labimotion 1.4.0.rc1 → 1.4.0.rc3

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
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-  data.tar.gz: 334b4f9d71132b30884e522a38cc11e770048d20d8ff4e34bc0f60ddaf45d3df
+  metadata.gz: a0e43bc1bdccd36b76e3c357c88b148f6af58a422ac15967b51018ad68cc570c
+  data.tar.gz: bf7e9b0ea4e21736bd9a71cca94b32f02c3d2eed96a1188c07a97be3e11a25f4
 SHA512:
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+  metadata.gz: b64d866c7f796c327b3a3f37b7ac5883a1e4ce8e604b0280dc3f47ea300ebbfb82251ea2e42ac2315377d24453f4323de13d10a6a6a85bd6fdf1f57671431d24
+  data.tar.gz: 90d185c4806b9e9f10ace66612bad2eb1e31d268a517890c01dd1304fcb53c1b42ef2433a2960d0da53e5c910c7fd8b526c6d4057845f394f663fd148d9e0e2b

data/lib/labimotion/entities/element_revision_entity.rb

@@ -23,7 +23,7 @@ module Labimotion
 
           object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS][idx]['value']['el_label'] = el.short_label if field['type'] == Labimotion::FieldType::DRAG_SAMPLE
           object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS][idx]['value']['el_tip'] = el.short_label if field['type'] == Labimotion::FieldType::DRAG_SAMPLE
-          object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS][idx]['value']['el_svg'] = field['type'] == Labimotion::FieldType::DRAG_SAMPLE ? el.get_svg_path : File.join('/images', 'molecules', el.molecule_svg_file)
+          object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS][idx]['value']['el_svg'] = field['type'] == Labimotion::FieldType::DRAG_SAMPLE ? el.get_svg_path : File.join('/images', 'molecules', el&.molecule_svg_file || 'nosvg')
         end
 
         field_tables = object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS].select { |ss| ss['type'] == Labimotion::FieldType::TABLE }
@@ -41,7 +41,7 @@ module Labimotion
               find_mol = Molecule.find_by(id: sub_value[col_id]['value']['el_id'])
               next unless find_mol.present?
 
-              sub_value[col_id]['value']['el_svg'] = File.join('/images', 'molecules', find_mol.molecule_svg_file)
+              sub_value[col_id]['value']['el_svg'] = File.join('/images', 'molecules', find_mol.molecule_svg_file) if find_mol&.molecule_svg_file&.present?
               sub_value[col_id]['value']['el_inchikey'] = find_mol.inchikey
               sub_value[col_id]['value']['el_smiles'] = find_mol.cano_smiles
               sub_value[col_id]['value']['el_iupac'] = find_mol.iupac_name

data/lib/labimotion/entities/eln_element_entity.rb

@@ -47,7 +47,7 @@ module Labimotion
               el.short_label
           end
           object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS][idx]['value']['el_svg'] =
-            field['type'] == Labimotion::FieldType::DRAG_SAMPLE ? el.get_svg_path : File.join('/images', 'molecules', el.molecule_svg_file)
+            field['type'] == Labimotion::FieldType::DRAG_SAMPLE ? el.get_svg_path : File.join('/images', 'molecules', el&.molecule_svg_file || 'nosvg')
         end
 
         field_tables = object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS].select { |ss| ss['type'] == Labimotion::FieldType::TABLE }
@@ -88,7 +88,7 @@ module Labimotion
 
           case obj
           when Labimotion::Prop::MOLECULE
-            sub_value[col_id]['value']['el_svg'] = File.join('/images', 'molecules', find_obj.molecule_svg_file)
+            sub_value[col_id]['value']['el_svg'] = File.join('/images', 'molecules', find_obj.molecule_svg_file) if find_obj&.molecule_svg_file&.present?
             sub_value[col_id]['value']['el_inchikey'] = find_obj.inchikey
             sub_value[col_id]['value']['el_smiles'] = find_obj.cano_smiles
             sub_value[col_id]['value']['el_iupac'] = find_obj.iupac_name

