Chore/find patients pagination

.gitignore

@@ -63,6 +63,15 @@ db/lims_metadata/*.json
 
 .solargraph.yml
 .vscode
+.idea
+vendor_bk
 
 # Ignore json files under hts_metadata
 db/hts_metadata/*.json
+
+# f bups
+db/data/facilities/backups/
+
+config/environments/development.rb
+config/environments/production.rb
+config/environments/test.rb

.mise.toml

@@ -0,0 +1,2 @@
+[tools]
+ruby = "3.2.0"

Docker-compose.yml

@@ -0,0 +1,80 @@
+version: '3.8'
+
+services:
+  db:
+    image: mysql:8.0
+    command: --default-authentication-plugin=mysql_native_password
+    restart: always
+    environment:
+      MYSQL_ROOT_PASSWORD: password
+      MYSQL_DATABASE: app_development
+      MYSQL_USER: app_user
+      MYSQL_PASSWORD: app_password
+    ports:
+      - "3306:3306"
+    volumes:
+      - mysql_data:/var/lib/mysql
+    healthcheck:
+      test: ["CMD", "mysqladmin", "ping", "-h", "localhost", "-u", "root", "-p$$MYSQL_ROOT_PASSWORD"]
+      interval: 10s
+      timeout: 5s
+      retries: 5
+
+  redis:
+    image: redis:7.0
+    ports:
+      - "6379:6379"
+    volumes:
+      - redis_data:/data
+    healthcheck:
+      test: ["CMD", "redis-cli", "ping"]
+      interval: 10s
+      timeout: 5s
+      retries: 5
+
+  app:
+    build: .
+    depends_on:
+      db:
+        condition: service_healthy
+      redis:
+        condition: service_healthy
+    ports:
+      - "3000:3000"
+    environment:
+      DATABASE_HOST: db
+      DATABASE_PORT: 3306
+      DATABASE_USERNAME: app_user
+      DATABASE_PASSWORD: app_password
+      DATABASE_NAME: app_development
+      REDIS_URL: redis://redis:6379/0
+      RAILS_ENV: development
+      ENABLE_SIDEKIQ: "true"
+    volumes:
+      - .:/app
+      - bundle_cache:/usr/local/bundle
+    command: rails server -b 0.0.0.0
+
+  sidekiq:
+    build: .
+    depends_on:
+      - app
+      - db
+      - redis
+    environment:
+      DATABASE_HOST: db
+      DATABASE_PORT: 3306
+      DATABASE_USERNAME: app_user
+      DATABASE_PASSWORD: app_password
+      DATABASE_NAME: app_development
+      REDIS_URL: redis://redis:6379/0
+      RAILS_ENV: development
+    volumes:
+      - .:/app
+      - bundle_cache:/usr/local/bundle
+    command: bundle exec sidekiq
+
+volumes:
+  mysql_data:
+  redis_data:
+  bundle_cache:

Dockerfile

@@ -0,0 +1,81 @@
+FROM ruby:3.2
+
+# Set DNS to use Google's public DNS as a fallback
+RUN echo "nameserver 8.8.8.8" >> /etc/resolv.conf
+
+# Install dependencies with retry mechanism
+RUN apt-get update -qq || (sleep 10 && apt-get update -qq) && \
+    apt-get install -y \
+    build-essential \
+    default-libmysqlclient-dev \
+    mariadb-client \
+    nodejs \
+    npm \
+    curl \
+    net-tools \
+    netcat \
+    && apt-get clean \
+    && rm -rf /var/lib/apt/lists/*
+
+# Install passenger
+RUN gem install passenger
+
+# Set up working directory
+WORKDIR /app
+
+# Copy Gemfile and Gemfile.lock
+COPY Gemfile Gemfile.lock ./
+
+# Install gems with retry
+RUN bundle install || (gem install bundler && bundle install)
+
+# Copy the rest of the application
+COPY . .
+
+# Expose port 3000
+EXPOSE 3000
+
+# Set environment variables
+ENV RAILS_ENV=development
+ENV RAILS_LOG_TO_STDOUT=true
+
+# Install foreman to run multiple processes
+RUN gem install foreman
+
+# Create entrypoint script
+RUN echo '#!/bin/bash\n\
+set -e\n\
+\n\
+# Wait for MySQL to be ready\n\
+if [ -n "$DATABASE_HOST" ]; then\n\
+  echo "Waiting for MySQL..."\n\
+  while ! nc -z $DATABASE_HOST ${DATABASE_PORT:-3306}; do\n\
+    sleep 1\n\
+  done\n\
+  echo "MySQL is up and running!"\n\
+fi\n\
+\n\
+# Remove a potentially pre-existing server.pid for Rails\n\
+rm -f tmp/pids/server.pid\n\
+\n\
+# Run database migrations if needed\n\
+if [ "$RAILS_ENV" = "development" ] || [ "$RAILS_ENV" = "test" ]; then\n\
+  bundle exec rails db:create db:migrate 2>/dev/null || echo "Database migrations not needed"\n\
+fi\n\
+\n\
+# Start Redis and Sidekiq in background if needed\n\
+if [ "$ENABLE_SIDEKIQ" = "true" ]; then\n\
+  redis-server --daemonize yes\n\
+  bundle exec sidekiq -C config/sidekiq.yml &\n\
+fi\n\
+\n\
+# Execute the main command\n\
+exec "$@"' > /app/entrypoint.sh
+
+RUN chmod +x /app/entrypoint.sh
+
+# Set entry point
+ENTRYPOINT ["/app/entrypoint.sh"]
+
+# Start Rails server
+CMD ["rails", "server", "-b", "0.0.0.0"]

Gemfile

@@ -5,6 +5,13 @@ git_source(:github) { |repo| "https://github.com/#{repo}.git" }
 
 ruby '~> 3.2.0'
 
+
+# Gems for managing background jobs
+gem 'sidekiq'
+gem 'sidekiq-cron'
+gem 'redis'
+gem 'activejob-uniqueness'
+
 # Bundle edge Rails instead: gem 'rails', github: 'rails/rails'
 gem 'rails', '~> 7.0.6'
 # Use sqlite3 as the database for Active Record
@@ -42,30 +49,31 @@ gem 'rest-client'
 
 gem 'test-unit'
 
+
 gem 'rswag-api'
 gem 'rswag-ui'
 
-# gem 'emr_ohsp_interface', '~> 1.2'
-# gem 'his_emr_api_lab', '~> 1.1.30'
-# gem 'his_emr_api_radiology', '~> 0.0.8'
+gem 'emr_ohsp_interface', '~> 2.2.5'
 
-gem 'emr_ohsp_interface', '~> 2.2.3'
-gem 'his_emr_api_lab', '~> 2.0.0'
+gem 'his_emr_api_lab', '2.0.9.pre.mahis'
+
+# gem 'emr_ohsp_interface', '~> 2.2.3'
+# gem 'his_emr_api_lab', '~> 2.0.5'
 # gem 'his_emr_api_radiology', '~> 1.0.9'
 
 gem 'parallel', '~> 1.20.1'
+gem 'time_difference'
+
+gem "audited"
 
 group :development, :test do
   # Call 'byebug' anywhere in the code to stop execution and get a debugger console
   gem 'byebug', platforms: %i[mri mingw x64_mingw]
-  gem 'spring'
-end
-
-group :test do
   gem 'factory_bot_rails'
   gem 'rspec'
   gem 'rspec-rails'
   gem 'rswag-specs'
+  gem 'spring'
 end
 
 group :development do
@@ -79,5 +87,10 @@ gem 'tzinfo-data', platforms: %i[mingw mswin x64_mingw jruby]
 
 gem 'whenever', '~> 1.0'
 
+gem 'concurrent-ruby', '= 1.3.4'
+
 # gems for reading excel and csv files
 gem 'roo', '~> 2.8'
+
+#gem for object matching
+gem 'whitesimilarity'