labimotion 1.5.0.rc9 → 2.0.0.rc2

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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+  metadata.gz: 608624a39eb174198e63db9cde2e4440425aa6bad1c604801c817ea13caea859
+  data.tar.gz: c691e2f9e670d301acc2494745e02836bf8ffcb1479c86c747f02ff9fadc6617
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-  data.tar.gz: 4fc728cf883e6d9a3f4fcf54193ab823993e424c2bf6d53fa4d924cfb3efec4b5dfc65ab7a122e19b9ac16e7057f392e93bed88e0f302046f77533d498f89e7c
+  metadata.gz: e3c03f09293537ad8993158d1e1871fff2bf6a84ff88d90ca5d55af663fa862df4907a72639a2cdfb4bb7a2371911bf37b146cc97fbf0030945d3c23b5777de9
+  data.tar.gz: c746e80182b677d03c5bf06608285441a7b7022fdfcf521aec2aeaab61470d7a774ce059919d35e4b671446890b4055e3707da8b9a7f2fa52b4446fe52fbf655

data/lib/labimotion/apis/vocabulary_api.rb

@@ -30,7 +30,7 @@ module Labimotion
             source_id: params[:source_id],
             layer_id: params[:layer_id],
             field_id: params[:name],
-            identifier: params[:source_id],
+            identifier: SecureRandom.uuid,
             created_by: current_user.id,
             properties: declared(params, include_missing: false),
           }

data/lib/labimotion/entities/properties_entity.rb

@@ -21,7 +21,7 @@ module Labimotion
       process_sample_and_molecule_fields(key, layer)
       process_reaction_fields(key, layer)
       process_table_fields(key, layer)
-      process_voc_fields(key, layer)
+      # process_voc_fields(key, layer)
     end
 
     def process_sample_and_molecule_fields(key, layer)
@@ -52,7 +52,7 @@ module Labimotion
       fields = layer[Labimotion::Prop::FIELDS]
       fields = fields.select { |f| types.include?(f['type']) } if types
       fields = fields.select { |f| f['is_voc'] == true } if is_voc
-      fields.map { |f| [f, fields.index(f)] }
+      fields.map { |f| [f, layer[Labimotion::Prop::FIELDS].index(f)] }
     end
 
     def update_sample_or_molecule_field(key, field, idx)
@@ -100,7 +100,6 @@ module Labimotion
 
     def update_voc_field(key, field, idx)
       root_element = get_root_element
-
       case field['source']
       when Labimotion::Prop::ELEMENT
         update_element_voc_field(key, field, idx, root_element)

data/lib/labimotion/entities/vocabulary_entity.rb

@@ -21,9 +21,10 @@ module Labimotion
 
       case voc['source']
       when Labimotion::Prop::ELEMENT
-        if voc['identifier'] == 'element.name'
+        voc['source_name'] = ElementKlass.find_by(identifier: voc['source_id'])&.label
+        # if voc['identifier'] == 'element.name'
           # voc['source_name'] = ElementKlass.find_by(identifier: voc['source_id'])&.name
-        end
+        # end
       when Labimotion::Prop::SEGMENT
         voc['source_name'] = SegmentKlass.find_by(identifier: voc['source_id'])&.label
       when Labimotion::Prop::DATASET

data/lib/labimotion/helpers/element_helpers.rb

@@ -113,7 +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]
@@ -124,15 +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
+      new_properties = update_vocabularies(element.properties, current_user, element)
+      element.update_column(:properties, new_properties)
       element
     rescue StandardError => e
       Labimotion.log_exception(e, current_user)

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/libs/data/vocab/Standard.json

@@ -1,6 +1,6 @@
 [
   {
-      "identifier": "atmosphere",
+      "identifier": "std-atmosphere",
       "name": "atmosphere",
       "label": "Atmosphere",
       "field_type": "text",
@@ -20,7 +20,7 @@
       "source": "Standard"
   },
   {
-      "identifier": "calibration",
+      "identifier": "std-calibration",
       "name": "calibration",
       "label": "Calibration",
       "field_type": "text",
@@ -40,7 +40,7 @@
       "source": "Standard"
   },
   {
-      "identifier": "coating",
+      "identifier": "std-coating",
       "name": "coating",
       "label": "Coating",
       "field_type": "text",
@@ -60,7 +60,7 @@
       "source": "Standard"
   },
   {
-      "identifier": "coating_material",
+      "identifier": "std-coating_material",
       "name": "coating_material",
       "label": "Coating Material",
       "field_type": "text",
@@ -80,7 +80,7 @@
       "source": "Standard"
   },
   {
-      "identifier": "wavelength",
+      "identifier": "std-wavelength",
       "name": "wavelength",
       "label": "Wavelength",
       "field_type": "text",

