labimotion 2.2.0.rc18 → 2.2.0.rc20

checksums.yaml

@@ -1,7 +1,7 @@
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+  data.tar.gz: b3a45b638d8d2cf2e44cdd97ec0b4306af12f3abc25e44c414b1f49783b38f5e
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data/lib/labimotion/apis/generic_element_api.rb

@@ -432,6 +432,7 @@ module Labimotion
       desc 'Return serialized elements of current user'
       params do
         optional :collection_id, type: Integer, desc: 'Collection id'
+        optional :sync_collection_id, type: Integer, desc: 'SyncCollectionsUser id'
         optional :el_type, type: String, desc: 'element klass name'
         optional :from_date, type: Integer, desc: 'created_date from in ms'
         optional :to_date, type: Integer, desc: 'created_date to in ms'

data/lib/labimotion/helpers/element_helpers.rb

@@ -215,7 +215,7 @@ module Labimotion
         layer, field = params[:sort_column].split('.')
 
         element_klass = Labimotion::ElementKlass.find_by(name: params[:el_type])
-        allowed_fields = element_klass&.properties_release&.dig(Labimotion::Prop::LAYERS, layer, Labimotion::Prop::FIELDS)&.pluck('field') || []
+        allowed_fields = element_klass.properties_release.dig(Labimotion::Prop::LAYERS, layer, Labimotion::Prop::FIELDS)&.pluck('field') || []
 
         if field.in?(allowed_fields)
           query = ActiveRecord::Base.sanitize_sql(
@@ -247,21 +247,27 @@ module Labimotion
     end
 
     def list_serialized_elements(params, current_user)
-      scope = Labimotion::Element.none
-
+      collection_id =
       if params[:collection_id]
-        begin
-          collection = Collection.accessible_for(current_user).find(params[:collection_id])
-          scope = collection.elements
-                            .joins(:element_klass)
-                            .where(element_klasses: { name: params[:el_type] })
-                            .includes(:tag)
-        rescue ActiveRecord::RecordNotFound
-          Labimotion::Element.none
-        end
+        Collection
+          .belongs_to_or_shared_by(current_user.id, current_user.group_ids)
+          .find_by(id: params[:collection_id])&.id
+      elsif params[:sync_collection_id]
+        current_user
+          .all_sync_in_collections_users
+          .find_by(id: params[:sync_collection_id])&.collection&.id
+      end
+
+      scope =
+      if collection_id
+        Labimotion::Element
+          .joins(:element_klass, :collections_elements)
+          .where(
+            element_klasses: { name: params[:el_type] },
+            collections_elements: { collection_id: collection_id },
+          ).includes(:tag, collections: :sync_collections_users)
       else
-        # All collection of current_user
-        scope = Labimotion::Element.for_user(current_user.id)
+        Labimotion::Element.none
       end
 
       ## TO DO: refactor labimotion
@@ -272,7 +278,7 @@ module Labimotion
         layer, field = params[:sort_column].split('.')
 
         element_klass = Labimotion::ElementKlass.find_by(name: params[:el_type])
-        allowed_fields = element_klass&.properties_release&.dig(Labimotion::Prop::LAYERS, layer, Labimotion::Prop::FIELDS)&.pluck('field') || []
+        allowed_fields = element_klass.properties_release.dig(Labimotion::Prop::LAYERS, layer, Labimotion::Prop::FIELDS)&.pluck('field') || []
 
