Implementing new in-house background for svs (#32)

WIP

HISTORY.rst

@@ -30,6 +30,7 @@ End-User Summary
 - Fixed smallvariant flags filter query (#502).
 - Added flags `segregates`, `doesnt_segregate` and `no_disease_association` to file export (#502).
 - Adjusting path to new varfish-annotator db download (#546).
+- Implement new in-house background database for structural variants (#32).
 
 Full Change List
 ================
@@ -59,6 +60,7 @@ Full Change List
 - Fixed smallvariant flags filter query (#502).
 - Added flags `segregates`, `doesnt_segregate` and `no_disease_association` to file export (#502).
 - Adjusting path to new varfish-annotator db download (#546).
+- Implement new in-house background database for structural variants (#32).
 
 ------
 v1.2.0

config/settings/base.py

@@ -508,6 +508,9 @@ def set_logging(level=None):
 # Number of cases to perform in one query for joint queries.
 QUERY_MAX_UNION = env.int("VARFISH_QUERY_MAX_UNION", 20)
 
+# Timeout (in hours) for VarFish cleaning up background SV sets in "building" state.
+SV_CLEANUP_BUILDING_SV_SETS = env.int("VARFISH_SV_CLEANUP_BUILDING_SV_SETS", 48)
+
 # Varfish: Exomiser
 # ------------------------------------------------------------------------------
 

importer/models.py

@@ -4,7 +4,6 @@
 import tempfile
 import uuid as uuid_object
 
-import aldjemy
 from bgjobs.models import BackgroundJob, LOG_LEVEL_ERROR, JobModelMessageMixin
 from django.contrib import auth
 from django.db import models, transaction

requirements/base.txt

@@ -154,3 +154,12 @@ django-saml2-auth-ai>=2.1.6, <2.2
 # Code formatting.
 black ==19.10b0
 click >=8.0,<8.1
+
+# Editable interval trees
+intervaltree >=3.1.0,<4.0.0
+
+# Pretty tables
+prettytable >=3.3.0,<4.0
+
+# process introspection
+psutil >=5.9.0,<6.0