labimotion 2.0.0 → 2.0.1

data/lib/labimotion/models/segment_klasses_revision.rb

@@ -1,9 +1,12 @@
 # frozen_string_literal: true
 
+require 'labimotion/models/concerns/klass_revision'
+
 module Labimotion
   class SegmentKlassesRevision < ApplicationRecord
     acts_as_paranoid
     self.table_name = :segment_klasses_revisions
-    has_one :segment_klass, class_name: 'Labimotion::SegmentKlass'
+    include KlassRevision
+    belongs_to :segment_klass, class_name: 'Labimotion::SegmentKlass'
   end
 end

data/lib/labimotion/models/template_submission.rb

@@ -0,0 +1,52 @@
+# frozen_string_literal: true
+
+# == Schema Information
+#
+# Table name: template_submissions
+#
+#  id            :bigint           not null, primary key
+#  template_klass :string           not null
+#  template      :jsonb            not null, default: {}
+#  metadata      :jsonb            not null, default: {}
+#  origin        :string           not null
+#  state         :integer          not null, default: 0
+#  created_at    :datetime         not null
+#  updated_at    :datetime
+#  deleted_at    :datetime
+#
+# Indexes
+#
+#  idx_template_submissions_template  (template) USING gin
+#  idx_template_submissions_metadata  (metadata) USING gin
+#
+
+module Labimotion
+  class TemplateSubmission < ApplicationRecord
+    acts_as_paranoid
+
+    # State enum
+    enum state: {
+      pending: 0,
+      approved: 1,
+      rejected: 2,
+      released: 3
+    }
+
+    # Validations
+    validates :template_klass, presence: true
+    validates :template, presence: true
+    validates :metadata, presence: true
+    validates :origin, presence: true
+
+    # Scopes
+    scope :by_template_klass, ->(klass) { where(template_klass: klass) }
+    scope :by_state, ->(state) { where(state: state) }
+    scope :by_origin, ->(origin) { where(origin: origin) }
+    scope :by_email, ->(email) { where("metadata->'submission'->>'email' = ?", email) }
+    scope :by_contact_email, ->(email) { where("metadata->'submission'->>'contact_email' = ?", email) }
+    scope :by_any_email, lambda { |email|
+      where("metadata->'submission'->>'email' = ? OR metadata->'submission'->>'contact_email' = ?", email, email)
+    }
+    scope :recent, -> { order(created_at: :desc) }
+  end
+end

data/lib/labimotion/utils/utils.rb

@@ -80,27 +80,6 @@ module Labimotion
       current_version
     end
 
-    def self.find_field(properties, field_path, separator = '.')
-      return if properties.nil? || field_path.nil?
-
-      layer_name, field_name = field_path.split(separator)
-      fields = properties.dig(Labimotion::Prop::LAYERS, layer_name, Labimotion::Prop::FIELDS)
-      return unless fields
-
-      fields.find { |f| f['field'] == field_name }
-    end
-
-    def self.find_options_val(field, properties)
-      return if field.nil? || properties.nil? || field['option_layers'].nil? || field['value'].nil?
-
-      option_layers = properties.dig(Labimotion::Prop::SEL_OPTIONS, field['option_layers'])
-      options = option_layers && option_layers['options']
-      return if options.nil?
-
-      sel_option = options.find { |o| o['key'] == field['value'] }
-      sel_option && sel_option['label']
-    end
-
     def self.pkg(pkg)
       pkg = {} if pkg.nil?
       pkg['eln'] = Chemotion::Application.config.version

data/lib/labimotion/version.rb

@@ -2,5 +2,5 @@
 
 ## Labimotion Version
 module Labimotion
-  VERSION = '2.0.0'
+  VERSION = '2.0.1'
 end

data/lib/labimotion.rb

@@ -1,8 +1,8 @@
 # In your_gem_name.rb or main Ruby file
 module Labimotion
+
   autoload :CONF, 'labimotion/conf'
   autoload :VERSION, 'labimotion/version'
-  autoload :Constants, 'labimotion/constants'
 
   def self.logger
     @@labimotion_logger ||= Logger.new(Rails.root.join('log/labimotion.log')) # rubocop:disable Style/ClassVars
@@ -13,7 +13,6 @@ module Labimotion
     Labimotion.logger.error(exception.backtrace.join("\n"))
   end
 
-  autoload :MapperUtils, 'labimotion/utils/mapper_utils'
   autoload :Utils, 'labimotion/utils/utils'
 
   ######## APIs
@@ -63,7 +62,6 @@ module Labimotion
 
   ######## Libs
   autoload :Converter, 'labimotion/libs/converter'
-  autoload :DatasetBuilder, 'labimotion/libs/dataset_builder'
   autoload :NmrMapper, 'labimotion/libs/nmr_mapper'
   autoload :NmrMapperRepo, 'labimotion/libs/nmr_mapper_repo' ## for Chemotion Repository
   autoload :TemplateHub, 'labimotion/libs/template_hub'
@@ -116,4 +114,6 @@ module Labimotion
   autoload :Datasetable, 'labimotion/models/concerns/datasetable'
   autoload :AttachmentConverter, 'labimotion/models/concerns/attachment_converter.rb'
   autoload :LinkedProperties, 'labimotion/models/concerns/linked_properties'
+
+
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: labimotion
 version: !ruby/object:Gem::Version
-  version: 2.0.0
+  version: 2.0.1
 platform: ruby
 authors:
 - Chia-Lin Lin
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2025-03-25 00:00:00.000000000 Z
+date: 2025-12-19 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rails
@@ -76,11 +76,9 @@ files:
 - lib/labimotion/helpers/vocabulary_helpers.rb
 - lib/labimotion/libs/attachment_handler.rb
 - lib/labimotion/libs/converter.rb
-- lib/labimotion/libs/data/mapper/Chemwiki.json
-- lib/labimotion/libs/data/mapper/Source.json
+- lib/labimotion/libs/data/layer/StdDataset.json
 - lib/labimotion/libs/data/vocab/Standard.json
 - lib/labimotion/libs/data/vocab/System.json
-- lib/labimotion/libs/dataset_builder.rb
 - lib/labimotion/libs/export_dataset.rb
 - lib/labimotion/libs/export_element.rb
 - lib/labimotion/libs/nmr_mapper.rb
@@ -93,6 +91,7 @@ files:
 - lib/labimotion/models/concerns/datasetable.rb
 - lib/labimotion/models/concerns/generic_klass_revisions.rb
 - lib/labimotion/models/concerns/generic_revisions.rb
+- lib/labimotion/models/concerns/klass_revision.rb
 - lib/labimotion/models/concerns/linked_properties.rb
 - lib/labimotion/models/concerns/segmentable.rb
 - lib/labimotion/models/concerns/workflow.rb
@@ -113,12 +112,12 @@ files:
 - lib/labimotion/models/segments_revision.rb
 - lib/labimotion/models/std_layer.rb
 - lib/labimotion/models/std_layers_revision.rb
+- lib/labimotion/models/template_submission.rb
 - lib/labimotion/models/vocabulary.rb
 - lib/labimotion/utils/con_state.rb
 - lib/labimotion/utils/export_utils.rb
 - lib/labimotion/utils/field_type.rb
 - lib/labimotion/utils/import_utils.rb
-- lib/labimotion/utils/mapper_utils.rb
 - lib/labimotion/utils/prop.rb
 - lib/labimotion/utils/search.rb
 - lib/labimotion/utils/serializer.rb

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

@@ -1,236 +0,0 @@
-{
-  "CHMO:0000025": {
-    "index": ["A", "B", "C", "D", "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"]
-      },
-      "D": {
-        "sources": ["redox"],
-        "separator": ","
-      },
-      "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"]
-      },
-      "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": 6,
-        "type": "spc"
-      },
-      "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

@@ -1,78 +0,0 @@
-{
-  "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/dataset_builder.rb

@@ -1,70 +0,0 @@
-# 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