labimotion 0.2.1 → 1.0.0

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: 23bcd1152eed5ceb0d7596e7f60ae6f302d6bef48d2c6972f450ff9b205e0a6f
+  metadata.gz: 387a4b4a47a140008970b10f005472e8ba882c80ddaab99863ced5acdb0dfa29
+  data.tar.gz: 90f5839a92d045e45861a2354354bf5ef1542799a484cda94fa9c1263c206d5e
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+  metadata.gz: cca4c43074754aefbe3f2b3ca09b55af69d25ebf2a4b7f456990bc692ee7ab19905020aed4505d6360b720d94e497e91ab5910b8c50d4b5b914a01d23e840796
+  data.tar.gz: 5280180e034e2bd2a38000b62e8001ebee247cae2dd29e30f5b66eb3292d11e0e9f0566986c5eb918e6f6dcfc9d95024553204d834da44e7a1aee2b13500d454

data/lib/labimotion/apis/generic_element_api.rb

@@ -225,7 +225,7 @@ module Labimotion
           @klz = fetch_klass(params[:klass], params[:id])
         end
         post do
-          update_template(params)
+          update_template(params, current_user)
         end
       end
 
@@ -237,10 +237,10 @@ module Labimotion
         optional :from_date, type: Integer, desc: 'created_date from in ms'
         optional :to_date, type: Integer, desc: 'created_date to in ms'
         optional :filter_created_at, type: Boolean, desc: 'filter by created at or updated at'
+        optional :sort_column, type: String, desc: 'sort by updated_at or selected layers property'
       end
       paginate per_page: 7, offset: 0, max_per_page: 100
       get do
-
         scope = list_serialized_elements(params, current_user)
 
         reset_pagination_page(scope)

data/lib/labimotion/helpers/dataset_helpers.rb

@@ -16,7 +16,8 @@ module Labimotion
     def create_repo_klass(params, current_user)
       response = Labimotion::TemplateHub.fetch_identifier('DatasetKlass', params[:identifier])
       attributes = response.slice('ols_term_id', 'label', 'desc', 'uuid', 'identifier', 'properties_release', 'version') # .except(:id, :is_active, :place, :created_by, :created_at, :updated_at)
-      attributes['properties_template'] = response['properties_release']
+      attributes['properties_release']['identifier'] = attributes['identifier']
+      attributes['properties_template'] = attributes['properties_release']
       attributes['place'] = ((Labimotion::DatasetKlass.all.length * 10) || 0) + 10
       attributes['is_active'] = false
       attributes['updated_by'] = current_user.id
@@ -29,7 +30,7 @@ module Labimotion
         attributes['created_by'] = current_user.id
         ds = Labimotion::DatasetKlass.create!(attributes)
       end
-      ds.create_klasses_revision(current_user.id)
+      ds.create_klasses_revision(current_user)
     rescue StandardError => e
       Labimotion.log_exception(e, current_user)
       # { error: e.message }

data/lib/labimotion/helpers/element_helpers.rb

@@ -20,12 +20,10 @@ module Labimotion
       uuid = SecureRandom.uuid
       template = { uuid: uuid, layers: {}, select_options: {} }
       attributes = declared(params, include_missing: false)
-      if attributes[:properties_template].present?
-        attributes[:properties_template]['uuid'] = uuid
-        attributes[:properties_template] = template
-        attributes[:properties_template]['pkg'] = Labimotion::Utils.pkg(attributes[:properties_template]['pkg'])
-        attributes[:properties_template]['klass'] = 'ElementKlass'
-      end
+      attributes[:properties_template] = template if attributes[:properties_template].nil?
+      attributes[:properties_template]['uuid'] = uuid
+      attributes[:properties_template]['pkg'] = Labimotion::Utils.pkg(attributes[:properties_template]['pkg'])
+      attributes[:properties_template]['klass'] = 'ElementKlass'
       attributes[:is_active] = false
       attributes[:uuid] = uuid
       attributes[:released_at] = DateTime.now
@@ -34,7 +32,7 @@ module Labimotion
 
