some corrections on docs, conf and get descendants

README.md

@@ -77,7 +77,7 @@ Remember to do this step every time you import new data!!
 You can create the necessary indexes running the following Python script:
 
 ```bash
-docker exec beacon python beacon/reindex.py
+docker exec beaconprod python /beacon/connections/mongo/reindex.py
 ```
 
 #### Fetch the ontologies and extract the filtering terms

beacon/conf/conf.py

@@ -12,7 +12,6 @@
 
 level=logging.NOTSET
 api_version='2.0.0'
-default_beacon_granularity='record'
 beacon_id = 'org.ega-archive.beacon-ri-demo'  # ID of the Beacon
 beacon_name = 'Beacon Reference Implementation demo'  # Name of the Beacon service
 api_version = 'v2.0.0' # Version of the Beacon implementation
@@ -24,7 +23,7 @@
 alternative_url = 'https://beacon.ega-archive.org/api'
 create_datetime = '2021-11-29T12:00:00.000000'
 update_datetime = ''
-default_beacon_granularity = "record"
+default_beacon_granularity = "record" # boolean, count or record
 security_levels = ['PUBLIC', 'REGISTERED', 'CONTROLLED']
 documentation_url = 'https://b2ri-documentation-demo.ega-archive.org/'
 alphanumeric_terms = ['libraryStrategy', 'molecularAttributes.geneIds', 'diseases.ageOfOnset.iso8601duration', 'molecularAttributes.aminoacidChanges']

beacon/connections/mongo/get_descendants.py

@@ -46,6 +46,7 @@ def __call__(self, block_num: int, block_size: int, total_size: int):
 
 def load_ontology(ontology_id: str):
     if ontology_id.isalpha():
+        print(ontology_id)
         url_alt = "https://www.ebi.ac.uk/efo/EFO.obo"
         url = "http://purl.obolibrary.org/obo/{}.obo".format(ontology_id.lower())
         path = "/beacon/connections/mongo/ontologies/{}.obo".format(ontology_id)
@@ -61,6 +62,8 @@ def load_ontology(ontology_id: str):
         except ValueError:
             #print("ERROR", ValueError)
             pass
+        except Exception:
+            pass
         try:
             #print (os.stat(path).st_size)
             if os.stat(path).st_size == 0:

ri-tools/conf/conf.py

@@ -6,6 +6,7 @@
 allele_frequency=1 # introduce float number, leave 1 if you want to convert all the variants
 reference_genome='GRCh38' # Choose one between NCBI36, GRCh37, GRCh38
 datasetId='coadread_tcga_pan_can_atlas_2018'
+case_level_data=True
 
 ### MongoDB parameters ###
 database_host = 'mongo'