Different rdf formats

app/controllers/assays_controller.rb

@@ -160,6 +160,7 @@ def show
     respond_to do |format|
       format.html { render(params[:only_content] ? { layout: false } : {}) }
       format.rdf { render template: 'rdf/show' }
+      format.ttl { render template: 'rdf/show' }
       format.json { render json: @assay, include: [params[:include]] }
     end
   end

app/controllers/collections_controller.rb

@@ -16,6 +16,7 @@ def show
     respond_to do |format|
       format.html
       format.rdf { render template: 'rdf/show' }
+      format.ttl { render template: 'rdf/show' }
       format.json { render json: @collection, include: json_api_include_param }
     end
   end

app/controllers/culture_growth_types_controller.rb

@@ -5,6 +5,7 @@ def show
     respond_to do |format|
       format.all { render plain: @culture_growth_type.title }
       format.rdf { render template: 'rdf/show' }
+      format.ttl { render template: 'rdf/show' }
     end
   end
 

app/controllers/people_controller.rb

@@ -31,6 +31,7 @@ def show
     respond_to do |format|
       format.html # show.html.erb
       format.rdf { render template: 'rdf/show' }
+      format.ttl { render template: 'rdf/show' }
       format.json {render json: @person, include: [params[:include]]}
     end
   end

app/controllers/placeholders_controller.rb

@@ -21,6 +21,7 @@ def show
     respond_to do |format|
         format.html
         format.rdf { render template: 'rdf/show' }
+      format.ttl { render template: 'rdf/show' }
         format.json { render json: @placeholder, include: json_api_include_param }
       end
     end

app/controllers/programmes_controller.rb

@@ -91,6 +91,7 @@ def show
       format.html
       format.json {render json: @programme, include: [params[:include]]}
       format.rdf { render template: 'rdf/show' }
+      format.ttl { render template: 'rdf/show' }
     end
   end
 

app/controllers/projects_controller.rb

@@ -525,6 +525,7 @@ def show
     respond_to do |format|
       format.html { render(params[:only_content] ? { layout: false } : {})} # show.html.erb
       format.rdf { render template: 'rdf/show' }
+      format.ttl { render template: 'rdf/show' }
       format.json { render json: @project, include: [params[:include]] }
     end
   end

app/controllers/publications_controller.rb

@@ -24,6 +24,7 @@ def show
     respond_to do |format|
       format.html { render(params[:only_content] ? { layout: false } : {})} # show.html.erb
       format.rdf { render template: 'rdf/show' }
+      format.ttl { render template: 'rdf/show' }
       format.json {render json: @publication, include: [params[:include]]}
       format.any( *Publication::EXPORT_TYPES.keys ) do
         begin

app/controllers/samples_controller.rb

@@ -76,6 +76,7 @@ def show
       format.html
       format.json {render json: @sample, include: [params[:include]]}
       format.rdf { render template: 'rdf/show' }
+      format.ttl { render template: 'rdf/show' }
     end
   end
 

app/controllers/strains_controller.rb

@@ -59,6 +59,7 @@ def index
   def show
     respond_to do |format|
       format.rdf { render template: 'rdf/show' }
+      format.ttl { render template: 'rdf/show' }
       format.html
       # format.json {render json: @strain}
       format.json {render json: :not_implemented, status: :not_implemented }

app/controllers/studies_controller.rb

@@ -109,6 +109,7 @@ def show
     respond_to do |format|
       format.html { render(params[:only_content] ? { layout: false } : {})}
       format.rdf { render template: 'rdf/show' }
+      format.ttl { render template: 'rdf/show' }
       format.json {render json: @study, include: [params[:include]]}
     end
   end

app/helpers/rdf_helper.rb

@@ -3,7 +3,8 @@ module RdfHelper
   include ResourceHelper
 
   def asset_rdf
-    resource_for_controller.to_rdf
+    format = request.format.symbol == :ttl ? :ttl : :rdf
+    resource_for_controller.to_rdf(format)
   end
 
