lims-core 3.2.3

checksums.yaml

@@ -0,0 +1,15 @@
+---
+!binary "U0hBMQ==":
+  metadata.gz: !binary |-
+    NmQ4MDBjZjVjMWRiZTkzMmU5MGQyODRjNzZiMTYxMjg1ZjU0ODRiMQ==
+  data.tar.gz: !binary |-
+    MjFlYjNmOGQ3NThmODI1Mzg2NWQxZGM2MjExZjI1MzE3YzRhYTAxZQ==
+SHA512:
+  metadata.gz: !binary |-
+    Y2U3NGI0MmYxMDA3OGMxNTI3Y2I2MzJlMGE1YWE4ZmE5Zjg2MmJiNjllYjlm
+    NWYwMDM0MjlkOTJkM2M2OTYzYTViOGVhZDA0ZTFkNjk3ZDE3ZjgzZTQyNWI1
+    YzkyMDExZjJkOTgxYjJkYzY2MDcxYjhkZDc5NzA4ZmYzMmZlMzI=
+  data.tar.gz: !binary |-
+    NTE4MzQ5MDMyMzM2NTFkYzg0YmFkNzRlNThjNDZmMjE3MGY1MWQ4NmNkMTg5
+    N2I3NTZhMzZjOTQwNWVkNTdlNTc1NTY0MzFhZTZiYTI5MjA4Yzg5ZTNkMDM0
+    ZTE1Njg3MmIyMmJmYmRiYjA4MTVhZDVjMzhiZDIxZmFmMjIxNjA=

data/.gitignore

@@ -0,0 +1,5 @@
+.yardoc
+*.db
+.bundle
+tags
+.DS_Store

data/.rspec

@@ -0,0 +1 @@
+--tag ~@wip

data/.rvmrc

@@ -0,0 +1,2 @@
+rvm use 1.9.3@lims-core --create
+

data/.travis.yml

@@ -0,0 +1,2 @@
+sudo: false
+install: bundle install --without debugging pry autotest yard showoff

data/.vimrc

@@ -0,0 +1,27 @@
+iabbr req require 'lims/core/
+iabbr mlims module Lims::Core
  module Labware
    # @todo doc
  end
+set path=lib/**,spec/**,showoff/core-2012-06-11/**,,*,**,$GEM_HOME/gems
+let g:ruby_path=&path
+set cdpath=lib/lims/core,spec
+
+set isk+=?,!
+
+set makeprg=rspec
+set errorformat=
+    \%-Z\ \ \ \ \ \#\ %f:%l:%.%#,%E\ \ %\\d%\\+)%.%#,%C%m,%Z,
+    \%-Z%f:%l:%.%#,%E%\\d%\\+)%.%#,%C%m,%Z,
+    \%+W'%.%#'\ FAILED,
+    \%+I'%.%#'\ FIXED,
+    \%-Cexpected:%.%#,
+    \%-C\ \ \ \ \ got:%.%#,
+    \%E%.%#:in\ `load':\ %f:%l:%m,
+    \%C%f:%l:,
+    \%W%f:%l:\ warning:\ %m,
+    \%E%f:%l:in\ %*[^:]:\ %m,
+    \%E%f:%l:\ %m,
+    \%-Z%\tfrom\ %f:%l,
+    \%-Z%p^%.%#,
+    \%-C%.%#,
+    \%-G%.%#
+
+