         if field.in?(allowed_fields)
           query = ActiveRecord::Base.sanitize_sql(

data/lib/labimotion/libs/data/datacite/labimotion_template.html.erb

@@ -0,0 +1,55 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<resource xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://datacite.org/schema/kernel-4" xsi:schemaLocation="http://datacite.org/schema/kernel-4 https://schema.datacite.org/meta/kernel-4/metadata.xsd">
+  <identifier identifierType="DOI">https://dx.doi.org/<%= full_doi %></identifier>
+  <creators>
+    <% if creators.empty? %>
+    <creator>
+      <creatorName>(:unav)</creatorName>
+    </creator>
+    <% end %>
+    <% creators.each do |creator| %>
+    <creator>
+      <creatorName nameType="Personal"><%= creator['familyName'] %>, <%= creator['givenName'] %></creatorName>
+      <givenName><%= creator['givenName'] %></givenName>
+      <familyName><%= creator['familyName'] %></familyName>
+      <% if creator['orcid'].present? %>
+      <nameIdentifier schemeURI="https://orcid.org/" nameIdentifierScheme="ORCID"><%= creator['orcid'] %></nameIdentifier>
+      <% end %>
+      <% if creator['affiliation'].present? %>
+      <affiliation><%= creator['affiliation'] %></affiliation>
+      <% end %>
+    </creator>
+    <% end %>
+  </creators>
+  <titles>
+    <title xml:lang="en-US"><%= title %></title>
+  </titles>
+  <%= render_publisher(publisher_config) %>
+  <publicationYear><%= publication_year %></publicationYear>
+  <subjects>
+    <subject>Chemistry</subject>
+  </subjects>
+  <% if contributor %>
+  <contributors>
+    <contributor contributorType="Researcher">
+      <contributorName nameType="Personal"><%= contributor['familyName'] %>, <%= contributor['givenName'] %></contributorName>
+      <givenName><%= contributor['givenName'] %></givenName>
+      <familyName><%= contributor['familyName'] %></familyName>
+      <% if contributor['orcid'].present? %>
+      <nameIdentifier schemeURI="https://orcid.org/" nameIdentifierScheme="ORCID"><%= contributor['orcid'] %></nameIdentifier>
+      <% end %>
+    </contributor>
+  </contributors>
+  <% end %>
+  <language>en</language>
+  <resourceType resourceTypeGeneral="Model"><%= resource_label %></resourceType>
+  <version><%= version %></version>
+  <rightsList>
+    <rights><%= license %></rights>
+  </rightsList>
+  <descriptions>
+    <% if description.present? %>
+    <description xml:lang="en-US" descriptionType="Abstract"><%= description %></description>
+    <% end %>
+  </descriptions>
+</resource>

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

@@ -26,9 +26,9 @@ module Labimotion
           joins(collections: :user).where(collections: { user_id: user_id })
         )
 
-        # Shared records
+        # Shared (synced) records
         shared = apply_filters.call(
-          left_joins(:collection_shares).where(collection_shares: { shared_with_id: user_id })
+          joins(collections: :sync_collections_users).where(sync_collections_users: { user_id: user_id })
         )
 