   def schema_ld_script_block

app/views/rdf/show.ttl.erb

@@ -0,0 +1 @@
+<%= asset_rdf.html_safe -%>

config/initializers/mime_types.rb

@@ -8,6 +8,7 @@
   Mime::Type.register_alias "image/svg+xml", :svg
   Mime::Type.register_alias "text/plain", :dot
   Mime::Type.register "text/turtle", :rdf, ["application/rdf", "application/x-turtle"]
+  Mime::Type.register "text/turtle", :ttl
   Mime::Type.register "application/vnd.wf4ever.robundle+zip", :ro
 
   api_mime_types = %W(

db/seeds/example_data/example_config_seeds.rb

@@ -0,0 +1,43 @@
+# Activity Logging and Configuration
+
+# Log activity
+[$project, $investigation, $study, $exp_assay, $model_assay, $data_file1, $data_file2, $model, $publication].each do |item|
+  ActivityLog.create(action: 'create',
+                     culprit: $guest_user,
+                     controller_name: item.class.name.underscore.pluralize,
+                     activity_loggable: item,
+                     data: item.title)
+end
+
+# Updating programme
+disable_authorization_checks do
+  $program.programme_administrators = [$guest_person, $admin_person]
+  $program.projects = [$project]
+  # $program.funding_codes_as_text = ['123456789'] # TODO cannot set funding codes
+  # Discussion links...
+  $program.save!
+end
+
+# Configuration
+Seek::Config.home_description = '<p style="text-align:center;font-size:larger;font-weight:bolder">Welcome to the SEEK Sandbox</p>
+<p style="text-align:center;font-size:larger;font-weight:bolder">You can log in with the username: <em>guest</em> and password: <em>guest</em></p>
+<p style="text-align:center">For more information about SEEK and to see a video, please visit our <a href="http://www.seek4science.org">Website</a>.</p>'
+
+Seek::Config.solr_enabled = true
+Seek::Config.isa_enabled = true
+Seek::Config.observation_units_enabled = true
+Seek::Config.programmes_enabled = true
+Seek::Config.programme_user_creation_enabled = true
+Seek::Config.noreply_sender = '[email protected]'
+Seek::Config.instance_name = 'SEEK SANDBOX'
+Seek::Config.application_name = 'FAIRDOM-SEEK'
+Seek::Config.exception_notification_enabled = true
+Seek::Config.exception_notification_recipients = ['[email protected]']
+Seek::Config.datacite_url = 'https://mds.test.datacite.org/'
+Seek::Config.doi_prefix = '10.5072'
+Seek::Config.doi_suffix = 'seek.5'
+Seek::Config.tag_threshold = 0 # TODO set to 0 or 1 so the tags created in this example_data seeds will be visiblw on the front page.
+puts 'Finish configuration'
+puts 'Please visit admin site for further configuration, e.g. site_base_host, pubmed_api_email, crossref_api_email, bioportal_api_key, email, doi, admin email'
+puts 'Admin account: username admin, password adminadmin. You might want to change admin password.'
+puts 'Then make sure solr, workers are running'

