sequencescape-client-api 0.3.5

data/lib/sequencescape-api/resource.rb

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+require 'sequencescape-api/associations'
+require 'sequencescape-api/composition'
+require 'sequencescape-api/actions'
+require 'sequencescape-api/error_handling'
+
+class Sequencescape::Api::JsonError < Sequencescape::Api::Error
+  def initialize(path, object)
+    super("Cannot find the JSON attributes for #{path.inspect} in #{object.inspect}")
+  end
+end
+
+class Sequencescape::Api::Resource
+  require 'sequencescape-api/resource/instance_methods'
+  require 'sequencescape-api/resource/modifications'
+  require 'sequencescape-api/resource/attributes'
+  require 'sequencescape-api/resource/active_model'
+  require 'sequencescape-api/resource/json'
+  require 'sequencescape-api/resource/attribute_groups'
+
+  include ActiveModel
+  extend Attributes
+  include InstanceMethods
+  include Modifications
+  include ::Sequencescape::Api::ErrorHandling
+  include Json
+
+  extend  Groups
+  include Groups::Json
+
+  def initialize(*args, &block)
+    super
+    after_load
+  end
+
+  def after_load
+    # Does nothing
+  end
+  private :after_load
+
+  extend Sequencescape::Api::Associations
+  extend Sequencescape::Api::Composition
+  extend Sequencescape::Api::Actions
+
+  def self.is_a_proxied_model?
+    false
+  end
+end

data/lib/sequencescape-api/resource_model_proxy.rb

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+require 'active_support'
+
+require 'sequencescape-api/finder_methods'
+require 'sequencescape-api/actions'
+
+require 'ostruct'
+
+# Any interaction with the API isn't done directly through a model but through an instance of this
+# class, that proxies the model and ensures that it uses the correct instance of Sequencescape::Api.
+class Sequencescape::Api::ResourceModelProxy
+  self.instance_methods.each { |m| undef_method(m) unless m.to_s =~ /^(__.+__|respond_to\?|object_id)$/ }
+
+  include ::Sequencescape::Api::FinderMethods
+  extend ::Sequencescape::Api::Actions
+
+  def initialize(api, model, actions)
+    @api, @model, @actions = api, model, OpenStruct.new(actions)
+    @model.send(:initialize_class_actions, self)
+  end
+
+  attr_reader :api, :actions, :model
+  private :api, :actions, :model
+
+  delegate :nil?, :inspect, :to => :model
+  delegate :read_timeout, :to => :api
+
+  has_create_action
+
+  def respond_to_missing?(name, include_private = false)
+    super or model.respond_to?(name, include_private)
+  end
+
+  def method_missing(name, *args, &block)
+    model.send(name, api, *args, &block)
+  end
+  protected :method_missing
+
+  def is_a_proxied_model?
+    true
+  end
+
+  # Here are some methods that need to be delegated directly.
+  delegate :ai, :to => :model
+end

data/lib/sequencescape-api/version.rb

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+module Sequencescape
+  class Api
+    VERSION = "0.3.5"
+  end
+end

data/lib/sequencescape-api.rb

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+require 'active_support'
+require 'active_support/core_ext/module/delegation'
+require 'active_support/core_ext/class'
+require 'active_support/core_ext/kernel/singleton_class'
+require 'active_support/core_ext/object/with_options'
+require 'active_support/core_ext/object/try'
+require 'active_support/core_ext/string/inflections'
+require 'active_support/inflections'
+
+require 'sequencescape-api/errors'
+require 'sequencescape-api/core'
+require 'sequencescape-api/resource'
+require 'sequencescape-api/rails'
+
+# Ensure that the I18n stuff has been properly configured
+I18n.config.load_path << File.expand_path(File.join(File.dirname(__FILE__), %w{sequencescape-api locale en.yml}))

