lims-core 3.2.3
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- checksums.yaml +15 -0
- data/.gitignore +5 -0
- data/.rspec +1 -0
- data/.rvmrc +2 -0
- data/.travis.yml +2 -0
- data/.vimrc +27 -0
- data/.yard_templates/default/layout/html/footer.erb +0 -0
- data/.yardopts +1 -0
- data/Gemfile +54 -0
- data/Gemfile.lock +197 -0
- data/Guardfile +21 -0
- data/Guardfile.tmux +28 -0
- data/README.markdown +67 -0
- data/Rakefile +16 -0
- data/config/database.yml +16 -0
- data/doc/Array.html +116 -0
- data/doc/Array/ArrayLoggerPersistor.html +152 -0
- data/doc/Lims.html +114 -0
- data/doc/Lims/Core.html +178 -0
- data/doc/Lims/Core/Action.html +91 -0
- data/doc/Lims/Core/Actions.html +116 -0
- data/doc/Lims/Core/Actions/Action.html +216 -0
- data/doc/Lims/Core/Actions/Action/AfterEval.html +853 -0
- data/doc/Lims/Core/Actions/Action/InvalidParameters.html +268 -0
- data/doc/Lims/Core/Actions/ActionGroup.html +196 -0
- data/doc/Lims/Core/Actions/ActionGroup/AfterEval.html +315 -0
- data/doc/Lims/Core/Actions/BulkAction.html +224 -0
- data/doc/Lims/Core/Actions/BulkAction/AfterEval.html +253 -0
- data/doc/Lims/Core/Actions/TestActionGroup.html +101 -0
- data/doc/Lims/Core/Actions/TestActionGroup/Action.html +133 -0
- data/doc/Lims/Core/Actions/TestActionGroup/ActionGroup.html +127 -0
- data/doc/Lims/Core/Base.html +287 -0
- data/doc/Lims/Core/Base/AccessibleViaSuper.html +252 -0
- data/doc/Lims/Core/Base/ClassMethod.html +177 -0
- data/doc/Lims/Core/Base/HashString.html +177 -0
- data/doc/Lims/Core/Base/IsArrayOf.html +606 -0
- data/doc/Lims/Core/Base/State.html +130 -0
- data/doc/Lims/Core/Organization.html +113 -0
- data/doc/Lims/Core/Organization/Batch.html +106 -0
- data/doc/Lims/Core/Persistence.html +267 -0
- data/doc/Lims/Core/Persistence/ComparisonFilter.html +318 -0
- data/doc/Lims/Core/Persistence/Filter.html +252 -0
- data/doc/Lims/Core/Persistence/IdentityMap.html +409 -0
- data/doc/Lims/Core/Persistence/IdentityMap/Class.html +144 -0
- data/doc/Lims/Core/Persistence/IdentityMap/DuplicateError.html +126 -0
- data/doc/Lims/Core/Persistence/IdentityMap/DuplicateIdError.html +136 -0
- data/doc/Lims/Core/Persistence/IdentityMap/DuplicateObjectError.html +136 -0
- data/doc/Lims/Core/Persistence/IdentityMapClass.html +133 -0
- data/doc/Lims/Core/Persistence/Logger.html +105 -0
- data/doc/Lims/Core/Persistence/Logger/Persistor.html +334 -0
- data/doc/Lims/Core/Persistence/Logger/Session.html +452 -0
- data/doc/Lims/Core/Persistence/Logger/Store.html +470 -0
- data/doc/Lims/Core/Persistence/MessageBus.html +871 -0
- data/doc/Lims/Core/Persistence/MessageBus/ConnectionError.html +123 -0
- data/doc/Lims/Core/Persistence/MessageBus/InvalidSettingsError.html +122 -0
- data/doc/Lims/Core/Persistence/MultiCriteriaFilter.html +293 -0
- data/doc/Lims/Core/Persistence/PersistAssociationTrait.html +91 -0
- data/doc/Lims/Core/Persistence/PersistableTrait.html +91 -0
- data/doc/Lims/Core/Persistence/Persistor.html +3072 -0
- data/doc/Lims/Core/Persistence/Persistor/DuplicateError.html +205 -0
- data/doc/Lims/Core/Persistence/Persistor/DuplicateIdError.html +147 -0
- data/doc/Lims/Core/Persistence/Persistor/DuplicateObjectError.html +147 -0
- data/doc/Lims/Core/Persistence/PersistorTrait.html +91 -0
- data/doc/Lims/Core/Persistence/ResourceState.html +1738 -0
- data/doc/Lims/Core/Persistence/Search.html +269 -0
- data/doc/Lims/Core/Persistence/Search/CreateSearch.html +251 -0
- data/doc/Lims/Core/Persistence/Search/SearchPersistor.html +240 -0
- data/doc/Lims/Core/Persistence/Search/SearchSequelPersistor.html +396 -0
- data/doc/Lims/Core/Persistence/Sequel.html +117 -0
- data/doc/Lims/Core/Persistence/Sequel/Filters.html +462 -0
- data/doc/Lims/Core/Persistence/Sequel/ForTest.html +101 -0
- data/doc/Lims/Core/Persistence/Sequel/ForTest/Name.html +137 -0
- data/doc/Lims/Core/Persistence/Sequel/ForTest/Name/NamePersitor.html +143 -0
- data/doc/Lims/Core/Persistence/Sequel/Migrations.html +266 -0
- data/doc/Lims/Core/Persistence/Sequel/Persistor.html +665 -0
- data/doc/Lims/Core/Persistence/Sequel/Session.html +501 -0
- data/doc/Lims/Core/Persistence/Sequel/Store.html +417 -0
- data/doc/Lims/Core/Persistence/Session.html +2751 -0
- data/doc/Lims/Core/Persistence/Session/UnmanagedObjectError.html +111 -0
- data/doc/Lims/Core/Persistence/StateGroup.html +696 -0