db/seeds/example_data/example_data.seeds.rb

@@ -1,229 +1,8 @@
-# Project, Institution, Workgroup
-project = Project.where(title: 'Default Project').first_or_create
-institution = Institution.where(title: 'Default Institution').first_or_create(country: 'United Kingdom')
-workgroup = WorkGroup.where(project_id: project.id, institution_id: institution.id).first_or_create
-
-admin_user = User.where(login: 'admin').first_or_create(
-  login: 'admin',
-  email: '[email protected]',
-  password: 'adminadmin', password_confirmation: 'adminadmin'
-)
-
-# Admin and guest
-admin_user.activate
-admin_user.build_person(first_name: 'Admin', last_name: 'User', email: '[email protected]') unless admin_user.person
-admin_user.save!
-admin_user.person.work_groups << workgroup
-admin_person = admin_user.person
-admin_person.save
-puts 'Seeded 1 admin.'
-
-guest_user = User.where(login: 'guest').first_or_create(
-  login: 'guest',
-  email: '[email protected]',
-  password: 'guestguest', password_confirmation: 'guestguest'
-)
-guest_user.activate
-guest_user.build_person(first_name: 'Guest', last_name: 'User', email: '[email protected]') unless guest_user.person
-guest_user.save!
-guest_user.person.work_groups << workgroup
-guest_person = guest_user.person
-guest_person.save
-puts 'Seeded 1 guest.'
-
-# ISA
-investigation = Investigation.new(title: 'Central Carbon Metabolism of Sulfolobus solfataricus',
-                                  description: 'An investigation in the CCM of S. solfataricus with a focus on the unique temperature adaptations and regulation; using a combined modelling and experimental approach.')
-investigation.projects = [project]
-investigation.contributor = guest_user
-investigation.policy = Policy.create(name: 'default policy', access_type: 1)
-investigation.save
-puts 'Seeded 1 investigation.'
-
-study = Study.new(title: 'Carbon loss at high T')
-study.contributor = guest_user
-study.policy = Policy.create(name: 'default policy', access_type: 1)
-study.investigation = investigation
-study.save
-puts 'Seeded 1 study.'
-
-exp_assay = Assay.new(title: 'Reconstituted system reference state',
-                      description: 'The four purified enzymes were incubated in assay buffer and consumption of 3PG and production of F6P were measured in time, together with GAP and DHAP concentrations.')
-exp_assay.contributor = guest_person
-exp_assay.policy = Policy.create(name: 'default policy', access_type: 1)
-exp_assay.study = study
-exp_assay.assay_class = AssayClass.first
-exp_assay.save
-puts 'Seeded 1 experimental assay.'
-
-model_assay = Assay.new(title: 'Model reconstituted system',
-                        description: 'Mathematical model for the reconstituted system with PGK, GAPDH, TPI and FBPAase.')
-model_assay.contributor = guest_person
-model_assay.policy = Policy.create(name: 'default policy', access_type: 1)
-model_assay.study = study
-model_assay.assay_class = AssayClass.last
-model_assay.save
-puts 'Seeded 1 modelling analysis.'
-
-# Assets
-# TODO check filesize
-data_file1 = DataFile.new(title: 'Metabolite concentrations during reconstituted enzyme incubation',
-                          description: 'The purified enzymes, PGK, GAPDH, TPI and FBPAase were incubated at 70 C en conversion of 3PG to F6P was followed.')
-data_file1.contributor = guest_user
-data_file1.projects = [project]
-relationship = RelationshipType.where(title: 'Validation data').first
-data_file1.policy = Policy.create(name: 'default policy', access_type: 1)
-data_file1.content_blob = ContentBlob.new(original_filename: 'ValidationReference.xlsx',
-                                          content_type: 'application/vnd.openxmlformats-officedocument.spreadsheetml.sheet')
-disable_authorization_checks do
-  data_file1.save
-  exp_assay.associate(data_file1)
-  model_assay.associate(data_file1, relationship: relationship)
-end
-AssetsCreator.create(asset_id: data_file1.id, creator_id: guest_user.id, asset_type: data_file1.class.name)
-# copy file
-FileUtils.cp File.dirname(__FILE__) + '/' + data_file1.content_blob.original_filename, data_file1.content_blob.filepath
-disable_authorization_checks { data_file1.content_blob.save }
-puts 'Seeded data file 1.'
-
-data_file2 = DataFile.new(title: 'Model simulation and Exp data for reconstituted system',
-                          description: 'Experimental data for the reconstituted system are plotted together with the model prediction.')
-data_file2.contributor = guest_user
