From d02d54ce196e036fa800da16fad70eb8245591ca Mon Sep 17 00:00:00 2001 From: Kevin De Pelseneer Date: Wed, 8 May 2024 12:31:40 +0200 Subject: [PATCH 001/131] Add 'assets/manage_specific_attributes' for assay streams --- app/views/isa_assays/_form.html.erb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/app/views/isa_assays/_form.html.erb b/app/views/isa_assays/_form.html.erb index 20fe51faaf..899e57ad4f 100644 --- a/app/views/isa_assays/_form.html.erb +++ b/app/views/isa_assays/_form.html.erb @@ -80,7 +80,11 @@ <%= assay_fields.hidden_field :assay_stream_id, value: assay_stream_id -%> <%= assay_fields.hidden_field :assay_class_id, value: assay_class_id -%> - <% unless is_assay_stream %> + <% if is_assay_stream %> + <% if User.current_user -%> + <%= render partial: 'assets/manage_specific_attributes', locals:{f:assay_fields} if show_form_manage_specific_attributes? %> + <% end %> + <% else %> <% if User.current_user -%> <%= render partial: 'assets/manage_specific_attributes', locals:{f:assay_fields} if show_form_manage_specific_attributes? %> <%= assay_fields.fancy_multiselect(:sops, other_projects_checkbox: true, name: "isa_assay[assay][sop_ids]")%> From ddd8a1b5def5095b06aaab7b359a5febae718fb4 Mon Sep 17 00:00:00 2001 From: Kevin De Pelseneer Date: Wed, 8 May 2024 13:15:27 +0200 Subject: [PATCH 002/131] Hide assay design in case of assay stream --- app/views/assays/show.html.erb | 2 +- app/views/general/_show_page_tab_definitions.html.erb | 3 ++- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/app/views/assays/show.html.erb b/app/views/assays/show.html.erb index fabd8c63f9..e0c12ee449 100644 --- a/app/views/assays/show.html.erb +++ b/app/views/assays/show.html.erb @@ -160,7 +160,7 @@ <%= tab_pane('related-items') do %> <%= render partial: 'general/items_related_to', object: @assay %> <% end %> - <% if Seek::Config.isa_json_compliance_enabled && @assay.is_isa_json_compliant? %> + <% if Seek::Config.isa_json_compliance_enabled && @assay.is_isa_json_compliant? && !@assay.is_assay_stream? %> <%= tab_pane('assay_design') do %> <%= render :partial=>"isa_assays/assay_design", locals: { assay: @assay} -%> <%= render partial: 'single_pages/change_batch_persmission_modal' %> diff --git a/app/views/general/_show_page_tab_definitions.html.erb b/app/views/general/_show_page_tab_definitions.html.erb index 5ea7c76dc3..612f1fecfe 100644 --- a/app/views/general/_show_page_tab_definitions.html.erb +++ b/app/views/general/_show_page_tab_definitions.html.erb @@ -18,7 +18,8 @@ <% end %> <% if resource %> - <% if Seek::Config.isa_json_compliance_enabled && resource.is_isa_json_compliant? %> + <% resource_is_assay_stream = resource_name == 'Assay' ? resource.is_assay_stream? : false %> + <% if Seek::Config.isa_json_compliance_enabled && resource.is_isa_json_compliant? && !resource_is_assay_stream %> <%= tab(resource_name&.downcase + "_design") do %> <%= resource.model_name.human %> design <% end %> From 5e8b1512e3ac878e62135d6351c5b236752f3409 Mon Sep 17 00:00:00 2001 From: Stuart Owen Date: Tue, 7 May 2024 11:10:51 +0100 Subject: [PATCH 003/131] new AuthLookupMaintenanceJob to check consistency, runs priority 3 on the authlookup queue every 8 hours #1866 --- app/jobs/auth_lookup_maintenance_job.rb | 33 ++++++++ app/jobs/regular_maintenance_job.rb | 23 ------ config/schedule.rb | 4 + .../jobs/auth_lookup_maintenance_job_test.rb | 76 +++++++++++++++++++ test/unit/jobs/regular_maintenace_job_test.rb | 59 -------------- 5 files changed, 113 insertions(+), 82 deletions(-) create mode 100644 app/jobs/auth_lookup_maintenance_job.rb create mode 100644 test/unit/jobs/auth_lookup_maintenance_job_test.rb diff --git a/app/jobs/auth_lookup_maintenance_job.rb b/app/jobs/auth_lookup_maintenance_job.rb new file mode 100644 index 0000000000..ca46761a34 --- /dev/null +++ b/app/jobs/auth_lookup_maintenance_job.rb @@ -0,0 +1,33 @@ +class AuthLookupMaintenanceJob < ApplicationJob + RUN_PERIOD = 8.hours.freeze + + queue_as QueueNames::AUTH_LOOKUP + queue_with_priority 3 + + def perform + check_authlookup_consistency + end + + # checks lookup_table_consistent? on each type for each user, and if not triggers a job to repopulate for that user + def check_authlookup_consistency + found_types = [].to_set + items_for_queue = [].to_set + User.where.not(person_id: nil).to_a.push(nil).each do |user| + + # will only deal with 1 type per user per run + found = Seek::Util.authorized_types.find do |type| + !type.lookup_table_consistent?(user) + end + + next unless found.present? + + found_types << found + missing = found.items_missing_from_authlookup(user) + items_for_queue.merge(missing) + end + + found_types.each(&:remove_invalid_auth_lookup_entries) + AuthLookupUpdateQueue.enqueue(items_for_queue.to_a) unless items_for_queue.empty? + end + +end \ No newline at end of file diff --git a/app/jobs/regular_maintenance_job.rb b/app/jobs/regular_maintenance_job.rb index 139fe3c52a..d42afdf85e 100644 --- a/app/jobs/regular_maintenance_job.rb +++ b/app/jobs/regular_maintenance_job.rb @@ -20,7 +20,6 @@ def perform clean_git_repositories resend_activation_emails remove_unregistered_users - check_authlookup_consistency end private @@ -73,26 +72,4 @@ def resend_activation_emails end end - # checks lookup_table_consistent? on each type for each user, and if not triggers a job to repopulate for that user - # if not already queued - def check_authlookup_consistency - found_types = [].to_set - items_for_queue = [].to_set - User.where.not(person_id: nil).to_a.push(nil).each do |user| - - # will only deal with 1 type per user per run - found = Seek::Util.authorized_types.find do |type| - !type.lookup_table_consistent?(user) - end - - next unless found.present? - - found_types << found - missing = found.items_missing_from_authlookup(user) - items_for_queue.merge(missing) - end - - found_types.each(&:remove_invalid_auth_lookup_entries) - AuthLookupUpdateQueue.enqueue(items_for_queue.to_a) unless items_for_queue.empty? - end end diff --git a/config/schedule.rb b/config/schedule.rb index 0718d9b395..ba8c045099 100644 --- a/config/schedule.rb +++ b/config/schedule.rb @@ -47,6 +47,10 @@ def offset(off_hours) runner "RegularMaintenanceJob.perform_later" end +every AuthLookupMaintenanceJob::RUN_PERIOD, at: offset(1) do + runner "AuthLookupMaintenanceJob.perform_later" +end + every LifeMonitorStatusJob::PERIOD, at: offset(2) do runner "LifeMonitorStatusJob.perform_later" end diff --git a/test/unit/jobs/auth_lookup_maintenance_job_test.rb b/test/unit/jobs/auth_lookup_maintenance_job_test.rb new file mode 100644 index 0000000000..95f1b543f2 --- /dev/null +++ b/test/unit/jobs/auth_lookup_maintenance_job_test.rb @@ -0,0 +1,76 @@ +require 'test_helper' + +class AuthLookupMaintenaceJobTest < ActiveSupport::TestCase + + test 'run period' do + assert_equal 8.hours, AuthLookupMaintenanceJob::RUN_PERIOD + end + + test 'priority' do + assert_equal 3, AuthLookupMaintenanceJob.priority + end + + test 'queue name' do + assert_equal QueueNames::AUTH_LOOKUP, AuthLookupMaintenanceJob.queue_name + end + + + test 'check authlookup consistency' do + #ensure a consistent initial state + disable_authorization_checks do + Seek::Util.authorized_types.each(&:destroy_all) + Seek::Util.authorized_types.each(&:clear_lookup_table) + end + + User.destroy_all + p = FactoryBot.create(:person) + p2 = FactoryBot.create(:person) + u = FactoryBot.create(:brand_new_user) + + assert_nil u.person + + with_config_value(:auth_lookup_enabled, true) do + assert AuthLookupUpdateQueue.queue_enabled? + + doc1 = FactoryBot.create(:document) + doc2 = FactoryBot.create(:document) + AuthLookupUpdateJob.perform_now + + assert Document.lookup_table_consistent?(p.user) + assert Document.lookup_table_consistent?(p2.user) + assert Document.lookup_table_consistent?(nil) + + assert_no_enqueued_jobs do + assert_no_difference('AuthLookupUpdateQueue.count') do + AuthLookupMaintenanceJob.perform_now + end + end + + # delete a record + Document.lookup_class.where(user_id:p.user.id,asset_id:doc1.id).last.delete + + #duplicate a record + Document.lookup_class.where(user_id:p2.user.id, asset_id:doc2.id).last.dup.save! + + refute Document.lookup_table_consistent?(p.user) + refute Document.lookup_table_consistent?(p2.user) + + #gets immmediately updated for anonymous user + assert Document.lookup_table_consistent?(nil) + + assert_enqueued_jobs(1) do + assert_difference('AuthLookupUpdateQueue.count',1) do + AuthLookupMaintenanceJob.perform_now + end + end + + # double check it will be fixed when the job runs + AuthLookupUpdateJob.perform_now + assert Document.lookup_table_consistent?(p.user) + assert Document.lookup_table_consistent?(p2.user) + assert Document.lookup_table_consistent?(nil) + end + + end + +end \ No newline at end of file diff --git a/test/unit/jobs/regular_maintenace_job_test.rb b/test/unit/jobs/regular_maintenace_job_test.rb index 0cff108369..7b627541b9 100644 --- a/test/unit/jobs/regular_maintenace_job_test.rb +++ b/test/unit/jobs/regular_maintenace_job_test.rb @@ -154,65 +154,6 @@ def setup assert_equal [person3, person4].sort, logs.collect(&:subject).sort end - test 'check authlookup consistency' do - #ensure a consistent initial state - disable_authorization_checks do - Seek::Util.authorized_types.each(&:destroy_all) - Seek::Util.authorized_types.each(&:clear_lookup_table) - end - - User.destroy_all - p = FactoryBot.create(:person) - p2 = FactoryBot.create(:person) - u = FactoryBot.create(:brand_new_user) - - assert_nil u.person - - with_config_value(:auth_lookup_enabled, true) do - assert AuthLookupUpdateQueue.queue_enabled? - - doc1 = FactoryBot.create(:document) - doc2 = FactoryBot.create(:document) - AuthLookupUpdateJob.perform_now - - assert Document.lookup_table_consistent?(p.user) - assert Document.lookup_table_consistent?(p2.user) - assert Document.lookup_table_consistent?(nil) - - assert_no_enqueued_jobs do - assert_no_difference('AuthLookupUpdateQueue.count') do - RegularMaintenanceJob.perform_now - end - end - - # delete a record - Document.lookup_class.where(user_id:p.user.id,asset_id:doc1.id).last.delete - - #duplicate a record - Document.lookup_class.where(user_id:p2.user.id, asset_id:doc2.id).last.dup.save! - - refute Document.lookup_table_consistent?(p.user) - refute Document.lookup_table_consistent?(p2.user) - - #gets immmediately updated for anonymous user - assert Document.lookup_table_consistent?(nil) - - assert_enqueued_jobs(1) do - assert_difference('AuthLookupUpdateQueue.count',1) do - RegularMaintenanceJob.perform_now - end - end - - # double check it will be fixed when the job runs - AuthLookupUpdateJob.perform_now - assert Document.lookup_table_consistent?(p.user) - assert Document.lookup_table_consistent?(p2.user) - assert Document.lookup_table_consistent?(nil) - end - - - end - test 'cleans redundant repositories' do redundant = FactoryBot.create(:blank_repository, created_at: 5.years.ago) redundant_but_in_grace = FactoryBot.create(:blank_repository, created_at: 1.second.ago) From b76db9e4d2540649b925d05a3a9d1dd1b8243ad9 Mon Sep 17 00:00:00 2001 From: Stuart Owen Date: Tue, 7 May 2024 11:23:28 +0100 Subject: [PATCH 004/131] skip users that are already queued when checking, probably a newly registered user #1866 --- app/jobs/auth_lookup_maintenance_job.rb | 3 ++ .../jobs/auth_lookup_maintenance_job_test.rb | 50 +++++++++++++++++++ 2 files changed, 53 insertions(+) diff --git a/app/jobs/auth_lookup_maintenance_job.rb b/app/jobs/auth_lookup_maintenance_job.rb index ca46761a34..2cfa216fed 100644 --- a/app/jobs/auth_lookup_maintenance_job.rb +++ b/app/jobs/auth_lookup_maintenance_job.rb @@ -14,6 +14,9 @@ def check_authlookup_consistency items_for_queue = [].to_set User.where.not(person_id: nil).to_a.push(nil).each do |user| + # skip if this user is queued up + next if AuthLookupUpdateQueue.where(item:user).any? + # will only deal with 1 type per user per run found = Seek::Util.authorized_types.find do |type| !type.lookup_table_consistent?(user) diff --git a/test/unit/jobs/auth_lookup_maintenance_job_test.rb b/test/unit/jobs/auth_lookup_maintenance_job_test.rb index 95f1b543f2..ae563886d4 100644 --- a/test/unit/jobs/auth_lookup_maintenance_job_test.rb +++ b/test/unit/jobs/auth_lookup_maintenance_job_test.rb @@ -73,4 +73,54 @@ class AuthLookupMaintenaceJobTest < ActiveSupport::TestCase end + test 'skip if user in the queue' do + #ensure a consistent initial state + disable_authorization_checks do + Seek::Util.authorized_types.each(&:destroy_all) + Seek::Util.authorized_types.each(&:clear_lookup_table) + end + + User.destroy_all + p = FactoryBot.create(:person) + + with_config_value(:auth_lookup_enabled, true) do + assert AuthLookupUpdateQueue.queue_enabled? + + doc1 = FactoryBot.create(:document) + AuthLookupUpdateJob.perform_now + + assert Document.lookup_table_consistent?(p.user) + + # delete a record + Document.lookup_class.where(user_id:p.user.id,asset_id:doc1.id).last.delete + + refute Document.lookup_table_consistent?(p.user) + + #gets immmediately updated for anonymous user + assert Document.lookup_table_consistent?(nil) + + refute AuthLookupUpdateQueue.any? + AuthLookupUpdateQueue.create!(item: p.user) + assert AuthLookupUpdateQueue.any? + + # nothing queued whilst user is queued + assert_no_enqueued_jobs do + assert_no_difference('AuthLookupUpdateQueue.count') do + AuthLookupMaintenanceJob.perform_now + end + end + + AuthLookupUpdateQueue.destroy_all + refute AuthLookupUpdateQueue.any? + + # queued after the user has been removed + assert_enqueued_jobs(1) do + assert_difference('AuthLookupUpdateQueue.count',1) do + AuthLookupMaintenanceJob.perform_now + end + end + + end + end + end \ No newline at end of file From beb0de6fa9cba72ae26f2c92eb5aa19f07fe2257 Mon Sep 17 00:00:00 2001 From: Stuart Owen Date: Tue, 7 May 2024 11:52:30 +0100 Subject: [PATCH 005/131] skip any types that are present in the queue #1866 --- app/jobs/auth_lookup_maintenance_job.rb | 3 + .../jobs/auth_lookup_maintenance_job_test.rb | 65 +++++++++++++++---- 2 files changed, 56 insertions(+), 12 deletions(-) diff --git a/app/jobs/auth_lookup_maintenance_job.rb b/app/jobs/auth_lookup_maintenance_job.rb index 2cfa216fed..3b06b727c4 100644 --- a/app/jobs/auth_lookup_maintenance_job.rb +++ b/app/jobs/auth_lookup_maintenance_job.rb @@ -19,6 +19,9 @@ def check_authlookup_consistency # will only deal with 1 type per user per run found = Seek::Util.authorized_types.find do |type| + # skip if there are any queued items of this type + next if AuthLookupUpdateQueue.where(item_type:type.name).any? + !type.lookup_table_consistent?(user) end diff --git a/test/unit/jobs/auth_lookup_maintenance_job_test.rb b/test/unit/jobs/auth_lookup_maintenance_job_test.rb index ae563886d4..9c40175428 100644 --- a/test/unit/jobs/auth_lookup_maintenance_job_test.rb +++ b/test/unit/jobs/auth_lookup_maintenance_job_test.rb @@ -2,6 +2,16 @@ class AuthLookupMaintenaceJobTest < ActiveSupport::TestCase + def setup + #ensure a consistent initial state + disable_authorization_checks do + Seek::Util.authorized_types.each(&:destroy_all) + Seek::Util.authorized_types.each(&:clear_lookup_table) + end + + User.destroy_all + end + test 'run period' do assert_equal 8.hours, AuthLookupMaintenanceJob::RUN_PERIOD end @@ -16,13 +26,7 @@ class AuthLookupMaintenaceJobTest < ActiveSupport::TestCase test 'check authlookup consistency' do - #ensure a consistent initial state - disable_authorization_checks do - Seek::Util.authorized_types.each(&:destroy_all) - Seek::Util.authorized_types.each(&:clear_lookup_table) - end - User.destroy_all p = FactoryBot.create(:person) p2 = FactoryBot.create(:person) u = FactoryBot.create(:brand_new_user) @@ -74,13 +78,7 @@ class AuthLookupMaintenaceJobTest < ActiveSupport::TestCase end test 'skip if user in the queue' do - #ensure a consistent initial state - disable_authorization_checks do - Seek::Util.authorized_types.each(&:destroy_all) - Seek::Util.authorized_types.each(&:clear_lookup_table) - end - User.destroy_all p = FactoryBot.create(:person) with_config_value(:auth_lookup_enabled, true) do @@ -123,4 +121,47 @@ class AuthLookupMaintenaceJobTest < ActiveSupport::TestCase end end + test 'skip if particular type is on the queue' do + p = FactoryBot.create(:person) + + with_config_value(:auth_lookup_enabled, true) do + assert AuthLookupUpdateQueue.queue_enabled? + + doc1 = FactoryBot.create(:document) + AuthLookupUpdateJob.perform_now + + assert Document.lookup_table_consistent?(p.user) + + # delete a record + Document.lookup_class.where(user_id:p.user.id,asset_id:doc1.id).last.delete + + refute Document.lookup_table_consistent?(p.user) + + #gets immmediately updated for anonymous user + assert Document.lookup_table_consistent?(nil) + + refute AuthLookupUpdateQueue.any? + AuthLookupUpdateQueue.create!(item: doc1) + assert AuthLookupUpdateQueue.any? + + # nothing queued whilst doc1 is queued + assert_no_enqueued_jobs do + assert_no_difference('AuthLookupUpdateQueue.count') do + AuthLookupMaintenanceJob.perform_now + end + end + + AuthLookupUpdateQueue.destroy_all + refute AuthLookupUpdateQueue.any? + + # queued after the doc1 has been removed + assert_enqueued_jobs(1) do + assert_difference('AuthLookupUpdateQueue.count',1) do + AuthLookupMaintenanceJob.perform_now + end + end + + end + end + end \ No newline at end of file From 106df34434ad68ad33366b341f7a1f91aaacdab5 Mon Sep 17 00:00:00 2001 From: Stuart Owen Date: Tue, 7 May 2024 13:17:11 +0100 Subject: [PATCH 006/131] updated schedule test #1866 --- test/integration/schedule_test.rb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/test/integration/schedule_test.rb b/test/integration/schedule_test.rb index 54f930f38d..b7aa273ccb 100644 --- a/test/integration/schedule_test.rb +++ b/test/integration/schedule_test.rb @@ -24,6 +24,11 @@ class ScheduleTest < ActionDispatch::IntegrationTest assert regular assert_equal [RegularMaintenanceJob::RUN_PERIOD, { at: '1:00am' }], regular[:every] + # AuthLookupMaintenanceJob + auth = pop_task(runners, "AuthLookupMaintenanceJob.perform_later") + assert auth + assert_equal [AuthLookupMaintenanceJob::RUN_PERIOD, { at: '1:00am' }], auth[:every] + # LifeMonitor status lm_status = pop_task(runners, "LifeMonitorStatusJob.perform_later") assert lm_status From 31fde85f4ce8fca93688a86866be79d2493a45a0 Mon Sep 17 00:00:00 2001 From: Stuart Owen Date: Tue, 7 May 2024 14:26:23 +0100 Subject: [PATCH 007/131] check each type, rather than just taking the first failing type #1866 --- app/jobs/auth_lookup_maintenance_job.rb | 29 ++++++----- .../jobs/auth_lookup_maintenance_job_test.rb | 48 ++++++++++++++++++- 2 files changed, 60 insertions(+), 17 deletions(-) diff --git a/app/jobs/auth_lookup_maintenance_job.rb b/app/jobs/auth_lookup_maintenance_job.rb index 3b06b727c4..fb9700549b 100644 --- a/app/jobs/auth_lookup_maintenance_job.rb +++ b/app/jobs/auth_lookup_maintenance_job.rb @@ -11,29 +11,28 @@ def perform # checks lookup_table_consistent? on each type for each user, and if not triggers a job to repopulate for that user def check_authlookup_consistency found_types = [].to_set - items_for_queue = [].to_set - User.where.not(person_id: nil).to_a.push(nil).each do |user| - # skip if this user is queued up - next if AuthLookupUpdateQueue.where(item:user).any? + Seek::Util.authorized_types.each do |type| + #skip if there are any items of this type queued + next if AuthLookupUpdateQueue.where(item_type: type.name).any? - # will only deal with 1 type per user per run - found = Seek::Util.authorized_types.find do |type| - # skip if there are any queued items of this type - next if AuthLookupUpdateQueue.where(item_type:type.name).any? + items_for_queue = [].to_set - !type.lookup_table_consistent?(user) - end + User.where.not(person_id: nil).to_a.push(nil).each do |user| - next unless found.present? + # skip if this user is queued up + next if AuthLookupUpdateQueue.where(item: user).any? + next if type.lookup_table_consistent?(user) - found_types << found - missing = found.items_missing_from_authlookup(user) - items_for_queue.merge(missing) + items_for_queue.merge(type.items_missing_from_authlookup(user)) + found_types << type + end + AuthLookupUpdateQueue.enqueue(items_for_queue.to_a) unless items_for_queue.empty? end found_types.each(&:remove_invalid_auth_lookup_entries) - AuthLookupUpdateQueue.enqueue(items_for_queue.to_a) unless items_for_queue.empty? end + + end \ No newline at end of file diff --git a/test/unit/jobs/auth_lookup_maintenance_job_test.rb b/test/unit/jobs/auth_lookup_maintenance_job_test.rb index 9c40175428..04d4dd8023 100644 --- a/test/unit/jobs/auth_lookup_maintenance_job_test.rb +++ b/test/unit/jobs/auth_lookup_maintenance_job_test.rb @@ -10,6 +10,7 @@ def setup end User.destroy_all + AuthLookupUpdateQueue.destroy_all end test 'run period' do @@ -94,7 +95,7 @@ def setup refute Document.lookup_table_consistent?(p.user) - #gets immmediately updated for anonymous user + #gets immediately updated for anonymous user assert Document.lookup_table_consistent?(nil) refute AuthLookupUpdateQueue.any? @@ -137,7 +138,7 @@ def setup refute Document.lookup_table_consistent?(p.user) - #gets immmediately updated for anonymous user + #gets immediately updated for anonymous user assert Document.lookup_table_consistent?(nil) refute AuthLookupUpdateQueue.any? @@ -164,4 +165,47 @@ def setup end end + test 'checks each type' do + p = FactoryBot.create(:person) + + with_config_value(:auth_lookup_enabled, true) do + assert AuthLookupUpdateQueue.queue_enabled? + + doc = FactoryBot.create(:document) + sample = FactoryBot.create(:sample) + sop = FactoryBot.create(:sop) + with_config_value(:auth_lookup_update_batch_size, 20) do + AuthLookupUpdateJob.perform_now + end + + assert Document.lookup_table_consistent?(p.user) + assert Sample.lookup_table_consistent?(p.user) + assert Sop.lookup_table_consistent?(p.user) + + # delete a record + Document.lookup_class.where(user_id:p.user.id,asset_id:doc.id).last.delete + Sample.lookup_class.where(user_id:p.user.id,asset_id:sample.id).last.delete + Sop.lookup_class.where(user_id:p.user.id,asset_id:sop.id).last.delete + + refute Document.lookup_table_consistent?(p.user) + refute Sample.lookup_table_consistent?(p.user) + refute Sop.lookup_table_consistent?(p.user) + + #gets immediately updated for anonymous user + assert Document.lookup_table_consistent?(nil) + assert Sample.lookup_table_consistent?(nil) + assert Sop.lookup_table_consistent?(nil) + + assert_enqueued_jobs(3) do + assert_difference('AuthLookupUpdateQueue.count',3) do + AuthLookupMaintenanceJob.perform_now + end + end + + assert AuthLookupUpdateQueue.where(item: doc).any? + assert AuthLookupUpdateQueue.where(item: sample).any? + assert AuthLookupUpdateQueue.where(item: sop).any? + end + end + end \ No newline at end of file From c7464fa52feaf03e958dcf140d7d33f160e97fc3 Mon Sep 17 00:00:00 2001 From: Stuart Owen Date: Tue, 7 May 2024 15:20:00 +0100 Subject: [PATCH 008/131] queue authupdate for user only after person_id is associated #1866 needs tests, but see what tests are affected first --- app/models/user.rb | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/app/models/user.rb b/app/models/user.rb index ed0e487e03..1f13990a0c 100644 --- a/app/models/user.rb +++ b/app/models/user.rb @@ -67,7 +67,7 @@ class User < ApplicationRecord delegate :is_admin_or_project_administrator?, to: :person, allow_nil: true delegate :is_programme_administrator?, to: :person, allow_nil: true - after_commit :queue_update_auth_table, on: :create + after_save_commit :queue_update_auth_table after_destroy :queue_auth_lookup_delete_job @@ -336,7 +336,9 @@ def email_available? end def queue_update_auth_table - AuthLookupUpdateQueue.enqueue(self) + if saved_changes.keys.include?("person_id") + AuthLookupUpdateQueue.enqueue(self) + end end def queue_auth_lookup_delete_job From 9749e094e327f1f1c36079b40be1ae2dc4d870dc Mon Sep 17 00:00:00 2001 From: Stuart Owen Date: Tue, 7 May 2024 16:09:40 +0100 Subject: [PATCH 009/131] updated to to check job is queued after registration #1866 --- app/models/user.rb | 2 +- .../permissions/auth_lookup_update_queue_test.rb | 13 ++++++++++--- 2 files changed, 11 insertions(+), 4 deletions(-) diff --git a/app/models/user.rb b/app/models/user.rb index 1f13990a0c..6d0f25e762 100644 --- a/app/models/user.rb +++ b/app/models/user.rb @@ -337,7 +337,7 @@ def email_available? def queue_update_auth_table if saved_changes.keys.include?("person_id") - AuthLookupUpdateQueue.enqueue(self) + AuthLookupUpdateQueue.enqueue(self, priority: 1) end end diff --git a/test/unit/permissions/auth_lookup_update_queue_test.rb b/test/unit/permissions/auth_lookup_update_queue_test.rb index a1cc616690..95b07d9a8c 100644 --- a/test/unit/permissions/auth_lookup_update_queue_test.rb +++ b/test/unit/permissions/auth_lookup_update_queue_test.rb @@ -161,10 +161,17 @@ def teardown end end - test 'updates when a user registers' do + test 'updates when a user registers but not until associated with a person' do + person = FactoryBot.create(:person) + user = assert_no_difference('AuthLookupUpdateQueue.count') do + FactoryBot.create(:brand_new_user) + end assert_difference('AuthLookupUpdateQueue.count', 1) do - user = FactoryBot.create(:brand_new_user) - assert_equal user, AuthLookupUpdateQueue.order(:id).last.item + user.person = person + user.save! + q = AuthLookupUpdateQueue.order(:id).last + assert_equal user, q.item + assert_equal 1, q.priority end end From 4aa490cf17c6e129322bb1295300171b1852515c Mon Sep 17 00:00:00 2001 From: Stuart Owen Date: Tue, 7 May 2024 17:35:10 +0100 Subject: [PATCH 010/131] give UserAuthLookupUpdateJob a longer timeout of 30 mins, and do in batches of 8000 #1866 --- app/jobs/user_auth_lookup_update_job.rb | 14 ++++++++++++-- 1 file changed, 12 insertions(+), 2 deletions(-) diff --git a/app/jobs/user_auth_lookup_update_job.rb b/app/jobs/user_auth_lookup_update_job.rb index 957c9320f0..d67ccf3d10 100644 --- a/app/jobs/user_auth_lookup_update_job.rb +++ b/app/jobs/user_auth_lookup_update_job.rb @@ -2,11 +2,21 @@ class UserAuthLookupUpdateJob < ApplicationJob queue_as QueueNames::AUTH_LOOKUP queue_with_priority 0 + BATCH_SIZE = 8000 - def perform(user, type) - type.constantize.includes(policy: :permissions).find_each do |item| + # needs longer, otherwise the samples can time out + def timelimit + 30.minutes + end + + def perform(user, type, offset = 0) + type.constantize.offset(offset).limit(BATCH_SIZE).includes(policy: :permissions).find_each do |item| item.update_lookup_table(user) end + + offset += BATCH_SIZE + + self.class.perform_later(user, type, offset) if offset < type.constantize.count end end From 12717cf18b20d28b1b22810f1ed9df6b0fd08232 Mon Sep 17 00:00:00 2001 From: Stuart Owen Date: Wed, 8 May 2024 10:30:55 +0100 Subject: [PATCH 011/131] also skip if person is on the queue, and added test to check for anonymous user checks #1866 --- app/jobs/auth_lookup_maintenance_job.rb | 5 +- .../jobs/auth_lookup_maintenance_job_test.rb | 55 ++++++++++++++----- 2 files changed, 43 insertions(+), 17 deletions(-) diff --git a/app/jobs/auth_lookup_maintenance_job.rb b/app/jobs/auth_lookup_maintenance_job.rb index fb9700549b..14c4d73fcd 100644 --- a/app/jobs/auth_lookup_maintenance_job.rb +++ b/app/jobs/auth_lookup_maintenance_job.rb @@ -20,8 +20,9 @@ def check_authlookup_consistency User.where.not(person_id: nil).to_a.push(nil).each do |user| - # skip if this user is queued up - next if AuthLookupUpdateQueue.where(item: user).any? + # skip if this user or person is queued up + next if user && AuthLookupUpdateQueue.where(item: user).or(AuthLookupUpdateQueue.where(item: user.person)).any? + next if type.lookup_table_consistent?