- data/doc/Lims/Core/Persistence/StateList.html +498 -0
- data/doc/Lims/Core/Persistence/Store.html +695 -0
- data/doc/Lims/Core/Persistence/UuidResource.html +1044 -0
- data/doc/Lims/Core/Persistence/UuidResource/InvalidUuidError.html +111 -0
- data/doc/Lims/Core/Persistence/UuidResource/UuidResourcePersistor.html +337 -0
- data/doc/Lims/Core/Persistence/Uuidable.html +799 -0
- data/doc/Lims/Core/Persistor.html +320 -0
- data/doc/Lims/Core/Resource.html +165 -0
- data/doc/Object.html +228 -0
- data/doc/SessionSpec.html +101 -0
- data/doc/SessionSpec/Model.html +279 -0
- data/doc/SessionSpec/Model/ModelPersistor.html +327 -0
- data/doc/_index.html +732 -0
- data/doc/class_list.html +47 -0
- data/doc/css/common.css +1 -0
- data/doc/css/full_list.css +55 -0
- data/doc/css/style.css +322 -0
- data/doc/file.README.html +127 -0
- data/doc/file_list.html +49 -0
- data/doc/frames.html +13 -0
- data/doc/index.html +127 -0
- data/doc/js/app.js +205 -0
- data/doc/js/full_list.js +167 -0
- data/doc/js/jquery.js +16 -0
- data/doc/method_list.html +1894 -0
- data/doc/top-level-namespace.html +100 -0
- data/lib/common.rb +18 -0
- data/lib/lims-core.rb +29 -0
- data/lib/lims-core/actions.rb +10 -0
- data/lib/lims-core/actions/action.rb +185 -0
- data/lib/lims-core/actions/action_group.rb +54 -0
- data/lib/lims-core/actions/bulk_action.rb +65 -0
- data/lib/lims-core/base.rb +132 -0
- data/lib/lims-core/helpers.rb +41 -0
- data/lib/lims-core/persistence.rb +15 -0
- data/lib/lims-core/persistence/comparison_filter.rb +54 -0
- data/lib/lims-core/persistence/filter.rb +23 -0
- data/lib/lims-core/persistence/identity_map.rb +55 -0
- data/lib/lims-core/persistence/logger/all.rb +5 -0
- data/lib/lims-core/persistence/logger/persistor.rb +35 -0
- data/lib/lims-core/persistence/logger/session.rb +30 -0
- data/lib/lims-core/persistence/logger/store.rb +37 -0
- data/lib/lims-core/persistence/message_bus.rb +131 -0
- data/lib/lims-core/persistence/multi_criteria_filter.rb +50 -0
- data/lib/lims-core/persistence/persist_association_trait.rb +96 -0
- data/lib/lims-core/persistence/persistable_trait.rb +150 -0
- data/lib/lims-core/persistence/persistor.rb +495 -0
- data/lib/lims-core/persistence/resource_state.rb +157 -0
- data/lib/lims-core/persistence/search.rb +3 -0
- data/lib/lims-core/persistence/search/all.rb +3 -0
- data/lib/lims-core/persistence/search/create_search.rb +55 -0
- data/lib/lims-core/persistence/search/search_persistor.rb +45 -0
- data/lib/lims-core/persistence/search/search_sequel_persistor.rb +40 -0
- data/lib/lims-core/persistence/sequel.rb +14 -0
- data/lib/lims-core/persistence/sequel/filters.rb +106 -0
- data/lib/lims-core/persistence/sequel/migrations.rb +14 -0
- data/lib/lims-core/persistence/sequel/migrations/add_audit_tables.rb +147 -0
- data/lib/lims-core/persistence/sequel/migrations/initial.rb +156 -0
- data/lib/lims-core/persistence/sequel/persistor.rb +200 -0
- data/lib/lims-core/persistence/sequel/session.rb +136 -0
- data/lib/lims-core/persistence/sequel/store.rb +37 -0
- data/lib/lims-core/persistence/session.rb +409 -0
- data/lib/lims-core/persistence/state_group.rb +97 -0
- data/lib/lims-core/persistence/state_list.rb +56 -0
- data/lib/lims-core/persistence/store.rb +73 -0
- data/lib/lims-core/persistence/uuid_resource.rb +115 -0
- data/lib/lims-core/persistence/uuid_resource_persistor.rb +43 -0
- data/lib/lims-core/persistence/uuidable.rb +107 -0
- data/lib/lims-core/resource.rb +21 -0
- data/lib/lims-core/subclass_tracker.rb +30 -0
- data/lib/lims-core/version.rb +5 -0
- data/lims-core.gemspec +40 -0
- data/makefile +52 -0
- data/showoff/core-2012-06-11/core/01_slide.md +237 -0
- data/showoff/core-2012-06-11/core/02_slide.md +110 -0
- data/showoff/core-2012-06-11/custom.css +44 -0
- data/showoff/core-2012-06-11/main/01_slide.md +53 -0
- data/showoff/core-2012-06-11/showoff.json +10 -0
- data/showoff/core-2012-06-11/tp1.tpl +1 -0
- data/spec/actions/action_group_spec.rb +39 -0
- data/spec/actions/spec_helper.rb +1 -0
- data/spec/persistence/identity_map_spec.rb +55 -0
- data/spec/persistence/logger/spec_helper.rb +7 -0
- data/spec/persistence/logger/store_spec.rb +48 -0
- data/spec/persistence/message_bus_spec.rb +76 -0
- data/spec/persistence/sequel/session_spec.rb +125 -0
- data/spec/persistence/sequel/spec_helper.rb +39 -0