-data_file2.projects = [project]
-data_file2.policy = Policy.create(name: 'default policy', access_type: 1)
-data_file2.content_blob = ContentBlob.new(original_filename: 'combinedPlot.jpg',
-                                          content_type: 'image/jpeg')
-disable_authorization_checks do
-  data_file2.save
-  exp_assay.associate(data_file2)
-  model_assay.associate(data_file2, relationship: relationship)
-end
-
-AssetsCreator.create(asset_id: data_file2.id, creator_id: guest_user.id, asset_type: data_file2.class.name)
-# copy file
-FileUtils.cp File.dirname(__FILE__) + '/' + data_file2.content_blob.original_filename, data_file2.content_blob.filepath
-disable_authorization_checks { data_file2.content_blob.save }
-puts 'Seeded data file 2.'
-
-# model
-model = Model.new(title: 'Mathematical model for the combined four enzyme system',
-                  description: 'The PGK, GAPDH, TPI and FBPAase were modelled together using the individual rate equations. Closed system.')
-model.model_format = ModelFormat.find_by_title('SBML')
-model.contributor = guest_user
-model.projects = [project]
-model.assays = [model_assay]
-model.policy = Policy.create(name: 'default policy', access_type: 1)
-model.model_type = ModelType.where(title: 'Ordinary differential equations (ODE)').first
-model.model_format = ModelFormat.where(title: 'SBML').first
-model.recommended_environment = RecommendedModelEnvironment.where(title: 'JWS Online').first
-model.organism = Organism.where(title: 'Sulfolobus solfataricus').first
-cb1 = ContentBlob.new(original_filename: 'ssolfGluconeogenesisOpenAnn.dat',
-                      content_type: 'text/x-uuencode')
-cb2 = ContentBlob.new(original_filename: 'ssolfGluconeogenesisOpenAnn.xml',
-                      content_type: 'text/xml')
-cb3 = ContentBlob.new(original_filename: 'ssolfGluconeogenesisOpenAnn.xml',
-                      content_type: 'text/xml')
-cb4 = ContentBlob.new(original_filename: 'ssolfGluconeogenesisAnn.xml',
-                      content_type: 'text/xml')
-cb5 = ContentBlob.new(original_filename: 'ssolfGluconeogenesisClosed.xml',
-                      content_type: 'text/xml')
-cb6 = ContentBlob.new(original_filename: 'ssolfGluconeogenesis.xml',
-                      content_type: 'text/xml')
-model.content_blobs = [cb1, cb2, cb3, cb4, cb5, cb6]
-disable_authorization_checks { model.save }
-AssetsCreator.create(asset_id: model.id, creator_id: guest_user.id, asset_type: model.class.name)
-# copy file
-model.content_blobs.each do |blob|
-  FileUtils.cp File.dirname(__FILE__) + '/' + blob.original_filename, blob.filepath
-  blob.save
-end
-puts 'Seeded 1 model.'
-
-# sop
-=begin
-sop = Sop.new(title: "Default title",
-                  description: "Default description"
-)
-sop.contributor = guest_user
-sop.projects = [project]
-sop.assays = [exp_assay]
-sop.policy = Policy.create(name: 'default policy', access_type: 1)
-sop.content_blob = ContentBlob.new(original_filename: 'test_sop.txt',
-                                      content_type: 'text'
-)
-disable_authorization_checks {sop.save}
-AssetsCreator.create(asset_id: sop.id, creator_id: guest_user.id, asset_type: sop.class.name)
-#copy file
-FileUtils.cp File.dirname(__FILE__) + '/' + sop.content_blob.original_filename, sop.content_blob.filepath
-puts "Seeded 1 sop."
-=end
-
-# publication
-publication = Publication.new(pubmed_id: '23865479',
-                              title: 'Intermediate instability at high temperature leads to low pathway efficiency for an in vitro reconstituted system of gluconeogenesis in Sulfolobus solfataricus',
-                              abstract: "Four enzymes of the gluconeogenic pathway in Sulfolobus solfataricus were purified and kinetically characterized. The enzymes were reconstituted in vitro to quantify the contribution of temperature instability of the pathway intermediates to carbon loss from the system.
-                                         The reconstituted system, consisting of phosphoglycerate kinase, glyceraldehyde 3-phosphate dehydrogenase, triose phosphate isomerase and the fructose 1,6-bisphosphate aldolase/phosphatase, maintained a constant consumption rate of 3-phosphoglycerate and production of
-                                         fructose 6-phosphate over a 1-h period. Cofactors ATP and NADPH were regenerated via pyruvate kinase and glucose dehydrogenase. A mathematical model was constructed on the basis of the kinetics of the purified enzymes and the measured half-life times of the pathway intermediates.
