labimotion 1.1.3 → 1.2.0.0

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Files changed (30) hide show
  1. checksums.yaml +4 -4
  2. data/lib/labimotion/apis/generic_element_api.rb +32 -38
  3. data/lib/labimotion/collection/export.rb +45 -84
  4. data/lib/labimotion/collection/import.rb +60 -54
  5. data/lib/labimotion/entities/element_revision_entity.rb +10 -10
  6. data/lib/labimotion/entities/eln_element_entity.rb +23 -23
  7. data/lib/labimotion/entities/properties_entity.rb +18 -19
  8. data/lib/labimotion/entities/segment_revision_entity.rb +11 -11
  9. data/lib/labimotion/helpers/element_helpers.rb +14 -4
  10. data/lib/labimotion/helpers/generic_helpers.rb +9 -9
  11. data/lib/labimotion/helpers/segment_helpers.rb +1 -2
  12. data/lib/labimotion/libs/converter.rb +12 -13
  13. data/lib/labimotion/libs/export_dataset.rb +32 -6
  14. data/lib/labimotion/libs/nmr_mapper.rb +27 -27
  15. data/lib/labimotion/libs/properties_handler.rb +95 -0
  16. data/lib/labimotion/libs/sample_association.rb +15 -15
  17. data/lib/labimotion/models/concerns/generic_klass_revisions.rb +1 -1
  18. data/lib/labimotion/models/concerns/generic_revisions.rb +3 -3
  19. data/lib/labimotion/models/concerns/linked_properties.rb +18 -0
  20. data/lib/labimotion/models/concerns/segmentable.rb +17 -12
  21. data/lib/labimotion/models/element.rb +26 -17
  22. data/lib/labimotion/utils/export_utils.rb +196 -0
  23. data/lib/labimotion/utils/field_type.rb +23 -0
  24. data/lib/labimotion/utils/import_utils.rb +244 -59
  25. data/lib/labimotion/utils/prop.rb +27 -0
  26. data/lib/labimotion/utils/search.rb +2 -2
  27. data/lib/labimotion/utils/serializer.rb +22 -22
  28. data/lib/labimotion/version.rb +1 -1
  29. data/lib/labimotion.rb +4 -1
  30. metadata +7 -2
@@ -6,39 +6,38 @@ module Labimotion
6
6
 
7
7
  # TODO: Refactor this method to something more readable/understandable
8
8
  def properties
9
- (object&.properties.is_a?(Hash) && object.properties['layers']&.keys || []).each do |key|
9
+ (object&.properties.is_a?(Hash) && object.properties[Labimotion::Prop::LAYERS]&.keys || []).each do |key|
10
10
  # layer = object.properties[key]
11
- field_sample_molecules = object.properties['layers'][key]['fields'].select { |ss| ss['type'] == 'drag_sample' || ss['type'] == 'drag_molecule' }
11
+ field_sample_molecules = object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS].select { |ss| ss['type'] == Labimotion::FieldType::DRAG_SAMPLE || ss['type'] == Labimotion::FieldType::DRAG_MOLECULE }
12
12
  field_sample_molecules.each do |field|
13
- idx = object.properties['layers'][key]['fields'].index(field)
13
+ idx = object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS].index(field)
14
14
  sid = field.dig('value', 'el_id')
15
15
  next unless sid.present?
16
16
 
17
- el = field['type'] == 'drag_sample' ? Sample.find_by(id: sid) : Molecule.find_by(id: sid)
17
+ el = field['type'] == Labimotion::FieldType::DRAG_SAMPLE ? Sample.find_by(id: sid) : Molecule.find_by(id: sid)
18
18
  next unless el.present?
19
- next unless object.properties.dig('layers', key, 'fields', idx, 'value').present?
19
+ next unless object.properties.dig(Labimotion::Prop::LAYERS, key, Labimotion::Prop::FIELDS, idx, 'value').present?
20
20
 
