i was having trouble with the inference due to the "large" file size so i broke it up into smaller parts.

- added samples to the list as well
- added a presentation with a single example slide

Author: jjkoehorst

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

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+# Assets - Data files, Models, SOPs
+# 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 = $guest_person
+data_file1.projects = [$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 = $guest_person
+data_file2.projects = [$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 = $guest_person
+model.projects = [$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_person.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 creation
+sop = Sop.new(title: 'Reconstituted Enzyme System Protocol',
+              description: 'Standard operating procedure for reconstituting the gluconeogenic enzyme system from Sulfolobus solfataricus to study metabolic pathway efficiency at high temperatures.')
+sop.contributor = $guest_person
+sop.projects = [$project]
+sop.assays = [$exp_assay, $model_assay]
+sop.policy = Policy.create(name: 'default policy', access_type: 1)
+sop.content_blob = ContentBlob.new(original_filename: 'test_sop.txt',
+                                   content_type: 'text')
+AssetsCreator.create(asset_id: sop.id, creator_id: $guest_person.id, asset_type: sop.class.name)
+FileUtils.cp File.dirname(__FILE__) + '/' + sop.content_blob.original_filename, sop.content_blob.filepath
+
+disable_authorization_checks {sop.save!}
+sop.annotate_with(['protocol', 'enzymology', 'thermophile'], 'tag', $guest_person)
+puts 'Seeded 1 SOP.'
+
+# Store references for other seed files
+$data_file1 = data_file1
+$data_file2 = data_file2
+$model = model
+$sop = sop

db/seeds/example_data/example_data_files_and_models_seeds.rb

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+# ISA - Investigation, Study, Assays, Observation Units
+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_person
+investigation.policy = Policy.create(name: 'default policy', access_type: 1)
+investigation.annotate_with(['metabolism', 'thermophile'], 'tag', $guest_person)
+investigation.save
+puts 'Seeded 1 investigation.'
+
+study = Study.new(title: 'Carbon loss at high T')
+study.contributor = $guest_person
+study.policy = Policy.create(name: 'default policy', access_type: 1)
+study.investigation = investigation
+study.annotate_with(['thermophile', 'high temperature'], 'tag', $guest_person)
+study.save
+puts 'Seeded 1 study.'
+
+## Observation unit
+observation_unit = ObservationUnit.new(title: 'Large scale bioreactor')
+observation_unit.description = 'A large scale bioreactor with a 1000 mL reservoir.'
+observation_unit.other_creators = [$admin_person.name, 'Jane Doe']
+observation_unit.contributor = $guest_person
+observation_unit.policy = Policy.create(name: 'default policy', access_type: 1)
+observation_unit.annotate_with(['bioreactor'], 'tag', $guest_person)
+observation_unit.study = study
+disable_authorization_checks { observation_unit.save }
+puts 'Seeded 1 observation unit'
+
+## Assays ##
+
+## Experimental assay?
+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 = $guest_person
+exp_assay.policy = Policy.create(name: 'default policy', access_type: 1)
+exp_assay.study = study
+# exp_assay.observation_units = [observation_unit] # TODO ActiveRecord::HasManyThroughNestedAssociationsAreReadonly: Cannot modify association 'Assay#observation_units' because it goes through more than one other association. (ActiveRecord::HasManyThroughNestedAssociationsAreReadonly)
+exp_assay.assay_class = AssayClass.experimental
+exp_assay.organisms = [$organism]
+exp_assay.save
+puts "exp_assay: Seeded 1 #{exp_assay.assay_class.long_key.downcase}."
+
+# Modeling 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.modelling
+model_assay.save
+puts "Seeded 1 #{model_assay.assay_class.long_key.downcase}."
+
+# Assay stream
+assay_stream = Assay.new(title: 'Assay stream',
+                         description: 'A stream of assays? This is a test assay stream for the example data.',)
+assay_stream.contributor = $guest_person
+assay_stream.policy = Policy.create(name: 'default policy', access_type: 1)
+assay_stream.study = study
+assay_stream.assay_class = AssayClass.assay_stream
+assay_stream.save
+puts "Seeded 1 assay stream #{model_assay.assay_class.long_key.downcase}."
+
+# Store references for other seed files
+$investigation = investigation
+$study = study
+$observation_unit = observation_unit
+$exp_assay = exp_assay
+$model_assay = model_assay
+$assay_stream = assay_stream