data/lib/labimotion/entities/properties_entity.rb

@@ -20,7 +20,27 @@ module Labimotion
 
           object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS][idx]['value']['el_label'] = el.short_label if field['type'] == Labimotion::FieldType::DRAG_SAMPLE
           object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS][idx]['value']['el_tip'] = el.short_label if field['type'] == Labimotion::FieldType::DRAG_SAMPLE
-          object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS][idx]['value']['el_svg'] = field['type'] == Labimotion::FieldType::DRAG_SAMPLE ? el.get_svg_path : File.join('/images', 'molecules', el.molecule_svg_file)
+          object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS][idx]['value']['el_svg'] = field['type'] == Labimotion::FieldType::DRAG_SAMPLE ? el.get_svg_path : File.join('/images', 'molecules', el&.molecule_svg_file || 'nosvg')
+        end
+
+        field_sys_reactions = object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS].select { |ss| ss['type'] == Labimotion::FieldType::SYS_REACTION }
+        field_sys_reactions.each do |field|
+          idx = object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS].index(field)
+          sid = field.dig('value', 'el_id')
+          next unless sid.present?
+
+          el = Reaction.find_by(id: sid)
+          if el.blank?
+            object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS][idx]['value']['el_tip'] = 'ERROR'
+            object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS][idx]['value']['el_svg'] = ''
+          end
+
+          next unless el.present?
+          next unless object.properties.dig(Labimotion::Prop::LAYERS, key, Labimotion::Prop::FIELDS, idx, 'value').present?
+
+          object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS][idx]['value']['el_label'] = el.short_label
+          object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS][idx]['value']['el_tip'] = el.short_label
+          object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS][idx]['value']['el_svg'] =  el.reaction_svg_file
         end
 
         field_tables = object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS].select { |ss| ss['type'] == Labimotion::FieldType::TABLE }
@@ -49,7 +69,7 @@ module Labimotion
 
           case obj
           when Labimotion::Prop::MOLECULE
-            sub_value[col_id]['value']['el_svg'] = File.join('/images', 'molecules', find_obj.molecule_svg_file)
+            sub_value[col_id]['value']['el_svg'] = File.join('/images', 'molecules', find_obj.molecule_svg_file) if find_obj&.molecule_svg_file&.present?
             sub_value[col_id]['value']['el_inchikey'] = find_obj.inchikey
             sub_value[col_id]['value']['el_smiles'] = find_obj.cano_smiles
             sub_value[col_id]['value']['el_iupac'] = find_obj.iupac_name

data/lib/labimotion/entities/segment_revision_entity.rb

@@ -22,7 +22,7 @@ module Labimotion
 
           object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS][idx]['value']['el_label'] = el.short_label if field['type'] == Labimotion::FieldType::DRAG_SAMPLE
           object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS][idx]['value']['el_tip'] = el.short_label if field['type'] == Labimotion::FieldType::DRAG_SAMPLE
-          object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS][idx]['value']['el_svg'] = field['type'] == Labimotion::FieldType::DRAG_SAMPLE ? el.get_svg_path : File.join('/images', 'molecules', el.molecule_svg_file)
+          object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS][idx]['value']['el_svg'] = field['type'] == Labimotion::FieldType::DRAG_SAMPLE ? el.get_svg_path : File.join('/images', 'molecules', el&.molecule_svg_file || 'nosvg')
         end
 
         field_tables = object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS].select { |ss| ss['type'] == Labimotion::FieldType::TABLE }
@@ -40,7 +40,7 @@ module Labimotion
               find_mol = Molecule.find_by(id: sub_value[col_id]['value']['el_id'])
               next unless find_mol.present?
 
-              sub_value[col_id]['value']['el_svg'] = File.join('/images', 'molecules', find_mol.molecule_svg_file)
+              sub_value[col_id]['value']['el_svg'] = File.join('/images', 'molecules', find_mol.molecule_svg_file) if find_mol&.molecule_svg_file&.present?
               sub_value[col_id]['value']['el_inchikey'] = find_mol.inchikey
               sub_value[col_id]['value']['el_smiles'] = find_mol.cano_smiles
               sub_value[col_id]['value']['el_iupac'] = find_mol.iupac_name

data/lib/labimotion/libs/export_element.rb

@@ -91,6 +91,20 @@ module Labimotion
           obj_final = OpenStruct.new(obj_os)
           field_obj[:structure] = Reporter::Docx::DiagramSample.new(obj: obj_final, format: 'png').generate
         end
+      when Labimotion::FieldType::SYS_REACTION
+        val = field.fetch('value', nil)
+        if val.present?
+          instance = Reaction.find_by(id: val['el_id'])
+          field_obj[:value] = val['el_label']
+          field_obj[:has_structure] = true
+          obj_os = Entities::ReactionReportEntity.new(
+            instance,
+            current_user: @current_user,
+            detail_levels: ElementDetailLevelCalculator.new(user: @current_user, element: instance).detail_levels,
+          ).serializable_hash
+          obj_final = OpenStruct.new(obj_os)
+          field_obj[:structure] = Reporter::Docx::DiagramReaction.new(obj: obj_final, format: 'png').generate
+        end
       when Labimotion::FieldType::DRAG_MOLECULE
         val = field.fetch('value', nil)
         if val.present?