data/lib/labimotion/libs/data/vocab/System.json

@@ -1,8 +1,8 @@
 [
   {
     "id": 1,
-    "identifier": "dateTime.create",
-    "name": "Create Time",
+    "identifier": "dateTime-create",
+    "name": "create_time",
     "label": "Create Time",
     "field_type": "datetime",
     "opid": 9,
@@ -27,8 +27,8 @@
   },
   {
     "id": 2,
-    "identifier": "dateTime.update",
-    "name": "Update Time",
+    "identifier": "dateTime-update",
+    "name": "update_time",
     "label": "Update Time",
     "field_type": "datetime",
     "opid": 9,
@@ -53,9 +53,9 @@
   },
   {
     "id": 4,
-    "identifier": "user.name",
+    "identifier": "user-name",
     "name": "creator",
-    "label": "creator",
+    "label": "Creator",
     "field_type": "text",
     "opid": 9,
     "term_id": "NCIT_C42628",
@@ -79,8 +79,8 @@
   },
   {
     "id": 2,
-    "identifier": "element.id",
-    "name": "Element Id",
+    "identifier": "element-id",
+    "name": "element_id",
     "label": "Element Id",
     "field_type": "text",
     "opid": 9,
@@ -92,8 +92,8 @@
   },
   {
     "id": 5,
-    "identifier": "element.name",
-    "name": "Element Name",
+    "identifier": "element-name",
+    "name": "element_name",
     "label": "Element Name",
     "field_type": "text",
     "opid": 8,
@@ -105,8 +105,8 @@
   },
   {
     "id": 3,
-    "identifier": "element.short_label",
-    "name": "Element Short Label",
+    "identifier": "element-short_label",
+    "name": "element_short_label",
     "label": "Element Short Label",
     "field_type": "text",
     "opid": 9,
@@ -118,8 +118,8 @@
   },
   {
     "id": 3,
-    "identifier": "element.class",
-    "name": "Element Class",
+    "identifier": "element-class",
+    "name": "element_class",
     "label": "Element Class",
     "field_type": "text",
     "opid": 9,

data/lib/labimotion/libs/sample_association.rb

@@ -78,6 +78,8 @@ module Labimotion
         field_samples = layer[Labimotion::Prop::FIELDS].select { |ss| ss['type'] == Labimotion::FieldType::DRAG_SAMPLE }
         field_samples.each do |field|
           idx = properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS].index(field)
+          return if field.is_a?(String) || properties.is_a?(String)
+
           sid = field.dig('value', 'el_id')
           next if sid.blank?
 
@@ -100,6 +102,8 @@ module Labimotion
         field_elements = layer[Labimotion::Prop::FIELDS].select { |ss| ss['type'] == Labimotion::FieldType::DRAG_ELEMENT }
         field_elements.each do |field|
           idx = properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS].index(field)
+          next if field['value'].is_a?(String)
+
           sid = field.dig('value', 'el_id')
           next if element.nil? || sid.blank? || sid == element.id
 

data/lib/labimotion/libs/vocabulary_handler.rb

@@ -24,7 +24,7 @@ module Labimotion
       private
 
       def update_layer_vocabularies(layer, key, properties, current_user, element)
-        field_vocabularies = layer[Labimotion::Prop::FIELDS].select { |field| field['is_voc'] && field['opid'] == 9 }
+        field_vocabularies = layer[Labimotion::Prop::FIELDS].select { |field| field['is_voc'] }
         field_vocabularies.each do |field|
           idx = layer[Labimotion::Prop::FIELDS].index(field)
           val = get_vocabulary_value(field, current_user, element)
@@ -51,29 +51,34 @@ module Labimotion
       def get_system_value(field)
         current_time = Time.now.strftime('%d/%m/%Y %H:%M')
         case field['identifier']
-        when 'dateTime.update'
+        when 'dateTime-update'
           current_time
-        when 'dateTime.create'
+        when 'dateTime-create'
           current_time if field['value'].blank?
         end
       end
 
       def get_user_value(field, current_user)
-        return current_user.name if field['identifier'] == 'user.name' && current_user.present?
+        current_user.name if field['identifier'] == 'user-name' && current_user.present?
       end
 
       def get_element_value(field, element)
         case field['identifier']
-        when 'element.id'
+        when 'element-id'
           element.id.to_s
-        when 'element.short_label'
+        when 'element-short_label'
           element.short_label if element.has_attribute?(:short_label)
-        when 'element.class'
-          if element.class.name === 'Labimotion::Element'
-            element.element_klass.label
-          else
-            element.class.name
-          end
+        when 'element-name'
+          element.name if element.has_attribute?(:name)
+        when 'element-class'
+          element.class.name === 'Labimotion::Element' ? element.element_klass.label : element.class.name
+        else
+          ek = element.element_klass
+          return if ek.nil? || ek.identifier != field['source_id']
+
+          el_prop = element.properties
+          fields = el_prop[Labimotion::Prop::LAYERS][field['layer_id']][Labimotion::Prop::FIELDS]
+          fields.find { |ss| ss['field'] == field['field_id'] }&.dig('value')
         end
       end
 
@@ -88,6 +93,7 @@ module Labimotion
 
       def update_field_value(properties, key, idx, val)
         properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS][idx]['value'] = val
+        properties
       end
 
       def load_from_files

data/lib/labimotion/models/std_layer.rb

@@ -3,7 +3,7 @@
 module Labimotion
   class StdLayer < ApplicationRecord
     acts_as_paranoid
-    self.table_name = :l_s_lyrs
-    has_many :l_s_lyrs_tracks, primary_key: 'identifier', foreign_key: 'identifier', class_name: 'Labimotion::StdLayersRevision'
+    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

@@ -3,7 +3,7 @@
 module Labimotion
   class StdLayersRevision < ApplicationRecord
     acts_as_paranoid
-    self.table_name = :l_s_lyrs_tracks
-    belongs_to :l_s_lyrs, primary_key: 'identifier', foreign_key: 'identifier', class_name: 'Labimotion::StdLayer'
+    self.table_name = :layer_tracks
+    belongs_to :layers, primary_key: 'identifier', foreign_key: 'identifier', class_name: 'Labimotion::StdLayer'
   end
 end

data/lib/labimotion/version.rb

@@ -2,5 +2,5 @@
 
 ## Labimotion Version
 module Labimotion
-  VERSION = '1.5.0.rc9'
+  VERSION = '2.0.0.rc2'
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: labimotion
 version: !ruby/object:Gem::Version
-  version: 1.5.0.rc9
+  version: 2.0.0.rc2
 platform: ruby
 authors:
 - Chia-Lin Lin
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2024-11-22 00:00:00.000000000 Z
+date: 2024-12-18 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rails