labimotion 1.4.1 → 2.0.0.rc2

data/lib/labimotion/libs/data/vocab/Standard.json

@@ -0,0 +1,385 @@
+[
+  {
+      "identifier": "std-atmosphere",
+      "name": "atmosphere",
+      "label": "Atmosphere",
+      "field_type": "text",
+      "ontology": {
+        "id": "ncit:class:http://purl.obolibrary.org/obo/NCIT_C54711",
+        "iri": "http://purl.obolibrary.org/obo/NCIT_C54711",
+        "short_form": "NCIT_C54711",
+        "obo_id": "NCIT:C54711",
+        "label": "Atmosphere",
+        "description": [
+          "Non-SI unit of pressure equal to 101 325 Pa."
+        ],
+        "ontology_name": "ncit",
+        "ontology_prefix": "NCIT",
+        "type": "class"
+      },
+      "source": "Standard"
+  },
+  {
+      "identifier": "std-calibration",
+      "name": "calibration",
+      "label": "Calibration",
+      "field_type": "text",
+      "ontology": {
+        "id": "ncit:class:http://purl.obolibrary.org/obo/NCIT_C69187",
+        "iri": "http://purl.obolibrary.org/obo/NCIT_C69187",
+        "short_form": "NCIT_C69187",
+        "obo_id": "NCIT:C69187",
+        "label": "Calibration",
+        "description": [
+          "The act of checking or adjusting (by comparison with a standard) the accuracy of a measuring instrument."
+        ],
+        "ontology_name": "ncit",
+        "ontology_prefix": "NCIT",
+        "type": "class"
+      },
+      "source": "Standard"
+  },
+  {
+      "identifier": "std-coating",
+      "name": "coating",
+      "label": "Coating",
+      "field_type": "text",
+      "ontology": {
+        "id": "afo:class:http://purl.allotrope.org/ontologies/process#AFP_0001986",
+        "iri": "http://purl.allotrope.org/ontologies/process#AFP_0001986",
+        "short_form": "AFP_0001986",
+        "obo_id": "AFP:0001986",
+        "label": "coating",
+        "description": [
+          "The application of a thin cover to a material. [CHMO]"
+        ],
+        "ontology_name": "afo",
+        "ontology_prefix": "AFO",
+        "type": "class"
+      },
+      "source": "Standard"
+  },
+  {
+      "identifier": "std-coating_material",
+      "name": "coating_material",
+      "label": "Coating Material",
+      "field_type": "text",
+      "ontology": {
+        "id": "ncit:class:http://purl.obolibrary.org/obo/NCIT_C172794",
+        "iri": "http://purl.obolibrary.org/obo/NCIT_C172794",
+        "short_form": "NCIT_C172794",
+        "obo_id": "NCIT:C172794",
+        "label": "Coating Material",
+        "description": [
+          "A layer of material covering the surface of a device."
+        ],
+        "ontology_name": "ncit",
+        "ontology_prefix": "NCIT",
+        "type": "class"
+      },
+      "source": "Standard"
+  },
+  {
+      "identifier": "std-wavelength",
+      "name": "wavelength",
+      "label": "Wavelength",
+      "field_type": "text",
+      "ontology": {
+        "id": "ncit:class:http://purl.obolibrary.org/obo/NCIT_C48158",
+        "iri": "http://purl.obolibrary.org/obo/NCIT_C48158",
+        "short_form": "NCIT_C48158",
+        "obo_id": "NCIT:C48158",
+        "label": "Wavelength",
+        "description": [
+          "The distance (measured in the direction of propagation) between two points in the same phase in consecutive cycles of a wave."
+        ],
+        "ontology_name": "ncit",
+        "ontology_prefix": "NCIT",
+        "type": "class"
+      },
+      "source": "Standard"
+  },
+  {
+      "identifier": "std-sample_size",
+      "name": "sample_size",
+      "label": "Sample Size",
+      "field_type": "text",
+      "ontology": {
+        "id": "ncit:class:http://purl.obolibrary.org/obo/NCIT_C53190",
+        "iri": "http://purl.obolibrary.org/obo/NCIT_C53190",
+        "short_form": "NCIT_C53190",
+        "obo_id": "NCIT:C53190",
+        "label": "Sample Size",
+        "ontology_name": "ncit",
+        "ontology_prefix": "NCIT",
+        "type": "class"
+      },
+      "source": "Standard"
+  },
+  {
+      "identifier": "std-instrument",
+      "name": "instrument",
+      "label": "Instrument",
+      "field_type": "text",
+      "ontology": {
+        "id": "nmrcv:class:http://nmrML.org/nmrCV#NMR:1000463",
