mostly hot fix - protected external_references

bycon/beaconServer/tests/GET-examples.md

@@ -2,17 +2,17 @@
 
 http://progenetix.test/beacon/biosamples/?datasetIds=progenetix&referenceName=refseq:NC_000009.12&variantType=EFO:0030067&start=21500000&start=21975098&end=21967753&end=22500000&filters=NCIT:C3058
 
-http://progenetix.org/beacon/genomicVariations/?referenceName=NC_000017.11&start=7577120&referenceBases=G&alternateBases=A&debug=1
+http://progenetix.org/beacon/genomicVariations/?referenceName=NC_000017.11&start=7577120&referenceBases=G&alternateBases=A
 
-https://progenetix.org/beacon/g_variants/?filters=NCIT:C7712&output=pgxseg&debug=1
+https://progenetix.org/beacon/g_variants/?filters=NCIT:C7712&output=pgxseg
 
-https://progenetix.org/beacon/analyses/?referenceName=17&variantType=DEL&start=5000000&start=7676592&end=7669607&end=10000000&filters=&output=pgxmatrix&debug=1
+https://progenetix.org/beacon/analyses/?referenceName=17&variantType=DEL&start=5000000&start=7676592&end=7669607&end=10000000&filters=&output=pgxmatrix
 
-https://progenetix.org/beacon/analyses?referenceName=17&variantType=DEL&start=5000000&start=7676592&end=7669607&end=10000000&filters=cellosaurus&output=pgxmatrix&debug=1
+https://progenetix.org/beacon/analyses?referenceName=17&variantType=DEL&start=5000000&start=7676592&end=7669607&end=10000000&filters=cellosaurus&output=pgxmatrix
 
-http://progenetix.org/beacon/biosamples?filters=NCIT:C3697&output=table&debug=1
+http://progenetix.org/beacon/biosamples?filters=NCIT:C3697&output=table
 
-http://progenetix.org/beacon/biosamples?referenceName=9&start=10000000,12000000&end=12500000,15000000&variantType=DEL&filters=pgx:icdom-81703&debug=1
+http://progenetix.org/beacon/biosamples?referenceName=9&start=10000000,12000000&end=12500000,15000000&variantType=DEL&filters=pgx:icdom-81703
 
 http://progenetix.org/beacon/biosamples/onekgbs-HG00142/g_variants
 

bycon/definitions/datatable_mappings.yaml

@@ -517,7 +517,7 @@ definitions:
       variant_state_id:
         type: string
         db_key: variant_state.id
-        indexed: True
+        indexed: True      # might not beneeded if first in a compound index
         compact: True
       variant_state_label:
         type: string

bycon/lib/bycon_helpers.py

@@ -12,8 +12,7 @@ def set_debug_state(debug=False) -> bool:
     """
     Function to provide a text response header for debugging purposes, i.e. to 
     print out the error or test parameters to a browser session.
-    The common way would be to add either a `/debug=1/` part to a REST path or
-    to provide a `...&debug=1` query parameter.
+    The common way would be to add either a `?debugMode=true` query parameter.
     """
     if BYC["DEBUG_MODE"] is True:
         return True

bycon/lib/cgi_parsing.py

@@ -110,23 +110,17 @@ def rest_path_elements(byc):
         |             |                 |               |
     required      required          optional        optional
     """
-
-    r_p_r = byc.get("request_path_root", "beacon")
-
     if not environ.get('REQUEST_URI'):
         return
 
+    r_p_r = byc.get("request_path_root", "beacon")
     url_comps = urlparse(environ.get('REQUEST_URI'))
     url_p = url_comps.path
     p_items = re.split('/', url_p)
 
     if not r_p_r in p_items:
         return
 
-    for d_k in ["&debug=1", "debug=1", "debug=true"]:
-        if d_k in p_items:
-            p_items.remove(d_k)
-
     p_items = list(filter(None, p_items))
     r_i = p_items.index(r_p_r)
 

bycon/lib/query_generation.py

@@ -254,22 +254,18 @@ def __query_from_variant_pars(self):
     def __create_geneVariantRequest_query(self):
         # query database for gene and use coordinates to create range query
         vp = self.varguments
-
         gene_data = GeneInfo().returnGene(vp["gene_id"])
-
         # TODO: error report/warning
         if not gene_data:
             return
-
         gene = gene_data[0]
 
         # Since this is a pre-processor to the range request
         self.varguments.update( {
-            "reference_name": "refseq:{}".format(gene["accession_version"]),
-            "start": [ gene["start"] ],
-            "end": [ gene["end"] ]
+            "reference_name": f'refseq:{gene.get("accession_version", "___none___")}',
+            "start": [ gene.get("start", 0) ],
+            "end": [ gene.get("end", 1) ]
         } )
-
         self.variant_request_type = "variantRangeRequest"
 
 
@@ -279,7 +275,6 @@ def __create_aminoacidChangeRequest_query(self):
         vp = self.varguments
         if not "aminoacid_change" in vp:
             return
-
         v_p_defs = self.argument_definitions
         v_q = { v_p_defs["aminoacid_change"]["db_key"]: vp.get("aminoacid_change", "___none___")}
 
@@ -304,7 +299,6 @@ def __create_variantTypeRequest_query(self):
         vp = self.varguments
         if not "variant_type" in vp:
             return
-
         v_q = self.__create_in_query_for_parameter("variant_type", v_p_defs["variant_type"]["db_key"], vp)
 
         return v_q

bycon/lib/response_remapping.py

@@ -162,6 +162,7 @@ def remap_biosamples(r_s_res, byc):
         e_r = []
         for r_k, r_v in bs_r.get("references", {}).items():
             e_r.append(__reference_object_from_ontology_term(r_k, r_v, byc))
+
         r_s_res[bs_i].update({
             "sample_origin_type": {"id": "OBI:0001479", "label": "specimen from organism"},
             "external_references": e_r
@@ -186,17 +187,15 @@ def remap_biosamples(r_s_res, byc):
 
 def __reference_object_from_ontology_term(filter_type, ontology_term, byc):
     if "label" in ontology_term:
-        ontology_term.update({"description": ontology_term.get("label")})
+        ontology_term.update({"description": ontology_term.get("label", "")})
         ontology_term.pop("label", None)
-
     f_t_d = byc["filter_definitions"].get(filter_type, {})
     r_d = f_t_d.get("reference")
     if not r_d:
         return ontology_term
     r_r = r_d.get("replace", [])
     if len(r_r) == 2:
         o_id = ontology_term.get("id", "___none___").replace(r_r[0], r_r[1])
-
     ontology_term.update({"reference": f'{r_d.get("root")}{o_id}'})
     return ontology_term
 
@@ -290,10 +289,13 @@ def phenopack_individual(ind, data_db, byc):
 ################################################################################
 
 def clean_empty_fields(this_object):
+    protected = ["external_references"]
     if not isinstance(this_object, dict):
         return this_object
 
     for k in list(this_object.keys()):
+        if k in protected:
+            continue
         if isinstance(this_object[k], dict):
             if not this_object[k]:
                 this_object.pop(k, None)

docs/changes.md

@@ -13,6 +13,11 @@ through the Perl based [**PGX** project](http://github.com/progenetix/PGX/).
 
 ## Changes Tracker
 
+### 2024-02-21 (v.1.5.1)
+
+* hot fix: added "protected" status for `external_references` in general empty
+  field clean-up since the object is required by the front-end (even if empty list)
+
 ### 2024-02-20 (v.1.5.0)
 
 * refactoring global configs into `bycon/config.py` to slowly get rid of some of