(user) items_for_queue.merge(type.items_missing_from_authlookup(user)) diff --git a/test/unit/jobs/auth_lookup_maintenance_job_test.rb b/test/unit/jobs/auth_lookup_maintenance_job_test.rb index 04d4dd8023..102aa8c5e2 100644 --- a/test/unit/jobs/auth_lookup_maintenance_job_test.rb +++ b/test/unit/jobs/auth_lookup_maintenance_job_test.rb @@ -60,9 +60,6 @@ def setup refute Document.lookup_table_consistent?(p.user) refute Document.lookup_table_consistent?(p2.user) - #gets immmediately updated for anonymous user - assert Document.lookup_table_consistent?(nil) - assert_enqueued_jobs(1) do assert_difference('AuthLookupUpdateQueue.count',1) do AuthLookupMaintenanceJob.perform_now @@ -78,7 +75,32 @@ def setup end - test 'skip if user in the queue' do + test 'test for anonymous user' do + + with_config_value(:auth_lookup_enabled, true) do + assert AuthLookupUpdateQueue.queue_enabled? + + doc = FactoryBot.create(:document) + AuthLookupUpdateJob.perform_now + + assert Document.lookup_table_consistent?(nil) + + # delete a record + Document.lookup_class.where(user_id:0,asset_id:doc.id).last.delete + + refute Document.lookup_table_consistent?(nil) + + # queued after the user has been removed + assert_enqueued_jobs(1) do + assert_difference('AuthLookupUpdateQueue.count',1) do + AuthLookupMaintenanceJob.perform_now + end + end + + end + end + + test 'skip if user or person in the queue' do p = FactoryBot.create(:person) @@ -95,9 +117,6 @@ def setup refute Document.lookup_table_consistent?(p.user) - #gets immediately updated for anonymous user - assert Document.lookup_table_consistent?(nil) - refute AuthLookupUpdateQueue.any? AuthLookupUpdateQueue.create!(item: p.user) assert AuthLookupUpdateQueue.any? @@ -109,8 +128,22 @@ def setup end end + AuthLookupUpdateQueue.destroy_all + AuthLookupUpdateQueue.create!(item: p) + assert AuthLookupUpdateQueue.any? + + # nothing queued whilst person is queued + assert_no_enqueued_jobs do + assert_no_difference('AuthLookupUpdateQueue.count') do + AuthLookupMaintenanceJob.perform_now + end + end + AuthLookupUpdateQueue.destroy_all refute AuthLookupUpdateQueue.any? + #add another item to make sure it's only checking for user/person + AuthLookupUpdateQueue.create!(item: FactoryBot.create(:sop)) + assert AuthLookupUpdateQueue.any? # queued after the user has been removed assert_enqueued_jobs(1) do @@ -138,9 +171,6 @@ def setup refute Document.lookup_table_consistent?(p.user) - #gets immediately updated for anonymous user - assert Document.lookup_table_consistent?(nil) - refute AuthLookupUpdateQueue.any? AuthLookupUpdateQueue.create!(item: doc1) assert AuthLookupUpdateQueue.any? @@ -191,11 +221,6 @@ def setup refute Sample.lookup_table_consistent?(p.user) refute Sop.lookup_table_consistent?(p.user) - #gets immediately updated for anonymous user - assert Document.lookup_table_consistent?(nil) - assert Sample.lookup_table_consistent?(nil) - assert Sop.lookup_table_consistent?(nil) - assert_enqueued_jobs(3) do assert_difference('AuthLookupUpdateQueue.count',3) do AuthLookupMaintenanceJob.perform_now From 3b5731c2896f23046abcb11dd3f60d82947c2a75 Mon Sep 17 00:00:00 2001 From: Stuart Owen Date: Wed, 8 May 2024 15:25:51 +0100 Subject: [PATCH 012/131] use each instead of find_each, due to an issue when combined with offset and limit #1866 --- app/jobs/user_auth_lookup_update_job.rb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/app/jobs/user_auth_lookup_update_job.rb b/app/jobs/user_auth_lookup_update_job.rb index d67ccf3d10..6ea614771d 100644 --- a/app/jobs/user_auth_lookup_update_job.rb +++ b/app/jobs/user_auth_lookup_update_job.rb @@ -10,7 +10,7 @@ def timelimit end def perform(user, type, offset = 0) - type.constantize.offset(offset).limit(BATCH_SIZE).includes(policy: :permissions).find_each do |item| + type.constantize.offset(offset).limit(BATCH_SIZE).includes(policy: :permissions).each do |item| item.update_lookup_table(user) end From 211896f092747f9b3fd1f6df6ab8fe1d9db01fe8 Mon Sep 17 00:00:00 2001 From: Stuart Owen Date: Thu, 9 May 2024 18:39:06 +0100 Subject: [PATCH 013/131] upgrade tweaks WIP #1861 --- lib/tasks/seek_upgrades.rake | 35 ++++++++++++++++++++--------------- 1 file changed, 20 insertions(+), 15 deletions(-) diff --git a/lib/tasks/seek_upgrades.rake b/lib/tasks/seek_upgrades.rake index ebd435c9ef..44726d19b1 100644 --- a/lib/tasks/seek_upgrades.rake +++ b/lib/tasks/seek_upgrades.rake @@ -113,15 +113,17 @@ namespace :seek do disable_authorization_checks do - Sample.includes(:originating_data_file).find_each do |sample| - # check if the sample was extracted from a datafile and their policies are linked - if sample.extracted? && sample.policy_id == sample.originating_data_file&.policy_id - policy = sample.policy.deep_copy - policy.save - sample.update_column(:policy_id, policy.id) - putc('.') - affected_samples << sample + Sample.includes(:originating_data_file).in_batches(of: 250) do |batch| + batch.each do |sample| + # check if the sample was extracted from a datafile and their policies are linked + #if sample.extracted? && sample.policy_id == sample.originating_data_file&.policy_id + policy = sample.policy.deep_copy + # policy.save + # sample.update_column(:policy_id, policy.id) + affected_samples << sample + #end end + putc('.') end end puts "..... finished creating independent policies of #{affected_samples.count} extracted samples" @@ -137,18 +139,21 @@ namespace :seek do decoupled = 0 hash_array = [] disable_authorization_checks do - Sample.find_each do |sample| - # check if the sample was extracted from a datafile and their projects are linked - if sample.extracted? && sample.project_ids.empty? - sample.originating_data_file.project_ids.each do |project_id| - hash_array << { project_id: project_id, sample_id: sample.id } + Sample.includes(:originating_data_file).in_batches(of: 250) do |batch| + batch.each do |sample| + # check if the sample was extracted from a datafile and their projects are linked + if sample.extracted? && sample.project_ids.empty? + sample.originating_data_file.project_ids.each do |project_id| + hash_array << { project_id: project_id, sample_id: sample.id } + end + decoupled += 1 end - decoupled += 1 end + putc('.') end unless hash_array.empty? class ProjectsSample < ActiveRecord::Base; end; - ProjectsSample.insert_all(hash_array) + #ProjectsSample.insert_all(hash_array) end end puts " ... finished copying project ids of #{decoupled.to_s} extracted samples" From 4ebf317e870e832de7516b8422c0255fb886733d Mon Sep 17 00:00:00 2001 From: Stuart Owen Date: Mon, 13 May 2024 09:31:24 +0100 Subject: [PATCH 014/131] finished improving the upgrade tasks for updating samples #1861 show progress for decouple_extracted_samples_policies and decouple_extracted_samples_projects, after every batch of 250 also update the query for decouple_extracted_samples_projects to select those without projects, making reruns quicker --- lib/tasks/seek_upgrades.rake | 19 +++++++++---------- 1 file changed, 9 insertions(+), 10 deletions(-) diff --git a/lib/tasks/seek_upgrades.rake b/lib/tasks/seek_upgrades.rake index 44726d19b1..14ce7516bf 100644 --- a/lib/tasks/seek_upgrades.rake +++ b/lib/tasks/seek_upgrades.rake @@ -112,16 +112,15 @@ namespace :seek do Permission.skip_callback :commit, :after, :queue_rdf_generation_job disable_authorization_checks do - Sample.includes(:originating_data_file).in_batches(of: 250) do |batch| batch.each do |sample| # check if the sample was extracted from a datafile and their policies are linked - #if sample.extracted? && sample.policy_id == sample.originating_data_file&.policy_id + if sample.extracted? && sample.policy_id == sample.originating_data_file&.policy_id policy = sample.policy.deep_copy - # policy.save - # sample.update_column(:policy_id, policy.id) + policy.save + sample.update_column(:policy_id, policy.id) affected_samples << sample - #end + end end putc('.') end @@ -136,27 +135,27 @@ namespace :seek do task(decouple_extracted_samples_projects: [:environment]) do puts '..... copying project ids for extracted samples...' - decoupled = 0 + decoupled_count = 0 hash_array = [] disable_authorization_checks do - Sample.includes(:originating_data_file).in_batches(of: 250) do |batch| + Sample.includes(:originating_data_file).where.missing(:projects).in_batches(of: 250) do |batch| batch.each do |sample| # check if the sample was extracted from a datafile and their projects are linked if sample.extracted? && sample.project_ids.empty? sample.originating_data_file.project_ids.each do |project_id| hash_array << { project_id: project_id, sample_id: sample.id } end - decoupled += 1 + decoupled_count += 1 end end putc('.') end unless hash_array.empty? class ProjectsSample < ActiveRecord::Base; end; - #ProjectsSample.insert_all(hash_array) + ProjectsSample.insert_all(hash_array) end end - puts " ... finished copying project ids of #{decoupled.to_s} extracted samples" + puts " ... finished copying project ids of #{decoupled_count.to_s} extracted samples" end task(link_sample_datafile_attributes: [:environment]) do From d209fa8686ea980d5a1d8619202f30d7e00faba1 Mon Sep 17 00:00:00 2001 From: Stuart Owen Date: Mon, 13 May 2024 09:42:54 +0100 Subject: [PATCH 015/131] removed upgrade tasks from 1.14 #1861 --- lib/tasks/seek_upgrades.rake | 50 ------------------------------------ 1 file changed, 50 deletions(-) diff --git a/lib/tasks/seek_upgrades.rake b/lib/tasks/seek_upgrades.rake index 14ce7516bf..769e95aed1 100644 --- a/lib/tasks/seek_upgrades.rake +++ b/lib/tasks/seek_upgrades.rake @@ -11,9 +11,6 @@ namespace :seek do decouple_extracted_samples_policies decouple_extracted_samples_projects link_sample_datafile_attributes - strip_sample_attribute_pids - rename_registered_sample_multiple_attribute_type - remove_ontology_attribute_type db:seed:007_sample_attribute_types db:seed:001_create_controlled_vocabs db:seed:017_minimal_starter_isa_templates @@ -55,53 +52,6 @@ namespace :seek do end end - task(rename_registered_sample_multiple_attribute_type: [:environment]) do - attr = SampleAttributeType.find_by(title:'Registered Sample (multiple)') - if attr - puts "..... Renaming sample attribute type 'Registered Sample (multiple)' to 'Registered Sample List'." - attr.update_column(:title, 'Registered Sample List') - end - end - - task(strip_sample_attribute_pids: [:environment]) do - puts '..... Stripping Sample Attribute PIds ...' - n = 0 - SampleAttribute.where('pid is NOT NULL AND pid !=?','').each do |attribute| - new_pid = attribute.pid.strip - if attribute.pid != new_pid - attribute.update_column(:pid, new_pid) - n += 1 - end - end - puts "..... Finished stripping #{n} Sample Attribute PIds." - end - - task(remove_ontology_attribute_type: [:environment]) do - ontology_attr_type = SampleAttributeType.find_by(title:'Ontology') - cv_attr_type = SampleAttributeType.find_by(title:'Controlled Vocabulary') - if ontology_attr_type - puts '..... Removing the Ontology sample attribute type ...' - if cv_attr_type - if ontology_attr_type.sample_attributes.any? - puts "..... Moving #{ontology_attr_type.sample_attributes.count} sample attributes to Controlled Vocabulary" - ontology_attr_type.sample_attributes.each do |attr_type| - attr_type.update_column(:sample_attribute_type_id, cv_attr_type.id) - end - end - if ontology_attr_type.isa_template_attributes.any? - puts "..... Moving #{ontology_attr_type.isa_template_attributes.count} template attributes to Controlled Vocabulary" - ontology_attr_type.isa_template_attributes.each do |attr_type| - attr_type.update_column(:sample_attribute_type_id, cv_attr_type.id) - end - end - - ontology_attr_type.destroy - else - puts '..... Target Controlled Vocabulary attribute type not found' - end - end - end - task(decouple_extracted_samples_policies: [:environment]) do puts '..... creating independent policies for extracted samples (this can take a while if there are many samples) ...' affected_samples = [] From 8ab176c531e227317c27a66fa4258f4adce43cb5 Mon Sep 17 00:00:00 2001 From: Stuart Owen Date: Mon, 13 May 2024 10:14:22 +0100 Subject: [PATCH 016/131] don't queue reindexing items or jobs, or create follow on jobs, if solr_enabled is false #1874 --- app/jobs/reindexing_job.rb | 2 +- app/models/reindexing_queue.rb | 6 ++++++ test/unit/jobs/reindexing_job_test.rb | 24 ++++++++++++++++++++++++ 3 files changed, 31 insertions(+), 1 deletion(-) diff --git a/app/jobs/reindexing_job.rb b/app/jobs/reindexing_job.rb index ff45e69e65..a19281775e 100644 --- a/app/jobs/reindexing_job.rb +++ b/app/jobs/reindexing_job.rb @@ -25,7 +25,7 @@ def gather_items end def follow_on_job? - ReindexingQueue.any? + Seek::Config.solr_enabled && ReindexingQueue.any? end def timelimit diff --git a/app/models/reindexing_queue.rb b/app/models/reindexing_queue.rb index e01186c0cd..40a988713c 100644 --- a/app/models/reindexing_queue.rb +++ b/app/models/reindexing_queue.rb @@ -1,7 +1,13 @@ class ReindexingQueue < ApplicationRecord include ResourceQueue + def self.enqueue(*items, priority: DEFAULT_PRIORITY, queue_job: true) + return unless Seek::Config.solr_enabled + super(items, priority: priority, queue_job: queue_job) + end + def self.job_class ReindexingJob end + end diff --git a/test/unit/jobs/reindexing_job_test.rb b/test/unit/jobs/reindexing_job_test.rb index 7bc3f20324..78e8804b89 100644 --- a/test/unit/jobs/reindexing_job_test.rb +++ b/test/unit/jobs/reindexing_job_test.rb @@ -27,6 +27,20 @@ class ReindexingJobTest < ActiveSupport::TestCase end end + test 'dont add items if search disabled' do + p = FactoryBot.create :person + ReindexingQueue.delete_all + + with_config_value(:solr_enabled, false) do + assert_no_enqueued_jobs(only: ReindexingJob) do + assert_no_difference('ReindexingQueue.count') do + ReindexingQueue.enqueue(p) + ReindexingQueue.enqueue(FactoryBot.create(:sop)) + end + end + end + end + test 'gather_items strips deleted (nil) items' do model1 = FactoryBot.create(:model) model2 = FactoryBot.create(:model) @@ -44,4 +58,14 @@ class ReindexingJobTest < ActiveSupport::TestCase assert_includes items, model2 assert_includes items, document end + + test 'follow on job' do + ReindexingQueue.delete_all + refute ReindexingJob.new.follow_on_job? + ReindexingQueue.enqueue(FactoryBot.create(:sop)) + assert ReindexingJob.new.follow_on_job? + with_config_value(:solr_enabled, false) do + refute ReindexingJob.new.follow_on_job? + end + end end From 0717937150a0b4518b5cfbc73e4177f9c9b1f682 Mon Sep 17 00:00:00 2001 From: Kevin De Pelseneer Date: Wed, 15 May 2024 09:14:59 +0200 Subject: [PATCH 017/131] internationalize the names in the search types --- app/helpers/search_helper.rb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/app/helpers/search_helper.rb b/app/helpers/search_helper.rb index 1960662ebf..39824e8ed8 100644 --- a/app/helpers/search_helper.rb +++ b/app/helpers/search_helper.rb @@ -3,7 +3,7 @@ module SearchHelper def search_type_options - [['All', '']] | Seek::Util.searchable_types.collect { |c| [(c.name.underscore.humanize == 'Sop' ? t('sop') : c.name.underscore.humanize.pluralize), c.name.underscore.pluralize] } + [['All', '']] | Seek::Util.searchable_types.collect { |c| [(c.name.underscore.humanize == 'Sop' ? t('sop') : t(c.name.underscore).humanize.pluralize), c.name.underscore.pluralize] } end def external_search_tooltip_text From bb7e941400c6c7fbdc1ec88ae7c568728ad6c0e3 Mon Sep 17 00:00:00 2001 From: Kevin De Pelseneer Date: Wed, 15 May 2024 13:59:54 +0200 Subject: [PATCH 018/131] Add test --- test/functional/homes_controller_test.rb | 45 ++++++++++++++++++++++++ 1 file changed, 45 insertions(+) diff --git a/test/functional/homes_controller_test.rb b/test/functional/homes_controller_test.rb index 51a9d86bc2..0c3ca05d19 100644 --- a/test/functional/homes_controller_test.rb +++ b/test/functional/homes_controller_test.rb @@ -726,6 +726,51 @@ class HomesControllerTest < ActionController::TestCase end + test 'Show aliases in search options' do + I18n.load_path += Dir[Rails.root.join('test', 'config', 'translation_override.en.yml')] + I18n.backend.load_translations + with_config_values({ isa_json_compliance_enabled: true, solr_enabled: true }) do + get :index + assert_response :success + assert_select 'select#search_type' do + assert_select 'option', text: 'Investigation tests', count: 1 + assert_select 'option', text: 'Study tests', count: 1 + assert_select 'option', text: 'Assay tests', count: 1 + assert_select 'option', text: 'Data file tests', count: 1 + assert_select 'option', text: 'Document tests', count: 1 + assert_select 'option', text: 'SOP_test', count: 1 # this is an exception, the alias is not in the translation file + assert_select 'option', text: 'Presentation tests', count: 1 + assert_select 'option', text: 'Event tests', count: 1 + assert_select 'option', text: 'Collection tests', count: 1 + assert_select 'option', text: 'Sample tests', count: 1 + assert_select 'option', text: 'Sample type tests', count: 1 + assert_select 'option', text: 'Template tests', count: 1 + assert_select 'option', text: 'Person tests', count: 1 + assert_select 'option', text: 'Project tests', count: 1 + assert_select 'option', text: 'Institution tests', count: 1 + assert_select 'option', text: 'Programme tests', count: 1 + + # Making sure the default values are not shown + assert_select 'option', text: 'Investigations', count: 0 + assert_select 'option', text: 'Studies', count: 0 + assert_select 'option', text: 'Assays', count: 0 + assert_select 'option', text: 'Data files', count: 0 + assert_select 'option', text: 'Documents', count: 0 + assert_select 'option', text: 'SOP', count: 0 + assert_select 'option', text: 'Presentations', count: 0 + assert_select 'option', text: 'Events', count: 0 + assert_select 'option', text: 'Collections', count: 0 + assert_select 'option', text: 'Samples', count: 0 + assert_select 'option', text: 'Sample types', count: 0 + assert_select 'option', text: 'Templates', count: 0 + assert_select 'option', text: 'People', count: 0 + assert_select 'option', text: 'Projects', count: 0 + assert_select 'option', text: 'Institutions', count: 0 + assert_select 'option', text: 'Programmes', count: 0 + end + end + end + test 'get dataset jsonld from index' do get :index, format: :jsonld assert_response :success From 45f779b2e8dfef5c357c8276096626ecb55acc7c Mon Sep 17 00:00:00 2001 From: Kevin De Pelseneer Date: Wed, 15 May 2024 14:38:09 +0200 Subject: [PATCH 019/131] Restore the internalisation settings afterwards --- test/functional/homes_controller_test.rb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/test/functional/homes_controller_test.rb b/test/functional/homes_controller_test.rb index 0c3ca05d19..a8bbc1c54f 100644 --- a/test/functional/homes_controller_test.rb +++ b/test/functional/homes_controller_test.rb @@ -727,6 +727,7 @@ class HomesControllerTest < ActionController::TestCase end test 'Show aliases in search options' do + original_load_path = I18n.load_path I18n.load_path += Dir[Rails.root.join('test', 'config', 'translation_override.en.yml')] I18n.backend.load_translations with_config_values({ isa_json_compliance_enabled: true, solr_enabled: true }) do @@ -769,6 +770,8 @@ class HomesControllerTest < ActionController::TestCase assert_select 'option', text: 'Programmes', count: 0 end end + I18n.load_path = original_load_path + I18n.backend.load_translations end test 'get dataset jsonld from index' do From e0d7cc5f26a4cd6e433f561a252a78b5eae23761 Mon Sep 17 00:00:00 2001 From: Kevin De Pelseneer <82407142+kdp-cloud@users.noreply.github.com> Date: Wed, 15 May 2024 15:12:31 +0200 Subject: [PATCH 020/131] Issue 1783 fix add new button (#1872) * Add to the config --- lib/seek/config.rb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/lib/seek/config.rb b/lib/seek/config.rb index 2f6df9fe27..a363d1986e 100644 --- a/lib/seek/config.rb +++ b/lib/seek/config.rb @@ -336,6 +336,10 @@ def templates_enabled isa_json_compliance_enabled end + def strains_enabled + organisms_enabled + end + def omniauth_elixir_aai_config if omniauth_elixir_aai_legacy_mode { From 51653bba80a0defca805da302c004f825529f580 Mon Sep 17 00:00:00 2001 From: Kevin De Pelseneer Date: Thu, 16 May 2024 09:28:42 +0200 Subject: [PATCH 021/131] Rewrite can_create? function in more clear way. --- app/models/template.rb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/app/models/template.rb b/app/models/template.rb index de1beeaf88..12131d9518 100644 --- a/app/models/template.rb +++ b/app/models/template.rb @@ -24,8 +24,7 @@ def can_edit?(user = User.current_user) end def self.can_create? - can = User.logged_in_and_member? && Seek::Config.samples_enabled - can && User.current_user.is_admin_or_project_administrator? + super && Seek::Config.samples_enabled && User.current_user.is_admin_or_project_administrator? end def resolve_inconsistencies From c3c0485e159b5289b61e7e64e19059ec3e3cef2a Mon Sep 17 00:00:00 2001 From: Kevin De Pelseneer Date: Thu, 16 May 2024 09:37:53 +0200 Subject: [PATCH 022/131] Filter out administered projects in a very very messy way --- app/views/projects/_project_selector.html.erb | 15 ++++++++++++--- app/views/templates/_form.html.erb | 4 ++-- 2 files changed, 14 insertions(+), 5 deletions(-) diff --git a/app/views/projects/_project_selector.html.erb b/app/views/projects/_project_selector.html.erb index 5d12d5efd5..ea7340f819 100644 --- a/app/views/projects/_project_selector.html.erb +++ b/app/views/projects/_project_selector.html.erb @@ -6,6 +6,7 @@ <% allow_nil ||= false allow_all ||= false + allow_only_administered ||= false resource ||= nil selected_projects = resource ? resource.projects : [] @@ -13,10 +14,18 @@ possible_projects = Project.all else possible_projects = [] - possible_projects |= User.current_user.person.current_projects if resource - possible_projects |= resource.projects - possible_projects |= resource.contributor.current_projects if resource.respond_to?(:contributor) && resource.contributor + if resource.respond_to?(:contributor) && resource.contributor + if allow_only_administered + possible_projects |= resource.contributor.current_projects.select{ |p| @current_user.person.is_project_administrator? p } + else + possible_projects |= resource.contributor.current_projects + end + else + possible_projects |= resource.projects + end + else + possible_projects |= @current_user.person.current_projects end end diff --git a/app/views/templates/_form.html.erb b/app/views/templates/_form.html.erb index d7acd30e54..bc3720dc59 100644 --- a/app/views/templates/_form.html.erb +++ b/app/views/templates/_form.html.erb @@ -15,7 +15,7 @@ <%= f.text_area :description, class: "form-control rich-text-edit", rows: 5, id: "template-description" -%> - <%= render partial: "projects/project_selector", locals: { resource: @template } -%> + <%= render partial: "projects/project_selector", locals: { resource: @template, allow_only_administered: true } -%> <%= render partial: 'assets/manage_specific_attributes', locals:{f:f} if show_form_manage_specific_attributes? %> @@ -85,7 +85,7 @@ <% if @template.children.none? %> - <%= button_link_to('Add new attribute', 'add', '#', id: 'add-attribute') %> + <%= button_link_to('Add new attribute', 'add', '#', id: 'add-attribute') if @template.level %> <% end %> From 42e5890434b501acff148c4322a38a0f304d0cdf Mon Sep 17 00:00:00 2001 From: Kevin De Pelseneer Date: Thu, 16 May 2024 11:12:06 +0200 Subject: [PATCH 023/131] Make current_person available as helper method and simplify logic. --- app/controllers/application_controller.rb | 1 + app/views/projects/_project_selector.html.erb | 15 ++++----------- 2 files changed, 5 insertions(+), 11 deletions(-) diff --git a/app/controllers/application_controller.rb b/app/controllers/application_controller.rb index 6d98f1920e..b5da0a292c 100644 --- a/app/controllers/application_controller.rb +++ b/app/controllers/application_controller.rb @@ -54,6 +54,7 @@ def with_current_user def current_person current_user.try(:person) end + helper_method :current_person def partially_registered? redirect_to register_people_path if current_user && !current_user.registration_complete? diff --git a/app/views/projects/_project_selector.html.erb b/app/views/projects/_project_selector.html.erb index ea7340f819..27a1ae2efc 100644 --- a/app/views/projects/_project_selector.html.erb +++ b/app/views/projects/_project_selector.html.erb @@ -14,21 +14,14 @@ possible_projects = Project.all else possible_projects = [] + possible_projects |= current_person.current_projects if resource - if resource.respond_to?(:contributor) && resource.contributor - if allow_only_administered - possible_projects |= resource.contributor.current_projects.select{ |p| @current_user.person.is_project_administrator? p } - else - possible_projects |= resource.contributor.current_projects - end - else - possible_projects |= resource.projects - end - else - possible_projects |= @current_user.person.current_projects + possible_projects |= resource.projects + possible_projects |= resource.contributor.current_projects if resource.respond_to?(:contributor) && resource.contributor end end + possible_projects = possible_projects.select { |p| current_person.is_project_administrator? p } if allow_only_administered possible_projects = possible_projects - selected_projects possible_projects_json, selected_projects_json = [possible_projects, selected_projects].map do |projects| From a768918fb029ba6f47093fc5f79d00dd0546d08e Mon Sep 17 00:00:00 2001 From: Kevin De Pelseneer Date: Thu, 16 May 2024 12:01:19 +0200 Subject: [PATCH 024/131] Hide 'Add new attribute button' when it's a new form and shows the button when an existing template is shown. --- app/assets/javascripts/templates.js | 5 ++++- app/views/templates/_form.html.erb | 16 ++++++++-------- 2 files changed, 12 insertions(+), 9 deletions(-) diff --git a/app/assets/javascripts/templates.js b/app/assets/javascripts/templates.js index 4b0c733526..e1430fc40d 100644 --- a/app/assets/javascripts/templates.js +++ b/app/assets/javascripts/templates.js @@ -293,9 +293,12 @@ const applyTemplate = () => { const template_id_tag = $j(`#isa_study${suffix}template_parent_id`); if (template_id_tag) $j(template_id_tag).val(id); + // Removes the hidden from the new attribute button + $j(`${attribute_table} ${addAttributeRow}`).find('#add-attribute').removeClass("hidden"); + SampleTypes.recalculatePositions(); SampleTypes.bindSortable(); - $j(".sample-type-attribute-type").trigger("change", [false]); + $j(".sample-type-attribute-type").trigger("change", [false]); }; // Shows the modal form diff --git a/app/views/templates/_form.html.erb b/app/views/templates/_form.html.erb index bc3720dc59..82d74be6c4 100644 --- a/app/views/templates/_form.html.erb +++ b/app/views/templates/_form.html.erb @@ -27,12 +27,6 @@

Template Information

- <% if @template.new_record? %> -
- -
- <% end %> -
<%= f.label :level, 'ISA Level' %> <%= f.text_field :level, { class: 'form-control', readonly: true } %> @@ -61,7 +55,13 @@ To ensure compliance with the original template, please do not modify the existing ISA-tags and attributes in the form below. You can always add new attributes.
