lims-core 3.2.3

data/utils/constant_tree.rb

@@ -0,0 +1,29 @@
+# this script lists all constants hierarchycally.
+# Usefull to see if what require <module> really requires.
+
+
+if ARGV[0]
+  require 'lims-core/' +  ARGV[0].tr(?-,?/)
+elsif  __FILE__ == $0  # file ran as a script, not required by another one
+  require 'lims-core'
+end
+
+
+def list_constants(m, name=nil, level="", done=Set.new)
+  return if done.include? m
+  done << m
+
+
+  puts "#{level}- #{name || m} (#{m.class})"
+  if m.respond_to?(:constants)
+    m.constants.each do |n|
+      c = m.const_get(n)
+
+      next unless c.respond_to? :name
+      next unless c.name.include? m.name
+      list_constants(c, n, "  #{level}", done) 
+    end
+  end
+end
+
+list_constants(Lims::Core)

data/utils/stack.rb

@@ -0,0 +1,48 @@
+    require 'sequel'
+    require 'logger'
+
+    DB=Sequel.sqlite '', :loggers => [Logger.new($stdout)]
+    # Create test table
+    DB.create_table :uuids do
+      primary_key :id
+      String :uuid, :fixed => true, :size => 4
+    end
+
+    U = DB[:uuids]
+
+
+    def test(msg)
+      U.delete
+      begin
+        puts
+        puts "==> #{msg}"
+        yield
+        puts"<== PASS", U.all.inspect
+      rescue
+        puts "<== FAIL", $!.inspect
+      end
+    end
+
+    def for_uuid(uuid)
+      print "================ Testing : #{uuid} ==========" 
+
+      test "using 'insert'" do
+        U.insert(:uuid => uuid)
+      end
+
+      test  "using raw sql" do
+        DB.run ("INSERT INTO uuids ('uuid') VALUES('#{uuid}')")
+      end
+
+      test  "using prepared statement" do
+        U.prepare(:insert, :p, :uuid => :$n)
+        DB.call(:p, "n" => uuid)
+      end
+      puts
+      puts
+
+    end
+
+    for_uuid('Helo')
+    # Create dodgy string
+    for_uuid(["53020100"].pack("H*"))

metadata

@@ -0,0 +1,402 @@
+--- !ruby/object:Gem::Specification
+name: lims-core
+version: !ruby/object:Gem::Version
+  version: 3.2.3
+platform: ruby
+authors:
+- Maxime Bourget
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2015-11-11 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: facets
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 2.9.3
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 2.9.3
+- !ruby/object:Gem::Dependency
+  name: virtus
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 0.2.0
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 0.2.0
+- !ruby/object:Gem::Dependency
+  name: aequitas
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: modularity
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 0.6.1
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 0.6.1
+- !ruby/object:Gem::Dependency
+  name: dm-validations
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: sequel
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: activesupport
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: uuid
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: state_machine
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: bunny
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 0.9.0.pre10
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 0.9.0.pre10
+- !ruby/object:Gem::Dependency
+  name: rspec
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '2'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '2'
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+description: provides all the necessary to interact with the core database
+email:
+- mb14@sanger.ac.uk
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- .gitignore
+- .rspec
+- .rvmrc
+- .travis.yml
+- .vimrc
+- .yard_templates/default/layout/html/footer.erb
+- .yardopts
+- Gemfile
+- Gemfile.lock
+- Guardfile
+- Guardfile.tmux
+- README.markdown
+- Rakefile
+- config/database.yml
+- doc/Array.html
+- doc/Array/ArrayLoggerPersistor.html
+- doc/Lims.html
+- doc/Lims/Core.html
+- doc/Lims/Core/Action.html
+- doc/Lims/Core/Actions.html
+- doc/Lims/Core/Actions/Action.html
+- doc/Lims/Core/Actions/Action/AfterEval.html
+- doc/Lims/Core/Actions/Action/InvalidParameters.html
+- doc/Lims/Core/Actions/ActionGroup.html
+- doc/Lims/Core/Actions/ActionGroup/AfterEval.html
+- doc/Lims/Core/Actions/BulkAction.html
+- doc/Lims/Core/Actions/BulkAction/AfterEval.html
+- doc/Lims/Core/Actions/TestActionGroup.html
+- doc/Lims/Core/Actions/TestActionGroup/Action.html
+- doc/Lims/Core/Actions/TestActionGroup/ActionGroup.html
+- doc/Lims/Core/Base.html
+- doc/Lims/Core/Base/AccessibleViaSuper.html
+- doc/Lims/Core/Base/ClassMethod.html
+- doc/Lims/Core/Base/HashString.html
+- doc/Lims/Core/Base/IsArrayOf.html
+- doc/Lims/Core/Base/State.html
+- doc/Lims/Core/Organization.html
+- doc/Lims/Core/Organization/Batch.html
+- doc/Lims/Core/Persistence.html
+- doc/Lims/Core/Persistence/ComparisonFilter.html
+- doc/Lims/Core/Persistence/Filter.html
+- doc/Lims/Core/Persistence/IdentityMap.html
+- doc/Lims/Core/Persistence/IdentityMap/Class.html
+- doc/Lims/Core/Persistence/IdentityMap/DuplicateError.html
+- doc/Lims/Core/Persistence/IdentityMap/DuplicateIdError.html
+- doc/Lims/Core/Persistence/IdentityMap/DuplicateObjectError.html
+- doc/Lims/Core/Persistence/IdentityMapClass.html
+- doc/Lims/Core/Persistence/Logger.html
+- doc/Lims/Core/Persistence/Logger/Persistor.html
+- doc/Lims/Core/Persistence/Logger/Session.html
+- doc/Lims/Core/Persistence/Logger/Store.html
+- doc/Lims/Core/Persistence/MessageBus.html
+- doc/Lims/Core/Persistence/MessageBus/ConnectionError.html
+- doc/Lims/Core/Persistence/MessageBus/InvalidSettingsError.html
+- doc/Lims/Core/Persistence/MultiCriteriaFilter.html
+- doc/Lims/Core/Persistence/PersistAssociationTrait.html
+- doc/Lims/Core/Persistence/PersistableTrait.html
+- doc/Lims/Core/Persistence/Persistor.html
+- doc/Lims/Core/Persistence/Persistor/DuplicateError.html
+- doc/Lims/Core/Persistence/Persistor/DuplicateIdError.html
+- doc/Lims/Core/Persistence/Persistor/DuplicateObjectError.html
+- doc/Lims/Core/Persistence/PersistorTrait.html
+- doc/Lims/Core/Persistence/ResourceState.html
+- doc/Lims/Core/Persistence/Search.html
+- doc/Lims/Core/Persistence/Search/CreateSearch.html
+- doc/Lims/Core/Persistence/Search/SearchPersistor.html
+- doc/Lims/Core/Persistence/Search/SearchSequelPersistor.html
+- doc/Lims/Core/Persistence/Sequel.html
+- doc/Lims/Core/Persistence/Sequel/Filters.html
+- doc/Lims/Core/Persistence/Sequel/ForTest.html
+- doc/Lims/Core/Persistence/Sequel/ForTest/Name.html
+- doc/Lims/Core/Persistence/Sequel/ForTest/Name/NamePersitor.html
+- doc/Lims/Core/Persistence/Sequel/Migrations.html
+- doc/Lims/Core/Persistence/Sequel/Persistor.html
+- doc/Lims/Core/Persistence/Sequel/Session.html
+- doc/Lims/Core/Persistence/Sequel/Store.html
+- doc/Lims/Core/Persistence/Session.html
+- doc/Lims/Core/Persistence/Session/UnmanagedObjectError.html
+- doc/Lims/Core/Persistence/StateGroup.html
+- doc/Lims/Core/Persistence/StateList.html
+- doc/Lims/Core/Persistence/Store.html
+- doc/Lims/Core/Persistence/UuidResource.html
+- doc/Lims/Core/Persistence/UuidResource/InvalidUuidError.html
+- doc/Lims/Core/Persistence/UuidResource/UuidResourcePersistor.html
+- doc/Lims/Core/Persistence/Uuidable.html
+- doc/Lims/Core/Persistor.html
+- doc/Lims/Core/Resource.html
+- doc/Object.html
+- doc/SessionSpec.html
+- doc/SessionSpec/Model.html
+- doc/SessionSpec/Model/ModelPersistor.html
+- doc/_index.html
+- doc/class_list.html
+- doc/css/common.css
+- doc/css/full_list.css
+- doc/css/style.css
+- doc/file.README.html
+- doc/file_list.html
+- doc/frames.html
+- doc/index.html
+- doc/js/app.js
+- doc/js/full_list.js
+- doc/js/jquery.js
+- doc/method_list.html
+- doc/top-level-namespace.html
+- lib/common.rb
+- lib/lims-core.rb
+- lib/lims-core/actions.rb
+- lib/lims-core/actions/action.rb
+- lib/lims-core/actions/action_group.rb
+- lib/lims-core/actions/bulk_action.rb
+- lib/lims-core/base.rb
+- lib/lims-core/helpers.rb
+- lib/lims-core/persistence.rb
+- lib/lims-core/persistence/comparison_filter.rb
+- lib/lims-core/persistence/filter.rb
+- lib/lims-core/persistence/identity_map.rb
+- lib/lims-core/persistence/logger/all.rb
+- lib/lims-core/persistence/logger/persistor.rb
+- lib/lims-core/persistence/logger/session.rb
+- lib/lims-core/persistence/logger/store.rb
+- lib/lims-core/persistence/message_bus.rb
+- lib/lims-core/persistence/multi_criteria_filter.rb
+- lib/lims-core/persistence/persist_association_trait.rb
+- lib/lims-core/persistence/persistable_trait.rb
+- lib/lims-core/persistence/persistor.rb
+- lib/lims-core/persistence/resource_state.rb
+- lib/lims-core/persistence/search.rb
+- lib/lims-core/persistence/search/all.rb
+- lib/lims-core/persistence/search/create_search.rb
+- lib/lims-core/persistence/search/search_persistor.rb
+- lib/lims-core/persistence/search/search_sequel_persistor.rb
+- lib/lims-core/persistence/sequel.rb
+- lib/lims-core/persistence/sequel/filters.rb
+- lib/lims-core/persistence/sequel/migrations.rb
+- lib/lims-core/persistence/sequel/migrations/add_audit_tables.rb
+- lib/lims-core/persistence/sequel/migrations/initial.rb
+- lib/lims-core/persistence/sequel/persistor.rb
+- lib/lims-core/persistence/sequel/session.rb
+- lib/lims-core/persistence/sequel/store.rb
+- lib/lims-core/persistence/session.rb
+- lib/lims-core/persistence/state_group.rb
+- lib/lims-core/persistence/state_list.rb
+- lib/lims-core/persistence/store.rb
+- lib/lims-core/persistence/uuid_resource.rb
+- lib/lims-core/persistence/uuid_resource_persistor.rb
+- lib/lims-core/persistence/uuidable.rb
+- lib/lims-core/resource.rb
+- lib/lims-core/subclass_tracker.rb
+- lib/lims-core/version.rb
+- lims-core.gemspec
+- makefile
+- showoff/core-2012-06-11/core/01_slide.md
+- showoff/core-2012-06-11/core/02_slide.md
+- showoff/core-2012-06-11/custom.css
+- showoff/core-2012-06-11/main/01_slide.md
+- showoff/core-2012-06-11/showoff.json
+- showoff/core-2012-06-11/tp1.tpl
+- spec/actions/action_group_spec.rb
+- spec/actions/spec_helper.rb
+- spec/persistence/identity_map_spec.rb
+- spec/persistence/logger/spec_helper.rb
+- spec/persistence/logger/store_spec.rb
+- spec/persistence/message_bus_spec.rb
+- spec/persistence/sequel/session_spec.rb
+- spec/persistence/sequel/spec_helper.rb
+- spec/persistence/sequel/store_shared.rb
+- spec/persistence/sequel/store_spec.rb
+- spec/persistence/session_spec.rb
+- spec/persistence/spec_helper.rb
+- spec/persistence/uuid_resource_spec.rb
+- spec/spec_helper.rb
+- spec/subclass_tracker_sperc.rb
+- utils/constant_tree.rb
+- utils/stack.rb
+homepage: ''
+licenses: []
+metadata: {}
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: lims-core
+rubygems_version: 2.4.8
+signing_key: 
+specification_version: 4
+summary: Core of new LIMS system
+test_files:
+- spec/actions/action_group_spec.rb
+- spec/actions/spec_helper.rb
+- spec/persistence/identity_map_spec.rb
+- spec/persistence/logger/spec_helper.rb
+- spec/persistence/logger/store_spec.rb
+- spec/persistence/message_bus_spec.rb
+- spec/persistence/sequel/session_spec.rb
+- spec/persistence/sequel/spec_helper.rb
+- spec/persistence/sequel/store_shared.rb
+- spec/persistence/sequel/store_spec.rb
+- spec/persistence/session_spec.rb
+- spec/persistence/spec_helper.rb
+- spec/persistence/uuid_resource_spec.rb
+- spec/spec_helper.rb
+- spec/subclass_tracker_sperc.rb
+has_rdoc: