Remove submodule svip_server

Author: falquaddoomi

.gitmodules

@@ -3,11 +3,6 @@
 	url = [email protected]:SVIPdb/g2p-aggregator.git 
 	branch = v0.11
 	update = merge
-[submodule "svip_server"]
-	path = svip_api
-	url = [email protected]:SVIPdb/svip_api.git
-	branch = master
-	update = merge
 [submodule "svip-o-vue"]
 	path = svip-o-vue
 	url = [email protected]:SVIPdb/frontend.git 

dc_private.sh

@@ -0,0 +1,4 @@
+#!/usr/bin/env bash
+
+docker-compose -f docker-compose.yml -f compose_configs/prod.yml -f compose_configs/sites/sib-svip-private.yml "$@"
+

sql_scratch/genes_by_sources.sql

@@ -0,0 +1,34 @@
+select AG.symbol, AV.name, count(*) from svip_curationentry CE
+inner join api_disease AD on AD.id = CE.disease_id
+inner join api_variant AV on AV.id = CE.variant_id
+inner join api_gene AG on AG.id = AV.gene_id
+where CE.status='unreviewed'
+group by AG.symbol, AV.name;
+
+select count(*) from svip_curationentry CE where CE.status='unreviewed';
+
+select * from (
+  select
+    symbol,
+    sum(compiled.civic_counts) as civic_counts,
+    sum(compiled.oncokb_counts) as oncokb_counts,
+    sum(compiled.clinvar_counts) as clinvar_counts,
+    sum(compiled.cosmic_counts) as cosmic_counts
+  from (
+    select
+      symbol,
+      (select cnt where name='civic') as civic_counts,
+      (select cnt where name='oncokb') as oncokb_counts,
+      (select cnt where name='clinvar') as clinvar_counts,
+      (select cnt where name='cosmic') as cosmic_counts
+    from (
+      select AG.symbol, AVS.name, count(*) as cnt from api_variantinsource VIS
+      inner join api_variant AV on VIS.variant_id = AV.id
+      inner join api_gene AG on AV.gene_id = AG.id
+      inner join api_source AVS on VIS.source_id = AVS.id
+      group by AG.symbol, AVS.name
+    ) as var_counts
+  ) as compiled
+  group by symbol
+) as Z
+order by civic_counts + oncokb_counts + clinvar_counts + cosmic_counts;