- + <% if @template.new_record? %> +
+ +
+ <% end %> + +
@@ -85,7 +85,7 @@ <% if @template.children.none? %> <% end %> From 7f6f50bd84026ca40d1696098bb9b81017b46990 Mon Sep 17 00:00:00 2001 From: Stuart Owen Date: Thu, 16 May 2024 11:56:22 +0100 Subject: [PATCH 025/131] update version numbers for 1.15.0 --- config/version.yml | 2 +- docker-compose-relative-root.yml | 4 ++-- docker-compose-virtuoso.yml | 4 ++-- docker-compose-with-email.yml | 4 ++-- docker-compose.yml | 4 ++-- 5 files changed, 9 insertions(+), 9 deletions(-) diff --git a/config/version.yml b/config/version.yml index 9fe2f4b4c9..4b76db861f 100644 --- a/config/version.yml +++ b/config/version.yml @@ -9,4 +9,4 @@ major: 1 minor: 15 -patch: 0-pre +patch: 0 diff --git a/docker-compose-relative-root.yml b/docker-compose-relative-root.yml index c9f214cbbf..7576847289 100644 --- a/docker-compose-relative-root.yml +++ b/docker-compose-relative-root.yml @@ -14,7 +14,7 @@ services: seek: # The SEEK application #build: . - image: fairdom/seek:main + image: fairdom/seek:1.15 container_name: seek command: docker/entrypoint.sh @@ -43,7 +43,7 @@ services: seek_workers: # The SEEK delayed job workers #build: . - image: fairdom/seek:main + image: fairdom/seek:1.15 container_name: seek-workers command: docker/start_workers.sh restart: always diff --git a/docker-compose-virtuoso.yml b/docker-compose-virtuoso.yml index 626485b5a5..8a3d78f05c 100644 --- a/docker-compose-virtuoso.yml +++ b/docker-compose-virtuoso.yml @@ -12,7 +12,7 @@ services: seek: # The SEEK application #build: . - image: fairdom/seek:main + image: fairdom/seek:1.15 container_name: seek command: docker/entrypoint.sh restart: always @@ -39,7 +39,7 @@ services: seek_workers: # The SEEK delayed job workers #build: . - image: fairdom/seek:main + image: fairdom/seek:1.15 container_name: seek-workers command: docker/start_workers.sh restart: always diff --git a/docker-compose-with-email.yml b/docker-compose-with-email.yml index 19beb35095..51685ce1d0 100644 --- a/docker-compose-with-email.yml +++ b/docker-compose-with-email.yml @@ -14,7 +14,7 @@ services: seek: # The SEEK application #build: . - image: fairdom/seek:main + image: fairdom/seek:1.15 container_name: seek command: docker/entrypoint.sh @@ -43,7 +43,7 @@ services: seek_workers: # The SEEK delayed job workers #build: . - image: fairdom/seek:main + image: fairdom/seek:1.15 container_name: seek-workers command: docker/start_workers.sh restart: always diff --git a/docker-compose.yml b/docker-compose.yml index e7dec9dd7e..c9dd6960b2 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -14,7 +14,7 @@ services: seek: # The SEEK application #build: . - image: fairdom/seek:1.15-dev + image: fairdom/seek:1.15 container_name: seek command: docker/entrypoint.sh @@ -42,7 +42,7 @@ services: seek_workers: # The SEEK delayed job workers #build: . - image: fairdom/seek:1.15-dev + image: fairdom/seek:1.15 container_name: seek-workers command: docker/start_workers.sh restart: always From b6bf4bbc752e24004c2a24a31692b6ed11106c85 Mon Sep 17 00:00:00 2001 From: Kevin De Pelseneer Date: Thu, 16 May 2024 13:15:25 +0200 Subject: [PATCH 026/131] Only lock attribute fields when template is applied on a sample type --- app/assets/javascripts/templates.js | 20 +++++++++++--------- 1 file changed, 11 insertions(+), 9 deletions(-) diff --git a/app/assets/javascripts/templates.js b/app/assets/javascripts/templates.js index e1430fc40d..a37cbe5e37 100644 --- a/app/assets/javascripts/templates.js +++ b/app/assets/javascripts/templates.js @@ -222,6 +222,7 @@ const applyTemplate = () => { $j('#template_level').val(data.level); $j('#template_parent_id').val(data.template_id); + const appliedToSampleType = $j('#template_level')[0] === undefined || $j('#template_level')[0] === null; // Make sure default sorted attributes are added to the table Templates.table.order([9, "asc"]).draw(); $j.each(Templates.table.rows().data(), (i, row) => { @@ -239,24 +240,25 @@ const applyTemplate = () => { row[7] === "Registered Sample List" && row[1].includes("Input") && row[11] === null; - const isInherited = row[14] !== "undefined" || row[14] !== null; const isRequired = row[0] ? "checked" : ""; newRow = $j(newRow.replace(/replace-me/g, index)); $j(newRow).find('[data-attr="required"]').prop("checked", row[0]); + if (appliedToSampleType) $j(newRow).find('[data-attr="required"]').prop("disabled", true); + $j(newRow).find(".sample-type-is-title").prop("checked", row[8]); + if (appliedToSampleType) $j(newRow).find('.sample-type-is-title').prop("disabled", true); $j(newRow).find('[data-attr="title"]').val(row[1]); - $j(newRow).find('[data-attr="title"]').addClass("disabled"); + if (appliedToSampleType) $j(newRow).find('[data-attr="title"]').addClass("disabled"); $j(newRow).find('[data-attr="description"]').val(row[2]); $j(newRow).find('[data-attr="type"]').val(row[3]); - $j(newRow).find('[data-attr="type"]').addClass("disabled"); + if (appliedToSampleType) $j(newRow).find('[data-attr="type"]').addClass("disabled"); $j(newRow).find('[data-attr="cv_id"]').val(row[4]); - $j(newRow).find('[data-attr="cv_id"]').parent().addClass("disabled"); + if (appliedToSampleType) $j(newRow).find('[data-attr="cv_id"]').parent().addClass("disabled"); $j(newRow).find('[data-attr="allow_cv_free_text"]').prop("checked", row[5]); - $j(newRow) - .find('[data-attr="allow_cv_free_text"]') - .addClass("disabled"); + if (appliedToSampleType) $j(newRow) + .find('[data-attr="allow_cv_free_text"]') + .addClass("disabled"); $j(newRow).find('[data-attr="unit"]').val(row[6]); - $j(newRow).find('[data-attr="unit"]').addClass("disabled"); - $j(newRow).find(".sample-type-is-title").prop("checked", row[8]); + if (appliedToSampleType) $j(newRow).find('[data-attr="unit"]').addClass("disabled"); $j(newRow).find('[data-attr="pid"]').val(row[9]); $j(newRow).find('[data-attr="isa_tag_id"]').val(row[11]); $j(newRow).find('[data-attr="isa_tag_title"]').val(row[11]); From 2a439007a322a15b6443fdc85c54e7440fd6229c Mon Sep 17 00:00:00 2001 From: Kevin De Pelseneer Date: Thu, 16 May 2024 13:40:33 +0200 Subject: [PATCH 027/131] Make sure template attributes can be removed, even when inherrited and/or mandatory --- app/assets/javascripts/templates.js | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/app/assets/javascripts/templates.js b/app/assets/javascripts/templates.js index a37cbe5e37..41d064d115 100644 --- a/app/assets/javascripts/templates.js +++ b/app/assets/javascripts/templates.js @@ -267,7 +267,10 @@ const applyTemplate = () => { .addClass("disabled"); $j(newRow).find('[data-attr="template_attribute_id"]').val(row[14]); // In case of a sample type $j(newRow).find('[data-attr="parent_attribute_id"]').val(row[14]); // In case of a template - if (isRequired) { + + // Hide the remove button if the attribute is required and it is applied to a sample type. + // Template attributes should always be removeable + if (isRequired && appliedToSampleType) { $j(newRow).find('label.btn.btn-danger').addClass("hidden"); } From 8b327a7b9fc32f94707830dd8b3dfd4ab738348d Mon Sep 17 00:00:00 2001 From: Kevin De Pelseneer Date: Thu, 16 May 2024 14:12:26 +0200 Subject: [PATCH 028/131] Add tests for the `Add new attribute` button --- test/functional/templates_controller_test.rb | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/test/functional/templates_controller_test.rb b/test/functional/templates_controller_test.rb index 753d43a28c..7e512e6301 100644 --- a/test/functional/templates_controller_test.rb +++ b/test/functional/templates_controller_test.rb @@ -623,6 +623,19 @@ class TemplatesControllerTest < ActionController::TestCase end end + test 'Should not see add new attribute button at template creation time' do + get :new + assert_response :success + assert_select 'a#add-attribute.hidden', text: /Add new attribute/, count: 1 + end + + test 'Should see add new attribute button at template edit time' do + my_template = FactoryBot.create(:isa_source_template, project_ids: @project_ids, contributor: @person) + get :edit, params: { id: my_template.id } + assert_response :success + assert_select 'a#add-attribute.hidden', text: /Add new attribute/, count: 0 + end + def create_template_from_parent_template(parent_template, person= @person, linked_sample_type= nil) child_template_attributes = parent_template.template_attributes.map do |ta| FactoryBot.create(:template_attribute, parent_attribute_id: ta.id, title: ta.title, isa_tag_id: ta.isa_tag_id, sample_attribute_type: ta.sample_attribute_type, is_title: ta.is_title, required: ta.required, sample_controlled_vocab: ta.sample_controlled_vocab, pos: ta.pos) From 0055e6f3ae8535f0a7d4e0a0d31a0cbc4ace1178 Mon Sep 17 00:00:00 2001 From: AndrewWood94 Date: Tue, 21 May 2024 15:53:42 +0100 Subject: [PATCH 029/131] Add authorised_assay_assets function to data_files_helper --- app/helpers/data_files_helper.rb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/app/helpers/data_files_helper.rb b/app/helpers/data_files_helper.rb index 67d9d12f46..917fe91da2 100644 --- a/app/helpers/data_files_helper.rb +++ b/app/helpers/data_files_helper.rb @@ -3,6 +3,10 @@ def authorised_data_files(projects = nil) authorised_assets(DataFile, projects) end + def authorised_assay_assets(data_file) + data_file.assay_assets.where(assay_id: authorised_assays.collect(&:id)) + end + def split_into_two(ahash = {}) return [{}, {}] if ahash.nil? return [ahash, {}] if ahash.length < 2 From a367ba69fe4f87665f6775da8339e684c1b89201 Mon Sep 17 00:00:00 2001 From: AndrewWood94 Date: Tue, 21 May 2024 15:55:49 +0100 Subject: [PATCH 030/131] Only show authorised assays when extracting samples --- app/views/data_files/confirm_extraction.html.erb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/app/views/data_files/confirm_extraction.html.erb b/app/views/data_files/confirm_extraction.html.erb index c163b63d65..66bc8d2084 100644 --- a/app/views/data_files/confirm_extraction.html.erb +++ b/app/views/data_files/confirm_extraction.html.erb @@ -56,11 +56,11 @@ <%= hidden_field_tag(:sample_type_id, @sample_type.id) if @sample_type %> <%= hidden_field_tag(:confirm, 'true') %> - <% if @data_file.assay_assets.any? %> + <% if authorised_assays.intersect?(@data_file.assays) %>

Link to assays

This data file is linked to the following assays. Check the corresponding checkbox to also link the above samples to that assay. - <% @data_file.assay_assets.each do |aa| %> + <% authorised_assay_assets(@data_file).each do |aa| %>
- + From e1505f1d093098ab8669f631aa0bedc7368fe9bf Mon Sep 17 00:00:00 2001 From: Kevin De Pelseneer Date: Mon, 27 May 2024 18:48:08 +0200 Subject: [PATCH 052/131] Revert last two commits --- app/models/sample_controlled_vocab_term.rb | 2 +- app/views/sample_controlled_vocabs/_term_form_row.html.erb | 5 +---- .../_term_form_row_disabled.html.erb | 1 - 3 files changed, 2 insertions(+), 6 deletions(-) diff --git a/app/models/sample_controlled_vocab_term.rb b/app/models/sample_controlled_vocab_term.rb index 092c85a9a5..4f1791e66f 100644 --- a/app/models/sample_controlled_vocab_term.rb +++ b/app/models/sample_controlled_vocab_term.rb @@ -1,7 +1,7 @@ class SampleControlledVocabTerm < ApplicationRecord belongs_to :sample_controlled_vocab, inverse_of: :sample_controlled_vocab_terms - validates :label, presence: true, length: { maximum: 500 }, uniqueness: { scope: :sample_controlled_vocab_id } + validates :label, presence: true, length: { maximum: 500 } before_validation :truncate_label diff --git a/app/views/sample_controlled_vocabs/_term_form_row.html.erb b/app/views/sample_controlled_vocabs/_term_form_row.html.erb index ffb2edf3b5..aa600c85a7 100644 --- a/app/views/sample_controlled_vocabs/_term_form_row.html.erb +++ b/app/views/sample_controlled_vocabs/_term_form_row.html.erb @@ -1,8 +1,5 @@ - + From 57819ece160249d9c21d1a389032275a2ed3bcf1 Mon Sep 17 00:00:00 2001 From: Kevin De Pelseneer Date: Wed, 29 May 2024 15:58:36 +0200 Subject: [PATCH 053/131] Revert changes --- app/helpers/bootstrap_helper.rb | 13 +++------- .../sharing/_group_permission_modal.html.erb | 14 ++--------- .../sharing/_person_permission_modal.html.erb | 24 ++++--------------- .../_programme_permission_modal.html.erb | 22 ++++------------- 4 files changed, 14 insertions(+), 59 deletions(-) diff --git a/app/helpers/bootstrap_helper.rb b/app/helpers/bootstrap_helper.rb index f222431a61..0ee54d45d2 100644 --- a/app/helpers/bootstrap_helper.rb +++ b/app/helpers/bootstrap_helper.rb @@ -161,17 +161,10 @@ def modal(options = {}, &block) end end - def modal_header(title, options = {}) - # If no_close_btn is set to true, the modal will not have a close button. - # Useful for multiple shown modals. - no_close_btn = options[:no_close_btn] if options[:no_close_btn] + def modal_header(title, _options = {}) content_tag(:div, class: 'modal-header') do - if no_close_btn - ''.html_safe - else - content_tag(:button, class: 'close', 'data-dismiss' => 'modal', 'aria-label' => 'Close' ) do - content_tag(:span, '×'.html_safe, 'aria-hidden' => 'true') - end + content_tag(:button, class: 'close', 'data-dismiss' => 'modal', 'aria-label' => 'Close') do + content_tag(:span, '×'.html_safe, 'aria-hidden' => 'true') end + content_tag(:h4, title, class: 'modal-title') end diff --git a/app/views/sharing/_group_permission_modal.html.erb b/app/views/sharing/_group_permission_modal.html.erb index 901d42de98..e31c09fb6f 100644 --- a/app/views/sharing/_group_permission_modal.html.erb +++ b/app/views/sharing/_group_permission_modal.html.erb @@ -1,7 +1,7 @@ <%= button_link_to("Share with a #{t('project')} / #{t('institution')}", 'add', '#', id: 'add-project-permission-button') %> <%= modal(id: 'add-project-permission-modal', size: 'm') do %> - <%= modal_header("Share with a #{t('project')} and/or #{t('institution')}", { no_close_btn: true }) %> + <%= modal_header("Share with a #{t('project')} and/or #{t('institution')}") %> <%= modal_body do %>
@@ -32,9 +32,7 @@
<% end %> <%= modal_footer do %> - <%= link_to('Add', '#', id: 'permission-project-confirm', class: 'btn btn-primary') %> - or - <%= link_to('Cancel', '#', id: 'cancel-project-selection', class: 'btn btn-default') %> + <%= link_to('Add', '#', id: 'permission-project-confirm', class: 'btn btn-primary pull-right', 'data-dismiss' => 'modal') %> <% end %> <% end %> @@ -79,17 +77,9 @@ } } - // Close this modal after clicking add button - $j('#add-project-permission-modal').modal('hide'); - Sharing.addPermission(permission); }); - // Close modal when cancel button is clicked - $j('#cancel-project-selection').click(function () { - $j('#add-project-permission-modal').modal('hide'); - }); - // Update the institution list when a project is selected $j('#permission-project-id').change(function () { var institutionSelect = $j('#permission-institution-id'); diff --git a/app/views/sharing/_person_permission_modal.html.erb b/app/views/sharing/_person_permission_modal.html.erb index b26b88c8dc..f10f4bf61a 100644 --- a/app/views/sharing/_person_permission_modal.html.erb +++ b/app/views/sharing/_person_permission_modal.html.erb @@ -1,7 +1,7 @@ <%= button_link_to("Share with a #{t('person')}", 'add', '#', id: 'add-person-permission-button') %> <%= modal(id: 'add-person-permission-modal', size: 'm') do %> - <%= modal_header("Share with #{t('person').pluralize}", { no_close_btn: true }) %> + <%= modal_header("Share with #{t('person').pluralize}") %> <%= modal_body do %>
@@ -18,18 +18,11 @@
<% end %> <%= modal_footer do %> - <%= link_to('Add', '#', id: 'permission-people-confirm', class: 'btn btn-primary') %> - or - <%= link_to('Cancel', '#', id: 'cancel-people-permission-selection', class: 'btn btn-default') %> + <%= link_to('Add', '#', id: 'permission-people-confirm', class: 'btn btn-primary pull-right', 'data-dismiss' => 'modal') %> <% end %> <% end %> diff --git a/app/views/sharing/_programme_permission_modal.html.erb b/app/views/sharing/_programme_permission_modal.html.erb index 994d35a336..94eb5e97e0 100644 --- a/app/views/sharing/_programme_permission_modal.html.erb +++ b/app/views/sharing/_programme_permission_modal.html.erb @@ -1,7 +1,7 @@ <%= button_link_to("Share with a #{t('programme')}", 'add', '#', id: 'add-programme-permission-button') %> <%= modal(id: 'add-programme-permission-modal', size: 'm') do %> - <%= modal_header("Share with #{t('programme').pluralize}", { no_close_btn: true }) %> + <%= modal_header("Share with #{t('programme').pluralize}") %> <%= modal_body do %>
@@ -18,18 +18,11 @@
<% end %> <%= modal_footer do %> - <%= link_to('Add', '#', id: 'permission-programmes-confirm', class: 'btn btn-primary') %> - or - <%= link_to('Cancel', '#', id: 'cancel-programme-permission-selection', class: 'btn btn-default') %> + <%= link_to('Add', '#', id: 'permission-programmes-confirm', class: 'btn btn-primary pull-right', 'data-dismiss' => 'modal') %> <% end %> <% end %> From 668852c41faa548058828914a5db75b4deec8c23 Mon Sep 17 00:00:00 2001 From: Kevin De Pelseneer Date: Wed, 29 May 2024 16:23:23 +0200 Subject: [PATCH 054/131] Add function to stop the propagation of the data-dismiss of the inner modals --- .../single_pages/sample_sharing_bulk_change_preview.html.erb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/app/views/single_pages/sample_sharing_bulk_change_preview.html.erb b/app/views/single_pages/sample_sharing_bulk_change_preview.html.erb index c0f86b7e72..75ef3baced 100644 --- a/app/views/single_pages/sample_sharing_bulk_change_preview.html.erb +++ b/app/views/single_pages/sample_sharing_bulk_change_preview.html.erb @@ -73,4 +73,7 @@ }); } + $j('#add-person-permission-modal').on('click', '[data-dismiss="modal"]', function(e){e.stopPropagation();}); + $j('#add-project-permission-modal').on('click', '[data-dismiss="modal"]', function(e){e.stopPropagation();}); + $j('#add-programme-permission-modal').on('click', '[data-dismiss="modal"]', function(e){e.stopPropagation();}); \ No newline at end of file From fdffeb9c2ff1a9145ab204b1b5ce37e8bdc2f6df Mon Sep 17 00:00:00 2001 From: Kevin De Pelseneer Date: Wed, 29 May 2024 16:32:08 +0200 Subject: [PATCH 055/131] Add static backdrop to the batch permissions modal --- app/views/isa_studies/_buttons.html.erb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/app/views/isa_studies/_buttons.html.erb b/app/views/isa_studies/_buttons.html.erb index 47466814c3..55d68466fb 100644 --- a/app/views/isa_studies/_buttons.html.erb +++ b/app/views/isa_studies/_buttons.html.erb @@ -48,7 +48,7 @@ uploadExcel||="studySampleUploadExcel()" if (res?.status == "unprocessable_entity"){ alert(res?.error) } else { - $j('#change-batch-permission-modal').modal('show').focus(); + $j('#change-batch-permission-modal').modal({backdrop: 'static', keyboard: false}).focus(); $j('#change-batch-permission').html(res); ObjectsInput.init(); } From 12935e0c93306b92daa3eba3a25469d74416dd65 Mon Sep 17 00:00:00 2001 From: Kevin De Pelseneer Date: Wed, 29 May 2024 16:49:15 +0200 Subject: [PATCH 056/131] Group all helper methods together --- app/controllers/application_controller.rb | 35 +++++++++++------------ 1 file changed, 17 insertions(+), 18 deletions(-) diff --git a/app/controllers/application_controller.rb b/app/controllers/application_controller.rb index b5da0a292c..6e2bc08abc 100644 --- a/app/controllers/application_controller.rb +++ b/app/controllers/application_controller.rb @@ -42,6 +42,8 @@ class ApplicationController < ActionController::Base include FairSignposting helper :all + helper_method %i[current_person is_condensed_view page_and_sort_params controller_model + displaying_single_page? display_isa_graph? safe_class_lookup] layout Seek::Config.main_layout @@ -54,7 +56,6 @@ def with_current_user def current_person current_user.try(:person) end - helper_method :current_person def partially_registered? redirect_to register_people_path if current_user && !current_user.registration_complete? @@ -119,7 +120,7 @@ def page_and_sort_params params.permit(:page, :sort, :order, :view, :table_cols, permitted_filter_params) end - helper_method :page_and_sort_params + def controller_model begin @@ -128,7 +129,6 @@ def controller_model end end - helper_method :controller_model def self.api_actions(*actions) @api_actions ||= [] @@ -234,7 +234,8 @@ def find_and_authorize_requested_item case privilege when :publish, :manage, :edit, :download, :delete if current_user.nil? - flash[:error] = "You are not authorized to #{privilege} this #{name.humanize}, you may need to login first." + flash[:error] = +"You are not authorized to #{privilege} this #{name.humanize}, you may need to login first." else flash[:error] = "You are not authorized to #{privilege} this #{name.humanize}." end @@ -290,14 +291,16 @@ def render_not_found_error(e) def render_unknown_attribute_error(e) respond_to do |format| - format.json { render json: { errors: [{ title: 'Unknown attribute', details: e.message }] }, status: :unprocessable_entity } + format.json { + render json: { errors: [{ title: 'Unknown attribute', details: e.message }] }, status: :unprocessable_entity } format.all { render plain: e.message, status: :unprocessable_entity } end end def render_not_implemented_error(e) respond_to do |format| - format.json { render json: { errors: [{ title: 'Not implemented', details: e.message }] }, status: :not_implemented } + format.json { + render json: { errors: [{ title: 'Not implemented', details: e.message }] }, status: :not_implemented } format.all { render plain: e.message, status: :not_implemented } end end @@ -319,8 +322,6 @@ def is_condensed_view? (!params.has_key?(:view) && session.has_key?(:view) && !session[:view].nil? && session[:view]!="default") end - helper_method :is_condensed_view - def log_event # FIXME: why is needed to wrap in this block when the around filter already does ? @@ -383,7 +384,8 @@ def log_event user_agent: user_agent, data: activity_loggable.title) end - when *Seek::Util.authorized_types.map { |t| t.name.underscore.pluralize.split('/').last } + ["sample_types"] # TODO: Find a nicer way of doing this... + when *Seek::Util.authorized_types.map { |t| + t.name.underscore.pluralize.split('/').last } + ["sample_types"] # TODO: Find a nicer way of doing this... action = 'create' if action == 'create_metadata' || action == 'create_from_template' action = 'update' if action == 'create_version' action = 'inline_view' if action == 'explore' @@ -531,7 +533,8 @@ def rdf_enabled? return unless request.format.rdf? unless Seek::Util.rdf_capable_types.include?