21
- object.properties['layers'][key]['fields'][idx]['value']['el_label'] = el.short_label if field['type'] == 'drag_sample'
22
- object.properties['layers'][key]['fields'][idx]['value']['el_tip'] = el.short_label if field['type'] == 'drag_sample'
23
- object.properties['layers'][key]['fields'][idx]['value']['el_svg'] = field['type'] == 'drag_sample' ? el.get_svg_path : File.join('/images', 'molecules', el.molecule_svg_file)
21
+ object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS][idx]['value']['el_label'] = el.short_label if field['type'] == Labimotion::FieldType::DRAG_SAMPLE
22
+ object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS][idx]['value']['el_tip'] = el.short_label if field['type'] == Labimotion::FieldType::DRAG_SAMPLE
23
+ object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS][idx]['value']['el_svg'] = field['type'] == Labimotion::FieldType::DRAG_SAMPLE ? el.get_svg_path : File.join('/images', 'molecules', el.molecule_svg_file)
24
24
  end
25
25
 
26
- field_tables = object.properties['layers'][key]['fields'].select { |ss| ss['type'] == 'table' }
26
+ field_tables = object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS].select { |ss| ss['type'] == Labimotion::FieldType::TABLE }
27
27
  field_tables.each do |field|
28
- idx = object.properties['layers'][key]['fields'].index(field)
29
- next unless field['sub_values'].present? && field['sub_fields'].present?
28
+ idx = object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS].index(field)
29
+ next unless field['sub_values'].present? && field[Labimotion::Prop::SUBFIELDS].present?
30
30
 
31
- field_table_molecules = field['sub_fields'].select { |ss| ss['type'] == 'drag_molecule' }
32
- object.properties['layers'][key]['fields'][idx] = set_table(field, field_table_molecules, 'Molecule') if field_table_molecules.present?
31
+ field_table_molecules = field[Labimotion::Prop::SUBFIELDS].select { |ss| ss['type'] == Labimotion::FieldType::DRAG_MOLECULE }
32
+ object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS][idx] = set_table(field, field_table_molecules, Labimotion::Prop::MOLECULE) if field_table_molecules.present?
33
33
 
34
- field_table_samples = field['sub_fields'].select { |ss| ss['type'] == 'drag_sample' }
35
- object.properties['layers'][key]['fields'][idx] = set_table(field, field_table_samples, 'Sample') if field_table_samples.present?
34
+ field_table_samples = field[Labimotion::Prop::SUBFIELDS].select { |ss| ss['type'] == Labimotion::FieldType::DRAG_SAMPLE }
35
+ object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS][idx] = set_table(field, field_table_samples, Labimotion::Prop::SAMPLE) if field_table_samples.present?
36
36
  end
37
37
  end
38
38
  object.properties
39
39
  end
40
40
 
41
-
42
41
  def set_table(field, field_table_objs, obj)
43
42
  col_ids = field_table_objs.map { |x| x.values[0] }
44
43
  col_ids.each do |col_id|
@@ -46,16 +45,16 @@ module Labimotion
46
45
  next unless sub_value[col_id].present? && sub_value[col_id]['value'].present? && sub_value[col_id]['value']['el_id'].present?
47
46
 
48
47
  find_obj = obj.constantize.find_by(id: sub_value[col_id]['value']['el_id'])
49
- next unless find_obj.present?
48
+ next if find_obj.blank?
50
49
 
51
50
  case obj
52
- when 'Molecule'
51
+ when Labimotion::Prop::MOLECULE
53
52
  sub_value[col_id]['value']['el_svg'] = File.join('/images', 'molecules', find_obj.molecule_svg_file)
54
53
  sub_value[col_id]['value']['el_inchikey'] = find_obj.inchikey
55
54
  sub_value[col_id]['value']['el_smiles'] = find_obj.cano_smiles
56
55
  sub_value[col_id]['value']['el_iupac'] = find_obj.iupac_name
57
56
  sub_value[col_id]['value']['el_molecular_weight'] = find_obj.molecular_weight
58
- when 'Sample'
57
+ when Labimotion::Prop::SAMPLE
59
58
  sub_value[col_id]['value']['el_svg'] = find_obj.get_svg_path
60
59
  sub_value[col_id]['value']['el_label'] = find_obj.short_label
61
60
  sub_value[col_id]['value']['el_short_label'] = find_obj.short_label
@@ -9,27 +9,27 @@ module Labimotion
9
9
  end
10
10
 