- data/spec/persistence/sequel/store_shared.rb +25 -0
- data/spec/persistence/sequel/store_spec.rb +22 -0
- data/spec/persistence/session_spec.rb +199 -0
- data/spec/persistence/spec_helper.rb +2 -0
- data/spec/persistence/uuid_resource_spec.rb +80 -0
- data/spec/spec_helper.rb +10 -0
- data/spec/subclass_tracker_sperc.rb +62 -0
- data/utils/constant_tree.rb +29 -0
- data/utils/stack.rb +48 -0
- metadata +402 -0
checksums.yaml
ADDED
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---
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!binary "U0hBMQ==":
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metadata.gz: !binary |-
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NmQ4MDBjZjVjMWRiZTkzMmU5MGQyODRjNzZiMTYxMjg1ZjU0ODRiMQ==
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data.tar.gz: !binary |-
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MjFlYjNmOGQ3NThmODI1Mzg2NWQxZGM2MjExZjI1MzE3YzRhYTAxZQ==
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SHA512:
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metadata.gz: !binary |-
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+
Y2U3NGI0MmYxMDA3OGMxNTI3Y2I2MzJlMGE1YWE4ZmE5Zjg2MmJiNjllYjlm
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+
NWYwMDM0MjlkOTJkM2M2OTYzYTViOGVhZDA0ZTFkNjk3ZDE3ZjgzZTQyNWI1
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+
YzkyMDExZjJkOTgxYjJkYzY2MDcxYjhkZDc5NzA4ZmYzMmZlMzI=
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data.tar.gz: !binary |-
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NTE4MzQ5MDMyMzM2NTFkYzg0YmFkNzRlNThjNDZmMjE3MGY1MWQ4NmNkMTg5
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+
N2I3NTZhMzZjOTQwNWVkNTdlNTc1NTY0MzFhZTZiYTI5MjA4Yzg5ZTNkMDM0
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+
ZTE1Njg3MmIyMmJmYmRiYjA4MTVhZDVjMzhiZDIxZmFmMjIxNjA=
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data/.rspec
ADDED
@@ -0,0 +1 @@
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1
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--tag ~@wip
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data/.rvmrc
ADDED
data/.travis.yml
ADDED
data/.vimrc
ADDED
@@ -0,0 +1,27 @@
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iabbr req require 'lims/core/
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iabbr mlims module Lims::Core
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module Labware
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1
4
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# @todo doc
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2
5
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end
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set path=lib/**,spec/**,showoff/core-2012-06-11/**,,*,**,$GEM_HOME/gems
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let g:ruby_path=&path
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set cdpath=lib/lims/core,spec
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set isk+=?,!
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set makeprg=rspec
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set errorformat=
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\%-Z\ \ \ \ \ \#\ %f:%l:%.%#,%E\ \ %\\d%\\+)%.%#,%C%m,%Z,
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\%-Z%f:%l:%.%#,%E%\\d%\\+)%.%#,%C%m,%Z,
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\%+W'%.%#'\ FAILED,
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\%+I'%.%#'\ FIXED,
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\%-Cexpected:%.%#,
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\%-C\ \ \ \ \ got:%.%#,
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\%E%.%#:in\ `load':\ %f:%l:%m,
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\%C%f:%l:,
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\%W%f:%l:\ warning:\ %m,
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\%E%f:%l:in\ %*[^:]:\ %m,
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\%E%f:%l:\ %m,
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\%-Z%\tfrom\ %f:%l,
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\%-Z%p^%.%#,
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\%-C%.%#,
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\%-G%.%#
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File without changes
