Updates to bin/setup to make installation easier

.env.mysql2

@@ -0,0 +1,48 @@
+# DMPRoadmap dotenv file
+
+# Rails log level
+RAILS_LOG_LEVEL=debug
+# Whether or not Rails should log to STDOUT. If false it will log to `./logs/[env].log`
+RAILS_LOG_TO_STDOUT=true
+# Whether or not Rails will be serving your static assets 
+RAILS_SERVE_STATIC_FILES=false
+# Maximum number of Puma threads
+RAILS_MAX_THREADS=5
+# Maximum number of Puma workers
+WEB_CONCURRENCY=2
+# The port puma will use to host the Rails app
+PORT=3000
+
+# Rails 6.1+ has a white-list of valid domains. You must set this for your production env!
+DMPROADMAP_HOST=localhost
+
+# The location of the wkhtmltopdf app. Once bundler has installed it, you can find it with
+# `which wkhtmltopdf` on linux/osx systems.
+WICKED_PDF_PATH=/usr/local/bin/wkhtmltopdf
+
+# Database settings.
+DB_ADAPTER=mysql2
+DB_HOST=localhost
+DB_PORT=3306
+DB_POOL_SIZE=16
+DB_NAME=roadmap
+
+# Whether or not the Dragonfly gem should use AWS S3 to store logos. If 'false' the logos will 
+# be stored on the local disk. If true, you must provide the `AWS_` prefixed values.
+DRAGONFLY_AWS=false
+AWS_REGION=
+AWS_BUCKET_NAME=
+
+# If you have a Rollbar account and want to redcord errors there, add your token here
+ROLLBAR_ACCESS_TOKEN=
+ROLLBAR_ENV=
+
+# Translation IO variables. The Domain can be either `app` or `client` and is typically defined
+# when running `bin/rails translations:sync DOMAIN=app`. `client` will use any of your 
+# customized content in ./app/views/branded and `app` is for the core roadmap translations.
+# Include your Translation.io API key for the appropriate domains:
+#    app => TRANSLATION_API_ROADMAP
+#    client => TRANSLATION_API_CLIENT
+# DOMAIN=app
+# TRANSLATION_API_ROADMAP=
+# TRANSLATION_API_CLIENT=

.env.postgresql

@@ -0,0 +1,48 @@
+# DMPRoadmap dotenv file
+
+# Rails log level
+RAILS_LOG_LEVEL=debug
+# Whether or not Rails should log to STDOUT. If false it will log to `./logs/[env].log`
+RAILS_LOG_TO_STDOUT=true
+# Whether or not Rails will be serving your static assets 
+RAILS_SERVE_STATIC_FILES=false
+# Maximum number of Puma threads
+RAILS_MAX_THREADS=5
+# Maximum number of Puma workers
+WEB_CONCURRENCY=2
+# The port puma will use to host the Rails app
+PORT=3000
+
+# Rails 6.1+ has a white-list of valid domains. You must set this for your production env!
+DMPROADMAP_HOST=localhost
+
+# The location of the wkhtmltopdf app. Once bundler has installed it, you can find it with
+# `which wkhtmltopdf` on linux/osx systems.
+WICKED_PDF_PATH=/usr/local/bin/wkhtmltopdf
+
+# Database settings.
+DB_ADAPTER=postgresql
+DB_HOST=localhost
+DB_PORT=5432
+DB_POOL_SIZE=16
+DB_NAME=roadmap
+
+# Whether or not the Dragonfly gem should use AWS S3 to store logos. If 'false' the logos will 
+# be stored on the local disk. If true, you must provide the `AWS_` prefixed values.
+DRAGONFLY_AWS=false
+AWS_REGION=
+AWS_BUCKET_NAME=
+
+# If you have a Rollbar account and want to redcord errors there, add your token here
+ROLLBAR_ACCESS_TOKEN=
+ROLLBAR_ENV=
+
+# Translation IO variables. The Domain can be either `app` or `client` and is typically defined
+# when running `bin/rails translations:sync DOMAIN=app`. `client` will use any of your 
+# customized content in ./app/views/branded and `app` is for the core roadmap translations.
+# Include your Translation.io API key for the appropriate domains:
+#    app => TRANSLATION_API_ROADMAP
+#    client => TRANSLATION_API_CLIENT
+DOMAIN=app
+TRANSLATION_API_ROADMAP=
+TRANSLATION_API_CLIENT=

.github/workflows/mysql.yml

@@ -28,15 +28,16 @@ jobs:
         cache: 'yarn'
 
     # Copy all of the example configs over
-    - name: 'Setup Default Configuration'
+    - name: 'Setup the application'
       run: |
         cp config/database.yml.sample config/database.yml
         cp config/initializers/contact_us.rb.example config/initializers/contact_us.rb
         cp config/initializers/wicked_pdf.rb.example config/initializers/wicked_pdf.rb
+        cp .env.mysql2 .env
 
