Seeds improvements

db/seeds/example_data/example_data_files_and_models_seeds.rb

@@ -22,6 +22,7 @@
 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 = $guest_person
+data_file2.license = 'CC-BY-SA-4.0'
 data_file2.projects = [$project]
 data_file2.policy = Policy.create(name: 'default policy', access_type: 1)
 data_file2.content_blob = ContentBlob.new(original_filename: 'combinedPlot.jpg',
@@ -32,7 +33,11 @@
   $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)
+AssetsCreator.create(asset_id: data_file2.id, creator_id: $admin_person.id, asset_type: data_file2.class.name)
+data_file2.other_creators = 'Person A, Person B'
+disable_authorization_checks { data_file2.save }
+User.with_current_user($guest_user) { data_file2.annotate_with(['metabolism', 'modelling', 'gluconeogenesis'], 'tag', $guest_person) }
+disable_authorization_checks { data_file2.save }
 # 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 }
@@ -77,15 +82,16 @@
               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.license = 'CC-BY-SA-4.0'
 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', $guest_person)
+User.with_current_user($guest_user) { sop.annotate_with(['protocol', 'enzymology', 'thermophile'], 'tag', $guest_person) }
+disable_authorization_checks { sop.save! }
 puts 'Seeded 1 SOP.'
 
 # Store references for other seed files

db/seeds/example_data/example_document.txt

@@ -0,0 +1 @@
+This is an example document for the SEEK sandbox. It describes the experimental setup for the reconstituted gluconeogenic enzyme system from Sulfolobus solfataricus.

db/seeds/example_data/example_isa_structure_seeds.rb

@@ -3,16 +3,19 @@
                                   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 = $guest_person
+investigation.creators = [$admin_person]
+investigation.other_creators = ['Person A', 'Person B']
 investigation.policy = Policy.create(name: 'default policy', access_type: 1)
-investigation.annotate_with(['metabolism', 'thermophile'], 'tag', $guest_person)
+User.with_current_user($guest_user) { investigation.annotate_with(['metabolism', 'thermophile'], 'tag', $guest_person) }
 investigation.save
 puts 'Seeded 1 investigation.'
 
 study = Study.new(title: 'Carbon loss at high T')
+study.description = 'The carbon loss at high T description will be here but I am currently not imaginative enough.'
 study.contributor = $guest_person
 study.policy = Policy.create(name: 'default policy', access_type: 1)
 study.investigation = investigation
-study.annotate_with(['thermophile', 'high temperature'], 'tag', $guest_person)
+User.with_current_user($guest_user) { study.annotate_with(['thermophile', 'high temperature'], 'tag', $guest_person) }
 study.save
 puts 'Seeded 1 study.'
 
@@ -22,7 +25,7 @@
 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', $guest_person)
+User.with_current_user($guest_user) { observation_unit.annotate_with(['bioreactor'], 'tag', $guest_person) }
 observation_unit.study = study
 disable_authorization_checks { observation_unit.save }
 puts 'Seeded 1 observation unit'

db/seeds/example_data/example_projects_and_basic_setup_seeds.rb

@@ -1,6 +1,7 @@
 # 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
+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
 
@@ -18,6 +19,7 @@
 
 # Create an organism
 organism = Organism.where(title: 'Sulfolobus solfataricus').first_or_create
+organism.concept_uri = '2287'
 organism.projects = [project]
 organism.strains = [strain]
 organism.save!

db/seeds/example_data/example_publications_and_presentations_seeds.rb

@@ -2,7 +2,7 @@
 
 # publication
 publication = Publication.new(
-  publication_type_id: PublicationType.where(title:"Journal").first.id,
+  publication_type_id: PublicationType.where(title: 'Journal').first_or_create!(title: 'Journal').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.
@@ -17,7 +17,7 @@
 # Set contributor and projects
 publication.contributor = $guest_person
 publication.projects << $project
-
+publication.registered_mode = 2
 # Build policy through the association
 publication.build_policy(name: 'default policy', access_type: 1)
 # Publication date
@@ -33,10 +33,11 @@
 ]
 # Citation
 publication.citation = "Kouril, T. et al. Intermediate instability at high temperature leads to low pathway efficiency for an in vitro reconstituted system of gluconeogenesis in Sulfolobus solfataricus. FEBS J. 2015;687:100-108."
-
 authors.each do |author_attrs|
   publication.publication_authors.build(author_attrs)
 end
+# Tags
+User.with_current_user($guest_user) { publication.annotate_with(['metabolism', 'thermophile'], 'tag', $guest_person) }
 
 # Save publication with all associations
 disable_authorization_checks do
@@ -60,26 +61,69 @@
 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')
+disable_authorization_checks { presentation.save! }
 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!
+FileUtils.cp File.dirname(__FILE__) + '/presentation.pptx', presentation.content_blob.filepath
+disable_authorization_checks { presentation.content_blob.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.url = 'http://www.seek4science.org'
 event.city = 'London'
 event.country = 'United Kingdom'
 event.address = 'Dunmore Terrace 123'
 
 event.save!
 puts 'Seeded 1 event.'
 
