labimotion 2.0.0.rc2 → 2.0.0.rc4

data/lib/labimotion/libs/data/mapper/Chemwiki.json

@@ -0,0 +1,236 @@
+{
+  "CHMO:0000025": {
+    "index": ["A", "B", "C", "Q1", "Q2", "Q3", "G", "H", "Q4", "Q5", "K", "L", "Q6", "N", "O", "P", "Q7", "R", "S", "T", "U", "V", "W", "X", "Q8", "Q9", "Q10"],
+    "mapper": {
+      "A": {
+        "sources": ["inchikey"]
+      },
+      "B": {
+        "sources": ["molfile"]
+      },
+      "C": {
+        "sources": ["concentration"]
+      },
+      "G": {
+        "sources": ["solvent_volume"]
+      },
+      "H": {
+        "sources": ["elect_inchikey"]
+      },
+      "K": {
+        "sources": ["elect_concentration"]
+      },
+      "L": {
+        "sources": ["reference_internal"]
+      },
+      "N": {
+        "sources": ["scan_rate"]
+      },
+      "O": {
+        "sources": ["scan_number"]
+      },
+      "P": {
+        "sources": ["voltage_limit_one", "voltage_limit_two"],
+        "separator": ","
+      },
+      "R": {
+        "sources": ["atmosphere"]
+      },
+      "S": {
+        "sources": ["temperature"]
+      },
+      "T": {
+        "sources": ["condition"]
+      },
+      "U": {
+        "sources": ["we"]
+      },
+      "V": {
+        "sources": ["we_area"]
+      },
+      "W": {
+        "sources": ["ce"]
+      },
+      "X": {
+        "sources": ["re"]
+      },
+      "Q1": {
+        "sources": ["redox"],
+        "separator": ","
+      },
+      "Q2": {
+        "sources": ["solvent"]
+      },
+      "Q3": {
+        "sources": ["solvent_molfile"]
+      },
+      "Q4": {
+        "sources": ["elect_molfile"]
+      },
+      "Q5": {
+        "sources": ["elect_purity"]
+      },
+      "Q6": {
+        "sources": ["reference_internal_compound_molfile"]
+      },
+      "Q7": {
+        "sources": ["scan_direction"],
+        "separator": ","
+      },
+      "Q8": {
+        "sources": ["details"],
+        "separator": ","
+      },
+      "Q9": {
+        "sources": ["includes"],
+        "separator": ","
+      },
+      "Q10": {
+        "sources": ["base_page"],
+        "separator": ","
+      }
+    },
+    "source": {
+      "concentration": {
+        "title": "Analyte concentration [mM]",
+        "param": "sample_preparation.concentration",
+        "type": "dataset"
+      },
+      "temperature": {
+        "title": "Temperature [°C]",
+        "param": "set.temperature",
+        "type": "dataset"
+      },
+      "condition": {
+        "title": "Condition",
+        "param": "set.conditions",
+        "type": "dataset"
+      },
+      "scan_rate": {
+        "title": "Scan rate [mV/s]",
+        "param": "meas.scan_rate",
+        "type": "dataset"
+      },
+      "atmosphere": {
+        "title": "Gas",
+        "param": "set.atmosphere",
+        "type": "dataset"
+      },
+      "scan_number": {
+        "title": "Scan number",
+        "param": "meas.cycles",
+        "type": "dataset"
+      },
+      "we": {
+        "title": "Working electrode",
+        "param": "electrodes.working",
+        "type": "dataset"
+      },
+      "we_area": {
+        "title": "Working electrode surface area",
+        "param": "electrodes.working_area",
+        "type": "dataset"
+      },
+      "ce": {
+        "title": "Counter electrode",
+        "param": "electrodes.counter",
+        "type": "dataset"
+      },
+      "re": {
+        "title": "Reference electrode",
+        "param": "electrodes.reference",
+        "type": "dataset"
+      },
+      "voltage_limit_one": {
+        "title": "Potential window",
+        "param": "meas.voltage_limit_one",
+        "type": "dataset"
+      },
+      "voltage_limit_two": {
+        "title": "Potential window",
+        "param": "meas.voltage_limit_two",
+        "type": "dataset"
+      },
+      "reference_internal": {
+        "title": "Internal reference compound_inchikey",
+        "param": "meas.reference_internal",
+        "type": "dataset"
+      },
+      "elect_inchikey": {
+        "title": "Electrolyte_inchikey",
+        "param": "sample_preparation.salt",
+        "type": "dataset"
+      },
+      "elect_concentration": {
+        "title": "Electrolyte concentration [M]",
+        "param": "sample_preparation.concentration_salt",
+        "type": "dataset"
+      },
+      "solvent": {
+        "title": "Solvent A_inchikey",
+        "param": "sample_preparation.solvent",
+        "type": "dataset"
+      },
+      "solvent_volume": {
+        "title": "Solvent volume [ml]",
+        "param": "sample_preparation.amount_sol",
+        "type": "dataset"
+      },
+      "solvent_molfile": {
+        "title": "Solvent A_molfile",
+        "param": "n/a",
+        "type": "string"
+      },
+      "scan_direction": {
+        "title": "Scan direction",
+        "param": "n/a",
+        "type": "string"
+      },
+      "reference_internal_compound_molfile": {
+        "title": "Internal reference compound_molfile",
+        "param": "n/a",
+        "type": "string"
+      },
+      "elect_purity": {
+        "title": "Electrolyte purity [%]",
+        "param": "n/a",
+        "type": "string"
+      },
+      "redox": {
+        "title": "Redox-Potential",
+        "param": "n/a",
+        "type": "string"
+      },
+      "elect_molfile": {
+        "title": "Electrolyte_inchikey",
+        "param": "n/a",
+        "type": "string"
+      },
+      "inchikey": {
+        "title": "Analyte_inchikey",
+        "param": "inchikey",
+        "type": "molecule"
+      },
+      "molfile": {
+        "title": "Analyte_molfile",
+        "param": "molfile",
+        "type": "sample"
+      },
+      "details": {
+        "title": "Details",
+        "param": "n/a",
+        "type": "string"
+      },
+      "includes": {
+        "title": "Included",
+        "param": "n/a",
+        "type": "string"
+      },
+      "base_page": {
+        "title": "BasePageName",
+        "param": "n/a",
+        "type": "string"
+      }
+    }
+  }
+}

