labimotion 2.1.0 → 2.1.2

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 0b97ee960a48914097f872e1b421ada368d5bdee1bb6b05e7f14a36248955020
-  data.tar.gz: 5dc30139a5c87ed6cd8a86f3f9c583f3973eceb7cb5fd01ac2c245630815c425
+  metadata.gz: 2be4b8936c18a5560a7aed2c4ca7ad3ea6f3fc17245b7442e3658255a0e84494
+  data.tar.gz: 88f5beed8cea656e69f5e9ba13aaa3acbe92dddce489a131e5238b09ca63cc87
 SHA512:
-  metadata.gz: abfbd09a8bcab8d5cfc47dea6c6ee098cbd0b54985d16d888f63a5ee2ba6f53673e4a105af59576d689c5b58cefbdde36a1c7649fa760dd4178a999df4975858
-  data.tar.gz: af957c39d2675b38d01a0c14c018c49b584c15f6b1785d76f36ca5c2833c408e82e396a88e82bb59d625069ac0dc267b24d91b16f2c8c4ab97de5bc6d77fd77b
+  metadata.gz: 98cfc7e3e0f672a3371a6fc523fd58de260e2cde2e83696be0976ad44c2efc79ebdf60fd414969b996cfa09f7d4f2c384168fd04503f0713c6ccdf4f5905da87
+  data.tar.gz: 22052eb592542f2e8a43368b6c08dac67e301352234f968ffc175a12d6af66133857876884b85ee1f35e449a4edcae3e37ff39c0233673f73323f9c7a39b8812

data/lib/labimotion/helpers/element_helpers.rb

@@ -87,12 +87,13 @@ module Labimotion
       }
       element = Labimotion::Element.new(attributes)
 
-      if params[:collection_id]
+      all_coll = Collection.get_all_collection_for_user(current_user.id)
+      element.collections << all_coll
+
+      if params[:collection_id] && params[:collection_id] != all_coll.id
         collection = current_user.collections.find(params[:collection_id])
         element.collections << collection
       end
-      all_coll = Collection.get_all_collection_for_user(current_user.id)
-      element.collections << all_coll
       element.save!
       element.properties = update_sample_association(params[:properties], current_user, element)
       # element.properties = update_vocabularies(_properties, current_user, element)

data/lib/labimotion/libs/converter.rb

@@ -6,6 +6,7 @@ require 'json'
 require 'date'
 require 'labimotion/version'
 require 'labimotion/utils/utils'
+require 'labimotion/utils/mapper_utils'
 require 'labimotion/helpers/converter_helpers'
 
 # rubocop: disable Metrics/AbcSize
@@ -20,27 +21,36 @@ module Labimotion
     end
 
     def self.process_ds(id, current_user = {})
-      att = Attachment.find_by(id: id, con_state: Labimotion::ConState::CONVERTED)
+      ctx = { att: nil, ols: nil, dsr: [] }
+      # Savepoint: a failure leaves no half-built dataset and keeps the caller's transaction usable
+      Attachment.transaction(requires_new: true) { map_ds(id, current_user, ctx) }
+    rescue StandardError => e
+      Labimotion::Converter.logger.error ["Att ID: #{ctx[:att]&.id}, OLS: #{ctx[:ols]}", "DSR: #{ctx[:dsr]}", e.message, *e.backtrace].join($INPUT_RECORD_SEPARATOR)
+      Labimotion.report_exception(e)
+      # Terminal state: do not fail the request, and do not retry on the next save
+      ctx[:att]&.update_column(:con_state, Labimotion::ConState::ERROR)
+      Labimotion::ConState::ERROR
+    end
+
+    def self.map_ds(id, current_user, ctx)
+      att = ctx[:att] = Attachment.find_by(id: id, con_state: Labimotion::ConState::CONVERTED)
       return if att.nil? || att.attachable_id.nil? || att.attachable_type != 'Container' || att.filename.split('.')&.last != 'zip'
 
       eln_ds = Container.find_by(id: att.attachable_id, container_type: 'dataset')
       return if eln_ds.nil? || eln_ds.parent.nil? || eln_ds.parent&.container_type != 'analysis'
 
