Remove pgloader, insert TCR data via Flyway migration, add migration …

…to populate query tables (#2496)

* Support pgsql infra

* Make infra work with next

* Remove dev win

* The real dev win fix

* add bash script

* update load script to add sqlite db

* update docker compose file to include loading the data

* cleanup

* [pre-commit.ci] auto fixes from pre-commit hooks

* add chmod cmd

* [pre-commit.ci] auto fixes from pre-commit hooks

* typo

* remove temp code

* add query_name to schema

* add oid as a column for query-to_valueset

* remove pgloader bash script from docker compose

* add migration 2 to load TCR data

* add migration 3 to populate data for query tables

* remove load tcr from docker compose

* [pre-commit.ci] auto fixes from pre-commit hooks

* remove loading script

---------

Co-authored-by: bamader <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

containers/tefca-viewer/docker-compose-dev.yaml

@@ -21,13 +21,3 @@ services:
       interval: 2s
       timeout: 5s
       retries: 20
-  load_tcr_data:
-    image: "postgres:alpine"
-    depends_on:
-      db:
-        condition: service_healthy
-    volumes:
-      - "./tefca.env:/tefca.env"
-      - "./load_tcr_data.sh:/load_tcr_data.sh"
-    entrypoint:
-      ["/bin/sh", "-c", "chmod +x /load_tcr_data.sh && /load_tcr_data.sh"]

containers/tefca-viewer/flyway/sql/V01_01__tcr_custom_query_schema.sql

@@ -52,6 +52,7 @@ CREATE TABLE IF NOT EXISTS icd_crosswalk (
 
 CREATE TABLE IF NOT EXISTS query (
     id UUID DEFAULT uuid_generate_v4 (),
+    query_name VARCHAR(255),
     author VARCHAR(255),
     date_created TIMESTAMP,
     date_last_modified TIMESTAMP,
@@ -63,6 +64,7 @@ CREATE TABLE IF NOT EXISTS query_to_valueset (
     id TEXT PRIMARY KEY,
     query_id UUID,
     valueset_id TEXT,
+    valueset_oid TEXT,
     FOREIGN KEY (query_id) REFERENCES query(id),
     FOREIGN KEY (valueset_id) REFERENCES valuesets(id)
 );