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EGA-archive · Jul 3, 2024 · 34f6dad · 34f6dad
1 parent 36d41de
commit 34f6dad
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Showing 4 changed files with 15 additions and 11 deletions.
diff --git a/beacon/conf.py b/beacon/conf.py
@@ -126,6 +126,6 @@
 #
 ontologies_folder = "ontologies"
 
-alphanumeric_terms = ['libraryStrategy', 'molecularAttributes.geneIds', 'diseases.ageOfOnset.iso8601duration']
+alphanumeric_terms = ['libraryStrategy', 'molecularAttributes.geneIds', 'diseases.ageOfOnset.iso8601duration', 'molecularAttributes.aminoacidChanges']
 
 ontology_files={"NCIT": "http://purl.obolibrary.org/obo/NCIT.obo"}
diff --git a/beacon/request/handlers.py b/beacon/request/handlers.py
@@ -27,6 +27,7 @@
 
 LOG = logging.getLogger(__name__)
 
+
 def collection_handler(db_fn, request=None):
     async def wrapper(request: Request):
         try:
@@ -58,8 +59,6 @@ async def wrapper(request: Request):
                     [r for r in records] if records else []
                 )
                 LOG.debug(entity_schema)
-                LOG.debug(response_converted)
-                LOG.debug(type(response_converted))
                 response = build_beacon_collection_response(
                     response_converted, count, qparams, lambda x, y: x, entity_schema
                 )
@@ -220,20 +219,16 @@ async def wrapper(request: Request):
                 #LOG.debug(response_datasets)
                 new_count=0
                 loop = asyncio.get_running_loop()
-                tasks=[]
                 for dataset in response_datasets:
                     with ThreadPoolExecutor() as pool:
-                        tasks.append(await loop.run_in_executor(pool, db_fn, entry_id, qparams, dataset))
-                    #LOG.debug(dataset)
-                asyncio.wait(tasks)
-                for task in tasks:
-                    entity_schema, count, dataset_count, records = task
+                        entity_schema, count, dataset_count, records = await loop.run_in_executor(pool, db_fn, entry_id, qparams, dataset)
                     #LOG.debug(dataset)
 
                     if dataset_count != -1:
                         new_count+=dataset_count
                         datasets_docs[dataset]=records
                         datasets_count[dataset]=dataset_count
+
                 if include != 'NONE':
                     count=new_count
                 else:

diff --git a/deploy/conf.py b/deploy/conf.py
@@ -126,6 +126,6 @@
 #
 ontologies_folder = "ontologies"
 
-alphanumeric_terms = ['libraryStrategy', 'molecularAttributes.geneIds', 'diseases.ageOfOnset.iso8601duration']
+alphanumeric_terms = ['libraryStrategy', 'molecularAttributes.geneIds', 'diseases.ageOfOnset.iso8601duration', 'molecularAttributes.aminoacidChanges']
 
 ontology_files={"NCIT": "http://purl.obolibrary.org/obo/NCIT.obo"}
diff --git a/permissions/public_datasets.yml b/permissions/public_datasets.yml
@@ -4,4 +4,13 @@ public_datasets:
 - AV_Dataset
 - rd-connect_dataset
 - coadread_tcga_pan_can_atlas_2018
-- B1MG-COADREAD
+- B1MG-COADREAD
+- HGI_BelCovid_2
+- HGI_BRACOVID
+- HGI_GEN-COVID
+- HGI_Hostage_1
+- HGI_Hostage_2
+- HGI_Hostage_3
+- HGI_Hostage_4
+- HGI_INMUNGEN_CoV2
+- HGI_SPGRX