1.3.7

... authorization stub etc.; see changes doc

bycon/beaconServer/beacon.py

@@ -63,6 +63,8 @@ def beacon():
         byc.update({"request_entity_path_id": e_p_id})
     r_p_id = byc.get("request_entity_path_id", "info")
 
+    prdbug(byc, f'beacon.py - request_entity_path_id: {r_p_id}')
+
     # check for rewrites
     if r_p_id in r_w:
         uri = environ.get('REQUEST_URI')

bycon/config/authorizations.yaml

@@ -0,0 +1,4 @@
+anonymous:
+  default: boolean
+local:
+  default: record

bycon/config/config.yaml

@@ -1,36 +1,42 @@
-byc_root_pars:
+args: {}
+debug_mode: false
+empty_query_all_count: false
+error_response: {}
+errors: []
+filters: []
+form_data: {}
+granularity_levels:
+  none: 0
+  boolean: 1
+  count: 2
+  record: 3
+pagination:
+  skip: 0
+  limit: 0
+include_handovers: false
+method: ''
+output: ''
+queries: {}
+query_meta: {}
+request_path_root: beacon
+request_entity_path_id:
+request_entity_path_id_value: false
+response_entity_path_id:
+request_entity_id: genomicVariant
+response_entity_id: genomicVariant
+response_entity:
+  is_entry_type: True
+  collection: variants
+  response_schema: beaconResultsetsResponse
+  beacon_schema:
+    entity_type: genomicVariant
+    schema: https://progenetix.org/services/schemas/genomicVariant/
+service_response: {}
+service_config: {}
+test_mode: false
+test_mode_count: 5
 
-  args:
-  request_path_root: beacon
-  request_entity_path_id:
-  request_entity_path_id_value: false
-  response_entity_path_id:
-  request_entity_id: genomicVariant
-  response_entity_id: genomicVariant
-  response_entity:
-    is_entry_type: True
-    collection: variants
-    response_schema: beaconResultsetsResponse
-    beacon_schema:
-      entity_type: genomicVariant
-      schema: https://progenetix.org/services/schemas/genomicVariant/
-  service_response: {}
-  error_response: {}
-  service_config: {}
-  filters: []
-  method: ''
-  output: ''
-  form_data: {}
-  queries: {}
-  query_meta: {}
-  include_handovers: false
-  empty_query_all_count: false
-  test_mode: false
-  test_mode_count: 5
-  check_args: true
-  debug_mode: false
-  download_mode: false
-  errors: []
+filtering_terms_coll: collations
 
 genomes_path:
   - rsrc
@@ -44,18 +50,10 @@ filter_flags:
   precision: exact
   include_descendant_terms: true
 
-resource_urls:
-  ncbi_geosoft: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?form=text&acc=
-  ncbi_geoweb: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=
-  europepmc_pmid: https://europepmc.org/article/MED/
-  cellosaurus_web: https://web.expasy.org/cellosaurus/
-
 ################################################################################
 # MongoDB configs
 ################################################################################
 
-filtering_terms_coll: collations
-
 # special database, auto-generated ######
 housekeeping_db: _byconHousekeepingDB
 beacon_info_coll: beaconinfo

bycon/lib/args_parsing.py

@@ -3,11 +3,10 @@
 
 from humps import decamelize
 
-
 ################################################################################
 
 def get_bycon_args(byc):
-    if byc.get("check_args", False) is False:
+    if byc.get("check_args", True) is False:
         return
 
     # Serves as "we've been here before" marker - before the env check.
@@ -65,6 +64,7 @@ def args_update_form(byc):
         else:
             byc["form_data"].update({p_d: arg_vars[p]})
 
+
 ################################################################################
 
 def filters_from_args(byc):
@@ -99,19 +99,19 @@ def set_collation_types(byc):
 def set_processing_modes(byc):
     byc.update({"update_mode": False})
 
-    try:
-        if byc["test_mode"] is True:
-            byc.update({"update_mode": False})
-            print("¡¡¡ TEST MODE - no db update !!!")
-            return
-    except:
-        pass
-
-    try:
-        if byc["args"].update:
-            byc.update({"update_mode": True})
-            print("¡¡¡ UPDATE MODE - may overwrite entries !!!")
-    except:
-        pass
+    tm = byc.get("test_mode", False)
+    env = byc.get("env", "server")
+
+    if not "local" in env:
+        return
+
+    if byc["test_mode"] is True:
+        print("¡¡¡ TEST MODE - no db update !!!")
+        return
+
+    if byc["args"].update:
+        byc.update({"update_mode": True})
+        print("¡¡¡ UPDATE MODE - may overwrite entries !!!")
+
+
 
-################################################################################

bycon/lib/beacon_response_generation.py

@@ -65,11 +65,13 @@ def __init__(self, byc: dict):
         self.byc = byc
         self.test_mode = byc.get("test_mode", False)
         self.beacon_defaults = byc.get("beacon_defaults", {})
+        self.authorized_granularities = byc.get("authorized_granularities", {})
+        self.user_name = byc.get("user_name", "anonymous")
         self.entity_defaults = self.beacon_defaults.get("entity_defaults", {"info":{}})
         self.form_data = byc.get("form_data", {})
         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.returned_granularity = self.form_data.get("returned_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 = {}
@@ -86,6 +88,7 @@ def __init__(self, byc: dict):
     # -------------------------------------------------------------------------#
 
     def resultsetResponse(self):
+        prdbug(self.byc, f'... resultsetResponse start, schema {self.response_schema}')
         if not "beaconResultsetsResponse" in self.response_schema:
             return
 
@@ -94,16 +97,7 @@ 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:
-            # 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)
+        self.__resultSetResponse_force_granularities()
 
         b_h_o = self.data_response.get("beacon_handovers", [])
         if len(b_h_o) < 1:
@@ -118,6 +112,7 @@ def resultsetResponse(self):
         self.__meta_add_received_request_summary_parameters()
         self.__meta_add_parameters()
         self.__meta_clean_parameters()
+        self.__response_clean_parameters()
         self.result_sets_end = datetime.datetime.now()
         self.result_sets_duration = self.result_sets_end - self.result_sets_start
         prdbug(self.byc, f'... data response duration was {self.result_sets_duration.total_seconds()} seconds')
@@ -140,6 +135,7 @@ def collectionsResponse(self):
         self.__meta_add_received_request_summary_parameters()
         self.__meta_add_parameters()
         self.__meta_clean_parameters()
+        self.__response_clean_parameters()
         return self.data_response
 
 
@@ -157,6 +153,7 @@ def filteringTermsResponse(self):
         self.__meta_add_received_request_summary_parameters()
         self.__meta_add_parameters()
         self.__meta_clean_parameters()
+        self.__response_clean_parameters()
         return self.data_response
 
 
@@ -191,6 +188,30 @@ def __check_switch_to_error_response(self):
             self.data_response = self.error_response
 
 
+    # -------------------------------------------------------------------------#
+
+    def __resultSetResponse_force_granularities(self):
+        prdbug(self.byc, f'authorized_granularities: {self.authorized_granularities}')
+        for rs in self.data_response["response"]["result_sets"]:
+            rs_granularity = self.authorized_granularities.get(rs["id"], "boolean")
+            prdbug(self.byc, f'rs_granularity ({rs["id"]}): {rs_granularity}')
+            if not "record" in rs_granularity:
+                # TODO /CUSTOM: This non-standard modification removes the results
+                # but keeps the resultSets structure (handovers ...)
+                rs.pop("results", None)
+            if "boolean" in rs_granularity:
+                rs.pop("results_count", None)
+        if "boolean" in self.returned_granularity:
+            self.data_response["response_summary"].pop("num_total_results", None)
+
+
+    # -------------------------------------------------------------------------#
+
+    def __response_clean_parameters(self):
+        r_m = self.data_response.get("response", {})
+        r_m.pop("$schema", None)
+
+
     # -------------------------------------------------------------------------#
 
     def __meta_clean_parameters(self):
@@ -221,8 +242,8 @@ def __meta_add_parameters(self):
         form = self.form_data
         # TODO: this is hacky; need a separate setting of the returned granularity
         # since the server may decide so...
-        if self.requested_granularity and "returned_granularity" in r_m:
-            r_m.update({"returned_granularity": form.get("requested_granularity")})
+        # if self.requested_granularity and "returned_granularity" in r_m:
+        #     r_m.update({"returned_granularity": form.get("requested_granularity")})
 
         service_meta = self.service_config.get("meta", {})
         for rrs_k, rrs_v in service_meta.items():
@@ -246,7 +267,7 @@ def __meta_add_received_request_summary_parameters(self):
             "requested_schemas": [self.beacon_schema]
         })
 
-        for name in ["dataset_ids", "test_mode"]:
+        for name in ["dataset_ids", "test_mode", "pagination"]:
             value = self.byc.get(name)
             if not value:
                 continue
@@ -442,6 +463,7 @@ def __return_filtering_terms(self):
 
         return
 
+
     # -------------------------------------------------------------------------#
 
     def __return_filter_resources(self):
@@ -596,7 +618,6 @@ def populatedResultSets(self):
         self.__retrieve_variants_data()
         self.__populate_result_sets()
         self.__result_sets_save_handovers()
-
         return self.result_sets, self.record_queries
 
