labimotion 0.3.3 → 1.0.0

data/lib/labimotion/models/element.rb

@@ -7,12 +7,10 @@ module Labimotion
   class Element < ApplicationRecord
     acts_as_paranoid
     self.table_name = :elements
-    include PgSearch if Labimotion::IS_RAILS5 == true
-    include PgSearch::Model if Labimotion::IS_RAILS5 == false
+    include PgSearch::Model
     include ElementUIStateScopes
     include Collectable
     ## include AnalysisCodes
-    include ElementCodes
     include Taggable
     include Workflow
     include Segmentable
@@ -59,7 +57,7 @@ module Labimotion
 
 
     def attachments
-      Attachment.where(attachable_id: self.id, attachable_type: self.class.name)
+      Attachment.where(attachable_id: self.id, attachable_type: 'Element')
     end
 
     def self.get_associated_samples(element_ids)
@@ -101,20 +99,13 @@ module Labimotion
     end
 
     def thumb_svg
-      if Labimotion::IS_RAILS5 == true
-        image_atts = attachments.select do |a_img|
-          a_img&.content_type&.match(Regexp.union(%w[jpg jpeg png tiff tif]))
-        end
-
-        attachment = image_atts[0] || attachments[0]
-        preview = attachment.read_thumbnail if attachment
-        preview && Base64.encode64(preview) || 'not available'
-      else
-        image_atts = attachments.select(&:type_image?)
-        attachment = image_atts[0] || attachments[0]
-        preview = attachment&.read_thumbnail
-        (preview && Base64.encode64(preview)) || 'not available'
+      image_atts = attachments.select do |a_img|
+        a_img&.content_type&.match(Regexp.union(%w[jpg jpeg png tiff tif]))
       end
+
+      attachment = image_atts[0] || attachments[0]
+      preview = attachment.read_thumbnail if attachment
+      preview && Base64.encode64(preview) || 'not available'
     end
 
 

data/lib/labimotion/models/element_klass.rb

@@ -23,5 +23,13 @@ module Labimotion
       )
     end
 
+    def migrate_workflow
+      return if properties_template.nil? || properties_release.nil?
+
+      return if properties_template['flow'].nil? && properties_release['flow'].nil?
+
+      update_column(:properties_template, split_workflow(properties_template)) if properties_template['flow']
+      update_column(:properties_release, split_workflow(properties_release)) if properties_release['flow']
+    end
   end
 end

data/lib/labimotion/models/segment_klass.rb

@@ -1,13 +1,11 @@
 # frozen_string_literal: true
 require 'labimotion/models/concerns/generic_klass_revisions'
-require 'labimotion/models/concerns/workflow'
 
 module Labimotion
   class SegmentKlass < ApplicationRecord
     self.table_name = :segment_klasses
     acts_as_paranoid
     include GenericKlassRevisions
-    include Workflow
     belongs_to :element_klass, class_name: 'Labimotion::ElementKlass'
     has_many :segments, dependent: :destroy, class_name: 'Labimotion::Segment'
     has_many :segment_klasses_revisions, dependent: :destroy, class_name: 'Labimotion::SegmentKlassesRevision'

data/lib/labimotion/{collection → utils}/export.rb

@@ -22,29 +22,6 @@ module Labimotion
       fetch_many.call(klasses, {'created_by' => 'User'})
     end
 
-    def self.fetch_elements(collection, segments, attachments, fetch_many, fetch_one, fetch_containers)
-      # fetch_many.call(collection.elements, {
-      #   'element_klass_id' => 'Labimotion::ElementKlass',
-      #   'created_by' => 'User',
-      # })
-      # fetch_many.call(collection.collections_elements, {
-      #         'collection_id' => 'Collection',
-      #         'element_id' => 'Labimotion::Element',
-      # })
-      collection.elements.each do |element|
-        element, attachments = Labimotion::Export.fetch_properties(data, element, attachments, &fetch_one)
-        fetch_one.call(element, {
-          'element_klass_id' => 'Labimotion::ElementKlass',
-          'created_by' => 'User',
-        })
-        fetch_containers.call(element)
-        segment, @attachments = Labimotion::Export.fetch_segments(element, attachments, &fetch_one)
-        segments += segment if segment.present?
-      end
-
-      [segments, attachments]
-
-    end
 
     def self.fetch_segments(element, attachments, &fetch_one)
       element_type = element.class.name
@@ -94,15 +71,6 @@ module Labimotion
           mol = Molecule.find(id) unless id.nil?
           properties['layers'][key]['fields'][idx]['value']['el_id'] = fetch_one.call(mol) unless mol.nil?
         end
-
-        field_samples = layer['fields'].select { |ss| ss['type'] == 'drag_sample' }
-        field_samples.each do |field|
-          # idx = properties['layers'][key]['fields'].index(field)
-          # id = field["value"] && field["value"]["el_id"] unless idx.nil?
-          # ss = Sample.find(id) unless id.nil?
-          # properties['layers'][key]['fields'][idx]['value']['el_id'] = fetch_one.call(ss) unless ss.nil?
-        end
-
         field_uploads = layer['fields'].select { |ss| ss['type'] == 'upload' }
         field_uploads.each do |upload|
           idx = properties['layers'][key]['fields'].index(upload)
@@ -135,6 +103,7 @@ module Labimotion
             end
           end
         end
+
       end
       instance.properties = properties
       [instance, attachments]

data/lib/labimotion/{collection → utils}/import.rb

@@ -1,6 +1,5 @@
 # frozen_string_literal: true
 
-require 'labimotion/utils/import_utils'
 module Labimotion
   class Import
 
@@ -51,7 +50,7 @@ module Labimotion
           element_type = fields.fetch('element_type')
           element = instances.fetch(element_type).fetch(element_uuid)
 
-          dataset_klass = Labimotion::DatasetKlass.find_by(identifier: dk_id) if dk_id.present?
+          dataset_klass = Labimotion::DatasetKlass.find_by(identifier: dk_id)
           next if gt == true && dataset_klass.nil?
 
           dkr = Labimotion::DatasetKlassesRevision.find_by(uuid: fields.fetch('klass_uuid'))
@@ -89,21 +88,33 @@ module Labimotion
           ek_obj = data.fetch('Labimotion::ElementKlass').fetch(sk_obj["element_klass_id"])
           element_klass = Labimotion::ElementKlass.find_by(name: ek_obj['name']) if ek_obj.present?
           next if element_klass.nil? || ek_obj.nil? || ek_obj['is_generic'] == true
-
           element_uuid = fields.fetch('element_id')
           element_type = fields.fetch('element_type')
           element = instances.fetch(element_type).fetch(element_uuid)
-          segment_klass = Labimotion::SegmentKlass.find_by(identifier: sk_id) if sk_id.present?
-          segment_klass = Labimotion::SegmentKlass.find_by(uuid: fields.fetch('klass_uuid')) if segment_klass.nil?
-
-          if segment_klass.nil?
-            skr = Labimotion::SegmentKlassesRevision.find_by(uuid: fields.fetch('klass_uuid'))
-            segment_klass = skr.segment_klass if segment_klass.nil? && skr.present?
-          end
-
-          next if segment_klass.nil? || element.nil?
-
-          ## segment_klass = Labimotion::ImportUtils.create_segment_klass(sk_obj, segment_klass, element_klass, current_user_id)
+          segment_klass = Labimotion::SegmentKlass.find_by(identifier: sk_id)
+          next if gt == true && segment_klass.nil?
+
+          skr = Labimotion::SegmentKlassesRevision.find_by(uuid: fields.fetch('klass_uuid'))
+          segment_klass = skr.segment_klass if segment_klass.nil? && skr.present?
+
+          # segment_klass = Labimotion::SegmentKlass.create!(sk_obj.slice(
+          #     'label',
+          #     'desc',
+          #     'properties_template',
+          #     'is_active',
+          #     'place',
+          #     'properties_release',
+          #     'uuid',
+          #     'identifier',
+          #     'sync_time'
+          #   ).merge(
+          #     element_klass: element_klass,
+          #     created_by: current_user_id,
+          #     released_at: DateTime.now
+          #   )
+          # ) if segment_klass.nil?
+
+          next if segment_klass.nil?
 