       new_klass = Labimotion::ElementKlass.create!(attributes)
       new_klass.reload
-      new_klass.create_klasses_revision(current_user.id)
+      new_klass.create_klasses_revision(current_user)
       klass_names_file = Rails.root.join('app/packs/klasses.json')
       klasses = Labimotion::ElementKlass.where(is_active: true)&.pluck(:name) || []
       File.write(klass_names_file, klasses)
@@ -71,6 +69,7 @@ module Labimotion
       params[:properties]['klass_uuid'] = klass[:uuid]
       params[:properties]['pkg'] = Labimotion::Utils.pkg(params[:properties]['pkg'])
       params[:properties]['klass'] = 'Element'
+      params[:properties]['identifier'] = klass[:identifier]
       properties = params[:properties]
       properties.delete('flow') unless properties['flow'].nil?
       properties.delete('flowObject') unless properties['flowObject'].nil?
@@ -247,7 +246,7 @@ module Labimotion
           .where(
             element_klasses: { name: params[:el_type] },
             collections_elements: { collection_id: collection_id },
-          ).includes(:tag, collections: :sync_collections_users).order('created_at DESC')
+          ).includes(:tag, collections: :sync_collections_users)
       else
         Labimotion::Element.none
       end
@@ -256,10 +255,35 @@ module Labimotion
       from = params[:from_date]
       to = params[:to_date]
       by_created_at = params[:filter_created_at] || false
-      scope = scope.created_time_from(Time.at(from)) if from && by_created_at
-      scope = scope.created_time_to(Time.at(to) + 1.day) if to && by_created_at
-      scope = scope.updated_time_from(Time.at(from)) if from && !by_created_at
-      scope = scope.updated_time_to(Time.at(to) + 1.day) if to && !by_created_at
+      if params[:sort_column]&.include?('.')
+        layer, field = params[:sort_column].split('.')
+
+        element_klass = Labimotion::ElementKlass.find_by(name: params[:el_type])
+        allowed_fields = element_klass.properties_release.dig('layers', layer, 'fields')&.pluck('field') || []
+
+        if field.in?(allowed_fields)
+          query = ActiveRecord::Base.sanitize_sql(
+            [
+              "LEFT JOIN LATERAL(
+                SELECT field->'value' AS value
+                FROM jsonb_array_elements(properties->'layers'->:layer->'fields') a(field)
+                WHERE field->>'field' = :field
+              ) a ON true",
+              { layer: layer, field: field },
+            ],
+          )
+          scope = scope.joins(query).order('value ASC NULLS FIRST')
+        else
+          scope = scope.order(updated_at: :desc)
+        end
+      else
+        scope = scope.order(updated_at: :desc)
+      end
+
+      scope = scope.elements_created_time_from(Time.at(from)) if from && by_created_at
+      scope = scope.elements_created_time_to(Time.at(to) + 1.day) if to && by_created_at
+      scope = scope.elements_updated_time_from(Time.at(from)) if from && !by_created_at
+      scope = scope.elements_updated_time_to(Time.at(to) + 1.day) if to && !by_created_at
       scope
     rescue StandardError => e
       Labimotion.log_exception(e, current_user)
@@ -268,8 +292,9 @@ module Labimotion
 
     def create_repo_klass(params, current_user)
       response = Labimotion::TemplateHub.fetch_identifier('ElementKlass', params[:identifier])
-      attributes = response.slice('name', 'label', 'desc', 'icon_name', 'klass_prefix', 'is_generic', 'identifier', 'properties_release', 'version') # .except(:id, :is_active, :place, :created_by, :created_at, :updated_at)
-      attributes['properties_template'] = response['properties_release']
+      attributes = response.slice('name', 'label', 'desc', 'icon_name', 'klass_prefix', 'is_generic', 'identifier', 'properties_release', 'version')
+      attributes['properties_release']['identifier'] = attributes['identifier']
+      attributes['properties_template'] = attributes['properties_release']
       attributes['place'] = ((Labimotion::DatasetKlass.all.length * 10) || 0) + 10
       attributes['is_active'] = false
       attributes['updated_by'] = current_user.id
@@ -283,7 +308,7 @@ module Labimotion
         attributes['created_by'] = current_user.id
         element_klass = Labimotion::ElementKlass.create!(attributes)
       end
-      element_klass.create_klasses_revision(current_user.id)
+      element_klass.create_klasses_revision(current_user)
     rescue StandardError => e
       Labimotion.log_exception(e, current_user)
       # { error: e.message }

data/lib/labimotion/helpers/generic_helpers.rb

@@ -41,22 +41,22 @@ module Labimotion
       raise e
     end
 
-    def update_template(params)
+    def update_template(params, current_user)
       klz = fetch_klass(params[:klass], params[:id])
       uuid = SecureRandom.uuid
       properties = params[:properties_template]
       properties['uuid'] = uuid
-
       klz.version = Labimotion::Utils.next_version(params[:release], klz.version)
       properties['version'] = klz.version
-      properties['pkg'] = Labimotion::Utils.pkg(params['pkg'] || klz.properties_template['pkg'])
+      properties['pkg'] = Labimotion::Utils.pkg(params['pkg'] || (klz.properties_template && klz.properties_template['pkg']))
       properties['klass'] = klz.class.name.split('::').last
+      properties['identifier'] = klz.identifier
       properties.delete('eln') if properties['eln'].present?
       klz.updated_by = current_user.id
       klz.properties_template = properties
       klz.save!
       klz.reload
-      klz.create_klasses_revision(current_user.id) if params[:release] != 'draft'
+      klz.create_klasses_revision(current_user) if params[:release] != 'draft'
       klz
     rescue StandardError => e
       Labimotion.log_exception(e, current_user)
@@ -188,9 +188,9 @@ module Labimotion
       raise e
     end
 
