labimotion 2.3.2 → 2.3.3

checksums.yaml

@@ -1,7 +1,7 @@
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data/CHANGELOG.md

@@ -8,6 +8,7 @@
   * `number`, `integer` and `system-defined` columns accept numbers only. A cell holding anything else is cleared with a warning rather than stored as text, which also cleans up text those columns already hold.
   * Import warnings name the cell they came from (`Cell I6: ...`), so the user can go straight to it in the spreadsheet.
 * Bug fixes:
+  * New records and element Reload build from the release's metadata (labimotion#326, port of labimotion#321 and labimotion#324, [chem-generic-ui#1438](https://github.com/cllde8/chem-generic-ui/issues/1438), port of [chem-generic-ui#1430](https://github.com/cllde8/chem-generic-ui/issues/1430)). A klass's `metadata` follows every save, drafts included, so a new element, segment or dataset, and an element brought up to the release by Reload, combined the released layers with the draft's layer groups and restrictions. Klass payloads now carry `metadata_release`: the metadata of the klass's active release, read from its revision row, or `null` when no revision matches the klass's uuid. Sent by `generic_elements/klass`, `segments/list_segment_klass` (nested element klasses included), `generic_dataset/klasses`, and on the nested `element_klass` of the element `GET`, create and update responses, with one revision query per klass family; every other payload is unchanged. A client reading `metadata_release ?? metadata` builds from one version. Read-only: no migration.
   * A copied element, segment or dataset keeps the template release its properties were built on (labimotion#301, labimotion#303). Saves used to stamp every new segment and every dataset save with the klass's current `uuid` and `properties_release`, and an element with whatever the client sent, so a copy of a v1.0.0 record was labelled v2.0.0 and the client never offered Reload. `Labimotion::KlassVersion` now resolves the submitted `properties['klass_uuid']` against the klass's current release and its `*_klasses_revisions`, deleted revisions included, and stores that uuid together with the matching `properties_release`. A new record whose uuid is missing or unknown follows the current release; an existing record keeps its stored uuid when none is sent, then the uuid its stored `properties_release` names, and follows the current release only when it has neither, and a uuid this instance never released (a record imported from an instance with its own release history) keeps the release stored with the record. A new element whose properties carry no uuid follows the template the client built it on; a new segment does the same, and a copied one falls back to the `klass_uuid` of the row it was copied from. The collection import stamps the release the archive names instead of the importing instance's current one: it tries the uuid inside the archived `properties_release`, then `properties['klass_uuid']`, then the `klass_uuid` column, and stores the first one this instance knows with the local release; when none resolves, the archived release keeps the uuid it names (or, naming none, the first uuid the archive carries), and the imported properties carry the same `klass_uuid` as the column. A `klass_uuid` that is not a string is ignored, and a dataset whose klass changed follows the new klass and ignores the client's release. Element create returns 404 when the template is missing or deleted, element update resolves a soft-deleted template (`with_deleted`) before writing anything, and segments and datasets of a deleted template are skipped on save. A new record whose `klass_uuid` this instance cannot resolve keeps it with the `properties_release` the client sent, only when that release names the same uuid. No migration and no client change.
   * `fetch_for_user`: the shared-records branch joined `collection_shares` directly on the element model (an association that only exists on `Collection`), raising `ActiveRecord::ConfigurationError` — rescued into empty search results. Now joins through `collections`. Fixed for both the basic elements (`ElementFetchable`) and the generic element (`Labimotion::Element`), so `search_by_like` and `search_basic_by_like` return shared records again.
 * Dependencies:

data/lib/labimotion/apis/generic_dataset_api.rb

@@ -13,7 +13,9 @@ module Labimotion
         desc 'get dataset klasses'
         get do
           list = klass_list(true, false)
-          present list.sort_by(&:place), with: Labimotion::DatasetKlassEntity, root: 'klass'
+          # New datasets are built from these klasses, so they need the release's metadata.
+          present list.sort_by(&:place), with: Labimotion::DatasetKlassEntity, root: 'klass',
+                                         metadata_releases: Labimotion::ReleaseMetadata.map_for(list)
         end
       end
 