db/seeds/example_data/example_isa_structure_seeds.rb

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+# Project, Institution, Workgroup, Program, Strains, Organisms
+program = Programme.where(title: 'Default Programme').first_or_create(web_page: 'http://www.seek4science.org', funding_details: 'Funding H2020X01Y001', description: 'This is a test programme for the SEEK sandbox.')
+project = Project.where(title: 'Default Project').first_or_create(:programme_id => program.id, description: 'A description for the default project') # TODO this link is not working
+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
+
+# Create a strain
+strain = Strain.where(title: 'Sulfolobus solfataricus strain 98/2').first_or_create
+strain.projects = [project]
+strain.policy = Policy.create(name: 'default policy', access_type: 1)
+strain.organism = Organism.where(title: 'Sulfolobus solfataricus').first_or_create
+strain.provider_name = 'BacDive'
+strain.provider_id = '123456789'
+strain.synonym = '98/2'
+strain.comment = 'This is a test strain.'
+strain.save!
+puts 'Seeded 1 strain.'
+
+# Create an organism
+organism = Organism.where(title: 'Sulfolobus solfataricus').first_or_create
+organism.projects = [project]
+organism.strains = [strain]
+organism.save!
+puts 'Seeded 1 organism.'
+
+# Store references for other seed files
+$program = program
+$project = project
+$institution = institution
+$workgroup = workgroup
+$strain = strain
+$organism = organism

db/seeds/example_data/example_projects_and_basic_setup_seeds.rb

@@ -0,0 +1,85 @@
+# Publications, Presentations and Events
+
+# publication
+publication = Publication.new(
+  publication_type_id: PublicationType.where(title:"Journal").first.id,
+  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'
+)
+
+# Set contributor and projects
+publication.contributor = $guest_person
+publication.projects << $project
+
+# Build policy through the association
+publication.build_policy(name: 'default policy', access_type: 1)
+# Publication date
+publication.published_date = Date.today.to_s
+# Build publication authors
+authors = [
+  { first_name: 'T.', last_name: 'Kouril', author_index: 1 },
+  { first_name: 'D.', last_name: 'Esser', author_index: 2 },
+  { first_name: 'J.', last_name: 'Kort', author_index: 3 },
+  { first_name: 'H. V.', last_name: 'Westerhoff', author_index: 4 },
+  { first_name: 'B.', last_name: 'Siebers', author_index: 5 },
+  { first_name: 'J.', last_name: 'Snoep', author_index: 6 }
+]
+# Citation
+publication.citation = "Kouril, T. et al. Intermediate instability at high temperature leads to low pathway efficiency for an in vitro reconstituted system of gluconeogenesis in Sulfolobus solfataricus. FEBS J. 2015;687:100-108."
+
+authors.each do |author_attrs|
+  publication.publication_authors.build(author_attrs)
+end
+
+# Save publication with all associations
+disable_authorization_checks do
+  publication.save!  # raises an error if something is invalid
+  publication.associate($exp_assay)
+  publication.associate($model_assay)
+end
+
+# Create asset
+AssetsCreator.create(asset_id: publication.id, creator_id: $guest_person.id, asset_type: publication.class.name)
+puts 'Seeded 1 publication.'
+
+# Presentation
+presentation = Presentation.new(
+  title: 'Intermediate instability at high temperature leads to low pathway efficiency for an in vitro reconstituted system of gluconeogenesis in Sulfolobus solfataricus',
+  description: "Four enzymes of the gluconeogenic pathway in Sulfolobus solfataricus were purified and kinetically characterized. The enzymes were reconstituted in vitro to quantify the contribution of temperature instability of the pathway intermediates to carbon loss from the system.
+             The reconstituted system, consisting of phosphoglycerate kinase, glyceraldehyde 3-phosphate dehydrogenase, triose phosphate isomerase and the fructose 1,6-bisphosphate aldolase/phosphatase, maintained a constant consumption rate of 3-phosphoglycerate and production of
+  ",
+)
+presentation.projects = [$project]
+presentation.contributor = $guest_person
+presentation.policy = Policy.create(name: 'default policy', access_type: 1)
+presentation.content_blob = ContentBlob.new(original_filename: 'presentation.pptx', content_type: 'application/vnd.openxmlformats-officedocument.presentationml.presentation')
+AssetsCreator.create(asset_id: presentation.id, creator_id: $guest_person.id, asset_type: presentation.class.name)
+FileUtils.cp File.dirname(__FILE__) + '/' + presentation.content_blob.original_filename, presentation.content_blob.filepath # TODO results in "This version is not available"
+presentation.version = 1
+presentation.save!
+puts 'Seeded 1 presentation.'
+
+# Create an event
+event = Event.new(title: 'Event for publication', description: 'Event for publication', start_date: Date.today, end_date: Date.today + 1.day)
+event.projects = [$project]
+event.contributor = $guest_person
+event.policy = Policy.create(name: 'default policy', access_type: 1)
+# event.website = 'http://www.seek4science.org'
+event.city = 'London'
+event.country = 'United Kingdom'
+event.address = 'Dunmore Terrace 123'
+
+event.save!
+puts 'Seeded 1 event.'
+
+# Store references for other seed files
+$publication = publication
+$presentation = presentation
+$event = event