     # Stub out the Rails credentials file so that we can start the Rails app
     - name: 'Setup Credentials'
-      run: EDITOR='echo "$(cat config/credentials.yml.example)" >' bundle exec rails credentials:edit
+      run: EDITOR='echo "$(cat config/credentials.yml.mysql2)" >' bundle exec rails credentials:edit
 
     # Set the path to the wkhtmltopdf executable
     - name: 'Determine wkhtmltopdf location'

.github/workflows/postgres.yml

@@ -55,12 +55,13 @@ jobs:
         cp config/database.yml.sample config/database.yml
         cp config/initializers/contact_us.rb.example config/initializers/contact_us.rb
         cp config/initializers/wicked_pdf.rb.example config/initializers/wicked_pdf.rb
+        cp .env.postgresql .env
 
     # Stub out the Rails credentials file so that we can start the Rails app
     - name: 'Setup Credentials'
       run: |
         # generate a default credential file and key
-        EDITOR='echo "$(cat config/credentials.yml.example)" >' bundle exec rails credentials:edit
+        EDITOR='echo "$(cat config/credentials.yml.postgresql)" >' bundle exec rails credentials:edit
 
     # Set the path to the wkhtmltopdf executable
     - name: 'Determine wkhtmltopdf location'

Gemfile.lock

@@ -268,6 +268,8 @@ GEM
     mysql2 (0.5.4)
     nenv (0.3.0)
     nio4r (2.5.8)
+    nokogiri (1.13.9-arm64-darwin)
+      racc (~> 1.4)
     nokogiri (1.13.9-x86_64-linux)
       racc (~> 1.4)
     notiffany (0.1.3)
@@ -498,6 +500,7 @@ GEM
     zeitwerk (2.6.1)
 
 PLATFORMS
+  arm64-darwin-21
   x86_64-linux
 
 DEPENDENCIES
@@ -580,4 +583,4 @@ RUBY VERSION
    ruby 2.7.6p219
 
 BUNDLED WITH
-   2.3.15
+   2.3.24

bin/setup

@@ -9,32 +9,65 @@ def system!(*args)
   system(*args) || abort("\n== Command #{args} failed ==")
 end
 
-chdir APP_ROOT do
-  # This script is a starting point to setup your application.
-  # Add necessary setup steps to this file.
-
-  puts '== Installing dependencies =='
-  system! 'gem install bundler --conservative'
-  system('bundle check') || system!('bundle install')
-
-  puts "\n== Copying sample files =="
-  %w[
-    config/database.yml.sample
-    config/initializers/wicked_pdf.rb.example
-  ].each do |file|
-    new_file = file.gsub('.sample', '').gsub('.example', '')
-    cp file, new_file unless File.exist?(new_file)
-  end
+valid_db = ARGV.length > 0 && %w[mysql postgres].include?(ARGV[0].to_s.downcase.strip)
 
-  puts "\n== Preparing database =="
-  system! 'bin/rails db:prepare'
+if valid_db
+  db_adapter = ARGV[0].to_s.downcase.strip == 'mysql' ? 'mysql2' : 'postgresql'
 
-  puts "\n== Fetching mime types and adding to database =="
-  system! 'bin/rails mime_types:load'
+  chdir APP_ROOT do
+    # This script is a starting point to setup your application.
+    # Add necessary setup steps to this file.
 
-  puts "\n== Removing old logs and tempfiles =="
-  system! 'bin/rails log:clear tmp:clear'
+    puts '== Installing dependencies =='
+    system! 'gem install bundler --conservative'
+    system('bundle check') || system!('bundle install')
+    system! 'yarn install'
 
-  puts "\n== Restarting application server =="
-  system! 'bin/rails restart'
-end
+    puts "\n== Copying sample files =="
+    cp 'config/database.yml.sample', 'config/database.yml'
+    cp 'config/initializers/contact_us.rb.example', 'config/initializers/contact_us.rb'
+    cp 'config/initializers/wicked_pdf.rb.example', 'config/initializers/wicked_pdf.rb'
+    cp ".env.#{db_adapter}", '.env'
+
+    puts "\n== Preparing credentials file =="
+    system! "EDITOR='echo \"$(cat config/credentials.yml.#{db_adapter})\" >' bin/rails credentials:edit"
+
+    # Set the editor based on the platform
+    ENV['EDITOR'] = Gem.win_platform? ? 'code --wait' : 'vim'
+
+    puts "\n== Opening .env in editor ... please update as needed =="
+    puts "    In particular make sure your DB settings are correct."
+    sleep(3)
+    system! '$EDITOR .env'
+
+    puts "\n== Opening credentials editor ... please update as needed =="
+    puts "    In particular make sure your DB settings are correct."
+    sleep(3)
+    system! 'bin/rails credentials:edit'
+
+    puts "\n== Preparing database =="
+    system! 'bin/rails db:setup'
+
+    puts "\n== Populating License table =="
+    system! 'bin/rails external_api:load_spdx_licenses'
+
+    puts "\n== Populating Metadata Standards table =="
+    system! 'bin/rails external_api:load_rdamsc_standards'
+
+    puts "\n== Populating Research Domains table =="
+    system! 'bin/rails external_api:add_field_of_science_to_research_domains'
+
+    puts "\n== Removing old logs and tempfiles =="
+    system! 'bin/rails log:clear tmp:clear'
+
+    puts "\n== Restarting application server =="
+    system! 'bin/rails restart'
+
+    puts "\n== !!We highly recommend that you populate the Repositories table, but this can take"
+    puts "in excess of 10 minutes so we do not run it as part of this setup!!"
+    puts "    To run it on your own: `bin/rails external_api:load_re3data_repos`"
+  end
+else
+  puts "\n== You MUST specify the type of DB you would like to use. Either mysql or postgres =="
+  puts "== For example: `ruby bin/setup postgres` =="
+end

