labimotion 1.0.13 → 1.0.18

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 6fee76937fb58a56cbe5ccbfa23deaf60ec7270ce18962697232baba381864bc
-  data.tar.gz: 4f9c52e1d367b7e267ffd2e1933e1a0986e714baf53095f06d4c3a740e4d5dff
+  metadata.gz: cb5fd5761e888bf207676bbf97543cf5636dec7ab38fb70ee1d9481bc2fce073
+  data.tar.gz: 99c3efcefccd2c5ac2460c2c1e5b31b4f3aa3740f95511efa9453f04f2218deb
 SHA512:
-  metadata.gz: '0578eec6bf64edda52b79d66dd635ced6b99c6d73e28cec5f4cd3e14bd8c669c5ef1b75a7464564f73f38492d6565cafa77ee3f0a6aa2e4ee1cd9af7d04dbc85'
-  data.tar.gz: f16f35d5efe1f6b06271c8675903137021d541acdd5e3dca9a58ee7a9cca08c69a73a508a2e972d206bf54e9ccb8b26dedd19032bd8ab35cc3709d4d8d2fe5a0
+  metadata.gz: 39cd347d558a49e57931c2d818530ea9cce85ea01e1a8950d04977cbe6794e3f777ec551bb37af058ca773083301a1bbd79d57d85733c882068d081a5d8b527d
+  data.tar.gz: 19c0ededc605def31634b210e0117411841afaad5c7b84dc9f57a96cfcab6177b54d11f5bf70bb0f70752589aebe37d0ed5f53a22bbaa486002a66d2830a3210

data/lib/labimotion/libs/converter.rb

@@ -19,28 +19,31 @@ module Labimotion
     end
 
     def self.process_ds(id, current_user = {})
-      att = Attachment.find_by(attachable_id: id, con_state: Labimotion::ConState::CONVERTED)
-      return if att.nil?
+      att = Attachment.find_by(id: id, con_state: Labimotion::ConState::CONVERTED)
+      return if att.nil? || att.attachable_id.nil? || att.attachable_type != 'Container'
 
       dsr = []
       ols = nil
-
-      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?
+      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
       end
       dsr.flatten!
-
-      dataset = build_ds(id, ols)
+      dataset = build_ds(att.attachable_id, ols)
       update_ds(dataset, dsr, current_user) if dataset.present?
-
-
+      att.update_column(:con_state, Labimotion::ConState::COMPLETED)
     rescue StandardError => e
       Labimotion::Converter.logger.error ["Att ID: #{att&.id}, OLS: #{ols}", "DSR: #{dsr}", e.message, *e.backtrace].join($INPUT_RECORD_SEPARATOR)
       raise e
-    ensure
-      ## tmp_file&.close
     end
 
     def self.uri(api_name)
@@ -149,19 +152,7 @@ module Labimotion
           primary_store = Rails.configuration.storage.primary_store
           att.update!(storage: primary_store)
         end
-
-        if Labimotion::IS_RAILS5 == true
-          Zip::File.open(tmp_file.path) do |zip_file|
-            res = Labimotion::Converter.collect_metadata(zip_file) if name.split('.')&.last == 'zip'
-            ols = res[:o] unless res&.dig(:o).nil?
-            dsr.push(res[:d]) unless res&.dig(:d).nil?
-          end
-
-          dsr.flatten!
-          if dsr.length.positive? && name.split('.')&.last == 'zip'
-            Labimotion::Converter.ts('write', att.attachable_id, ols: ols, info: dsr)
-          end
-        end
+        process_ds(att.id)
       rescue StandardError => e
         raise e
       ensure
@@ -205,23 +196,20 @@ module Labimotion
     end
 
     def self.jcamp_converter(id)
-      resp = nil
-      begin
-
-        data = Labimotion::Converter.vor_conv(id)
-        return if data.nil?
+      data = Labimotion::Converter.vor_conv(id)
+      return if data.nil?
 
