Merge pull request #26 from EGA-archive/urgent-fix

Applying granularity restrictions from source
EGA-archive · Jan 7, 2025 · eeabc63 · eeabc63
2 parents 9f42772 + 01393f5
commit eeabc63
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Showing 3 changed files with 24 additions and 19 deletions.
diff --git a/beacon/conf/api_version.yml b/beacon/conf/api_version.yml
@@ -1 +1 @@
-api_version: v2.0-154384d
+api_version: v2.0-9f42772
diff --git a/beacon/response/builder.py b/beacon/response/builder.py
@@ -14,36 +14,56 @@ async def builder(self, request: Request, datasets, qparams, entry_type, entry_i
             source_entry_type = source_entry_type[1]
             if source_entry_type == 'analyses':
                 source = analyses['database']
+                source_granularity = analyses['granularity']
             elif source_entry_type == 'biosamples':
                 source = biosamples['database']
+                source_granularity = biosamples['granularity']
             elif source_entry_type == 'individuals':
                 source = individuals['database']
+                source_granularity = individuals['granularity']
             elif source_entry_type == 'runs':
                 source = runs['database']
+                source_granularity = runs['granularity']
         elif entry_type == 'g_variants':
             source = g_variants['database']
+            source_granularity = g_variants['granularity']
         elif '_' in entry_type:
             source = g_variants['database']
+            source_granularity = g_variants['granularity']
         elif entry_type == 'analyses':
             source = analyses['database']
+            source_granularity = analyses['granularity']
         elif entry_type == 'biosamples':
             source = biosamples['database']
+            source_granularity = biosamples['granularity']
         elif entry_type == 'individuals':
             source = individuals['database']
+            source_granularity = individuals['granularity']
         elif entry_type == 'runs':
             source = runs['database']
+            source_granularity = runs['granularity']
+        if source_granularity['record']==True:
+            allowed_granularity='record'
+        elif source_granularity['count']==True:
+            allowed_granularity='count'
+        else:
+            allowed_granularity='boolean'
         complete_module='beacon.connections.'+source+'.executor'
         import importlib
         module = importlib.import_module(complete_module, package=None)
         testMode = qparams.query.test_mode
         if testMode == True:
             datasets = ['test']
         datasets_docs, datasets_count, count, entity_schema, include, datasets = await module.execute_function(self, entry_type, datasets, qparams, entry_id)
-        if include != 'NONE' and granularity == Granularity.RECORD and max_beacon_granularity == 'record':
+        if include != 'NONE' and granularity == Granularity.RECORD and max_beacon_granularity == 'record' and allowed_granularity=='record':
             response = build_beacon_record_response_by_dataset(self, datasets, datasets_docs, datasets_count, count, qparams, entity_schema)
-        elif include == 'NONE' and granularity == Granularity.RECORD and max_beacon_granularity == 'record':
+        elif include == 'NONE' and granularity == Granularity.RECORD and max_beacon_granularity == 'record' and allowed_granularity=='record':
             response = build_beacon_none_response(self, datasets_docs["NONE"], count, qparams, entity_schema)
-        elif granularity == Granularity.COUNT and max_beacon_granularity in ['count', 'record'] or granularity == Granularity.RECORD and max_beacon_granularity in ['count']:
+        elif granularity == Granularity.COUNT and max_beacon_granularity in ['count', 'record'] and allowed_granularity in ['count', 'record']:
+            response = build_beacon_count_response(self, count, qparams, entity_schema)
+        elif granularity == Granularity.RECORD and max_beacon_granularity in ['count'] and allowed_granularity in ['count', 'record']:
+            response = build_beacon_count_response(self, count, qparams, entity_schema)
+        elif granularity == Granularity.RECORD and allowed_granularity in ['count'] and max_beacon_granularity in ['count', 'record']:
             response = build_beacon_count_response(self, count, qparams, entity_schema)
         else:
             response = build_beacon_boolean_response(self, count, qparams, entity_schema)

diff --git a/beacon/source/manage.py b/beacon/source/manage.py
@@ -2,7 +2,6 @@
 
 analyses={
     'granularity': {
-        'boolean': True,
         'count': True,
         'record': True
     },
@@ -15,7 +14,6 @@
 }
 biosamples={
     'granularity': {
-        'boolean': True,
         'count': True,
         'record': True
     },
@@ -29,11 +27,6 @@
     'database': 'mongo'
 }
 cohorts={
-    'granularity': {
-        'boolean': True,
-        'count': True,
-        'record': True
-    },
     'singleEntryUrl': True,
     'endpoints': {
         'analysis': True,
@@ -44,11 +37,6 @@
     'database': 'mongo'
 }
 datasets={
-    'granularity': {
-        'boolean': True,
-        'count': True,
-        'record': True
-    },
     'singleEntryUrl': True,
     'endpoints': {
         'analysis': True,
@@ -62,7 +50,6 @@
 }
 g_variants={
     'granularity': {
-        'boolean': True,
         'count': True,
         'record': True
     },
@@ -78,7 +65,6 @@
 }
 individuals={
     'granularity': {
-        'boolean': True,
         'count': True,
         'record': True
     },
@@ -94,7 +80,6 @@
 }
 runs={
     'granularity': {
-        'boolean': True,
         'count': True,
         'record': True
     },
Original file line number	Diff line number	Diff line change
		@@ -1 +1 @@
		api_version: v2.0-154384d
		api_version: v2.0-9f42772