move of installers & housekeepers

... from byconaut

bycon/schemas/models/src/progenetix-database-schemas/pgxBiosample.yaml

@@ -26,6 +26,8 @@ properties:
     examples:
       - breast carcinoma
       - adenocarcinoma [cell line HeLa]
+      - rectal adenocarcinoma [MSI, grade 3, metastasized]
+      - rectal adenocarcinoma [MSI, brain metastasis]
   externalReferences:
     type: array
     items:

bycon/services/ontologymaps.py

@@ -70,7 +70,7 @@ def ontologymaps():
     c_g = [ ]
     u_c_d = { }
     mongo_client = MongoClient(host=DB_MONGOHOST)
-    mongo_coll = mongo_client["progenetix"]["ontologymaps"]
+    mongo_coll = mongo_client["_byconServicesDB"]["ontologymaps"]
     for o in mongo_coll.find( query, { '_id': False } ):
         for c in o["code_group"]:
             pre, code = re.split("[:-]", c["id"], maxsplit=1)

bycon/services/publications.py

@@ -52,7 +52,7 @@ def publications():
         BeaconErrorResponse().response(422)
 
     mongo_client = MongoClient(host=DB_MONGOHOST)
-    pub_coll = mongo_client[ "progenetix" ][ "publications" ]
+    pub_coll = mongo_client[ "_byconServicesDB" ][ "publications" ]
     p_re = re.compile( f_d_s["pubmed"]["pattern"] )
     d_k = set_selected_delivery_keys(s_c.get("method_keys"))
     p_l = [ ]
@@ -134,7 +134,7 @@ def _create_filters_query():
     if BYC["TEST_MODE"] is True:
         test_mode_count = int(BYC_PARS.get('test_mode_count', 5))
         mongo_client = MongoClient(host=DB_MONGOHOST)
-        data_coll = mongo_client[ "progenetix" ][ "publications" ]
+        data_coll = mongo_client[ "_byconServicesDB" ][ "publications" ]
 
         rs = list(data_coll.aggregate([{"$sample": {"size": test_mode_count}}]))
         query = {"_id": {"$in": list(s["_id"] for s in rs)}}

docs/changes.md

@@ -21,6 +21,10 @@ 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.
 
+### 2023-09-13 (v.1.9.3)
+
+* services moved to bycon from byconaut
+
 ### 2023-09-12 (v.1.9.2)
 
 * mostly `byconaut` additions (housekeeping scripts etc. and map plot fix)