(controller_model) respond_to do |format| - format.rdf { render plain: 'This resource does not support RDF', status: :not_acceptable, content_type: 'text/plain' } + format.rdf { + render plain: 'This resource does not support RDF', status: :not_acceptable, content_type: 'text/plain' } end end end @@ -607,9 +610,11 @@ def relationify_collection(collection) def determine_extended_metadata_keys(asset = nil) keys = [] if asset - type_id = params.dig(controller_name.singularize.to_sym, asset, :extended_metadata_attributes, :extended_metadata_type_id) + type_id = params.dig(controller_name.singularize.to_sym, asset, :extended_metadata_attributes, + :extended_metadata_type_id) else - type_id = params.dig(controller_name.singularize.to_sym, :extended_metadata_attributes, :extended_metadata_type_id) + type_id = params.dig(controller_name.singularize.to_sym, :extended_metadata_attributes, + :extended_metadata_type_id) end if type_id.present? metadata_type = ExtendedMetadataType.find(type_id) @@ -651,14 +656,10 @@ def displaying_single_page? @single_page || false end - helper_method :displaying_single_page? - def display_isa_graph? !displaying_single_page? end - helper_method :display_isa_graph? - def creator_related_params [:other_creators, @@ -678,6 +679,4 @@ def creator_related_params def safe_class_lookup(class_name, raise: true) Seek::Util.lookup_class(class_name, raise: raise) end - - helper_method :safe_class_lookup end From d143bd4d212d3c6f2826ed0ff1a241e790d32117 Mon Sep 17 00:00:00 2001 From: Kevin De Pelseneer Date: Mon, 27 May 2024 19:04:45 +0200 Subject: [PATCH 057/131] Add hidden id fields to the CV terms form and add a uniqueness clause to the validation --- app/models/sample_controlled_vocab_term.rb | 2 +- app/views/sample_controlled_vocabs/_term_form_row.html.erb | 5 ++++- .../_term_form_row_disabled.html.erb | 1 + 3 files changed, 6 insertions(+), 2 deletions(-) diff --git a/app/models/sample_controlled_vocab_term.rb b/app/models/sample_controlled_vocab_term.rb index 4f1791e66f..092c85a9a5 100644 --- a/app/models/sample_controlled_vocab_term.rb +++ b/app/models/sample_controlled_vocab_term.rb @@ -1,7 +1,7 @@ class SampleControlledVocabTerm < ApplicationRecord belongs_to :sample_controlled_vocab, inverse_of: :sample_controlled_vocab_terms - validates :label, presence: true, length: { maximum: 500 } + validates :label, presence: true, length: { maximum: 500 }, uniqueness: { scope: :sample_controlled_vocab_id } before_validation :truncate_label diff --git a/app/views/sample_controlled_vocabs/_term_form_row.html.erb b/app/views/sample_controlled_vocabs/_term_form_row.html.erb index aa600c85a7..ffb2edf3b5 100644 --- a/app/views/sample_controlled_vocabs/_term_form_row.html.erb +++ b/app/views/sample_controlled_vocabs/_term_form_row.html.erb @@ -1,5 +1,8 @@ - + From 624f8d6ec1ea7f0ddcc404b5e9faf8aaa17a034c Mon Sep 17 00:00:00 2001 From: AndrewWood94 Date: Mon, 27 May 2024 16:56:57 +0100 Subject: [PATCH 058/131] Update data_files_controller.rb Set sample extraction status to 'cancelled' before re-extracting a datafile --- app/controllers/data_files_controller.rb | 1 + 1 file changed, 1 insertion(+) diff --git a/app/controllers/data_files_controller.rb b/app/controllers/data_files_controller.rb index d42906f834..0d0b66e81f 100644 --- a/app/controllers/data_files_controller.rb +++ b/app/controllers/data_files_controller.rb @@ -169,6 +169,7 @@ def extract_samples SampleDataPersistJob.new(@data_file, @sample_type, User.current_user, assay_ids: params["assay_ids"]).queue_job flash[:notice] = 'Started creating extracted samples' else + @data_file.sample_persistence_task.update(status: "cancelled") if @data_file.sample_persistence_task&.success? SampleDataExtractionJob.new(@data_file, @sample_type).queue_job end From 13e46470f2934e82a170e878db63350cae1f5a57 Mon Sep 17 00:00:00 2001 From: AndrewWood94 Date: Thu, 30 May 2024 17:18:43 +0100 Subject: [PATCH 059/131] Destroy existing sample_persistence_task if re-extracting --- app/controllers/data_files_controller.rb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/app/controllers/data_files_controller.rb b/app/controllers/data_files_controller.rb index 0d0b66e81f..6143dfcee1 100644 --- a/app/controllers/data_files_controller.rb +++ b/app/controllers/data_files_controller.rb @@ -169,7 +169,7 @@ def extract_samples SampleDataPersistJob.new(@data_file, @sample_type, User.current_user, assay_ids: params["assay_ids"]).queue_job flash[:notice] = 'Started creating extracted samples' else - @data_file.sample_persistence_task.update(status: "cancelled") if @data_file.sample_persistence_task&.success? + @data_file.sample_persistence_task.destroy if @data_file.sample_persistence_task&.success? SampleDataExtractionJob.new(@data_file, @sample_type).queue_job end From f35182de0f0ef0e5c6941058175206e28ba53d16 Mon Sep 17 00:00:00 2001 From: Kevin De Pelseneer Date: Fri, 31 May 2024 15:34:21 +0200 Subject: [PATCH 060/131] Simplify assay linkage --- app/controllers/isa_assays_controller.rb | 23 +++++++++-------------- 1 file changed, 9 insertions(+), 14 deletions(-) diff --git a/app/controllers/isa_assays_controller.rb b/app/controllers/isa_assays_controller.rb index 7e93c82ab4..d6c12551dd 100644 --- a/app/controllers/isa_assays_controller.rb +++ b/app/controllers/isa_assays_controller.rb @@ -5,8 +5,8 @@ class IsaAssaysController < ApplicationController before_action :set_up_instance_variable before_action :find_requested_item, only: %i[edit update] before_action :initialize_isa_assay, only: :create - before_action :fix_assay_linkage_for_new_assays, only: :create after_action :rearrange_assay_positions_create_isa_assay, only: :create + after_action :fix_assay_linkage_for_new_assays, only: :create def new study = Study.find(params[:study_id]) @@ -93,23 +93,18 @@ def update def fix_assay_linkage_for_new_assays return unless @isa_assay.assay.is_isa_json_compliant? return if @isa_assay.assay.is_assay_stream? # Should not fix anything when creating an assay stream + return unless @isa_assay.sample_type.present? # Just to be sure previous_sample_type = SampleType.find(params[:isa_assay][:input_sample_type_id]) - previous_assay = previous_sample_type.assays.first + next_sample_types = previous_sample_type.next_linked_sample_types + next_sample_types.delete @isa_assay.sample_type + next_sample_type = next_sample_types.first - # In case an assay is inserted right at the beginning of an assay stream, - # the next assay is the current first one in the assay stream. - next_assay = previous_assay.nil? ? @isa_assay.assay.assay_stream.next_linked_child_assay : previous_assay.next_linked_child_assay + # In case an assay is inserted right at the end of an assay stream, + # there is no next sample type and also no linkage to fix + return if next_sample_type.nil? - # In case no next assay (an assay was appended to the end of the stream), assay linkage does not have to be fixed. - return unless next_assay - - next_assay_input_attribute_id = next_assay.sample_type.sample_attributes.detect(&:input_attribute?).id - return unless next_assay_input_attribute_id - - # Add link of next assay sample type to currently created assay sample type - updated_lsai = @isa_assay.assay.sample_type.linked_sample_attribute_ids.push(next_assay_input_attribute_id) - @isa_assay.assay.sample_type.update(linked_sample_attribute_ids: updated_lsai) + next_sample_type.sample_attributes.detect(&:input_attribute?).update_column(:linked_sample_type_id, @isa_assay.sample_type.id) end def rearrange_assay_positions_create_isa_assay From 8e37e73c27e913cf8d2ac7193dc7c95b38e49e97 Mon Sep 17 00:00:00 2001 From: Kevin De Pelseneer Date: Fri, 31 May 2024 16:28:05 +0200 Subject: [PATCH 061/131] Make use of `:is_input?` instead --- app/forms/isa_assay.rb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/app/forms/isa_assay.rb b/app/forms/isa_assay.rb index 7c6679d4b3..7e90b8751f 100644 --- a/app/forms/isa_assay.rb +++ b/app/forms/isa_assay.rb @@ -21,7 +21,7 @@ def save if valid? if @assay.new_record? && !@assay.is_assay_stream? # connect the sample type multi link attribute to the last sample type of the assay's study - input_attribute = @sample_type.sample_attributes.detect(&:seek_sample_multi?) + input_attribute = @sample_type.sample_attributes.detect(&:input_attribute?) input_attribute.linked_sample_type_id = @input_sample_type_id title = SampleType.find(@input_sample_type_id).sample_attributes.detect(&:is_title).title input_attribute.title = "Input (#{title})" From d1878731d59820b5e4ed560dc7c69c005ff781be Mon Sep 17 00:00:00 2001 From: Kevin De Pelseneer Date: Fri, 31 May 2024 16:54:23 +0200 Subject: [PATCH 062/131] Simplification + update even when not authorized --- app/controllers/assays_controller.rb | 12 ++++-------- 1 file changed, 4 insertions(+), 8 deletions(-) diff --git a/app/controllers/assays_controller.rb b/app/controllers/assays_controller.rb index 140b5c0dd6..4aa210b8b5 100644 --- a/app/controllers/assays_controller.rb +++ b/app/controllers/assays_controller.rb @@ -171,15 +171,11 @@ def fix_assay_linkage_when_deleting_assays return unless @assay.is_isa_json_compliant? return unless @assay.has_linked_child_assay? - previous_assay_linked_st_id = @assay.previous_linked_sample_type&.id + previous_st = @assay.sample_type&.previous_linked_sample_type + next_st = @assay.sample_type&.next_linked_sample_types&.first + return unless previous_st && next_st - next_assay = @assay.next_linked_child_assay - - next_assay_st_attr = next_assay.sample_type&.sample_attributes&.detect(&:input_attribute?) - - return unless next_assay && previous_assay_linked_st_id && next_assay_st_attr - - next_assay_st_attr.update(linked_sample_type_id: previous_assay_linked_st_id) + next_st.sample_attributes.detect(&:input_attribute?).update_column(:linked_sample_type_id, previous_st&.id) end def rearrange_assay_positions_at_destroy From 77f8bdd1e46fbfffa84875ce5c40c52ff0a803ac Mon Sep 17 00:00:00 2001 From: Kevin De Pelseneer Date: Fri, 31 May 2024 17:34:27 +0200 Subject: [PATCH 063/131] Add unit test for uniqueness clause --- test/unit/sample_controlled_vocab_test.rb | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/test/unit/sample_controlled_vocab_test.rb b/test/unit/sample_controlled_vocab_test.rb index 6918c77450..c9253225d3 100644 --- a/test/unit/sample_controlled_vocab_test.rb +++ b/test/unit/sample_controlled_vocab_test.rb @@ -312,4 +312,12 @@ class SampleControlledVocabTest < ActiveSupport::TestCase assert vocab.ontology_based? end + test 'should not allow to add term with same label' do + vocab = FactoryBot.create(:apples_sample_controlled_vocab) + vocab.sample_controlled_vocab_terms.create(label: 'Golden Delicious') + assert_raises ActiveRecord::RecordInvalid do + vocab.sample_controlled_vocab_terms.create!(label: 'Golden Delicious') + end + end + end From feb52ca1593ce0abd5d0881103ab1e105e5f0f80 Mon Sep 17 00:00:00 2001 From: Kevin De Pelseneer Date: Fri, 31 May 2024 17:38:33 +0200 Subject: [PATCH 064/131] Fix current controller tests --- test/functional/sample_controlled_vocabs_controller_test.rb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/functional/sample_controlled_vocabs_controller_test.rb b/test/functional/sample_controlled_vocabs_controller_test.rb index f8a450e584..1bcab9cb8b 100644 --- a/test/functional/sample_controlled_vocabs_controller_test.rb +++ b/test/functional/sample_controlled_vocabs_controller_test.rb @@ -299,7 +299,7 @@ class SampleControlledVocabsControllerTest < ActionController::TestCase assert_select 'table#new-terms' do # 3 hidden fields for each field, and an extra one for the remove button default - assert_select 'tr.sample-cv-term input[type=hidden]', count:cv.sample_controlled_vocab_terms.length * 4 + assert_select 'tr.sample-cv-term input[type=hidden]', count:cv.sample_controlled_vocab_terms.length * 5 assert_select 'div.disabled-cv-field', count: cv.sample_controlled_vocab_terms.length * 3 end From 94c2964fa35dc46f9924bae5e00f7fc339ac55f1 Mon Sep 17 00:00:00 2001 From: Kevin De Pelseneer Date: Fri, 31 May 2024 18:44:37 +0200 Subject: [PATCH 065/131] Add test for duplicated CV terms --- ...ample_controlled_vocabs_controller_test.rb | 261 ++++++++++++------ 1 file changed, 169 insertions(+), 92 deletions(-) diff --git a/test/functional/sample_controlled_vocabs_controller_test.rb b/test/functional/sample_controlled_vocabs_controller_test.rb index 1bcab9cb8b..4abdce9459 100644 --- a/test/functional/sample_controlled_vocabs_controller_test.rb +++ b/test/functional/sample_controlled_vocabs_controller_test.rb @@ -70,11 +70,10 @@ class SampleControlledVocabsControllerTest < ActionController::TestCase assert_difference('SampleControlledVocab.count') do assert_difference('SampleControlledVocabTerm.count', 2) do post :create, params: { sample_controlled_vocab: { title: 'fish', description: 'About fish', - sample_controlled_vocab_terms_attributes: { - '0' => { label: 'goldfish', _destroy: '0' }, - '1' => { label: 'guppy', _destroy: '0' } - } - } } + sample_controlled_vocab_terms_attributes: { + '0' => { label: 'goldfish', _destroy: '0' }, + '1' => { label: 'guppy', _destroy: '0' } + } } } end end assert cv = assigns(:sample_controlled_vocab) @@ -89,11 +88,10 @@ class SampleControlledVocabsControllerTest < ActionController::TestCase assert_no_difference('SampleControlledVocab.count') do assert_no_difference('SampleControlledVocabTerm.count') do post :create, params: { sample_controlled_vocab: { title: 'fish', description: 'About fish', - sample_controlled_vocab_terms_attributes: { - '0' => { label: 'goldfish', _destroy: '0' }, - '1' => { label: 'guppy', _destroy: '0' } - } - } } + sample_controlled_vocab_terms_attributes: { + '0' => { label: 'goldfish', _destroy: '0' }, + '1' => { label: 'guppy', _destroy: '0' } + } } } end end assert_response :redirect @@ -105,11 +103,10 @@ class SampleControlledVocabsControllerTest < ActionController::TestCase assert_no_difference('SampleControlledVocab.count') do assert_no_difference('SampleControlledVocabTerm.count', 2) do post :create, params: { sample_controlled_vocab: { title: 'fish', description: 'About fish', - sample_controlled_vocab_terms_attributes: { - '0' => { label: 'goldfish', _destroy: '0' }, - '1' => { label: 'guppy', _destroy: '0' } - } - } } + sample_controlled_vocab_terms_attributes: { + '0' => { label: 'goldfish', _destroy: '0' }, + '1' => { label: 'guppy', _destroy: '0' } + } } } end end assert_response :redirect @@ -123,14 +120,16 @@ class SampleControlledVocabsControllerTest < ActionController::TestCase assert_no_difference('SampleControlledVocab.count') do assert_no_difference('SampleControlledVocabTerm.count') do put :update, params: { id: cv, sample_controlled_vocab: { title: 'the apples', description: 'About apples', - sample_controlled_vocab_terms_attributes: { - '0' => { label: 'Granny Smith', _destroy: '0', id: term_ids[0] }, - '1' => { _destroy: '1', id: term_ids[1] }, - '2' => { label: 'Bramley', _destroy: '0', id: term_ids[2] }, - '3' => { label: 'Cox', _destroy: '0', id: term_ids[3] }, - '4' => { label: 'Jazz', _destroy: '0' } - } - } } + sample_controlled_vocab_terms_attributes: { + '0' => { label: 'Granny Smith', _destroy: '0', + id: term_ids[0] }, + '1' => { _destroy: '1', id: term_ids[1] }, + '2' => { label: 'Bramley', _destroy: '0', + id: term_ids[2] }, + '3' => { label: 'Cox', _destroy: '0', + id: term_ids[3] }, + '4' => { label: 'Jazz', _destroy: '0' } + } } } end end assert cv = assigns(:sample_controlled_vocab) @@ -147,14 +146,16 @@ class SampleControlledVocabsControllerTest < ActionController::TestCase assert_no_difference('SampleControlledVocab.count') do assert_no_difference('SampleControlledVocabTerm.count') do put :update, params: { id: cv, sample_controlled_vocab: { title: 'the apples', description: 'About apples', - sample_controlled_vocab_terms_attributes: { - '0' => { label: 'Granny Smith', _destroy: '0', id: term_ids[0] }, - '1' => { _destroy: '1', id: term_ids[1] }, - '2' => { label: 'Bramley', _destroy: '0', id: term_ids[2] }, - '3' => { label: 'Cox', _destroy: '0', id: term_ids[3] }, - '4' => { label: 'Jazz', _destroy: '0' } - } - } } + sample_controlled_vocab_terms_attributes: { + '0' => { label: 'Granny Smith', _destroy: '0', + id: term_ids[0] }, + '1' => { _destroy: '1', id: term_ids[1] }, + '2' => { label: 'Bramley', _destroy: '0', + id: term_ids[2] }, + '3' => { label: 'Cox', _destroy: '0', + id: term_ids[3] }, + '4' => { label: 'Jazz', _destroy: '0' } + } } } end end assert_response :redirect @@ -294,7 +295,7 @@ class SampleControlledVocabsControllerTest < ActionController::TestCase login_as(person) cv = FactoryBot.create(:ontology_sample_controlled_vocab) assert cv.ontology_based? - get :edit, params:{id: cv.id} + get :edit, params:{ id: cv.id } assert_response :success assert_select 'table#new-terms' do @@ -310,7 +311,7 @@ class SampleControlledVocabsControllerTest < ActionController::TestCase login_as(person) cv = FactoryBot.create(:apples_sample_controlled_vocab) refute cv.ontology_based? - get :edit, params:{id: cv.id} + get :edit, params:{ id: cv.id } assert_response :success assert_select 'table#new-terms' do @@ -329,8 +330,8 @@ class SampleControlledVocabsControllerTest < ActionController::TestCase login_as(person) VCR.use_cassette('ols/fetch_obo_bad_term') do get :fetch_ols_terms_html, params: { source_ontology_id: 'go', - root_uris: 'http://purl.obolibrary.org/obo/banana', - include_root_term: '1' } + root_uris: 'http://purl.obolibrary.org/obo/banana', + include_root_term: '1' } assert_response :unprocessable_entity assert_equal '404 Not Found', response.body @@ -348,18 +349,29 @@ class SampleControlledVocabsControllerTest < ActionController::TestCase assert_response :success assert_select 'tr.sample-cv-term', count: 4 - assert_select 'input[type=hidden]#sample_controlled_vocab_sample_controlled_vocab_terms_attributes_0_iri[value=?]','http://purl.obolibrary.org/obo/GO_0090395' + assert_select 'input[type=hidden]#sample_controlled_vocab_sample_controlled_vocab_terms_attributes_0_iri[value=?]', +'http://purl.obolibrary.org/obo/GO_0090395' assert_select 'input[type=hidden]#sample_controlled_vocab_sample_controlled_vocab_terms_attributes_0_parent_iri:not([value])' - assert_select 'input[type=hidden]#sample_controlled_vocab_sample_controlled_vocab_terms_attributes_0_label[value=?]','plant cell papilla' - assert_select 'input[type=hidden]#sample_controlled_vocab_sample_controlled_vocab_terms_attributes_1_iri[value=?]','http://purl.obolibrary.org/obo/GO_0090397' - assert_select 'input[type=hidden]#sample_controlled_vocab_sample_controlled_vocab_terms_attributes_1_parent_iri[value=?]','http://purl.obolibrary.org/obo/GO_0090395' - assert_select 'input[type=hidden]#sample_controlled_vocab_sample_controlled_vocab_terms_attributes_1_label[value=?]','stigma papilla' - assert_select 'input[type=hidden]#sample_controlled_vocab_sample_controlled_vocab_terms_attributes_2_iri[value=?]','http://purl.obolibrary.org/obo/GO_0090396' - assert_select 'input[type=hidden]#sample_controlled_vocab_sample_controlled_vocab_terms_attributes_2_parent_iri[value=?]','http://purl.obolibrary.org/obo/GO_0090395' - assert_select 'input[type=hidden]#sample_controlled_vocab_sample_controlled_vocab_terms_attributes_2_label[value=?]','leaf papilla' - assert_select 'input[type=hidden]#sample_controlled_vocab_sample_controlled_vocab_terms_attributes_3_iri[value=?]','http://purl.obolibrary.org/obo/GO_0090705' - assert_select 'input[type=hidden]#sample_controlled_vocab_sample_controlled_vocab_terms_attributes_3_parent_iri[value=?]','http://purl.obolibrary.org/obo/GO_0090395' - assert_select 'input[type=hidden]#sample_controlled_vocab_sample_controlled_vocab_terms_attributes_3_label[value=?]','trichome papilla' + assert_select 'input[type=hidden]#sample_controlled_vocab_sample_controlled_vocab_terms_attributes_0_label[value=?]', +'plant cell papilla' + assert_select 'input[type=hidden]#sample_controlled_vocab_sample_controlled_vocab_terms_attributes_1_iri[value=?]', +'http://purl.obolibrary.org/obo/GO_0090397' + assert_select 'input[type=hidden]#sample_controlled_vocab_sample_controlled_vocab_terms_attributes_1_parent_iri[value=?]', +'http://purl.obolibrary.org/obo/GO_0090395' + assert_select 'input[type=hidden]#sample_controlled_vocab_sample_controlled_vocab_terms_attributes_1_label[value=?]', +'stigma papilla' + assert_select 'input[type=hidden]#sample_controlled_vocab_sample_controlled_vocab_terms_attributes_2_iri[value=?]', +'http://purl.obolibrary.org/obo/GO_0090396' + assert_select 'input[type=hidden]#sample_controlled_vocab_sample_controlled_vocab_terms_attributes_2_parent_iri[value=?]', +'http://purl.obolibrary.org/obo/GO_0090395' + assert_select 'input[type=hidden]#sample_controlled_vocab_sample_controlled_vocab_terms_attributes_2_label[value=?]', +'leaf papilla' + assert_select 'input[type=hidden]#sample_controlled_vocab_sample_controlled_vocab_terms_attributes_3_iri[value=?]', +'http://purl.obolibrary.org/obo/GO_0090705' + assert_select 'input[type=hidden]#sample_controlled_vocab_sample_controlled_vocab_terms_attributes_3_parent_iri[value=?]', +'http://purl.obolibrary.org/obo/GO_0090395' + assert_select 'input[type=hidden]#sample_controlled_vocab_sample_controlled_vocab_terms_attributes_3_label[value=?]', +'trichome papilla' end test 'create with root uris' do @@ -369,10 +381,11 @@ class SampleControlledVocabsControllerTest < ActionController::TestCase post :create, params: { sample_controlled_vocab: { title: 'plant_cell_papilla and haustorium', description: 'multiple root uris', ols_root_term_uris: 'http://purl.obolibrary.org/obo/GO_0090395, http://purl.obolibrary.org/obo/GO_0085035', sample_controlled_vocab_terms_attributes: { - '0' => { label: 'plant cell papilla', iri:'http://purl.obolibrary.org/obo/GO_0090395', parent_iri:'', _destroy: '0' }, - '1' => { label: 'haustorium', iri:'http://purl.obolibrary.org/obo/GO_0085035', parent_iri:'', _destroy: '0' } - } - } } + '0' => { label: 'plant cell papilla', + iri: 'http://purl.obolibrary.org/obo/GO_0090395', parent_iri:'', _destroy: '0' }, + '1' => { label: 'haustorium', + iri: 'http://purl.obolibrary.org/obo/GO_0085035', parent_iri:'', _destroy: '0' } + } } } end end assert cv = assigns(:sample_controlled_vocab) @@ -381,8 +394,10 @@ class SampleControlledVocabsControllerTest < ActionController::TestCase assert_equal 'multiple root uris', cv.description assert_equal 2, cv.sample_controlled_vocab_terms.count assert_equal ['plant cell papilla','haustorium'], cv.labels - assert_equal ['http://purl.obolibrary.org/obo/GO_0090395','http://purl.obolibrary.org/obo/GO_0085035'], cv.sample_controlled_vocab_terms.collect(&:iri) - assert_equal 'http://purl.obolibrary.org/obo/GO_0090395, http://purl.obolibrary.org/obo/GO_0085035', cv.ols_root_term_uris + assert_equal ['http://purl.obolibrary.org/obo/GO_0090395','http://purl.obolibrary.org/obo/GO_0085035'], +cv.sample_controlled_vocab_terms.collect(&:iri) + assert_equal 'http://purl.obolibrary.org/obo/GO_0090395, http://purl.obolibrary.org/obo/GO_0085035', +cv.ols_root_term_uris end test 'fetch ols terms as HTML with multiple root uris and root term included' do @@ -398,25 +413,41 @@ class SampleControlledVocabsControllerTest < ActionController::TestCase assert_response :success assert_select 'tr.sample-cv-term', count: 6 - assert_select 'input[type=hidden]#sample_controlled_vocab_sample_controlled_vocab_terms_attributes_0_iri[value=?]','http://purl.obolibrary.org/obo/GO_0090395' + assert_select 'input[type=hidden]#sample_controlled_vocab_sample_controlled_vocab_terms_attributes_0_iri[value=?]', +'http://purl.obolibrary.org/obo/GO_0090395' assert_select 'input[type=hidden]#sample_controlled_vocab_sample_controlled_vocab_terms_attributes_0_parent_iri:not([value])' - assert_select 'input[type=hidden]#sample_controlled_vocab_sample_controlled_vocab_terms_attributes_0_label[value=?]','plant cell papilla' - assert_select 'input[type=hidden]#sample_controlled_vocab_sample_controlled_vocab_terms_attributes_1_iri[value=?]','http://purl.obolibrary.org/obo/GO_0090397' - assert_select 'input[type=hidden]#sample_controlled_vocab_sample_controlled_vocab_terms_attributes_1_parent_iri[value=?]','http://purl.obolibrary.org/obo/GO_0090395' - assert_select 'input[type=hidden]#sample_controlled_vocab_sample_controlled_vocab_terms_attributes_1_label[value=?]','stigma papilla' - assert_select 'input[type=hidden]#sample_controlled_vocab_sample_controlled_vocab_terms_attributes_2_iri[value=?]','http://purl.obolibrary.org/obo/GO_0090396' - assert_select 'input[type=hidden]#sample_controlled_vocab_sample_controlled_vocab_terms_attributes_2_parent_iri[value=?]','http://purl.obolibrary.org/obo/GO_0090395' - assert_select 'input[type=hidden]#sample_controlled_vocab_sample_controlled_vocab_terms_attributes_2_label[value=?]','leaf papilla' - assert_select 'input[type=hidden]#sample_controlled_vocab_sample_controlled_vocab_terms_attributes_3_iri[value=?]','http://purl.obolibrary.org/obo/GO_0090705' - assert_select 'input[type=hidden]#sample_controlled_vocab_sample_controlled_vocab_terms_attributes_3_parent_iri[value=?]','http://purl.obolibrary.org/obo/GO_0090395' - assert_select 'input[type=hidden]#sample_controlled_vocab_sample_controlled_vocab_terms_attributes_3_label[value=?]','trichome papilla' - - assert_select 'input[type=hidden]#sample_controlled_vocab_sample_controlled_vocab_terms_attributes_4_iri[value=?]','http://purl.obolibrary.org/obo/GO_0085035' + assert_select 'input[type=hidden]#sample_controlled_vocab_sample_controlled_vocab_terms_attributes_0_label[value=?]', +'plant cell papilla' + assert_select 'input[type=hidden]#sample_controlled_vocab_sample_controlled_vocab_terms_attributes_1_iri[value=?]', +'http://purl.obolibrary.org/obo/GO_0090397' + assert_select 'input[type=hidden]#sample_controlled_vocab_sample_controlled_vocab_terms_attributes_1_parent_iri[value=?]', +'http://purl.obolibrary.org/obo/GO_0090395' + assert_select 'input[type=hidden]#sample_controlled_vocab_sample_controlled_vocab_terms_attributes_1_label[value=?]', +'stigma papilla' + assert_select 'input[type=hidden]#sample_controlled_vocab_sample_controlled_vocab_terms_attributes_2_iri[value=?]', +'http://purl.obolibrary.org/obo/GO_0090396' + assert_select 'input[type=hidden]#sample_controlled_vocab_sample_controlled_vocab_terms_attributes_2_parent_iri[value=?]', +'http://purl.obolibrary.org/obo/GO_0090395' + assert_select 'input[type=hidden]#sample_controlled_vocab_sample_controlled_vocab_terms_attributes_2_label[value=?]', +'leaf papilla' + assert_select 'input[type=hidden]#sample_controlled_vocab_sample_controlled_vocab_terms_attributes_3_iri[value=?]', +'http://purl.obolibrary.org/obo/GO_0090705' + assert_select 'input[type=hidden]#sample_controlled_vocab_sample_controlled_vocab_terms_attributes_3_parent_iri[value=?]', +'http://purl.obolibrary.org/obo/GO_0090395' + assert_select 'input[type=hidden]#sample_controlled_vocab_sample_controlled_vocab_terms_attributes_3_label[value=?]', +'trichome papilla' + + assert_select 'input[type=hidden]#sample_controlled_vocab_sample_controlled_vocab_terms_attributes_4_iri[value=?]', +'http://purl.obolibrary.org/obo/GO_0085035' assert_select 'input[type=hidden]#sample_controlled_vocab_sample_controlled_vocab_terms_attributes_4_parent_iri:not([value])' - assert_select 'input[type=hidden]#sample_controlled_vocab_sample_controlled_vocab_terms_attributes_4_label[value=?]','haustorium' - assert_select 'input[type=hidden]#sample_controlled_vocab_sample_controlled_vocab_terms_attributes_5_iri[value=?]','http://purl.obolibrary.org/obo/GO_0085041' - assert_select 'input[type=hidden]#sample_controlled_vocab_sample_controlled_vocab_terms_attributes_5_parent_iri[value=?]','http://purl.obolibrary.org/obo/GO_0085035' - assert_select 'input[type=hidden]#sample_controlled_vocab_sample_controlled_vocab_terms_attributes_5_label[value=?]','arbuscule' + assert_select 'input[type=hidden]#sample_controlled_vocab_sample_controlled_vocab_terms_attributes_4_label[value=?]', +'haustorium' + assert_select 'input[type=hidden]#sample_controlled_vocab_sample_controlled_vocab_terms_attributes_5_iri[value=?]', +'http://purl.obolibrary.org/obo/GO_0085041' + assert_select 'input[type=hidden]#sample_controlled_vocab_sample_controlled_vocab_terms_attributes_5_parent_iri[value=?]', +'http://purl.obolibrary.org/obo/GO_0085035' + assert_select 'input[type=hidden]#sample_controlled_vocab_sample_controlled_vocab_terms_attributes_5_label[value=?]', +'arbuscule' end @@ -434,19 +465,31 @@ class SampleControlledVocabsControllerTest < ActionController::TestCase assert_response :success assert_select 'tr.sample-cv-term', count: 4 - assert_select 'input[type=hidden]#sample_controlled_vocab_sample_controlled_vocab_terms_attributes_0_iri[value=?]','http://purl.obolibrary.org/obo/GO_0090397' - assert_select 'input[type=hidden]#sample_controlled_vocab_sample_controlled_vocab_terms_attributes_0_parent_iri[value=?]','http://purl.obolibrary.org/obo/GO_0090395' - assert_select 'input[type=hidden]#sample_controlled_vocab_sample_controlled_vocab_terms_attributes_0_label[value=?]','stigma papilla' - assert_select 'input[type=hidden]#sample_controlled_vocab_sample_controlled_vocab_terms_attributes_1_iri[value=?]','http://purl.obolibrary.org/obo/GO_0090396' - assert_select 'input[type=hidden]#sample_controlled_vocab_sample_controlled_vocab_terms_attributes_1_parent_iri[value=?]','http://purl.obolibrary.org/obo/GO_0090395' - assert_select 