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cleaned up the upgrade tasks for 1.14 #1580

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Sep 11, 2023
Merged

cleaned up the upgrade tasks for 1.14 #1580

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217 changes: 0 additions & 217 deletions lib/tasks/seek_upgrades.rake
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Original file line number Diff line number Diff line change
Expand Up @@ -8,28 +8,6 @@ namespace :seek do
# these are the tasks required for this version upgrade
task upgrade_version_tasks: %i[
environment
db:seed:007_sample_attribute_types
update_missing_openbis_istest
update_missing_publication_versions
update_edam_controlled_vocab_keys
db:seed:011_topics_controlled_vocab
db:seed:012_operations_controlled_vocab
db:seed:013_formats_controlled_vocab
db:seed:014_data_controlled_vocab
db:seed:015_isa_tags
db:seed:003_model_formats
db:seed:004_model_recommended_environments
remove_orphaned_versions
refresh_workflow_internals
remove_scale_annotations
remove_spreadsheet_annotations
remove_node_annotations
convert_roles
update_edam_annotation_attributes
remove_orphaned_project_subscriptions
remove_node_activity_logs
remove_node_asset_creators
set_default_sample_type_creators
]

# these are the tasks that are executes for each upgrade as standard, and rarely change
Expand Down Expand Up @@ -66,201 +44,6 @@ namespace :seek do
end
end

task(update_missing_openbis_istest: :environment) do
puts '... creating missing is_test for OpenbisEndpoint...'
create = 0
disable_authorization_checks do
OpenbisEndpoint.find_each do |openbis_endpoint|
# check if the publication has a version
# then create one if missing
if openbis_endpoint.is_test.nil?
openbis_endpoint.is_test = false # default -> prod, https
openbis_endpoint.save
unless openbis_endpoint.is_test.nil?
create += 1
end
end
# publication.save
end
end
puts " ... finished creating missing is_test for #{create.to_s} OpenbisEndpoint(s)"
end

task(update_missing_publication_versions: :environment) do
puts '... creating missing publications versions ...'
create = 0
disable_authorization_checks do
Publication.find_each do |publication|
# check if the publication has a version
# then create one if missing
if publication.latest_version.nil?
publication.save_as_new_version 'Version for legacy entries'
unless publication.latest_version.nil?
create += 1
end
end
# publication.save
end
end
puts " ... finished creating missing publications versions for #{create.to_s} publications"
end

task(remove_orphaned_versions: [:environment]) do
puts 'Removing orphaned versions ...'
count = 0
types = [DataFile::Version, Document::Version, Sop::Version, Model::Version, Presentation::Version,
Sop::Version, Workflow::Version]
disable_authorization_checks do
types.each do |type|
found = type.where.missing(:parent)
count += found.length
found.each(&:destroy)
end
end
puts "... finished removing #{count} orphaned versions"
end

task(remove_scale_annotations: [:environment]) do
a = Annotation.joins(:annotation_attribute).where(annotation_attribute: { name: ['additional_scale_info', 'scale'] })
count = a.count
a.destroy_all
AnnotationAttribute.where(name:['scale','additional_scale_info']).destroy_all
puts "Removed #{count} scale related annotations" if count > 0
end

task(remove_spreadsheet_annotations: [:environment]) do
annotations = Annotation.where(annotatable_type: 'CellRange')
count = annotations.count
values = TextValue.joins(:annotations).where(annotations: { annotatable_type: 'CellRange' })
values.select{|v| v.annotations.count == 1}.each(&:destroy)
annotations.destroy_all
AnnotationAttribute.where(name:'annotation').destroy_all
puts "Removed #{count} spreadsheet related annotations" if count > 0
end

task(remove_node_annotations: [:environment]) do
annotations = Annotation.where(annotatable_type: 'Node')
count = annotations.count
values = TextValue.joins(:annotations).where(annotations: { annotatable_type: 'Node' })
values.select{|v| v.annotations.count == 1}.each(&:destroy)
annotations.destroy_all
puts "Removed #{count} Node related annotations" if count > 0
end

task(convert_roles: [:environment]) do
puts 'Converting roles...'
disable_authorization_checks do
Person.find_each do |person|
RoleType.for_system.each do |rt|
mask = rt.id
if (person.roles_mask & mask) != 0
Role.where(role_type_id: rt.id, person_id: person.id, scope: nil).first_or_create!
end
end
end

class AdminDefinedRoleProject < ActiveRecord::Base; end

AdminDefinedRoleProject.find_each do |role|
RoleType.for_projects.each do |rt|
mask = rt.id
if (role.role_mask & mask) != 0
Role.where(role_type_id: rt.id, person_id: role.person_id,
scope_type: 'Project', scope_id: role.project_id).first_or_create!
end
end
end

class AdminDefinedRoleProgramme < ActiveRecord::Base; end

AdminDefinedRoleProgramme.find_each do |role|
RoleType.for_programmes.each do |rt|
mask = rt.id
if (role.role_mask & mask) != 0
Role.where(role_type_id: rt.id, person_id: role.person_id,
scope_type: 'Programme', scope_id: role.programme_id).first_or_create!
end
end
end
end
end

task(update_edam_annotation_attributes: [:environment]) do
defs = {
"edam_formats": "data_format_annotations",
"edam_topics": "topic_annotations",
"edam_operations": "operation_annotations",
"edam_data": "data_type_annotations"
}
defs.each do |old_name,new_name|
query = AnnotationAttribute.where(name: old_name)
if query.any?
puts "Updating EDAM based #{old_name} Annotation Attributes"
query.update_all(name: new_name)
end
end
end

task(update_edam_controlled_vocab_keys: [:environment]) do
defs = {
topics: 'edam_topics',
operations: 'edam_operations',
data_formats: 'edam_formats',
data_types: 'edam_data'
}

defs.each do |property, old_key|
new_key = SampleControlledVocab::SystemVocabs.database_key_for_property(property)
query = SampleControlledVocab.where(key: old_key)
if query.any?
puts "Updating key for #{old_key} controlled vocabulary"
query.update_all(key: new_key)
end
end
end

task(remove_orphaned_project_subscriptions: [:environment]) do
disable_authorization_checks do
ProjectSubscription.where.missing(:project).destroy_all
end
end

task(remove_node_activity_logs: [:environment]) do
logs = ActivityLog.where(activity_loggable_type: 'Node')
puts "Removing #{logs.count} Node related activity logs" if logs.count > 0
logs.delete_all
end

task(remove_node_asset_creators: [:environment]) do
creators = AssetsCreator.where(asset_type: 'Node')
puts "Removing #{creators.count} Node related asset creators" if creators.count > 0
creators.delete_all
end

task(refresh_workflow_internals: [:environment]) do |task|
ran = only_once(task) do
Rake::Task['seek:rebuild_workflow_internals'].invoke
end

puts "Skipping workflow internals rebuild, already done" unless ran
end

task(set_default_sample_type_creators: [:environment]) do
ran = only_once('set_default_sample_type_creators') do
puts "Setting default Sample Type creators"
count = 0
SampleType.all.each do |sample_type|
if sample_type.assets_creators.empty?
sample_type.assets_creators.build(creator: sample_type.contributor).save!
count += 1
end
end
puts "#{count} Sample Types updated"
end

puts "Skipping setting default Sample Type creators, as already set" unless ran
end

private

##
Expand Down
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