feat: cleanup (#1911)

Author: JackScanlon

.dockerignore

@@ -4,6 +4,8 @@ docs
 LICENSE
 README.md
 renovate.json
+**/Thumbs.db
+**/.DS_Store
 **/staticroot
 **/__pycache__
 **/.pytest_cache

.github/workflows/sonarqube.yaml

@@ -8,7 +8,6 @@ on:
       - '.github/workflows/sonarqube.yaml'
       - 'CodeListLibrary_project/**'
       - 'docker/**'
-      - 'docs/**'
   push:
     branches:
       # We're using the free version of Sonarqube so we can only scan a single branch and not PRs

.gitignore

@@ -51,7 +51,8 @@ CodeListLibrary_project/staticroot/*
 
 # Platform / OS files
 .idea
-.DS_Stores
+**/Thumbs.db
+**/.DS_Store
 
 # Misc. files
 docs/~$plication Guide.docx

CodeListLibrary_project/cll/static/js/clinicalcode/services/organisationService/view.js

@@ -451,6 +451,10 @@ const initMetrics = (accordion, mapping) => {
     }
 
     if (isNullOrUndefined(dataset.promise) || isResolved(dataset.promise)) {
+      const spinner = startLoadingSpinner(container, true);
+      dataset?.spinner?.remove?.();
+
+      dataset.spinner = spinner;
       dataset.promise = fetch(
         getCurrentURL(),
         {
@@ -481,6 +485,12 @@ const initMetrics = (accordion, mapping) => {
           .catch((e) => {
             console.error(`Failed to resolve metrics w/ err:\n${e}`);
           })
+          .finally(() => {
+            spinner?.remove?.();
+            if (dataset.spinner === spinner) {
+              dataset.spinner = null;
+            }
+          })
     }
   })
 };

docs/dev.cleanup.sql

@@ -0,0 +1,149 @@
+-- vacuum (analyze, verbose);
+
+-- do $$declare r record;
+-- begin
+--   for r in (
+--     select table_name
+--       from information_schema.tables
+--      where table_name ~ '^(django_|auth_|easyaudit_|clinicalcode_).*$'
+--   )
+--     loop
+--       execute format('reindex table %s.%s;', quote_ident('public'), quote_ident(r.table_name));
+--     end loop;
+-- end$$;
+
+-- vacuum (full, analyze, verbose);
+
+select
+    table_name as name,
+    pg_size_pretty(pg_total_relation_size(quote_ident(table_name))) as total_size,
+    pg_size_pretty(pg_relation_size(quote_ident(table_name))) as table_size,
+    pg_size_pretty(pg_indexes_size(quote_ident(table_name))) as index_size
+  from information_schema.tables
+ where table_schema = 'public'
+ order by pg_total_relation_size(quote_ident(table_name)) desc;
+
+-- truncate table public.django_session;
+
+-- truncate
+--    table public.django_admin_log
+--  restart identity;
+
+-- truncate
+--    table public.easyaudit_crudevent
+--  restart identity;
+
+-- truncate
+--    table public.easyaudit_loginevent
+--  restart identity;
+
+-- truncate
+--    table public.easyaudit_requestevent
+--  restart identity;
+
+-- truncate
+--    table public.django_celery_beat_periodictask
+--  restart identity;
+
+-- truncate
+--    table public.django_celery_results_taskresult
+--  restart identity;
+
+-- alter sequence public.django_admin_log_id_seq restart with 1;
+
+-- alter sequence public.easyaudit_crudevent_id_seq restart with 1;
+
+-- alter sequence public.easyaudit_loginevent_id_seq restart with 1;
+
+-- alter sequence public.easyaudit_requestevent_id_seq restart with 1;
+
+-- alter sequence public.django_celery_beat_periodictask_id_seq restart with 1;
+
+-- alter sequence public.django_celery_results_taskresult_id_seq restart with 1;
+
+-- begin;
+--   create temporary table tmp_code(
+--     code text
+--   );
+
+--   with
+--     ont as (
+--       select cast(t0.properties::json->'code' as varchar) as code
+--         from public.clinicalcode_ontologytag as t0
+--       where json_typeof(t0.properties::json->'code') = 'string'
+--       union all
+--       select t0.code::varchar
+--         from public.clinicalcode_code as t0
+--     ),
+--     unq as (
+--       select code::varchar
+--         from ont
+--       group by code
+--     )
+--   insert into tmp_code(code) (
+--     select t0.code
+--       from public.clinicalcode_snomed_codes as t0
+--       left join unq as t1
+--         on t0.code = t1.code
+--     where t1.code is null
+--   );
+--   delete
+--     from public.clinicalcode_snomed_codes as t0
+--   using tmp_code as t1
+--   where t0.code = t1.code;
+-- commit;
+
+-- begin;
+--   create temporary table tmp_code(
+--     code text
+--   );
+
+--   with
+--     unq as (
+--       select code
+--         from public.clinicalcode_code
+--       group by code
+--     )
+--   insert into tmp_code(code) (
+--     select t0.term_id as code
+--       from public.clinicalcode_read_cd_cv3_terms_scd as t0
+--       left join unq as t1
+--         on t0.term_id = t1.code
+--     where t1.code is null
+--   );
+--   delete
+--     from public.clinicalcode_read_cd_cv3_terms_scd as t0
+--   using tmp_code as t1
+--   where t0.term_id = t1.code;
+-- commit;
+
+-- with
+--   used as (
+--     select t1.value::text::bigint
+--       from public.clinicalcode_genericentity as t0,
+--            json_array_elements(t0.template_data::json->'ontology') as t1
+--      where json_typeof(t0.template_data::json->'ontology') = 'array'
+--        and json_array_length(t0.template_data::json->'ontology') > 0
+--      union all
+--     select t1.value::text::bigint
+--       from public.clinicalcode_historicalgenericentity as t0,
+--            json_array_elements(t0.template_data::json->'ontology') as t1
+--      where json_typeof(t0.template_data::json->'ontology') = 'array'
+--        and json_array_length(t0.template_data::json->'ontology') > 0
+--   ),
+--   unq_used as (
+--     select value
+--       from used
+--     group by value
+--   )
+-- delete
+--   from public.clinicalcode_ontologytag as t0
+--  where t0.id not in (table unq_used)
+--    and t0.id > 100;
+
+
+-- select t0.*
+--   from public.clinicalcode_ontologytag as t0
+--  where t0.id in (table unq_used)
+  -- join public.clinicalcode_ontologytag as t1
+  --   on t0.template_data::json->'ontology' @> t1.id,