           segment = Labimotion::Segment.create!(
             fields.slice(
@@ -117,7 +128,52 @@ module Labimotion
             )
           )
 
-          properties = Labimotion::ImportUtils.properties_handler(data, segment.properties)
+          properties = segment.properties
+          properties['layers'].keys.each do |key|
+            layer = properties['layers'][key]
+            field_molecules = layer['fields'].select { |ss| ss['type'] == 'drag_molecule' }
+            field_molecules.each do |field|
+              idx = properties['layers'][key]['fields'].index(field)
+              id = field["value"] && field["value"]["el_id"] unless idx.nil?
+              mol = Molecule.find_or_create_by_molfile(data.fetch('Molecule')[id]['molfile']) unless id.nil?
+              unless mol.nil?
+                properties['layers'][key]['fields'][idx]['value']['el_id'] = mol.id
+                properties['layers'][key]['fields'][idx]['value']['el_tip'] = "#{mol.inchikey}@@#{mol.cano_smiles}"
+                properties['layers'][key]['fields'][idx]['value']['el_label'] = mol.iupac_name
+              end
+            end
+
+            field_tables = layer['fields'].select { |ss| ss['type'] == 'table' }
+            field_tables&.each do |field|
+              tidx = layer['fields'].index(field)
+              next unless field['sub_values'].present? && field['sub_fields'].present?
+
+              field_table_molecules = field['sub_fields'].select { |ss| ss['type'] == 'drag_molecule' }
+              if field_table_molecules.present?
+                col_ids = field_table_molecules.map { |x| x.values[0] }
+                col_ids.each do |col_id|
+                  field['sub_values'].each_with_index do |sub_value, vdx|
+                    next unless sub_value[col_id].present? && sub_value[col_id]['value'].present? && sub_value[col_id]['value']['el_id'].present?
+
+                    svalue = sub_value[col_id]['value']
+                    next unless svalue['el_id'].present? && svalue['el_inchikey'].present?
+
+                    tmol = Molecule.find_or_create_by_molfile(data.fetch('Molecule')[svalue['el_id']]['molfile']) unless svalue['el_id'].nil?
+                    unless tmol.nil?
+                      properties['layers'][key]['fields'][tidx]['sub_values'][vdx][col_id]['value']['el_id'] = tmol.id
+                      properties['layers'][key]['fields'][tidx]['sub_values'][vdx][col_id]['value']['el_tip'] = "#{tmol.inchikey}@@#{tmol.cano_smiles}"
+                      properties['layers'][key]['fields'][tidx]['sub_values'][vdx][col_id]['value']['el_label'] = tmol.cano_smiles
+                      properties['layers'][key]['fields'][tidx]['sub_values'][vdx][col_id]['value']['el_smiles'] = tmol.cano_smiles
+                      properties['layers'][key]['fields'][tidx]['sub_values'][vdx][col_id]['value']['el_iupac'] = tmol.iupac_name
+                      properties['layers'][key]['fields'][tidx]['sub_values'][vdx][col_id]['value']['el_inchikey'] = tmol.inchikey
+                      properties['layers'][key]['fields'][tidx]['sub_values'][vdx][col_id]['value']['el_svg'] = File.join('/images', 'molecules', tmol.molecule_svg_file)
+                      properties['layers'][key]['fields'][tidx]['sub_values'][vdx][col_id]['value']['el_molecular_weight'] = tmol.molecular_weight
+                    end
+                  end
+                end
+              end
+            end
+          end
           segment.update!(properties: properties)
           update_instances.call(uuid, segment)
         end
@@ -126,43 +182,5 @@ module Labimotion
         raise
       end
     end
-
-    def self.import_elements(data, instances, gt, current_user_id, fetch_many, &update_instances)
-      data.fetch('Labimotion::Element', {}).each do |uuid, fields|
-        klass_id = fields["element_klass_id"]
-        ek_obj = data.fetch('Labimotion::ElementKlass', {})[klass_id]
-        ek_id = ek_obj["identifier"]
-        element_klass = Labimotion::ElementKlass.find_by(identifier: ek_id) if ek_id.present?
-        element_klass = Labimotion::ElementKlass.find_by(uuid: fields.fetch('klass_uuid')) if element_klass.nil?
-
-        if element_klass.nil?
-          ekr = Labimotion::ElementKlassesRevision.find_by(uuid: fields.fetch('klass_uuid'))
-          element_klass = ekr.element_klass if element_klass.nil? && ekr.present?
-        end
-        next if element_klass.nil?
-
-        element = Labimotion::Element.create!(
-          fields.slice(
-            'name', 'properties', 'properties_release'
-          ).merge(
-            created_by: current_user_id,
-            element_klass: element_klass,
-            collections: fetch_many.call(
-              'Collection', 'Labimotion::CollectionsElement', 'element_id', 'collection_id', uuid
-            ),
-            uuid: SecureRandom.uuid,
-            klass_uuid: ekr&.uuid || element_klass.uuid
-          )
-        )
-
-        properties = Labimotion::ImportUtils.properties_handler(data, element.properties)
-        element.update!(properties: properties)
-        update_instances.call(uuid, element)
-        element.container = Container.create_root_container
-      end
-    rescue StandardError => e
-      Rails.logger.error(e.backtrace)
-      raise
-    end
   end
 end

data/lib/labimotion/version.rb

@@ -1,11 +1,7 @@
 # frozen_string_literal: true
 
-## Labimotion Version
 module Labimotion
-  IS_RAILS5 = true
-  VERSION_ELN = '1.0.17'
-  VERSION_REPO = '0.3.3'
-
-  VERSION = Labimotion::VERSION_REPO if Labimotion::IS_RAILS5 == true
-  VERSION = Labimotion::VERSION_ELN if Labimotion::IS_RAILS5 == false
+  # VERSION = '0.1.4'
+  VERSION = '1.0.0'
+  IS_RAILS5 = false
 end

data/lib/labimotion.rb

@@ -61,11 +61,8 @@ module Labimotion
   autoload :ConState, 'labimotion/utils/con_state'
   autoload :Serializer, 'labimotion/utils/serializer'
   autoload :Search, 'labimotion/utils/search'
-
-
-  ######## Collection
-  autoload :Export, 'labimotion/collection/export'
-  autoload :Import, 'labimotion/collection/import'
+  autoload :Export, 'labimotion/utils/export'
+  autoload :Import, 'labimotion/utils/import'
 
   ######## Models
   autoload :Element, 'labimotion/models/element'

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: labimotion
 version: !ruby/object:Gem::Version
-  version: 0.3.3
+  version: 1.0.0
 platform: ruby
 authors:
 - Chia-Lin Lin
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2023-10-19 00:00:00.000000000 Z
+date: 2023-08-24 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rails
@@ -17,14 +17,14 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 5.2.0
+        version: 6.1.7
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 5.2.0
+        version: 6.1.7
 description: 
 email:
 - chia-lin.lin@kit.edu
@@ -34,13 +34,12 @@ extensions: []
 extra_rdoc_files: []
 files:
 - lib/labimotion.rb
+- lib/labimotion/api.rb
 - lib/labimotion/apis/converter_api.rb
 - lib/labimotion/apis/generic_dataset_api.rb
 - lib/labimotion/apis/generic_element_api.rb
 - lib/labimotion/apis/labimotion_hub_api.rb
 - lib/labimotion/apis/segment_api.rb
-- lib/labimotion/collection/export.rb
-- lib/labimotion/collection/import.rb
 - lib/labimotion/entities/application_entity.rb
 - lib/labimotion/entities/dataset_entity.rb
 - lib/labimotion/entities/dataset_klass_entity.rb
@@ -66,6 +65,7 @@ files:
 - lib/labimotion/libs/converter.rb
 - lib/labimotion/libs/export_dataset.rb
 - lib/labimotion/libs/nmr_mapper.rb
+- lib/labimotion/libs/nmr_mapper_repo.rb
 - lib/labimotion/libs/template_hub.rb
 - lib/labimotion/models/collections_element.rb
 - lib/labimotion/models/concerns/attachment_converter.rb
@@ -84,20 +84,20 @@ files:
 - lib/labimotion/models/elements_element.rb
 - lib/labimotion/models/elements_revision.rb
 - lib/labimotion/models/elements_sample.rb
-- lib/labimotion/models/hub_log.rb
 - lib/labimotion/models/segment.rb
 - lib/labimotion/models/segment_klass.rb
 - lib/labimotion/models/segment_klasses_revision.rb
 - lib/labimotion/models/segments_revision.rb
 - lib/labimotion/utils/con_state.rb
-- lib/labimotion/utils/import_utils.rb
+- lib/labimotion/utils/export.rb
+- lib/labimotion/utils/import.rb
 - lib/labimotion/utils/search.rb
 - lib/labimotion/utils/serializer.rb
 - lib/labimotion/utils/utils.rb
 - lib/labimotion/version.rb
-homepage: https://gitlab.kit.edu/kit/labimotion/labimotion
+homepage: https://github.com/phuang26/labimotion
 licenses:
-- GPL-3.0
+- MIT
 metadata: {}
 post_install_message: 
 rdoc_options: []

data/lib/labimotion/models/hub_log.rb

@@ -1,8 +0,0 @@
-# frozen_string_literal: true
-
-module Labimotion
-  class HubLog < ApplicationRecord
-    self.table_name = :hub_logs
-    belongs_to :klass, polymorphic: true, optional: true
-  end
-end

data/lib/labimotion/utils/import_utils.rb

@@ -1,116 +0,0 @@
-# frozen_string_literal: true
-
-module Labimotion
-  ## Import Utils
-  class ImportUtils
-    def self.proc_sample(layer, key, data, properties)
-      field_samples = layer['fields'].select { |ss| ss['type'] == 'drag_sample' }
-      field_samples.each do |field|
-        idx = properties['layers'][key]['fields'].index(field)
-        id = field["value"] && field["value"]["el_id"] unless idx.nil?
-
-        # mol = Molecule.find_or_create_by_molfile(data.fetch('Molecule')[id]['molfile']) unless id.nil?
-        # unless mol.nil?
-        #   properties['layers'][key]['fields'][idx]['value']['el_id'] = mol.id
-        #   properties['layers'][key]['fields'][idx]['value']['el_tip'] = "#{mol.inchikey}@@#{mol.cano_smiles}"
-        #   properties['layers'][key]['fields'][idx]['value']['el_label'] = mol.iupac_name
-        # end
-      end
-      properties
-    rescue StandardError => e
-      Rails.logger.error(e.backtrace)
-      raise
-    end
-
-    def self.proc_molecule(layer, key, data, properties)
-      field_molecules = layer['fields'].select { |ss| ss['type'] == 'drag_molecule' }
-      field_molecules.each do |field|
-        idx = properties['layers'][key]['fields'].index(field)
-        id = field["value"] && field["value"]["el_id"] unless idx.nil?
-        mol = Molecule.find_or_create_by_molfile(data.fetch('Molecule')[id]['molfile']) unless id.nil?
-        unless mol.nil?
-          properties['layers'][key]['fields'][idx]['value']['el_id'] = mol.id
-          properties['layers'][key]['fields'][idx]['value']['el_tip'] = "#{mol.inchikey}@@#{mol.cano_smiles}"
-          properties['layers'][key]['fields'][idx]['value']['el_label'] = mol.iupac_name
-        end
-      end
-      properties
-    rescue StandardError => e
-      Rails.logger.error(e.backtrace)
-      raise
-    end
-
-    def self.proc_table(layer, key, data, properties)
-      field_tables = layer['fields'].select { |ss| ss['type'] == 'table' }
-      field_tables&.each do |field|
-        tidx = layer['fields'].index(field)
-        next unless field['sub_values'].present? && field['sub_fields'].present?
-
-        field_table_molecules = field['sub_fields'].select { |ss| ss['type'] == 'drag_molecule' }
-        if field_table_molecules.present?
-          col_ids = field_table_molecules.map { |x| x.values[0] }
-          col_ids.each do |col_id|
-            field['sub_values'].each_with_index do |sub_value, vdx|
-              next unless sub_value[col_id].present? && sub_value[col_id]['value'].present? && sub_value[col_id]['value']['el_id'].present?
-
-              svalue = sub_value[col_id]['value']
-              next unless svalue['el_id'].present? && svalue['el_inchikey'].present?
-
-              tmol = Molecule.find_or_create_by_molfile(data.fetch('Molecule')[svalue['el_id']]['molfile']) unless svalue['el_id'].nil?
-              unless tmol.nil?
-                properties['layers'][key]['fields'][tidx]['sub_values'][vdx][col_id]['value']['el_id'] = tmol.id
-                properties['layers'][key]['fields'][tidx]['sub_values'][vdx][col_id]['value']['el_tip'] = "#{tmol.inchikey}@@#{tmol.cano_smiles}"
-                properties['layers'][key]['fields'][tidx]['sub_values'][vdx][col_id]['value']['el_label'] = tmol.cano_smiles
-                properties['layers'][key]['fields'][tidx]['sub_values'][vdx][col_id]['value']['el_smiles'] = tmol.cano_smiles
-                properties['layers'][key]['fields'][tidx]['sub_values'][vdx][col_id]['value']['el_iupac'] = tmol.iupac_name
-                properties['layers'][key]['fields'][tidx]['sub_values'][vdx][col_id]['value']['el_inchikey'] = tmol.inchikey
-                properties['layers'][key]['fields'][tidx]['sub_values'][vdx][col_id]['value']['el_svg'] = File.join('/images', 'molecules', tmol.molecule_svg_file)
-                properties['layers'][key]['fields'][tidx]['sub_values'][vdx][col_id]['value']['el_molecular_weight'] = tmol.molecular_weight
-              end
-            end
-          end
-        end
-      end
-      properties
-    rescue StandardError => e
-      Rails.logger.error(e.backtrace)
-      raise
-    end
-
-    def self.properties_handler(data, properties)
-      properties && properties['layers'] && properties['layers'].keys&.each do |key|
-        layer = properties['layers'][key]
-        properties = proc_molecule(layer, key, data, properties)
-        properties = proc_table(layer, key, data, properties)
-        # properties = proc_sample(layer, key, data, properties)
-      end
-      properties
-    rescue StandardError => e
-      Rails.logger.error(e.backtrace)
-      raise
-    end
-
-    def self.create_segment_klass(sk_obj, segment_klass, element_klass, current_user_id)
-      return if segment_klass.present? || element_klass.nil? || sk_obj.nil?
-
-      segment_klass = Labimotion::SegmentKlass.create!(sk_obj.slice(
-          'label',
-          'desc',
-          'properties_template',
-          'is_active',
-          'place',
-          'properties_release',
-          'uuid',
-          'identifier',
-          'sync_time'
-        ).merge(
-          element_klass: element_klass,
-          created_by: current_user_id,
-          released_at: DateTime.now
-        )
-      )
-
-      segment_klass
-    end
-  end
-end