labimotion 1.4.1 → 2.0.0.rc6

data/lib/labimotion/helpers/element_helpers.rb

@@ -93,7 +93,8 @@ module Labimotion
       all_coll = Collection.get_all_collection_for_user(current_user.id)
       element.collections << all_coll
       element.save!
-      element.properties = update_sample_association(params[:properties], current_user, element)
+      _properties = update_sample_association(params[:properties], current_user, element)
+      element.properties = update_vocabularies(_properties, current_user, element)
       element.container = update_datamodel(params[:container], current_user)
       element.save!
       update_element_labels(element, params[:user_labels], current_user.id)
@@ -112,7 +113,6 @@ module Labimotion
       params.delete(:properties)
       update_element_labels(element, params[:user_labels], current_user.id)
       params.delete(:user_labels)
-
       attributes = declared(params.except(:segments), include_missing: false)
       properties['pkg'] = Labimotion::Utils.pkg(properties['pkg'])
       if element.klass_uuid != properties['klass_uuid'] || element.properties != properties || element.name != params[:name]
@@ -123,15 +123,16 @@ module Labimotion
         properties.delete('flow') unless properties['flow'].nil?
         properties.delete('flowObject') unless properties['flowObject'].nil?
         properties.delete('select_options') unless properties['select_options'].nil?
-
         attributes['properties'] = properties
         attributes['properties']['uuid'] = uuid
         attributes['uuid'] = uuid
         attributes['klass_uuid'] = properties['klass_uuid']
-
         element.update(attributes)
       end
       element.save_segments(segments: params[:segments], current_user_id: current_user.id)
+      element.reload
+      element.properties = update_vocabularies(element.properties, current_user, element)
+      element.save!
       element
     rescue StandardError => e
       Labimotion.log_exception(e, current_user)
@@ -321,7 +322,6 @@ module Labimotion
           return { status: 'success', message: "The element: #{attributes['name']} has been created using version: #{attributes['version']}!" }
         end
       end
-
     rescue StandardError => e
       Labimotion.log_exception(e, current_user)
       return { status: 'error', message: e.message }
@@ -351,7 +351,9 @@ module Labimotion
         _att
       end
       attachments
+    rescue StandardError => e
+      Labimotion.log_exception(e)
+      attachments
     end
-
   end
 end

data/lib/labimotion/helpers/generic_helpers.rb

@@ -9,7 +9,12 @@ module Labimotion
     extend Grape::API::Helpers
 
     def authenticate_admin!(type)
-      error!('401 Unauthorized', 401) unless current_user.generic_admin[type]
+      unauthorized = -> { error!('401 Unauthorized', 401) }
+      if %w[standard_layers vocabularies].include?(type)
+        unauthorized.call unless current_user.generic_admin.values_at('elements', 'segments', 'datasets').any?
+      else
+        unauthorized.call unless current_user.generic_admin[type]
+      end
     end
 
     def fetch_klass(name, id)

data/lib/labimotion/helpers/param_helpers.rb

@@ -6,94 +6,133 @@ module Labimotion
   ## Generic Helpers
   module ParamHelpers
     extend Grape::API::Helpers
-       ## Element Klass Params
-      params :upload_element_klass_params do
-        requires :name, type: String, desc: 'Klass Name'
-        optional :label, type: String, desc: 'Klass label'
-        optional :desc, type: String, desc: 'Klass desc'
-        optional :klass_prefix, type: String, desc: 'Klass klass_prefix'
-        optional :icon_name, type: String, desc: 'Klass icon_name'
-        requires :properties_template, type: Hash, desc: 'Klass template'
-        optional :properties_release, type: Hash, desc: 'Klass release'
-        optional :released_at, type: DateTime, desc: 'Klass released_at'
-        requires :uuid, type: String, desc: 'Klass uuid'
-        requires :place, type: Integer, desc: 'Klass place'
-        requires :identifier, type: String, desc: 'Klass identifier'
-        optional :sync_time, type: DateTime, desc: 'Klass sync_time'
-        optional :version, type: String, desc: 'Klass version'
-      end
+    ## Element Klass Params
+    params :upload_element_klass_params do
+      requires :name, type: String, desc: 'Klass Name'
+      optional :label, type: String, desc: 'Klass label'
+      optional :desc, type: String, desc: 'Klass desc'
+      optional :klass_prefix, type: String, desc: 'Klass klass_prefix'
+      optional :icon_name, type: String, desc: 'Klass icon_name'
+      requires :properties_template, type: Hash, desc: 'Klass template'
+      optional :properties_release, type: Hash, desc: 'Klass release'
+      optional :released_at, type: DateTime, desc: 'Klass released_at'
+      requires :uuid, type: String, desc: 'Klass uuid'
+      requires :place, type: Integer, desc: 'Klass place'
+      requires :identifier, type: String, desc: 'Klass identifier'
+      optional :sync_time, type: DateTime, desc: 'Klass sync_time'
+      optional :version, type: String, desc: 'Klass version'
+    end
 