         # Combine (remove duplicates), order, and limit

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

@@ -0,0 +1,113 @@
+# frozen_string_literal: true
+
+# TemplateDoi concern
+#
+# LabIMotion template DOI logic for the host's Doi model. The host owns the DOI
+# record and the generic DataCite plumbing (build_suffix/align_suffix, the MDS
+# client, the DataCitePublisher concern); this adds only the LabIMotion-specific
+# class methods that the gem's template DOI usecases and APIs call on ::Doi.
+#
+# The host wires it up with a single line:
+#   class Doi < ApplicationRecord
+#     include Labimotion::TemplateDoi
+#   end
+#
+# Assumes the host `dois` table has a jsonb `metadata` column (the DOI version
+# is stamped there) and that the deterministic suffix survives Doi#align_suffix
+# unchanged (reserve sets inchikey == suffix and version_count: 0 for that).
+module Labimotion
+  module TemplateDoi
+    extend ActiveSupport::Concern
+
+    # Literal namespace shared by every LabIMotion template DOI suffix.
+    LABIMOTION_DOI_NAMESPACE = 'labimotion'
+
+    # ActiveSupport::Concern extends this into the including class, so every
+    # method below becomes a class method on the host's Doi.
+    module ClassMethods
+      # Deterministic DOI suffix for a LabIMotion template klass. The same suffix
+      # is used at reserve and at release time, so both share one DOI:
+      #   element -> labimotion/element/<name>/<identifier>/<doi_version>
+      #   segment -> labimotion/segment/<element>/<identifier>/<doi_version>
+      #   dataset -> labimotion/dataset/<ols_term_id>/<identifier>/<doi_version>
+      # `<identifier>` is the first UUID group (8 hex chars) of the template's
+      # identifier/uuid, falling back to the record id. `<doi_version>` is the DOI
+      # version (see .labimotion_version_segment). Callers may pass an explicit
+      # template version; otherwise the record's current version is used.
+      def build_labimotion_suffix(record, version = nil)
+        parts = labimotion_suffix_parts(record)
+        raise ArgumentError, "unsupported template: #{record.class}" if parts.nil?
+
+        segment = labimotion_version_segment(record, version)
+        return nil if segment.blank?
+
+        segments = parts.map { |part| sanitize_doi_part(part) }.reject(&:empty?)
+        "#{segments.join('/')}/#{segment}"
+      end
+
+      # The DOI version segment for a template version. A DOI is published per major
+      # release: the .0 release opens that version (X.0 -> "X") and later minor
+      # revisions roll into the NEXT DOI (X.y, y>=1 -> "X+1"). Sub-1.0 and
+      # unversioned/blank templates map to the first DOI (v1).
+      #   0.x -> "1"   1.0 -> "1"   1.1..2.0 -> "2"   2.1..3.0 -> "3"
+      def labimotion_version_segment(record, version = nil)
+        raw = (version.presence || record.try(:version)).to_s.strip
+        parts = raw.split('.')
+        major = parts[0].to_i
+        minor = parts[1].to_i
+        return '1' if major.zero?
+        return major.to_s if minor.zero?
+
+        (major + 1).to_s
+      end
+
+      # The DOIs reserved for a LabIMotion template, in reservation order.
+      def labimotion_dois(record)
+        where(doiable_id: record.id, doiable_type: record.class.name).order(:id).to_a
+      end
+
+      # The current (most recently reserved) DOI for a template, or nil.
+      def labimotion_latest_doi(record)
+        labimotion_dois(record).last
+      end
+
+      # The DOI version (next-major integer) recorded on a reserved template DOI.
+      def labimotion_doi_version(doi)
+        doi.metadata.to_h.dig('labimotion', 'doi_version')
+      end
+
+      # Metadata stamped on a reserved template DOI so the version it represents
+      # survives on the record (used to gate reserving the next version).
+      def labimotion_doi_metadata(record, version = nil)
+        { 'labimotion' => { 'doi_version' => labimotion_version_segment(record, version) } }
+      end
+
+      def labimotion_suffix_parts(record)
+        # identifier/uuid may both be blank for a draft, which would collapse the
+        # scope (colliding across templates). Fall back to the stable record id so
+        # every template gets a unique, deterministic suffix. Resolved lazily so an
+        # unsupported record (no #id) still falls through to the ArgumentError in the
+        # caller. The identifier is shortened to its first UUID group (8 hex chars).
+        # A segment's <element> is the name of the ElementKlass it belongs to.
+        identifier = lambda do
+          raw = record.try(:identifier).presence || record.try(:uuid).presence || record.id
+          raw.to_s.split('-').first
+        end
+        case record
+        when ::Labimotion::ElementKlass
+          [LABIMOTION_DOI_NAMESPACE, 'element', record.name, identifier.call]
+        when ::Labimotion::SegmentKlass
+          [LABIMOTION_DOI_NAMESPACE, 'segment', record.element_klass&.name, identifier.call]
+        when ::Labimotion::DatasetKlass
+          [LABIMOTION_DOI_NAMESPACE, 'dataset', record.ols_term_id, identifier.call]
+        end
+      end
+
+      # Keeps a suffix segment DOI-safe: trims, collapses whitespace to hyphens and
+      # drops anything outside [A-Za-z0-9._-] (colons stripped, as elsewhere here).
+      def sanitize_doi_part(value)
+        value.to_s.strip.gsub(/\s+/, '-').gsub(/[^A-Za-z0-9._-]/, '')
+      end
+    end
+  end
+end

data/lib/labimotion/models/element.rb

@@ -141,9 +141,9 @@ module Labimotion
         joins(collections: :user).where(collections: { user_id: user_id })
       )
 
-      # Shared elements
+      # Shared (synced) elements
       shared = apply_filters.call(
-        left_joins(:collection_shares).where(collection_shares: { shared_with_id: user_id })
+        joins(collections: :sync_collections_users).where(sync_collections_users: { user_id: user_id })
       )
 
       # Combine (remove duplicates), order, and limit

data/lib/labimotion/usecases/build_template_doi_xml.rb

@@ -11,7 +11,11 @@ module Labimotion
   class BuildTemplateDoiXml
     include ::DataCitePublisher
 
-    TEMPLATE_PATH = Rails.root.join('app/publish/datacite_metadata_labimotion_template.html.erb')
+    # The template ships with the gem. A host app may still override it by
+    # placing its own copy at HOST_TEMPLATE_PATH, which is how it used to be
+    # sourced — hence the lookup order below.
+    GEM_TEMPLATE_PATH = File.expand_path('../libs/data/datacite/labimotion_template.html.erb', __dir__)
+    HOST_TEMPLATE_PATH = 'app/publish/datacite_metadata_labimotion_template.html.erb'
 
     RESOURCE_LABEL = {
       'element' => 'LabIMotion Element Template',
@@ -29,11 +33,19 @@ module Labimotion
     def call
       return nil if @doi.nil?
 