data/lib/sequencescape.rb

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+require 'sequencescape-api'
+
+module Sequencescape
+
+end
+
+require 'sequencescape/user'
+
+require 'sequencescape/request'
+require 'sequencescape/pipeline'
+require 'sequencescape/batch'
+require 'sequencescape/study'
+require 'sequencescape/project'
+
+require 'sequencescape/asset'
+require 'sequencescape/barcoded_asset'
+require 'sequencescape/asset_group'
+
+require 'sequencescape/tube_purpose'
+require 'sequencescape/library_tube'
+require 'sequencescape/multiplexed_library_tube'
+require 'sequencescape/sample_tube'
+require 'sequencescape/sample'
+
+require 'sequencescape/comment'
+require 'sequencescape/plate'
+require 'sequencescape/plate_purpose'
+require 'sequencescape/well'
+
+require 'sequencescape/qc_file'
+
+require 'sequencescape/asset_audit'
+
+require 'sequencescape/submission'
+require 'sequencescape/submission_pool'
+require 'sequencescape/order_template'
+require 'sequencescape/order'
+
+require 'sequencescape/search'
+require 'sequencescape/work_completion'
+require 'sequencescape/custom_metadatum_collection'
+
+require 'sequencescape/transfer_request_collection'
+require 'sequencescape/transfer_request'
+
+# Pulldown API support
+require 'sequencescape/plate_creation'
+require 'sequencescape/pooled_plate_creation'
+require 'sequencescape/tube_creation'
+require 'sequencescape/tube_from_tube_creation'
+require 'sequencescape/specific_tube_creation'
+require 'sequencescape/state_change'
+require 'sequencescape/transfer_template'
+require 'sequencescape/transfer'
+require 'sequencescape/bulk_transfer'
+require 'sequencescape/tag_layout_template'
+require 'sequencescape/tag_group'
+require 'sequencescape/volume_update'
+require 'sequencescape/tag_layout'
+require 'sequencescape/bait_library_layout'
+require 'sequencescape/barcode_printer'
+
+# TagQC support
+require 'sequencescape/lot'
+require 'sequencescape/robot'
+require 'sequencescape/lot_type'
+require 'sequencescape/qcable'
+require 'sequencescape/stamp'
+require 'sequencescape/template'
+require 'sequencescape/tag2_layout_template'
+require 'sequencescape/tag2_layout'
+require 'sequencescape/plate_template'
+require 'sequencescape/qcable_creator'
+require 'sequencescape/qc_decision'
+require 'sequencescape/plate_conversion'
+
+# Events
+require 'sequencescape/library_event'
+
+# Ensure that the I18n stuff has been properly configured
+I18n.config.load_path << File.expand_path(File.join(File.dirname(__FILE__), %w{sequencescape locale en.yml}))

data/sequencescape-api.gemspec

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+# -*- encoding: utf-8 -*-
+$:.push File.expand_path("../lib", __FILE__)
+require "sequencescape-api/version"
+
+Gem::Specification.new do |s|
+  s.name        = "sequencescape-client-api"
+  s.version     = Sequencescape::Api::VERSION
+  s.platform    = Gem::Platform::RUBY
+  s.authors     = ["Matthew Denner","James Glover","Eduardo Martin Rojo"]
+  s.email       = ["md12@sanger.ac.uk","james.glover@sanger.ac.uk","emr@sanger.ac.uk"]
+  s.homepage    = ""
+  s.summary     = %q{Gem for the client side of the Sequencescape API}
+  s.description = %q{Provides all of the necessary code for interacting with the Sequencescape API}
+
+  s.rubyforge_project = "sequencescape-client-api"
+
+  s.files         = `git ls-files`.split("\n")
+  s.test_files    = `git ls-files -- {test,spec,features}/*`.split("\n")
+  s.executables   = `git ls-files -- bin/*`.split("\n").map{ |f| File.basename(f) }
+  s.require_paths = ["lib"]
+
+  s.add_dependency('activesupport', '>= 4.0.0', '< 5.2')
+  s.add_dependency('activemodel', '>= 4.0.0', '< 5.2')
+  s.add_dependency('i18n')
+  s.add_dependency('yajl-ruby', '>= 1.3.1')
+
+  s.add_development_dependency('rspec', '~> 2.11.0')
+  s.add_development_dependency('pry')
+  s.add_development_dependency('webmock')
+  s.add_development_dependency('yard')
+  s.add_development_dependency('redcarpet')
+end

data/spec/sequencescape-api/associations_spec.rb

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+require 'spec_helper'
+
+describe 'Various associations' do
+  is_working_as_an_unauthorised_client
+
+  context 'has_many' do
+    context 'with size included in the JSON' do
+      stub_request_from('retrieve-model') { response('model-a-instance') }
+
+      subject { api.model_a.find('UUID').model_bs }
+
+      its(:size) { should == 3 }
+
+      context do
+        stub_request_and_response('results-page-1')
+        stub_request_and_response('results-page-2')
+        stub_request_and_response('results-page-3')
+
+        it_behaves_like 'a paged result'
+      end
+
+      context '#first' do
+        stub_request_and_response('results-page-1')
+
+        it 'only loads the page needed' do
+          subject.first.should_not be_nil
+        end
+      end
+
+      context '#last' do
+        stub_request_and_response('results-page-1')
+        stub_request_and_response('results-page-3')
+
+        it 'only loads the pages needed' do
+          subject.last.should_not be_nil
+        end
+      end
+    end
+
+    context ':disposition => :inline' do
+      stub_request_from('retrieve-model') { response('model-c-instance') }
+
+      subject { api.model_c.find('UUID').model_bs }
+
+      its(:size) { should == 3 }
+
+      it_behaves_like 'a paged result'
+    end
+
+    context 'with create action' do
+      stub_request_from('retrieve-model') { response('model-a-instance') }
+      stub_request_from('create-via-has-many') { response('model-b-instance') }
+
+      subject { api.model_a.find('UUID').model_bs.create!() }
+
+      its(:class) { should == Unauthorised::ModelB }
+    end
+  end
+
+  context 'belongs_to' do
+    stub_request_from('retrieve-model') { response('model-b-instance') }
+
+    let(:resource) { api.model_b.find('UUID') }
+
+    [ :model_a, :model_by_simple_name, :model_by_full_name ].each do |association_name|
+      context "expressed as #{association_name.inspect}" do
+        stub_request_and_response('belongs-to-association')
+
+        subject { resource.send(association_name) }
+
+        its(:name) { should == 'name from JSON' }
+
+        it 'will not load the association twice' do
+          subject.name.should == 'name from JSON'
+          subject.name.should == 'name from JSON'
+        end
+      end
+    end
+
+    context 'when some data is included in the association' do
+      subject { resource.model_with_early_data }
+
+      its(:name) { should == 'early data from JSON' }
+
+      it 'has grouped data' do
+        subject.group.data.should == 'early group data from JSON'
+      end
+
+      context do
+        stub_request_and_response('belongs-to-association')
+        its(:data) { should == 'data from JSON' }
+      end
+    end
+  end
+end

data/spec/sequencescape-api/contracts/belongs-to-association.txt

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+HTTP/1.1 200 OK
+Content-Type: application/json
+
+{
+  "model_a": {
+    "actions": {
+      "read": "http://localhost:3000/BELONGS_TO_UUID"
+    },
+
+    "uuid": "BELONGS_TO_UUID",
+    "name": "name from JSON",
+    "data": "data from JSON"
+  }
+}

data/spec/sequencescape-api/contracts/client-fails-authentication.txt

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+HTTP/1.1 401 Unauthorised
+Content-Type: application/json
+
+{
+  "general": [ "the sign on cookie is invalid" ]
+}

data/spec/sequencescape-api/contracts/create-invalid-resource.txt

@@ -0,0 +1,10 @@
+POST /model_c/create HTTP/1.1
+Accept: application/json
+Content-Type: application/json
+Cookie: WTSISignOn=single-sign-on-cookie
+
+{
+  "model_c": {
+    "attribute_validated_at_server": "please error"
+  }
+}

data/spec/sequencescape-api/contracts/create-model-c-has-many-inline-nested.txt

@@ -0,0 +1,10 @@
+POST /model_c/create HTTP/1.1
+Accept: application/json
+Content-Type: application/json
+Cookie: WTSISignOn=single-sign-on-cookie
+
+{
+  "model_c": {
+    "model_bs": [{"test_attribute":"test_value"}]
+  }
+}

data/spec/sequencescape-api/contracts/create-model-c-has-many-inline.txt

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+POST /model_c/create HTTP/1.1
+Accept: application/json
+Content-Type: application/json
+Cookie: WTSISignOn=single-sign-on-cookie
+
+{
+  "model_c": {
+    "model_bs": ["model-b-uuids"]
+  }
+}

data/spec/sequencescape-api/contracts/create-model-c-has-many.txt

@@ -0,0 +1,10 @@
+POST /model_c/create HTTP/1.1
+Accept: application/json
+Content-Type: application/json
+Cookie: WTSISignOn=single-sign-on-cookie
+
+{
+  "model_c": {
+    "model_as": ["model-a-uuids"]
+  }
+}

data/spec/sequencescape-api/contracts/create-model-c.txt

@@ -0,0 +1,11 @@
+POST /model_c/create HTTP/1.1
+Accept: application/json
+Content-Type: application/json
+Cookie: WTSISignOn=single-sign-on-cookie
+
+{
+  "model_c": {
+    "changes_during_update": "sent from client",
+    "remains_same_during_update": "from JSON"
+  }
+}

data/spec/sequencescape-api/contracts/create-via-has-many.txt

@@ -0,0 +1,9 @@
+POST /UUID/model_bs HTTP/1.1
+Accept: application/json
+Content-Type: application/json
+Cookie: WTSISignOn=single-sign-on-cookie
+
+{
+  "model_b": {
+  }
+}

data/spec/sequencescape-api/contracts/model-a-instance.txt

@@ -0,0 +1,21 @@
+HTTP/1.1 200 OK
+Content-Type: application/json
+
+{
+  "model_a": {
+    "actions": {
+      "read": "http://localhost:3000/UUID"
+    },
+
+    "uuid": "UUID",
+
+    "model_bs": {
+      "actions": {
+        "read": "http://localhost:3000/pages/1",
+        "create": "http://localhost:3000/UUID/model_bs"
+      },
+      "size": 3
+    }
+  }
+}
+