-      dsr = []
-      ols = nil
-      Zip::File.open(att.attachment_attacher.file.url) do |zip_file|
-        res = Labimotion::Converter.collect_metadata(zip_file, current_user) 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)
-      update_ds(dataset, dsr, current_user) if dataset.present?
+      # Never close: closing can rewrite the stored file in place
+      zip_file = Zip::File.new(att.attachment_attacher.file.url)
+      res = Labimotion::Converter.collect_metadata(zip_file, current_user)
+      ctx[:ols] = res[:o] unless res&.dig(:o).nil?
+      ctx[:dsr].push(res[:d]) unless res&.dig(:d).nil?
+      ctx[:dsr].flatten!
+      dataset = build_ds(att.attachable_id, ctx[:ols])
+      update_ds(dataset, ctx[: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
+      Labimotion::ConState::COMPLETED
     end
+    private_class_method :map_ds
 
     def self.uri(api_name)
       url = Rails.configuration.converter.url
@@ -99,7 +109,7 @@ module Labimotion
       zip_file.each do |entry|
         next unless entry.name == 'metadata/converter.json'
 
-        metadata = entry.get_input_stream.read.force_encoding('UTF-8')
+        metadata = Labimotion::MapperUtils.read_entry(entry).force_encoding('UTF-8')
         jdata = JSON.parse(metadata)
 
         ols = jdata['ols']
@@ -164,8 +174,9 @@ module Labimotion
           )
         end
         if response.ok?
-          Labimotion::Converter.handle_response(data[:a], response, current_user)
-          Labimotion::ConState::PROCESSED
+          state = Labimotion::Converter.handle_response(data[:a], response, current_user)
+          # A failed dataset mapping also marks the source attachment as ERROR
+          state == Labimotion::ConState::ERROR ? state : Labimotion::ConState::PROCESSED
         else
           Labimotion::Converter.logger.error ["Converter Response Error: id: [#{data[:a]&.id}], filename: [#{data[:a]&.filename}], response: #{response}"].join($INPUT_RECORD_SEPARATOR)
           Labimotion::ConState::ERROR

data/lib/labimotion/libs/nmr_mapper.rb

@@ -30,7 +30,21 @@ module Labimotion
 
     class << self
       def process_ds(id, current_user = {})
-        att = find_attachment(id)
+        ctx = { att: nil }
+        # Savepoint: a failure leaves no half-built dataset and keeps the caller's transaction usable
+        Attachment.transaction(requires_new: true) { map_ds(id, current_user, ctx) }
+      rescue StandardError => e
+        Labimotion.log_exception(e, current_user)
+        # Not a readable zip: nothing to map, and not an error
+        return Labimotion::ConState::NONE if invalid_archive?(e, ctx[:att])
+
+        # Terminal state: do not fail the request, and do not retry on the next save
+        Labimotion.report_exception(e)
+        Labimotion::ConState::ERROR
+      end
+
+      def map_ds(id, current_user, ctx)
+        att = ctx[:att] = find_attachment(id)
         return Labimotion::ConState::NONE if att.nil?
 
         result = process(att)
@@ -132,6 +146,20 @@ module Labimotion
         Attachment.find_by(id: id, con_state: Labimotion::ConState::NMR)
       end
 
+      # True when the upload itself is not a readable zip. A missing or changed file, an encrypted zip
+      # or an unsupported compression method is not covered and stays ERROR.
+      def invalid_archive?(error, att)
+        return false unless error.instance_of?(Zip::Error) || error.is_a?(Zip::DecompressionError)
+
+        file = att&.attachment_attacher&.file
+        path = file&.url
+        on_disk = path && File.size?(path)
+        return false if on_disk.nil?
+
+        recorded = file.size
+        recorded.nil? || recorded == on_disk
+      end
+
       def handle_process_result(result, att, id, current_user)
         if result[:is_bagit]
           handle_bagit_result(att, id, current_user)
@@ -145,7 +173,8 @@ module Labimotion
       def handle_bagit_result(att, id, current_user)
         att.update_column(:con_state, Labimotion::ConState::CONVERTED)
         Labimotion::Converter.metadata(id, current_user)
-        Labimotion::ConState::COMPLETED
+        # Return the state Converter.metadata stored; CONVERTED means still waiting for an analysis dataset
+        Attachment.find_by(id: id)&.con_state || Labimotion::ConState::NONE
       end
 
       def invalid_metadata?(result)

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

@@ -1,5 +1,7 @@
 # frozen_string_literal: true
 
+require 'zip'
+
 module Labimotion
   module AttachmentConverter
     ACCEPTED_FORMATS = (Rails.configuration.try(:converter).try(:ext) || []).freeze
@@ -27,6 +29,8 @@ module Labimotion
 
         return if attachable_id.nil? && con_state != Labimotion::ConState::WAIT
 
+        # No attachable_id-changed guard: an attachment created already attached must still be processed.
+        # Each branch leaves its pending state, so the work runs once.
         current_user = User.find_by(id: created_by)
         case con_state
         when Labimotion::ConState::NMR
@@ -39,6 +43,26 @@ module Labimotion
           Labimotion::Converter.metadata(id, current_user)
         end
       end
+
+      # Run the zip mapping again for an attachment in ERROR, e.g. after its file was restored.
+      # Returns the new con_state.
+      def reprocess_converter!
+        return con_state unless has_attribute?(:con_state) && File.extname(filename.to_s.downcase) == '.zip'
+
+        path = attachment_attacher&.file&.url
+        return con_state unless path && File.size?(path)
+
+        self.con_state = converter_output?(path) ? Labimotion::ConState::CONVERTED : Labimotion::ConState::NMR
+        update_column(:con_state, con_state)
+        exec_converter
+        reload.con_state
+      end
+
+      private def converter_output?(path)
+        !Zip::File.new(path).find_entry('metadata/converter.json').nil?
+      rescue Zip::Error
+        false # not a readable zip: the NMR mapper classifies it
+      end
     end
   end
 end

data/lib/labimotion/utils/mapper_utils.rb

@@ -6,8 +6,18 @@ require 'zip'
 require 'labimotion/constants'
 
 module Labimotion
+  # rubyzip 2.x does not detect encrypted entries and would inflate them as garbage
+  class EncryptedZipError < Zip::Error; end
+
   class MapperUtils
     class << self
+      # Read an entry and close its stream, so no handle on the stored file stays open
+      def read_entry(entry)
+        raise EncryptedZipError, "Encrypted zip entry: #{entry.name}" if entry.encrypted?
+
+        entry.get_input_stream(&:read)
+      end
+
       def load_config(config_json)
         JSON.parse(config_json)
       rescue JSON::ParserError => e
@@ -37,13 +47,8 @@ module Labimotion
       def extract_data_from_zip(zip_file_url, source_map)
         return nil if zip_file_url.nil?
 
+        # nil means nothing to map; errors are raised so the caller can record ERROR
         process_zip_file(zip_file_url, source_map)
-      rescue Zip::Error => e
-        Rails.logger.error "Zip file error: #{e.message}"
-        nil
-      rescue StandardError => e
-        Rails.logger.error "Unexpected error extracting metadata: #{e.message}"
-        nil
       end
 
       def extract_parameters(file_content, parameter_names)
@@ -121,10 +126,12 @@ module Labimotion
       def process_zip_file(zip_file_url, source_map)
         final_parameters = {}
 
