labimotion 1.3.0.rc2 → 1.3.0.rc4

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: ee43dfba01f84786e6b1dc59d125c6c8cd3a7594e6f3d9e5179268995b8366dd
-  data.tar.gz: e15bf2f064a847b950f3320a2707de508f3c8169a966519280b71f8426a20f3e
+  metadata.gz: 99c322d38e4cd89d9983147d40d2ceb98aee8342fe9d036f6757034a52fc8b81
+  data.tar.gz: ccf53a3066ff47347a29f45594fbac4436fb6161078c56ef5461a672fa99e0db
 SHA512:
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-  data.tar.gz: db9c675738091bd749bdea7ece8eb3e555b6063694691d81a58832b19be3f92618d61a69228ad8a820c11a4b14d7ff8b77ef817378740e0f2af108aa43867316
+  metadata.gz: ce7a434025855de8eafc83450b4bb8808d77e237f306bc5c0f986bdbfb7cc72f46199d615eca43085353af365ea4315ca89f44bedc2ff487dc24d1c69e9a781d
+  data.tar.gz: fff821b8cf75223a50feb3d630eb229bb709de42c8644e1175cbe5c0cfad7a560e6ac9ca2548bfdecb1f2b6372c1e6ba9739ffbd712f82d017793b61e8b0e85b

data/lib/labimotion/apis/generic_element_api.rb

@@ -46,11 +46,19 @@ module Labimotion
       namespace :export do
         desc 'export element'
         params do
-          optional :id, type: Integer, desc: 'element id'
+          requires :id, type: Integer, desc: 'element id'
+          requires :klass, type: String, desc: 'Klass', values: %w[Element Segment Dataset]
           optional :export_format, type: String, desc: 'export format'
         end
         get do
-          element = Labimotion::Element.find(params[:id])
+          case params[:klass]
+          when 'Element'
+            element = Labimotion::Element.find(params[:id])
+          when 'Segment'
+            element = Labimotion::Segment.find(params[:id])
+          when 'Dataset'
+            element = Labimotion::Dataset.find(params[:id])
+          end
           ## byebug
           export = Labimotion::ExportElement.new current_user, element, params[:export_format]
           env['api.format'] = :binary
@@ -340,21 +348,14 @@ module Labimotion
 
         get do
           element = Labimotion::Element.find(params[:id])
-          if Labimotion::IS_RAILS5 == true
-            {
-              element: ElementPermissionProxy.new(current_user, element, user_ids).serialized,
-              attachments: attach_thumbnail(element&.attachments)
-            }
-          else
-            {
-              element: Labimotion::ElementEntity.represent(
-                element,
-                detail_levels: ElementDetailLevelCalculator.new(user: current_user, element: element).detail_levels,
-                policy: @element_policy
-              ),
-              attachments: attach_thumbnail(element&.attachments)
-            }
-          end
+          {
+            element: Labimotion::ElementEntity.represent(
+              element,
+              detail_levels: ElementDetailLevelCalculator.new(user: current_user, element: element).detail_levels,
+              policy: @element_policy
+            ),
+            attachments: attach_thumbnail(element&.attachments)
+          }
         rescue StandardError => e
           Labimotion.log_exception(e, current_user)
         end

data/lib/labimotion/collection/import.rb

@@ -89,7 +89,7 @@ module Labimotion
         sk_id = sk_obj["identifier"]
         ek_obj = data.fetch(Labimotion::Prop::L_ELEMENT_KLASS).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
+        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')
@@ -99,7 +99,7 @@ module Labimotion
 
         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?
+          segment_klass = Labimotion::SegmentKlass.find_by(id: skr.segment_klass_id) if skr.present?
         end
 
         next if segment_klass.nil? || element.nil?
@@ -133,7 +133,7 @@ module Labimotion
       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"]
+        ek_id = ek_obj["identifier"] if ek_obj.present?
         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?
 

data/lib/labimotion/helpers/element_helpers.rb

@@ -176,11 +176,6 @@ module Labimotion
         )
       end
       (attach_ary << att_ary).flatten! unless att_ary&.empty?
-
-      if Labimotion::IS_RAILS5 == true
-        TransferThumbnailToPublicJob.set(queue: "transfer_thumbnail_to_public_#{current_user.id}").perform_now(attach_ary) unless attach_ary.empty?
-        TransferFileFromTmpJob.set(queue: "transfer_file_from_tmp_#{current_user.id}").perform_now(attach_ary) unless attach_ary.empty?
-      end
       true
     rescue StandardError => e
       Labimotion.log_exception(e, current_user)