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data/.yardopts
ADDED
@@ -0,0 +1 @@
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1
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--private -p .yard_templates lib spec/**/*_spec.rb
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data/Gemfile
ADDED
@@ -0,0 +1,54 @@
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1
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# vim:ft=ruby:ts=2:et:sw=2:sts=2
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source "http://rubygems.org"
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# Specify your gem's dependencies in lims-core.gemspec
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gemspec
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gem 'oj', :platforms => :mri
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gem 'jrjackson', :platforms => :jruby
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group :debugging do
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gem 'debugger', :platforms => :mri
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gem 'debugger-completion', :platforms => :mri
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gem 'ruby-debug', :platforms => :jruby
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end
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group :pry do
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gem 'debugger-pry', :require => 'debugger/pry', :platforms => :mri
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end
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group :autotest do
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gem 'autotest'
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gem 'autotest-growl'
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gem 'autotest-fsevent'
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end
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group :guard do
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gem "guard", '>= 1.3.0', :platforms => :mri
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gem "guard-rspec", :platforms => :mri
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gem "guard-bundler", :platforms => :mri
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gem "guard-yard", :platforms => :mri
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gem "terminal-notifier-guard", :platforms => :mri
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gem "rb-fsevent", '~> 0.9.1', :platforms => :mri
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end
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group :development do
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gem 'sqlite3', :platforms => :mri
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gem 'mysql2', :platforms => :mri
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gem 'ruby-prof', :platforms => :mri
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gem 'jdbc-sqlite3', :platforms => :jruby
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gem 'jdbc-mysql', :platforms => :jruby
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end
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group :yard do
|
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gem 'yard', '= 0.7.3', :platforms => :mri
|
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gem 'yard-rspec', '0.1', :platforms => :mri
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gem 'yard-state_machine', :platforms => :mri
|
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gem 'redcarpet', :platforms => :mri
|
49
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gem 'ruby-graphviz', :platforms => :mri
|
50
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end
|
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group :showoff do
|
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gem 'showoff', :platforms => :mri
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54
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end
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data/Gemfile.lock
ADDED
@@ -0,0 +1,197 @@
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PATH
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remote: .
