a bunch of trials

Gemfile

@@ -33,6 +33,7 @@ gem 'linkeddata'
 gem 'openseek-api'
 gem 'jbuilder'
 gem 'jbuilder-json_api'
+gem 'jsonapi-serializers'
 
 gem 'equivalent-xml'
 gem 'breadcrumbs_on_rails'

Gemfile.lock

@@ -360,6 +360,8 @@ GEM
     json-ld (1.1.8)
       rdf (~> 1.1, >= 1.1.7)
     kgio (2.11.0)
+    jsonapi-serializers (0.16.1)
+      activesupport
     latex-decode (0.2.2)
       unicode (~> 0.4)
     libxml-ruby (2.8.0)
@@ -866,7 +868,12 @@ DEPENDENCIES
   jbuilder-json_api
   jquery-rails (~> 3)
   jquery-ui-rails (~> 3)
+<<<<<<< HEAD
   libxml-ruby (~> 2.8.0)
+=======
+  jsonapi-serializers
+  libxml-ruby (>= 2.6.0)
+>>>>>>> 1540dac... a bunch of trials
   linkeddata
   lograge
   magic_lamp

ansible_vars.yml

@@ -0,0 +1,60 @@
+---
+java_product: jdk # jdk vs jre required due to rjb gem
+java_version: 8
+java_shell_profile: true
+
+eclipse_distro: mars 
+eclipse_package: php
+eclipse_plugins_install:
+  - egit
+  - aptana_studio
+#  - redmine_mylyn
+
+package_list_eclipse:
+  - name: firefox
+  - name: chromium-browser
+
+rvm1_rubies:
+  - ruby-2.1.9
+
+mysql_databases:
+  - name:  seek_vagrant
+    state: present
+  - name:  seek_development
+    state: present
+  - name:  seek_test
+    state: present
+  - name:  seek_production
+    state: present
+
+mysql_users:
+  - name:     "mysqluser"
+    password: "mysqlpassword"
+    priv:     "seek%.*:ALL"
+    host:     "localhost"
+    state:    present
+
+# seek specific variables
+seek_initd:
+  - delayed_job-seek
+  - soffice
+  - solr-seek
+www_user: vagrant
+seek_project_root: /project
+rails_env: production
+
+# nginx setup
+nginx_remove_default_vhost: true
+passenger_ruby: /home/vagrant/sw/rvm/gems/{{ rvm1_rubies[0] }}@seek-1-3/wrappers/ruby
+
+nginx_vhosts:
+  - listen: "80 default_server"
+    server_name: "seek.local"
+    root: "{{ seek_project_root }}/public"
+    error_log:   /var/log/nginx/seek_error.log
+    access_log:  /var/log/nginx/seek_access.log
+    passenger_user: vagrant
+    passenger_enabled: "on"
+    passenger_app_env: "{{ rails_env }}"
+    # https://www.phusionpassenger.com/library/indepth/ruby/spawn_methods/#smart-spawning-caveats
+    extra_parameters: "passenger_spawn_method direct;"

app/controllers/institutions_controller.rb

@@ -58,6 +58,9 @@ def edit
   # POST /institutions
   # POST /institutions.xml
   def create
+
+    #if not params has attr ("title") do
+    #    params = process_jsonapi(params)
     @institution = Institution.new(params[:institution])
 
     respond_to do |format|

app/helpers/api_helper.rb

@@ -3,8 +3,10 @@
 # Copyright (c) 2008-2009, University of Manchester, The European Bioinformatics
 # Institute (EMBL-EBI) and the University of Southampton.
 # See license.txt for details.
-
+require 'jbuilder'
+require 'jbuilder/json_api/version'
 module ApiHelper
+  Jbuilder.include JsonAPI
   def xml_root_attributes
     { 'xmlns' => 'http://www.sysmo-db.org/2010/xml/rest',
       'xmlns:xsi' => 'http://www.w3.org/2001/XMLSchema-instance',
@@ -281,6 +283,18 @@ def associated_resources_xml(builder, object)
     end
   end
 
+  #TO DO: there is still redundancy with the parallel xml method with deleting ignored associated resources
+  def associated_resources_json(builder, object)
+    associated = get_related_resources(object)
+    to_ignore = ignore_associated_types.collect(&:name)
+    associated.delete_if { |k, _v| to_ignore.include?(k) }
+    associated.each_value do |value|
+      if (value[:items] != [])
+        builder.api_format! value[:items]
+      end
+    end
+  end
+
   # types that should be ignored from the related resources. It may be desirable to add items in this list to the schema
   def ignore_associated_types
     [Strain, TavernaPlayer::Run, Workflow, Sweep]

app/models/institution.rb

@@ -57,9 +57,10 @@ def json_api_attrs (options = {})
     attrs
   end
 
-  def json_api_relations (options = {})
-    %w(projects people avatar programmes)
-  end
+  # TO DO: is it redundant to have people and projects here?
+  #def json_api_relations (options = {})
+  #  %w(projects people avatar programmes)
+  #end
 
   def json_api_meta (options = {})
     { uuid: self.uuid, created: self.created_at, modified: self.updated_at }

app/serializers/base_serializer.rb

@@ -0,0 +1,7 @@
+class BaseSerializer
+  include JSONAPI::Serializer
+
+  def self_link
+    "/api/v1#{super}"
+  end
+end

app/views/institutions/show.json.jbuilder

@@ -1,11 +1,14 @@
 json.api_format! @institution
 #json.api_format! Person.all[2] #works
-associated = get_related_resources(@institution)
-associated.each_value do |value|
-  if (value[:items] != [])
-    json.api_format! value[:items]
-  end
-end
+
+associated_resources_json(json, @institution)
+
+# associated = get_related_resources(@institution)
+# associated.each_value do |value|
+#   if (value[:items] != [])
+#     json.api_format! value[:items]
+#   end
+# end
 
 #json.api_format! associated["Project"][:items]
 #json.api_format! associated["Person"][:items]

db/schema.rb

@@ -1234,6 +1234,13 @@
   add_index "publication_auth_lookup", ["user_id", "asset_id", "can_view"], :name => "index_pub_user_id_asset_id_can_view"
   add_index "publication_auth_lookup", ["user_id", "can_view"], :name => "index_publication_auth_lookup_on_user_id_and_can_view"
 
+  create_table "publication_author_orders", :force => true do |t|
+    t.integer "order"
+    t.integer "author_id"
+    t.string  "author_type"
+    t.integer "publication_id"
+  end
+
   create_table "publication_authors", :force => true do |t|
     t.string   "first_name"
     t.string   "last_name"