1.3.3

Most of the "special outputs" code has been moved to byconaut -> services.
For legacy reasons (e.g. use by pgxRpi) the webserver configuration needed some
rewrites ... They only apply for the Progenetix use case and are not needed if
sticking to the Beacon formats or if following the use of the new apps like
`services/vcfvariants`).

bycon/__init__.py

@@ -17,18 +17,16 @@
     from cgi_parsing import *
     from clustering_utils import *
     from dataset_parsing import *
-    from datatable_utils import *
     from handover_generation import *
     from interval_utils import *
-    from file_utils import *
     from filter_parsing import *
     from query_execution import *
     from query_generation import *
     from read_specs import *
     from response_remapping import *
     from schema_parsing import *
     from service_utils import *
-    from export_file_generation import *
+    # from export_file_generation import *
     from variant_mapping import *
     from variant_parsing import *
 

bycon/config/datatable_mappings.yaml

@@ -465,6 +465,15 @@ definitions:
         db_key: info.annotation_derived
         default: False
         indexed: True
+      aminoacid_changes:
+        type: array
+        items: string
+        db_key: molecular_attributes.aminoacid_changes
+        indexed: True
+      genomic_hgvs_id:
+        type: string
+        db_key: identifiers.genomicHGVS_id
+        indexed: True
 
       # special pgxseg columns
 

bycon/config/handover_definitions.yaml

@@ -55,7 +55,7 @@ h->o_types:
       - biosample
       - analysis
     h->o_key: 'biosamples.id'
-    script_path_web: '/beacon/biosamples'
+    script_path_web: '/services/sampletable'
 
   phenopackets:
     handoverType:
@@ -104,7 +104,7 @@ h->o_types:
     paginated_entities:
       - all
     h->o_key: 'variants._id'
-    script_path_web: '/beacon/genomicVariations'
+    script_path_web: '/services/pgxsegvariants'
 
   vcf:
     handoverType:
@@ -116,7 +116,7 @@ h->o_types:
     paginated_entities:
       - all
     h->o_key: 'variants._id'
-    script_path_web: '/beacon/genomicVariations'
+    script_path_web: '/services/vcfvariants'
 
   UCSClink:    
     handoverType:

bycon/lib/beacon_response_generation.py

@@ -4,9 +4,7 @@
 
 from bycon_helpers import mongo_result_list, mongo_test_mode_query, return_paginated_list
 from cgi_parsing import prdbug
-from datatable_utils import export_datatable_download
-from export_file_generation import *
-from file_utils import ByconBundler, callset_guess_probefile_path
+# from export_file_generation import *
 from handover_generation import dataset_response_add_handovers
 from query_execution import execute_bycon_queries
 from query_generation import ByconQuery
@@ -584,30 +582,18 @@ def __init__(self, byc: dict):
 
     def populatedResultSets(self):
 
-        # some methods for non-standard responses (i.e. beyond Beacon ...)
-        # first the methods which use data streaming, i.e. do not retrieve the data first
-        self.__check_datasets_0_results_pgxseg_export()
-        self.__check_datasets_0_results_vcf_export()
-        self.__check_result_sets_matrix_export()
-        # retrieving the data if not exited above
         self.__retrieve_datasets_data()
         self.__retrieve_variants_data()
-        # tables before reshaping ...
-        self.__check_datasets_data_table_export()
-        # self.__check_datasets_results_histoplot_delivery()
-        # self.__check_datasets_results_samplesplot_delivery()
-        self.__check_biosamples_map_delivery()
-        # finally populating the standard Beacon response
         self.__populate_result_sets()
-        # if still here (i.e. non of the above was successful) now saving
-        # this could be separate ...
         self.__result_sets_save_handovers()
 
         return self.result_sets, self.record_queries
 
     # -------------------------------------------------------------------------#
 
     def datasetsData(self):
+        self.__retrieve_datasets_data()
+        self.__retrieve_variants_data()
         return self.datasets_data
 
 
@@ -638,88 +624,6 @@ def __get_handover_access_key(self):
         return
 
 
-    # -------------------------------------------------------------------------#
-
-    def __check_datasets_data_table_export(self):
-        if not "table" in self.output:
-            return
-
-        collated_results = []
-        for ds_id, data in self.datasets_data.items():
-            collated_results += data
-
-        export_datatable_download(collated_results, self.byc)
-
-
-    # -------------------------------------------------------------------------#
-
-    def __check_datasets_0_results_pgxseg_export(self):
-        """
-
-        """
-        if not "pgxseg" in self.output:
-            return
-
-        ds_id = list(self.datasets_results.keys())[0]
-        export_pgxseg_download(self.datasets_results, ds_id, self.byc)
-        return
-
-
-    # -------------------------------------------------------------------------#
-
-    def __check_datasets_0_results_vcf_export(self):
-        """
-
-        """
-        if not "vcf" in self.output:
-            return
-
-        ds_id = list(self.datasets_results.keys())[0]
-        export_vcf_download(self.datasets_results, ds_id, self.byc)
-
-        return
-
-
-    # -------------------------------------------------------------------------#
-
-    def __check_result_sets_matrix_export(self):
-        if not "pgxmatrix" in self.output:
-            return
-
-        ds_id = list(self.datasets_results.keys())[0]
-        export_callsets_matrix(self.datasets_results, ds_id, self.byc)
-        return
-
-
-    # -------------------------------------------------------------------------#
-
-    def __check_biosamples_map_delivery(self):
-        """
-        TBD
-        """
-
-
-        return
-
-
-    # -------------------------------------------------------------------------#
-
-    def __check_datasets_results_samplesplot_delivery(self):
-        if not "samplesplot" in self.output:
-            return
-        self.__datasets_results_samplesplot_generation()
-        print_svg_response(self.svg, self.env)
-
-
-    # -------------------------------------------------------------------------#
-
-    def __check_datasets_results_histoplot_delivery(self):
-        if not "histo" in self.output:
-            return
-        self.__datasets_results_histoplot_generation()
-        print_svg_response(self.svg, self.env)
-
-
     # -------------------------------------------------------------------------#
 
     def __result_sets_save_handovers(self):

bycon/lib/bycon_helpers.py

@@ -120,3 +120,108 @@ def mongo_test_mode_query(db_name, coll_name, test_mode_count=5):
 
     return query, error
 
+################################################################################
+
+def assign_nested_value(parent, dotted_key, v, parameter_definitions={}):
+
+    parameter_type = parameter_definitions.get("type", "string")
+    parameter_default = parameter_definitions.get("default")
+
+    if v is None:
+        if parameter_default:
+            v = parameter_default
+
+    if v is None:
+        return parent
+
+    if "num" in parameter_type:
+        if str(v).strip().lstrip('-').replace('.','',1).isdigit():
+            v = float(v)
+    elif "integer" in parameter_type:
+        if str(v).strip().isdigit():
+            v = int(v)
+    else:
+        v = str(v)
+
+    ps = dotted_key.split('.')
+
+    if len(ps) == 1:
+        if "array" in parameter_type:
+            parent.update({ps[0]: v.split(',')})
+        else:
+            parent.update({ps[0]: v })
+        return parent
+
+    if ps[0] not in parent or parent[ ps[0] ] is None:
+        parent.update({ps[0]: {}})
+
+    if len(ps) == 2:
+        if "array" in parameter_type:
+            parent[ ps[0] ].update({ps[1]: v.split(',')})
+        else:
+            parent[ ps[0] ].update({ps[1]: v })
+        return parent
+
+    if  ps[1] not in parent[ ps[0] ] or parent[ ps[0] ][ ps[1] ] is None:
+        parent[ ps[0] ].update({ps[1]: {}})
+    if len(ps) == 3:
+        if "array" in parameter_type:
+            parent[ ps[0] ][ ps[1] ].update({ps[2]: v.split(',')})
+        else:
+            parent[ ps[0] ][ ps[1] ].update({ps[2]: v })
+        return parent
+
+    if  ps[2] not in parent[ ps[0] ][ ps[1] ] or parent[ ps[0] ][ ps[1] ][ ps[2] ] is None:
+        parent[ ps[0] ][ ps[1] ].update({ps[2]: {}})
+    if len(ps) == 4:
+        if "array" in parameter_type:
+            parent[ ps[0] ][ ps[1] ][ ps[2] ].update({ps[3]: v.split(',')})
+        else:
+            parent[ ps[0] ][ ps[1] ][ ps[2] ].update({ps[3]: v })
+        return parent
+
+    if len(ps) > 4:
+        print("¡¡¡ Parameter key "+dotted_key+" nested too deeply (>4) !!!")
+        return '_too_deep_'
+
+    return parent
+
+################################################################################
+
+def get_nested_value(parent, dotted_key, parameter_type="string"):
+
+    ps = dotted_key.split('.')
+
+    v = ""
+
+    if len(ps) == 1:
+        try:
+            v = parent[ ps[0] ]
+        except:
+            v = ""
+    elif len(ps) == 2:
+        try:
+            v = parent[ ps[0] ][ ps[1] ]
+        except:
+            v = ""
+    elif len(ps) == 3:
+        try:
+            v = parent[ ps[0] ][ ps[1] ][ ps[2] ]
+        except:
+            v = ""
+    elif len(ps) == 4:
+        try:
+            v = parent[ ps[0] ][ ps[1] ][ ps[2] ][ ps[3] ]
+        except:
+            v = ""
+    elif len(ps) == 5:
+        try:
+            v = parent[ ps[0] ][ ps[1] ][ ps[2] ][ ps[3] ][ ps[4] ]
+        except:
+            v = ""
+    elif len(ps) > 5:
+        print("¡¡¡ Parameter key "+dotted_key+" nested too deeply (>5) !!!")
+        return '_too_deep_'
+
+    return v
+