-        Zip::File.open(zip_file_url) do |zip_file|
-          source_map['sourceSelector'].each do |source_name|
-            process_source(zip_file, source_map[source_name], final_parameters)
-          end
+        # Never close: closing can rewrite the stored file in place
+        zip_file = Zip::File.new(zip_file_url)
+        source_map['sourceSelector'].each do |source_name|
+          result = process_source(zip_file, source_map[source_name], final_parameters)
+          # A BagIt zip is mapped by the converter instead
+          return result if result&.dig(:is_bagit)
         end
 
         return { is_bagit: false, metadata: final_parameters } if final_parameters.present?
@@ -136,6 +143,8 @@ module Labimotion
         return if invalid_source_config?(source_config)
 
         zip_file.each do |entry|
+          next if entry.directory?
+
           if source_file?(entry, source_config)
             process_file_entry(entry, source_config['parameters'], final_parameters)
           elsif bagit_metadata_file?(entry)
@@ -145,7 +154,7 @@ module Labimotion
       end
 
       def process_file_entry(entry, parameters, final_parameters)
-        file_content = entry.get_input_stream.read.force_encoding(Constants::File::ENCODING)
+        file_content = read_entry(entry).force_encoding(Constants::File::ENCODING)
         extracted_parameters = extract_parameters(file_content, parameters)
         final_parameters.merge!(extracted_parameters) if extracted_parameters.present?
       end

data/lib/labimotion/version.rb

@@ -2,5 +2,5 @@
 
 ## Labimotion Version
 module Labimotion
-  VERSION = '2.1.0'
+  VERSION = '2.1.2'
 end

data/lib/labimotion.rb

@@ -13,6 +13,11 @@ module Labimotion
     Labimotion.logger.error(exception.backtrace.join("\n"))
   end
 
+  # Report a rescued exception to Sentry, if the host app uses it
+  def self.report_exception(exception)
+    Sentry.capture_exception(exception) if defined?(Sentry)
+  end
+
   autoload :MapperUtils, 'labimotion/utils/mapper_utils'
   autoload :Utils, 'labimotion/utils/utils'
 

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: labimotion
 version: !ruby/object:Gem::Version
-  version: 2.1.0
+  version: 2.1.2
 platform: ruby
 authors:
 - Chia-Lin Lin
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2026-01-29 00:00:00.000000000 Z
+date: 2026-10-01 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: caxlsx
@@ -98,7 +98,6 @@ files:
 - lib/labimotion/helpers/vocabulary_helpers.rb
 - lib/labimotion/libs/attachment_handler.rb
 - lib/labimotion/libs/converter.rb
-- lib/labimotion/libs/data/layer/StdDataset.json
 - lib/labimotion/libs/data/mapper/Chemwiki.json
 - lib/labimotion/libs/data/mapper/Source.json
 - lib/labimotion/libs/data/vocab/Standard.json