'input[type=hidden]#sample_controlled_vocab_sample_controlled_vocab_terms_attributes_1_label[value=?]','leaf papilla' - assert_select 'input[type=hidden]#sample_controlled_vocab_sample_controlled_vocab_terms_attributes_2_iri[value=?]','http://purl.obolibrary.org/obo/GO_0090705' - assert_select 'input[type=hidden]#sample_controlled_vocab_sample_controlled_vocab_terms_attributes_2_parent_iri[value=?]','http://purl.obolibrary.org/obo/GO_0090395' - assert_select 'input[type=hidden]#sample_controlled_vocab_sample_controlled_vocab_terms_attributes_2_label[value=?]','trichome papilla' - - assert_select 'input[type=hidden]#sample_controlled_vocab_sample_controlled_vocab_terms_attributes_3_iri[value=?]','http://purl.obolibrary.org/obo/GO_0085041' - assert_select 'input[type=hidden]#sample_controlled_vocab_sample_controlled_vocab_terms_attributes_3_parent_iri[value=?]','http://purl.obolibrary.org/obo/GO_0085035' - assert_select 'input[type=hidden]#sample_controlled_vocab_sample_controlled_vocab_terms_attributes_3_label[value=?]','arbuscule' + assert_select 'input[type=hidden]#sample_controlled_vocab_sample_controlled_vocab_terms_attributes_0_iri[value=?]', +'http://purl.obolibrary.org/obo/GO_0090397' + assert_select 'input[type=hidden]#sample_controlled_vocab_sample_controlled_vocab_terms_attributes_0_parent_iri[value=?]', +'http://purl.obolibrary.org/obo/GO_0090395' + assert_select 'input[type=hidden]#sample_controlled_vocab_sample_controlled_vocab_terms_attributes_0_label[value=?]', +'stigma papilla' + assert_select 'input[type=hidden]#sample_controlled_vocab_sample_controlled_vocab_terms_attributes_1_iri[value=?]', +'http://purl.obolibrary.org/obo/GO_0090396' + assert_select 'input[type=hidden]#sample_controlled_vocab_sample_controlled_vocab_terms_attributes_1_parent_iri[value=?]', +'http://purl.obolibrary.org/obo/GO_0090395' + assert_select 'input[type=hidden]#sample_controlled_vocab_sample_controlled_vocab_terms_attributes_1_label[value=?]', +'leaf papilla' + assert_select 'input[type=hidden]#sample_controlled_vocab_sample_controlled_vocab_terms_attributes_2_iri[value=?]', +'http://purl.obolibrary.org/obo/GO_0090705' + assert_select 'input[type=hidden]#sample_controlled_vocab_sample_controlled_vocab_terms_attributes_2_parent_iri[value=?]', +'http://purl.obolibrary.org/obo/GO_0090395' + assert_select 'input[type=hidden]#sample_controlled_vocab_sample_controlled_vocab_terms_attributes_2_label[value=?]', +'trichome papilla' + + assert_select 'input[type=hidden]#sample_controlled_vocab_sample_controlled_vocab_terms_attributes_3_iri[value=?]', +'http://purl.obolibrary.org/obo/GO_0085041' + assert_select 'input[type=hidden]#sample_controlled_vocab_sample_controlled_vocab_terms_attributes_3_parent_iri[value=?]', +'http://purl.obolibrary.org/obo/GO_0085035' + assert_select 'input[type=hidden]#sample_controlled_vocab_sample_controlled_vocab_terms_attributes_3_label[value=?]', +'arbuscule' end @@ -471,19 +514,28 @@ class SampleControlledVocabsControllerTest < ActionController::TestCase login_as(person) VCR.use_cassette('ols/fetch_obo_plant_cell_papilla') do get :fetch_ols_terms_html, params: { source_ontology_id: 'go', - root_uris: 'http://purl.obolibrary.org/obo/GO_0090395' } + root_uris: 'http://purl.obolibrary.org/obo/GO_0090395' } end assert_response :success assert_select 'tr.sample-cv-term', count: 3 - assert_select 'input[type=hidden]#sample_controlled_vocab_sample_controlled_vocab_terms_attributes_0_iri[value=?]','http://purl.obolibrary.org/obo/GO_0090397' - assert_select 'input[type=hidden]#sample_controlled_vocab_sample_controlled_vocab_terms_attributes_0_parent_iri[value=?]','http://purl.obolibrary.org/obo/GO_0090395' - assert_select 'input[type=hidden]#sample_controlled_vocab_sample_controlled_vocab_terms_attributes_0_label[value=?]','stigma papilla' - assert_select 'input[type=hidden]#sample_controlled_vocab_sample_controlled_vocab_terms_attributes_1_iri[value=?]','http://purl.obolibrary.org/obo/GO_0090396' - assert_select 'input[type=hidden]#sample_controlled_vocab_sample_controlled_vocab_terms_attributes_1_parent_iri[value=?]','http://purl.obolibrary.org/obo/GO_0090395' - assert_select 'input[type=hidden]#sample_controlled_vocab_sample_controlled_vocab_terms_attributes_1_label[value=?]','leaf papilla' - assert_select 'input[type=hidden]#sample_controlled_vocab_sample_controlled_vocab_terms_attributes_2_iri[value=?]','http://purl.obolibrary.org/obo/GO_0090705' - assert_select 'input[type=hidden]#sample_controlled_vocab_sample_controlled_vocab_terms_attributes_2_parent_iri[value=?]','http://purl.obolibrary.org/obo/GO_0090395' - assert_select 'input[type=hidden]#sample_controlled_vocab_sample_controlled_vocab_terms_attributes_2_label[value=?]','trichome papilla' + assert_select 'input[type=hidden]#sample_controlled_vocab_sample_controlled_vocab_terms_attributes_0_iri[value=?]', +'http://purl.obolibrary.org/obo/GO_0090397' + assert_select 'input[type=hidden]#sample_controlled_vocab_sample_controlled_vocab_terms_attributes_0_parent_iri[value=?]', +'http://purl.obolibrary.org/obo/GO_0090395' + assert_select 'input[type=hidden]#sample_controlled_vocab_sample_controlled_vocab_terms_attributes_0_label[value=?]', +'stigma papilla' + assert_select 'input[type=hidden]#sample_controlled_vocab_sample_controlled_vocab_terms_attributes_1_iri[value=?]', +'http://purl.obolibrary.org/obo/GO_0090396' + assert_select 'input[type=hidden]#sample_controlled_vocab_sample_controlled_vocab_terms_attributes_1_parent_iri[value=?]', +'http://purl.obolibrary.org/obo/GO_0090395' + assert_select 'input[type=hidden]#sample_controlled_vocab_sample_controlled_vocab_terms_attributes_1_label[value=?]', +'leaf papilla' + assert_select 'input[type=hidden]#sample_controlled_vocab_sample_controlled_vocab_terms_attributes_2_iri[value=?]', +'http://purl.obolibrary.org/obo/GO_0090705' + assert_select 'input[type=hidden]#sample_controlled_vocab_sample_controlled_vocab_terms_attributes_2_parent_iri[value=?]', +'http://purl.obolibrary.org/obo/GO_0090395' + assert_select 'input[type=hidden]#sample_controlled_vocab_sample_controlled_vocab_terms_attributes_2_label[value=?]', +'trichome papilla' end test 'can access typeahead with samples disabled' do @@ -498,4 +550,29 @@ class SampleControlledVocabsControllerTest < ActionController::TestCase assert_equal 'Sample collections', res.first['text'] end end + + test 'should not duplicate terms when updating' do + person = FactoryBot.create(:person) + login_as(person) + cv = FactoryBot.create(:apples_sample_controlled_vocab) + term_ids = cv.sample_controlled_vocab_terms.map(&:id) + + assert_no_difference('SampleControlledVocabTerm.count') do + put :update, params: { id: cv, sample_controlled_vocab: { title: 'the apples', description: 'About apples', + sample_controlled_vocab_terms_attributes: { + '0' => { label: 'Granny Smith', _destroy: '0', + id: term_ids[0] }, + '1' => { label: 'Red Delicious', _destroy: '0', + id: term_ids[1] }, + '2' => { label: 'Bramley', _destroy: '0', + id: term_ids[2] }, + '3' => { label: 'Cox', _destroy: '0', + id: term_ids[3] }, + '4' => { label: 'Granny Smith', _destroy: '0' } + } } } + end + assert_response :unprocessable_entity + assert_template :edit + assert flash[:error] = 'Validation failed: Labels have already been taken' + end end From fce8e3433a3b89d0611415417889df9e2f523a3c Mon Sep 17 00:00:00 2001 From: Kevin De Pelseneer Date: Mon, 3 Jun 2024 16:33:16 +0200 Subject: [PATCH 066/131] Pass errors to partials --- app/views/single_pages/sample_upload_content.html.erb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/app/views/single_pages/sample_upload_content.html.erb b/app/views/single_pages/sample_upload_content.html.erb index 139062d970..b8b1f51dc2 100644 --- a/app/views/single_pages/sample_upload_content.html.erb +++ b/app/views/single_pages/sample_upload_content.html.erb @@ -9,7 +9,7 @@
<%# General information panel %> - <%= render partial: 'general_panel' %> + <%= render partial: 'general_panel', locals: {errors: } %> <%# New Samples panel %> <%= render partial: 'new_samples_panel' %> @@ -21,7 +21,7 @@ <%= render partial: 'duplicate_samples_panel' %> <%# Panel for Sample with wrong permissions %> - <%= render partial: 'unauthorized_samples_panel' %> + <%= render partial: 'unauthorized_samples_panel', locals: {errors: } %>
<% unless @can_upload %> From f666d69a8027f9e3e0544847aae6422ef179598d Mon Sep 17 00:00:00 2001 From: Kevin De Pelseneer Date: Mon, 3 Jun 2024 17:13:42 +0200 Subject: [PATCH 067/131] Add test for unauthorized samples [JSON response] --- .../single_pages_controller_test.rb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) diff --git a/test/functional/single_pages_controller_test.rb b/test/functional/single_pages_controller_test.rb index 7350c73411..f78e9785d0 100644 --- a/test/functional/single_pages_controller_test.rb +++ b/test/functional/single_pages_controller_test.rb @@ -221,6 +221,37 @@ def setup end end + test 'Should show permission conflicts for samples' do + with_config_value(:project_single_page_enabled, true) do + unauthorized_user = FactoryBot.create(:user) + login_as unauthorized_user + project, source_sample_type = setup_file_upload.values_at( + :project, :source_sample_type + ) + + file_path = 'upload_single_page/01_combo_update_sources_spreadsheet.xlsx' + file = fixture_file_upload(file_path, 'application/vnd.openxmlformats-officedocument.spreadsheetml.sheet') + + post :upload_samples, as: :json, params: { file:, project_id: project.id, + sample_type_id: source_sample_type.id } + + response_data = JSON.parse(response.body)['uploadData'] + assert_response :success + + updated_samples = response_data['updateSamples'] + assert(updated_samples.size, 0) + + new_samples = response_data['unauthorized_samples'] + assert(new_samples.size, 2) + + new_samples = response_data['newSamples'] + assert(new_samples.size, 2) + + possible_duplicates = response_data['possibleDuplicates'] + assert(possible_duplicates.size, 1) + end + end + def setup_file_upload id_label = "#{Seek::Config.instance_name} id" person = @member.person From 2ffba238bd98e4e05c4b6247295e64233d2bc001 Mon Sep 17 00:00:00 2001 From: Kevin De Pelseneer Date: Mon, 3 Jun 2024 17:19:39 +0200 Subject: [PATCH 068/131] typo --- test/functional/single_pages_controller_test.rb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/test/functional/single_pages_controller_test.rb b/test/functional/single_pages_controller_test.rb index f78e9785d0..c7746c13a5 100644 --- a/test/functional/single_pages_controller_test.rb +++ b/test/functional/single_pages_controller_test.rb @@ -241,8 +241,8 @@ def setup updated_samples = response_data['updateSamples'] assert(updated_samples.size, 0) - new_samples = response_data['unauthorized_samples'] - assert(new_samples.size, 2) + unauthorized_samples = response_data['unauthorized_samples'] + assert(unauthorized_samples.size, 2) new_samples = response_data['newSamples'] assert(new_samples.size, 2) From f1247bb5cdd3c8411b6b52e9688a1a4f25922f6f Mon Sep 17 00:00:00 2001 From: Kevin De Pelseneer Date: Mon, 3 Jun 2024 18:05:42 +0200 Subject: [PATCH 069/131] Set empty cells to nil --- app/controllers/single_pages_controller.rb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/app/controllers/single_pages_controller.rb b/app/controllers/single_pages_controller.rb index e25a7db2c6..004b48f372 100644 --- a/app/controllers/single_pages_controller.rb +++ b/app/controllers/single_pages_controller.rb @@ -244,7 +244,7 @@ def get_spreadsheet_data(samples_sheet) next if sample_cells.all? { |cell| (cell&.value == '' || cell&.value.nil?) } sample_cells.map do |cell| - cell&.value + cell&.value unless cell&.value == '' end.drop(1) end.compact From c371563650c9bc2c4100e95582409ac7463c85eb Mon Sep 17 00:00:00 2001 From: Kevin De Pelseneer Date: Mon, 3 Jun 2024 18:06:22 +0200 Subject: [PATCH 070/131] Skip id and uuid columns when comparing metadata --- app/controllers/single_pages_controller.rb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/app/controllers/single_pages_controller.rb b/app/controllers/single_pages_controller.rb index 004b48f372..3229d54df0 100644 --- a/app/controllers/single_pages_controller.rb +++ b/app/controllers/single_pages_controller.rb @@ -334,7 +334,7 @@ def separate_unauthorized_samples(existing_excel_samples, db_samples, authorized is_changed = false db_sample.map do |k, v| - unless ees[k] == v + unless ees[k] == v || %w[id uuid].include?(k) is_changed = true break end From ace380fc31197adab7f77121fffa6bf7583acc5a Mon Sep 17 00:00:00 2001 From: Kevin De Pelseneer Date: Mon, 3 Jun 2024 20:08:41 +0200 Subject: [PATCH 071/131] Fix existing tests --- .../03_combo_update_samples_spreadsheet.xlsx | Bin 27970 -> 27981 bytes ...ombo_update_assay_samples_spreadsheet.xlsx | Bin 27918 -> 28043 bytes .../single_pages_controller_test.rb | 54 ++++++++---------- 3 files changed, 24 insertions(+), 30 deletions(-) diff --git a/test/fixtures/files/upload_single_page/03_combo_update_samples_spreadsheet.xlsx b/test/fixtures/files/upload_single_page/03_combo_update_samples_spreadsheet.xlsx index 357e00d721ae982c86652b2af6cbf4a8b9ce7828..18e303862283bed56125b5264e7346c1bc2091bd 100644 GIT binary patch delta 9377 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source_sample_type.id } response_data = JSON.parse(response.body)['uploadData'] - assert_response :success - + db_samples = response_data['dbSamples'] updated_samples = response_data['updateSamples'] - assert(updated_samples.size, 2) - new_samples = response_data['newSamples'] - assert(new_samples.size, 2) - possible_duplicates = response_data['possibleDuplicates'] - assert(possible_duplicates.size, 1) + + assert_response :success + assert_equal db_samples.size, 5 + assert_equal updated_samples.size, 2 + assert_equal new_samples.size, 2 + assert_equal possible_duplicates.size, 1 end end @@ -182,16 +182,14 @@ def setup sample_type_id: sample_collection_sample_type.id } response_data = JSON.parse(response.body)['uploadData'] - assert_response :success - updated_samples = response_data['updateSamples'] - assert(updated_samples.size, 2) - new_samples = response_data['newSamples'] - assert(new_samples.size, 2) - possible_duplicates = response_data['possibleDuplicates'] - assert(possible_duplicates.size, 1) + + assert_response :success + assert_equal updated_samples.size, 2 + assert_equal new_samples.size, 2 + assert_equal possible_duplicates.size, 1 end end @@ -208,16 +206,14 @@ def setup sample_type_id: assay_sample_type.id } response_data = JSON.parse(response.body)['uploadData'] - assert_response :success - updated_samples = response_data['updateSamples'] - assert(updated_samples.size, 2) - new_samples = response_data['newSamples'] - assert(new_samples.size, 1) - possible_duplicates = response_data['possibleDuplicates'] - assert(possible_duplicates.size, 1) + + assert_response :success + assert_equal updated_samples.size, 2 + assert_equal new_samples.size, 1 + assert_equal possible_duplicates.size, 1 end end @@ -236,16 +232,14 @@ def setup sample_type_id: source_sample_type.id } response_data = JSON.parse(response.body)['uploadData'] - assert_response :success - updated_samples = response_data['updateSamples'] - assert(updated_samples.size, 0) - unauthorized_samples = response_data['unauthorized_samples'] - assert(unauthorized_samples.size, 2) - new_samples = response_data['newSamples'] - assert(new_samples.size, 2) + + assert_response :success + assert_equal updated_samples.size, 0 + assert_equal unauthorized_samples.size, 2 + assert_equal new_samples.size, 2 possible_duplicates = response_data['possibleDuplicates'] assert(possible_duplicates.size, 1) @@ -289,12 +283,12 @@ def setup_file_upload FactoryBot.create( :sample, id: 10_010 + n, - title: "source#{n}", + title: "source_#{n}", sample_type: source_sample_type, project_ids: [project.id], contributor: person, data: { - 'Source Name': 'Source Name', + 'Source Name': "Source #{n}", 'Source Characteristic 1': 'Source Characteristic 1', 'Source Characteristic 2': source_sample_type From 04a82a46e525ad4d4e4569c67535bcbb8f10426c Mon Sep 17 00:00:00 2001 From: Kevin De Pelseneer Date: Mon, 3 Jun 2024 20:42:45 +0200 Subject: [PATCH 072/131] Add thead and tbody elements --- .../_duplicate_samples_panel.html.erb | 69 +++++++++++-------- .../single_pages/_new_samples_panel.html.erb | 33 +++++---- .../_unauthorized_samples_panel.html.erb | 13 ++-- .../_update_samples_panel.html.erb | 29 +++++--- 4 files changed, 86 insertions(+), 58 deletions(-) diff --git a/app/views/single_pages/_duplicate_samples_panel.html.erb b/app/views/single_pages/_duplicate_samples_panel.html.erb index b05064fdd6..6a623a4286 100644 --- a/app/views/single_pages/_duplicate_samples_panel.html.erb +++ b/app/views/single_pages/_duplicate_samples_panel.html.erb @@ -1,8 +1,9 @@ <% unless @possible_duplicates.nil? or @possible_duplicates.compact.none? %> - <%= folding_panel("Possible Duplicates #{@possible_duplicates.size}", true, :id => "duplicate-samples-panel", :body_options => {:id => "duplicate-samples-panel-content"}, - :help_text => "These new samples have been matched to already existing samples.") do %> + <%= folding_panel("Possible Duplicates #{@possible_duplicates.size}", true, :id => "duplicate-samples-panel", :body_options => { :id => "duplicate-samples-panel-content" }, + :help_text => "These new samples have been matched to already existing samples.") do %>
Order
- <%= button_link_to('Add new attribute', 'add', '#', id: 'add-attribute') if @template.level %> + <%= button_link_to('Add new attribute', 'add', '#', id: 'add-attribute', class: @template.new_record? ? 'hidden' : '') %>
<%= hidden_field_tag "#{field_name_prefix}[required]", '0' %> - <%= check_box_tag "#{field_name_prefix}[required]", '1', required, disabled: !allow_required, data: { attr: "required" } %> + <%= check_box_tag "#{field_name_prefix}[required]", '1', required, class: "#{ allow_required ? '' : 'disabled' }", data: { attr: "required" } %>
<%= hidden_field_tag "#{field_name_prefix}[is_title]", '0' %> - <%= check_box_tag "#{field_name_prefix}[is_title]", '1', is_title, class:'sample-type-is-title',disabled: seek_sample_multi || !allow_required %> + <%= check_box_tag "#{field_name_prefix}[is_title]", '1', is_title, class: "sample-type-is-title #{ allow_required ? '' : 'disabled' }"%>
From 0fec474d2a7a2bc40feb0dd2050247699d11a1e4 Mon Sep 17 00:00:00 2001 From: Kevin De Pelseneer Date: Thu, 23 May 2024 10:03:55 +0200 Subject: [PATCH 033/131] Make `is_title` and `required` attributes read-only if inherited --- lib/seek/samples/sample_type_editing_constraints.rb | 1 + 1 file changed, 1 insertion(+) diff --git a/lib/seek/samples/sample_type_editing_constraints.rb b/lib/seek/samples/sample_type_editing_constraints.rb index 39f5a64cd7..d5c35aa78d 100644 --- a/lib/seek/samples/sample_type_editing_constraints.rb +++ b/lib/seek/samples/sample_type_editing_constraints.rb @@ -22,6 +22,7 @@ def samples? def allow_required?(attr) if attr.is_a?(SampleAttribute) return true if attr.new_record? + return false if inherited?(attr) attr = attr.accessor_name end From 646919347a4756fb1e18e062099ab500d0ffb5f6 Mon Sep 17 00:00:00 2001 From: Kevin De Pelseneer Date: Thu, 23 May 2024 10:04:27 +0200 Subject: [PATCH 034/131] Replace 'disabled' prop with bootstrap class --- app/assets/javascripts/templates.js | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/app/assets/javascripts/templates.js b/app/assets/javascripts/templates.js index 41d064d115..0947bfa8d1 100644 --- a/app/assets/javascripts/templates.js +++ b/app/assets/javascripts/templates.js @@ -243,9 +243,9 @@ const applyTemplate = () => { const isRequired = row[0] ? "checked" : ""; newRow = $j(newRow.replace(/replace-me/g, index)); $j(newRow).find('[data-attr="required"]').prop("checked", row[0]); - if (appliedToSampleType) $j(newRow).find('[data-attr="required"]').prop("disabled", true); + if (appliedToSampleType) $j(newRow).find('[data-attr="required"]').addClass("disabled"); $j(newRow).find(".sample-type-is-title").prop("checked", row[8]); - if (appliedToSampleType) $j(newRow).find('.sample-type-is-title').prop("disabled", true); + if (appliedToSampleType) $j(newRow).find('.sample-type-is-title').addClass("disabled"); $j(newRow).find('[data-attr="title"]').val(row[1]); if (appliedToSampleType) $j(newRow).find('[data-attr="title"]').addClass("disabled"); $j(newRow).find('[data-attr="description"]').val(row[2]); From 579f5e356e0b282265f9c0b066d0749c989c5404 Mon Sep 17 00:00:00 2001 From: Kevin De Pelseneer Date: Thu, 23 May 2024 10:08:30 +0200 Subject: [PATCH 035/131] make isa_json_compliant sample_type editable when project member instead --- app/models/sample_type.rb | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/app/models/sample_type.rb b/app/models/sample_type.rb index d64709da02..b7ba82c750 100644 --- a/app/models/sample_type.rb +++ b/app/models/sample_type.rb @@ -128,7 +128,13 @@ def self.can_create? def can_edit?(user = User.current_user) return false if user.nil? || user.person.nil? || !Seek::Config.samples_enabled return true if user.is_admin? - contributor == user.person || projects.detect { |project| project.can_manage?(user) }.present? + + # Make the ISA JSON compliant sample types editable when a user is a project member instead of a project admin + if is_isa_json_compliant? + contributor == user.person || projects.detect { |project| project.has_member? user.person }.present? + else + contributor == user.person || projects.detect { |project| project.can_manage?(user) }.present? + end end def can_delete?(user = User.current_user) From 66a9e6a5a04ddcaebe4911b825c9e261188c2f67 Mon Sep 17 00:00:00 2001 From: Kevin De Pelseneer Date: Thu, 23 May 2024 10:31:19 +0200 Subject: [PATCH 036/131] Add sample type constraint test for `allow_required?` of inherited sample attributes --- .../sample_type_editing_constraints_test.rb | 18 +++++++++++++++++- 1 file changed, 17 insertions(+), 1 deletion(-) diff --git a/test/unit/samples/sample_type_editing_constraints_test.rb b/test/unit/samples/sample_type_editing_constraints_test.rb index ace957c974..4cfdc03a7a 100644 --- a/test/unit/samples/sample_type_editing_constraints_test.rb +++ b/test/unit/samples/sample_type_editing_constraints_test.rb @@ -87,13 +87,29 @@ class SampleTypeEditingConstraintsTest < ActiveSupport::TestCase assert c.allow_required?(:age) assert c.allow_required?('full name') - # accespts attribute + # accepts attribute attr = c.sample_type.sample_attributes.detect { |t| t.accessor_name == 'address' } refute_nil attr refute c.allow_required?(attr) attr = c.sample_type.sample_attributes.detect { |t| t.accessor_name == 'age' } refute_nil attr assert c.allow_required?(attr) + + # should refute if inherited from a template + template = FactoryBot.create(:isa_source_template) + sample_type_from_template = create_sample_type_from_template(template, c.sample_type.projects.first, c.sample_type.contributor) + sample_type_from_template.sample_attributes << FactoryBot.create(:sample_attribute, title: 'Extra Source Characteristic', sample_attribute_type: FactoryBot.create(:string_sample_attribute_type), required: false, isa_tag_id: FactoryBot.create(:source_characteristic_isa_tag).id, sample_type: sample_type_from_template) + + c_inherited = Seek::Samples::SampleTypeEditingConstraints.new(sample_type_from_template) + sample_type_from_template.sample_attributes.each do |attr| + if attr.title == 'Extra Source Characteristic' + refute c_inherited.send(:inherited?, attr) + assert c_inherited.allow_required?(attr) + else + assert c_inherited.send(:inherited?, attr) + refute c_inherited.allow_required?(attr) + end + end end test 'allow_attribute_removal?' do From 52e30617c7d301557552833d7ecd187ca17e415e Mon Sep 17 00:00:00 2001 From: Kevin De Pelseneer Date: Fri, 24 May 2024 10:36:09 +0200 Subject: [PATCH 037/131] Remove all logic from the views and transfer to controller --- app/controllers/isa_assays_controller.rb | 49 +++++++++++++++--- app/views/isa_assays/_form.html.erb | 63 +++++------------------- 2 files changed, 52 insertions(+), 60 deletions(-) diff --git a/app/controllers/isa_assays_controller.rb b/app/controllers/isa_assays_controller.rb index 8681f2a23f..710001a1d7 100644 --- a/app/controllers/isa_assays_controller.rb +++ b/app/controllers/isa_assays_controller.rb @@ -9,20 +9,53 @@ class IsaAssaysController < ApplicationController after_action :rearrange_assay_positions_create_isa_assay, only: :create def new - if params[:is_assay_stream] - @isa_assay = IsaAssay.new({ assay: { assay_class_id: AssayClass.assay_stream.id } }) - else - @isa_assay = IsaAssay.new({ assay: { assay_class_id: AssayClass.experimental.id } }) - end + new_position = + if params[:is_assay_stream] || params[:source_assay_id].nil? || (params[:source_assay_id] == params[:assay_stream_id]) + 0 + else + Assay.find(params[:source_assay_id]).position + 1 + end + + study = Study.find(params[:study_id]) + source_assay = Assay.find(params[:source_assay_id]) if params[:source_assay_id] + + input_sample_type_id = + if params[:is_assay_stream] + study.sample_types.second.id + else + source_assay.previous_linked_sample_type.id if source_assay + end + + projects = [] + + @isa_assay = + if params[:is_assay_stream] + IsaAssay.new({ assay: { assay_class_id: AssayClass.assay_stream.id, + study_id: study.id, + position: 0 }, + input_sample_type_id: input_sample_type_id}) + else + IsaAssay.new({ assay: { assay_class_id: AssayClass.experimental.id, + assay_stream_id: params[:assay_stream_id], + study_id: study.id, + position: new_position }, + input_sample_type_id: input_sample_type_id}) + end end def create if @isa_assay.save - redirect_to single_page_path(id: @isa_assay.assay.projects.first, item_type: 'assay', - item_id: @isa_assay.assay, notice: 'The ISA assay was created successfully!') + flash[:notice] = "The #{t('isa_assay')} was succesfully created.
".html_safe + respond_to do |format| + format.html do + redirect_to single_page_path(id: @isa_assay.assay.projects.first, item_type: 'assay', + item_id: @isa_assay.assay) + end + format.json { render json: @isa_assay, include: [params[:include]] } + end else respond_to do |format| - format.html { render action: 'new' } + format.html { render action: 'new', status: :unprocessable_entity } format.json { render json: json_api_errors(@isa_assay), status: :unprocessable_entity } end end diff --git a/app/views/isa_assays/_form.html.erb b/app/views/isa_assays/_form.html.erb index 899e57ad4f..020972f4d0 100644 --- a/app/views/isa_assays/_form.html.erb +++ b/app/views/isa_assays/_form.html.erb @@ -1,46 +1,6 @@ -<% assay = params[:isa_assay][:assay] if params.dig(:isa_assay, :assay) %> -<% study = Study.find(params[:study_id] || assay[:study_id]) %> -<% def first_assay_in_stream? - params[:source_assay_id].nil? || (params[:source_assay_id] == params[:assay_stream_id]) - end -%> <% - source_assay = Assay.find(params[:source_assay_id]) if params[:source_assay_id] - assay_stream_id = params[:assay_stream_id] if params[:assay_stream_id] - - if @isa_assay.assay.new_record? - if params[:is_assay_stream] - assay_position = study.assay_streams.any? ? study.assay_streams.map(&:position).max + 1 : 0 - assay_class_id = AssayClass.assay_stream.id - is_assay_stream = true - else - assay_position = first_assay_in_stream? ? 0 : source_assay.position + 1 - assay_class_id = AssayClass.experimental.id - is_assay_stream = false - end - else - assay_position = @isa_assay.assay.position - assay_class_id = @isa_assay.assay.assay_class_id - is_assay_stream = @isa_assay.assay.is_assay_stream? - end - - input_sample_type_id ||= - if is_assay_stream || source_assay&.assay_class&.is_assay_stream? - study.sample_types.second.id - else - source_assay.sample_type.id if source_assay - end - - show_extended_metadata = - if is_assay_stream - true - elsif source_assay&.position&.zero? && !@isa_assay.assay.new_record? - true # Custom metadata should be shown in edit as well if assay position is 0. - else - false - end + is_assay_stream = @isa_assay.assay.is_assay_stream? %> - <%= error_messages_for :isa_assay %> <%= f.fields_for @isa_assay.assay do |assay_fields| %> @@ -55,30 +15,28 @@ <%= assay_fields.text_area :description, rows: 5, class: "form-control rich-text-edit" -%> - <% if show_extended_metadata %> + # Show extended metadata is assay is of class assay_stream + <% if is_assay_stream %> <%= render partial: 'extended_metadata/extended_metadata_type_selection', locals:{f:assay_fields, resource:@isa_assay.assay} %> <%= render partial: 'extended_metadata/extended_metadata_attribute_input', locals:{f:assay_fields,resource:@isa_assay.assay, parent_resource: "isa_assay"} %> <% end %> - + <%= assay_fields.hidden_field :study_id %> <% if is_assay_stream %>
<%= assay_fields.label "Assay position" -%>
- <%= assay_fields.number_field :position, rows: 5, class: "form-control", value: assay_position %> + <%= assay_fields.number_field :position, rows: 5, class: "form-control" %>
<% else %> <% end %> - <%= assay_fields.hidden_field :assay_stream_id, value: assay_stream_id -%> - <%= assay_fields.hidden_field :assay_class_id, value: assay_class_id -%> + <%= assay_fields.hidden_field :assay_stream_id -%> + <%= assay_fields.hidden_field :assay_class_id -%> <% if is_assay_stream %> <% if User.current_user -%> @@ -97,7 +55,7 @@ <% end -%> <% end -%> -<%= f.hidden_field :input_sample_type_id, value: input_sample_type_id -%> +<%= f.hidden_field :input_sample_type_id -%> <% unless is_assay_stream %> <%= folding_panel("Define #{t(:sample_type)} for #{t(:assay)}") do %> @@ -110,7 +68,8 @@ <%= render partial: 'projects/implicit_project_selector', locals: { action: action, select_id: '#isa_assay_assay_study_id', - parents: Study.authorized_for('edit') } %> + parents: Study.authorized_for('edit'), + skip_on_page_load: true} %> From 723f6420125f7457ee196c13f0e533983130a96b Mon Sep 17 00:00:00 2001 From: Kevin De Pelseneer Date: Fri, 24 May 2024 13:17:20 +0200 Subject: [PATCH 041/131] Remove investigation list partial that conflicts with default policy prompt --- app/views/isa_studies/_form.html.erb | 4 ---- 1 file changed, 4 deletions(-) diff --git a/app/views/isa_studies/_form.html.erb b/app/views/isa_studies/_form.html.erb index 77d5b45858..d59bc9887f 100644 --- a/app/views/isa_studies/_form.html.erb +++ b/app/views/isa_studies/_form.html.erb @@ -23,10 +23,6 @@ <% end %> - -
<%= study_fields.label "Study position" -%>
<%= study_fields.number_field :position, :rows => 5, :class=>"form-control" -%> From 3c32ab05643eaaae7a92133a6c1c34c346553107 Mon Sep 17 00:00:00 2001 From: Kevin De Pelseneer Date: Fri, 24 May 2024 13:22:46 +0200 Subject: [PATCH 042/131] Prepopulate the investigation ID when assigning `@isa_study` --- app/controllers/isa_studies_controller.rb | 2 +- app/views/isa_studies/_form.html.erb | 9 --------- 2 files changed, 1 insertion(+), 10 deletions(-) diff --git a/app/controllers/isa_studies_controller.rb b/app/controllers/isa_studies_controller.rb index a060bf16bc..990169a543 100644 --- a/app/controllers/isa_studies_controller.rb +++ b/app/controllers/isa_studies_controller.rb @@ -6,7 +6,7 @@ class IsaStudiesController < ApplicationController before_action :find_requested_item, only: %i[edit update] def new - @isa_study = IsaStudy.new + @isa_study = IsaStudy.new({ study: { investigation_id: params[:investigation_id] } }) end def create diff --git a/app/views/isa_studies/_form.html.erb b/app/views/isa_studies/_form.html.erb index d59bc9887f..92d47194a5 100644 --- a/app/views/isa_studies/_form.html.erb +++ b/app/views/isa_studies/_form.html.erb @@ -76,15 +76,6 @@ } $j(document).ready(function () { - const urlSearchParams = new URLSearchParams(window.location.search); - const params = Object.fromEntries(urlSearchParams.entries()); - const investigation_id = params["investigation_id"] - // Prevent setting the hidden field on redirect (query string parameters are missing) - if(investigation_id) { - $j("#isa_study_study_investigation_id").val(investigation_id); - $j("#study_investigation_id").val(investigation_id).change(); - } - if (templates.length > 0) { Templates.init($j('#template-attributes')); } From 2bf968aa736c21978d83fe98eb22fa151c272656 Mon Sep 17 00:00:00 2001 From: Kevin De Pelseneer Date: Fri, 24 May 2024 13:56:39 +0200 Subject: [PATCH 043/131] Simplification + better error messages --- app/controllers/isa_assays_controller.rb | 4 +++- app/controllers/isa_studies_controller.rb | 23 +++++++++++++++-------- 2 files changed, 18 insertions(+), 9 deletions(-) diff --git a/app/controllers/isa_assays_controller.rb b/app/controllers/isa_assays_controller.rb index dbf1ce9807..b343b2b2d4 100644 --- a/app/controllers/isa_assays_controller.rb +++ b/app/controllers/isa_assays_controller.rb @@ -212,7 +212,9 @@ def find_requested_item end if @isa_assay.errors.any? - error_messages = @isa_assay.errors.full_messages.map { |msg| "
  • [#{t('isa_assay')}]: #{msg}
    • " }.join('') + error_messages = @isa_assay.errors.map do |error| + "
  • [#{error.attribute.to_s}]: #{error.message}
    • " + end.join('') flash[:error] = "
      #{error_messages}
    ".html_safe redirect_to single_page_path(id: @isa_assay.assay.projects.first, item_type: 'assay', item_id: @isa_assay.assay) diff --git a/app/controllers/isa_studies_controller.rb b/app/controllers/isa_studies_controller.rb index 990169a543..791575e4d2 100644 --- a/app/controllers/isa_studies_controller.rb +++ b/app/controllers/isa_studies_controller.rb @@ -36,12 +36,7 @@ def create end def edit - @isa_study.source = nil unless requested_item_authorized?(@isa_study.source) - @isa_study.sample_collection = nil unless requested_item_authorized?(@isa_study.sample_collection) - - respond_to do |format| - format.html - end + respond_to(&:html) end def update @@ -132,8 +127,20 @@ def set_up_instance_variable def find_requested_item @isa_study = IsaStudy.new @isa_study.populate(params[:id]) - unless requested_item_authorized?(@isa_study.study) - flash[:error] = "You are not authorized to edit this #{t('isa_study')}" + + @isa_study.errors.add(:study, "The #{t('isa_study')} was not found.") if @isa_study.study.nil? + @isa_study.errors.add(:study, "You are not authorized to edit this #{t('isa_study')}.") unless requested_item_authorized?(@isa_study.study) + + @isa_study.errors.add(:sample_type, "'Study source' #{t('sample_type')} not found.") if @isa_study.source.nil? + @isa_study.errors.add(:sample_type, "You are not authorized to edit the 'study source' #{t('sample_type')}.") unless requested_item_authorized?(@isa_study.source) + @isa_study.errors.add(:sample_type, "'Study sample' #{t('sample_type')} not found.") if @isa_study.sample_collection.nil? + @isa_study.errors.add(:sample_type, "You are not authorized to edit the 'study sample' #{t('sample_type')}.") unless requested_item_authorized?(@isa_study.sample_collection) + + if @isa_study.errors.any? + error_messages = @isa_study.errors.map do |error| + "
  • [#{error.attribute.to_s}]: #{error.message}
    • " + end.join('') + flash[:error] = "
      #{error_messages}
    ".html_safe redirect_to single_page_path(id: @isa_study.study.projects.first, item_type: 'study', item_id: @isa_study.study) end From b926597d6e5dac7edf8b20a8c01fe880f32fd5d4 Mon Sep 17 00:00:00 2001 From: Kevin De Pelseneer Date: Fri, 24 May 2024 14:18:46 +0200 Subject: [PATCH 044/131] Skip value if ID is blank --- app/helpers/samples_helper.rb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/app/helpers/samples_helper.rb b/app/helpers/samples_helper.rb index bd4bfd36dd..5c37ad0c79 100644 --- a/app/helpers/samples_helper.rb +++ b/app/helpers/samples_helper.rb @@ -81,6 +81,8 @@ def sample_form_field(attribute, element_name, value, limit = 1) value = [value] unless value.is_a?(Array) value.compact.each do |v| id = v[:id] + next if id.blank? # Skip value if there is no ID + title = v[:title] title = 'Hidden' unless Sample.find(id).can_view? existing_objects << str.new(id, title) @@ -379,5 +381,3 @@ def attribute_form_element(attribute, value, element_name, element_class, depth= end end - - From a62a0c763b0d7390c72cb7e0446c0a07447017c2 Mon Sep 17 00:00:00 2001 From: Kevin De Pelseneer Date: Fri, 24 May 2024 14:32:48 +0200 Subject: [PATCH 045/131] Rename registeredSamplesObjectsInput --- app/assets/javascripts/single_page/dynamic_table.js.erb | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/app/assets/javascripts/single_page/dynamic_table.js.erb b/app/assets/javascripts/single_page/dynamic_table.js.erb index ae1a9cc598..a0c2f4556a 100644 --- a/app/assets/javascripts/single_page/dynamic_table.js.erb +++ b/app/assets/javascripts/single_page/dynamic_table.js.erb @@ -90,7 +90,7 @@ const handleSelect = (e) => { if(c.linked_sample_type){ data = sanitizedData && Array.isArray(sanitizedData) ? sanitizedData : [sanitizedData]; data = data[0]?.id ? data : []; - return inputObjectsInput(c, data, options, linkedSamplesUrl); + return registeredSamplesObjectsInput(c, data, options, linkedSamplesUrl); } else if(c.is_cv_list && sanitizedData !== "#HIDDEN"){ data = sanitizedData && Array.isArray(sanitizedData) ? sanitizedData : [sanitizedData]; data = data.map((e) => { @@ -569,7 +569,7 @@ function retrieveLinkedSamples(url){ return linkedSamples; } -function inputObjectsInput(column, data, options, url){ +function registeredSamplesObjectsInput(column, data, options, url){ const existingOptions = data.map((e) => { isHiddenInput = (e.title == '#HIDDEN'); if (isHiddenInput) { @@ -584,7 +584,6 @@ function inputObjectsInput(column, data, options, url){ const typeaheadTemplate = 'typeahead/single_pages_samples' const objectInputName = data.map((e) => e.id).join('-') + '-' + crypto.randomUUID(); - const unLinkedSamples = data.reduce(function(filtered, sample) { if(!column.linkedSampleIds.includes(parseInt(sample.id)) && sample.title != '#HIDDEN'){ filtered.push(sample); From e286ad2458fded128248a74a5a0c305984f94cf9 Mon Sep 17 00:00:00 2001 From: Kevin De Pelseneer Date: Fri, 24 May 2024 15:09:57 +0200 Subject: [PATCH 046/131] Replace drop-down with objects input with limit of 1 for registered sample attributes --- .../javascripts/single_page/dynamic_table.js.erb | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/app/assets/javascripts/single_page/dynamic_table.js.erb b/app/assets/javascripts/single_page/dynamic_table.js.erb index a0c2f4556a..63627432bc 100644 --- a/app/assets/javascripts/single_page/dynamic_table.js.erb +++ b/app/assets/javascripts/single_page/dynamic_table.js.erb @@ -48,7 +48,7 @@ function sanitizeData(data) { const objectInputTemp = '' + ''; const typeaheadSamplesUrl = "<%= typeahead_samples_path(linked_sample_type_id: '_LINKED_') %>"; @@ -86,7 +86,8 @@ const handleSelect = (e) => { } c["render"] = function(data_, type, full, meta) { - sanitizedData = sanitizeData(data_); + let sanitizedData = sanitizeData(data_); + let data; if(c.linked_sample_type){ data = sanitizedData && Array.isArray(sanitizedData) ? sanitizedData : [sanitizedData]; data = data[0]?.id ? data : []; @@ -592,7 +593,7 @@ function registeredSamplesObjectsInput(column, data, options, url){ }, []); const hasUnlinkedSamples = unLinkedSamples.length > 0 ? true : false; - const hasMultipleInputs = column.multi_link ? 'multiple="multiple"' : '' + const hasMultipleInputs = column.multi_link ? '100' : '1' const extraClass = hasUnlinkedSamples ? 'select2__error' : ''; const titleText = hasUnlinkedSamples ? `Sample(s) '${unLinkedSamples.map(uls => uls.title).join(', ')}' not recognised as input. Please correct this issue!` : ''; setTimeout(ObjectsInput.init); @@ -604,7 +605,7 @@ function registeredSamplesObjectsInput(column, data, options, url){ .replace('_OPTIONS_', existingOptions) .replace('_EXTRACLASS_', extraClass) .replace('_TITLE_', titleText) - .replace('_MULTIPLE?_', hasMultipleInputs) + .replace('_LIMIT?_', hasMultipleInputs) .replace('_ALLOW_FREE_TEXT_', false); } } @@ -628,7 +629,7 @@ function cvListObjectsInput(column, data, options, url){ .replace('_OPTIONS_', existingOptions) .replace('_EXTRACLASS_', extraClass) .replace('_TITLE_', titleText) - .replace('_MULTIPLE?_', 'multiple="multiple"') + .replace('_LIMIT?_', '') .replace('_ALLOW_FREE_TEXT_', allowNewItems); } } From 1bb74c5e25b1fc030fb3d315b09e9da8e61ef8d3 Mon Sep 17 00:00:00 2001 From: Kevin De Pelseneer Date: Mon, 27 May 2024 09:32:46 +0200 Subject: [PATCH 047/131] Fix tests --- app/controllers/isa_assays_controller.rb | 26 ++++++++++++------- app/views/isa_assays/_form.html.erb | 2 +- test/functional/isa_assays_controller_test.rb | 11 ++++---- 3 files changed, 23 insertions(+), 16 deletions(-) diff --git a/app/controllers/isa_assays_controller.rb b/app/controllers/isa_assays_controller.rb index b343b2b2d4..7e93c82ab4 100644 --- a/app/controllers/isa_assays_controller.rb +++ b/app/controllers/isa_assays_controller.rb @@ -9,17 +9,19 @@ class IsaAssaysController < ApplicationController after_action :rearrange_assay_positions_create_isa_assay, only: :create def new + study = Study.find(params[:study_id]) new_position = - if params[:is_assay_stream] || params[:source_assay_id].nil? || (params[:source_assay_id] == params[:assay_stream_id]) + if params[:is_assay_stream] || params[:source_assay_id].nil? # If first assay is of class assay stream + study.assay_streams.any? ? study.assay_streams.map(&:position).max + 1 : 0 + elsif params[:source_assay_id] == params[:assay_stream_id] # If first assay in the stream 0 else Assay.find(params[:source_assay_id]).position + 1 end - study = Study.find(params[:study_id]) source_assay = Assay.find(params[:source_assay_id]) if params[:source_assay_id] input_sample_type_id = - if params[:is_assay_stream] || source_assay.is_assay_stream? + if params[:is_assay_stream] || source_assay&.is_assay_stream? study.sample_types.second.id else source_assay&.sample_type&.id @@ -29,7 +31,7 @@ def new if params[:is_assay_stream] IsaAssay.new({ assay: { assay_class_id: AssayClass.assay_stream.id, study_id: study.id, - position: 0 }, + position: new_position }, input_sample_type_id: }) else IsaAssay.new({ assay: { assay_class_id: AssayClass.experimental.id, @@ -67,7 +69,7 @@ def update @isa_assay.assay.attributes = isa_assay_params[:assay] # update the sample_type - unless @isa_assay.assay.is_assay_stream? + unless @isa_assay&.assay&.is_assay_stream? if requested_item_authorized?(@isa_assay.sample_type) @isa_assay.sample_type.update(isa_assay_params[:sample_type]) @isa_assay.sample_type.resolve_inconsistencies @@ -202,13 +204,19 @@ def find_requested_item @isa_assay = IsaAssay.new @isa_assay.populate(params[:id]) - @isa_assay.errors.add(:assay, "The #{t('isa_assay')} was not found.") if @isa_assay.assay.nil? - @isa_assay.errors.add(:assay, "You are not authorized to edit this #{t('isa_assay')}.") unless requested_item_authorized?(@isa_assay.assay) + if @isa_assay.assay.nil? + @isa_assay.errors.add(:assay, "The #{t('isa_assay')} was not found.") + else + @isa_assay.errors.add(:assay, "You are not authorized to edit this #{t('isa_assay')}.") unless requested_item_authorized?(@isa_assay.assay) + end # Should not deal with sample type if assay has assay_class assay stream unless @isa_assay.assay&.is_assay_stream? - @isa_assay.errors.add(:sample_type, 'Sample type not found.') if @isa_assay.sample_type.nil? - @isa_assay.errors.add(:sample_type, "You are not authorized to edit this assay's #{t('sample_type')}.") unless requested_item_authorized?(@isa_assay.sample_type) + if @isa_assay.sample_type.nil? + @isa_assay.errors.add(:sample_type, 'Sample type not found.') + else + @isa_assay.errors.add(:sample_type, "You are not authorized to edit this assay's #{t('sample_type')}.") unless requested_item_authorized?(@isa_assay.sample_type) + end end if @isa_assay.errors.any? diff --git a/app/views/isa_assays/_form.html.erb b/app/views/isa_assays/_form.html.erb index 15d980b68e..81b4c064d1 100644 --- a/app/views/isa_assays/_form.html.erb +++ b/app/views/isa_assays/_form.html.erb @@ -15,7 +15,7 @@ <%= assay_fields.text_area :description, rows: 5, class: "form-control rich-text-edit" -%>
    - # Show extended metadata is assay is of class assay_stream + <%# Show extended metadata is assay is of class assay_stream %> <% if is_assay_stream %> <%= render partial: 'extended_metadata/extended_metadata_type_selection', locals:{f:assay_fields, resource:@isa_assay.assay} %> <%= render partial: 'extended_metadata/extended_metadata_attribute_input', locals:{f:assay_fields,resource:@isa_assay.assay, parent_resource: "isa_assay"} %> diff --git a/test/functional/isa_assays_controller_test.rb b/test/functional/isa_assays_controller_test.rb index ba746b6d70..1ad8afd286 100644 --- a/test/functional/isa_assays_controller_test.rb +++ b/test/functional/isa_assays_controller_test.rb @@ -76,8 +76,7 @@ def setup end isa_assay = assigns(:isa_assay) assert_redirected_to controller: 'single_pages', action: 'show', id: isa_assay.assay.projects.first.id, - params: { notice: 'The ISA assay was created successfully!', - item_type: 'assay', item_id: Assay.last.id } + params: { item_type: 'assay', item_id: Assay.last.id } sample_types = SampleType.last(2) title = sample_types[0].sample_attributes.detect(&:is_title).title @@ -139,7 +138,7 @@ def setup assay = FactoryBot.create(:assay, study:, contributor: person) put :update, params: { id: assay, isa_assay: { assay: { title: 'assay title' } } } assert_redirected_to single_page_path(id: project, item_type: 'assay', item_id: assay.id) - assert flash[:error].include?('Resource not found.') + assert flash[:error].include?('Sample type not found.') assay = FactoryBot.create(:assay, study:, sample_type: assay_type, contributor: person) @@ -359,7 +358,7 @@ def setup end isa_assay = assigns(:isa_assay) - assert_redirected_to single_page_path(id: project, item_type: 'assay', item_id: isa_assay.assay.id, notice: 'The ISA assay was created successfully!') + assert_redirected_to single_page_path(id: project, item_type: 'assay', item_id: isa_assay.assay.id) assert_equal isa_assay.assay.sample_type.previous_linked_sample_type, study.sample_types.second assert_equal isa_assay.assay.next_linked_child_assay, end_assay @@ -455,7 +454,7 @@ def setup end isa_assay = assigns(:isa_assay) - assert_redirected_to single_page_path(id: project, item_type: 'assay', item_id: isa_assay.assay.id, notice: 'The ISA assay was created successfully!') + assert_redirected_to single_page_path(id: project, item_type: 'assay', item_id: isa_assay.assay.id) assert_equal begin_assay.previous_linked_sample_type, study.sample_types.second assert_equal isa_assay.assay.sample_type.previous_linked_sample_type, begin_assay.sample_type @@ -619,7 +618,7 @@ def setup # New assay stream should have position 1 and is of type 'number' assert_select 'input[type=number][value=1]#isa_assay_assay_position', count: 1 - assay_stream2 = FactoryBot.create(:assay_stream, study: , contributor: person, position: 5) + FactoryBot.create(:assay_stream, study: , contributor: person, position: 5) get :new, params: { study_id: study.id, is_assay_stream: true } assert_response :success # New assay stream should have position 6 and is of type 'number' From 36ba2e339a360a076c3a6c2c2bfc6bccac0b4d5b Mon Sep 17 00:00:00 2001 From: Kevin De Pelseneer Date: Mon, 27 May 2024 14:21:12 +0200 Subject: [PATCH 048/131] Remove the data-dismiss attribute and add a function that hides the modal --- app/views/sharing/_group_permission_modal.html.erb | 5 ++++- app/views/sharing/_person_permission_modal.html.erb | 6 ++++-- app/views/sharing/_programme_permission_modal.html.erb | 9 ++++++--- 3 files changed, 14 insertions(+), 6 deletions(-) diff --git a/app/views/sharing/_group_permission_modal.html.erb b/app/views/sharing/_group_permission_modal.html.erb index e31c09fb6f..fd0748ec2f 100644 --- a/app/views/sharing/_group_permission_modal.html.erb +++ b/app/views/sharing/_group_permission_modal.html.erb @@ -32,7 +32,7 @@ <% end %> <%= modal_footer do %> - <%= link_to('Add', '#', id: 'permission-project-confirm', class: 'btn btn-primary pull-right', 'data-dismiss' => 'modal') %> + <%= link_to('Add', '#', id: 'permission-project-confirm', class: 'btn btn-primary pull-right') %> <% end %> <% end %> @@ -77,6 +77,9 @@ } } + // Close this modal + $j('#add-project-permission-modal').modal('hide'); + Sharing.addPermission(permission); }); diff --git a/app/views/sharing/_person_permission_modal.html.erb b/app/views/sharing/_person_permission_modal.html.erb index f10f4bf61a..5e9f0a4903 100644 --- a/app/views/sharing/_person_permission_modal.html.erb +++ b/app/views/sharing/_person_permission_modal.html.erb @@ -18,7 +18,7 @@ <% end %> <%= modal_footer do %> - <%= link_to('Add', '#', id: 'permission-people-confirm', class: 'btn btn-primary pull-right', 'data-dismiss' => 'modal') %> + <% link_to('Add', '#', id: 'permission-people-confirm', class: 'btn btn-primary pull-right') %> <% end %> <% end %> @@ -44,9 +44,11 @@ access_type: parseInt($j('#permission-people-access-type').val()) }); }); - // Reset form $j('select#permission-people-ids').val([]).change(); $j('#permission-people-access-type').val('<%= Policy::ACCESSIBLE %>').change(); + + // Close this modal + $j('#add-person-permission-modal').modal('hide'); }); diff --git a/app/views/sharing/_programme_permission_modal.html.erb b/app/views/sharing/_programme_permission_modal.html.erb index 94eb5e97e0..3e35b25a79 100644 --- a/app/views/sharing/_programme_permission_modal.html.erb +++ b/app/views/sharing/_programme_permission_modal.html.erb @@ -18,7 +18,7 @@ <% end %> <%= modal_footer do %> - <%= link_to('Add', '#', id: 'permission-programmes-confirm', class: 'btn btn-primary pull-right', 'data-dismiss' => 'modal') %> + <%= link_to('Add', '#', id: 'permission-programmes-confirm', class: 'btn btn-primary pull-right') %> <% end %> <% end %> @@ -44,7 +44,10 @@ }); // Reset form - $j('select#permission-programmes-ids').val([]).change(); - $j('#permission-programmes-access-type').val('<%= Policy::ACCESSIBLE %>').change(); + $j('select#permission-programmes-ids').val([]).change(); + $j('#permission-programmes-access-type').val('<%= Policy::ACCESSIBLE %>').change(); + + // Close this modal + $j('#add-programme-permission-modal').modal('hide'); }); From 52c636cf0f29db99783ac8411b951019e2dcf320 Mon Sep 17 00:00:00 2001 From: Kevin De Pelseneer Date: Mon, 27 May 2024 16:21:16 +0200 Subject: [PATCH 049/131] Add functionality for cancel button --- app/helpers/bootstrap_helper.rb | 13 +++++++++--- .../sharing/_group_permission_modal.html.erb | 13 +++++++++--- .../sharing/_person_permission_modal.html.erb | 20 ++++++++++++++---- .../_programme_permission_modal.html.erb | 21 ++++++++++++++----- 4 files changed, 52 insertions(+), 15 deletions(-) diff --git a/app/helpers/bootstrap_helper.rb b/app/helpers/bootstrap_helper.rb index 0ee54d45d2..f222431a61 100644 --- a/app/helpers/bootstrap_helper.rb +++ b/app/helpers/bootstrap_helper.rb @@ -161,10 +161,17 @@ def modal(options = {}, &block) end end - def modal_header(title, _options = {}) + def modal_header(title, options = {}) + # If no_close_btn is set to true, the modal will not have a close button. + # Useful for multiple shown modals. + no_close_btn = options[:no_close_btn] if options[:no_close_btn] content_tag(:div, class: 'modal-header') do - content_tag(:button, class: 'close', 'data-dismiss' => 'modal', 'aria-label' => 'Close') do - content_tag(:span, '×'.html_safe, 'aria-hidden' => 'true') + if no_close_btn + ''.html_safe + else + content_tag(:button, class: 'close', 'data-dismiss' => 'modal', 'aria-label' => 'Close' ) do + content_tag(:span, '×'.html_safe, 'aria-hidden' => 'true') + end end + content_tag(:h4, title, class: 'modal-title') end diff --git a/app/views/sharing/_group_permission_modal.html.erb b/app/views/sharing/_group_permission_modal.html.erb index fd0748ec2f..901d42de98 100644 --- a/app/views/sharing/_group_permission_modal.html.erb +++ b/app/views/sharing/_group_permission_modal.html.erb @@ -1,7 +1,7 @@ <%= button_link_to("Share with a #{t('project')} / #{t('institution')}", 'add', '#', id: 'add-project-permission-button') %> <%= modal(id: 'add-project-permission-modal', size: 'm') do %> - <%= modal_header("Share with a #{t('project')} and/or #{t('institution')}") %> + <%= modal_header("Share with a #{t('project')} and/or #{t('institution')}", { no_close_btn: true }) %> <%= modal_body do %>
