labimotion 2.1.1 → 2.2.0.rc1

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
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-  data.tar.gz: 16f3da4ab02efa4ac7e4bd0848640b35df87e3d5115809543dde0279cb0e43a1
+  metadata.gz: 4397eed28e8f2c6f0e21e022191d842dbb7a42000a2efe72731a89ab8bf9e77b
+  data.tar.gz: 3ae429541da0f787d6d0f544307b5acfbf3e922d83c7fc7cd27e47738eb5880e
 SHA512:
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-  data.tar.gz: 6e4fe1c4dba90988961c704671bc43ed57a310fc0fcf3c410b99e5797de3a6e247e82635ac94edd3d3f271b61091bc83230f57888a94decdc3254de6e73d1d53
+  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

@@ -222,8 +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/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/version.rb

@@ -2,5 +2,5 @@
 
 ## Labimotion Version
 module Labimotion
-  VERSION = '2.1.1'
+  VERSION = '2.2.0.rc1'
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: labimotion
 version: !ruby/object:Gem::Version
-  version: 2.1.1
+  version: 2.2.0.rc1
 platform: ruby
 authors:
 - Chia-Lin Lin
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2026-03-25 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: