increased timeout limit for annotation service and reenabled annotati…

…on jobs
GC-HBOC · Jul 25, 2024 · 9747ef7 · 9747ef7
1 parent e05c763
commit 9747ef7
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Showing 2 changed files with 24 additions and 24 deletions.
diff --git a/src/annotation_service/main.py b/src/annotation_service/main.py
@@ -19,41 +19,41 @@
 def get_default_job_config():
     job_config = {
         # heredicare annotations
-        'do_heredicare': False,
+        'do_heredicare': True,
 
         # external programs
-        'do_phylop': False,
-        'do_spliceai': False,
-        'do_hexplorer': False,
-        'do_maxentscan': False,
+        'do_phylop': True,
+        'do_spliceai': True,
+        'do_hexplorer': True,
+        'do_maxentscan': True,
 
         # consequences
-        'do_consequence': False,
-        'do_vep': False,
+        'do_consequence': True,
+        'do_vep': True,
 
         #vcf annotate from vcf
-        'do_dbsnp': False,
-        'do_revel': False,
-        'do_cadd': False,
-        'do_clinvar': False,
-        'do_gnomad': False,
-        'do_brca_exchange': False,
-        'do_flossies': False,
+        'do_dbsnp': True,
+        'do_revel': True,
+        'do_cadd': True,
+        'do_clinvar': True,
+        'do_gnomad': True,
+        'do_brca_exchange': True,
+        'do_flossies': True,
 
-        'do_tp53_database': False,
-        'do_priors': False,
-        'do_bayesdel': False,
-        'do_cosmic': False,
+        'do_tp53_database': True,
+        'do_priors': True,
+        'do_bayesdel': True,
+        'do_cosmic': True,
 
         # assays
-        'do_cspec_brca_assays': False,
+        'do_cspec_brca_assays': True,
 
         # additional annotations
-        'do_cancerhotspots': False,
-        'do_taskforce_domains': False,
-        'do_coldspots': False,
+        'do_cancerhotspots': True,
+        'do_taskforce_domains': True,
+        'do_coldspots': True,
         'do_litvar': True,
-        'do_auto_class': False
+        'do_auto_class': True
 
         # outdated
         #'do_arup': True,

diff --git a/src/frontend_celery/webapp/tasks.py b/src/frontend_celery/webapp/tasks.py
@@ -763,7 +763,7 @@ def start_annotation_service(variant_id, user_id, conn: Connection, job_config =
 # this uses exponential backoff in case there is a http error
 # this will retry 3 times before giving up
 # first retry after 5 seconds, second after 25 seconds, third after 125 seconds (if task queue is empty that is)
-@celery.task(bind=True, retry_backoff=5, max_retries=3, time_limit=600)
+@celery.task(bind=True, retry_backoff=5, max_retries=3, time_limit=6000)
 def annotate_variant(self, annotation_queue_id, job_config):
     """Background task for running the annotation service"""
     self.update_state(state='PROGRESS')