data/lib/labimotion/libs/converter.rb

@@ -27,18 +27,10 @@ module Labimotion
 
       dsr = []
       ols = nil
-      if Labimotion::IS_RAILS5 == true
-        Zip::File.open(att.store.path) do |zip_file|
-          res = Labimotion::Converter.collect_metadata(zip_file) if att.filename.split('.')&.last == 'zip'
-          ols = res[:o] unless res&.dig(:o).nil?
-          dsr.push(res[:d]) unless res&.dig(:d).nil?
-        end
-      else
-        Zip::File.open(att.attachment_attacher.file.url) do |zip_file|
-          res = Labimotion::Converter.collect_metadata(zip_file) if att.filename.split('.')&.last == 'zip'
-          ols = res[:o] unless res&.dig(:o).nil?
-          dsr.push(res[:d]) unless res&.dig(:d).nil?
-        end
+      Zip::File.open(att.attachment_attacher.file.url) do |zip_file|
+        res = Labimotion::Converter.collect_metadata(zip_file) if att.filename.split('.')&.last == 'zip'
+        ols = res[:o] unless res&.dig(:o).nil?
+        dsr.push(res[:d]) unless res&.dig(:d).nil?
       end
       dsr.flatten!
       dataset = build_ds(att.attachable_id, ols)
@@ -145,16 +137,9 @@ module Labimotion
           created_by: oat.created_by,
           created_for: oat.created_for,
         )
-        # att.attachment_attacher.attach(tmp_file)
-        if att.valid? && Labimotion::IS_RAILS5 == false
-          ## att.attachment_attacher.create_derivatives
-          att.save!
-        end
-        if att.valid? && Labimotion::IS_RAILS5 == true
-          att.save!
-          primary_store = Rails.configuration.storage.primary_store
-          att.update!(storage: primary_store)
-        end
+
+        att.save! if att.valid?
+
         process_ds(att.id)
       rescue StandardError => e
         raise e
@@ -168,11 +153,7 @@ module Labimotion
       response = nil
       begin
         ofile = Rails.root.join(data[:f], data[:a].filename)
-        if Labimotion::IS_RAILS5 == true
-          FileUtils.cp(data[:a].store.path, ofile)
-        else
-          FileUtils.cp(data[:a].attachment_url, ofile)
-        end
+        FileUtils.cp(data[:a].attachment_url, ofile)
 
         File.open(ofile, 'r') do |f|
           body = { file: f }

data/lib/labimotion/libs/export_dataset.rb

@@ -145,18 +145,9 @@ module Labimotion
         sheet_name = "Sheet#{idx+1}"
         sheet = @xfile.workbook.add_worksheet(name: sheet_name)
         name_mapping.push([sheet_name, att.filename])
-
-        if Labimotion::IS_RAILS5 == true
-          File.open(att.store.path) do |fi|
-            fi.each_line do |line|
-              sheet.add_row(line.split(','))
-            end
-          end
-        else
-          File.open(att.attachment_url) do |fi|
-            fi.each_line do |line|
-              sheet.add_row(line.split(','))
-            end
+        File.open(att.attachment_url) do |fi|
+          fi.each_line do |line|
+            sheet.add_row(line.split(','))
           end
         end
       end

data/lib/labimotion/libs/export_element.rb

@@ -1,6 +1,7 @@
 # frozen_string_literal: true
 require 'export_table'
 require 'labimotion/version'
+require 'labimotion/utils/units'
 require 'sablon'
 
 module Labimotion
@@ -8,6 +9,25 @@ module Labimotion
     def initialize(current_user, element, export_format)
       @current_user = current_user
       @element = element
+      @parent =
+        case element.class.name
+        when 'Labimotion::Segment'
+          element&.element
+        when 'Labimotion::Dataset'
+          element&.element&.root_element
+        end
+      @element_klass =
+        case element.class.name
+        when 'Labimotion::Element'
+          element.element_klass
+        when 'Labimotion::Segment'
+          element.segment_klass
+        when 'Labimotion::Dataset'
+          element.dataset_klass
+        end
+      @name = @element.instance_of?(Labimotion::Element) ? element.name : @parent&.name
+      @short_label = @element.instance_of?(Labimotion::Element) ? element.short_label : @parent&.short_label
+      @element_name = "#{@element_klass.label}_#{@short_label}".gsub(/\s+/, '')
       @properties = element.properties
       @options = element.properties_release[Labimotion::Prop::SEL_OPTIONS]
       @export_format = export_format
@@ -17,7 +37,12 @@ module Labimotion
 
     def build_layers
       objs = []
-      @properties[Labimotion::Prop::LAYERS]&.keys&.sort_by { |key| @properties[Labimotion::Prop::LAYERS][key]['position'] }&.each do |key|
+      @properties[Labimotion::Prop::LAYERS]&.keys&.sort_by do |key|
+        [
+          @properties[Labimotion::Prop::LAYERS].fetch(key, nil)&.fetch('position', 0) || 0,
+          @properties[Labimotion::Prop::LAYERS].fetch(key, nil)&.fetch('wf_position', 0) || 0
+        ]
+      end&.each do |key|
         layer = @properties[Labimotion::Prop::LAYERS][key] || {}
 
         ## Build fields html
@@ -53,23 +78,25 @@ module Labimotion
         field_obj[:value] = (field['value'] && field['value']['el_label']) || ''
         field_obj[:obj] = field['value']  ### change to object
       when Labimotion::FieldType::DRAG_SAMPLE
-        val = field.fetch('value', {})
-        instance = Sample.find_by(id: val['el_id'])
-        field_obj[:value] = val['el_label']
-        field_obj[:has_structure] = true
-        obj_os = Entities::SampleReportEntity.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::DiagramSample.new(obj: obj_final, format: 'png').generate
+        val = field.fetch('value', nil)
+        if val.present?
+          instance = Sample.find_by(id: val['el_id'])
+          field_obj[:value] = val['el_label']
+          field_obj[:has_structure] = true
+          obj_os = Entities::SampleReportEntity.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::DiagramSample.new(obj: obj_final, format: 'png').generate
+        end
       when Labimotion::FieldType::DRAG_MOLECULE
-        val = field.fetch('value', {})
-        obj = Molecule.find_by(id: val['el_id'])
-        field_obj[:value] = val['el_label']
-        # field_obj[:has_structure] = true
-        # field_obj[:structure] = Reporter::Docx::DiagramSample.new(obj: obj, format: 'png').generate
+        val = field.fetch('value', nil)
+        if val.present?
+          obj = Molecule.find_by(id: val['el_id'])
+          field_obj[:value] = val['el_label']
+        end
       when Labimotion::FieldType::SELECT
         field_obj[:value] = @options.fetch(field['option_layers'], nil)&.fetch('options', nil)&.find { |ss| ss['key'] == field['value'] }&.fetch('label', nil) || field['value']
       when Labimotion::FieldType::UPLOAD
@@ -82,7 +109,6 @@ module Labimotion
         tbl = []
         ## tbl_idx = []
         header = {}
-
         sub_fields = field.fetch('sub_fields', [])
         sub_fields.each_with_index do |sub_field, idx|
           header["col#{idx}"] = sub_field['col_name']
@@ -107,6 +133,25 @@ module Labimotion
           end
         end
         field_obj[:value] = val.join(' ')
+      when Labimotion::FieldType::WF_NEXT
+        if field['value'].present? && field['wf_options'].present?
+          field_obj[:value] = field['wf_options'].find { |ss| ss['key'] == field['value'] }&.fetch('label', nil)&.split('(')&.first&.strip
+        end
+      when Labimotion::FieldType::SYSTEM_DEFINED
+        _field = field
+        unit = Labimotion::Units::FIELDS.find { |o| o[:field] == _field['option_layers'] }&.fetch(:units, []).find { |u| u[:key] == _field['value_system'] }&.fetch(:label, '')
+        val = _field['value'].to_s + ' ' + unit
+        val = Sablon.content(:html, "<div>" + val + "</div>") if val.include? '<'
+        field_obj[:value] = val
+      when Labimotion::FieldType::TEXT_FORMULA
+        field.fetch('text_sub_fields', []).each do |sub_field|
+          va = @properties['layers'][sub_field.fetch('layer','')]['fields'].find { |f| f['field'] == sub_field.fetch('field','') }&.fetch('value',nil)
+          field_obj[:value] = (field_obj[:value] || '') + va.to_s + sub_field.fetch('separator','') if va.present?
+        end
+        # field_obj[:value] = (field['value'] && field['value']['el_label']) || ''
+        # field_obj[:obj] = field['value']  ### change to object
+      else
+        field_obj[:value] = field['value']
       end
       field_obj
     rescue StandardError => e
@@ -117,10 +162,27 @@ module Labimotion
       return '' if sub_field.fetch('id', nil).nil? || sub_val[sub_field['id']].nil?
 
       case sub_field['type']
+      when Labimotion::FieldType::DRAG_SAMPLE
+        val = sub_val[sub_field['id']]['value'] || {}
+        label = val['el_label'].present? ? "Short Label: [#{val['el_label']}] \n" : ''
+        name = val['el_name'].present? ? "Name: [#{val['el_name']}] \n" : ''
+        ext = val['el_external_label'].present? ? "Ext. Label: [#{val['el_external_label']}] \n" : ''
+        mass = val['el_molecular_weight'].present? ? "Mass: [#{val['el_molecular_weight']}] \n" : ''
+        "#{label}#{name}#{ext}#{mass}"
+      when Labimotion::FieldType::DRAG_MOLECULE
+        val = sub_val[sub_field['id']]['value'] || {}
+        smile = val['el_smiles'].present? ? "SMILES: [#{val['el_smiles']}] \n" : ''
+        inchikey = val['el_inchikey'].present? ? "InChiKey:[#{val['el_inchikey']}] \n" : ''
+        iupac = val['el_iupac'].present? ? "IUPAC:[#{val['el_iupac']}] \n" : ''
+        mass = val['el_molecular_weight'].present? ? "MASS: [#{val['el_molecular_weight']}] \n" : ''
+        "#{smile}#{inchikey}#{iupac}#{mass}"
       when Labimotion::FieldType::SELECT
         sub_val[sub_field['id']]['value']
       when Labimotion::FieldType::SYSTEM_DEFINED
-        "#{sub_val[sub_field['id']]['value']} #{sub_val[sub_field['id']]['value_system']}"
+        unit = Labimotion::Units::FIELDS.find { |o| o[:field] == sub_field['option_layers'] }&.fetch(:units, [])&.find { |u| u[:key] == sub_field['value_system'] }&.fetch(:label, '')
+        val = sub_val[sub_field['id']]['value'].to_s + ' ' + unit
+        val = Sablon.content(:html, "<div>" + val + "</div>") if val.include? '<'
+        val
       else
         sub_val[sub_field['id']]
       end
@@ -148,8 +210,11 @@ module Labimotion
       template = Sablon.template(location)
       layers = build_layers
       context = {
-        name: @element.name,
-        short_label: @element.short_label,
+        label: @element_klass.label,
+        desc: @element_klass.desc,
+        name: @name,
+        parent_klass: @parent.present? ? "#{@parent&.class&.name&.split('::')&.last}: " : '',
+        short_label: @short_label,
         date: Time.now.strftime('%d/%m/%Y'),
         author: @current_user.name,
         layers: layers
@@ -162,14 +227,13 @@ module Labimotion
       Labimotion.log_exception(e)
     ensure
       # Close and delete the temporary file
-      tempfile.close
-      tempfile.unlink
+      tempfile&.close
+      tempfile&.unlink
     end
 
 
     def res_name
-      element_name = @element.short_label
-      "#{element_name}_#{Time.now.strftime('%Y%m%d%H%M')}.docx"
+      "#{@element_name}_#{Time.now.strftime('%Y%m%d%H%M')}.docx"
     rescue StandardError => e
       Labimotion.log_exception(e)
     end

data/lib/labimotion/libs/nmr_mapper.rb

@@ -28,8 +28,8 @@ module Labimotion
       att = Attachment.find_by(id: id, con_state: Labimotion::ConState::NMR)
       return if att.nil?
 
-      if Labimotion::IS_RAILS5 == true
-        Zip::File.open(att.store.path) do |zip_file|
+      if att&.attachment_attacher&.file&.url
+        Zip::File.open(att.attachment_attacher.file.url) do |zip_file|
           zip_file.each do |entry|
             if entry.name.include?('/pdata/') && entry.name.include?('parm.txt')
               metadata = entry.get_input_stream.read.force_encoding('UTF-8')
@@ -39,19 +39,6 @@ module Labimotion
             end
           end
         end
-      else
-        if att&.attachment_attacher&.file&.url
-          Zip::File.open(att.attachment_attacher.file.url) do |zip_file|
-            zip_file.each do |entry|
-              if entry.name.include?('/pdata/') && entry.name.include?('parm.txt')
-                metadata = entry.get_input_stream.read.force_encoding('UTF-8')
-                return { is_bagit: false, metadata: metadata }
-              elsif entry.name.include?('metadata/') && entry.name.include?('converter.json')
-                return { is_bagit: true, metadata: nil }
-              end
-            end
-          end
-        end
       end
       { is_bagit: false, metadata: nil }
     end

data/lib/labimotion/utils/field_type.rb

@@ -8,6 +8,8 @@ module Labimotion
     SELECT = 'select'.freeze
     INTEGER = 'integer'.freeze
     INPUT_GROUP = 'input-group'.freeze
+    WF_NEXT = 'wf-next'.freeze
+    TEXT_FORMULA = 'text-formula'.freeze
     SYSTEM_DEFINED = 'system-defined'.freeze
     DRAG = 'drag'.freeze
     DRAG_ELEMENT = 'drag_element'.freeze