+# Document
+document = Document.new(
+  title: 'Experimental setup for the reconstituted gluconeogenic enzyme system',
+  description: 'This document describes the experimental setup and procedures used for reconstituting the gluconeogenic enzyme system from Sulfolobus solfataricus.'
+)
+document.projects = [$project]
+document.contributor = $guest_person
+document.license = 'CC-BY-4.0'
+document.policy = Policy.create(name: 'default policy', access_type: 1)
+document.content_blob = ContentBlob.new(original_filename: 'example_document.txt', content_type: 'text/plain')
+User.with_current_user($guest_user) { document.annotate_with(['gluconeogenesis', 'protocol', 'thermophile'], 'tag', $guest_person) }
+disable_authorization_checks { document.save! }
+AssetsCreator.create(asset_id: document.id, creator_id: $admin_person.id, asset_type: document.class.name)
+FileUtils.cp File.dirname(__FILE__) + '/example_document.txt', document.content_blob.filepath
+disable_authorization_checks { document.content_blob.save }
+puts 'Seeded 1 document.'
+
+# Collection
+collection = Collection.new(
+  title: 'Gluconeogenesis in Sulfolobus solfataricus',
+  description: 'A collection of data files, models, SOPs and publications related to the reconstituted gluconeogenic enzyme system from Sulfolobus solfataricus.'
+)
+collection.projects = [$project]
+collection.contributor = $guest_person
+collection.license = 'CC-BY-4.0'
+collection.policy = Policy.create(name: 'default policy', access_type: 1)
+User.with_current_user($guest_user) { collection.annotate_with(['gluconeogenesis', 'thermophile', 'metabolism'], 'tag', $guest_person) }
+disable_authorization_checks { collection.save! }
+[
+  { asset: $data_file1,   comment: 'Metabolite concentration data', order: 1 },
+  { asset: $data_file2,   comment: 'Model simulation vs experimental data plot', order: 2 },
+  { asset: $model,        comment: 'Mathematical model of the four-enzyme system', order: 3 },
+  { asset: $sop,          comment: 'Protocol for reconstituting the enzyme system', order: 4 },
+  { asset: document,      comment: 'Experimental setup description', order: 5 },
+  { asset: publication,   comment: 'Key publication for this work', order: 6 },
+  { asset: presentation,  comment: 'Conference presentation', order: 7 },
+].each do |item|
+  CollectionItem.create!(collection: collection, asset: item[:asset], comment: item[:comment], order: item[:order])
+end
+puts 'Seeded 1 collection.'
+
 # Store references for other seed files
 $publication = publication
 $presentation = presentation
-$event = event
+$event = event
+$document = document
+$collection = collection

db/seeds/example_data/example_samples_seeds.rb

@@ -61,8 +61,8 @@
   description: 'Whether the culture has reached stationary phase'
 )
 
+User.with_current_user($guest_user) { culture_sample_type.annotate_with(['bacterial culture', 'thermophile', 'microbiology'], 'tag', $guest_person) }
 disable_authorization_checks { culture_sample_type.save! }
-culture_sample_type.annotate_with(['bacterial culture', 'thermophile', 'microbiology'], 'tag', $guest_person)
 puts 'Seeded bacterial culture sample type.'
 
 # Create a sample type for enzyme preparations
@@ -120,8 +120,8 @@
   description: 'Number of purification steps performed'
 )
 
+User.with_current_user($guest_user) { enzyme_sample_type.annotate_with(['enzyme', 'protein', 'purification'], 'tag', $guest_person) }
 disable_authorization_checks { enzyme_sample_type.save! }
-enzyme_sample_type.annotate_with(['enzyme', 'protein', 'purification'], 'tag', $guest_person)
 puts 'Seeded enzyme preparation sample type.'
 
 # Now create actual samples

db/seeds/example_data/example_users_seeds.rb

@@ -11,9 +11,17 @@
 # TODO, check if admin really has access to the admin environment
 admin_user.build_person(first_name: 'Admin', last_name: 'User', email: 'admin@test1000.com') unless admin_user.person
 admin_user.save!
-admin_user.person.work_groups << $workgroup
 admin_person = admin_user.person
-admin_person.save
+admin_person.first_name = 'Admin'
+admin_person.last_name = 'User'
+admin_person.orcid = 'https://orcid.org/0000-0002-1825-0097'
+admin_person.web_page = 'https://example.org'
+admin_person.phone = '00-0000-0000-0000'
+admin_person.work_groups << $workgroup unless admin_person.work_groups.include?($workgroup)
+disable_authorization_checks { admin_person.save! }
+# TODO, bug, annotations are not shown in the web interface
+admin_person.add_annotations(['administration', 'data management'], 'expertise', admin_person)
+admin_person.add_annotations(['SEEK', 'Ruby on Rails'], 'tool', admin_person)
 puts 'Seeded 1 admin.'
 
 ## Guest
@@ -25,15 +33,18 @@
 guest_user.activate
 guest_user.build_person(first_name: 'Guest', last_name: 'User', email: 'guest@example.com') unless guest_user.person
 guest_user.save!
-guest_user.person.work_groups << $workgroup
 guest_person = guest_user.person
-guest_person.save
+guest_person.first_name = 'Guest'
+guest_person.last_name = 'User'
+guest_person.work_groups << $workgroup unless guest_person.work_groups.include?($workgroup)
+disable_authorization_checks { guest_person.save! }
 puts 'Seeded 1 guest.'
 
 # Update project
 disable_authorization_checks do
   $project.description = 'This is a test project for the SEEK sandbox.'
   $project.web_page = 'http://www.seek4science.org'
+  $project.wiki_page = 'http://www.wiki.org/' # TODO, rename wiki_page to internal_page?
   $project.pals = [guest_person]
   $project.save!
   puts 'Seeded 1 project.'