 
@@ -640,8 +661,8 @@ def __get_handover_access_key(self):
     def __result_sets_save_handovers(self):
 
         ho_client = MongoClient(host=environ.get("BYCON_MONGO_HOST", "localhost"))
-        ho_db = ho_client[ self.byc["config"]["housekeeping_db"] ]
-        ho_coll = ho_db[ self.byc["config"][ "handover_coll" ] ]
+        ho_db = ho_client[ self.byc["housekeeping_db"] ]
+        ho_coll = ho_db[ self.byc["handover_coll"] ]
 
         for ds_id, d_s in self.datasets_results.items():
             if not d_s:

bycon/lib/cgi_parsing.py

@@ -130,7 +130,6 @@ def parse_POST(byc):
             "query_meta": jbod.get("meta", {})
         })
 
-
 ################################################################################
 
 def parse_GET(byc):

bycon/lib/dataset_parsing.py

@@ -42,8 +42,8 @@ def ds_id_from_accessid(byc):
     # test of existence...
 
     accessid = byc["form_data"].get("accessid", False)
-    ho_db = byc["config"].get("housekeeping_db", False)
-    ho_collname = byc["config"].get("handover_coll", False)
+    ho_db = byc.get("housekeeping_db", False)
+    ho_collname = byc.get("handover_coll", False)
 
     if any(x is False for x in [accessid, ho_db, ho_collname]):
         return False
@@ -89,12 +89,13 @@ def ds_ids_from_args(byc):
     if "args" not in byc or byc["args"] is None:
         return False
 
-    if byc["args"].datasetIds:
-        ds_ids = re.split(",", byc["args"].datasetIds)
-        byc.update({"dataset_ids": ds_ids})
-        return True
+    dsid_s = byc["args"].get("datasetIds")
+    if not dsid_s:
+        return False
 
-    return False
+    ds_ids = re.split(",", dsid_s)
+    byc.update({"dataset_ids": ds_ids})
+    return True
 
 
 ################################################################################

bycon/lib/genome_utils.py

@@ -39,7 +39,7 @@ def set_genome_rsrc_path(byc):
     if genome in g_map.keys():
         genome = g_map[ genome ]
 
-    byc.update({"genome_rsrc_path": path.join( pkg_path, *byc["config"]["genomes_path"], genome ) })
+    byc.update({"genome_rsrc_path": path.join( pkg_path, *byc["genomes_path"], genome ) })
 
 
 ################################################################################
@@ -130,11 +130,11 @@ def retrieve_gene_id_coordinates(gene_id, precision, byc):
     mongo_client = MongoClient(host=environ.get("BYCON_MONGO_HOST", "localhost"))
     db_names = list(mongo_client.list_database_names())
 
-    services_db = byc["config"].get("services_db", "___none___")
+    services_db = byc.get("services_db", "___none___")
     if services_db not in db_names:
         return [], f"services db `{services_db}` does not exist"
 
-    genes_coll = byc["config"].get("genes_coll")
+    genes_coll = byc.get("genes_coll")
     if not genes_coll:
         return [], "no `genes_coll` parameter in `config.yaml`"
 

bycon/lib/handover_generation.py

@@ -117,8 +117,8 @@ def query_results_save_handovers(byc):
 def dataset_results_save_handovers(ds_id, byc):
 
     ho_client = MongoClient(host=environ.get("BYCON_MONGO_HOST", "localhost"))
-    ho_db = ho_client[ byc["config"]["housekeeping_db"] ]
-    ho_coll = ho_db[ byc["config"][ "handover_coll" ] ]
+    ho_db = ho_client[ byc["housekeeping_db"] ]
+    ho_coll = ho_db[ byc[ "handover_coll" ] ]
 
     for h_o_k in byc["dataset_results"][ds_id].keys():
 

bycon/lib/parse_filters_request.py

@@ -15,9 +15,9 @@ def parse_filters(byc):
 def get_global_filter_flags(byc):
 
     ff = {
-        "logic": byc[ "config" ][ "filter_flags" ][ "logic" ],
-        "precision": byc[ "config" ][ "filter_flags" ][ "precision" ],
-        "descendants": byc[ "config" ][ "filter_flags" ][ "include_descendant_terms" ]
+        "logic": byc["filter_flags"]["logic"],
+        "precision": byc["filter_flags"]["precision"],
+        "descendants": byc["filter_flags"]["include_descendant_terms"]
     }
 
     if "form_data" in byc: