lims-core 3.2.3

data/showoff/core-2012-06-11/custom.css

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+.content {
+  color: black;
+  font-family: helvetica, arial;
+}
+
+h1, h2 {
+  color: rgb(79, 180, 226);
+  font-family: Georgia;
+	margin : 1em;
+}
+
+h3 {
+	font-size : 2.5 em;
+	text-align : left;
+	margin-left : 1em;
+}
+
+.subsection h1 {
+	color : white;
+	background :  rgb(79, 180, 226);
+	font-size : 3em;
+	text-align : right;
+
+}
+
+h2 {
+	#background : #ccc;
+	text-align : left;
+	margin-left : 1em;
+}
+.content::after {
+  position: absolute;
+  right: 120px;
+  bottom: 120px;
+  content: url(jay_small.png);
+}
+
+.red { color: #f33;}
+
+pre.sh_sourceCode {
+	background-color : #eee;
+	#border-radius : 0.5em;
+	box-shadow: -10px 10px 5px #888;
+}

data/showoff/core-2012-06-11/main/01_slide.md

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+!SLIDE top
+# New LIMS Core
+Maxime Bourget - Monday 2012/06/11
+!SLIDE subsection transition=scrollLeft
+# Overview
+* What it is and why.
+* How it works/design.
+* What's done
+* To do
+
+!SLIDE transition=scrollUp  small subsection
+# New LIMS Core
+##  Set of gems, core of the new LIMS.  
+
+* Contains the  domain model.
+* Interface for different persistence layers.
+* Organized in components.
+* No web/GUI *knowledge*.
+
+### Needs to be embedded in a server/application.
+
+
+!SLIDE smaller subsection transition=scrollUp
+# New LIMS Core
+## Lessons learned from Sequencescape
+### Persistence mixed with the domain implementation, adds *noise* to the code :
+
+* Domain code *aware* of persistence (`reload`, no identity map).
+* Domain tests have to take persistence into account (`save`, `reload`).
+* Object model too close from database model.
+* No identity map.
+* Tests slow.
+* Hard to maintain.
+
+.notes ActiveRecord is magic, but hard to customize and optimize.
+
+!SLIDE small subsection transition=scrollUp
+# New LIMS Core
+## Goal
+### Decouple domain model from persistence layer.
+* Code easier to split into component.
+* Domains of *responsibilities* clearer.
+* Less side effect.
+* Test suites small and faster.
+### ...     How do we do it ?
+
+
+!SLIDE small transition=scrollLeft
+# New LIMS server internal architecture
+
+*  `lims::api`  Sinatra application
+* Core extensions (clients specific) (optional)
+* `lims:core` gem domain  model + persistence.

data/showoff/core-2012-06-11/showoff.json

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+{ "name": "New core"
+	,
+	"author" : "Maxime Bourget"
+	, "description" : "Prestentation of the new core"
+	, "sections": [
+		{ "section" : "main" }, 
+		{ "section" : "core" }
+	]
+	, "templates": { "default" : "tp1.tpl" }
+}

data/showoff/core-2012-06-11/tp1.tpl

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+Hello, this is my template

data/spec/actions/action_group_spec.rb

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+require 'actions/spec_helper'
+
+require 'lims-core/actions/action_group'
+module Lims::Core
+  module Actions
+    module TestActionGroup
+      class Action
+        include  Actions::Action
+      end
+      class ActionGroup
+        include Actions::ActionGroup
+      end
+      describe ActionGroup do
+        context "with 2 actions" do
+          let(:store) { Lims::Core::Persistence::Store.new }
+          let(:user) { mock :user }
+          let(:application) { "test" }
+          let(:action_parameters) { {:user => user, :application => application, :store => store } }
+          let!(:action1) { Action.new(action_parameters).tap do |action|
+            end }
+          let!(:action2) { Action.new(action_parameters).tap do |action|
+            end }
+
+          subject{ ActionGroup.new(action_parameters.merge(:actions => [action1, action2])) do |action, session|
+            end
+          }
+
+          it "executes both action" do
+            action1.should_receive(:_call_in_session) { :result_1 }
+            action2.should_receive(:_call_in_session) { :result_2 }
+
+            subject.call();
+            subject.result.should == [:result_1, :result_2]
+          end
+        end
+      end
+    end
+  end
+end

data/spec/actions/spec_helper.rb

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+require 'spec_helper'

