labimotion 2.2.0.rc15 → 2.2.0.rc17

checksums.yaml

@@ -1,7 +1,7 @@
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+  data.tar.gz: df0c4bca0642d4d29cd9844088a7a2bd656fb240c1e573e63a366bd26a3bff36
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+  metadata.gz: 2b1522bf995bf6d7ecc88b5f80d2c4c24bed210501cd328a79e91d07bdeda984c51aca9259f5f70b80588f6b43e19b8eb090634071b6c2ae8fd2f08481099fe2
+  data.tar.gz: df75a698a49478ae259c64bbfc854ad855ad8ed3fe096225a5bcd4a0390ebca6f04b0ccb82122d58f689d675b4b5d07dcaa3d107d35ba1ae6a3f9e9b81c6ad10

data/lib/labimotion/apis/labimotion_api.rb

@@ -17,5 +17,6 @@ module Labimotion
     mount Labimotion::ElementVariationAPI
     mount Labimotion::LabimotionDoiAPI
     mount Labimotion::LabimotionTemplateBrowseAPI
+    mount Labimotion::WellplateAPI
   end
 end

data/lib/labimotion/apis/wellplate_api.rb

@@ -0,0 +1,60 @@
+# frozen_string_literal: true
+
+module Labimotion
+  # API for wellplates linked to a generic element
+  class WellplateAPI < Grape::API
+    resource :wellplates do
+      namespace :by_generic_element do
+        desc 'Get wellplates for a generic element'
+        params do
+          requires :element_id, type: Integer, desc: 'Generic element id'
+        end
+        route_param :element_id do
+          get do
+            element = Labimotion::Element.find_by(id: params[:element_id])
+            error!('404 Not Found', 404) unless element
+            error!('401 Unauthorized', 401) unless ElementPolicy.new(current_user, element).read?
+
+            wellplate_ids = Labimotion::ElementsWellplate.where(element_id: element.id).pluck(:wellplate_id)
+            wellplates = Wellplate.where(id: wellplate_ids)
+                                  .includes(:wells, wells: :sample)
+
+            serialized_wellplates = wellplates.map do |wellplate|
+              detail_levels = ElementDetailLevelCalculator.new(user: current_user, element: wellplate).detail_levels
+              Entities::WellplateEntity.represent(wellplate, detail_levels: detail_levels)
+            end
+
+            { wellplates: serialized_wellplates }
+          end
+
+          desc 'Update wellplates for a generic element'
+          params do
+            requires :wellplate_ids, type: Array, desc: 'Wellplate IDs'
+          end
+          put do
+            element = Labimotion::Element.find_by(id: params[:element_id])
+            error!('404 Not Found', 404) unless element
+            error!('401 Unauthorized', 401) unless ElementPolicy.new(current_user, element).update?
+
+            ActiveRecord::Base.transaction do
+              current_ids = Labimotion::ElementsWellplate.where(element_id: element.id).pluck(:wellplate_id)
+              new_ids = params[:wellplate_ids] || []
+
+              ids_to_remove = current_ids - new_ids
+              if ids_to_remove.any?
+                Labimotion::ElementsWellplate.where(element_id: element.id, wellplate_id: ids_to_remove).destroy_all
+              end
+
+              ids_to_add = new_ids - current_ids
+              ids_to_add.each do |wellplate_id|
+                Labimotion::ElementsWellplate.create!(element_id: element.id, wellplate_id: wellplate_id)
+              end
+            end
+
+            { wellplate_ids: Labimotion::ElementsWellplate.where(element_id: element.id).pluck(:wellplate_id) }
+          end
+        end
+      end
+    end
+  end
+end

data/lib/labimotion/libs/data/mapper/Source.json

@@ -9,7 +9,6 @@
       "file": "acqus",
       "parameters": [
         "DATE",
-        "D1",
         "INSTRUM",
         "NS",
         "NUC1",
@@ -23,7 +22,10 @@
         "TD",
         "TE",
         "TITLE"
-      ]
+      ],
+      "arrayParameters": {
+        "D1": { "name": "D", "index": 1 }
+      }
     },
     "procs": {
       "file": "pdata/1/procs",

data/lib/labimotion/models/elements_wellplate.rb

@@ -0,0 +1,10 @@
+# frozen_string_literal: true
+
+module Labimotion
+  class ElementsWellplate < ApplicationRecord
+    acts_as_paranoid
+    self.table_name = :elements_wellplates
+    belongs_to :element, class_name: 'Labimotion::Element'
+    belongs_to :wellplate
+  end
+end

data/lib/labimotion/utils/mapper_utils.rb

@@ -70,6 +70,37 @@ module Labimotion
         extracted_parameters
       end
 
+      # Extracts scalar values from Bruker array parameters such as
+      #   ##$D= (0..63)
+      #   0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.0002 ...
+      # where the values live on the line(s) following the header. The config maps
+      # each output key to an array name + index, e.g.
+      #   { "D1" => { "name" => "D", "index" => 1 } } => D1 = the 2nd value (here 1).
+      def extract_array_parameters(file_content, array_parameters)
+        return {} if file_content.blank? || array_parameters.blank?
+
+        lines = file_content.lines
+        extracted = {}
+        lines.each_with_index do |line, idx|
+          header = line.match(/^\s*##\$(?<name>[A-Za-z0-9_]+)\s*=\s*\(\s*\d+\s*\.\.\s*\d+\s*\)/)
+          next unless header
+
+          targets = array_parameters.select { |_key, cfg| cfg['name'] == header[:name] }
+          next if targets.empty?
+
+          values = collect_array_values(lines, idx + 1)
+          targets.each do |out_key, cfg|
+            value = values[cfg['index'].to_i]
+            extracted[out_key] = clean_value(value) if value.present?
+          end
+        end
+        extracted.compact_blank!
+        extracted
+      rescue StandardError => e
+        Rails.logger.error "Error extracting array parameters: #{e.message}"
+        {}
+      end
+
       def format_timestamp(timestamp_str, give_format = nil)
         return nil if timestamp_str.blank?
 
@@ -118,6 +149,21 @@ module Labimotion
         value
       end
 
+      # Collects whitespace-separated values from the line(s) following an array
+      # header, stopping at the next directive (line starting with '##') or a blank line.
+      def collect_array_values(lines, start_index)
+        values = []
+        index = start_index
+        while index < lines.length
+          stripped = lines[index].strip
+          break if stripped.empty? || stripped.start_with?('##')
+
+          values.concat(stripped.split(/\s+/))
+          index += 1
+        end
+        values
+      end
+
       def process_zip_file(zip_file_url, source_map)
         final_parameters = {}
 
@@ -137,23 +183,28 @@ module Labimotion
 
         zip_file.each do |entry|
           if source_file?(entry, source_config)
-            process_file_entry(entry, source_config['parameters'], final_parameters)
+            process_file_entry(entry, source_config, final_parameters)
           elsif bagit_metadata_file?(entry)
             return { is_bagit: true, metadata: nil }
           end
         end
       end
 
-      def process_file_entry(entry, parameters, final_parameters)
+      def process_file_entry(entry, source_config, final_parameters)
         file_content = entry.get_input_stream.read.force_encoding(Constants::File::ENCODING)
-        extracted_parameters = extract_parameters(file_content, parameters)
+        extracted_parameters = extract_parameters(file_content, source_config['parameters'])
         final_parameters.merge!(extracted_parameters) if extracted_parameters.present?
+
+        # Array parameters (e.g. D1 from acqus ##$D) are a fallback: they only fill a
+        # value that an earlier/higher-priority source (e.g. parm.txt D1) did not provide.
+        array_parameters = extract_array_parameters(file_content, source_config['arrayParameters'])
+        final_parameters.reverse_merge!(array_parameters) if array_parameters.present?
       end
 
       def invalid_source_config?(source_config)
         source_config.nil? ||
           source_config['file'].nil? ||
-          source_config['parameters'].nil?
+          (source_config['parameters'].nil? && source_config['arrayParameters'].nil?)
       end
 
       def source_file?(entry, source_config)

data/lib/labimotion/version.rb

@@ -2,5 +2,5 @@
 
 ## Labimotion Version
 module Labimotion
-  VERSION = '2.2.0.rc15'
+  VERSION = '2.2.0.rc17'
 end

data/lib/labimotion.rb

@@ -32,6 +32,7 @@ module Labimotion
   autoload :ElementVariationAPI, 'labimotion/apis/element_variation_api'
   autoload :LabimotionDoiAPI, 'labimotion/apis/labimotion_doi_api'
   autoload :LabimotionTemplateBrowseAPI, 'labimotion/apis/labimotion_template_browse_api'
+  autoload :WellplateAPI, 'labimotion/apis/wellplate_api'
 
   ######## Entities
   autoload :PropertiesEntity, 'labimotion/entities/properties_entity'
@@ -123,6 +124,7 @@ module Labimotion
 
   autoload :ElementsSample, 'labimotion/models/elements_sample'
   autoload :ElementsElement, 'labimotion/models/elements_element'
+  autoload :ElementsWellplate, 'labimotion/models/elements_wellplate'
   autoload :CollectionsElement, 'labimotion/models/collections_element'
 
   autoload :StdLayer, 'labimotion/models/std_layer'

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: labimotion
 version: !ruby/object:Gem::Version
-  version: 2.2.0.rc15
+  version: 2.2.0.rc17
 platform: ruby
 authors:
 - Chia-Lin Lin
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2026-06-23 00:00:00.000000000 Z
+date: 2026-06-30 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: caxlsx
@@ -73,6 +73,7 @@ files:
 - lib/labimotion/apis/standard_layer_api.rb
 - lib/labimotion/apis/user_api.rb
 - lib/labimotion/apis/vocabulary_api.rb
+- lib/labimotion/apis/wellplate_api.rb
 - lib/labimotion/collection/export.rb
 - lib/labimotion/collection/import.rb
 - lib/labimotion/conf.rb
@@ -150,6 +151,7 @@ files:
 - lib/labimotion/models/elements_element.rb
 - lib/labimotion/models/elements_revision.rb
 - lib/labimotion/models/elements_sample.rb
+- lib/labimotion/models/elements_wellplate.rb
 - lib/labimotion/models/hub_log.rb
 - lib/labimotion/models/reaction.rb
 - lib/labimotion/models/research_plan.rb