rename Isa -> ISA

seek4science · Dec 16, 2024 · 698ad57 · 698ad57
1 parent f7d4cd4
commit 698ad57
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Showing 51 changed files with 142 additions and 141 deletions.
diff --git a/app/controllers/assays_controller.rb b/app/controllers/assays_controller.rb
@@ -23,7 +23,7 @@ class AssaysController < ApplicationController
 
   include Seek::Publishing::PublishingCommon
 
-  include Seek::IsaGraphExtensions
+  include Seek::ISAGraphExtensions
 
   api_actions :index, :show, :create, :update, :destroy
 

diff --git a/app/controllers/collections_controller.rb b/app/controllers/collections_controller.rb
@@ -8,7 +8,7 @@ class CollectionsController < ApplicationController
 
   include Seek::Publishing::PublishingCommon
 
-  include Seek::IsaGraphExtensions
+  include Seek::ISAGraphExtensions
 
   api_actions :index, :show, :create, :update, :destroy
 

diff --git a/app/controllers/data_files_controller.rb b/app/controllers/data_files_controller.rb
@@ -30,7 +30,7 @@ class DataFilesController < ApplicationController
 
   include Seek::Doi::Minting
 
-  include Seek::IsaGraphExtensions
+  include Seek::ISAGraphExtensions
 
   api_actions :index, :show, :create, :update, :destroy
 

diff --git a/app/controllers/documents_controller.rb b/app/controllers/documents_controller.rb
@@ -13,7 +13,7 @@ class DocumentsController < ApplicationController
 
   include Seek::Doi::Minting
 
-  include Seek::IsaGraphExtensions
+  include Seek::ISAGraphExtensions
 
   api_actions :index, :show, :create, :update, :destroy
 

diff --git a/app/controllers/file_templates_controller.rb b/app/controllers/file_templates_controller.rb
@@ -18,7 +18,7 @@ class FileTemplatesController < ApplicationController
 
   include Seek::Doi::Minting
 
-  include Seek::IsaGraphExtensions
+  include Seek::ISAGraphExtensions
 
   api_actions :index, :show, :create, :update, :destroy
 

diff --git a/app/controllers/investigations_controller.rb b/app/controllers/investigations_controller.rb
@@ -19,7 +19,7 @@ class InvestigationsController < ApplicationController
 
   include Seek::AnnotationCommon
 
-  include Seek::IsaGraphExtensions
+  include Seek::ISAGraphExtensions
 
   api_actions :index, :show, :create, :update, :destroy
 
@@ -60,12 +60,12 @@ def submit_fairdata_station
   end
 
   def export_isatab_json
-    the_hash = IsaTabConverter.convert_investigation(Investigation.find(params[:id]))
+    the_hash = ISATabConverter.convert_investigation(Investigation.find(params[:id]))
     send_data JSON.pretty_generate(the_hash) , filename: 'isatab.json'
   end
 
   def export_isa
-    isa = IsaExporter::Exporter.new(Investigation.find(params[:id]), current_user).export
+    isa = ISAExporter::Exporter.new(Investigation.find(params[:id]), current_user).export
     send_data isa, filename: 'isa.json', type: 'application/json', deposition: 'attachment'
   rescue Exception => e
     respond_to do |format|

diff --git a/app/controllers/isa_assays_controller.rb b/app/controllers/isa_assays_controller.rb
@@ -1,4 +1,4 @@
-class IsaAssaysController < ApplicationController
+class ISAAssaysController < ApplicationController
   include Seek::AssetsCommon
   include Seek::Publishing::PublishingCommon
 