data/spec/persistence/identity_map_spec.rb

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+# Spec requirements
+require 'persistence/spec_helper'
+
+# Model requirements
+require 'lims-core/persistence/identity_map'
+
+
+
+
+module Lims::Core::Persistence
+  class IdentityMapClass
+    include IdentityMap
+  end
+
+  describe IdentityMapClass, :identity_map => true, :persistence => true do
+
+    context "with a object mapped to an id" do
+      let(:id) { 1 }
+      let(:object) { "Object 1" }
+      before {subject.map_id_object(id,object) }
+
+      it "must find the object by id" do
+        subject.object_for(id).should == object
+      end
+
+      it "must find the id by object" do
+        subject.id_for(object).should == id
+      end
+
+      it "must fail when mapping another object with the same id" do
+        expect { subject.map_id_object(id, "Object #2") }.to raise_error(IdentityMap::DuplicateIdError)
+      end
+
+      it "must fail when mapping another id with the same object" do
+        expect { subject.map_id_object(2, object) }.to raise_error(IdentityMap::DuplicateObjectError)
+      end
+
+      it "must not fail when mapping it again" do
+        expect { subject.map_id_object(id, object) }.not_to raise_error(IdentityMap::DuplicateError)
+      end
+
+      it "must yield the object" do
+        subject.object_for(id) do |o|
+          o.should == object
+        end
+      end
+
+      it "must not yield if the object can't be found" do
+        subject.object_for("wrong id") do |o|
+          raise "not found"
+        end.should be_nil
+      end
+    end
+  end
+end

data/spec/persistence/logger/spec_helper.rb

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+require 'spec_helper'
+
+require 'lims-core/persistence/logger/store'
+
+RSpec.configure do |c|
+  c.filter_run_excluding :logger => true
+end

data/spec/persistence/logger/store_spec.rb

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+# Spec requirements
+require 'persistence/logger/spec_helper'
+
+# Model requirements
+require 'logger'
+require 'lims-core/persistence/logger/store'
+require 'lims-core/persistence/logger/persistor'
+
+class Array
+  class ArrayLoggerPersistor <  Lims::Core::Persistence::Persistor
+    include Lims::Core::Persistence::Logger::Persistor
+  end
+end
+
+module Lims::Core
+  module Persistence
+    describe Logger::Store, :store => true, :logger => true, :persistence => true do
+      def self.initialized_with_a_logger(method)
+        context "initialized with a logger" do
+          let (:logger) { ::Logger.new($stdout) }
+          subject { described_class.new(logger, method) }
+          it "should log objects to stdout" do
+            logger.should_receive(:send).with(method, '["A1", "A2", "B1", "B2"]')
+            subject.with_session do |session|
+              session << %w(A1 A2 B1 B2)
+            end
+          end
+        end
+      end
+      def self.initialized_with_an_IO(io)
+        context "initialized to stdout" do
+          subject { described_class.new(io) }
+          it "should log objects to stdout" do
+            io.should_receive(:write)
+            subject.with_session do |session|
+              session << %w(A1 A2 B1 B2)
+            end
+          end
+        end
+      end
+      initialized_with_an_IO(STDOUT)
+      initialized_with_an_IO(STDERR)
+
+      initialized_with_a_logger(:info)
+      initialized_with_a_logger(:warn)
+    end
+  end
+end

data/spec/persistence/message_bus_spec.rb

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+require 'lims-core/persistence/message_bus'
+
+module Lims::Core
+  module Persistence
+    describe MessageBus, :message_bus => true do
+      context "to be valid" do
+        let(:url) { "amqp://user:password@localhost:55672" }
+        let(:exchange_name) { "exchange_name" }
+        let(:durable) { true }
+        let(:prefetch_number) { 30 }
+        let(:heart_beat) { 0 }
+        let(:backend_application_id) { "test backend app" }
+        let(:another_backend_application_id) { "another backend app id" }
+        let(:bus_settings) { {  "url"                     => url,
+                                "exchange_name"           => exchange_name,
+                                "durable"                 => durable,
+                                "prefetch_number"         => prefetch_number,
+                                "heart_beat"              => heart_beat,
+                                "backend_application_id"  => backend_application_id}
+        }
+
+        it "requires a RabbitMQ host" do
+          described_class.new(bus_settings - ["url"]).valid?.should == false
+        end
+
+        it "requires an exchange name" do
+          described_class.new(bus_settings - ["exchange_name"]).valid?.should == false
+        end
+
+        it "requires the durable option" do
+          described_class.new(bus_settings - ["durable"]).valid?.should == false
+        end
+
+        it "requires a prefetch number" do
+          described_class.new(bus_settings - ["prefetch_number"]).valid?.should == false
+        end
+
+        it "not requires a heart_beat value" do
+          described_class.new(bus_settings - ["heart_beat"]).valid?.should == true
+        end
+
+        it "requires the backend_application_id value" do
+          described_class.new(bus_settings - ["backend_application_id"]).valid?.should == false
+        end
+
+        it "requires correct settings" do
+          described_class.new(bus_settings).valid?.should == true
+        end
+  
+        it "sets the exchange type to topic by default" do
+          described_class.new(bus_settings).exchange_type.should == "topic"
+        end
+
+        it "requires correct settings to connect to the message bus" do
+          expect do
+            described_class.new(bus_settings - ["url"]).connect
+          end.to raise_error(MessageBus::InvalidSettingsError)
+        end
+
+        it "requires an exchange to publish a message" do
+          expect do
+            described_class.new(bus_settings).publish("message")
+          end.to raise_error(MessageBus::ConnectionError)
+        end
+
+        it "raise an error if set the backend app id more then once" do
+          expect do
+            message_bus = described_class.new(bus_settings)
+            message_bus.backend_application_id = another_backend_application_id
+          end.to raise_error(MessageBus::InvalidSettingsError)
+        end
+      end
+    end
+  end 
+end
+