+        "iri": "http://nmrML.org/nmrCV#NMR:1000463",
+        "short_form": "NMR:1000463",
+        "label": "instrument",
+        "description": [
+          "Description of the instrument or the mass spectrometer."
+        ],
+        "ontology_name": "nmrcv",
+        "ontology_prefix": "NMRCV",
+        "type": "class"
+      },
+      "source": "Standard"
+  },
+  {
+      "identifier": "std-irr_freq",
+      "name": "irr_freq",
+      "label": "Irradiation frequency",
+      "field_type": "text",
+      "ontology": {
+        "id": "nmrcv:class:http://nmrML.org/nmrCV#NMR:1000463",
+        "iri": "http://nmrML.org/nmrCV#NMR:1000463",
+        "short_form": "NMR:1000463",
+        "label": "instrument",
+        "description": [
+          "Description of the instrument or the mass spectrometer."
+        ],
+        "ontology_name": "nmrcv",
+        "ontology_prefix": "NMRCV",
+        "type": "class"
+      },
+      "source": "Standard"
+  },
+  {
+      "identifier": "std-num_scans",
+      "name": "num_scans",
+      "label": "Number of scans",
+      "field_type": "text",
+      "ontology": {
+        "id": "nmrcv:class:http://nmrML.org/nmrCV#NMR:1400087",
+        "iri": "http://nmrML.org/nmrCV#NMR:1400087",
+        "short_form": "NMR:1400087",
+        "label": "number of scans",
+        "description": [
+          "def: The number of repeat scans performed and summed to create the data set for an NMR sample."
+        ],
+        "ontology_name": "nmrcv",
+        "ontology_prefix": "NMRCV",
+        "type": "class"
+      },
+      "source": "Standard"
+  },
+  {
+      "identifier": "std-sample_ph",
+      "name": "sample_ph",
+      "label": "Sample pH",
+      "field_type": "text",
+      "ontology": {
+        "id": "nmrcv:class:http://nmrML.org/nmrCV#NMR:1000019",
+        "iri": "http://nmrML.org/nmrCV#NMR:1000019",
+        "short_form": "NMR:1000019",
+        "label": "sample pH",
+        "ontology_name": "nmrcv",
+        "ontology_prefix": "NMRCV",
+        "type": "class"
+      },
+      "source": "Standard"
+  },
+  {
+      "identifier": "std-pulse_seq",
+      "name": "pulse_seq",
+      "label": "NMR pulse sequence",
+      "field_type": "text",
+      "ontology": {
+        "id": "nmrcv:class:http://nmrML.org/nmrCV#NMR:1400037",
+        "iri": "http://nmrML.org/nmrCV#NMR:1400037",
+        "short_form": "NMR:1400037",
+        "label": "NMR pulse sequence",
+        "description": [
+          "def: A sequence of excitation pulses.",
+          "http://www.bmrb.wisc.edu/tools/choose_pulse_info.php"
+        ],
+        "ontology_name": "nmrcv",
+        "ontology_prefix": "NMRCV",
+        "type": "class"
+      },
+      "source": "Standard"
+  },
+  {
+      "identifier": "std-sample_conc",
+      "name": "sample_conc",
+      "label": "sample concentration",
+      "field_type": "text",
+      "ontology": {
+        "id": "nmrcv:class:http://nmrML.org/nmrCV#NMR:1000006",
+        "iri": "http://nmrML.org/nmrCV#NMR:1000006",
+        "short_form": "NMR:1000006",
+        "label": "sample concentration",
+        "description": [
+          "Concentration of sample in picomol/ul, femtomol/ul or attomol/ul solution used."
+        ],
+        "ontology_name": "nmrcv",
+        "ontology_prefix": "NMRCV",
+        "type": "class"
+      },
+      "source": "Standard"
+  },
+  {
+      "identifier": "std-scan_range",
+      "name": "scan_range",
+      "label": "scan range",
+      "field_type": "text",
+      "ontology": {
+        "id": "afo:class:http://purl.allotrope.org/ontologies/result#AFR_0001957",
+        "iri": "http://purl.allotrope.org/ontologies/result#AFR_0001957",
+        "short_form": "AFR_0001957",
+        "obo_id": "AFR:0001957",
+        "label": "detector scan rate setting",
+        "description": [
+          "A detector setting that sets the frequency of scans per time unit. [Allotrope]"
+        ],
+        "ontology_name": "afo",
+        "ontology_prefix": "AFO",
+        "type": "class"
+      },
+      "source": "Standard"
+  },
+  {
+      "identifier": "std-software_name",
+      "name": "software_name",
+      "label": "Software Name",
+      "field_type": "text",