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specs:
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lims-core (3.2.3)
|
5
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activesupport
|
6
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aequitas
|
7
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bunny (= 0.9.0.pre10)
|
8
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dm-validations
|
9
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facets (= 2.9.3)
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10
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modularity (= 0.6.1)
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11
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sequel
|
12
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state_machine
|
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uuid
|
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virtus (= 0.2.0)
|
15
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GEM
|
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remote: http://rubygems.org/
|
18
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specs:
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ZenTest (4.11.0)
|
20
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+
activesupport (4.2.4)
|
21
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+
i18n (~> 0.7)
|
22
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+
json (~> 1.7, >= 1.7.7)
|
23
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minitest (~> 5.1)
|
24
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+
thread_safe (~> 0.3, >= 0.3.4)
|
25
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+
tzinfo (~> 1.1)
|
26
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+
addressable (2.3.8)
|
27
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+
aequitas (0.0.2)
|
28
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+
amq-protocol (1.9.2)
|
29
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autotest (4.4.6)
|
30
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ZenTest (>= 4.4.1)
|
31
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+
autotest-fsevent (0.2.8)
|
32
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sys-uname
|
33
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+
autotest-growl (0.2.16)
|
34
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+
blankslate (2.1.2.4)
|
35
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+
bluecloth (2.2.0)
|
36
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+
bond (0.4.3)
|
37
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+
bunny (0.9.0.pre10)
|
38
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amq-protocol (>= 1.4.0)
|
39
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+
coderay (1.0.9)
|
40
|
+
columnize (0.9.0)
|
41
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+
debugger (1.6.8)
|
42
|
+