-      params :create_element_klass_params do
-        requires :name, type: String, desc: 'Element Klass Name'
-        requires :label, type: String, desc: 'Element Klass Label'
-        requires :klass_prefix, type: String, desc: 'Element Klass Short Label Prefix'
-        optional :icon_name, type: String, desc: 'Element Klass Icon Name'
-        optional :desc, type: String, desc: 'Element Klass Desc'
-        optional :properties_template, type: Hash, desc: 'Element Klass properties template'
-      end
+    params :create_element_klass_params do
+      requires :name, type: String, desc: 'Element Klass Name'
+      requires :label, type: String, desc: 'Element Klass Label'
+      requires :klass_prefix, type: String, desc: 'Element Klass Short Label Prefix'
+      optional :icon_name, type: String, desc: 'Element Klass Icon Name'
+      optional :desc, type: String, desc: 'Element Klass Desc'
+      optional :properties_template, type: Hash, desc: 'Element Klass properties template'
+    end
 
-      params :update_element_klass_params do
-        requires :id, type: Integer, desc: 'Element Klass ID'
-        optional :label, type: String, desc: 'Element Klass Label'
-        optional :klass_prefix, type: String, desc: 'Element Klass Short Label Prefix'
-        optional :icon_name, type: String, desc: 'Element Klass Icon Name'
-        optional :desc, type: String, desc: 'Element Klass Desc'
-        optional :place, type: String, desc: 'Element Klass Place'
-      end
+    params :update_element_klass_params do
+      requires :id, type: Integer, desc: 'Element Klass ID'
+      optional :label, type: String, desc: 'Element Klass Label'
+      optional :klass_prefix, type: String, desc: 'Element Klass Short Label Prefix'
+      optional :icon_name, type: String, desc: 'Element Klass Icon Name'
+      optional :desc, type: String, desc: 'Element Klass Desc'
+      optional :place, type: String, desc: 'Element Klass Place'
+    end
 
-      ## Element Params
-      params :create_element_params do
-        requires :element_klass, type: Hash
-        requires :name, type: String
-        optional :properties, type: Hash
-        optional :properties_release, type: Hash
-        optional :collection_id, type: Integer
-        requires :container, type: Hash
-        optional :user_labels, type: Array
-        optional :segments, type: Array, desc: 'Segments'
-      end
+    ## Element Params
+    params :create_element_params do
+      requires :element_klass, type: Hash
+      requires :name, type: String
+      optional :properties, type: Hash
+      optional :properties_release, type: Hash
+      optional :collection_id, type: Integer
+      requires :container, type: Hash
+      optional :user_labels, type: Array
+      optional :segments, type: Array, desc: 'Segments'
+    end
 
-      params :update_element_params do
-        requires :id, type: Integer, desc: 'element id'
-        optional :name, type: String
-        requires :properties, type: Hash
-        optional :properties_release, type: Hash
-        requires :container, type: Hash
-        optional :user_labels, type: Array
-        optional :segments, type: Array, desc: 'Segments'
-      end
+    params :update_element_params do
+      requires :id, type: Integer, desc: 'element id'
+      optional :name, type: String
+      requires :properties, type: Hash
+      optional :properties_release, type: Hash
+      requires :container, type: Hash
+      optional :user_labels, type: Array
+      optional :segments, type: Array, desc: 'Segments'
+    end
 