data/lib/labimotion/apis/generic_element_api.rb

@@ -39,7 +39,9 @@ module Labimotion
         end
         get do
           ek = Labimotion::ElementKlass.find_by(name: params[:name])
-          present ek, with: Labimotion::ElementKlassEntity, root: 'klass'
+          # The ELN builds a new element from this klass, so it needs the release's metadata.
+          present ek, with: Labimotion::ElementKlassEntity, root: 'klass',
+                      metadata_releases: Labimotion::ReleaseMetadata.map_for([ek])
         rescue StandardError => e
           Labimotion.log_exception(e, current_user)
           { klass: [] }
@@ -474,7 +476,10 @@ module Labimotion
             element: Labimotion::ElementEntity.represent(
               element,
               detail_levels: ElementDetailLevelCalculator.new(user: current_user, element: element).detail_levels,
-              policy: @element_policy
+              policy: @element_policy,
+              # Reload brings the record up to the release, so it needs the release's metadata,
+              # not the latest save's.
+              metadata_releases: Labimotion::ReleaseMetadata.map_for([element.element_klass])
             ),
             attachments: Entities::AttachmentEntity.represent(element&.attachments)
           }
@@ -495,6 +500,7 @@ module Labimotion
             with: Labimotion::ElementEntity,
             root: :element,
             detail_levels: ElementDetailLevelCalculator.new(user: current_user, element: element).detail_levels,
+            metadata_releases: Labimotion::ReleaseMetadata.map_for([element.element_klass])
           )
         rescue StandardError => e
           Labimotion.log_exception(e, current_user)
@@ -518,6 +524,7 @@ module Labimotion
               element: Labimotion::ElementEntity.represent(
                 element,
                 detail_levels: ElementDetailLevelCalculator.new(user: current_user, element: element).detail_levels,
+                metadata_releases: Labimotion::ReleaseMetadata.map_for([element.element_klass])
               ),
               attachments: Entities::AttachmentEntity.represent(element&.attachments),
             }

data/lib/labimotion/apis/segment_api.rb

@@ -26,7 +26,11 @@ module Labimotion
         end
         get do
           list = klass_list(nil, params[:is_active], false)
-          present list, with: Labimotion::SegmentKlassEntity, root: 'klass', displayed_in_list: false
+          # New segments are built from these klasses. The nested element klasses read the same
+          # map, since they are serialized with the same options.
+          metadata_releases = Labimotion::ReleaseMetadata.map_for(list.to_a + list.map(&:element_klass))
+          present list, with: Labimotion::SegmentKlassEntity, root: 'klass', displayed_in_list: false,
+                        metadata_releases: metadata_releases
         end
       end
 

data/lib/labimotion/constants.rb

@@ -32,7 +32,7 @@ module Labimotion
     module Tpa
       # Segments and layers sent along with reaction variations to a third-party
       # app (see ExportTpaSegments), as segment-klass label => layer keys.
-      SEGMENT_LAYERS = { 'Mol interactions' => %w[binding_props bind_partners].freeze }.freeze
+      SEGMENT_LAYERS = { 'Mol interactions' => %w[general binding_props bind_partners].freeze }.freeze
     end
   end
 end

data/lib/labimotion/entities/generic_klass_entity.rb

@@ -10,5 +10,16 @@ module Labimotion
     expose :properties_release, **DISPLAYED_IN_LIST_CONDITION, anonymize_with: {}
     expose :metadata, **DISPLAYED_IN_LIST_CONDITION, anonymize_with: {}
     expose_timestamps(timestamp_fields: %i[released_at created_at updated_at sync_time])
+
+    # The klass's own `metadata` follows every save, drafts included, so a client building a
+    # record from `properties_release` reads this instead: the metadata that release was cut
+    # with, or nil when no revision matches the klass's uuid (never released, or imported
+    # without one). Exposed only where the endpoint preloaded the map, so no other payload pays
+    # a revision query per row.
+    expose :metadata_release, **DISPLAYED_IN_LIST_CONDITION, if: :metadata_releases
+
+    def metadata_release
+      options[:metadata_releases][Labimotion::ReleaseMetadata.key_of(object)]
+    end
   end
 end