    @@ -32,7 +32,9 @@
    <% end %> <%= modal_footer do %> - <%= link_to('Add', '#', id: 'permission-project-confirm', class: 'btn btn-primary pull-right') %> + <%= link_to('Add', '#', id: 'permission-project-confirm', class: 'btn btn-primary') %> + or + <%= link_to('Cancel', '#', id: 'cancel-project-selection', class: 'btn btn-default') %> <% end %> <% end %> @@ -77,12 +79,17 @@ } } - // Close this modal + // Close this modal after clicking add button $j('#add-project-permission-modal').modal('hide'); Sharing.addPermission(permission); }); + // Close modal when cancel button is clicked + $j('#cancel-project-selection').click(function () { + $j('#add-project-permission-modal').modal('hide'); + }); + // Update the institution list when a project is selected $j('#permission-project-id').change(function () { var institutionSelect = $j('#permission-institution-id'); diff --git a/app/views/sharing/_person_permission_modal.html.erb b/app/views/sharing/_person_permission_modal.html.erb index 5e9f0a4903..b26b88c8dc 100644 --- a/app/views/sharing/_person_permission_modal.html.erb +++ b/app/views/sharing/_person_permission_modal.html.erb @@ -1,7 +1,7 @@ <%= button_link_to("Share with a #{t('person')}", 'add', '#', id: 'add-person-permission-button') %> <%= modal(id: 'add-person-permission-modal', size: 'm') do %> - <%= modal_header("Share with #{t('person').pluralize}") %> + <%= modal_header("Share with #{t('person').pluralize}", { no_close_btn: true }) %> <%= modal_body do %>
    @@ -18,11 +18,18 @@
    <% end %> <%= modal_footer do %> - <% link_to('Add', '#', id: 'permission-people-confirm', class: 'btn btn-primary pull-right') %> + <%= link_to('Add', '#', id: 'permission-people-confirm', class: 'btn btn-primary') %> + or + <%= link_to('Cancel', '#', id: 'cancel-people-permission-selection', class: 'btn btn-default') %> <% end %> <% end %> diff --git a/app/views/sharing/_programme_permission_modal.html.erb b/app/views/sharing/_programme_permission_modal.html.erb index 3e35b25a79..994d35a336 100644 --- a/app/views/sharing/_programme_permission_modal.html.erb +++ b/app/views/sharing/_programme_permission_modal.html.erb @@ -1,7 +1,7 @@ <%= button_link_to("Share with a #{t('programme')}", 'add', '#', id: 'add-programme-permission-button') %> <%= modal(id: 'add-programme-permission-modal', size: 'm') do %> - <%= modal_header("Share with #{t('programme').pluralize}") %> + <%= modal_header("Share with #{t('programme').pluralize}", { no_close_btn: true }) %> <%= modal_body do %>
    @@ -18,11 +18,18 @@
    <% end %> <%= modal_footer do %> - <%= link_to('Add', '#', id: 'permission-programmes-confirm', class: 'btn btn-primary pull-right') %> + <%= link_to('Add', '#', id: 'permission-programmes-confirm', class: 'btn btn-primary') %> + or + <%= link_to('Cancel', '#', id: 'cancel-programme-permission-selection', class: 'btn btn-default') %> <% end %> <% end %> From 60bcd97cbecbb64dbfd220dfbd32253e8186cc9c Mon Sep 17 00:00:00 2001 From: Kevin De Pelseneer Date: Mon, 27 May 2024 17:25:13 +0200 Subject: [PATCH 050/131] Make terms unique within a sample controlled vocab --- app/models/sample_controlled_vocab_term.rb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/app/models/sample_controlled_vocab_term.rb b/app/models/sample_controlled_vocab_term.rb index 4f1791e66f..092c85a9a5 100644 --- a/app/models/sample_controlled_vocab_term.rb +++ b/app/models/sample_controlled_vocab_term.rb @@ -1,7 +1,7 @@ class SampleControlledVocabTerm < ApplicationRecord belongs_to :sample_controlled_vocab, inverse_of: :sample_controlled_vocab_terms - validates :label, presence: true, length: { maximum: 500 } + validates :label, presence: true, length: { maximum: 500 }, uniqueness: { scope: :sample_controlled_vocab_id } before_validation :truncate_label From ec659ad0f0f750039806c619e4ccf03db4e3c871 Mon Sep 17 00:00:00 2001 From: Kevin De Pelseneer Date: Mon, 27 May 2024 17:59:25 +0200 Subject: [PATCH 051/131] Add id as a hidden field to also pass the ID to the controller when updating the CV --- app/views/sample_controlled_vocabs/_term_form_row.html.erb | 5 ++++- .../_term_form_row_disabled.html.erb | 1 + 2 files changed, 5 insertions(+), 1 deletion(-) diff --git a/app/views/sample_controlled_vocabs/_term_form_row.html.erb b/app/views/sample_controlled_vocabs/_term_form_row.html.erb index aa600c85a7..ffb2edf3b5 100644 --- a/app/views/sample_controlled_vocabs/_term_form_row.html.erb +++ b/app/views/sample_controlled_vocabs/_term_form_row.html.erb @@ -1,5 +1,8 @@
    <%= text_field_tag "sample_controlled_vocab[sample_controlled_vocab_terms_attributes][#{index}][label]", term.label %> + <%= hidden_field_tag "sample_controlled_vocab[sample_controlled_vocab_terms_attributes][#{index}][id]", term.id %> + <%= text_field_tag "sample_controlled_vocab[sample_controlled_vocab_terms_attributes][#{index}][label]", term.label %> + <%= text_field_tag "sample_controlled_vocab[sample_controlled_vocab_terms_attributes][#{index}][iri]", term.iri %> <%= text_field_tag "sample_controlled_vocab[sample_controlled_vocab_terms_attributes][#{index}][parent_iri]", term.parent_iri %> diff --git a/app/views/sample_controlled_vocabs/_term_form_row_disabled.html.erb b/app/views/sample_controlled_vocabs/_term_form_row_disabled.html.erb index 2be8514245..a331b87914 100644 --- a/app/views/sample_controlled_vocabs/_term_form_row_disabled.html.erb +++ b/app/views/sample_controlled_vocabs/_term_form_row_disabled.html.erb @@ -8,6 +8,7 @@ %>
    + <%= hidden_field_tag "sample_controlled_vocab[sample_controlled_vocab_terms_attributes][#{index}][id]", term.id %> <%= hidden_field_tag "sample_controlled_vocab[sample_controlled_vocab_terms_attributes][#{index}][label]", term.label %>
    <%= term.label %>
    - <%= hidden_field_tag "sample_controlled_vocab[sample_controlled_vocab_terms_attributes][#{index}][id]", term.id %> - <%= text_field_tag "sample_controlled_vocab[sample_controlled_vocab_terms_attributes][#{index}][label]", term.label %> - <%= text_field_tag "sample_controlled_vocab[sample_controlled_vocab_terms_attributes][#{index}][label]", term.label %> <%= text_field_tag "sample_controlled_vocab[sample_controlled_vocab_terms_attributes][#{index}][iri]", term.iri %> <%= text_field_tag "sample_controlled_vocab[sample_controlled_vocab_terms_attributes][#{index}][parent_iri]", term.parent_iri %> diff --git a/app/views/sample_controlled_vocabs/_term_form_row_disabled.html.erb b/app/views/sample_controlled_vocabs/_term_form_row_disabled.html.erb index a331b87914..2be8514245 100644 --- a/app/views/sample_controlled_vocabs/_term_form_row_disabled.html.erb +++ b/app/views/sample_controlled_vocabs/_term_form_row_disabled.html.erb @@ -8,7 +8,6 @@ %>
    - <%= hidden_field_tag "sample_controlled_vocab[sample_controlled_vocab_terms_attributes][#{index}][id]", term.id %> <%= hidden_field_tag "sample_controlled_vocab[sample_controlled_vocab_terms_attributes][#{index}][label]", term.label %>
    <%= term.label %>
    <%= text_field_tag "sample_controlled_vocab[sample_controlled_vocab_terms_attributes][#{index}][label]", term.label %> + <%= hidden_field_tag "sample_controlled_vocab[sample_controlled_vocab_terms_attributes][#{index}][id]", term.id %> + <%= text_field_tag "sample_controlled_vocab[sample_controlled_vocab_terms_attributes][#{index}][label]", term.label %> + <%= text_field_tag "sample_controlled_vocab[sample_controlled_vocab_terms_attributes][#{index}][iri]", term.iri %> <%= text_field_tag "sample_controlled_vocab[sample_controlled_vocab_terms_attributes][#{index}][parent_iri]", term.parent_iri %> diff --git a/app/views/sample_controlled_vocabs/_term_form_row_disabled.html.erb b/app/views/sample_controlled_vocabs/_term_form_row_disabled.html.erb index 2be8514245..a331b87914 100644 --- a/app/views/sample_controlled_vocabs/_term_form_row_disabled.html.erb +++ b/app/views/sample_controlled_vocabs/_term_form_row_disabled.html.erb @@ -8,6 +8,7 @@ %>
    + <%= hidden_field_tag "sample_controlled_vocab[sample_controlled_vocab_terms_attributes][#{index}][id]", term.id %> <%= hidden_field_tag "sample_controlled_vocab[sample_controlled_vocab_terms_attributes][#{index}][label]", term.label %>
    <%= term.label %>
    + <% for key in @possible_duplicates[0].keys %> @@ -11,56 +12,64 @@ <% end %> <% end %> + + <% for dupl_sample in @possible_duplicates %> - ' > - - <% dupl_sample.map do |key, val| %> - <% val = '' if key =='id' %> - <% unless %w[uuid duplicate].include?(key) %> - <% if @multiple_input_fields.include?(key)%> - - <% elsif @cv_list_fields.include?(key) %> - - <% elsif @registered_sample_fields.include?(key) %> - - <% else %> - + '> + + <% dupl_sample.map do |key, val| %> + <% val = '' if key == 'id' %> + <% unless %w[uuid duplicate].include?(key) %> + <% if @multiple_input_fields.include?(key) %> + + <% elsif @cv_list_fields.include?(key) %> + + <% elsif @registered_sample_fields.include?(key) %> + + <% else %> + + <% end %> <% end %> <% end %> - <% end %> ' class="danger"> <% dupl_sample['duplicate'].map do |key, val| %> <% unless %w[uuid duplicate].include?(key) %> - <% if @multiple_input_fields.include?(key)%> + <% if @multiple_input_fields.include?(key) %> <% elsif @cv_list_fields.include?(key) %> <% elsif @registered_sample_fields.include?(key) %> - + <% else %> - + <% end %> <% end %> <% end %> - + <% end %> +
    - <% val.each do |sub_sample| %> - ' data-attr_type="seek-sample-multi"><%= sub_sample['title'] %> - <% end %> - - <% val.each do |cv_term| %> - <%= cv_term %> - <% end %> - ' data-attr_type="seek-sample"><%= val['title'] %>' ><%= val %>
    + + <% val.each do |sub_sample| %> + ' data-attr_type="seek-sample-multi"><%= sub_sample['title'] %> + <% end %> + + <% val.each do |cv_term| %> + <%= cv_term %> + <% end %> + + ' data-attr_type="seek-sample"><%= val['title'] %> + '><%= val %>
    <% val.each do |sub_sample| %> - '><%= sub_sample['title'] %> + '><%= sub_sample['title'] %> <% end %> <% val.each do |cv_term| %> - <%= cv_term %> + <%= cv_term %> <% end %> '><%= val['title'] %>'><%= val['title'] %><%= val%><%= val %>
    <% end %> diff --git a/app/views/single_pages/_new_samples_panel.html.erb b/app/views/single_pages/_new_samples_panel.html.erb index 1b163ec3da..4fd18ae27b 100644 --- a/app/views/single_pages/_new_samples_panel.html.erb +++ b/app/views/single_pages/_new_samples_panel.html.erb @@ -1,8 +1,9 @@ <% unless @new_samples.nil? or @new_samples.compact.none? %> - <%= folding_panel("New Samples #{@new_samples.size}", true, :id => "new-samples-panel", :body_options => {:id => "new-samples-panel-content"}, - :help_text => "These samples have been detected as new samples and will be created.") do %> + <%= folding_panel("New Samples #{@new_samples.size}", true, :id => "new-samples-panel", :body_options => { :id => "new-samples-panel-content" }, + :help_text => "These samples have been detected as new samples and will be created.") do %>
    + <% for key in @new_samples[0].keys %> @@ -11,36 +12,42 @@ <% end %> <% end %> + + <% for new_sample in @new_samples %> <% new_sample_id = UUID.generate %> - - <% new_sample.map do |key, val| %> - <% val = '' if key =='id' %> + + <% new_sample.map do |key, val| %> + <% val = '' if key == 'id' %> <% unless key == 'uuid' %> - <% if @multiple_input_fields.include?(key)%> - <% elsif @cv_list_fields.include?(key) %> - <% elsif @registered_sample_fields.include?(key) %> - <% else %> - + <% end %> <% end %> <% end %> <% end %> +
    + + <% if @multiple_input_fields.include?(key) %> + <% val.each do |sub_sample| %> - ' data-attr_type="seek-sample-multi"><%= sub_sample['title'] %> + ' data-attr_type="seek-sample-multi"><%= sub_sample['title'] %> <% end %> + <% val.each do |cv_term| %> - <%= cv_term %> + <%= cv_term %> <% end %> - ' data-attr_type="seek-sample"><%= val['title'] %> + + ' data-attr_type="seek-sample"><%= val['title'] %> <%= val %><%= val %>
    <% end %> diff --git a/app/views/single_pages/_unauthorized_samples_panel.html.erb b/app/views/single_pages/_unauthorized_samples_panel.html.erb index 8ad35705d2..4d69e2a741 100644 --- a/app/views/single_pages/_unauthorized_samples_panel.html.erb +++ b/app/views/single_pages/_unauthorized_samples_panel.html.erb @@ -1,15 +1,17 @@ <% unless @unauthorized_samples.nil? or @unauthorized_samples.compact.none? %> <% @can_upload = false %> <% errors.append("There are unauthorized samples present in the spreadsheet.") %> - <%= folding_panel("Unauthorized Samples", false, :id => "unauthorized-samples-panel", :body_options => {:id => "unauthorized-samples-panel-content"}, - :help_text => "Sample the current user does not have permission to edit them.") do %> + <%= folding_panel("Unauthorized Samples", false, :id => "unauthorized-samples-panel", :body_options => { :id => "unauthorized-samples-panel-content" }, + :help_text => "Sample the current user does not have permission to edit them.") do %>

    - You don't have permission to edit the samples listed below. Please contact the submitter of these samples or revert the changes in the spreadsheet to its original values. + You don't have permission to edit the samples listed below. Please contact the submitter of these samples or + revert the changes in the spreadsheet to its original values.

    + <% for key in @unauthorized_samples[0].keys %> <% unless key == 'uuid' %> @@ -17,6 +19,8 @@ <% end %> <% end %> + + <% for unauthorized_sample in @unauthorized_samples %> ' class=""> <% unauthorized_sample.map do |key, val| %> @@ -24,7 +28,7 @@ <% if @multiple_input_fields.include?(key) %> <% else %> @@ -34,6 +38,7 @@ <% end %> <% end %> +
    <% val.each do |sub_sample| %> - '><%= sub_sample['title'] %> + '><%= sub_sample['title'] %> <% end %>
    <% end %> diff --git a/app/views/single_pages/_update_samples_panel.html.erb b/app/views/single_pages/_update_samples_panel.html.erb index 4349edd71b..1d339a2bba 100644 --- a/app/views/single_pages/_update_samples_panel.html.erb +++ b/app/views/single_pages/_update_samples_panel.html.erb @@ -1,8 +1,9 @@ <% unless @update_samples.nil? or @update_samples.compact.none? %> - <%= folding_panel("Samples to Update #{@update_samples.size}", true, :id => "existing-samples-panel", :body_options => {:id => "existing-samples-panel-content"}, - :help_text => "These samples were detected existing samples and will be updated.") do %> + <%= folding_panel("Samples to Update #{@update_samples.size}", true, :id => "existing-samples-panel", :body_options => { :id => "existing-samples-panel-content" }, + :help_text => "These samples were detected existing samples and will be updated.") do %>
    + <% for key in @update_samples[0].keys %> @@ -11,38 +12,43 @@ <% end %> <% end %> + + <% for update_sample in @update_samples %> - ' > + '> <% db_sample = @authorized_db_samples.select { |s| s['id'] == update_sample['id'] }.first %> - + <% update_sample.map do |key, val| %> <% unless key == 'uuid' %> - <% if @multiple_input_fields.include?(key)%> - <% elsif @cv_list_fields.include?(key) %> - <% elsif @registered_sample_fields.include?(key) %> - <% else %> - + <% end %> <% end %> <% end %> - ' > + '> <% db_sample.map do |key, val| %> <% unless key == 'uuid' %> - <% if @multiple_input_fields.include?(key)%> + <% if @multiple_input_fields.include?(key) %> <% end %> +
    + ' > + <% if @multiple_input_fields.include?(key) %> + '> <% val.each do |sub_sample| %> ' data-attr_type="seek-sample-multi"><%= sub_sample['title'] %> <% end %> ' > + '> <% val.each do |cv_term| %> <%= cv_term %> <% end %> '> + '> ' data-attr_type="seek-sample"><%= val['title'] %> ' ><%= val %>'><%= val %>
    <% val.each do |sub_sample| %> '><%= sub_sample['title'] %> @@ -63,6 +69,7 @@ <% end %>
    <% end %> From b76c1f6e967cad88d911c04ab11ec10225c5f6c4 Mon Sep 17 00:00:00 2001 From: Kevin De Pelseneer Date: Mon, 3 Jun 2024 20:43:02 +0200 Subject: [PATCH 073/131] Test the rendered HTML --- .../single_pages_controller_test.rb | 106 ++++++++++++++++++ 1 file changed, 106 insertions(+) diff --git a/test/functional/single_pages_controller_test.rb b/test/functional/single_pages_controller_test.rb index e37bb58102..e7fdb075e2 100644 --- a/test/functional/single_pages_controller_test.rb +++ b/test/functional/single_pages_controller_test.rb @@ -166,6 +166,35 @@ def setup assert_equal updated_samples.size, 2 assert_equal new_samples.size, 2 assert_equal possible_duplicates.size, 1 + + post :upload_samples, as: :html, params: { file:, project_id: project.id, + sample_type_id: source_sample_type.id } + + assert_response :success + + assert_select 'table#create-samples-table', count: 1 do + assert_select "tbody tr", count: new_samples.size + end + + assert_select 'table#update-samples-table', count: 1 do + update_sample_ids = updated_samples.map { |s| s['id'] } + update_sample_ids.map do |sample_id| + row_id_updated = "update-sample-#{sample_id}-updated" + assert_select "tr##{row_id_updated}", count: 1 + + row_id_original = "update-sample-#{sample_id}-original" + assert_select "tr##{row_id_original}", count: 1 + end + end + + assert_select 'table#duplicate-samples-table', count: 1 do + dup_sample_ids = possible_duplicates.map { |s| s['duplicate']['id'] } + dup_sample_ids.map do |sample_id| + row_id = "duplicate-sample-#{sample_id}" + assert_select "tr##{row_id}-1", count: 1 + assert_select "tr##{row_id}-2", count: 1 + end + end end end @@ -190,6 +219,35 @@ def setup assert_equal updated_samples.size, 2 assert_equal new_samples.size, 2 assert_equal possible_duplicates.size, 1 + + post :upload_samples, as: :html, params: { file:, project_id: project.id, + sample_type_id: sample_collection_sample_type.id } + + assert_response :success + + assert_select 'table#create-samples-table', count: 1 do + assert_select "tbody tr", count: new_samples.size + end + + assert_select 'table#update-samples-table', count: 1 do + update_sample_ids = updated_samples.map { |s| s['id'] } + update_sample_ids.map do |sample_id| + row_id_updated = "update-sample-#{sample_id}-updated" + assert_select "tr##{row_id_updated}", count: 1 + + row_id_original = "update-sample-#{sample_id}-original" + assert_select "tr##{row_id_original}", count: 1 + end + end + + assert_select 'table#duplicate-samples-table', count: 1 do + dup_sample_ids = possible_duplicates.map { |s| s['duplicate']['id'] } + dup_sample_ids.map do |sample_id| + row_id = "duplicate-sample-#{sample_id}" + assert_select "tr##{row_id}-1", count: 1 + assert_select "tr##{row_id}-2", count: 1 + end + end end end @@ -214,6 +272,35 @@ def setup assert_equal updated_samples.size, 2 assert_equal new_samples.size, 1 assert_equal possible_duplicates.size, 1 + + post :upload_samples, as: :html, params: { file:, project_id: project.id, + sample_type_id: assay_sample_type.id } + + assert_response :success + + assert_select 'table#create-samples-table', count: 1 do + assert_select "tbody tr", count: new_samples.size + end + + assert_select 'table#update-samples-table', count: 1 do + update_sample_ids = updated_samples.map { |s| s['id'] } + update_sample_ids.map do |sample_id| + row_id_updated = "update-sample-#{sample_id}-updated" + assert_select "tr##{row_id_updated}", count: 1 + + row_id_original = "update-sample-#{sample_id}-original" + assert_select "tr##{row_id_original}", count: 1 + end + end + + assert_select 'table#duplicate-samples-table', count: 1 do + dup_sample_ids = possible_duplicates.map { |s| s['duplicate']['id'] } + dup_sample_ids.map do |sample_id| + row_id = "duplicate-sample-#{sample_id}" + assert_select "tr##{row_id}-1", count: 1 + assert_select "tr##{row_id}-2", count: 1 + end + end end end @@ -243,6 +330,25 @@ def setup possible_duplicates = response_data['possibleDuplicates'] assert(possible_duplicates.size, 1) + + post :upload_samples, as: :html, params: { file:, project_id: project.id, + sample_type_id: source_sample_type.id } + + assert_response :success + + assert_select 'table#create-samples-table', count: 1 do + assert_select "tbody tr", count: new_samples.size + end + + assert_select 'table#update-samples-table', count: 0 + + assert_select 'table#unauthorized-samples-table', count: 1 do + unauthorized_sample_ids = unauthorized_samples.map { |s| s['id'] } + unauthorized_sample_ids.map do |sample_id| + row_id = "unauthorized-sample-#{sample_id}" + assert_select "tr##{row_id}", count: 1 + end + end end end From 10a321e2e530dfba606bb670b3318be5e51401e9 Mon Sep 17 00:00:00 2001 From: Kevin De Pelseneer Date: Mon, 3 Jun 2024 21:10:31 +0200 Subject: [PATCH 074/131] Redirect to correct item in SP view --- app/controllers/single_pages_controller.rb | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/app/controllers/single_pages_controller.rb b/app/controllers/single_pages_controller.rb index 3229d54df0..b3015c123d 100644 --- a/app/controllers/single_pages_controller.rb +++ b/app/controllers/single_pages_controller.rb @@ -47,7 +47,7 @@ def dynamic_table_data rescue Exception => e render json: { status: :unprocessable_entity, error: e.message } end - + def download_samples_excel sample_ids, sample_type_id, study_id, assay_id = Rails.cache.read(params[:uuid]).values_at(:sample_ids, :sample_type_id, :study_id, :assay_id) @@ -94,7 +94,10 @@ def download_samples_excel rescue StandardError => e flash[:error] = e.message respond_to do |format| - format.html { redirect_to single_page_path(@project.id) } + format.html do + redirect_to single_page_path(id: @project.id, item_type: @assay.nil? ? 