README

A simple Ruby on Rails application to manage biology specimens. The goal of this app is to make it simple to maintain accurate, complete and error-free specimen data.

A specimen belongs to a site, which is the time and place that the specimen was collected. Sites belong to a project. Multiple specimens may have been collected at a single site. A specimen may be identified as having a taxon (e.g. a species). Specimens can have photos.

A design goal is to make it as easy as possible to access the data. There are no access restrictions. Photos are stored in the public/images folder so they are served directly by the web server for maximum speed. This means that anyone with access to the server can see and edit all of the data and photos.

It uses a vanilla RoR setup.

• TODO

  • Allow relative urls in taxon descriptions.

• Ruby version (output of ruby --version): ruby 2.5.3p105 (2018-10-18 revision 65156) [x64-mingw32]

• Installed gems (output of gem list)

  • actioncable (5.2.2, 5.0.7)
  • actionmailer (5.2.2, 5.0.7)
  • actionpack (5.2.2, 5.0.7)
  • actionview (5.2.2, 5.0.7)
  • activejob (5.2.2, 5.0.7)
  • activemodel (5.2.2, 5.0.7)
  • activerecord (5.2.2, 5.0.7)
  • activestorage (5.2.2)
  • activesupport (5.2.2, 5.0.7)
  • addressable (2.7.0)
  • annotate (2.7.3)
  • arel (9.0.0, 7.1.4)
  • bigdecimal (default: 1.3.4)
  • bindex (0.5.0)
  • builder (3.2.4, 3.2.3)
  • bundler (1.17.1)
  • cmath (default: 1.0.0)
  • coffee-rails (4.2.2)
  • coffee-script (2.4.1)
  • coffee-script-source (1.12.2)
  • concurrent-ruby (1.1.5, 1.0.5)
  • crass (1.0.5, 1.0.4)
  • csv (default: 1.0.0)
  • date (default: 1.0.0)
  • dbm (default: 1.0.0)
  • did_you_mean (1.2.0)
  • erubi (1.7.1)
  • erubis (2.7.0)
  • etc (default: 1.0.0)
  • execjs (2.7.0)
  • faraday (0.17.0)
  • fcntl (default: 1.0.0)
  • ffi (1.9.25 x64-mingw32)
  • fiddle (default: 1.0.0)
  • fileutils (default: 1.0.2)
  • gdbm (default: 2.0.0)
  • globalid (0.4.1)
  • google-cloud-vision (0.37.0)
  • google-gax (1.8.1)
  • google-protobuf (3.10.1 x64-mingw32)
  • googleapis-common-protos (1.3.9)
  • googleapis-common-protos-types (1.0.4)
  • googleauth (0.10.0)
  • grpc (1.24.0 x64-mingw32)
  • i18n (1.7.0, 1.0.1)
  • io-console (default: 0.4.6)
  • ipaddr (default: 1.2.0)
  • jbuilder (2.7.0)
  • jquery-rails (4.3.3)
  • jquery-ui-rails (6.0.1)
  • json (default: 2.1.0)
  • jwt (2.2.1)
  • lazyload-rails (0.3.1)
  • loofah (2.4.0, 2.2.2)
  • mail (2.7.0)
  • marcel (0.3.3)
  • memoist (0.16.0)
  • method_source (0.9.0)
  • mimemagic (0.3.2)
  • mini_mime (1.0.0)
  • mini_portile2 (2.4.0, 2.3.0)
  • minitest (5.13.0, 5.11.3, 5.10.3)
  • multi_json (1.13.1)
  • multipart-post (2.1.1)
  • net-telnet (0.1.1)
  • nio4r (2.3.1)
  • nokogiri (1.10.7 x64-mingw32, 1.8.2 x64-mingw32)
  • openssl (default: 2.1.2)
  • os (1.0.1)
  • power_assert (1.1.1)
  • psych (default: 3.0.2)
  • public_suffix (4.0.1)
  • puma (3.11.4)
  • rack (2.0.5)
  • rack-test (0.6.3)
  • rails (5.2.2, 5.0.7)
  • rails-dom-testing (2.0.3)
  • rails-html-sanitizer (1.3.0, 1.0.4)
  • rails_autolink (1.1.6)
  • railties (5.2.2, 5.0.7)
  • rake (12.3.1, 12.3.0)
  • rb-fsevent (0.10.3)
  • rb-inotify (0.9.10)
  • rdoc (default: 6.0.1)
  • rly (0.2.3)
  • sass (3.5.6)
  • sass-listen (4.0.0)
  • sass-rails (5.0.7)
  • scanf (default: 1.0.0)
  • sdbm (default: 1.0.0)
  • signet (0.12.0)
  • sprockets (3.7.2)
  • sprockets-rails (3.2.1)
  • sqlite3 (1.4.2, 1.3.13 x64-mingw32)
  • stringio (default: 0.0.1)
  • strscan (default: 1.0.0)
  • test-unit (3.2.7)
  • thor (0.20.0)
  • thread_safe (0.3.6)
  • tilt (2.0.8)
  • turbolinks (5.1.1)
  • turbolinks-source (5.1.0)
  • tzinfo (1.2.5)
  • tzinfo-data (1.2018.5)
  • uglifier (4.1.10)
  • web-console (3.6.2)
  • webrick (default: 1.4.2)
  • websocket-driver (0.6.5)
  • websocket-extensions (0.1.3)
  • will_paginate (3.1.6)

• System dependencies

• Configuration

• Database creation

• Database initialization

• How to run the test suite

• Services (job queues, cache servers, search engines, etc.)

• Deployment instructions

Install Ruby and Ruby on Rails.

Pre-compiled assets are not checked in to revision control. That means it is necessary to precompile them as part of a production deployment. To do so, run the command $ bundle exec rake assets:precompile

On Windows, the server can be run using server.bat [-p]. If running production (-p option), it is necessary to first create a file called SECRET_KEY_BASE.bat which sets the environment variable SECRET_KEY_BASE. The file should contain:
set SECRET_KEY_BASE=<secret>
where <secret> can be generated with the command:
bundle exec rake secret

For managing secret keys etc. on Ubuntu, refer to this tutorial.

Various external image utilities are used to construct thumbnails and so on. Currently the executable names (and sometimes paths) are simply hard-wired. See lib/image_utils.rb.