data/lib/labimotion/libs/release_metadata.rb

@@ -0,0 +1,56 @@
+# frozen_string_literal: true
+
+# `underscore`, `constantize` and `index_by` are ActiveSupport core extensions, not plain
+# Ruby. A booted host always has them; declaring them here keeps this file from depending on
+# load order.
+require 'active_support/core_ext/enumerable'
+require 'active_support/core_ext/string/inflections'
+
+module Labimotion
+  ## ReleaseMetadata
+  # Builds the `metadata_releases:` option the klass entities read: each klass's metadata as
+  # of its active release. The klass row's own `metadata` follows every save, drafts included,
+  # so a client building a record from `properties_release` needs the copy kept on the revision.
+  # The active revision is the one whose uuid equals the klass's, which changes only on release.
+  class ReleaseMetadata
+    # A klass with no revision matching its uuid (never released, or imported without one)
+    # is left out of the map, and the entity reads it as nil.
+    def self.map_for(klasses)
+      Array(klasses).compact.group_by(&:class).each_with_object({}) do |(model, group), map|
+        map.merge!(map_for_family(model, group))
+      end
+    end
+
+    # Family as well as id: a segment klass payload nests its element klass, and ids repeat
+    # across the klass tables.
+    def self.key_of(klass)
+      "#{klass.class.name.split('::').last}:#{klass.id}"
+    end
+
+    def self.map_for_family(model, klasses)
+      by_pair = klasses.reject { |klass| klass.uuid.nil? }.index_by { |klass| [klass.id, klass.uuid] }
+      return {} if by_pair.empty?
+
+      revisions_for(model, by_pair.keys).each_with_object({}) do |(klass_id, uuid, metadata), map|
+        # The IN lists cross-match: a revision of one listed klass can carry the uuid of
+        # another. Only the exact pair is that klass's active release.
+        klass = by_pair[[klass_id, uuid]]
+        map[key_of(klass)] = metadata unless klass.nil?
+      end
+    rescue StandardError => e
+      # The release metadata is an addition to a list that must still render, and a failing
+      # family must not blank the families that resolved.
+      Labimotion.log_exception(e)
+      {}
+    end
+
+    # The revision model and its foreign key are named after the klass model.
+    def self.revisions_for(model, pairs)
+      foreign_key = "#{model.name.underscore.split('/').last}_id"
+      "#{model.name}esRevision".constantize
+                               .where(foreign_key => pairs.map(&:first), uuid: pairs.map(&:last))
+                               .pluck(foreign_key, :uuid, :metadata)
+    end
+    private_class_method :map_for_family, :revisions_for
+  end
+end

data/lib/labimotion/version.rb

@@ -2,5 +2,5 @@
 
 ## Labimotion Version
 module Labimotion
-  VERSION = '2.3.2'
+  VERSION = '2.3.3'
 end

data/lib/labimotion.rb

@@ -95,6 +95,7 @@ module Labimotion
   autoload :SampleAssociation, 'labimotion/libs/sample_association'
   autoload :PropertiesHandler, 'labimotion/libs/properties_handler'
   autoload :KlassVersion, 'labimotion/libs/klass_version'
+  autoload :ReleaseMetadata, 'labimotion/libs/release_metadata'
   autoload :AttachmentHandler, 'labimotion/libs/attachment_handler'
   autoload :VocabularyHandler, 'labimotion/libs/vocabulary_handler'
   autoload :XlsxExporter, 'labimotion/libs/xlsx_exporter'

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: labimotion
 version: !ruby/object:Gem::Version
-  version: 2.3.2
+  version: 2.3.3
 platform: ruby
 authors:
 - Chia-Lin Lin
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2026-10-02 00:00:00.000000000 Z
+date: 2026-10-19 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: caxlsx
@@ -140,6 +140,7 @@ files:
 - lib/labimotion/libs/klass_version.rb
 - lib/labimotion/libs/nmr_mapper.rb
 - lib/labimotion/libs/properties_handler.rb
+- lib/labimotion/libs/release_metadata.rb
 - lib/labimotion/libs/sample_association.rb
 - lib/labimotion/libs/template_hub.rb
 - lib/labimotion/libs/template_matcher.rb