+      "ontology": {
+        "id": "ncit:class:http://purl.obolibrary.org/obo/NCIT_C150832",
+        "iri": "http://purl.obolibrary.org/obo/NCIT_C150832",
+        "short_form": "NCIT_C150832",
+        "obo_id": "NCIT:C150832",
+        "label": "Software Name",
+        "description": [
+          "The literal identifier of the software program."
+        ],
+        "ontology_name": "ncit",
+        "ontology_prefix": "NCIT",
+        "type": "class"
+      },
+      "source": "Standard"
+  },
+  {
+      "identifier": "std-software_ver",
+      "name": "software_ver",
+      "label": "Software Version",
+      "field_type": "text",
+      "ontology": {
+        "id": "ncit:class:http://purl.obolibrary.org/obo/NCIT_C111093",
+        "iri": "http://purl.obolibrary.org/obo/NCIT_C111093",
+        "short_form": "NCIT_C111093",
+        "obo_id": "NCIT:C111093",
+        "label": "Software Version",
+        "description": [
+          "A form or variant of software; one of a sequence of copies of a software program, each incorporating new modifications."
+        ],
+        "ontology_name": "ncit",
+        "ontology_prefix": "NCIT",
+        "type": "class"
+      },
+      "source": "Standard"
+  },
+  {
+    "identifier": "std-solvent",
+    "name": "nmr_solvent",
+    "label": "NMR Solvent",
+    "field_type": "text",
+    "ontology": {
+      "id": "nmrcv:class:http://nmrML.org/nmrCV#NMR:1000330",
+      "iri": "http://nmrML.org/nmrCV#NMR:1000330",
+      "short_form": "NMR:1000330",
+      "label": "NMR solvent",
+      "description": [
+        "Use Chebi entities here."
+      ],
+      "ontology_name": "nmrcv",
+      "ontology_prefix": "NMRCV",
+      "type": "class"
+    },
+    "source": "Standard"
+  },
+  {
+    "identifier": "std-sample_volume",
+    "name": "sample_volume",
+    "label": "sample volume",
+    "field_type": "text",
+    "ontology": {
+      "id": "nmrcv:class:http://nmrML.org/nmrCV#NMR:1000005",
+      "iri": "http://nmrML.org/nmrCV#NMR:1000005",
+      "short_form": "NMR:1000005",
+      "label": "sample volume",
+      "description": [
+        "Total volume of solution used."
+      ],
+      "ontology_name": "nmrcv",
+      "ontology_prefix": "NMRCV",
+      "type": "class"
+    },
+    "source": "Standard"
+  },
+  {
+    "identifier": "std-solvent_info",
+    "name": "solvent_info",
+    "label": "NMR solvent information",
+    "field_type": "text",
+    "ontology": {
+      "id": "nmrcv:class:http://nmrML.org/nmrCV#NMR:1002010",
+      "iri": "http://nmrML.org/nmrCV#NMR:1002010",
+      "short_form": "NMR:1002010",
+      "label": "NMR solvent information",
+      "ontology_name": "nmrcv",
+      "ontology_prefix": "NMRCV",
+      "type": "class"
+    },
+    "source": "Standard"
+  },
+  {
+    "identifier": "std-sample_tube",
+    "name": "sample_tube",
+    "label": "NMR sample tube",
+    "field_type": "text",
+    "ontology": {
+      "id": "nmrcv:class:http://nmrML.org/nmrCV#NMR:1400132",
+      "iri": "http://nmrML.org/nmrCV#NMR:1400132",
+      "short_form": "NMR:1400132",
+      "label": "NMR sample tube",
+      "description": [
+        "http://en.wikipedia.org/wiki/NMR_tube",
+        "sortal dimensions are Vendor, Size (Diameter, length), Material (glass, quarz, pyrex ...), Frequency, Concentricity, OD and ID",
+        "The sample-tube holds the NMR sample and sits in the NMR probe. It is usually a glass tube of 5-20mm diameter."
+      ],
+      "ontology_name": "nmrcv",
+      "ontology_prefix": "NMRCV",
+      "type": "class"
+    },
+    "source": "Standard"
+  },
+  {
+    "identifier": "temperature",
+    "name": "Temperature",
+    "label": "Temperature",
+    "field_type": "text",
+    "ontology": {
+      "id": "nmrcv:class:http://nmrML.org/nmrCV#NMR:1400025",
+      "iri": "http://nmrML.org/nmrCV#NMR:1400025",
+      "short_form": "NMR:1400025",
+      "label": "sample temperature in magnet",
+      "description": [
+        "def: The temperature of an NMR sample whilst in the magnet of an NMR instrument."
+      ],
+      "ontology_name": "nmrcv",
+      "ontology_prefix": "NMRCV",
+      "type": "class"
+    },
+    "source": "Standard"
+  }
+]

data/lib/labimotion/libs/data/vocab/System.json

@@ -0,0 +1,131 @@
+[
+  {
+    "id": 1,
+    "identifier": "dateTime-create",
+    "name": "create_time",
+    "label": "Create Time",
+    "field_type": "datetime",
+    "opid": 9,
+    "term_id": "NCIT_C164483",
+    "ontology": {
+      "id": "ncit:class:http://purl.obolibrary.org/obo/NCIT_C164483",
+      "iri": "http://purl.obolibrary.org/obo/NCIT_C164483",
+      "type": "class",
+      "label": "Created Date",
+      "obo_id": "NCIT:C164483",
+      "short_form": "NCIT_C164483",
+      "description": [
+        "The date on which the activity or entity is created."
+      ],
+      "ontology_name": "ncit",
+      "ontology_prefix": "NCIT"
+    },
+    "source": "System",
+    "voc": {
+      "source": "System"
+    }
+  },
+  {
+    "id": 2,
+    "identifier": "dateTime-update",
+    "name": "update_time",
+    "label": "Update Time",
+    "field_type": "datetime",
+    "opid": 9,
+    "term_id": "NCIT_C25164",
+    "ontology": {
+      "id": "ncit:class:http://purl.obolibrary.org/obo/NCIT_C25710",
+      "iri": "http://purl.obolibrary.org/obo/NCIT_C25710",
+      "short_form": "NCIT_C25710",
+      "obo_id": "NCIT:C25710",
+      "label": "Update",
+      "description": [
+        "Make current; supply with recent information or technology."
+      ],
+      "ontology_name": "ncit",
+      "ontology_prefix": "NCIT",
+      "type": "class"
+    },
+    "source": "System",
+    "voc": {
+      "source": "System"
+    }
+  },
+  {
+    "id": 4,
+    "identifier": "user-name",
+    "name": "creator",
+    "label": "Creator",
+    "field_type": "text",
+    "opid": 9,
+    "term_id": "NCIT_C42628",
+    "ontology": {
+      "id": "ncit:class:http://purl.obolibrary.org/obo/NCIT_C42628",
+      "iri": "http://purl.obolibrary.org/obo/NCIT_C42628",
+      "type": "class",
+      "label": "Created By",
+      "obo_id": "NCIT:C42628",
+      "short_form": "NCIT_C42628",
+      "description": [
+        "Indicates the person or authoritative body who brought the item into existence."
+      ],
+      "ontology_name": "ncit",
+      "ontology_prefix": "NCIT"
+    },
+    "source": "User",
+    "voc": {
+      "source": "User"
+    }
+  },
+  {
+    "id": 2,
+    "identifier": "element-id",
+    "name": "element_id",
+    "label": "Element Id",
+    "field_type": "text",
+    "opid": 9,
+    "term_id": "NCIT_C25364",
+    "source": "Element",
+    "voc": {
+      "source": "Element"
+    }
+  },
+  {
+    "id": 5,
+    "identifier": "element-name",
+    "name": "element_name",
+    "label": "Element Name",
+    "field_type": "text",
+    "opid": 8,
+    "term_id": "NCIT_C42694",
+    "source": "Element",
+    "voc": {
+      "source": "Element"
+    }
+  },
+  {
+    "id": 3,
+    "identifier": "element-short_label",
+    "name": "element_short_label",
+    "label": "Element Short Label",
+    "field_type": "text",
+    "opid": 9,
+    "term_id": "NCIT_C45561",
+    "source": "Element",
+    "voc": {
+      "source": "Element"
+    }
+  },
+  {
+    "id": 3,
+    "identifier": "element-class",
+    "name": "element_class",
+    "label": "Element Class",
+    "field_type": "text",
+    "opid": 9,
+    "source": "Element",
+    "voc": {
+      "source": "Element"
+    }
+  }
+]

data/lib/labimotion/libs/nmr_mapper.rb

@@ -13,7 +13,7 @@ module Labimotion
       result = is_brucker_binary(id)
       if result[:is_bagit] == true
         att.update_column(:con_state, Labimotion::ConState::CONVERTED)
-        Labimotion::Converter.metadata(id)
+        Labimotion::Converter.metadata(id, current_user)
         Labimotion::ConState::COMPLETED
       elsif result[:metadata] == nil
         Labimotion::ConState::NONE
@@ -256,6 +256,7 @@ module Labimotion
           new_prop[Labimotion::Prop::LAYERS]['set'][Labimotion::Prop::FIELDS][idx] = fi
         end
       end
+      new_prop = Labimotion::VocabularyHandler.update_vocabularies(new_prop, current_user, element)
       dataset.properties = new_prop
       dataset.save!
     end

data/lib/labimotion/libs/sample_association.rb

@@ -78,6 +78,8 @@ module Labimotion
         field_samples = layer[Labimotion::Prop::FIELDS].select { |ss| ss['type'] == Labimotion::FieldType::DRAG_SAMPLE }
         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)
+
           sid = field.dig('value', 'el_id')
           next if sid.blank?
 
@@ -100,6 +102,8 @@ 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)
+
           sid = field.dig('value', 'el_id')
           next if element.nil? || sid.blank? || sid == element.id
 

data/lib/labimotion/libs/vocabulary_handler.rb

@@ -0,0 +1,118 @@
+# frozen_string_literal: true
+
+module Labimotion
+  class VocabularyHandler
+    class << self
+      def update_vocabularies(properties, current_user, element)
+        properties[Labimotion::Prop::LAYERS].each do |key, layer|
+          update_layer_vocabularies(layer, key, properties, current_user, element)
+        end
+        properties
+      rescue StandardError => e
+        Labimotion.log_exception(e, current_user)
+        properties
+      end
+
+      def load_all_vocabularies
+        load_from_files + load_from_database
+      end
+
+      def load_app_vocabularies
+        load_from_files
+      end
+
+      private
+
+      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?
+        end
+      end
+
+      def get_vocabulary_value(field, current_user, element)
+        case field['source']
+        when 'System'
+          get_system_value(field)
+        when 'User'
+          get_user_value(field, current_user)
+        when 'Element'
+          get_element_value(field, element)
+        when 'Segment'
+          get_segment_value(field, element)
+        when 'Dataset'
+          # TODO: Implement Dataset logic here
+          nil
+        end
+      end
+
+      def get_system_value(field)
+        current_time = Time.now.strftime('%d/%m/%Y %H:%M')
+        case field['identifier']
+        when 'dateTime-update'
+          current_time
+        when 'dateTime-create'
+          current_time if field['value'].blank?
+        end
+      end
+
+      def get_user_value(field, current_user)
+        current_user.name if field['identifier'] == 'user-name' && current_user.present?
+      end
+
+      def get_element_value(field, element)
+        case field['identifier']
+        when 'element-id'
+          element.id.to_s
+        when 'element-short_label'
+          element.short_label if element.has_attribute?(:short_label)
+        when 'element-name'
+          element.name if element.has_attribute?(:name)
+        when 'element-class'
+          element.class.name === 'Labimotion::Element' ? element.element_klass.label : element.class.name
+        else
+          ek = element.element_klass
+          return if ek.nil? || ek.identifier != field['source_id']
+
+          el_prop = element.properties
+          fields = el_prop[Labimotion::Prop::LAYERS][field['layer_id']][Labimotion::Prop::FIELDS]
+          fields.find { |ss| ss['field'] == field['field_id'] }&.dig('value')
+        end
+      end
+
+      def get_segment_value(field, element)
+        segments = element.segments.joins(:segment_klass).find_by('segment_klasses.identifier = ?', field['source_id'])
+        return if segments.nil?
+
+        seg_prop = segments.properties
+        fields = seg_prop[Labimotion::Prop::LAYERS][field['layer_id']][Labimotion::Prop::FIELDS]
+        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
+      end
+
+      def load_from_files
+        merged_data = []
+        merged_data.concat(load_json_file('System.json'))
+        merged_data.concat(load_json_file('Standard.json'))
+        merged_data
+      end
+
+      def load_json_file(filename)
+        file_path = File.join(__dir__, 'data', 'vocab', filename)
+        file_content = File.read(file_path)
+        JSON.parse(file_content)
+      end
+
+      def load_from_database
+        vocabularies = Labimotion::Vocabulary.all.sort_by(&:name)
+        Labimotion::VocabularyEntity.represent(vocabularies, serializable: true)
+      end
+    end
+  end
+end