-    def create_attachments(files, del_files, type, id, user_id)
+    def create_attachments(files, del_files, type, id, identifier, user_id)
       attach_ary = []
-      (files || []).each do |file|
+      (files || []).each_with_index do |file, index|
         next unless (tempfile = file[:tempfile])
 
         a = Attachment.new(
@@ -200,13 +200,14 @@ module Labimotion
           file_path: file[:tempfile],
           created_by: user_id,
           created_for: user_id,
+          identifier: identifier[index],
           content_type: file[:type],
           attachable_type: type,
           attachable_id: id,
         )
-        begin
-          a.save!
-          attach_ary.push(a.id)
+        ActiveRecord::Base.transaction do
+          att.save!
+          attach_ary.push(att.id)
         ensure
           tempfile.close
           tempfile.unlink

data/lib/labimotion/helpers/segment_helpers.rb

@@ -38,7 +38,7 @@ module Labimotion
       attributes[:properties_release] = attributes[:properties_template]
       klass = Labimotion::SegmentKlass.create!(attributes)
       klass.reload
-      klass.create_klasses_revision(current_user.id)
+      klass.create_klasses_revision(current_user)
       klass
     rescue StandardError => e
       Labimotion.log_exception(e, current_user)
@@ -65,8 +65,9 @@ module Labimotion
 
     def create_repo_klass(params, current_user)
       response = Labimotion::TemplateHub.fetch_identifier('SegmentKlass', params[:identifier])
-      attributes = response.slice('label', 'desc', 'uuid', 'identifier', 'released_at', 'properties_release', 'version') # .except(:id, :is_active, :place, :created_by, :created_at, :updated_at)
-      attributes['properties_template'] = response['properties_release']
+      attributes = response.slice('label', 'desc', 'uuid', 'identifier', 'released_at', 'properties_release', 'version')
+      attributes['properties_release']['identifier'] = attributes['identifier']
+      attributes['properties_template'] = attributes['properties_release']
       attributes['place'] = ((Labimotion::SegmentKlass.all.length * 10) || 0) + 10
       attributes['is_active'] = false
       attributes['updated_by'] = current_user.id
@@ -89,7 +90,7 @@ module Labimotion
         attributes['created_by'] = current_user.id
         segment_klass = Labimotion::SegmentKlass.create!(attributes)
       end
-      segment_klass.create_klasses_revision(current_user.id)
+      segment_klass.create_klasses_revision(current_user)
     rescue StandardError => e
       Labimotion.log_exception(e, current_user)
       raise e

data/lib/labimotion/libs/converter.rb

@@ -4,6 +4,7 @@ require 'net/http'
 require 'uri'
 require 'json'
 require 'date'
+require 'labimotion/version'
 require 'labimotion/utils/utils'
 
 # rubocop: disable Metrics/AbcSize
@@ -116,7 +117,7 @@ module Labimotion
         )
         # att.attachment_attacher.attach(tmp_file)
         if att.valid? && Labimotion::IS_RAILS5 == false
-          att.attachment_attacher.create_derivatives
+          ## att.attachment_attacher.create_derivatives
           att.save!
         end
         if att.valid? && Labimotion::IS_RAILS5 == true
@@ -148,7 +149,12 @@ module Labimotion
       response = nil
       begin
         ofile = Rails.root.join(data[:f], data[:a].filename)
-        FileUtils.cp(data[:a].store.path, ofile)
+        if Labimotion::IS_RAILS5 == true
+          FileUtils.cp(data[:a].store.path, ofile)
+        else
+          FileUtils.cp(data[:a].attachment_url, ofile)
+        end
+
         File.open(ofile, 'r') do |f|
           body = { file: f }
           response = HTTParty.post(

data/lib/labimotion/libs/export_dataset.rb

@@ -1,5 +1,6 @@
 # frozen_string_literal: true
 require 'export_table'
+require 'labimotion/version'
 
 module Labimotion
   ## ExportDataset
@@ -101,9 +102,18 @@ module Labimotion
       cds.attachments.where(aasm_state: 'csv').each do |att|
         name = File.basename(att.filename, '.csv')
         sheet = @xfile.workbook.add_worksheet(name: name)
-        File.open(att.store.path) do |fi|
-          fi.each_line do |line|
-            sheet.add_row(line.split(','))
+
+        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
           end
         end
       end

data/lib/labimotion/libs/nmr_mapper.rb

@@ -1,5 +1,6 @@
 # frozen_string_literal: true
 
+require 'labimotion/version'
 require 'labimotion/utils/utils'
 
 module Labimotion
@@ -7,8 +8,8 @@ module Labimotion
   class NmrMapper
     def self.is_brucker_binary(id)
       att = Attachment.find(id)
-      if att&.attachment_attacher&.file&.url
-        Zip::File.open(att.attachment_attacher.file.url) do |zip_file|
+      if Labimotion::IS_RAILS5 == true
+        Zip::File.open(att.store.path) 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')
@@ -16,6 +17,17 @@ 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 metadata
+              end
+            end
+          end
+        end
       end
       nil
     end

data/lib/labimotion/libs/nmr_mapper_repo.rb

@@ -1,18 +1,33 @@
 # frozen_string_literal: true
+require 'labimotion/version'
 require 'labimotion/utils/utils'
 
 module Labimotion
   class NmrMapperRepo
     def self.is_brucker_binary(id)
       att = Attachment.find(id)
-      Zip::File.open(att.store.path) 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 metadata
+      if Labimotion::IS_RAILS5 == true
+        Zip::File.open(att.store.path) 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 metadata
+            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 metadata
+              end
+            end
           end
         end
       end
+
       nil
     end
 

data/lib/labimotion/models/concerns/datasetable.rb

@@ -23,6 +23,7 @@ module Labimotion
       uuid = SecureRandom.uuid
       props = args[:properties]
       props['pkg'] = Labimotion::Utils.pkg(props['pkg'])
+      props['identifier'] = klass.identifier
       props['uuid'] = uuid
       props['klass'] = 'Dataset'
 

data/lib/labimotion/models/concerns/generic_klass_revisions.rb

@@ -1,13 +1,14 @@
 # frozen_string_literal: true
 
 module Labimotion
-    module GenericKlassRevisions
+  ## Generic Klass Revisions Helpers
+  module GenericKlassRevisions
     extend ActiveSupport::Concern
     included do
       # has_many :element_klasses_revisions, dependent: :destroy
     end
 
-    def create_klasses_revision(user_id=0)
+    def create_klasses_revision(current_user)
       properties_release = properties_template
       migrate_workflow if properties_release['flow'].present?
 
@@ -21,11 +22,19 @@ module Labimotion
         end
         properties_release['flowObject']['nodes'] = elements
       end
+      klass_attributes = {
+        uuid: properties_template['uuid'],
+        properties_template: properties_release,
+        properties_release: properties_release,
+        released_at: DateTime.now,
+        updated_by: current_user&.id,
+        released_by: current_user&.id,
+      }
 
-      self.update!({ uuid: properties_template['uuid'], properties_template: properties_release, properties_release: properties_release, released_at: DateTime.now })
+      self.update!(klass_attributes)
       reload
       attributes = {
-        released_by: user_id,
+        released_by: released_by,
         uuid: uuid,
         version: version,
         properties_release: properties_release,

data/lib/labimotion/models/concerns/segmentable.rb

@@ -48,6 +48,7 @@ module Labimotion
         uuid = SecureRandom.uuid
         props = seg['properties']
         props['pkg'] = Labimotion::Utils.pkg(props['pkg'])
+        props['identifier'] = identifier
         props['uuid'] = uuid
         props['klass'] = 'Segment'
         segment = Labimotion::Segment.find_by(element_type: Labimotion::Utils.element_name(self.class.name), element_id: self.id, segment_klass_id: seg['segment_klass_id'])

data/lib/labimotion/utils/utils.rb

@@ -81,7 +81,6 @@ module Labimotion
     end
 
     def self.pkg(pkg)
-byebug
       pkg = {} if pkg.nil?
       pkg['eln'] = Chemotion::Application.config.version
       pkg['labimotion'] = Labimotion::VERSION

data/lib/labimotion/version.rb

@@ -2,6 +2,6 @@
 
 module Labimotion
   # VERSION = '0.1.4'
-  VERSION = '0.2.1'
+  VERSION = '1.0.0'
   IS_RAILS5 = false
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: labimotion
 version: !ruby/object:Gem::Version
-  version: 0.2.1
+  version: 1.0.0
 platform: ruby
 authors:
 - Chia-Lin Lin
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2023-08-23 00:00:00.000000000 Z
+date: 2023-08-24 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rails