labimotion 2.1.2 → 2.2.0.rc1

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 2be4b8936c18a5560a7aed2c4ca7ad3ea6f3fc17245b7442e3658255a0e84494
-  data.tar.gz: 88f5beed8cea656e69f5e9ba13aaa3acbe92dddce489a131e5238b09ca63cc87
+  metadata.gz: 4397eed28e8f2c6f0e21e022191d842dbb7a42000a2efe72731a89ab8bf9e77b
+  data.tar.gz: 3ae429541da0f787d6d0f544307b5acfbf3e922d83c7fc7cd27e47738eb5880e
 SHA512:
-  metadata.gz: 98cfc7e3e0f672a3371a6fc523fd58de260e2cde2e83696be0976ad44c2efc79ebdf60fd414969b996cfa09f7d4f2c384168fd04503f0713c6ccdf4f5905da87
-  data.tar.gz: 22052eb592542f2e8a43368b6c08dac67e301352234f968ffc175a12d6af66133857876884b85ee1f35e449a4edcae3e37ff39c0233673f73323f9c7a39b8812
+  metadata.gz: 12a5d77d600daaf1a45640ab5ff7d253a608cd683fac28a5286019a7990e85cb7c1f0c957240fab625d3dbb703196dcb918b652bcc86457c6ac88cc085990ea0
+  data.tar.gz: 28453642570e3e177c0c2684590cdb715016c4043645d9f2e097eca0a4f41e9e3ff30564df8a0b7d5800bfb36a2fd224aa40cb91a107a2bc53adddc1db133070

data/lib/labimotion/apis/generic_element_api.rb

@@ -474,7 +474,7 @@ module Labimotion
               detail_levels: ElementDetailLevelCalculator.new(user: current_user, element: element).detail_levels,
               policy: @element_policy
             ),
-            attachments: Entities::AttachmentEntity.represent(element&.attachments)
+            attachments: attach_thumbnail(element&.attachments)
           }
         rescue StandardError => e
           Labimotion.log_exception(e, current_user)
@@ -517,7 +517,7 @@ module Labimotion
                 element,
                 detail_levels: ElementDetailLevelCalculator.new(user: current_user, element: element).detail_levels,
               ),
-              attachments: Entities::AttachmentEntity.represent(element&.attachments),
+              attachments: attach_thumbnail(element&.attachments),
             }
           rescue StandardError => e
             Labimotion.log_exception(e, current_user)

data/lib/labimotion/collection/import.rb

@@ -69,7 +69,7 @@ module Labimotion
 
           dataset = Labimotion::Dataset.create!(
             fields.slice(
-              'properties', 'properties_release', 'metadata'
+              'properties', 'properties_release'
             ).merge(
               ## created_by: current_user_id,
               element: element,
@@ -112,7 +112,7 @@ module Labimotion
 
         segment = Labimotion::Segment.create!(
           fields.slice(
-            'properties', 'properties_release', 'metadata'
+            'properties', 'properties_release'
           ).merge(
             created_by: current_user_id,
             element: element,
@@ -149,7 +149,7 @@ module Labimotion
 
         element = Labimotion::Element.create!(
           fields.slice(
-            'name', 'properties', 'properties_release', 'metadata'
+            'name', 'properties', 'properties_release'
           ).merge(
             created_by: current_user_id,
             element_klass: element_klass,

data/lib/labimotion/helpers/element_helpers.rb

@@ -82,18 +82,16 @@ module Labimotion
         klass_uuid: klass[:uuid],
         properties: properties,
         properties_release: params[:properties_release],
-        metadata: params[:metadata] || {},
-        created_by: current_user.id
+        created_by: current_user.id,
       }
       element = Labimotion::Element.new(attributes)
 