-        Labimotion::Converter.process(data)
-      rescue StandardError => e
-        Labimotion::Converter.logger.error ["jcamp_converter fail: #{id}", e.message, *e.backtrace].join($INPUT_RECORD_SEPARATOR)
-        Labimotion::ConState::ERROR
-      end
+      Labimotion::Converter.process(data)
+    rescue StandardError => e
+      Labimotion::Converter.logger.error ["jcamp_converter fail: #{id}", e.message, *e.backtrace].join($INPUT_RECORD_SEPARATOR)
+      Labimotion::ConState::ERROR
     end
 
     def self.generate_ds(att_id, current_user = {})
       dsr_info = Labimotion::Converter.fetch_dsr(att_id)
       begin
         return unless dsr_info && dsr_info[:info]&.length.positive?
+
         dataset = Labimotion::Converter.build_ds(att_id, dsr_info[:ols])
         Labimotion::Converter.update_ds(dataset, dsr_info[:info], current_user) if dataset.present?
       rescue StandardError => e
@@ -351,6 +339,15 @@ module Labimotion
       end
       res
     end
+
+    def self.metadata(id)
+      att = Attachment.find(id)
+      return if att.nil? || att.attachable_id.nil? || att.attachable_type != 'Container'
+
+      ds = Labimotion::Dataset.find_by(element_type: 'Container', element_id: att.attachable_id)
+      att.update_column(:con_state, Labimotion::ConState::COMPLETED) if ds.present?
+      process_ds(att.id) if ds.nil?
+    end
   end
 end
 

data/lib/labimotion/libs/nmr_mapper.rb

@@ -7,21 +7,23 @@ module Labimotion
   ## NmrMapper
   class NmrMapper
     def self.process_ds(id, current_user = {})
-      att = Attachment.find_by(attachable_id: id, con_state: Labimotion::ConState::NMR)
+      att = Attachment.find_by(id: id, con_state: Labimotion::ConState::NMR)
       return if att.nil?
 
-      content = is_brucker_binary(id, att)
+      content = is_brucker_binary(id)
       if content.nil?
-        att.update_column(:con_state, Labimotion::ConState::NONE)
+        Labimotion::ConState::NONE
       else
         data = process(att, id, content)
-        generate_ds(id, data, current_user)
-        att.update_column(:con_state, Labimotion::ConState::PROCESSED)
+        generate_ds(id, att.attachable_id, data, current_user)
+        Labimotion::ConState::COMPLETED
       end
     end
 
-    def self.is_brucker_binary(id, att)
-      # att = Attachment.find(id)
+    def self.is_brucker_binary(id)
+      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|
           zip_file.each do |entry|
@@ -76,16 +78,14 @@ module Labimotion
     end
 
 
-    def self.generate_ds(id, data, current_user = {})
-      # data = Labimotion::NmrMapper.fetch_content(id)
-      return if data.nil?
+    def self.generate_ds(id, cid, data, current_user = {})
+      return if data.nil? || cid.nil?
 
-      obj = Labimotion::NmrMapper.build_ds(id, data[:content])
+      obj = Labimotion::NmrMapper.build_ds(cid, data[:content])
       return if obj.nil? || obj[:ols].nil?
 
-      Labimotion::NmrMapper.update_ds_1h(id, obj, current_user) if obj[:ols] == 'CHMO:0000593'
-      Labimotion::NmrMapper.update_ds_1h(id, obj, current_user) if obj[:ols] == 'CHMO:0000595'
-      Labimotion::NmrMapper.clean(id)
+      Labimotion::NmrMapper.update_ds_1h(cid, obj, current_user) if obj[:ols] == 'CHMO:0000593'
+      Labimotion::NmrMapper.update_ds_1h(cid, obj, current_user) if obj[:ols] == 'CHMO:0000595'
     end
 
     def self.update_ds_13c(id, obj)

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

@@ -10,6 +10,7 @@ module Labimotion
       after_update :exec_converter
       def init_converter
         return if self.has_attribute?(:con_state) == false || con_state.present?
+
         if Rails.configuration.try(:converter).try(:url) && ACCEPTED_FORMATS.include?(File.extname(filename&.downcase))
           self.con_state = Labimotion::ConState::WAIT
         end
@@ -22,34 +23,20 @@ module Labimotion
       end
 
       def exec_converter
-        return if self.has_attribute?(:con_state) == false || !con_state.present?
-
-        #return if attachable_id.nil?
-        return if Labimotion::IS_RAILS5 == false && self.con_state != Labimotion::ConState::WAIT
-
         return if self.has_attribute?(:con_state) == false || self.con_state.nil? || self.con_state == Labimotion::ConState::NONE
 
+        return if attachable_id.nil? && self.con_state != Labimotion::ConState::WAIT
+
         case con_state
         when Labimotion::ConState::NMR
-          if Labimotion::IS_RAILS5 == true
-            content = Labimotion::NmrMapperRepo.is_brucker_binary(id)
-          else
-            content = Labimotion::NmrMapper.is_brucker_binary(id)
-          end
-          if content.nil?
-            self.con_state = Labimotion::ConState::NONE
-          else
-            if Labimotion::IS_RAILS5 == true
-              Labimotion::NmrMapperRepo.process(id, content)
-            else
-              Labimotion::NmrMapper.process(id, content)
-            end
-            self.con_state = Labimotion::ConState::PROCESSED
-          end
+          self.con_state = Labimotion::NmrMapper.process_ds(id)
+          update_column(:con_state, con_state)
         when Labimotion::ConState::WAIT
           self.con_state = Labimotion::Converter.jcamp_converter(id)
+          update_column(:con_state, con_state)
+        when Labimotion::ConState::CONVERTED
+          Labimotion::Converter.metadata(id)
         end
-        update_column(:con_state, con_state)
       end
     end
   end

data/lib/labimotion/models/element.rb

@@ -11,8 +11,6 @@ module Labimotion
     include PgSearch::Model if Labimotion::IS_RAILS5 == false
     include ElementUIStateScopes
     include Collectable
-    ## include AnalysisCodes
-    include ElementCodes
     include Taggable
     include Workflow
     include Segmentable

data/lib/labimotion/version.rb

@@ -3,7 +3,7 @@
 ## Labimotion Version
 module Labimotion
   IS_RAILS5 = false
-  VERSION_ELN = '1.0.13'
+  VERSION_ELN = '1.0.18'
   VERSION_REPO = '0.3.1'
 
   VERSION = Labimotion::VERSION_REPO if Labimotion::IS_RAILS5 == true

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: labimotion
 version: !ruby/object:Gem::Version
-  version: 1.0.13
+  version: 1.0.18
 platform: ruby
 authors:
 - Chia-Lin Lin
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2023-10-13 00:00:00.000000000 Z
+date: 2023-10-20 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rails
@@ -66,7 +66,6 @@ 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

data/lib/labimotion/libs/nmr_mapper_repo.rb

@@ -1,278 +0,0 @@
-# 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)
-      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
-
-    def self.process(id, content)
-      att = Attachment.find(id)
-      lines = content.split("\n").reject(&:empty?)
-      metadata = {}
-      lines.map do |ln|
-        arr = ln.split(/\s+/)
-        metadata[arr[0]] = arr[1..-1].join(' ') if arr.length > 1
-      end
-      ols = 'CHMO:0000593' if metadata['NUC1'] == '1H'
-      ols = 'CHMO:0000595' if metadata['NUC1'] == '13C'
-      if content.present? && att.present?
-        Labimotion::NmrMapper.ts('write', att.attachable_id,
-                              content: { metadata: metadata, ols: ols })
-      end
-    end
-
-    def self.fetch_content(id)
-      Labimotion::NmrMapper.ts('read', id)
-    end
-
-    def self.generate_ds(id, current_user = {})
-      data = Labimotion::NmrMapper.fetch_content(id)
-      return if data.nil?
-
-      obj = Labimotion::NmrMapper.build_ds(id, data[:content])
-      return if obj.nil? || obj[:ols].nil?
-
-      Labimotion::NmrMapper.update_ds_1h(id, obj, current_user) if obj[:ols] == 'CHMO:0000593'
-      Labimotion::NmrMapper.update_ds_1h(id, obj, current_user) if obj[:ols] == 'CHMO:0000595'
-      Labimotion::NmrMapper.clean(id)
-    end
-
-    def self.update_ds_13c(id, obj)
-      # dataset = obj[:dataset]
-      # metadata = obj[:metadata]
-      # new_prop = dataset.properties
-
-      # dataset.properties = new_prop
-      # dataset.save!
-    end
-
-    def self.set_data(prop, field, idx, layer_name, field_name, value)
-      return if field['field'] != field_name || value&.empty?
-
-      field['value'] = value
-      prop['layers'][layer_name]['fields'][idx] = field
-      prop
-    end
-
-    def self.update_ds_1h(id, obj, current_user)
-      dataset = obj[:dataset]
-      metadata = obj[:metadata]
-      new_prop = dataset.properties
-      new_prop.dig('layers', 'general', 'fields')&.each_with_index do |fi, idx|
-      #  new_prop = set_data(new_prop, fi, idx, 'general', 'title', metadata['NAME'])
-        if fi['field'] == 'title' && metadata['NAME'].present?
-          ## fi['label'] = fi['label']
-          fi['value'] = metadata['NAME']
-          fi['device'] = metadata['NAME']
-          fi['dkey'] = 'NAME'
-          new_prop['layers']['general']['fields'][idx] = fi
-        end
-
-        if fi['field'] == 'date' && metadata['Date_'].present?
-          ## fi['label'] = fi['label']
-          fi['value'] = metadata['Date_']
-          fi['device'] = metadata['Date_']
-          fi['dkey'] = 'Date_'
-          new_prop['layers']['general']['fields'][idx] = fi
-        end
-
-        if fi['field'] == 'time' && metadata['Time'].present?
-          ## fi['label'] = fi['label']
-          fi['value'] = metadata['Time']
-          fi['device'] = metadata['Time']
-          fi['dkey'] = 'Time'
-          new_prop['layers']['general']['fields'][idx] = fi
-        end
-
-        if fi['field'] == 'creator' && current_user.present?
-          ## fi['label'] = fi['label']
-          fi['value'] = current_user.name
-          new_prop['layers']['general']['fields'][idx] = fi
-        end
-      end
-      element = Container.find(id)&.root_element
-      element.present? && element&.class&.name == 'Sample' && new_prop.dig('layers', 'sample_details', 'fields')&.each_with_index do |fi, idx|
-        if fi['field'] == 'label'
-          fi['value'] = element.short_label
-          new_prop['layers']['sample_details']['fields'][idx] = fi
-        end
-        if fi['field'] == 'id'
-          fi['value'] = element.id
-          new_prop['layers']['sample_details']['fields'][idx] = fi
-        end
-      end
-
-      new_prop.dig('layers', 'instrument', 'fields')&.each_with_index do |fi, idx|
-        if fi['field'] == 'instrument' && metadata['INSTRUM'].present?
-          # fi['label'] = fi['label']
-          fi['value'] = metadata['INSTRUM']
-          fi['device'] = metadata['INSTRUM']
-          fi['dkey'] = 'INSTRUM'
-          new_prop['layers']['instrument']['fields'][idx] = fi
-        end
-      end
-
-
-      new_prop.dig('layers', 'equipment', 'fields')&.each_with_index do |fi, idx|
-        if fi['field'] == 'probehead' && metadata['PROBHD'].present?
-          # fi['label'] = fi['label']
-          fi['value'] = metadata['PROBHD']
-          fi['device'] = metadata['PROBHD']
-          fi['dkey'] = 'PROBHD'
-          new_prop['layers']['equipment']['fields'][idx] = fi
-        end
-      end
-
-      new_prop.dig('layers', 'sample_preparation', 'fields')&.each_with_index do |fi, idx|
-        if fi['field'] == 'solvent' && metadata['SOLVENT'].present?
-          # fi['label'] = fi['label']
-          fi['value'] = metadata['SOLVENT']
-          fi['device'] = metadata['SOLVENT']
-          fi['dkey'] = 'SOLVENT'
-          fi['value'] = 'chloroform-D1 (CDCl3)' if metadata['SOLVENT'] == 'CDCl3'
-          new_prop['layers']['sample_preparation']['fields'][idx] = fi
-        end
-      end
-
-
-      new_prop.dig('layers', 'set', 'fields')&.each_with_index do |fi, idx|
-        if fi['field'] == 'temperature' && metadata['TE'].present?
-          # fi['label'] = fi['label']
-          fi['value'] = metadata['TE'].split(/\s+/).first
-          fi['device'] = metadata['TE']
-          fi['dkey'] = 'TE'
-          fi['value_system'] = metadata['TE'].split(/\s+/).last
-          new_prop['layers']['set']['fields'][idx] = fi
-        end
-        if fi['field'] == 'ns' && metadata['NS'].present?
-          # fi['label'] = fi['label']
-          fi['value'] = metadata['NS']
-          fi['device'] = metadata['NS']
-          fi['dkey'] = 'NS'
-          new_prop['layers']['set']['fields'][idx] = fi
-        end
-        if fi['field'] == 'PULPROG' && metadata['PULPROG'].present?
-          # fi['label'] = fi['label']
-          fi['value'] = metadata['PULPROG']
-          fi['device'] = metadata['PULPROG']
-          fi['dkey'] = 'PULPROG'
-          new_prop['layers']['set']['fields'][idx] = fi
-        end
-        if fi['field'] == 'td' && metadata['TD'].present?
-          # fi['label'] = fi['label']
-          fi['value'] = metadata['TD']
-          fi['device'] = metadata['TD']
-          fi['dkey'] = 'TD'
-          new_prop['layers']['set']['fields'][idx] = fi
-        end
-        if fi['field'] == 'done' && metadata['D1'].present?
-          # fi['label'] = fi['label']
-          fi['value'] = metadata['D1']
-          fi['device'] = metadata['D1']
-          fi['dkey'] = 'D1'
-          new_prop['layers']['set']['fields'][idx] = fi
-        end
-        if fi['field'] == 'sf' && metadata['SF'].present?
-          ## fi['label'] = fi['label']
-          fi['value'] = metadata['SF']
-          fi['device'] = metadata['SF']
-          fi['dkey'] = 'SF'
-          new_prop['layers']['set']['fields'][idx] = fi
-        end
-        if fi['field'] == 'sfoone' && metadata['SFO1'].present?
-          ## fi['label'] = fi['label']
-          fi['value'] = metadata['SFO1']
-          fi['device'] = metadata['SFO1']
-          fi['dkey'] = 'SFO1'
-          new_prop['layers']['set']['fields'][idx] = fi
-        end
-        if fi['field'] == 'sfotwo' && metadata['SFO2'].present?
-          ## fi['label'] = fi['label']
-          fi['value'] = metadata['SFO2']
-          fi['device'] = metadata['SFO2']
-          fi['dkey'] = 'SFO2'
-          new_prop['layers']['set']['fields'][idx] = fi
-        end
-        if fi['field'] == 'nucone' && metadata['NUC1'].present?
-          ## fi['label'] = fi['label']
-          fi['value'] = metadata['NUC1']
-          fi['device'] = metadata['NUC1']
-          fi['dkey'] = 'NUC1'
-          new_prop['layers']['set']['fields'][idx] = fi
-        end
-        if fi['field'] == 'nuctwo' && metadata['NUC2'].present?
-          ## fi['label'] = fi['label']
-          fi['value'] = metadata['NUC2']
-          fi['device'] = metadata['NUC2']
-          fi['dkey'] = 'NUC2'
-          new_prop['layers']['set']['fields'][idx] = fi
-        end
-      end
-      dataset.properties = new_prop
-      dataset.save!
-    end
-
-
-    def self.ts(method, identifier, params = nil)
-      Rails.cache.send(method, "#{Labimotion::NmrMapper.new.class.name}#{identifier}", params)end
-
-    def self.clean(id)
-      Labimotion::NmrMapper.ts('delete', id)
-    end
-
-    def self.build_ds(id, content)
-      ds = Container.find_by(id: id)
-      return if ds.nil? || content.nil?
-
-      ols = content[:ols]
-      metadata = content[:metadata]
-
-      return if ols.nil? || metadata.nil?
-
-      klass = Labimotion::DatasetKlass.find_by(ols_term_id: ols)
-      return if klass.nil?
-
-      uuid = SecureRandom.uuid
-      props = klass.properties_release
-      props['uuid'] = uuid
-      props['pkg'] = Labimotion::Utils.pkg(props['pkg'])
-      props['klass'] = 'Dataset'
-      dataset = Labimotion::Dataset.create!(
-        uuid: uuid,
-        dataset_klass_id: klass.id,
-        element_type: 'Container',
-        element_id: ds.id,
-        properties: props,
-        properties_release: klass.properties_release,
-        klass_uuid: klass.uuid
-      )
-      { dataset: dataset, metadata: metadata, ols: ols }
-    end
-  end
-end