data/lib/labimotion/utils/export_utils.rb

@@ -20,6 +20,8 @@ module Labimotion
         case name
         when Labimotion::FieldType::DRAG_ELEMENT
           Labimotion::Prop::L_ELEMENT
+        when Labimotion::FieldType::SYS_REACTION
+          Labimotion::Prop::REACTION
         when Labimotion::FieldType::DRAG_SAMPLE
           Labimotion::Prop::SAMPLE
         when Labimotion::FieldType::DRAG_MOLECULE
@@ -167,6 +169,7 @@ module Labimotion
       properties[Labimotion::Prop::LAYERS].keys.each do |key|
         properties = set_seg_prop(properties, uuids, key, Labimotion::FieldType::DRAG_ELEMENT)
         properties = set_seg_prop(properties, uuids, key, Labimotion::FieldType::DRAG_SAMPLE)
+        properties = set_seg_prop(properties, uuids, key, Labimotion::FieldType::SYS_REACTION)
       end
       segment['properties'] = properties
       segment
@@ -183,6 +186,7 @@ module Labimotion
         properties = set_prop(properties, uuids, key, Labimotion::FieldType::DRAG_ELEMENT, &fetch_one)
         properties = set_prop(properties, uuids, key, Labimotion::FieldType::DRAG_MOLECULE, &fetch_one)
         properties = set_prop(properties, uuids, key, Labimotion::FieldType::DRAG_SAMPLE, &fetch_one)
+        properties = set_prop(properties, uuids, key, Labimotion::FieldType::SYS_REACTION, &fetch_one)
         properties, attachments = set_upload(instance, properties, attachments, uuids, key, Labimotion::FieldType::UPLOAD, &fetch_one)
         properties = set_table(properties, uuids, key, Labimotion::FieldType::TABLE, &fetch_one)
       end

data/lib/labimotion/utils/field_type.rb

@@ -11,13 +11,14 @@ module Labimotion
     WF_NEXT = 'wf-next'.freeze
     TEXT_FORMULA = 'text-formula'.freeze
     SYSTEM_DEFINED = 'system-defined'.freeze
+    SYS_REACTION = 'sys-reaction'.freeze
     DRAG = 'drag'.freeze
     DRAG_ELEMENT = 'drag_element'.freeze
     DRAG_MOLECULE = 'drag_molecule'.freeze
     DRAG_SAMPLE = 'drag_sample'.freeze
     DRAG_REACTION = 'drag_reaction'.freeze
     DRAG_MS = [DRAG_MOLECULE, DRAG_SAMPLE].freeze
-    DRAG_ALL = [DRAG_ELEMENT, DRAG_MOLECULE, DRAG_SAMPLE, DRAG_REACTION].freeze
+    DRAG_ALL = [DRAG_ELEMENT, DRAG_MOLECULE, DRAG_SAMPLE, DRAG_REACTION, SYS_REACTION].freeze
     TABLE = 'table'.freeze
     UPLOAD = 'upload'.freeze
     TEXT = 'text'.freeze

data/lib/labimotion/utils/import_utils.rb

@@ -24,7 +24,7 @@ module Labimotion
         value['el_id'] = molecule.id
         value['el_tip'] = "#{molecule.inchikey}@@#{molecule.cano_smiles}"
         value['el_label'] = molecule.iupac_name
-        value['el_svg'] = File.join('/images', 'molecules', molecule.molecule_svg_file)
+        value['el_svg'] = File.join('/images', 'molecules', molecule&.molecule_svg_file) if molecule&.molecule_svg_file.present?
         value['el_inchikey'] = molecule.inchikey
         value['el_smiles'] = molecule.cano_smiles
         value['el_type'] = 'molecule' if value['el_type'].nil?
@@ -51,6 +51,21 @@ module Labimotion
         value
       end
 
+      def proc_assign_reaction(value, reaction)
+        return {} if reaction.nil?
+
+        value = {} if value.nil? || value.is_a?(String)
+        value['el_id'] = reaction.id
+        value['el_type'] = 'reaction' if value['el_type'].nil?
+        value['el_tip'] = reaction.short_label
+        value['el_label'] = reaction.short_label
+        value['el_svg'] = reaction.reaction_svg_file
+        value
+      rescue StandardError => e
+        Labimotion.log_exception(e)
+        value
+      end
+
       def proc_assign_element(value, element)
         return {} if element.nil?
 
@@ -136,6 +151,22 @@ module Labimotion
       end
     end
 
+    def self.proc_reaction(layer, key, data, instances, properties)
+      fields = layer[Labimotion::Prop::FIELDS].select { |ss| ss['type'] == Labimotion::FieldType::SYS_REACTION }
+      fields.each do |field|
+        idx = properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS].index(field)
+        id = field["value"] && field["value"]["el_id"] unless idx.nil?
+        reaction = instances.fetch(Labimotion::Prop::REACTION, nil)&.fetch(id, nil)
+        val = properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS][idx]['value']
+        val = proc_assign_reaction(val, reaction)
+        properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS][idx]['value'] = val
+      end
+      properties
+    rescue StandardError => e
+      Labimotion.log_exception(e)
+      properties
+    end
+
     def self.proc_sample(layer, key, data, instances, properties)
       fields = layer[Labimotion::Prop::FIELDS].select { |ss| ss['type'] == Labimotion::FieldType::DRAG_SAMPLE }
       fields.each do |field|
@@ -149,7 +180,7 @@ module Labimotion
       properties
     rescue StandardError => e
       Labimotion.log_exception(e)
-      raise
+      properties
     end
 
     def self.proc_element(layer, key, data, instances, properties, elements)
@@ -169,7 +200,7 @@ module Labimotion
       properties
     rescue StandardError => e
       Labimotion.log_exception(e)
-      raise
+      properties
     end
 
     def self.proc_upload(layer, key, data, instances, attachments, element)
@@ -221,7 +252,7 @@ module Labimotion
       properties
     rescue StandardError => e
       Labimotion.log_exception(e)
-      raise
+      properties
     end
 
 
@@ -237,7 +268,7 @@ module Labimotion
       properties
     rescue StandardError => e
       Labimotion.log_exception(e)
-      raise
+      properties
     end
 
     def self.properties_handler(data, instances, attachments, elmenet, elements)
@@ -246,6 +277,7 @@ module Labimotion
         layer = properties[Labimotion::Prop::LAYERS][key]
         properties = proc_molecule(layer, key, data, properties)
         properties = proc_upload(layer, key, data, instances, attachments, elmenet)
+        properties = proc_reaction(layer, key, data, instances, properties)
         properties = proc_sample(layer, key, data, instances, properties)
         properties = proc_element(layer, key, data, instances, properties, elements) # unless elements.nil?
         properties = proc_table(layer, key, data, instances, properties)
@@ -253,7 +285,7 @@ module Labimotion
       properties
     rescue StandardError => e
       Labimotion.log_exception(e)
-      raise
+      properties
     end
 
     def self.process_ai(data, instances)
@@ -272,7 +304,7 @@ module Labimotion
       end
     rescue StandardError => e
       Labimotion.log_exception(e)
-      raise
+      properties
     end
 
     def self.create_segment_klass(sk_obj, segment_klass, element_klass, current_user_id)

data/lib/labimotion/utils/serializer.rb

@@ -13,7 +13,7 @@ module Labimotion
 
           case obj
           when Labimotion::Prop::MOLECULE
-            sub_value[col_id]['value']['el_svg'] = File.join('/images', 'molecules', find_obj.molecule_svg_file)
+            sub_value[col_id]['value']['el_svg'] = File.join('/images', 'molecules', find_obj.molecule_svg_file) if find_obj&.molecule_svg_file&.present?
             sub_value[col_id]['value']['el_inchikey'] = find_obj.inchikey
             sub_value[col_id]['value']['el_smiles'] = find_obj.cano_smiles
             sub_value[col_id]['value']['el_iupac'] = find_obj.iupac_name
@@ -56,7 +56,7 @@ module Labimotion
           object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS][idx]['value']['el_tip'] = el.short_label if %w[drag_sample].include?(field['type'])
           object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS][idx]['value']['el_tip'] = "#{el.element_klass&.label}@@#{el.name}" if %w[drag_element].include?(field['type'])
           object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS][idx]['value']['icon_name'] = el.element_klass&.icon_name || '' if %w[drag_element].include?(field['type'])
-          object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS][idx]['value']['el_svg'] = field['type'] == Labimotion::FieldType::DRAG_SAMPLE ? el.get_svg_path : File.join('/images', 'molecules', el.molecule_svg_file) if Labimotion::FieldType::DRAG_MS.include?(field['type'])
+          object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS][idx]['value']['el_svg'] = field['type'] == Labimotion::FieldType::DRAG_SAMPLE ? el.get_svg_path : File.join('/images', 'molecules', el&.molecule_svg_file || 'nosvg') if Labimotion::FieldType::DRAG_MS.include?(field['type'])
           object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS][idx]['value']['el_decoupled'] = el.decoupled if %w[drag_sample].include?(field['type'])
         end
 

data/lib/labimotion/version.rb

@@ -2,5 +2,5 @@
 
 ## Labimotion Version
 module Labimotion
-  VERSION = '1.4.0.rc1'
+  VERSION = '1.4.0.rc3'
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: labimotion
 version: !ruby/object:Gem::Version
-  version: 1.4.0.rc1
+  version: 1.4.0.rc3
 platform: ruby
 authors:
 - Chia-Lin Lin
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2024-05-16 00:00:00.000000000 Z
+date: 2024-06-03 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rails