data/.yardopts

@@ -0,0 +1 @@
+--private -p .yard_templates lib spec/**/*_spec.rb

data/Gemfile

@@ -0,0 +1,54 @@
+# vim:ft=ruby:ts=2:et:sw=2:sts=2
+source "http://rubygems.org"
+
+# Specify your gem's dependencies in lims-core.gemspec
+gemspec
+
+gem 'oj', :platforms => :mri
+gem 'jrjackson', :platforms => :jruby
+
+group :debugging do
+  gem 'debugger', :platforms => :mri
+  gem 'debugger-completion', :platforms => :mri
+  gem 'ruby-debug', :platforms => :jruby
+end
+
+group :pry do
+  gem 'debugger-pry', :require => 'debugger/pry', :platforms => :mri
+end
+
+group :autotest do
+  gem 'autotest'
+  gem 'autotest-growl'
+  gem 'autotest-fsevent'
+end
+
+group :guard do
+  gem "guard", '>= 1.3.0', :platforms => :mri
+  gem "guard-rspec", :platforms => :mri
+  gem "guard-bundler", :platforms => :mri
+  gem "guard-yard", :platforms => :mri
+  gem "terminal-notifier-guard", :platforms => :mri
+  gem "rb-fsevent", '~> 0.9.1', :platforms => :mri
+end
+
+group :development do
+  gem 'sqlite3', :platforms => :mri
+  gem 'mysql2', :platforms => :mri
+  gem 'ruby-prof', :platforms => :mri
+  gem 'jdbc-sqlite3', :platforms => :jruby
+  gem 'jdbc-mysql', :platforms => :jruby
+end
+
+
+group :yard do
+  gem 'yard', '= 0.7.3', :platforms => :mri
+  gem 'yard-rspec', '0.1', :platforms => :mri
+  gem 'yard-state_machine', :platforms => :mri
+  gem 'redcarpet', :platforms => :mri
+  gem 'ruby-graphviz', :platforms => :mri
+end
+
+group :showoff do
+  gem 'showoff', :platforms => :mri
+end

data/Gemfile.lock

@@ -0,0 +1,197 @@
+PATH
+  remote: .
+  specs:
+    lims-core (3.2.3)
+      activesupport
+      aequitas
+      bunny (= 0.9.0.pre10)
+      dm-validations
+      facets (= 2.9.3)
+      modularity (= 0.6.1)
+      sequel
+      state_machine
+      uuid
+      virtus (= 0.2.0)
+
+GEM
+  remote: http://rubygems.org/
+  specs:
+    ZenTest (4.11.0)
+    activesupport (4.2.4)
+      i18n (~> 0.7)
+      json (~> 1.7, >= 1.7.7)
+      minitest (~> 5.1)
+      thread_safe (~> 0.3, >= 0.3.4)
+      tzinfo (~> 1.1)
+    addressable (2.3.8)
+    aequitas (0.0.2)
+    amq-protocol (1.9.2)
+    autotest (4.4.6)
+      ZenTest (>= 4.4.1)
+    autotest-fsevent (0.2.8)
+      sys-uname
+    autotest-growl (0.2.16)
+    blankslate (2.1.2.4)
+    bluecloth (2.2.0)
+    bond (0.4.3)
+    bunny (0.9.0.pre10)
+      amq-protocol (>= 1.4.0)
+    coderay (1.0.9)
+    columnize (0.9.0)
+    debugger (1.6.8)
+      columnize (>= 0.3.1)
+      debugger-linecache (~> 1.2.0)
+      debugger-ruby_core_source (~> 1.3.5)
+    debugger-completion (1.0.0)
+      bond (>= 0.4.2)
+      debugger (~> 1.1)
+    debugger-linecache (1.2.0)
+    debugger-pry (0.1.1)
+      debugger (~> 1)
+      pry (>= 0.9.9)
+    debugger-ruby_core_source (1.3.8)
+    diff-lcs (1.1.3)
+    dm-core (1.2.1)
+      addressable (~> 2.3)
+    dm-validations (1.2.0)
+      dm-core (~> 1.2.0)
+    facets (2.9.3)
+    ffi (1.9.0)
+    ffi (1.9.0-java)
+    formatador (0.2.4)
+    gli (2.7.0)
+    guard (1.8.2)
+      formatador (>= 0.2.4)
+      listen (>= 1.0.0)
+      lumberjack (>= 1.0.2)
+      pry (>= 0.9.10)
+      thor (>= 0.14.6)
+    guard-bundler (1.0.0)
+      bundler (~> 1.0)
+      guard (~> 1.1)
+    guard-rspec (1.2.1)
+      guard (>= 1.1)
+    guard-yard (2.1.0)
+      guard (>= 1.1.0)
+      yard (>= 0.7.0)
+    i18n (0.7.0)
+    jdbc-mysql (5.1.27)
+    jdbc-sqlite3 (3.7.2.1)
+    jrjackson (0.2.3)
+    json (1.8.0)
+    listen (1.3.0)
+      rb-fsevent (>= 0.9.3)
+      rb-inotify (>= 0.9)
+      rb-kqueue (>= 0.2)
+    lumberjack (1.0.4)
+    macaddr (1.6.7)
+      systemu (~> 2.6.2)
+    method_source (0.8.2)
+    mini_portile (0.5.1)
+    minitest (5.8.2)
+    modularity (0.6.1)
+    mysql2 (0.3.13)
+      blankslate (~> 2.0)
+    nokogiri (1.6.0)
+      mini_portile (~> 0.5.0)
+    oj (2.1.7)
+    parslet (1.5.0)
+    pry (0.9.12.2)
+      coderay (~> 1.0.5)
+      method_source (~> 0.8)
+      slop (~> 3.4)
+    rack (1.5.2)
+    rack-protection (1.5.0)
+      rack
+    rake (10.1.0)
+    rb-fsevent (0.9.3)
+    rb-inotify (0.9.1)
+      ffi (>= 0.5.0)
+    rb-kqueue (0.2.0)
+      ffi (>= 0.5.0)
+    redcarpet (3.0.0)
+    rspec (2.8.0)
+      rspec-core (~> 2.8.0)
+      rspec-expectations (~> 2.8.0)
+      rspec-mocks (~> 2.8.0)
+    rspec-core (2.8.0)
+    rspec-expectations (2.8.0)
+      diff-lcs (~> 1.1.2)
+    rspec-mocks (2.8.0)
+    ruby-debug (0.10.4)
+      columnize (>= 0.1)
+      ruby-debug-base (~> 0.10.4.0)
+    ruby-debug-base (0.10.4-java)
+    ruby-graphviz (1.0.8)
+    ruby-prof (0.13.0)
+    sequel (4.8.0)
+    showoff (0.7.0)
+      bluecloth
+      gli (>= 1.3.2)
+      json
+      nokogiri
+      parslet
+      sinatra
+    sinatra (1.4.3)
+      rack (~> 1.4)
+      rack-protection (~> 1.4)
+      tilt (~> 1.3, >= 1.3.4)
+    slop (3.4.6)
+    sqlite3 (1.3.8)
+    state_machine (1.2.0)
+    sys-uname (0.9.2)
+      ffi (>= 1.0.0)
+    systemu (2.6.4)
+    terminal-notifier-guard (1.5.3)
+    thor (0.18.1)
+    thread_safe (0.3.5)
+    tilt (1.4.1)
+    tzinfo (1.2.2)
+      thread_safe (~> 0.1)
+    uuid (2.3.7)
+      macaddr (~> 1.0)
+    virtus (0.2.0)
+    yard (0.7.3)
+    yard-rspec (0.1)
+      yard
+    yard-state_machine (0.0.1)
+      ruby-graphviz (~> 1.0.0)
+      yard (~> 0.7.3)
+
+PLATFORMS
+  java
+  ruby
+
+DEPENDENCIES
+  autotest
+  autotest-fsevent
+  autotest-growl
+  debugger
+  debugger-completion
+  debugger-pry
+  guard (>= 1.3.0)
+  guard-bundler
+  guard-rspec
+  guard-yard
+  jdbc-mysql
+  jdbc-sqlite3
+  jrjackson
+  lims-core!
+  mysql2
+  oj
+  rake
+  rb-fsevent (~> 0.9.1)
+  redcarpet
+  rspec (~> 2)
+  ruby-debug
+  ruby-graphviz
+  ruby-prof
+  showoff
+  sqlite3
+  terminal-notifier-guard
+  yard (= 0.7.3)
+  yard-rspec (= 0.1)
+  yard-state_machine
+
+BUNDLED WITH
+   1.10.6

data/Guardfile

@@ -0,0 +1,21 @@
+# A sample Guardfile
+# More info at https://github.com/guard/guard#readme
+
+guard 'bundler' do
+  watch('Gemfile')
+  # Uncomment next line if Gemfile contain `gemspec' command
+  # watch(/^.+\.gemspec/)
+end
+
+guard 'rspec', :version => 2 do
+  watch(%r{^spec/.+_spec\.rb$})
+  watch(%r{^lib/[^\/]+\/(.+)\.rb$})     { |m| "spec/#{m[1]}_spec.rb" }
+  watch('spec/spec_helper.rb')  { "spec" }
+
+end
+
+guard 'yard' do
+  watch(%r{app/.+\.rb})
+  watch(%r{lib/.+\.rb})
+  watch(%r{ext/.+\.c})
+end

data/Guardfile.tmux

@@ -0,0 +1,28 @@
+# A sample Guardfile
+# More info at https://github.com/guard/guard#readme
+
+guard 'bundler' do
+  watch('Gemfile')
+  # Uncomment next line if Gemfile contain `gemspec' command
+  # watch(/^.+\.gemspec/)
+end
+
+guard 'rspec', :version => 2 do
+  watch(%r{^spec/.+_spec\.rb$})
+  watch(%r{^lib/[^\/]+\/(.+)\.rb$})     { |m| "spec/#{m[1]}_spec.rb" }
+  watch('spec/spec_helper.rb')  { "spec" }
+
+end
+
+guard 'yard' do
+  watch(%r{app/.+\.rb})
+  watch(%r{lib/.+\.rb})
+  watch(%r{ext/.+\.c})
+end
+
+notification :tmux,
+	:display_message => true,
+	:timeout => 5,
+	:default_message_format => '%s >> %s',
+	:line_separator => ' > '
+

data/README.markdown

@@ -0,0 +1,67 @@
+<!-- vim: spell:spelllang=en tw=80
+Yard markup
+# @markup markdown
+# @title README
+-->
+
+Overview 
+=======
+
+This gem implements the core functionalities of the LIMS (Laboratory Information Management System).
+It's not meant to be a stand alone application but the core library of the LIMS
+server.
+
+For more information consult the documentation.
+
+Installation
+============
+
+    gem install lims-core
+
+Or, if you are using [bundler](http://gembundler.com/) , add the following line
+
+     gem :lims-core, :git => "git+ssh://git@github.com/sanger/lims-core.git'
+
+in your `Gemfile`.
+
+Documentation
+=============
+The documentation is generated using [yard](http://yardoc.org/index.html) and can
+be found under the `doc/` directory or using a `yard server`
+
+Developers Guide
+================
+Gem requirements
+----------------
+Ideally each should be loadable on its own. This mean that every file should
+require everything it needs. The exception is for gems re-opening ruby basic
+classes as facet do. The common requirements are grouped in the `lib/common.rb`
+file.
+
+For the user convenience, requiring a directory should requires everything
+underneath. However, requiring `lims-core` will require `Persistence`, but not 
+the subdirectories of it (specific to each different stores like `Sequel`, or
+`Logger`). This to not force to install all the dependencies specific to each
+store.
+
+Documentation Guide
+-------------------
+
+The documentation is written using [yard](http://yardoc.org/index.html).
+It allows to write documentation within the doc and add *typing* hints/
+expectations.
+The recommended format for stand alone documentation files is
+[markdown](http://daringfireball.net/projects/markdown/), however
+it's easier to keep the native markup language used by **yard**, i.e. the
+[rdoc](http://rdoc.sourceforge.net/) one.
+This allows the code to be parsed via **rdoc** and doesn't need the extra spaces at
+the end of a line needed by **markdown**.
+
+However, when the usage of pure **markdown** seems appropriate, it's still
+possible to the use `@markup` switch.
+
+Some documentation can also be added in the specs.
+
+Tests
+-----
+We are using [rspec](http://rspec.info/).