config/brakeman.ignore

@@ -23,33 +23,14 @@
       ],
       "note": ""
     },
-    {
-      "warning_type": "Unmaintained Dependency",
-      "warning_code": 121,
-      "fingerprint": "9a3951031616a07c8e02c86652f537e92c08685da97f5ec2b12d5d3602b55bb8",
-      "check_name": "EOLRuby",
-      "message": "Support for Ruby 2.6.3 ended on 2022-03-31",
-      "file": "Gemfile.lock",
-      "line": 325,
-      "link": "https://brakemanscanner.org/docs/warning_types/unmaintained_dependency/",
-      "code": null,
-      "render_path": null,
-      "location": null,
-      "user_input": null,
-      "confidence": "High",
-      "cwe_id": [
-        1104
-      ],
-      "note": ""
-    },
     {
       "warning_type": "Redirect",
       "warning_code": 18,
       "fingerprint": "c94d0d02516558699b49eb76787d02665041a45b490686266e4f42d5c19088d6",
       "check_name": "Redirect",
       "message": "Possible unprotected redirect",
       "file": "app/controllers/plans_controller.rb",
-      "line": 393,
+      "line": 392,
       "link": "https://brakemanscanner.org/docs/warning_types/redirect/",
       "code": "redirect_to(Plan.deep_copy(Plan.find(params[:id])), :notice => success_message(Plan.deep_copy(Plan.find(params[:id])), _(\"copied\")))",
       "render_path": null,
@@ -65,25 +46,6 @@
       ],
       "note": ""
     },
-    {
-      "warning_type": "Unmaintained Dependency",
-      "warning_code": 120,
-      "fingerprint": "d84924377155b41e094acae7404ec2e521629d86f97b0ff628e3d1b263f8101c",
-      "check_name": "EOLRails",
-      "message": "Support for Rails 5.2.8.1 ended on 2022-06-01",
-      "file": "Gemfile.lock",
-      "line": 325,
-      "link": "https://brakemanscanner.org/docs/warning_types/unmaintained_dependency/",
-      "code": null,
-      "render_path": null,
-      "location": null,
-      "user_input": null,
-      "confidence": "High",
-      "cwe_id": [
-        1104
-      ],
-      "note": ""
-    },
     {
       "warning_type": "Redirect",
       "warning_code": 18,
@@ -108,6 +70,6 @@
       "note": ""
     }
   ],
-  "updated": "2022-08-10 07:47:14 -0700",
+  "updated": "2022-10-28 11:43:26 -0700",
   "brakeman_version": "5.3.1"
 }

config/credentials.yml.mysql2

@@ -0,0 +1,26 @@
+# DMPRoadmap Rails credentials file
+# To generate secrets and peppers, run the following in another tab/window `bin/rails secret`
+
+# Used as the base secret for all MessageVerifiers in Rails, including the one protecting cookies.
+secret_key_base: my_secret_key
+
+# Database credentials
+db_username: root
+db_password:
+
+# Devise credentials (used for user password encryption)
+secret_key: my_secret_key
+devise_pepper: my_pepper
+
+# Used by the Dragonfly gem for creating random hashes for org logos
+dragonfly_secret: my_secret_key
+
+# AWS credentials used by the config/initializers/dragonfly.rb to access your S3 bucket (if applicable)
+# aws:
+#   access_key_id: 12345
+#   secret_access_key: 34567
+
+# Recaptcha credentials
+recaptcha:
+  site_key: 11111
+  secret_key: 22222

config/credentials.yml.postgresql

@@ -0,0 +1,26 @@
+# DMPRoadmap Rails credentials file
+# To generate secrets and peppers, run the following in another tab/window `bin/rails secret`
+
+# Used as the base secret for all MessageVerifiers in Rails, including the one protecting cookies.
+secret_key_base: my_secret_key
+
+# Database credentials
+db_username: postgres
+db_password:
+
+# Devise credentials (used for user password encryption)
+secret_key: my_secret_key
+devise_pepper: my_pepper
+
+# Used by the Dragonfly gem for creating random hashes for org logos
+dragonfly_secret: my_secret_key
+
+# AWS credentials used by the config/initializers/dragonfly.rb to access your S3 bucket (if applicable)
+# aws:
+#   access_key_id: 12345
+#   secret_access_key: 34567
+
+# Recaptcha credentials
+recaptcha:
+  site_key: 11111
+  secret_key: 22222