-      ERB.new(File.read(TEMPLATE_PATH), trim_mode: '-').result(binding)
+      ERB.new(File.read(template_path), trim_mode: '-').result(binding)
     end
 
     private
 
+    # Resolved per call rather than at load time, so the class no longer needs
+    # Rails to be booted just to be autoloaded.
+    def template_path
+      # `Rails.root` is still nil if Rails is loaded but the app has not booted.
+      host = defined?(Rails) && Rails.respond_to?(:root) ? Rails.root&.join(HOST_TEMPLATE_PATH) : nil
+      host && File.exist?(host) ? host : GEM_TEMPLATE_PATH
+    end
+
     def full_doi
       @doi.full_doi
     end

data/lib/labimotion/utils/search.rb

@@ -12,7 +12,7 @@ module Labimotion
     end
 
     def self.elements_search(params, current_user, c_id, dl)
-      collection = Collection.accessible_for(current_user).find(c_id)
+      collection = Collection.belongs_to_or_shared_by(current_user.id, current_user.group_ids).find(c_id)
       element_scope = Labimotion::Element.joins(:collections_elements).where('collections_elements.collection_id = ?', collection.id).joins(:element_klass).where('element_klasses.id = elements.element_klass_id AND element_klasses.name = ?', params[:selection][:genericElName])
       element_scope = element_scope.where('elements.name like (?)', "%#{params[:selection][:searchName]}%") if params[:selection][:searchName].present?
       element_scope = element_scope.where('elements.short_label like (?)', "%#{params[:selection][:searchShowLabel]}%") if params[:selection][:searchShowLabel].present?
@@ -97,7 +97,7 @@ module Labimotion
     def self.samples_search(c_id = @c_id)
       sqls = []
       sps = params[:selection][:searchProperties]
-      collection = Collection.accessible_for(current_user).find(c_id)
+      collection = Collection.belongs_to_or_shared_by(current_user.id, current_user.group_ids).find(c_id)
       element_scope = Sample.joins(:collections_samples).where('collections_samples.collection_id = ?', collection.id)
       return element_scope if sps.empty?
 

data/lib/labimotion/version.rb

@@ -2,5 +2,5 @@
 
 ## Labimotion Version
 module Labimotion
-  VERSION = '2.2.0.rc18'
+  VERSION = '2.2.0.rc20'
 end

data/lib/labimotion.rb

@@ -148,4 +148,5 @@ module Labimotion
   autoload :Datasetable, 'labimotion/models/concerns/datasetable'
   autoload :AttachmentConverter, 'labimotion/models/concerns/attachment_converter'
   autoload :LinkedProperties, 'labimotion/models/concerns/linked_properties'
+  autoload :TemplateDoi, 'labimotion/models/concerns/template_doi'
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: labimotion
 version: !ruby/object:Gem::Version
-  version: 2.2.0.rc18
+  version: 2.2.0.rc20
 platform: ruby
 authors:
 - Chia-Lin Lin
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2026-07-01 00:00:00.000000000 Z
+date: 2026-07-27 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: caxlsx
@@ -111,6 +111,7 @@ files:
 - lib/labimotion/helpers/vocabulary_helpers.rb
 - lib/labimotion/libs/attachment_handler.rb
 - lib/labimotion/libs/converter.rb
+- lib/labimotion/libs/data/datacite/labimotion_template.html.erb
 - lib/labimotion/libs/data/mapper/Chemwiki.json
 - lib/labimotion/libs/data/mapper/Source.json
 - lib/labimotion/libs/data/vocab/Standard.json
@@ -136,6 +137,7 @@ files:
 - lib/labimotion/models/concerns/linked_properties.rb
 - lib/labimotion/models/concerns/metadata_validation.rb
 - lib/labimotion/models/concerns/segmentable.rb
+- lib/labimotion/models/concerns/template_doi.rb
 - lib/labimotion/models/concerns/workflow.rb
 - lib/labimotion/models/dataset.rb
 - lib/labimotion/models/dataset_klass.rb