Add pgloader bash script to port TCR SQLite DB (#2471)

* 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

---------

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

@@ -21,3 +21,13 @@ 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/load_tcr_data.sh

@@ -0,0 +1,41 @@
+#!/bin/bash
+
+source tefca.env
+
+# Define the database connection
+PG_CONN="postgresql://postgres:pw@db:5432/tefca_db"
+
+tables=("concepts" "valuesets" "conditions")
+
+# Function to check if tables contain data
+check_tables() {
+  for table in "${tables[@]}"; do
+    count=$(psql "$PG_CONN" -c "SELECT COUNT(*) FROM $table;" -tA)
+    if [ "$count" -eq 0 ]; then
+      return 1
+    fi
+  done
+  return 0
+}
+
+# Check if the tables contain data
+check_tables
+if [ $? -ne 0 ]; then
+  echo "Tables are empty. Proceeding with data loading..."
+
+  # Install pgloader if not already installed
+  if ! command -v pgloader &> /dev/null; then
+    echo "Installing pgloader..."
+    apk add --no-cache pgloader
+  fi
+
+  # Download the ERSD SQLite file
+  echo "Downloading ERSD SQLite file..."
+  wget -O /tmp/ersd.db https://github.com/CDCgov/phdi/raw/main/containers/trigger-code-reference/seed-scripts/ersd.db
+
+  echo "Loading data into PostgreSQL..."
+  pgloader sqlite://tmp/ersd.db "$PG_CONN"
+
+  echo "Successfully loaded TCR data into tefca_db"
+
+fi