columnize (>= 0.3.1)
|
43
|
+
debugger-linecache (~> 1.2.0)
|
44
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+
debugger-ruby_core_source (~> 1.3.5)
|
45
|
+
debugger-completion (1.0.0)
|
46
|
+
bond (>= 0.4.2)
|
47
|
+
debugger (~> 1.1)
|
48
|
+
debugger-linecache (1.2.0)
|
49
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+
debugger-pry (0.1.1)
|
50
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+
debugger (~> 1)
|
51
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+
pry (>= 0.9.9)
|
52
|
+
debugger-ruby_core_source (1.3.8)
|
53
|
+
diff-lcs (1.1.3)
|
54
|
+
dm-core (1.2.1)
|
55
|
+
addressable (~> 2.3)
|
56
|
+
dm-validations (1.2.0)
|
57
|
+
dm-core (~> 1.2.0)
|
58
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facets (2.9.3)
|
59
|
+
ffi (1.9.0)
|
60
|
+
ffi (1.9.0-java)
|
61
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+
formatador (0.2.4)
|
62
|
+
gli (2.7.0)
|
63
|
+
guard (1.8.2)
|
64
|
+
formatador (>= 0.2.4)
|
65
|
+
listen (>= 1.0.0)
|
66
|
+
lumberjack (>= 1.0.2)
|
67
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+
pry (>= 0.9.10)
|
68
|
+
thor (>= 0.14.6)
|
69
|
+
guard-bundler (1.0.0)
|
70
|
+
bundler (~> 1.0)
|
71
|
+
guard (~> 1.1)
|
72
|
+
guard-rspec (1.2.1)
|
73
|
+
guard (>= 1.1)
|
74
|
+
guard-yard (2.1.0)
|
75
|
+
guard (>= 1.1.0)
|
76
|
+
yard (>= 0.7.0)
|
77
|
+
i18n (0.7.0)
|
78
|
+
jdbc-mysql (5.1.27)
|
79
|
+
jdbc-sqlite3 (3.7.2.1)
|
80
|
+
jrjackson (0.2.3)
|
81
|
+
json (1.8.0)
|
82
|
+
listen (1.3.0)
|
83
|
+
rb-fsevent (>= 0.9.3)
|
84
|
+
rb-inotify (>= 0.9)
|
85
|
+
rb-kqueue (>= 0.2)
|
86
|
+
lumberjack (1.0.4)
|
87
|
+
macaddr (1.6.7)
|
88
|
+
systemu (~> 2.6.2)
|
89
|
+
method_source (0.8.2)
|
90
|
+
mini_portile (0.5.1)
|
91
|
+
minitest (5.8.2)
|
92
|
+
modularity (0.6.1)
|
93
|
+
mysql2 (0.3.13)
|
94
|
+
blankslate (~> 2.0)
|
95
|
+
nokogiri (1.6.0)
|
96
|
+
mini_portile (~> 0.5.0)
|
97
|
+
oj (2.1.7)
|
98
|
+
parslet (1.5.0)
|
99
|
+
pry (0.9.12.2)
|
100
|
+
coderay (~> 1.0.5)
|
101
|
+
method_source (~> 0.8)
|
102
|
+
slop (~> 3.4)
|
103
|
+
rack (1.5.2)
|
104
|
+
rack-protection (1.5.0)
|
105
|
+
rack
|
106
|
+
rake (10.1.0)
|
107
|
+
rb-fsevent (0.9.3)
|
108
|
+
rb-inotify (0.9.1)
|
109
|
+
ffi (>= 0.5.0)
|
110
|
+
rb-kqueue (0.2.0)
|
111
|
+
ffi (>= 0.5.0)
|
112
|
+
redcarpet (3.0.0)
|
113
|
+
rspec (2.8.0)
|
114
|
+
rspec-core (~> 2.8.0)
|
115
|
+
rspec-expectations (~> 2.8.0)
|
116
|
+
rspec-mocks (~> 2.8.0)
|
117
|
+
rspec-core (2.8.0)
|
118
|
+
rspec-expectations (2.8.0)
|
119
|
+
diff-lcs (~> 1.1.2)
|
120
|
+
rspec-mocks (2.8.0)
|
121
|
+
ruby-debug (0.10.4)
|
122
|
+
columnize (>= 0.1)
|
123
|
+
ruby-debug-base (~> 0.10.4.0)
|
124
|
+
ruby-debug-base (0.10.4-java)
|
125
|
+
ruby-graphviz (1.0.8)
|
126
|
+
ruby-prof (0.13.0)
|
127
|
+
sequel (4.8.0)
|
128
|
+
showoff (0.7.0)
|
129
|
+
bluecloth
|
130
|
+
gli (>= 1.3.2)
|
131
|
+
json
|
132
|
+
nokogiri
|
133
|
+
parslet
|