-      ## Segment Klass Params
-      params :upload_segment_klass_params do
-        requires :label, type: String, desc: 'Klass label'
-        optional :desc, type: String, desc: 'Klass desc'
-        requires :properties_template, type: Hash, desc: 'Klass template'
-        optional :properties_release, type: Hash, desc: 'Klass release'
-        optional :released_at, type: DateTime, desc: 'Klass released_at'
-        requires :uuid, type: String, desc: 'Klass uuid'
-        requires :place, type: Integer, desc: 'Klass place'
-        requires :identifier, type: String, desc: 'Klass identifier'
-        optional :sync_time, type: DateTime, desc: 'Klass sync_time'
-        optional :version, type: String, desc: 'Klass version'
-        requires :element_klass, type: Hash do
-          use :upload_element_klass_params
-        end
+    ## Segment Klass Params
+    params :upload_segment_klass_params do
+      requires :label, type: String, desc: 'Klass label'
+      optional :desc, type: String, desc: 'Klass desc'
+      requires :properties_template, type: Hash, desc: 'Klass template'
+      optional :properties_release, type: Hash, desc: 'Klass release'
+      optional :released_at, type: DateTime, desc: 'Klass released_at'
+      requires :uuid, type: String, desc: 'Klass uuid'
+      requires :place, type: Integer, desc: 'Klass place'
+      requires :identifier, type: String, desc: 'Klass identifier'
+      optional :sync_time, type: DateTime, desc: 'Klass sync_time'
+      optional :version, type: String, desc: 'Klass version'
+      requires :element_klass, type: Hash do
+        use :upload_element_klass_params
       end
+    end
 
-      params :update_segment_klass_params do
-        requires :id, type: Integer, desc: 'Segment Klass ID'
-        optional :label, type: String, desc: 'Segment Klass Label'
-        optional :desc, type: String, desc: 'Segment Klass Desc'
-        optional :place, type: String, desc: 'Segment Klass Place', default: '100'
-        optional :identifier, type: String, desc: 'Segment Identifier'
-      end
+    params :update_segment_klass_params do
+      requires :id, type: Integer, desc: 'Segment Klass ID'
+      optional :label, type: String, desc: 'Segment Klass Label'
+      optional :desc, type: String, desc: 'Segment Klass Desc'
+      optional :place, type: String, desc: 'Segment Klass Place', default: '100'
+      optional :identifier, type: String, desc: 'Segment Identifier'
+    end
 
-      params :create_segment_klass_params do
-        requires :label, type: String, desc: 'Segment Klass Label'
-        requires :element_klass, type: Integer, desc: 'Element Klass Id'
-        optional :desc, type: String, desc: 'Segment Klass Desc'
-        optional :place, type: String, desc: 'Segment Klass Place', default: '100'
-        optional :properties_template, type: Hash, desc: 'Element Klass properties template'
-      end
+    params :create_segment_klass_params do
+      requires :label, type: String, desc: 'Segment Klass Label'
+      requires :element_klass, type: Integer, desc: 'Element Klass Id'
+      optional :desc, type: String, desc: 'Segment Klass Desc'
+      optional :place, type: String, desc: 'Segment Klass Place', default: '100'
+      optional :properties_template, type: Hash, desc: 'Element Klass properties template'
+    end
+
+    params :create_std_layer_params do
+      requires :name, type: String, desc: 'Element Klass Name'
+      requires :label, type: String, desc: 'Element Klass Label'
+      requires :klass_prefix, type: String, desc: 'Element Klass Short Label Prefix'
+      optional :icon_name, type: String, desc: 'Element Klass Icon Name'
+      optional :desc, type: String, desc: 'Element Klass Desc'
+      optional :properties_template, type: Hash, desc: 'Element Klass properties template'
+    end
+
+    params :std_layer_save do
+      requires :key, type: String, desc: 'key'
+      requires :cols, type: Integer, desc: 'key'
+      requires :label, type: String, desc: 'Label'
+      optional :position, type: Integer, desc: 'position'
+      optional :wf_position, type: Integer, desc: 'wf position'
+      optional :fields, type: Array, desc: 'fields'
+      optional :select_options, type: Hash, desc: 'selections'
+    end
+
+    params :std_layer_criteria do
+      requires :name, type: String, desc: 'Layer name'
+    end
+
+    params :vocab_save do
+      optional :name, type: String, desc: 'field'
+      optional :label, type: String, desc: 'Label'
+      optional :term_id, type: String, desc: 'ontology term_id'
+      requires :ontology, type: Hash, desc: 'ontology'
+      optional :source, type: String, desc: 'source'
+      optional :source_id, type: String, desc: 'source_id'
+      optional :layer_id, type: String, desc: 'layer_id'
+      optional :sub_fields, type: Array, desc: 'sub_fields'
+      optional :text_sub_fields, type: Array, desc: 'text_sub_fields'
+      requires :field_type, type: String, desc: 'field type'
+      requires :voc, type: Hash, desc: 'vocabulary references'
+      optional :select_options, type: Hash, desc: 'selections'
+      optional :option_layers, type: String, desc: 'option'
+    end
   end
-end
+end

data/lib/labimotion/helpers/segment_helpers.rb

@@ -72,7 +72,7 @@ module Labimotion
       # el_attributes['properties_template'] = response['element_klass']['properties_release']
       # Labimotion::ElementKlass.create!(el_attributes)
       attributes['element_klass_id'] = element_klass.id
-      segment_klass = Labimotion::SegmentKlass.find_by(identifier: attributes['identifier'])
+      segment_klass = Labimotion::SegmentKlass.find_by(identifier: attributes['identifier']) if attributes['identifier'].present?
       if segment_klass.present?
         if segment_klass['uuid'] == attributes['uuid'] && segment_klass['version'] == attributes['version']
           return { status: 'success', message: "This segment: #{attributes['label']} has the latest version!" }

data/lib/labimotion/helpers/vocabulary_helpers.rb

@@ -0,0 +1,16 @@
+# frozen_string_literal: true
+
+module Labimotion
+  # Helper for associated sample
+  module VocabularyHelpers
+    extend Grape::API::Helpers
+
+    def update_vocabularies(properties, current_user, element)
+      Labimotion::VocabularyHandler.update_vocabularies(properties, current_user, element)
+    rescue StandardError => e
+      Labimotion.log_exception(e, current_user)
+      properties
+    end
+
+  end
+end

data/lib/labimotion/libs/converter.rb

@@ -28,7 +28,7 @@ module Labimotion
       dsr = []
       ols = nil
       Zip::File.open(att.attachment_attacher.file.url) do |zip_file|
-        res = Labimotion::Converter.collect_metadata(zip_file) if att.filename.split('.')&.last == 'zip'
+        res = Labimotion::Converter.collect_metadata(zip_file, current_user) if att.filename.split('.')&.last == 'zip'
         ols = res[:o] unless res&.dig(:o).nil?
         dsr.push(res[:d]) unless res&.dig(:d).nil?
       end
@@ -92,7 +92,7 @@ module Labimotion
       { a: oa, f: folder }
     end
 
-    def self.collect_metadata(zip_file) # rubocop: disable Metrics/PerceivedComplexity
+    def self.collect_metadata(zip_file, current_user = {}) # rubocop: disable Metrics/PerceivedComplexity
       dsr = []
       ols = nil
       zip_file.each do |entry|
@@ -114,7 +114,7 @@ module Labimotion
       { d: dsr, o: ols }
     end
 
-    def self.handle_response(oat, response) # rubocop: disable Metrics/PerceivedComplexity
+    def self.handle_response(oat, response, current_user = {}) # rubocop: disable Metrics/PerceivedComplexity
       dsr = []
       ols = nil
 
@@ -123,10 +123,8 @@ module Labimotion
         tmp_file.write(response.parsed_response)
         tmp_file.rewind
 
-        name = response&.headers && response&.headers['content-disposition']&.split('=')&.last
         filename = oat.filename
         name = "#{File.basename(filename, '.*')}.zip"
-
         att = Attachment.new(
           filename: name,
           file_path: tmp_file.path,
@@ -140,7 +138,7 @@ module Labimotion
 
         att.save! if att.valid?
 
-        process_ds(att.id)
+        process_ds(att.id, current_user)
       rescue StandardError => e
         raise e
       ensure
@@ -148,7 +146,7 @@ module Labimotion
       end
     end
 
-    def self.process(data)
+    def self.process(data, current_user = {}) # rubocop: disable Metrics/PerceivedComplexity
       return data[:a].con_state if data[:a]&.attachable_type != 'Container'
       response = nil
       begin
@@ -165,25 +163,25 @@ module Labimotion
           )
         end
         if response.ok?
-          Labimotion::Converter.handle_response(data[:a], response)
+          Labimotion::Converter.handle_response(data[:a], response, current_user)
           Labimotion::ConState::PROCESSED
         else
           Labimotion::Converter.logger.error ["Converter Response Error: id: [#{data[:a]&.id}], filename: [#{data[:a]&.filename}], response: #{response}"].join($INPUT_RECORD_SEPARATOR)
           Labimotion::ConState::ERROR
         end
       rescue StandardError => e
-        Labimotion::Converter.logger.error ["process fail: [#{data[:a]&.id}]", e.message, *e.backtrace].join($INPUT_RECORD_SEPARATOR)
+        Labimotion::Converter.logger.error ["process fail: #{data[:a]&.id}", e.message, *e.backtrace].join($INPUT_RECORD_SEPARATOR)
         Labimotion::ConState::ERROR
       ensure
         FileUtils.rm_f(ofile)
       end
     end
 
-    def self.jcamp_converter(id)
+    def self.jcamp_converter(id, current_user = {})
       data = Labimotion::Converter.vor_conv(id)
       return if data.nil?
 
-      Labimotion::Converter.process(data)
+      Labimotion::Converter.process(data, current_user)
     rescue StandardError => e
       Labimotion::Converter.logger.error ["jcamp_converter fail: #{id}", e.message, *e.backtrace].join($INPUT_RECORD_SEPARATOR)
       Labimotion::ConState::ERROR
@@ -243,27 +241,8 @@ module Labimotion
         fi['device'] = ds[:device] || ds[:value]
         new_prop[Labimotion::Prop::LAYERS][ds[:layer]][Labimotion::Prop::FIELDS][idx] = fi
       end
-      new_prop.dig(Labimotion::Prop::LAYERS, 'general', Labimotion::Prop::FIELDS)&.each_with_index do |fi, idx|
-        if fi['field'] == 'creator' && current_user.present?
-          fi['value'] = current_user.name
-          fi['system'] = current_user.name
-          new_prop[Labimotion::Prop::LAYERS]['general'][Labimotion::Prop::FIELDS][idx] = fi
-        end
-      end
       element = Container.find(dataset.element_id)&.root_element
-      element.present? && element&.class&.name == 'Sample' && new_prop.dig(Labimotion::Prop::LAYERS, 'sample_details', Labimotion::Prop::FIELDS)&.each_with_index do |fi, idx|
-        if fi['field'] == 'id'
-          fi['value'] = element.id
-          fi['system'] = element.id
-          new_prop[Labimotion::Prop::LAYERS]['sample_details'][Labimotion::Prop::FIELDS][idx] = fi
-        end
-
-        if fi['field'] == 'label'
-          fi['value'] = element.short_label
-          fi['system'] = element.short_label
-          new_prop[Labimotion::Prop::LAYERS]['sample_details'][Labimotion::Prop::FIELDS][idx] = fi
-        end
-      end
+      new_prop = Labimotion::VocabularyHandler.update_vocabularies(new_prop, current_user, element)
       dataset.properties = new_prop
       dataset.save!
     end
@@ -325,13 +304,13 @@ module Labimotion
       res
     end
 
-    def self.metadata(id)
+    def self.metadata(id, current_user)
       att = Attachment.find(id)
       return if att.nil? || att.attachable_id.nil? || att.attachable_type != Labimotion::Prop::CONTAINER
 
       ds = Labimotion::Dataset.find_by(element_type: Labimotion::Prop::CONTAINER, element_id: att.attachable_id)
       att.update_column(:con_state, Labimotion::ConState::COMPLETED) if ds.present?
-      process_ds(att.id) if ds.nil?
+      process_ds(att.id, current_user) if ds.nil?
     end
   end
 end