@@ -29,12 +29,12 @@ def new
 
     @isa_assay =
       if params[:is_assay_stream]
-        IsaAssay.new({ assay: { assay_class_id: AssayClass.assay_stream.id,
+        ISAAssay.new({ assay: { assay_class_id: AssayClass.assay_stream.id,
                                 study_id: study.id,
                                 position: new_position },
                        input_sample_type_id: })
       else
-        IsaAssay.new({ assay: { assay_class_id: AssayClass.experimental.id,
+        ISAAssay.new({ assay: { assay_class_id: AssayClass.experimental.id,
                                 assay_stream_id: params[:assay_stream_id],
                                 study_id: study.id,
                                 position: new_position },
@@ -118,7 +118,7 @@ def rearrange_assay_positions_create_isa_assay
   end
 
   def initialize_isa_assay
-    @isa_assay = IsaAssay.new(isa_assay_params)
+    @isa_assay = ISAAssay.new(isa_assay_params)
     update_sharing_policies @isa_assay.assay
     @isa_assay.assay.contributor = current_person
     @isa_assay.sample_type.contributor = User.current_user.person if isa_assay_params[:sample_type]
@@ -199,7 +199,7 @@ def set_up_instance_variable
   end
 
   def find_requested_item
-    @isa_assay = IsaAssay.new
+    @isa_assay = ISAAssay.new
     @isa_assay.populate(params[:id])
 
     if @isa_assay.assay.nil?

diff --git a/app/controllers/isa_studies_controller.rb b/app/controllers/isa_studies_controller.rb
@@ -1,16 +1,16 @@
-class IsaStudiesController < ApplicationController
+class ISAStudiesController < ApplicationController
   include Seek::AssetsCommon
   include Seek::Publishing::PublishingCommon
 
   before_action :set_up_instance_variable
   before_action :find_requested_item, only: %i[edit update]
 
   def new
-    @isa_study = IsaStudy.new({ study: { investigation_id: params[:investigation_id] } })
+    @isa_study = ISAStudy.new({ study: { investigation_id: params[:investigation_id] } })
   end
 
   def create
-    @isa_study = IsaStudy.new(isa_study_params)
+    @isa_study = ISAStudy.new(isa_study_params)
     update_sharing_policies @isa_study.study
     @isa_study.source.policy = @isa_study.study.policy
     @isa_study.sample_collection.policy = @isa_study.study.policy
@@ -129,7 +129,7 @@ def set_up_instance_variable
   end
 
   def find_requested_item
-    @isa_study = IsaStudy.new
+    @isa_study = ISAStudy.new
     @isa_study.populate(params[:id])
 
     @isa_study.errors.add(:study, "The #{t('isa_study')} was not found.") if @isa_study.study.nil?

diff --git a/app/controllers/models_controller.rb b/app/controllers/models_controller.rb
@@ -18,7 +18,7 @@ class ModelsController < ApplicationController
   include Bives
   include Seek::Doi::Minting
 
-  include Seek::IsaGraphExtensions
+  include Seek::ISAGraphExtensions
 
   api_actions :index, :show, :create, :update, :destroy
 

diff --git a/app/controllers/observation_units_controller.rb b/app/controllers/observation_units_controller.rb
@@ -11,7 +11,7 @@ class ObservationUnitsController < ApplicationController
   before_action :find_assets, only: [:index]
 
   include Seek::Publishing::PublishingCommon
-  include Seek::IsaGraphExtensions
+  include Seek::ISAGraphExtensions
 
   api_actions :index, :show, :create, :update, :destroy
 

diff --git a/app/controllers/presentations_controller.rb b/app/controllers/presentations_controller.rb
@@ -12,7 +12,7 @@ class PresentationsController < ApplicationController
 
   include Seek::Publishing::PublishingCommon
 
-  include Seek::IsaGraphExtensions
+  include Seek::ISAGraphExtensions
 
   api_actions :index, :show, :create, :update, :destroy
 

diff --git a/app/controllers/programmes_controller.rb b/app/controllers/programmes_controller.rb
@@ -14,7 +14,7 @@ class ProgrammesController < ApplicationController
 
   skip_before_action :project_membership_required
 
-  include Seek::IsaGraphExtensions
+  include Seek::ISAGraphExtensions
 
   respond_to :html, :json
 

diff --git a/app/controllers/projects_controller.rb b/app/controllers/projects_controller.rb
@@ -47,7 +47,7 @@ class ProjectsController < ApplicationController
 
   cache_sweeper :projects_sweeper, only: %i[update create destroy]
 