134
|
+
sinatra
|
135
|
+
sinatra (1.4.3)
|
136
|
+
rack (~> 1.4)
|
137
|
+
rack-protection (~> 1.4)
|
138
|
+
tilt (~> 1.3, >= 1.3.4)
|
139
|
+
slop (3.4.6)
|
140
|
+
sqlite3 (1.3.8)
|
141
|
+
state_machine (1.2.0)
|
142
|
+
sys-uname (0.9.2)
|
143
|
+
ffi (>= 1.0.0)
|
144
|
+
systemu (2.6.4)
|
145
|
+
terminal-notifier-guard (1.5.3)
|
146
|
+
thor (0.18.1)
|
147
|
+
thread_safe (0.3.5)
|
148
|
+
tilt (1.4.1)
|
149
|
+
tzinfo (1.2.2)
|
150
|
+
thread_safe (~> 0.1)
|
151
|
+
uuid (2.3.7)
|
152
|
+
macaddr (~> 1.0)
|
153
|
+
virtus (0.2.0)
|
154
|
+
yard (0.7.3)
|
155
|
+
yard-rspec (0.1)
|
156
|
+
yard
|
157
|
+
yard-state_machine (0.0.1)
|
158
|
+
ruby-graphviz (~> 1.0.0)
|
159
|
+
yard (~> 0.7.3)
|
160
|
+
|
161
|
+
PLATFORMS
|
162
|
+
java
|
163
|
+
ruby
|
164
|
+
|
165
|
+
DEPENDENCIES
|
166
|
+
autotest
|
167
|
+
autotest-fsevent
|
168
|
+
autotest-growl
|
169
|
+
debugger
|
170
|
+
debugger-completion
|
171
|
+
debugger-pry
|
172
|
+
guard (>= 1.3.0)
|
173
|
+
guard-bundler
|
174
|
+
guard-rspec
|
175
|
+
guard-yard
|
176
|
+
jdbc-mysql
|
177
|
+
jdbc-sqlite3
|
178
|
+
jrjackson
|
179
|
+
lims-core!
|
180
|
+
mysql2
|
181
|
+
oj
|
182
|
+
rake
|
183
|
+
rb-fsevent (~> 0.9.1)
|
184
|
+
redcarpet
|
185
|
+
rspec (~> 2)
|
186
|
+
ruby-debug
|
187
|
+
ruby-graphviz
|
188
|
+
ruby-prof
|
189
|
+
showoff
|
190
|
+
sqlite3
|
191
|
+
terminal-notifier-guard
|
192
|
+
yard (= 0.7.3)
|
193
|
+
yard-rspec (= 0.1)
|
194
|
+
yard-state_machine
|
195
|
+
|
196
|
+
BUNDLED WITH
|
197
|
+
1.10.6
|
data/Guardfile
ADDED
@@ -0,0 +1,21 @@
|
|
1
|
+
# A sample Guardfile
|
2
|
+
# More info at https://github.com/guard/guard#readme
|
3
|
+
|
4
|
+
guard 'bundler' do
|
5
|
+
watch('Gemfile')
|
6
|
+
# Uncomment next line if Gemfile contain `gemspec' command
|
7
|
+
# watch(/^.+\.gemspec/)
|
8
|
+
end
|
9
|
+
|
10
|
+
guard 'rspec', :version => 2 do
|
11
|
+
watch(%r{^spec/.+_spec\.rb$})
|
12
|
+
watch(%r{^lib/[^\/]+\/(.+)\.rb$}) { |m| "spec/#{m[1]}_spec.rb" }
|
13
|
+
watch('spec/spec_helper.rb') { "spec" }
|
14
|
+
|
15
|
+
end
|
16
|
+
|
17
|
+
guard 'yard' do
|
18
|
+
watch(%r{app/.+\.rb})
|
19
|
+
watch(%r{lib/.+\.rb})
|
20
|
+
watch(%r{ext/.+\.c})
|
21
|
+
end
|
data/Guardfile.tmux
ADDED
@@ -0,0 +1,28 @@
|
|
1
|
+
# A sample Guardfile
|
2
|
+
# More info at https://github.com/guard/guard#readme
|
3
|
+
|
4
|
+
guard 'bundler' do
|
5
|
+
watch('Gemfile')
|
6
|
+
# Uncomment next line if Gemfile contain `gemspec' command
|
7
|
+
# watch(/^.+\.gemspec/)
|
8
|
+
end
|
9
|
+
|
10
|
+
guard 'rspec', :version => 2 do
|
11
|
+
watch(%r{^spec/.+_spec\.rb$})
|
12
|
+
watch(%r{^lib/[^\/]+\/(.+)\.rb$}) { |m| "spec/#{m[1]}_spec.rb" }
|
13
|
+
watch('spec/spec_helper.rb') { "spec" }
|
14
|
+
|
15
|
+
end
|
16
|
+
|
17
|
+
guard 'yard' do
|
18
|
+
watch(%r{app/.+\.rb})
|
19
|
+
watch(%r{lib/.+\.rb})
|
20
|
+
watch(%r{ext/.+\.c})
|
21
|
+
end
|
22
|
+
|
23
|
+
notification :tmux,
|
24
|
+
:display_message => true,
|
25
|
+
:timeout => 5,
|
26
|
+
:default_message_format => '%s >> %s',
|
27
|
+
:line_separator => ' > '
|
28
|
+
|
data/README.markdown
ADDED
@@ -0,0 +1,67 @@
|
|
1
|
+
<!-- vim: spell:spelllang=en tw=80
|
2
|
+
Yard markup
|
3
|
+
# @markup markdown
|
4
|
+
# @title README
|
5
|
+
-->
|
6
|
+
|
7
|
+
Overview
|
8
|
+
=======
|
9
|
+
|
10
|
+
This gem implements the core functionalities of the LIMS (Laboratory Information Management System).
|
11
|
+
It's not meant to be a stand alone application but the core library of the LIMS
|
12
|
+
server.
|
13
|
+
|
14
|
+
For more information consult the documentation.
|
15
|
+
|
16
|
+
Installation
|
17
|
+
============
|
18
|
+
|
19
|
+
gem install lims-core
|
20
|
+
|
21
|
+
Or, if you are using [bundler](http://gembundler.com/) , add the following line
|
22
|
+
|
23
|
+
gem :lims-core, :git => "git+ssh://git@github.com/sanger/lims-core.git'
|
24
|
+
|
25
|
+
in your `Gemfile`.
|
26
|
+
|
27
|
+
Documentation
|
28
|
+
=============
|
29
|
+
The documentation is generated using [yard](http://yardoc.org/index.html) and can
|
30
|
+
be found under the `doc/` directory or using a `yard server`
|
31
|
+
|
32
|
+
Developers Guide
|
33
|
+
================
|
34
|
+
Gem requirements
|
35
|
+
----------------
|
36
|
+
Ideally each should be loadable on its own. This mean that every file should
|
37
|
+
require everything it needs. The exception is for gems re-opening ruby basic
|
38
|
+
classes as facet do. The common requirements are grouped in the `lib/common.rb`
|
39
|
+
file.
|
40
|
+
|
41
|
+
For the user convenience, requiring a directory should requires everything
|
42
|
+
underneath. However, requiring `lims-core` will require `Persistence`, but not
|
43
|
+
the subdirectories of it (specific to each different stores like `Sequel`, or
|
44
|
+
`Logger`). This to not force to install all the dependencies specific to each
|
45
|
+
store.
|
46
|
+
|
47
|
+
Documentation Guide
|
48
|
+
-------------------
|
49
|
+
|
50
|
+
The documentation is written using [yard](http://yardoc.org/index.html).
|
51
|
+
It allows to write documentation within the doc and add *typing* hints/
|
52
|
+
expectations.
|
53
|
+
The recommended format for stand alone documentation files is
|
54
|
+
[markdown](http://daringfireball.net/projects/markdown/), however
|
55
|
+
it's easier to keep the native markup language used by **yard**, i.e. the
|
56
|
+
[rdoc](http://rdoc.sourceforge.net/) one.
|
57
|
+
This allows the code to be parsed via **rdoc** and doesn't need the extra spaces at
|
58
|
+
the end of a line needed by **markdown**.
|
59
|
+
|
60
|
+
However, when the usage of pure **markdown** seems appropriate, it's still
|
61
|
+
possible to the use `@markup` switch.
|
62
|
+
|
63
|
+
Some documentation can also be added in the specs.
|
64
|
+
|
65
|
+
Tests
|
66
|
+
-----
|
67
|
+
We are using [rspec](http://rspec.info/).
|