labimotion 1.4.1 → 2.0.0.rc1

data/lib/labimotion/models/concerns/attachment_converter.rb

@@ -25,17 +25,18 @@ module Labimotion
       def exec_converter
         return if self.has_attribute?(:con_state) == false || self.con_state.nil? || self.con_state == Labimotion::ConState::NONE
 
-        return if attachable_id.nil? && self.con_state != Labimotion::ConState::WAIT
+        return if attachable_id.nil? && con_state != Labimotion::ConState::WAIT
 
+        current_user = User.find_by(id: created_by)
         case con_state
         when Labimotion::ConState::NMR
-          self.con_state = Labimotion::NmrMapper.process_ds(id)
+          self.con_state = Labimotion::NmrMapper.process_ds(id, current_user)
           update_column(:con_state, con_state)
         when Labimotion::ConState::WAIT
-          self.con_state = Labimotion::Converter.jcamp_converter(id)
+          self.con_state = Labimotion::Converter.jcamp_converter(id, current_user)
           update_column(:con_state, con_state)
         when Labimotion::ConState::CONVERTED
-          Labimotion::Converter.metadata(id)
+          Labimotion::Converter.metadata(id, current_user)
         end
       end
     end

data/lib/labimotion/models/concerns/datasetable.rb

@@ -42,6 +42,7 @@ module Labimotion
       props['identifier'] = klass.identifier if klass.identifier.present?
       props['uuid'] = uuid
       props['klass'] = 'Dataset'
+      props = Labimotion::VocabularyHandler.update_vocabularies(props, args[:current_user], args[:element])
 
       ds = Labimotion::Dataset.find_by(element_type: self.class.name, element_id: id)
       if ds.present? && (ds.klass_uuid != props['klass_uuid'] || ds.properties != props)

data/lib/labimotion/models/concerns/segmentable.rb

@@ -59,6 +59,8 @@ module Labimotion
         props['uuid'] = uuid
         props['klass'] = 'Segment'
         props = Labimotion::SampleAssociation.update_sample_association(props, args[:current_user_id])
+        current_user = User.find_by(id: args[:current_user_id])
+        props = Labimotion::VocabularyHandler.update_vocabularies(props, current_user, self)
         segment = Labimotion::Segment.where(element_type: self.class.name, element_id: self.id, segment_klass_id: seg['segment_klass_id']).order(id: :desc).first
         if segment.present? && (segment.klass_uuid != props['klass_uuid'] || segment.properties != props)
           segment.update!(properties_release: klass.properties_release, properties: props, uuid: uuid, klass_uuid: props['klass_uuid'])

data/lib/labimotion/models/std_layer.rb

@@ -0,0 +1,9 @@
+# frozen_string_literal: true
+
+module Labimotion
+  class StdLayer < ApplicationRecord
+    acts_as_paranoid
+    self.table_name = :layers
+    has_many :layer_tracks, primary_key: 'identifier', foreign_key: 'identifier', class_name: 'Labimotion::StdLayersRevision'
+  end
+end

data/lib/labimotion/models/std_layers_revision.rb

@@ -0,0 +1,9 @@
+# frozen_string_literal: true
+
+module Labimotion
+  class StdLayersRevision < ApplicationRecord
+    acts_as_paranoid
+    self.table_name = :layer_tracks
+    belongs_to :layers, primary_key: 'identifier', foreign_key: 'identifier', class_name: 'Labimotion::StdLayer'
+  end
+end

data/lib/labimotion/models/vocabulary.rb

@@ -0,0 +1,12 @@
+# frozen_string_literal: true
+require 'labimotion/models/concerns/generic_klass_revisions'
+require 'labimotion/models/concerns/workflow'
+
+module Labimotion
+  class Vocabulary < ApplicationRecord
+    self.table_name = :vocabularies
+    acts_as_paranoid
+
+
+  end
+end

data/lib/labimotion/version.rb

@@ -2,5 +2,5 @@
 
 ## Labimotion Version
 module Labimotion
-  VERSION = '1.4.1'
+  VERSION = '2.0.0.rc1'
 end

data/lib/labimotion.rb

@@ -16,12 +16,15 @@ module Labimotion
   autoload :Utils, 'labimotion/utils/utils'
 
   ######## APIs
+  autoload :LabimotionAPI, 'labimotion/apis/labimotion_api'
   autoload :GenericKlassAPI, 'labimotion/apis/generic_klass_api'
   autoload :GenericElementAPI, 'labimotion/apis/generic_element_api'
   autoload :GenericDatasetAPI, 'labimotion/apis/generic_dataset_api'
   autoload :SegmentAPI, 'labimotion/apis/segment_api'
   autoload :LabimotionHubAPI, 'labimotion/apis/labimotion_hub_api'
   autoload :ConverterAPI, 'labimotion/apis/converter_api'
+  autoload :StandardLayerAPI, 'labimotion/apis/standard_layer_api'
+  autoload :VocabularyAPI, 'labimotion/apis/vocabulary_api'
 
   ######## Entities
   autoload :PropertiesEntity, 'labimotion/entities/properties_entity'
@@ -43,6 +46,7 @@ module Labimotion
   autoload :ElementRevisionEntity, 'labimotion/entities/element_revision_entity'
   autoload :SegmentRevisionEntity, 'labimotion/entities/segment_revision_entity'
   ## autoload :DatasetRevisionEntity, 'labimotion/entities/dataset_revision_entity'
+  autoload :VocabularyEntity, 'labimotion/entities/vocabulary_entity'
 
