labimotion 0.2.2 → 1.0.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
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-  data.tar.gz: 118586faba049e9b0db78533e912c1ea1143a27314e4d13395dca19469c9cecd
+  metadata.gz: 387a4b4a47a140008970b10f005472e8ba882c80ddaab99863ced5acdb0dfa29
+  data.tar.gz: 90f5839a92d045e45861a2354354bf5ef1542799a484cda94fa9c1263c206d5e
 SHA512:
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+  metadata.gz: cca4c43074754aefbe3f2b3ca09b55af69d25ebf2a4b7f456990bc692ee7ab19905020aed4505d6360b720d94e497e91ab5910b8c50d4b5b914a01d23e840796
+  data.tar.gz: 5280180e034e2bd2a38000b62e8001ebee247cae2dd29e30f5b66eb3292d11e0e9f0566986c5eb918e6f6dcfc9d95024553204d834da44e7a1aee2b13500d454

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

data/lib/labimotion/helpers/generic_helpers.rb

@@ -46,10 +46,9 @@ module Labimotion
       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?
@@ -189,9 +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(
@@ -201,13 +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/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/version.rb

@@ -2,6 +2,6 @@
 
 module Labimotion
   # VERSION = '0.1.4'
-  VERSION = '0.2.2'
+  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: 0.2.2
+  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