'study' : 'assay', + item_id: @assay.nil? ? @study.id : @assay.id) + end format.json do render json: { parameters: { sample_ids:, sample_type_id:, study_id: }, errors: e }, status: :bad_request end From e6d7223c40127016caa40db5b23ad52199e2a9e6 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Tue, 4 Jun 2024 23:09:42 +0000 Subject: [PATCH 075/131] Bump actionpack from 6.1.7.7 to 6.1.7.8 Bumps [actionpack](https://github.com/rails/rails) from 6.1.7.7 to 6.1.7.8. - [Release notes](https://github.com/rails/rails/releases) - [Changelog](https://github.com/rails/rails/blob/v7.1.3.4/actionpack/CHANGELOG.md) - [Commits](https://github.com/rails/rails/compare/v6.1.7.7...v6.1.7.8) --- updated-dependencies: - dependency-name: actionpack dependency-type: indirect ... Signed-off-by: dependabot[bot] --- Gemfile.lock | 126 ++++++++++++++++++++++++++------------------------- 1 file changed, 64 insertions(+), 62 deletions(-) diff --git a/Gemfile.lock b/Gemfile.lock index 0de2621a2b..1836f41939 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -51,40 +51,40 @@ GEM remote: https://rubygems.org/ specs: RedCloth (4.3.3) - actioncable (6.1.7.7) - actionpack (= 6.1.7.7) - activesupport (= 6.1.7.7) + actioncable (6.1.7.8) + actionpack (= 6.1.7.8) + activesupport (= 6.1.7.8) nio4r (~> 2.0) websocket-driver (>= 0.6.1) - actionmailbox (6.1.7.7) - actionpack (= 6.1.7.7) - activejob (= 6.1.7.7) - activerecord (= 6.1.7.7) - activestorage (= 6.1.7.7) - activesupport (= 6.1.7.7) + actionmailbox (6.1.7.8) + actionpack (= 6.1.7.8) + activejob (= 6.1.7.8) + activerecord (= 6.1.7.8) + activestorage (= 6.1.7.8) + activesupport (= 6.1.7.8) mail (>= 2.7.1) - actionmailer (6.1.7.7) - actionpack (= 6.1.7.7) - actionview (= 6.1.7.7) - activejob (= 6.1.7.7) - activesupport (= 6.1.7.7) + actionmailer (6.1.7.8) + actionpack (= 6.1.7.8) + actionview (= 6.1.7.8) + activejob (= 6.1.7.8) + activesupport (= 6.1.7.8) mail (~> 2.5, >= 2.5.4) rails-dom-testing (~> 2.0) - actionpack (6.1.7.7) - actionview (= 6.1.7.7) - activesupport (= 6.1.7.7) + actionpack (6.1.7.8) + actionview (= 6.1.7.8) + activesupport (= 6.1.7.8) rack (~> 2.0, >= 2.0.9) rack-test (>= 0.6.3) rails-dom-testing (~> 2.0) rails-html-sanitizer (~> 1.0, >= 1.2.0) - actiontext (6.1.7.7) - actionpack (= 6.1.7.7) - activerecord (= 6.1.7.7) - activestorage (= 6.1.7.7) - activesupport (= 6.1.7.7) + actiontext (6.1.7.8) + actionpack (= 6.1.7.8) + activerecord (= 6.1.7.8) + activestorage (= 6.1.7.8) + activesupport (= 6.1.7.8) nokogiri (>= 1.8.5) - actionview (6.1.7.7) - activesupport (= 6.1.7.7) + actionview (6.1.7.8) + activesupport (= 6.1.7.8) builder (~> 3.1) erubi (~> 1.4) rails-dom-testing (~> 2.0) @@ -94,14 +94,14 @@ GEM activemodel (>= 4.1, < 7.1) case_transform (>= 0.2) jsonapi-renderer (>= 0.1.1.beta1, < 0.3) - activejob (6.1.7.7) - activesupport (= 6.1.7.7) + activejob (6.1.7.8) + activesupport (= 6.1.7.8) globalid (>= 0.3.6) - activemodel (6.1.7.7) - activesupport (= 6.1.7.7) - activerecord (6.1.7.7) - activemodel (= 6.1.7.7) - activesupport (= 6.1.7.7) + activemodel (6.1.7.8) + activesupport (= 6.1.7.8) + activerecord (6.1.7.8) + activemodel (= 6.1.7.8) + activesupport (= 6.1.7.8) activerecord-import (1.3.0) activerecord (>= 4.2) activerecord-session_store (2.0.0) @@ -110,14 +110,14 @@ GEM multi_json (~> 1.11, >= 1.11.2) rack (>= 2.0.8, < 3) railties (>= 5.2.4.1) - activestorage (6.1.7.7) - actionpack (= 6.1.7.7) - activejob (= 6.1.7.7) - activerecord (= 6.1.7.7) - activesupport (= 6.1.7.7) + activestorage (6.1.7.8) + actionpack (= 6.1.7.8) + activejob (= 6.1.7.8) + activerecord (= 6.1.7.8) + activesupport (= 6.1.7.8) marcel (~> 1.0) mini_mime (>= 1.1.0) - activesupport (6.1.7.7) + activesupport (6.1.7.8) concurrent-ruby (~> 1.0, >= 1.0.2) i18n (>= 1.6, < 2) minitest (>= 5.1) @@ -198,7 +198,7 @@ GEM execjs coffee-script-source (1.12.2) commonmarker (0.23.10) - concurrent-ruby (1.2.3) + concurrent-ruby (1.3.1) connection_pool (2.3.0) countries (5.2.0) unaccent (~> 0.3) @@ -322,7 +322,7 @@ GEM httpclient (2.8.3) httpi (1.1.1) rack - i18n (1.14.4) + i18n (1.14.5) concurrent-ruby (~> 1.0) i18n-js (3.9.0) i18n (>= 0.6.6) @@ -460,7 +460,7 @@ GEM nokogiri (~> 1) rake mini_mime (1.1.5) - mini_portile2 (2.8.5) + mini_portile2 (2.8.7) minitest (5.20.0) minitest-reporters (1.5.0) ansi @@ -492,7 +492,7 @@ GEM net-protocol netrc (0.11.0) nio4r (2.7.0) - nokogiri (1.16.2) + nokogiri (1.16.5) mini_portile2 (~> 2.8.2) racc (~> 1.4) nori (1.1.5) @@ -566,8 +566,8 @@ GEM puma (5.6.8) nio4r (~> 2.0) pyu-ruby-sasl (0.0.3.3) - racc (1.7.3) - rack (2.2.8.1) + racc (1.8.0) + rack (2.2.9) rack-attack (6.6.0) rack (>= 1.0, < 3) rack-cors (1.1.1) @@ -584,20 +584,20 @@ GEM rack rack-test (2.1.0) rack (>= 1.3) - rails (6.1.7.7) - actioncable (= 6.1.7.7) - actionmailbox (= 6.1.7.7) - actionmailer (= 6.1.7.7) - actionpack (= 6.1.7.7) - actiontext (= 6.1.7.7) - actionview (= 6.1.7.7) - activejob (= 6.1.7.7) - activemodel (= 6.1.7.7) - activerecord (= 6.1.7.7) - activestorage (= 6.1.7.7) - activesupport (= 6.1.7.7) + rails (6.1.7.8) + actioncable (= 6.1.7.8) + actionmailbox (= 6.1.7.8) + actionmailer (= 6.1.7.8) + actionpack (= 6.1.7.8) + actiontext (= 6.1.7.8) + actionview (= 6.1.7.8) + activejob (= 6.1.7.8) + activemodel (= 6.1.7.8) + activerecord (= 6.1.7.8) + activestorage (= 6.1.7.8) + activesupport (= 6.1.7.8) bundler (>= 1.15.0) - railties (= 6.1.7.7) + railties (= 6.1.7.8) sprockets-rails (>= 2.0.0) rails-controller-testing (1.0.5) actionpack (>= 5.0.1.rc1) @@ -625,9 +625,9 @@ GEM json require_all (~> 3.0) ruby-progressbar - railties (6.1.7.7) - actionpack (= 6.1.7.7) - activesupport (= 6.1.7.7) + railties (6.1.7.8) + actionpack (= 6.1.7.8) + activesupport (= 6.1.7.8) method_source rake (>= 12.2) thor (~> 1.0) @@ -728,7 +728,8 @@ GEM netrc (~> 0.8) reverse_markdown (2.1.1) nokogiri - rexml (3.2.5) + rexml (3.2.8) + strscan (>= 3.0.9) rfc-822 (0.4.1) rmagick (5.3.0) pkg-config (~> 1.4) @@ -861,6 +862,7 @@ GEM sqlite3 (1.4.2) stackprof (0.2.25) stringio (3.0.1.1) + strscan (3.1.0) sunspot (2.6.0) pr_geohash (~> 1.0) rsolr (>= 1.1.1, < 3) @@ -950,7 +952,7 @@ GEM rails (>= 3.0) rake (>= 0.8.7) yard (0.9.36) - zeitwerk (2.6.13) + zeitwerk (2.6.15) zip-container (4.0.2) rubyzip (~> 2.0.0) @@ -1028,7 +1030,7 @@ DEPENDENCIES my_responds_to_parent! mysql2 net-ftp - nokogiri (~> 1.16.2) + nokogiri (~> 1.16.5) omniauth (~> 2.1.0) omniauth-github omniauth-rails_csrf_protection From 3ec31c0d94c05e3266db58150dcfdb21cf1104f3 Mon Sep 17 00:00:00 2001 From: Stuart Owen Date: Wed, 5 Jun 2024 09:48:28 +0100 Subject: [PATCH 076/131] fix nokogiri version mismatch --- Gemfile | 2 +- Gemfile.lock | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/Gemfile b/Gemfile index 1ba5c08b17..1077041082 100644 --- a/Gemfile +++ b/Gemfile @@ -52,7 +52,7 @@ gem 'will_paginate', '~> 3.1' gem 'yaml_db' gem 'rails_autolink' gem 'rfc-822' -gem 'nokogiri', '~> 1.16.2' +gem 'nokogiri', '~> 1.16' #necessary for newer hashie dependency, original api_smith is no longer active gem 'api_smith', git: 'https://github.com/youroute/api_smith.git', ref: '1fb428cebc17b9afab25ac9f809bde87b0ec315b' gem 'rdf-virtuoso', '>= 0.2.0' diff --git a/Gemfile.lock b/Gemfile.lock index 1836f41939..1a31a36a38 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -1030,7 +1030,7 @@ DEPENDENCIES my_responds_to_parent! mysql2 net-ftp - nokogiri (~> 1.16.5) + nokogiri (~> 1.16) omniauth (~> 2.1.0) omniauth-github omniauth-rails_csrf_protection From 842fc554e0be7f0c75d2ab96a69255e2b9d74b08 Mon Sep 17 00:00:00 2001 From: Finn Bacall Date: Thu, 6 Jun 2024 10:28:38 +0100 Subject: [PATCH 077/131] Typo fix --- app/views/assets/_asset_buttons.html.erb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/app/views/assets/_asset_buttons.html.erb b/app/views/assets/_asset_buttons.html.erb index 9d26ddbc7f..cba08d71d2 100644 --- a/app/views/assets/_asset_buttons.html.erb +++ b/app/views/assets/_asset_buttons.html.erb @@ -33,7 +33,7 @@ <% if can_download_asset?(asset, params[:code]) -%> <% if asset.is_a?(Workflow) %> <% if display_asset.is_git_versioned? || asset.content_blob&.file_exists? %> - <%= button_link_to('Download RO Crate', 'ro_crate_file', ro_crate_workflow_path(asset, version: version, code: params[:code]), + <%= button_link_to('Download RO-Crate', 'ro_crate_file', ro_crate_workflow_path(asset, version: version, code: params[:code]), 'data-tooltip' => tooltip("The Workflow RO-Crate is a package containing the workflow definition, its metadata and supporting resources like test data")) %> <% if asset.can_run? %> <%= button_link_to("Run on Galaxy", 'run_galaxy', display_asset.run_url) %> From af0ecb4fd76c25a6c13226763b1292c657ec0a99 Mon Sep 17 00:00:00 2001 From: Stuart Owen Date: Wed, 5 Jun 2024 11:22:02 +0100 Subject: [PATCH 078/131] fix pid uri validation, and handle gracefully in short_pid for existing entries #1865 --- app/models/sample_attribute.rb | 11 +++++++++-- test/unit/sample_attribute_test.rb | 6 ++++++ 2 files changed, 15 insertions(+), 2 deletions(-) diff --git a/app/models/sample_attribute.rb b/app/models/sample_attribute.rb index 740f673e21..79de668b7b 100644 --- a/app/models/sample_attribute.rb +++ b/app/models/sample_attribute.rb @@ -11,7 +11,7 @@ class SampleAttribute < ApplicationRecord auto_strip_attributes :pid validates :sample_type, presence: true - validates :pid, format: { with: URI::regexp, allow_blank: true, allow_nil: true, message: 'not a valid URI' } + validates :pid, format: { with: URI::ABS_URI, allow_blank: true, allow_nil: true, message: 'not a valid URI' } validate :validate_against_editing_constraints, if: -> { sample_type.present? } before_save :store_accessor_name @@ -64,7 +64,14 @@ def template_column_definition def short_pid return '' unless pid.present? - URI.parse(pid).fragment || pid.gsub(/.*\//,'') || pid + begin + URI.parse(pid).fragment || pid.gsub(/.*\//,'') || pid + rescue URI::InvalidURIError + # likely a space that managed to pass through earlier uri validation + fixed_pid = pid.gsub(' ','_') + URI.parse(fixed_pid).fragment || fixed_pid.gsub(/.*\//,'') || fixed_pid + end + end def linked_extended_metadata_type diff --git a/test/unit/sample_attribute_test.rb b/test/unit/sample_attribute_test.rb index 4ab9f2f82e..006f8cdbc5 100644 --- a/test/unit/sample_attribute_test.rb +++ b/test/unit/sample_attribute_test.rb @@ -67,6 +67,9 @@ class SampleAttributeTest < ActiveSupport::TestCase sample_type: FactoryBot.create(:simple_sample_type) refute attribute.valid? + attribute.pid = 'Source:bacterial culture' + refute attribute.valid? + attribute.pid = 'http://somewhere.org#fish' assert attribute.valid? attribute.pid = 'dc:fish' @@ -333,6 +336,9 @@ class SampleAttributeTest < ActiveSupport::TestCase attribute = FactoryBot.create(:string_sample_attribute_with_description_and_pid, is_title: true, pid: 'http://pid.org/attr/title', sample_type: FactoryBot.create(:simple_sample_type)) assert_equal 'title',attribute.short_pid + attribute.pid = 'Source:bacterial culture' + assert_equal 'Source:bacterial_culture',attribute.short_pid + attribute = FactoryBot.create(:sample_sample_attribute, sample_type: FactoryBot.create(:simple_sample_type)) assert_equal '', attribute.short_pid end From 91d0dcf073c894f0bf853ac38f64f11a70ec9d2b Mon Sep 17 00:00:00 2001 From: Stuart Owen Date: Wed, 5 Jun 2024 16:06:49 +0100 Subject: [PATCH 079/131] fix factory pid to conform to fixed validation #1865 --- test/factories/sample_attributes.rb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/factories/sample_attributes.rb b/test/factories/sample_attributes.rb index de36f107c7..9aad6646f9 100644 --- a/test/factories/sample_attributes.rb +++ b/test/factories/sample_attributes.rb @@ -50,7 +50,7 @@ factory(:string_sample_attribute_with_description_and_pid, parent: :sample_attribute) do association :sample_attribute_type, factory: :string_sample_attribute_type description { "sample_attribute_description" } - pid { "sample_attribute:pid" } + pid { "sample-attribute:pid" } required { true } end end From 24751349dbc29d10ba1bb20530398447a5b16ad3 Mon Sep 17 00:00:00 2001 From: Stuart Owen Date: Wed, 5 Jun 2024 17:14:05 +0100 Subject: [PATCH 080/131] replace space with - instead of _ #1865 --- app/models/sample_attribute.rb | 2 +- test/unit/sample_attribute_test.rb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/app/models/sample_attribute.rb b/app/models/sample_attribute.rb index 79de668b7b..9740e0c3fe 100644 --- a/app/models/sample_attribute.rb +++ b/app/models/sample_attribute.rb @@ -68,7 +68,7 @@ def short_pid URI.parse(pid).fragment || pid.gsub(/.*\//,'') || pid rescue URI::InvalidURIError # likely a space that managed to pass through earlier uri validation - fixed_pid = pid.gsub(' ','_') + fixed_pid = pid.gsub(' ','-') URI.parse(fixed_pid).fragment || fixed_pid.gsub(/.*\//,'') || fixed_pid end diff --git a/test/unit/sample_attribute_test.rb b/test/unit/sample_attribute_test.rb index 006f8cdbc5..abe11a0df8 100644 --- a/test/unit/sample_attribute_test.rb +++ b/test/unit/sample_attribute_test.rb @@ -337,7 +337,7 @@ class SampleAttributeTest < ActiveSupport::TestCase assert_equal 'title',attribute.short_pid attribute.pid = 'Source:bacterial culture' - assert_equal 'Source:bacterial_culture',attribute.short_pid + assert_equal 'Source:bacterial-culture',attribute.short_pid attribute = FactoryBot.create(:sample_sample_attribute, sample_type: FactoryBot.create(:simple_sample_type)) assert_equal '', attribute.short_pid From 2f122b065329095fba19a74d8822a3297653ba62 Mon Sep 17 00:00:00 2001 From: Finn Bacall Date: Thu, 6 Jun 2024 10:32:28 +0100 Subject: [PATCH 081/131] Account for git in `contains_downloadable_items?`. Fixes #1915 --- lib/seek/acts_as_asset.rb | 4 ++++ lib/seek/acts_as_asset/content_blobs.rb | 5 ----- lib/seek/versioned_resource.rb | 6 ------ test/unit/asset_test.rb | 21 ++++++++++++++------- 4 files changed, 18 insertions(+), 18 deletions(-) diff --git a/lib/seek/acts_as_asset.rb b/lib/seek/acts_as_asset.rb index 1c5de8cb75..e8abef8742 100644 --- a/lib/seek/acts_as_asset.rb +++ b/lib/seek/acts_as_asset.rb @@ -23,6 +23,10 @@ def is_downloadable_asset? is_asset? && is_downloadable? end + def contains_downloadable_items? + respond_to?(:all_content_blobs) && all_content_blobs.compact.any?(&:is_downloadable?) || is_git_versioned? + end + def have_misc_links? self.class.have_misc_links? end diff --git a/lib/seek/acts_as_asset/content_blobs.rb b/lib/seek/acts_as_asset/content_blobs.rb index 6ff53183ba..2ddc88cc24 100644 --- a/lib/seek/acts_as_asset/content_blobs.rb +++ b/lib/seek/acts_as_asset/content_blobs.rb @@ -10,11 +10,6 @@ module ClassMethods end module InstanceMethods - - def contains_downloadable_items? - all_content_blobs.compact.any?(&:is_downloadable?) - end - def all_content_blobs if self.respond_to?(:content_blobs) content_blobs diff --git a/lib/seek/versioned_resource.rb b/lib/seek/versioned_resource.rb index 4bf7ab5794..31979c487e 100644 --- a/lib/seek/versioned_resource.rb +++ b/lib/seek/versioned_resource.rb @@ -59,12 +59,6 @@ def attributions_objects end end - # assumes all versioned resources are also taggable - - def contains_downloadable_items? - all_content_blobs.compact.any?(&:is_downloadable?) - end - def all_content_blobs blobs = [] blobs << content_blob if respond_to?(:content_blob) diff --git a/test/unit/asset_test.rb b/test/unit/asset_test.rb index fc966488e5..4d4a15ad3c 100644 --- a/test/unit/asset_test.rb +++ b/test/unit/asset_test.rb @@ -78,12 +78,12 @@ class AssetTest < ActiveSupport::TestCase assert df.latest_version.contains_downloadable_items? df = FactoryBot.create :data_file, content_blob: FactoryBot.create(:content_blob, url: 'http://webpage.com', external_link: true) - assert !df.contains_downloadable_items? - assert !df.latest_version.contains_downloadable_items? + refute df.contains_downloadable_items? + refute df.latest_version.contains_downloadable_items? model = FactoryBot.create :model_with_urls - assert !model.contains_downloadable_items? - assert !model.latest_version.contains_downloadable_items? + refute model.contains_downloadable_items? + refute model.latest_version.contains_downloadable_items? model = FactoryBot.create :teusink_model assert model.contains_downloadable_items? @@ -94,10 +94,10 @@ class AssetTest < ActiveSupport::TestCase assert model.latest_version.contains_downloadable_items? df = DataFile.new - assert !df.contains_downloadable_items? + refute df.contains_downloadable_items? model = Model.new - assert !model.contains_downloadable_items? + refute model.contains_downloadable_items? # test for versions model = FactoryBot.create :teusink_model @@ -112,7 +112,14 @@ class AssetTest < ActiveSupport::TestCase assert_equal(2, model.versions.count) assert model.find_version(1).contains_downloadable_items? - assert !model.find_version(2).contains_downloadable_items? + refute model.find_version(2).contains_downloadable_items? + + workflow = FactoryBot.create(:nfcore_git_workflow) + assert workflow.contains_downloadable_items? + assert workflow.git_version.contains_downloadable_items? + + workflow = Workflow.new + refute workflow.contains_downloadable_items? end test 'supports_spreadsheet_explore?' do From 69edef8bc337a17d6a594d55a877bb2cbcaf255c Mon Sep 17 00:00:00 2001 From: Finn Bacall Date: Wed, 5 Jun 2024 12:24:20 +0100 Subject: [PATCH 082/131] Bump nf-core rnaseq fixture --- .../git/nf-core-rnaseq/_git/FETCH_HEAD | 7 +------ .../git/nf-core-rnaseq/_git/ORIG_HEAD | 1 + test/fixtures/git/nf-core-rnaseq/_git/index | Bin 0 -> 32411 bytes .../git/nf-core-rnaseq/_git/logs/HEAD | 2 ++ .../_git/logs/refs/heads/master | 1 + .../_git/logs/refs/remotes/origin/TEMPLATE | 1 + .../_git/logs/refs/remotes/origin/arm | 1 + .../refs/remotes/origin/change_testing_logic | 1 + .../_git/logs/refs/remotes/origin/dev | 1 + .../remotes/origin/document_fastp_sampling | 1 + .../remotes/origin/feat/implement-ci-nf-tests | 1 + .../refs/remotes/origin/fix_bbsplit_config | 1 + .../logs/refs/remotes/origin/fix_gtf_unzip | 1 + .../logs/refs/remotes/origin/fix_salmon_args | 1 + .../remotes/origin/improve_rseqc_strandedness | 1 + .../_git/logs/refs/remotes/origin/master | 1 + .../logs/refs/remotes/origin/nf-test-cicd | 1 + .../refs/remotes/origin/optimized-resources | 1 + .../origin/update_default_pipeline_test | 1 + ...198e3e69261a07440f01e7393b0d0cfb8f9dc9.idx | Bin 0 -> 405224 bytes ...98e3e69261a07440f01e7393b0d0cfb8f9dc9.pack | Bin 0 -> 10599746 bytes .../git/nf-core-rnaseq/_git/refs/heads/master | 2 +- .../_git/refs/remotes/origin/TEMPLATE | 2 +- .../_git/refs/remotes/origin/arm | 1 + .../refs/remotes/origin/change_testing_logic | 1 + .../_git/refs/remotes/origin/dev | 2 +- .../remotes/origin/document_fastp_sampling | 1 + .../remotes/origin/feat/implement-ci-nf-tests | 1 + .../refs/remotes/origin/fix_bbsplit_config | 1 + .../_git/refs/remotes/origin/fix_gtf_unzip | 1 + .../_git/refs/remotes/origin/fix_salmon_args | 1 + .../remotes/origin/improve_rseqc_strandedness | 1 + .../_git/refs/remotes/origin/master | 2 +- .../_git/refs/remotes/origin/nf-test-cicd | 1 + .../refs/remotes/origin/optimized-resources | 1 + .../origin/update_default_pipeline_test | 1 + .../git/nf-core-rnaseq/_git/refs/tags/3.1 | 1 + .../git/nf-core-rnaseq/_git/refs/tags/3.10 | 1 + .../git/nf-core-rnaseq/_git/refs/tags/3.10.1 | 1 + .../git/nf-core-rnaseq/_git/refs/tags/3.11.0 | 1 + .../git/nf-core-rnaseq/_git/refs/tags/3.11.1 | 1 + .../git/nf-core-rnaseq/_git/refs/tags/3.11.2 | 1 + .../git/nf-core-rnaseq/_git/refs/tags/3.12.0 | 1 + .../git/nf-core-rnaseq/_git/refs/tags/3.13.0 | 1 + .../git/nf-core-rnaseq/_git/refs/tags/3.13.1 | 1 + .../git/nf-core-rnaseq/_git/refs/tags/3.13.2 | 1 + .../git/nf-core-rnaseq/_git/refs/tags/3.14.0 | 1 + .../git/nf-core-rnaseq/_git/refs/tags/3.2 | 1 + .../git/nf-core-rnaseq/_git/refs/tags/3.3 | 1 + .../git/nf-core-rnaseq/_git/refs/tags/3.4 | 1 + .../git/nf-core-rnaseq/_git/refs/tags/3.5 | 1 + .../git/nf-core-rnaseq/_git/refs/tags/3.6 | 1 + .../git/nf-core-rnaseq/_git/refs/tags/3.7 | 1 + .../git/nf-core-rnaseq/_git/refs/tags/3.8 | 1 + .../git/nf-core-rnaseq/_git/refs/tags/3.8.1 | 1 + .../git/nf-core-rnaseq/_git/refs/tags/3.9 | 1 + 56 files changed, 54 insertions(+), 10 deletions(-) create mode 100644 test/fixtures/git/nf-core-rnaseq/_git/ORIG_HEAD create mode 100644 test/fixtures/git/nf-core-rnaseq/_git/index create mode 100644 test/fixtures/git/nf-core-rnaseq/_git/logs/HEAD create mode 100644 test/fixtures/git/nf-core-rnaseq/_git/logs/refs/heads/master create mode 100644 test/fixtures/git/nf-core-rnaseq/_git/logs/refs/remotes/origin/arm create mode 100644 test/fixtures/git/nf-core-rnaseq/_git/logs/refs/remotes/origin/change_testing_logic create mode 100644 test/fixtures/git/nf-core-rnaseq/_git/logs/refs/remotes/origin/document_fastp_sampling create mode 100644 test/fixtures/git/nf-core-rnaseq/_git/logs/refs/remotes/origin/feat/implement-ci-nf-tests create mode 100644 test/fixtures/git/nf-core-rnaseq/_git/logs/refs/remotes/origin/fix_bbsplit_config create mode 100644 test/fixtures/git/nf-core-rnaseq/_git/logs/refs/remotes/origin/fix_gtf_unzip create mode 100644 test/fixtures/git/nf-core-rnaseq/_git/logs/refs/remotes/origin/fix_salmon_args create mode 100644 test/fixtures/git/nf-core-rnaseq/_git/logs/refs/remotes/origin/improve_rseqc_strandedness create mode 100644 test/fixtures/git/nf-core-rnaseq/_git/logs/refs/remotes/origin/nf-test-cicd create mode 100644 test/fixtures/git/nf-core-rnaseq/_git/logs/refs/remotes/origin/optimized-resources create mode 100644 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create mode 100644 test/fixtures/git/nf-core-rnaseq/_git/refs/remotes/origin/improve_rseqc_strandedness create mode 100644 test/fixtures/git/nf-core-rnaseq/_git/refs/remotes/origin/nf-test-cicd create mode 100644 test/fixtures/git/nf-core-rnaseq/_git/refs/remotes/origin/optimized-resources create mode 100644 test/fixtures/git/nf-core-rnaseq/_git/refs/remotes/origin/update_default_pipeline_test create mode 100644 test/fixtures/git/nf-core-rnaseq/_git/refs/tags/3.1 create mode 100644 test/fixtures/git/nf-core-rnaseq/_git/refs/tags/3.10 create mode 100644 test/fixtures/git/nf-core-rnaseq/_git/refs/tags/3.10.1 create mode 100644 test/fixtures/git/nf-core-rnaseq/_git/refs/tags/3.11.0 create mode 100644 test/fixtures/git/nf-core-rnaseq/_git/refs/tags/3.11.1 create mode 100644 test/fixtures/git/nf-core-rnaseq/_git/refs/tags/3.11.2 create mode 100644 test/fixtures/git/nf-core-rnaseq/_git/refs/tags/3.12.0 create mode 100644 test/fixtures/git/nf-core-rnaseq/_git/refs/tags/3.13.0 create mode 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