Merge pull request #317 from EGA-archive/develop

filtering terms scopes fixed
EGA-archive · Apr 15, 2024 · 04ebcd7 · 04ebcd7
2 parents 369a0f5 + 75f3c61
commit 04ebcd7
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Showing 12 changed files with 23 additions and 20 deletions.
diff --git a/beacon/db/analyses.py b/beacon/db/analyses.py
@@ -99,7 +99,7 @@ def get_variants_of_analysis(entry_id: Optional[str], qparams: RequestParams, da
     return schema, count, dataset_count, docs
 
 def get_filtering_terms_of_analyse(entry_id: Optional[str], qparams: RequestParams):
-    query = {'scope': 'analyses'}
+    query = {'scopes': 'analysis'}
     schema = DefaultSchemas.FILTERINGTERMS
     count = get_count(client.beacon.filtering_terms, query)
     remove_id={'_id':0}

diff --git a/beacon/db/biosamples.py b/beacon/db/biosamples.py
@@ -136,7 +136,7 @@ def get_runs_of_biosample(entry_id: Optional[str], qparams: RequestParams, datas
     return schema, count, dataset_count, docs
 
 def get_filtering_terms_of_biosample(entry_id: Optional[str], qparams: RequestParams):
-    query = {'scope': 'biosamples'}
+    query = {'scopes': 'biosample'}
     schema = DefaultSchemas.FILTERINGTERMS
     count = get_count(client.beacon.filtering_terms, query)
     remove_id={'_id':0}

diff --git a/beacon/db/cohorts.py b/beacon/db/cohorts.py
@@ -173,7 +173,7 @@ def get_biosamples_of_cohort(entry_id: Optional[str], qparams: RequestParams, da
 
 
 def get_filtering_terms_of_cohort(entry_id: Optional[str], qparams: RequestParams):
-    query = {'scope': 'cohorts'}
+    query = {'scopes': 'cohort'}
     schema = DefaultSchemas.FILTERINGTERMS
     count = get_count(client.beacon.filtering_terms, query)
     remove_id={'_id':0}

diff --git a/beacon/db/datasets.py b/beacon/db/datasets.py
@@ -207,7 +207,7 @@ def filter_public_datasets(requested_datasets_ids):
 
 
 def get_filtering_terms_of_dataset(entry_id: Optional[str], qparams: RequestParams):
-    query = {'scope': 'datasets'}
+    query = {'scopes': 'dataset'}
     schema = DefaultSchemas.FILTERINGTERMS
     count = get_count(client.beacon.filtering_terms, query)
     docs = get_documents(

diff --git a/beacon/db/extract_filtering_terms.py b/beacon/db/extract_filtering_terms.py
@@ -283,30 +283,30 @@ def get_filtering_object(terms_ids: list, collection_name: str):
                                         'label': ontology_label,
                                         # TODO: Use conf.py -> beaconGranularity to not disclouse counts in the filtering terms
                                         #'count': get_ontology_term_count(collection_name, onto),
-                                        'scope': [collection_name[0:-1]]                 
+                                        'scopes': [collection_name[0:-1]]                 
                                     })
 
                         terms.append({
                                                 'type': 'alphanumeric',
                                                 'id': field,
                                                 # TODO: Use conf.py -> beaconGranularity to not disclouse counts in the filtering terms
                                                 #'count': get_ontology_term_count(collection_name, onto),
-                                                'scope': [collection_name[0:-1]]     
+                                                'scopes': [collection_name[0:-1]]     
                                             })
                         terms.append({
                                         'type': 'custom',
                                         'id': '{}:{}'.format(field,label),
                                         # TODO: Use conf.py -> beaconGranularity to not disclouse counts in the filtering terms
                                         #'count': get_ontology_term_count(collection_name, onto),
-                                        'scope': [collection_name[0:-1]]                        
+                                        'scopes': [collection_name[0:-1]]                        
                                     })
                     if value_id is not None:
                         terms.append({
                                                 'type': 'alphanumeric',
                                                 'id': value_id,
                                                 # TODO: Use conf.py -> beaconGranularity to not disclouse counts in the filtering terms
                                                 #'count': get_ontology_term_count(collection_name, onto),
-                                                'scope': [collection_name[0:-1]]     
+                                                'scopes': [collection_name[0:-1]]     
                                             })
 