data/spec/persistence/sequel/session_spec.rb

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+# Spec requirements
+require 'persistence/sequel/spec_helper'
+
+# Model requirements
+require 'lims-core/persistence/sequel/store'
+require 'lims-core/persistence/sequel/session'
+require 'lims-core/persistence/sequel/persistor'
+
+module Lims::Core::Persistence
+  module ForTest
+    class Name
+      include Lims::Core::Resource
+      attribute :name, String
+      class NamePersitor < Lims::Core::Persistence::Persistor
+        Model = Name
+      end
+    end
+  end
+
+  module Sequel
+    describe Session, :session => true, :persistence => true, :persistence => true, :sequel => true do
+      context "with mysql underlying" do
+        include_context "mysql db"
+        let(:store) { Store.new(db).tap do
+          db.create_table :sessions do
+            primary_key :id
+            String :user
+            String :backend_application_id
+            String :parameters, :text => true
+            boolean :success
+            timestamp :start_time
+            DateTime :end_time
+          end unless db.table_exists?(:sessions)
+        end}
+        xit "sets a new session_id to work with" do
+          begin
+            my_session_id=nil
+            store.with_session do |s|
+              my_session_id = s.get_current_session
+            end
+          rescue
+          end
+          (my_session_id == nil).should == false
+        end
+        xit "session is reseted after scope" do
+          begin
+            my_session_id=nil
+            store.with_session do |s|
+              my_session_id = s.get_current_session
+            end
+            my_session_after_scope = s.get_current_session
+          rescue
+          end
+          (my_session_after_scope == my_session_id).should == false
+          (my_session_after_scope == nil).should == true
+        end
+        xit "a different session if I create a new scope" do
+          begin
+            my_session_id=nil
+            my_session_id_2=nil
+            store.with_session do |s|
+              my_session_id = s.get_current_session
+            end
+            my_session_after_scope = s.get_current_session
+            store.with_session do |s|
+              my_session_id_2 = s.get_current_session
+            end
+            my_session_after_scope_2 = s.get_current_session
+          rescue
+          end
+          (my_session_id == my_session_id_2).should == false
+        end
+      end
+
+      context "with sqlite underlying" do
+        include_context "sqlite db"
+        let(:store) { Store.new(db).tap do
+            db.create_table :primary_keys do
+              primary_key :id
+              String :table_name
+              Integer :current_key
+            end
+          end
+        }
+
+        context "#transaction" do
+          let(:a) { ForTest::Name.new(:name => "A") }
+          let(:b) { ForTest::Name.new(:name => "B") }
+          let(:c) { ForTest::Name.new(:name => "C") }
+
+          before() do
+            db.create_table :names do
+              primary_key :id
+              String :name
+            end
+
+            c.stub(:attributes) do
+              raise RuntimeError, "Can't save '#{inspect}'"
+            end
+          end
+
+          it "save the 2 if no problem" do
+            expect { store.with_session do |s|
+                s << a << b
+              end }.to change{db[:names].count}.by(2)
+          end
+
+          it "saves 0 if the second doesn't save" do
+            expect {
+              begin
+                store.with_session do |s|
+                  s << a << c
+                end
+              rescue
+              end
+            }.to change{db[:names].count}.by(0)
+          end
+
+          xit "saves 0 if the second is not valid" do
+          end
+        end
+      end
+    end
+  end
+end