data/lib/labimotion/libs/data/layer/StdDataset.json

@@ -1,212 +0,0 @@
-{
-  "layers": {
-    "std_general": {
-      "wf": false,
-      "key": "std_general",
-      "std": true,
-      "cols": 4,
-      "color": "default",
-      "label": "Standard General description",
-      "style": "panel_generic_heading",
-      "fields": [
-        {
-          "type": "text",
-          "field": "title",
-          "label": "title",
-          "default": "",
-          "ontology": {
-            "id": "afo:class:http://purl.allotrope.org/ontologies/result#AFR_0001080",
-            "iri": "http://purl.allotrope.org/ontologies/result#AFR_0001080",
-            "type": "class",
-            "label": "title",
-            "obo_id": "AFR:0001080",
-            "short_form": "AFR_0001080",
-            "description": [
-              "A title is a prefix or suffix added to a personal name. A title can be a title of honor, that is a title bestowed as an award,  a honorary title (academic), that is a recognition of contributions by a non-employee or employee, a hereditary title, that is a title that remains in a family or a job title, that is a designation of a person's position in an organization. [Wikipedia]"
-            ],
-            "ontology_name": "afo",
-            "ontology_prefix": "AFO"
-          },
-          "position": 1,
-          "required": false,
-          "sub_fields": [],
-          "text_sub_fields": []
-        },
-        {
-          "type": "text",
-          "field": "data_type",
-          "label": "Type of the data ",
-          "default": "",
-          "readonly": true,
-          "position": 2,
-          "required": false,
-          "sub_fields": [],
-          "description": "Ontologies!!!! type of entity",
-          "placeholder": "e.g. sample or reaction analysis",
-          "text_sub_fields": []
-        },
-        {
-          "type": "text",
-          "field": "date",
-          "label": "date",
-          "default": "",
-          "position": 3,
-          "required": false,
-          "sub_fields": [],
-          "text_sub_fields": []
-        },
-        {
-          "type": "text",
-          "field": "time",
-          "label": "starting time",
-          "default": "",
-          "position": 4,
-          "required": false,
-          "sub_fields": [],
-          "text_sub_fields": []
-        },
-        {
-          "type": "text",
-          "field": "contributor",
-          "label": "contributor",
-          "default": "",
-          "position": 5,
-          "required": false,
-          "sub_fields": [],
-          "description": "",
-          "text_sub_fields": []
-        },
-        {
-          "type": "text",
-          "field": "creator",
-          "label": "creator",
-          "default": "",
-          "position": 6,
-          "required": false,
-          "sub_fields": [],
-          "description": "the person who upload the analysis",
-          "text_sub_fields": []
-        },
-        {
-          "type": "text",
-          "field": "operator",
-          "label": "operator",
-          "default": "",
-          "position": 7,
-          "required": false,
-          "sub_fields": [],
-          "text_sub_fields": []
-        },
-        {
-          "type": "text",
-          "field": "comments",
-          "label": "comments",
-          "default": "",
-          "position": 8,
-          "required": false,
-          "sub_fields": [],
-          "text_sub_fields": []
-        },
-        {
-          "opid": 8,
-          "type": "text",
-          "field": "Producer",
-          "label": "Producer of the sample",
-          "is_voc": true,
-          "source": "Segment",
-          "default": "",
-          "field_id": "Producer",
-          "layer_id": "bsi",
-          "ontology": {
-            "id": "schema:property:https://schema.org/producer",
-            "iri": "https://schema.org/producer",
-            "type": "property",
-            "label": "producer",
-            "obo_id": "schema:producer",
-            "short_form": "schema_producer",
-            "description": [
-              "The person or organization who produced the work (e.g. music album, movie, TV/radio series etc.)."
-            ],
-            "ontology_name": "schema",
-            "ontology_prefix": "schema"
-          },
-          "position": 9,
-          "source_id": "dce363d5-56d0-4324-9914-0476be999016",
-          "identifier": "357b7cd3-ca47-49e0-be47-154d907c2cf5",
-          "sub_fields": [],
-          "text_sub_fields": []
-        }
-      ],
-      "position": -2,
-      "condition": "",
-      "wf_position": 0
-    },
-    "std_sample_details": {
-      "wf": false,
-      "key": "std_sample_details",
-      "cols": 3,
-      "std": true,
-      "color": "none",
-      "label": "Standard Sample details",
-      "style": "panel_generic_heading",
-      "fields": [
-        {
-          "type": "text",
-          "field": "label",
-          "label": "label",
-          "default": "",
-          "position": 1,
-          "required": false,
-          "sub_fields": [],
-          "text_sub_fields": []
-        },
-        {
-          "type": "text",
-          "field": "id",
-          "label": "id",
-          "default": "",
-          "position": 2,
-          "required": false,
-          "sub_fields": [],
-          "text_sub_fields": []
-        },
-        {
-          "type": "text",
-          "field": "amount",
-          "label": "amount",
-          "default": "",
-          "position": 3,
-          "required": false,
-          "sub_fields": [],
-          "text_sub_fields": []
-        },
-        {
-          "type": "text",
-          "field": "volume",
-          "label": "volume",
-          "default": "",
-          "position": 4,
-          "required": false,
-          "sub_fields": [],
-          "text_sub_fields": []
-        },
-        {
-          "type": "text",
-          "field": "size",
-          "label": "size",
-          "default": "",
-          "position": 5,
-          "required": false,
-          "sub_fields": [],
-          "text_sub_fields": []
-        }
-      ],
-      "position": -1,
-      "timeRecord": "",
-      "wf_position": 0
-    }
-  },
-  "version": "0.1",
-  "select_options": {
-  }
-}