-      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
+      if params[:collection_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)
@@ -118,8 +116,7 @@ module Labimotion
       params.delete(:user_labels)
       attributes = declared(params.except(:segments), include_missing: false)
       properties['pkg'] = Labimotion::Utils.pkg(properties['pkg'])
-      metadata = params[:metadata] || element.metadata || {}
-      if element.klass_uuid != properties['klass_uuid'] || element.properties != properties || element.name != params[:name] || element.metadata != metadata
+      if element.klass_uuid != properties['klass_uuid'] || element.properties != properties || element.name != params[:name]
         properties['klass'] = 'Element'
         uuid = SecureRandom.uuid
         properties['uuid'] = uuid
@@ -131,7 +128,6 @@ module Labimotion
         attributes['properties']['uuid'] = uuid
         attributes['uuid'] = uuid
         attributes['klass_uuid'] = properties['klass_uuid']
-        attributes['metadata'] = metadata
         attributes['updated_at'] = Time.current
         element.update_columns(attributes)
       end

data/lib/labimotion/helpers/param_helpers.rb

@@ -13,7 +13,6 @@ module Labimotion
       optional :desc, type: String, desc: 'Klass desc'
       optional :klass_prefix, type: String, desc: 'Klass klass_prefix'
       optional :icon_name, type: String, desc: 'Klass icon_name'
-      optional :metadata, type: Hash, desc: 'Klass metadata'
       requires :properties_template, type: Hash, desc: 'Klass template'
       optional :properties_release, type: Hash, desc: 'Klass release'
       optional :released_at, type: DateTime, desc: 'Klass released_at'
@@ -30,7 +29,6 @@ module Labimotion
       requires :klass_prefix, type: String, desc: 'Element Klass Short Label Prefix'
       optional :icon_name, type: String, desc: 'Element Klass Icon Name'
       optional :desc, type: String, desc: 'Element Klass Desc'
-      optional :metadata, type: Hash, desc: 'Element Klass metadata'
       optional :properties_template, type: Hash, desc: 'Element Klass properties template'
     end
 
@@ -71,7 +69,6 @@ module Labimotion
     params :upload_segment_klass_params do
       requires :label, type: String, desc: 'Klass label'
       optional :desc, type: String, desc: 'Klass desc'
-      optional :metadata, type: Hash, desc: 'Klass metadata'
       requires :properties_template, type: Hash, desc: 'Klass template'
       optional :properties_release, type: Hash, desc: 'Klass release'
       optional :released_at, type: DateTime, desc: 'Klass released_at'
@@ -98,7 +95,6 @@ module Labimotion
       requires :element_klass, type: Integer, desc: 'Element Klass Id'
       optional :desc, type: String, desc: 'Segment Klass Desc'
       optional :place, type: String, desc: 'Segment Klass Place', default: '100'
-      optional :metadata, type: Hash, desc: 'Klass metadata'
       optional :properties_template, type: Hash, desc: 'Element Klass properties template'
     end
 

data/lib/labimotion/libs/converter.rb

@@ -6,7 +6,6 @@ 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
@@ -21,36 +20,27 @@ module Labimotion
     end
 
     def self.process_ds(id, current_user = {})
-      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)
+      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'
 
-      # 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?
+      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?
       att.update_column(:con_state, Labimotion::ConState::COMPLETED)
-      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
     end
-    private_class_method :map_ds
 
     def self.uri(api_name)
       url = Rails.configuration.converter.url
@@ -109,7 +99,7 @@ module Labimotion
       zip_file.each do |entry|
         next unless entry.name == 'metadata/converter.json'
 
-        metadata = Labimotion::MapperUtils.read_entry(entry).force_encoding('UTF-8')
+        metadata = entry.get_input_stream.read.force_encoding('UTF-8')
         jdata = JSON.parse(metadata)
 
         ols = jdata['ols']
@@ -174,9 +164,8 @@ module Labimotion
           )
         end
         if response.ok?
-          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
+          Labimotion::Converter.handle_response(data[:a], response, current_user)
+          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
@@ -233,8 +222,7 @@ module Labimotion
         element_id: cds.id,
         properties: props,
         properties_release: klass.properties_release,
-        klass_uuid: klass.uuid,
-        metadata: klass.metadata
+        klass_uuid: klass.uuid
       )
     end
 

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

@@ -0,0 +1,212 @@
+{
+  "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": {
+  }
+}

data/lib/labimotion/libs/dataset_builder.rb

@@ -44,8 +44,7 @@ module Labimotion
         element_id: container.id,
         properties: props,
         properties_release: klass.properties_release,
-        klass_uuid: klass.uuid,
-        metadata: klass.metadata
+        klass_uuid: klass.uuid
       )
     end
 

data/lib/labimotion/libs/nmr_mapper.rb

@@ -30,21 +30,7 @@ module Labimotion
 
     class << self
       def process_ds(id, current_user = {})
-        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)
+        att = find_attachment(id)
         return Labimotion::ConState::NONE if att.nil?
 
         result = process(att)
@@ -146,20 +132,6 @@ 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)
@@ -173,8 +145,7 @@ module Labimotion
       def handle_bagit_result(att, id, current_user)
         att.update_column(:con_state, Labimotion::ConState::CONVERTED)
         Labimotion::Converter.metadata(id, current_user)
-        # Return the state Converter.metadata stored; CONVERTED means still waiting for an analysis dataset
-        Attachment.find_by(id: id)&.con_state || Labimotion::ConState::NONE
+        Labimotion::ConState::COMPLETED
       end
 
       def invalid_metadata?(result)

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

@@ -1,7 +1,5 @@
 # frozen_string_literal: true
 
-require 'zip'
-
 module Labimotion
   module AttachmentConverter
     ACCEPTED_FORMATS = (Rails.configuration.try(:converter).try(:ext) || []).freeze
@@ -29,8 +27,6 @@ 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
@@ -43,26 +39,6 @@ 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/models/concerns/datasetable.rb

@@ -29,7 +29,6 @@ module Labimotion
         properties: ods.properties,
         properties_release: ods.properties_release,
         klass_uuid: ods.klass_uuid,
-        metadata: ods.metadata || {}
       )
     end
 
@@ -50,8 +49,8 @@ module Labimotion
       props = Labimotion::VocabularyHandler.update_vocabularies(props, dataset_args[:current_user], dataset_args[:element])
 
       ds = Labimotion::Dataset.find_by(element_type: self.class.name, element_id: id)
-      if ds.present? && (ds.klass_uuid != klass.uuid || ds.properties != props || ds.metadata != metadata)
-        ds.update!(properties_release: klass.properties_release, uuid: uuid, dataset_klass_id: dataset_klass_id, properties: props, klass_uuid: klass.uuid, metadata: metadata)
+      if ds.present? && (ds.klass_uuid != klass.uuid || ds.properties != props)
+        ds.update!(properties_release: klass.properties_release, uuid: uuid, dataset_klass_id: dataset_klass_id, properties: props, klass_uuid: klass.uuid)
       end
       return if ds.present?
 

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

@@ -9,6 +9,7 @@ module Labimotion
       before_save :check_identifier
     end
 
+
     def check_identifier
       self.identifier = identifier || SecureRandom.uuid if self.has_attribute?(:identifier)
     end
@@ -33,7 +34,7 @@ module Labimotion
         properties_release: properties_release,
         released_at: DateTime.now,
         updated_by: current_user&.id,
-        released_by: current_user&.id
+        released_by: current_user&.id,
       }
 
       self.update!(klass_attributes)
@@ -45,7 +46,7 @@ module Labimotion
         created_by: updated_by,
         properties_release: properties_release,
         released_at: released_at,
-        metadata: metadata || {}
+        metadata: metadata
       }
       attributes["#{self.class.name.underscore.split('/').last}_id"] = id
       "#{self.class.name}esRevision".constantize.create(attributes)

data/lib/labimotion/utils/mapper_utils.rb

@@ -6,18 +6,8 @@ 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
@@ -47,8 +37,13 @@ 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)
@@ -126,12 +121,10 @@ module Labimotion
       def process_zip_file(zip_file_url, source_map)
         final_parameters = {}
 
-        # 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)
+        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
         end
 
         return { is_bagit: false, metadata: final_parameters } if final_parameters.present?
@@ -143,8 +136,6 @@ 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)
@@ -154,7 +145,7 @@ module Labimotion
       end
 
       def process_file_entry(entry, parameters, final_parameters)
-        file_content = read_entry(entry).force_encoding(Constants::File::ENCODING)
+        file_content = entry.get_input_stream.read.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 = '2.1.2'
+  VERSION = '2.2.0.rc1'
 end

data/lib/labimotion.rb

@@ -13,11 +13,6 @@ 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: 2.1.2
+  version: 2.2.0.rc1
 platform: ruby
 authors:
 - Chia-Lin Lin
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2026-10-01 00:00:00.000000000 Z
+date: 2025-12-25 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: caxlsx
@@ -98,6 +98,7 @@ 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
@@ -182,9 +183,9 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '3.4'
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
-  - - ">="
+  - - ">"
     - !ruby/object:Gem::Version
-      version: '0'
+      version: 1.3.1
 requirements: []
 rubygems_version: 3.1.6
 signing_key: