labimotion 2.0.0 → 2.1.0.rc11

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/data/mapper/Chemwiki.json

@@ -197,7 +197,7 @@
         "type": "string"
       },
       "redox": {
-        "title": "Redox-Potential",
+        "title": "Redox potential",
         "param": 6,
         "type": "spc"
       },
@@ -233,4 +233,4 @@
       }
     }
   }
-}
+}

data/lib/labimotion/libs/dataset_builder.rb

@@ -29,7 +29,8 @@ module Labimotion
     end
 
     def self.find_dataset_klass(ols_term_id)
-      Labimotion::DatasetKlass.find_by(ols_term_id: ols_term_id)
+      result = Labimotion::TemplateMatcher.find_best_match(ols_term_id)
+      result[:template]
     end
 
     def self.create_dataset(container, klass)

data/lib/labimotion/libs/export_element.rb

@@ -1,4 +1,5 @@
 # frozen_string_literal: true
+require 'ostruct'
 require 'export_table'
 require 'labimotion/version'
 require 'labimotion/utils/units'
@@ -35,6 +36,13 @@ module Labimotion
       Labimotion.log_exception(e)
     end
 
+    def sample_url
+      protocol = Rails.env.production? ? 'https' : 'http'
+      host = ENV['PUBLIC_URL'] || 'localhost:3000'
+      api = 'mydb/collection/all/sample'
+      "#{protocol}://#{host}/#{api}"
+    end
+
     def build_layers
       objs = []
       @properties[Labimotion::Prop::LAYERS]&.keys&.sort_by do |key|
@@ -182,7 +190,8 @@ module Labimotion
         name = val['el_name'].present? ? "Name: [#{val['el_name']}] \n" : ''
         ext = val['el_external_label'].present? ? "Ext. Label: [#{val['el_external_label']}] \n" : ''
         mass = val['el_molecular_weight'].present? ? "Mass: [#{val['el_molecular_weight']}] \n" : ''
-        "#{label}#{name}#{ext}#{mass}"
+        url = val['el_id'].present? ? "#{sample_url}/#{val['el_id']}" : ''
+        "#{label}#{name}#{ext}#{mass}#{url}"
       when Labimotion::FieldType::DRAG_MOLECULE
         val = sub_val[sub_field['id']]['value'] || {}
         smile = val['el_smiles'].present? ? "SMILES: [#{val['el_smiles']}] \n" : ''
@@ -193,7 +202,7 @@ module Labimotion
       when Labimotion::FieldType::SELECT
         sub_val[sub_field['id']]['value']
       when Labimotion::FieldType::SYSTEM_DEFINED
-        unit = Labimotion::Units::FIELDS.find { |o| o[:field] == sub_field['option_layers'] }&.fetch(:units, [])&.find { |u| u[:key] == sub_field['value_system'] }&.fetch(:label, '')
+        unit = Labimotion::Units::FIELDS.find { |o| o[:field] == sub_field['option_layers'] }&.fetch(:units, [])&.find { |u| u[:key] == sub_val[sub_field['id']]['value_system'] }&.fetch(:label, '')
         val = sub_val[sub_field['id']]['value'].to_s + ' ' + unit
         val = Sablon.content(:html, "<div>" + val + "</div>") if val.include? '<'
         val

data/lib/labimotion/libs/nmr_mapper.rb

@@ -4,6 +4,7 @@ require 'labimotion/libs/dataset_builder'
 require 'labimotion/version'
 require 'labimotion/utils/mapper_utils'
 require 'labimotion/utils/utils'
+require 'labimotion/helpers/converter_helpers'
 
 module Labimotion
   ## NmrMapper
@@ -61,6 +62,7 @@ module Labimotion
 
       def update_ds(_cid, obj, current_user, element)
         dataset = obj[:dataset]
+        process_general_description(obj, current_user, element)
         dataset.properties = process_prop(obj, current_user, element)
         dataset.save!
       end
@@ -106,6 +108,17 @@ module Labimotion
         new_prop
       end
 
+      def process_general_description(obj, current_user, element)
+        container = obj[:dataset]&.element
+        return unless container.present?
+
+        dt = obj[:metadata]&.dig('DATE')
+        date = Labimotion::MapperUtils.format_timestamp(dt, 'date') if dt.present?
+        time = Labimotion::MapperUtils.format_timestamp(dt, 'time') if dt.present?
+
+        Labimotion::ConverterHelpers.update_general_description(container, current_user, date: date, time: time)
+      end
+
       def process_prop(obj, current_user, element)
         new_prop = obj[:dataset].properties
         new_prop

data/lib/labimotion/libs/properties_handler.rb

@@ -8,9 +8,9 @@ module Labimotion
       def check_val(field, type)
         case type
         when Labimotion::FieldType::DRAG_SAMPLE, Labimotion::FieldType::DRAG_ELEMENT
-          return field.dig('value', 'el_id').present?
+          return field['value'].is_a?(Hash) && field.dig('value', 'el_id').present?
         when Labimotion::FieldType::UPLOAD
-          return field.dig('value', 'files')&.length&.positive?
+          return field['value'].is_a?(Hash) && field.dig('value', 'files')&.length&.positive?
         when Labimotion::FieldType::TABLE
           return field[Labimotion::Prop::SUBFIELDS]&.length&.positive? && field['sub_values']&.length&.positive?
         end
@@ -91,5 +91,15 @@ module Labimotion
       Labimotion.log_exception(e)
       properties
     end
+
+    # Update field with value
+    def self.update_field_value!(properties, layer_key, field_index, value)
+      properties[Labimotion::Prop::LAYERS][layer_key][Labimotion::Prop::FIELDS][field_index]['value'] = value
+    end
+
+    # Delete field key
+    def self.delete_field_key!(properties, layer_key, field_index, key)
+      properties[Labimotion::Prop::LAYERS][layer_key][Labimotion::Prop::FIELDS][field_index].delete(key)
+    end
   end
 end

data/lib/labimotion/libs/sample_association.rb

@@ -79,6 +79,7 @@ module Labimotion
         field_samples.each do |field|
           idx = properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS].index(field)
           return if field.is_a?(String) || properties.is_a?(String)
+          next unless field['value'].is_a?(Hash)
 
           sid = field.dig('value', 'el_id')
           next if sid.blank?
@@ -102,7 +103,8 @@ module Labimotion
         field_elements = layer[Labimotion::Prop::FIELDS].select { |ss| ss['type'] == Labimotion::FieldType::DRAG_ELEMENT }
         field_elements.each do |field|
           idx = properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS].index(field)
-          next if field['value'].is_a?(String)
+          return if field.is_a?(String) || properties.is_a?(String)
+          next unless field['value'].is_a?(Hash)
 
           sid = field.dig('value', 'el_id')
           next if element.nil? || sid.blank? || sid == element.id
@@ -113,11 +115,12 @@ module Labimotion
           Labimotion::ElementsElement.find_or_create_by(parent_id: element.id, element_id: el.id)
           els << el.id
         end
-
       end
       if element.present?
-        es_list = Labimotion::ElementsSample.where(element_id: element.id).where.not(sample_id: sds)
-        ee_list = Labimotion::ElementsElement.where(parent_id: element.id).where.not(element_id: els&.flatten)
+        sds = sds.flatten.uniq
+        els = els.flatten.uniq
+        es_list = sds.present? ? Labimotion::ElementsSample.where(element_id: element.id).where.not(sample_id: sds) : Labimotion::ElementsSample.where(element_id: element.id)
+        ee_list = els.present? ? Labimotion::ElementsElement.where(parent_id: element.id).where.not(element_id: els) : Labimotion::ElementsElement.where(parent_id: element.id)
         es_list.destroy_all if es_list.present?
         ee_list.destroy_all if ee_list.present?
       end

data/lib/labimotion/libs/template_matcher.rb

@@ -0,0 +1,39 @@
+# frozen_string_literal: true
+
+module Labimotion
+  class TemplateMatcher
+    def self.find_best_match(ols_term_id)
+      return { template: nil, match_type: nil, info_messages: [] } if ols_term_id.blank?
+
+      info_messages = []
+
+      # Step 1: Find "assigned" mode templates
+      assigned = Labimotion::DatasetKlass.find_assigned_templates(ols_term_id)
+      if assigned.any?
+        handle_multiple_results(assigned, :assigned, info_messages)
+        return { template: assigned.first, match_type: 'assigned', info_messages: info_messages }
+      end
+
+      # Step 2: Find exact match template
+      exact = Labimotion::DatasetKlass.find_by(ols_term_id: ols_term_id)
+      return { template: exact, match_type: 'exact', info_messages: info_messages } if exact
+
+      # Step 3: Find "inferred" mode templates
+      info_messages << 'Using parent template'
+      inferred = Labimotion::DatasetKlass.find_inferred_templates(ols_term_id)
+      if inferred.any?
+        handle_multiple_results(inferred, :inferred, info_messages)
+        return { template: inferred.first, match_type: 'inferred', info_messages: info_messages }
+      end
+
+      { template: nil, match_type: nil, info_messages: info_messages }
+    end
+
+    def self.handle_multiple_results(templates, mode, info_messages)
+      return unless templates.size > 1
+
+      ols_ids = templates.map(&:ols_term_id).join(', ')
+      info_messages << "Multiple #{mode} templates found, ols_term_id(s) are #{ols_ids}"
+    end
+  end
+end

data/lib/labimotion/libs/vocabulary_handler.rb

@@ -4,8 +4,10 @@ module Labimotion
   class VocabularyHandler
     class << self
       def update_vocabularies(properties, current_user, element)
+        return properties if properties.nil? || !properties.is_a?(Hash) || properties[Labimotion::Prop::LAYERS].nil?
+
         properties[Labimotion::Prop::LAYERS].each do |key, layer|
-          update_layer_vocabularies(layer, key, properties, current_user, element)
+          update_layer_vocabularies!(layer, key, properties, current_user, element)
         end
         properties
       rescue StandardError => e
@@ -23,12 +25,12 @@ module Labimotion
 
       private
 
-      def update_layer_vocabularies(layer, key, properties, current_user, element)
+      def update_layer_vocabularies!(layer, key, properties, current_user, element)
         field_vocabularies = layer[Labimotion::Prop::FIELDS].select { |field| field['is_voc'] }
         field_vocabularies.each do |field|
           idx = layer[Labimotion::Prop::FIELDS].index(field)
           val = get_vocabulary_value(field, current_user, element)
-          update_field_value(properties, key, idx, val) if val.present?
+          update_field_value!(properties, key, idx, val)
         end
       end
 
@@ -44,6 +46,7 @@ module Labimotion
           get_segment_value(field, element)
         when 'Dataset'
           # TODO: Implement Dataset logic here
+          # TODO: Update datasetable.save_dataset
           nil
         end
       end
@@ -91,9 +94,8 @@ module Labimotion
         fields.find { |ss| ss['field'] == field['field_id'] }&.dig('value')
       end
 
-      def update_field_value(properties, key, idx, val)
-        properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS][idx]['value'] = val
-        properties
+      def update_field_value!(properties, key, idx, val)
+        Labimotion::PropertiesHandler.update_field_value!(properties, key, idx, val)
       end
 
       def load_from_files