-                                         The model quantitatively predicted the system fluxes and metabolite concentrations. Relative enzyme concentrations were chosen such that half the carbon in the system was lost due to degradation of the thermolabile intermediates dihydroxyacetone phosphate, glyceraldehyde 3-phosphate
-                                         and 1,3-bisphosphoglycerate, indicating that intermediate instability at high temperature can significantly affect pathway efficiency.",
-                              published_date: '2015',
-                              journal: 'FEBS J')
-
-publication.contributor = guest_user
-publication.projects = [project]
-publication.policy = Policy.create(name: 'default policy', access_type: 1)
-publication_author1 = PublicationAuthor.new(first_name: 'T.',
-                                            last_name: 'Kouril',
-                                            author_index: 1)
-publication_author2 = PublicationAuthor.new(first_name: 'D.',
-                                            last_name: 'Esser',
-                                            author_index: 1)
-publication_author3 = PublicationAuthor.new(first_name: 'J.',
-                                            last_name: 'Kort',
-                                            author_index: 1)
-publication_author4 = PublicationAuthor.new(first_name: 'H. V.',
-                                            last_name: 'Westerhoff',
-                                            author_index: 1)
-publication_author5 = PublicationAuthor.new(first_name: 'B.',
-                                            last_name: 'Siebers',
-                                            author_index: 1)
-publication_author6 = PublicationAuthor.new(first_name: 'J.',
-                                            last_name: 'Snoep',
-                                            author_index: 1)
-
-publication.publication_authors = [publication_author1, publication_author2, publication_author3, publication_author4, publication_author5, publication_author6]
-disable_authorization_checks do
-  publication.save
-  publication.associate(exp_assay)
-  publication.associate(model_assay)
-end
-AssetsCreator.create(asset_id: publication.id, creator_id: guest_user.id, asset_type: publication.class.name)
-puts 'Seeded 1 publication.'
-
-[project, investigation, study, exp_assay, model_assay, data_file1, data_file2, model, publication].each do |item|
-  ActivityLog.create(action: 'create',
-                     culprit: guest_user,
-                     controller_name: item.class.name.underscore.pluralize,
-                     activity_loggable: item,
-                     data: item.title)
-end
-
-Seek::Config.home_description = '<p style="text-align:center;font-size:larger;font-weight:bolder">Welcome to the SEEK Sandbox</p>
-<p style="text-align:center;font-size:larger;font-weight:bolder">You can log in with the username: <em>guest</em> and password: <em>guest</em></p>
-<p style="text-align:center">For more information about SEEK and to see a video, please visit our <a href="http://www.seek4science.org">Website</a>.</p>'
-
-Seek::Config.solr_enabled = true
-Seek::Config.programmes_enabled = true
-Seek::Config.programme_user_creation_enabled = true
-Seek::Config.noreply_sender = '[email protected]'
-Seek::Config.instance_name = 'SEEK SANDBOX'
-Seek::Config.application_name = 'FAIRDOM-SEEK'
-Seek::Config.exception_notification_enabled = true
-Seek::Config.exception_notification_recipients = ['[email protected]']
-Seek::Config.datacite_url = 'https://mds.test.datacite.org/'
-Seek::Config.doi_prefix = '10.5072'
-Seek::Config.doi_suffix = 'seek.5'
-puts 'Finish configuration'
-puts 'Please visit admin site for further configuration, e.g. site_base_host, pubmed_api_email, crossref_api_email, bioportal_api_key, email, doi, admin email'
-puts 'Admin account: username admin, password adminadmin. You might want to change admin password.'
-puts 'Then make sure solr, workers are running'
+# Load modular seed files in order
+require_relative 'example_projects_and_basic_setup_seeds'
+require_relative 'example_users_seeds'
+require_relative 'example_isa_structure_seeds'
+require_relative 'example_samples_seeds'
+require_relative 'example_data_files_and_models_seeds'
+require_relative 'example_publications_and_presentations_seeds'
+require_relative 'example_config_seeds'