-  include Seek::IsaGraphExtensions
+  include Seek::ISAGraphExtensions
 
   respond_to :html, :json
 

diff --git a/app/controllers/publications_controller.rb b/app/controllers/publications_controller.rb
@@ -13,7 +13,7 @@ class PublicationsController < ApplicationController
   before_action :suggest_authors, only: [:manage]
   before_action :find_display_asset, :only=>[:show, :download]
 
-  include Seek::IsaGraphExtensions
+  include Seek::ISAGraphExtensions
   include PublicationsHelper
 
   api_actions :index, :show

diff --git a/app/controllers/samples_controller.rb b/app/controllers/samples_controller.rb
@@ -13,7 +13,7 @@ class SamplesController < ApplicationController
 
   before_action :auth_to_create, only: %i[new create batch_create]
 
-  include Seek::IsaGraphExtensions
+  include Seek::ISAGraphExtensions
   include Seek::Publishing::PublishingCommon
 
   api_actions :index, :show, :create, :update, :destroy, :batch_create

diff --git a/app/controllers/sops_controller.rb b/app/controllers/sops_controller.rb
@@ -14,7 +14,7 @@ class SopsController < ApplicationController
 
   include Seek::Doi::Minting
 
-  include Seek::IsaGraphExtensions
+  include Seek::ISAGraphExtensions
 
   api_actions :index, :show, :create, :update, :destroy
 

diff --git a/app/controllers/studies_controller.rb b/app/controllers/studies_controller.rb
@@ -18,7 +18,7 @@ class StudiesController < ApplicationController
 
   include Seek::Publishing::PublishingCommon
   include Seek::AnnotationCommon
-  include Seek::IsaGraphExtensions
+  include Seek::ISAGraphExtensions
 
   api_actions :index, :show, :create, :update, :destroy
 

diff --git a/app/controllers/templates_controller.rb b/app/controllers/templates_controller.rb
@@ -124,7 +124,7 @@ def template_attributes
 
   def filter_isa_tags_by_level
     level = params[:level]
-    all_isa_tags_options = IsaTag.all.map { |it| { text: it.title, value: it.id } }
+    all_isa_tags_options = ISATag.all.map { |it| { text: it.title, value: it.id } }
 
     case level
     when 'study source'

diff --git a/app/controllers/workflows_controller.rb b/app/controllers/workflows_controller.rb
@@ -17,7 +17,7 @@ class WorkflowsController < ApplicationController
 
   include Seek::Publishing::PublishingCommon
   include Seek::Doi::Minting
-  include Seek::IsaGraphExtensions
+  include Seek::ISAGraphExtensions
   include RoCrateHandling
   include Legacy::WorkflowSupport
 

diff --git a/app/forms/isa_assay.rb b/app/forms/isa_assay.rb
@@ -1,4 +1,4 @@
-class IsaAssay
+class ISAAssay
   include ActiveModel::Model
 
   attr_accessor :assay, :sample_type, :input_sample_type_id

diff --git a/app/forms/isa_study.rb b/app/forms/isa_study.rb
@@ -1,4 +1,4 @@
-class IsaStudy
+class ISAStudy
   include ActiveModel::Model
 
   attr_accessor :study, :source_sample_type, :sample_collection_sample_type

diff --git a/app/helpers/isa_helper.rb b/app/helpers/isa_helper.rb
@@ -1,6 +1,6 @@
 require 'tempfile'
 
-module IsaHelper
+module ISAHelper
   OLD_FILL_COLOURS = {
       'Sop' => '#7AC5CD', # cadetblue3
       'Model' => '#CDCD00', # yellow3

diff --git a/app/helpers/isa_tab_converter.rb b/app/helpers/isa_tab_converter.rb
@@ -1,5 +1,5 @@
 # noinspection ALL
-class IsaTabConverter
+class ISATabConverter
   include Seek::Util.routes
 
   JERM_ONTOLOGY_URL = 'http://jermontology.org/ontology/JERMOntology'

diff --git a/app/jobs/populate_templates_job.rb b/app/jobs/populate_templates_job.rb
@@ -5,6 +5,6 @@ class PopulateTemplatesJob < ApplicationJob
   def perform
     return unless Seek::Config.isa_json_compliance_enabled
 
-    Seek::IsaTemplates::TemplateExtractor.extract_templates
+    Seek::ISATemplates::TemplateExtractor.extract_templates
   end
 end
diff --git a/app/models/application_record.rb b/app/models/application_record.rb
@@ -14,7 +14,7 @@ class ApplicationRecord < ActiveRecord::Base
   include Seek::GroupedPagination
   include Seek::TitleTrimmer
   include Seek::ActsAsAsset
-  include Seek::ActsAsIsa
+  include Seek::ActsAsISA
   include HasExtendedMetadata
   include Seek::Doi::ActsAsDoiMintable
   include Seek::Doi::ActsAsDoiParent

diff --git a/app/models/isa_tag.rb b/app/models/isa_tag.rb
@@ -1,63 +1,63 @@
-class IsaTag < ApplicationRecord
+class ISATag < ApplicationRecord
   validates :title, presence: true
 
-  has_many :template_attributes, inverse_of: :isa_tag
-  has_many :sample_attributes, inverse_of: :isa_tag
+  has_many :template_attributes, inverse_of: :ISATag
+  has_many :sample_attributes, inverse_of: :ISATag
 
   def isa_source?
-    title == Seek::Isa::TagType::SOURCE
+    title == Seek::ISA::TagType::SOURCE
   end
 
   def isa_source_characteristic?
-    title == Seek::Isa::TagType::SOURCE_CHARACTERISTIC
+    title == Seek::ISA::TagType::SOURCE_CHARACTERISTIC
   end
 
   def isa_sample?
-    title == Seek::Isa::TagType::SAMPLE
+    title == Seek::ISA::TagType::SAMPLE
   end
 
   def isa_sample_characteristic?
-    title == Seek::Isa::TagType::SAMPLE_CHARACTERISTIC
+    title == Seek::ISA::TagType::SAMPLE_CHARACTERISTIC
   end
 
   def isa_protocol?
-    title == Seek::Isa::TagType::PROTOCOL
+    title == Seek::ISA::TagType::PROTOCOL
   end
 
   def isa_other_material?
-    title == Seek::Isa::TagType::OTHER_MATERIAL
+    title == Seek::ISA::TagType::OTHER_MATERIAL
   end
 
   def isa_other_material_characteristic?
-    title == Seek::Isa::TagType::OTHER_MATERIAL_CHARACTERISTIC
+    title == Seek::ISA::TagType::OTHER_MATERIAL_CHARACTERISTIC
   end
 
   def isa_data_file?
-    title == Seek::Isa::TagType::DATA_FILE
+    title == Seek::ISA::TagType::DATA_FILE
   end
 
   def isa_data_file_comment?
-    title == Seek::Isa::TagType::DATA_FILE_COMMENT
+    title == Seek::ISA::TagType::DATA_FILE_COMMENT
   end
 
   def isa_parameter_value?
-    title == Seek::Isa::TagType::PARAMETER_VALUE
+    title == Seek::ISA::TagType::PARAMETER_VALUE
   end
 
   def self.allowed_isa_tags_for_level(level)
     tags = case level
     when 'study source'
-      Seek::Isa::TagType::SOURCE_TAGS
+      Seek::ISA::TagType::SOURCE_TAGS
     when 'study sample'
-      Seek::Isa::TagType::SAMPLE_TAGS
+      Seek::ISA::TagType::SAMPLE_TAGS
     when 'assay - material'
-      Seek::Isa::TagType::OTHER_MATERIAL_TAGS
+      Seek::ISA::TagType::OTHER_MATERIAL_TAGS
     when 'assay - data file'
-      Seek::Isa::TagType::DATA_FILE_TAGS
+      Seek::ISA::TagType::DATA_FILE_TAGS
     else
-      Seek::Isa::TagType::ALL_TYPES
+      Seek::ISA::TagType::ALL_TYPES
     end
 
-    tags.map { |tag| IsaTag.find_by(title: tag) }
+    tags.map { |tag| ISATag.find_by(title: tag) }
   end
 end