data/lib/labimotion/libs/data/mapper/Source.json

@@ -0,0 +1,78 @@
+{
+  "sourceMap": {
+    "sourceSelector": [
+      "parm",
+      "acqus",
+      "procs"
+    ],
+    "acqus": {
+      "file": "acqus",
+      "parameters": [
+        "DATE",
+        "D1",
+        "INSTRUM",
+        "NS",
+        "NUC1",
+        "NUC2",
+        "PROBHD",
+        "PULPROG",
+        "SFO1",
+        "SFO2",
+        "SOLVENT",
+        "SW",
+        "TD",
+        "TE",
+        "TITLE"
+      ]
+    },
+    "procs": {
+      "file": "pdata/1/procs",
+      "parameters": [
+        "SI",
+        "SF",
+        "WDW",
+        "LB",
+        "GB"
+      ]
+    },
+    "parm": {
+      "file": "pdata/1/parm.txt",
+      "parameters": [
+        "Date_",
+        "Time",
+        "INSTRUM",
+        "PROBHD",
+        "SOLVENT",
+        "TE",
+        "NS",
+        "PULPROG",
+        "TD",
+        "D1",
+        "SF",
+        "SFO1",
+        "SFO2",
+        "NUC1",
+        "NUC2"
+      ]
+    },
+    "parameters": {
+      "DATE": "general.date",
+      "D1": "set.done",
+      "INSTRUM": "instrument.instrument",
+      "NS": "set.ns",
+      "NUC1": "set.nucone",
+      "NUC2": "set.nuctwo",
+      "SF": "set.sf",
+      "SFO1": "set.sfoone",
+      "SFO2": "set.sfotwo",
+      "PROBHD": "equipment.probehead",
+      "PULPROG": "set.PULPROG",
+      "SOLVENT": "sample_preparation.solvent",
+      "TD": "set.td",
+      "TE": "set.temperature",
+      "TITLE": "software.Name",
+      "Version": "software.Version",
+      "Time": "general.time"
+    }
+  }
+}

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

@@ -55,7 +55,7 @@
     "id": 4,
     "identifier": "user-name",
     "name": "creator",
-    "label": "Creator",
+    "label": "creator",
     "field_type": "text",
     "opid": 9,
     "term_id": "NCIT_C42628",

data/lib/labimotion/libs/dataset_builder.rb

@@ -0,0 +1,70 @@
+# frozen_string_literal: true
+
+require 'labimotion/utils/utils'
+require 'labimotion/version'
+
+module Labimotion
+  class DatasetBuilder
+    def self.build(container, content)
+      return unless valid_input?(container, content)
+
+      create_dataset_with_metadata(container, content)
+    end
+
+    private
+
+    def self.valid_input?(container, content)
+      container.present? &&
+        content.present? &&
+        content[:ols].present? &&
+        content[:metadata].present?
+    end
+
+    def self.create_dataset_with_metadata(container, content)
+      klass = find_dataset_klass(content[:ols])
+      return unless klass
+
+      dataset = create_dataset(container, klass)
+      build_result(dataset, content)
+    end
+
+    def self.find_dataset_klass(ols_term_id)
+      Labimotion::DatasetKlass.find_by(ols_term_id: ols_term_id)
+    end
+
+    def self.create_dataset(container, klass)
+      uuid = SecureRandom.uuid
+      props = prepare_properties(klass, uuid)
+
+      Labimotion::Dataset.create!(
+        uuid: uuid,
+        dataset_klass_id: klass.id,
+        element_type: 'Container',
+        element_id: container.id,
+        properties: props,
+        properties_release: klass.properties_release,
+        klass_uuid: klass.uuid
+      )
+    end
+
+    def self.prepare_properties(klass, uuid)
+      props = klass.properties_release
+      props['uuid'] = uuid
+      props['pkg'] = Labimotion::Utils.pkg(props['pkg'])
+      props['klass'] = 'Dataset'
+      props
+    end
+
+    def self.build_result(dataset, content)
+      {
+        dataset: dataset,
+        metadata: content[:metadata],
+        ols: content[:ols],
+        parameters: content[:parameters]
+      }
+    end
+
+    private_class_method :valid_input?, :create_dataset_with_metadata, :find_dataset_klass, :create_dataset,
+                         :prepare_properties, :build_result
+  end
+end

data/lib/labimotion/libs/export_dataset.rb

@@ -8,47 +8,190 @@ module Labimotion
     DEFAULT_ROW_WIDTH = 100
     DEFAULT_ROW_HEIGHT = 20
 
-    def initialize(**args)
+    def initialize(id)
       @xfile = Axlsx::Package.new
-      @file_extension = 'xlsx'
       @xfile.workbook.styles.fonts.first.name = 'Calibri'
+      @file_extension = 'xlsx'
+
+      @id = id
+      @dataset = Labimotion::Dataset.find_by(element_id: @id, element_type: 'Container')
+      return if @dataset.nil?
+
+      @klass = @dataset.dataset_klass
+      @ols_term_id = @klass.ols_term_id
+      @label = @klass.label
+      @analysis = @dataset&.element&.parent
+      @element = @analysis&.root&.containable if @analysis.present?
+      @element_type = @element.class.name if @element.present?
+    end
+
+    def read
+      @xfile.to_stream.read
     end
 
-    def res_name(id)
-      element_name = Container.find(id)&.root_element&.short_label
-      ols = ols_name(id)
+    def res_name
+      element_name = Container.find(@id)&.root_element&.short_label
+      ols = ols_name
       "#{element_name}_#{ols.gsub(' ', '_')}.xlsx"
     rescue StandardError => e
       Labimotion.log_exception(e)
     end
 
-    def ols_name(id)
-      ds = Labimotion::Dataset.find_by(element_id: id, element_type: 'Container')
-      return nil if ds.nil?
+    def spectra
+      name_mapping = []
+      ## gds = Labimotion::Dataset.find_by(element_id: id, element_type: 'Container')
+      cds = Container.find(@id)
+      cds_csv = cds.attachments.where(aasm_state: 'csv').order(:filename)
+      csv_length = cds_csv.length
+      return if csv_length.zero?
+
+      cds_csv.each_with_index do |att, idx|
+        sheet_name = "Sheet#{idx+1}"
+        sheet = @xfile.workbook.add_worksheet(name: sheet_name)
+        name_mapping.push([sheet_name, att.filename])
+        File.open(att.attachment_url) do |fi|
+          fi.each_line do |line|
+            sheet.add_row(line.split(','))
+          end
+        end
+      end
+      return unless name_mapping.length > 1
+
+      first_sheet = @xfile.workbook.worksheets&.first
+      header_style = first_sheet&.styles.add_style(sz: 12, fg_color: 'FFFFFF', bg_color: '00008B', border: { style: :thick, color: 'FF777777', edges: [:bottom] })
+      first_sheet&.add_row(['Sheet name', 'File name'], style: header_style)
+      name_mapping&.each do |mapping|
+        next if mapping.length < 2
+
+        @xfile.workbook.worksheets&.first&.add_row([mapping[0].to_s, mapping[1].to_s])
+      end
+    rescue StandardError => e
+      Labimotion.log_exception(e)
+    end
+
+    def export
+      return if @dataset.nil? || @analysis.nil? || @element.nil?
+
+      description
+      dataset_info
+      # element_info
+      chemwiki_info
+    rescue StandardError => e
+      Labimotion.log_exception(e)
+    end
+
+    private
+
+    def chemwiki_info
+      config = Labimotion::MapperUtils.load_config(File.read(Constants::Mapper::WIKI_CONFIG))
+      return if config.nil? || config[@ols_term_id].nil?
 