   ######## Helpers
   autoload :GenericHelpers, 'labimotion/helpers/generic_helpers'
@@ -54,6 +58,7 @@ module Labimotion
   autoload :ConverterHelpers, 'labimotion/helpers/converter_helpers'
   autoload :SampleAssociationHelpers, 'labimotion/helpers/sample_association_helpers'
   autoload :RepositoryHelpers, 'labimotion/helpers/repository_helpers'
+  autoload :VocabularyHelpers, 'labimotion/helpers/vocabulary_helpers'
 
   ######## Libs
   autoload :Converter, 'labimotion/libs/converter'
@@ -64,6 +69,7 @@ module Labimotion
   autoload :SampleAssociation, 'labimotion/libs/sample_association'
   autoload :PropertiesHandler, 'labimotion/libs/properties_handler'
   autoload :AttachmentHandler, 'labimotion/libs/attachment_handler'
+  autoload :VocabularyHandler, 'labimotion/libs/vocabulary_handler'
 
   ######## Utils
   autoload :Prop, 'labimotion/utils/prop'
@@ -84,6 +90,7 @@ module Labimotion
   autoload :ElementKlass, 'labimotion/models/element_klass'
   autoload :SegmentKlass, 'labimotion/models/segment_klass'
   autoload :DatasetKlass, 'labimotion/models/dataset_klass'
+  autoload :Vocabulary, 'labimotion/models/vocabulary'
 
   autoload :ElementsRevision, 'labimotion/models/elements_revision'
   autoload :SegmentsRevision, 'labimotion/models/segments_revision'
@@ -97,6 +104,9 @@ module Labimotion
   autoload :ElementsElement, 'labimotion/models/elements_element'
   autoload :CollectionsElement, 'labimotion/models/collections_element'
 
+  autoload :StdLayer, 'labimotion/models/std_layer'
+  autoload :StdLayersRevision, 'labimotion/models/std_layers_revision'
+
   ######## Models/Concerns
   autoload :GenericKlassRevisions, 'labimotion/models/concerns/generic_klass_revisions'
   autoload :GenericRevisions, 'labimotion/models/concerns/generic_revisions'

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: labimotion
 version: !ruby/object:Gem::Version
-  version: 1.4.1
+  version: 2.0.0.rc1
 platform: ruby
 authors:
 - Chia-Lin Lin
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2024-10-24 00:00:00.000000000 Z
+date: 2024-12-06 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rails
@@ -38,8 +38,12 @@ files:
 - lib/labimotion/apis/generic_dataset_api.rb
 - lib/labimotion/apis/generic_element_api.rb
 - lib/labimotion/apis/generic_klass_api.rb
+- lib/labimotion/apis/labimotion_api.rb
 - lib/labimotion/apis/labimotion_hub_api.rb
 - lib/labimotion/apis/segment_api.rb
+- lib/labimotion/apis/standard_api.rb
+- lib/labimotion/apis/standard_layer_api.rb
+- lib/labimotion/apis/vocabulary_api.rb
 - lib/labimotion/collection/export.rb
 - lib/labimotion/collection/import.rb
 - lib/labimotion/conf.rb
@@ -58,6 +62,7 @@ files:
 - lib/labimotion/entities/segment_entity.rb
 - lib/labimotion/entities/segment_klass_entity.rb
 - lib/labimotion/entities/segment_revision_entity.rb
+- lib/labimotion/entities/vocabulary_entity.rb
 - lib/labimotion/helpers/converter_helpers.rb
 - lib/labimotion/helpers/dataset_helpers.rb
 - lib/labimotion/helpers/element_helpers.rb
@@ -67,14 +72,18 @@ files:
 - lib/labimotion/helpers/sample_association_helpers.rb
 - lib/labimotion/helpers/search_helpers.rb
 - lib/labimotion/helpers/segment_helpers.rb
+- lib/labimotion/helpers/vocabulary_helpers.rb
 - lib/labimotion/libs/attachment_handler.rb
 - lib/labimotion/libs/converter.rb
+- lib/labimotion/libs/data/vocab/Standard.json
+- lib/labimotion/libs/data/vocab/System.json
 - lib/labimotion/libs/export_dataset.rb
 - lib/labimotion/libs/export_element.rb
 - lib/labimotion/libs/nmr_mapper.rb
 - lib/labimotion/libs/properties_handler.rb
 - lib/labimotion/libs/sample_association.rb
 - lib/labimotion/libs/template_hub.rb
+- lib/labimotion/libs/vocabulary_handler.rb
 - lib/labimotion/models/collections_element.rb
 - lib/labimotion/models/concerns/attachment_converter.rb
 - lib/labimotion/models/concerns/datasetable.rb
@@ -98,6 +107,9 @@ files:
 - lib/labimotion/models/segment_klass.rb
 - lib/labimotion/models/segment_klasses_revision.rb
 - lib/labimotion/models/segments_revision.rb
+- lib/labimotion/models/std_layer.rb
+- lib/labimotion/models/std_layers_revision.rb
+- lib/labimotion/models/vocabulary.rb
 - lib/labimotion/utils/con_state.rb
 - lib/labimotion/utils/export_utils.rb
 - lib/labimotion/utils/field_type.rb
@@ -111,7 +123,10 @@ files:
 homepage: https://github.com/LabIMotion/labimotion
 licenses:
 - AGPL-3.0
-metadata: {}
+metadata:
+  homepage_uri: https://github.com/LabIMotion/labimotion
+  source_code_uri: https://github.com/LabIMotion/labimotion
+  bug_tracker_uri: https://github.com/LabIMotion/labimotion/discussions
 post_install_message: 
 rdoc_options: []
 require_paths:
@@ -123,9 +138,9 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
-  - - ">="
+  - - ">"
     - !ruby/object:Gem::Version
-      version: '0'
+      version: 1.3.1
 requirements: []
 rubygems_version: 3.1.6
 signing_key: