Allow excluding cases from in-house database (#579)

Closes: #579
Related-Issue: #579
Projected-Results-Impact: require-revalidation

HISTORY.rst

@@ -38,6 +38,7 @@ End-User Summary
   A full re-import after re-annotation with varfish-annotator v0.23 or above is recommended.
   Alternatively, you can use ``python manage.py svs_sv_fill_nulls`` to update the records on the fly.
 - Implement new in-house background database for structural variants (#32).
+- Allow to exclude cases from in-house database through project settings (#579).
 
 Full Change List
 ================
@@ -65,11 +66,12 @@ Full Change List
 - Fixed broken VariantValidator query (#523).
 - Converted not cooperative tooltip to standard title on Filter & Display button (#508).
 - Fixed smallvariant flags filter query (#502).
-- Added flags `segregates`, `doesnt_segregate` and `no_disease_association` to file export (#502).
+- Added flags ``segregates``, ``doesnt_segregate`` and ``no_disease_association`` to file export (#502).
 - Adjusting path to new varfish-annotator db download (#546).
 - Fixing issue with sync-from-remote when no remote is defined (#570).
 - Adding feature to enable and configure link-out to HGMD (#576).
 - Implement new in-house background database for structural variants (#32).
+- Allow to exclude cases from in-house database through project settings (#579).
 
 ------
 v1.2.0

docs_manual/admin_upgrade.rst

@@ -30,6 +30,19 @@ You can find out more details, give feedback, and ask for help `in this Github d
 v1.2.* to v2.*.*
 ----------------
 
+**In-House Background Database.**
+A number of changes were made to the implementation of the background database.
+The upgrade will re-create the in-house database as empty.
+
+You will have to re-build the database manually with the command ``python manage.py rebuild_variant_summary``.
+Assuming that you are running within ``varfish-docker-compose``, you can use the following command directly.
+
+::
+
+    $ docker exec -it varfish-docker-compose_varfish-web_1 python /usr/src/app/manage.py \
+        rebuild_variant_summary
+
+
 **Structural Variants.**
 In case that the support for structural variants has been used, it is **strongly recommended** to re-annotate the structural variants with an updated version of ``varfish-annotator`` (v0.24 or above).
 You will need to use ``varfish-cli`` in a recent version (v0.3.4 or above) for being able to import the data into VarFish.

svs/migrations/0018_extend_structuralvariant.py

@@ -104,7 +104,7 @@
                 DROP COLUMN num_het,
                 DROP COLUMN num_hemi_alt,
                 DROP COLUMN num_hemi_ref;
-            """
+            """,
         ),
     ]
 

variants/plugins.py

@@ -119,6 +119,17 @@ class ProjectAppPlugin(ProjectAppPluginPoint):
                 "Use this if the sex is unknown."
             ),
         },
+        "exclude_from_inhouse_db": {
+            "scope": SODAR_CONSTANTS["APP_SETTING_SCOPE_PROJECT"],
+            "type": "BOOLEAN",
+            "default": False,
+            "label": "Exclude from in-house database",
+            "description": (
+                "Exclude project's cases from in-house database.  This is intended to be used for cases containing "
+                "training data that may exist with multiple copies and thus introduce artifacts in the in-house "
+                "database (such as no variant of a case showing up because being in the in-house database many times)."
+            ),
+        },
     }
 
     #: Additional columns to display for the projects.