-      name = ds.dataset_klass.label
+      sheet = @xfile.workbook.add_worksheet(name: 'ChemWiki')
+      map_index = config.dig(@ols_term_id, 'index')
+      map_mapper = config.dig(@ols_term_id, 'mapper')
+      map_source = config.dig(@ols_term_id, 'source')
 
-      match = name.match(/\((.*?)\)/)
-      name = match && match.length > 1 ? match[1] : name
+      return if map_index.nil? || map_mapper.nil? || map_source.nil?
 
-      name = '1H NMR' if ds.dataset_klass.ols_term_id == 'CHMO:0000593'
-      name = '13C NMR' if ds.dataset_klass.ols_term_id == 'CHMO:0000595'
+      return unless map_index.is_a?(Array) && map_mapper.is_a?(Hash) && map_source.is_a?(Hash)
+
+      # sheet.column_info.each { |col| col.width = map_width }
+
+      array_header = []
+      array_data = []
+      map_index.each do |key|
+        mapper = map_mapper.dig(key)
+        next if mapper.nil? || mapper['sources'].nil? || !mapper.is_a?(Hash)
+
+        col_header = ''
+        col_value = ''
+        mapper['sources'].each_with_index do |source_key, idx|
+          source = map_source&.dig(source_key)
+          next if source.nil? || source['title'].nil?
+
+          col_header = source['title']
+
+          if col_value.present?
+            col_value += (mapper['separator'] || '') + source_data(source)
+          else
+            col_value = source_data(source)
+          end
+        end
+        array_header.push(col_header || '')
+        array_data.push(col_value || '')
+      end
+      sheet.add_row(array_header)
+      sheet.add_row(array_data)
+    rescue StandardError => e
+      Labimotion.log_exception(e)
+    end
+
+
+    def conv_value(field, properties)
+      return '' if field.nil?
+
+      case field['type']
+      when 'select'
+        Labimotion::Utils.find_options_val(field, properties) || field['value']
+      else
+        field['value']
+      end
+    end
+
+    def source_data(source)
+      param = source['param']
+      return '' if param.nil? || source['type'].nil?
+
+      val = case source['type']
+            when 'string'
+              param
+            when 'sample'
+              @element.send(param) if @element.respond_to?(param)
+            when 'molecule'
+              @element.molecule.send(param) if @element_type == 'Sample' && @element&.molecule&.respond_to?(param)
+            when 'dataset'
+              field = Labimotion::Utils.find_field(@dataset.properties, param)
+              # (field && field['value']) || ''
+              conv_value(field, @dataset.properties)
+            end
+      val || ''
+    rescue StandardError => e
+      Labimotion.log_exception(e)
+    end
+
+    def element_info
+      if @element.class.name == 'Sample'
+        sheet = @xfile.workbook.add_worksheet(name: 'Element')
+        sheet.add_row(['inchikey', @element.molecule_inchikey])
+        sheet.add_row(['molfile', @element.molfile])
+      end
+    rescue StandardError => e
+      Labimotion.log_exception(e)
+    end
+
+    def ols_name
+      #name = @dataset.dataset_klass.label
+
+      match = @label.match(/\((.*?)\)/)
+      name = match && match.length > 1 ? match[1] : @label
+
+      name = '1H NMR' if @ols_term_id == 'CHMO:0000593'
+      name = '13C NMR' if @ols_term_id == 'CHMO:0000595'
       name.slice(0, 26)
     rescue StandardError => e
       Labimotion.log_exception(e)
       'ols_name'
     end
 
-    def description(ds, id)
-      wb = @xfile.workbook
+    def description
       sheet = @xfile.workbook.add_worksheet(name: 'Description')
       header_style = sheet.styles.add_style(sz: 12, fg_color: 'FFFFFF', bg_color: '00008B', border: { style: :thick, color: 'FF777777', edges: [:bottom] })
-      sheet.add_row(['File name', res_name(id)])
+      sheet.add_row(['File name', res_name])
       sheet.add_row(['Time', Time.now.strftime("%Y-%m-%d %H:%M:%S %Z")] )
       sheet.add_row(['(This file is automatically generated by the system.)'])
       sheet.add_row([''])
       sheet.add_row([''])
-      sheet.add_row(['Fields description of sheet:' + ds.dataset_klass.label])
+      sheet.add_row(['Fields description of sheet:' + @dataset.dataset_klass.label])
       sheet.add_row(['Fields', 'Field description'], style: header_style)
       sheet.add_row(['Layer Label', 'The label of the layer'])
       sheet.add_row(['Field Label', 'The label of the field'])
@@ -65,24 +208,18 @@ module Labimotion
       Labimotion.log_exception(e)
     end
 
-    def export(id)
-      ds = Labimotion::Dataset.find_by(element_id: id, element_type: 'Container')
-      return if ds.nil?
-
-      description(ds, id)
-
-      wb = @xfile.workbook
-      name = ols_name(id)
+    def dataset_info
+      name = ols_name
       return if name.nil?
 
       sheet = @xfile.workbook.add_worksheet(name: name)
-      sheet.add_row([ds.dataset_klass.label])
+      sheet.add_row([@dataset.dataset_klass.label])
       header_style = sheet.styles.add_style(sz: 12, fg_color: 'FFFFFF', bg_color: '00008B', border: { style: :thick, color: 'FF777777', edges: [:bottom] })
       layer_style = sheet.styles.add_style(b: true, bg_color: 'CEECF5')
       sheet.add_row(header, style: header_style)
 
-      layers = ds.properties[Labimotion::Prop::LAYERS] || {}
-      options = ds.properties[Labimotion::Prop::SEL_OPTIONS]
+      layers = @dataset.properties[Labimotion::Prop::LAYERS] || {}
+      options = @dataset.properties[Labimotion::Prop::SEL_OPTIONS]
       layer_keys = layers.keys.sort_by { |key| layers[key]['position'] }
       layer_keys.each do |key|
         layer = layers[key]
@@ -116,8 +253,6 @@ module Labimotion
           end
           sheet.rows.last.cells[2].value = show_value
           sheet.rows.last.cells[8].value = field['system'] || field['device']
-
-
         end
         # sheet.column_widths nil, nil, nil, nil, 0, 0, 0, 0, 0
       end
@@ -136,45 +271,9 @@ module Labimotion
       field['value']
     end
 
-    def spectra(id)
-      name_mapping = []
-      wb = @xfile.workbook
-      gds = Labimotion::Dataset.find_by(element_id: id, element_type: 'Container')
-      cds = Container.find(id)
-      cds_csv = cds.attachments.where(aasm_state: 'csv').order(:filename)
-      csv_length = cds_csv.length
-      return if csv_length.zero?
-      cds_csv.each_with_index do |att, idx|
-        sheet_name = "Sheet#{idx+1}"
-        sheet = @xfile.workbook.add_worksheet(name: sheet_name)
-        name_mapping.push([sheet_name, att.filename])
-        File.open(att.attachment_url) do |fi|
-          fi.each_line do |line|
-            sheet.add_row(line.split(','))
-          end
-        end
-      end
-
-      if name_mapping.length > 1
-        first_sheet = @xfile.workbook.worksheets&.first
-        header_style = first_sheet&.styles.add_style(sz: 12, fg_color: 'FFFFFF', bg_color: '00008B', border: { style: :thick, color: 'FF777777', edges: [:bottom] })
-        first_sheet&.add_row(['Sheet name', 'File name'], style: header_style)
-        name_mapping&.each do |mapping|
-          next if mapping.length < 2
-
-          @xfile.workbook.worksheets&.first&.add_row([mapping[0].to_s, mapping[1].to_s])
-        end
-      end
-
-    end
-
     def header
       ['Layer Label', 'Field Label', 'Value', 'Unit', 'Name', 'Type', 'Source?', 'Source identifier', 'Source data', 'Ontology', 'Ontology Label', 'iri'].freeze
     end
 
-    def read
-      @xfile.to_stream.read
-    end
-
   end
 end