                 print(terms)
@@ -369,17 +369,17 @@ def merge_terms():
             #print(repeated_term)
             id=repeated_term["id"]
             label=repeated_term["label"]
-            if repeated_term['scope'] != []:
-                if repeated_term['scope'][0] not in array_of_scopes:
-                    array_of_scopes.append(repeated_term['scope'][0])
+            if repeated_term['scopes'] != []:
+                if repeated_term['scopes'][0] not in array_of_scopes:
+                    array_of_scopes.append(repeated_term['scopes'][0])
         if array_of_scopes != []:
             new_terms.append({
                 'type': 'ontology',
                 'id': id,
                 'label': label,
                 # TODO: Use conf.py -> beaconGranularity to not disclouse counts in the filtering terms
                 #'count': get_ontology_term_count(collection_name, onto),
-                'scope': array_of_scopes        
+                'scopes': array_of_scopes        
                         })
         client.beacon.filtering_terms.delete_many({"id": repeated_id})
     client.beacon.filtering_terms.insert_many(new_terms)

diff --git a/beacon/db/filters.py b/beacon/db/filters.py
@@ -439,7 +439,7 @@ def apply_ontology_filter(query: dict, filter: OntologyFilter, collection: str,
         final_term_list.append(filter.id)
         query_filtering={}
         query_filtering['$and']=[]
-        dict_scope['scope']=scope
+        dict_scope['scopes']=scope
         query_filtering['$and'].append(dict_scope)
         dict_id={}
         dict_id['id']=filter.id
@@ -514,7 +514,7 @@ def apply_ontology_filter(query: dict, filter: OntologyFilter, collection: str,
         query_filtering['$and']=[]
         dict_scope={}
 
-        dict_scope['scope']=scope
+        dict_scope['scopes']=scope
         dict_id={}
         dict_id['id']=filter.id
         query_filtering['$and'].append(dict_id)
@@ -540,7 +540,7 @@ def apply_ontology_filter(query: dict, filter: OntologyFilter, collection: str,
         dict_id={}
         dict_id['id']=dict_regex
         dict_scope={}
-        dict_scope['scope']=scope
+        dict_scope['scopes']=scope
         query_filtering['$and'].append(dict_id)
         query_filtering['$and'].append(dict_scope)
         docs_2 = get_documents(
@@ -573,7 +573,7 @@ def apply_ontology_filter(query: dict, filter: OntologyFilter, collection: str,
         query_filtering={}
         query_filtering['$and']=[]
         dict_scope={}
-        dict_scope['scope']=scope
+        dict_scope['scopes']=scope
         query_filtering['$and'].append(dict_scope)
         dict_id={}
         dict_id['id']=filter.id

diff --git a/beacon/db/g_variants.py b/beacon/db/g_variants.py
@@ -360,7 +360,7 @@ def get_analyses_of_variant(entry_id: Optional[str], qparams: RequestParams, dat
     return schema, count, dataset_count, docs
 
 def get_filtering_terms_of_genomicvariation(entry_id: Optional[str], qparams: RequestParams):
-    query = {'scope': 'genomicVariations'}
+    query = {'scopes': 'genomicVariation'}
     schema = DefaultSchemas.FILTERINGTERMS
     count = get_count(client.beacon.filtering_terms, query)
     remove_id={'_id':0}

diff --git a/beacon/db/individuals.py b/beacon/db/individuals.py
@@ -297,7 +297,7 @@ def get_biosamples_of_individual(entry_id: Optional[str], qparams: RequestParams
 
 
 def get_filtering_terms_of_individual(entry_id: Optional[str], qparams: RequestParams):
-    query = {'scope': 'individuals'}
+    query = {'scopes': 'individual'}
     schema = DefaultSchemas.FILTERINGTERMS
     count = get_count(client.beacon.filtering_terms, query)
     remove_id={'_id':0}

diff --git a/beacon/db/runs.py b/beacon/db/runs.py
@@ -228,7 +228,7 @@ def get_analyses_of_run(entry_id: Optional[str], qparams: RequestParams, dataset
     return schema, count, dataset_count, docs
 
 def get_filtering_terms_of_run(entry_id: Optional[str], qparams: RequestParams):
-    query = {'scope': 'runs'}
+    query = {'scopes': 'run'}
     schema = DefaultSchemas.FILTERINGTERMS
     count = get_count(client.beacon.filtering_terms, query)
     remove_id={'_id':0}

diff --git a/beacon/request/cohorts.yml b/beacon/request/cohorts.yml
diff --git a/beacon/request/datasets.yml b/beacon/request/datasets.yml
diff --git a/permissions/public_datasets.yml b/permissions/public_datasets.yml
@@ -3,4 +3,5 @@ public_datasets:
 - CINECA_dataset
 - AV_Dataset
 - rd-connect_dataset
-- coadread_tcga_pan_can_atlas_2018
+- coadread_tcga_pan_can_atlas_2018
+- B1MG-COADREAD