] } } )
-        p_n = "variant_max_length"
-        if "variant_max_length" in vp:
-            v_q.update( { v_p_defs[p_n]["db_key"]: { "$lte" : vp[p_n] } } )
+        if (l_q := self.__request_variant_size_limits(v_pars)):
+            v_q.update(l_q)
 
         p_n = "variant_type"
         if p_n in vp:
@@ -565,6 +561,28 @@ def __create_variantRangeRequest_query(self, v_pars):
 
     #--------------------------------------------------------------------------#
 
+    def __request_variant_size_limits(self, v_pars):
+        vp = v_pars
+        v_p_defs = self.argument_definitions
+        l_k = v_p_defs["variant_max_length"]["db_key"]
+        s_q = {l_k: {}}
+
+        p_n = "variant_min_length"
+        if (minl := vp.get(p_n)):
+            { v_p_defs["variant_max_length"]["db_key"]: {}}
+            s_q[l_k].update( { "$gte" : minl } )
+        p_n = "variant_max_length"
+        if (maxl := vp.get(p_n)):
+            s_q[l_k].update( { "$lte" : maxl } )
+
+        if s_q[l_k].keys():
+            return s_q
+
+        return None
+
+    #--------------------------------------------------------------------------#
+
+
     def __create_variantBracketRequest_query(self, v_pars):
         vp = v_pars
         prdbug(f'...__create_variantBracketRequest_query parameters: {vp}')
@@ -788,7 +806,7 @@ def __query_from_hoid(self):
             return
 
         ho_client = MongoClient(host=DB_MONGOHOST)
-        ho_coll = ho_client[HOUSEKEEPING_DB].ho_db[HOUSEKEEPING_HO_COLL]
+        ho_coll = ho_client[HOUSEKEEPING_DB][HOUSEKEEPING_HO_COLL]
         h_o = ho_coll.find_one({"id": accessid})
 
         # accessid overrides ... ?

diff --git a/bycon/lib/service_utils.py b/bycon/lib/service_utils.py
@@ -26,6 +26,7 @@ def initialize_bycon_service():
     update_requested_schema_from_request()
     set_special_modes()
     select_dataset_ids()
+    prdbug(f'initialize_bycon_service - ds_id: {BYC["BYC_DATASET_IDS"]}')
     set_user_name()
     set_returned_granularities()    
     parse_filters()

diff --git a/docs/changes.md b/docs/changes.md
@@ -21,6 +21,16 @@ While changes are documented for individual point versions we actually do not
 push releases out for all of them; they serve more as internal development
 milestones.
 
+### 2023-06-24 (v.1.8.5)
+
+* bug fix: `variantMinSize` wasn't evaluated if also `variantMaxSize` was given
+* `byconaut`: change in datastructure of status maps and frequencies
+    - we have abandoned the "max value ..." concepts which weren't used anyway
+      and switched to  bin coverage and frequency values for high level changes
+      additionally to the all CNV values
+    - this allows now a simple overplotting of high level gains and losses over
+      the low level/combined CNV histograms
+
 ### 2023-06-19 (v.1.8.4)
 
 * changed the values for individual.sex from PATO to EFO (see the [Progenetix data notes](https://docs.progenetix.org/changelog/#2024-06-18-switching-ontology-use-for-individualsex))

diff --git a/docs/generated/argument_definitions.md b/docs/generated/argument_definitions.md
@@ -71,7 +71,7 @@ requested schema, e.g. biosample
 * include resultset responses, e.g. HIT, MISS     
 * kind of a holdover from Beacon pre-v1 but HIT & ALL might have
   some use in networks    
-**default:** `ALL`    
+**default:** `HIT`    
 
 ### `dataset_ids` 
 **type:** array    

diff --git a/setup.py b/setup.py
@@ -11,7 +11,7 @@
 
 setup(
     name="bycon",
-    version="1.8.4",
+    version="1.8.5",
     description="A Python-based environment for the Beacon v2 genomics API",
     long_description=long_description,
     long_description_content_type="text/markdown",

diff --git a/updev.sh b/updev.sh
@@ -9,7 +9,7 @@ BY=(./dist/*tar.gz)
 pip3 install $BY --break-system-packages
 # pipreqs --force .
 # python3 -m build --wheel && twine upload dist/*
-# git tag v1.8.0  & git push --tags
+# git tag v1.8.4  & git push --tags
 ./install.py
 # TODO: the caller for this should be external
 ../byconaut/install.py