11
11
  def properties
12
- object.properties['layers']&.keys.each do |key|
13
- field_sample_molecules = object.properties['layers'][key]['fields'].select { |ss| ss['type'] == 'drag_sample' || ss['type'] == 'drag_molecule' }
12
+ object.properties[Labimotion::Prop::LAYERS]&.keys.each do |key|
13
+ field_sample_molecules = object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS].select { |ss| ss['type'] == Labimotion::FieldType::DRAG_SAMPLE || ss['type'] == Labimotion::FieldType::DRAG_MOLECULE }
14
14
  field_sample_molecules.each do |field|
15
- idx = object.properties['layers'][key]['fields'].index(field)
15
+ idx = object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS].index(field)
16
16
  sid = field.dig('value', 'el_id')
17
17
  next unless sid.present?
18
18
 
19
- el = field['type'] == 'drag_sample' ? Sample.find_by(id: sid) : Molecule.find_by(id: sid)
19
+ el = field['type'] == Labimotion::FieldType::DRAG_SAMPLE ? Sample.find_by(id: sid) : Molecule.find_by(id: sid)
20
20
  next unless el.present?
21
- next unless object.properties.dig('layers', key, 'fields', idx, 'value').present?
21
+ next unless object.properties.dig(Labimotion::Prop::LAYERS, key, Labimotion::Prop::FIELDS, idx, 'value').present?
22
22
 
23
- object.properties['layers'][key]['fields'][idx]['value']['el_label'] = el.short_label if field['type'] == 'drag_sample'
24
- object.properties['layers'][key]['fields'][idx]['value']['el_tip'] = el.short_label if field['type'] == 'drag_sample'
25
- object.properties['layers'][key]['fields'][idx]['value']['el_svg'] = field['type'] == 'drag_sample' ? el.get_svg_path : File.join('/images', 'molecules', el.molecule_svg_file)
23
+ object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS][idx]['value']['el_label'] = el.short_label if field['type'] == Labimotion::FieldType::DRAG_SAMPLE
24
+ object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS][idx]['value']['el_tip'] = el.short_label if field['type'] == Labimotion::FieldType::DRAG_SAMPLE
25
+ object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS][idx]['value']['el_svg'] = field['type'] == Labimotion::FieldType::DRAG_SAMPLE ? el.get_svg_path : File.join('/images', 'molecules', el.molecule_svg_file)
26
26
  end
27
27
 
28
- field_tables = object.properties['layers'][key]['fields'].select { |ss| ss['type'] == 'table' }
28
+ field_tables = object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS].select { |ss| ss['type'] == Labimotion::FieldType::TABLE }
29
29
  field_tables.each do |field|
30
- next unless field['sub_values'].present? && field['sub_fields'].present?
30
+ next unless field['sub_values'].present? && field[Labimotion::Prop::SUBFIELDS].present?
31
31
 
32
- field_table_molecules = field['sub_fields'].select { |ss| ss['type'] == 'drag_molecule' }
32
+ field_table_molecules = field[Labimotion::Prop::SUBFIELDS].select { |ss| ss['type'] == Labimotion::FieldType::DRAG_MOLECULE }
33
33
  next unless field_table_molecules.present?
34
34
 
35
35
  col_ids = field_table_molecules.map { |x| x.values[0] }
@@ -133,10 +133,20 @@ module Labimotion
133
133
  raise e
134
134
  end
135
135
 
136
+ def split_elements(ui_state, current_user)
137
+ col_id = ui_state[:currentCollectionId] || 0
138
+ element_ids = Labimotion::Element.for_user(current_user.id).for_ui_state_with_collection(ui_state[:element], Labimotion::CollectionsElement, col_id)
139
+ klass_id = Labimotion::ElementKlass.find_by(name: ui_state[:element][:name])&.id
140
+ Labimotion::Element.where(id: element_ids, element_klass_id: klass_id).each do |element|
141
+ element.split(current_user, col_id)
142
+ end
143
+ {}
144
+ end
145
+
136
146
  def upload_generics_files(current_user, params)
137
147
  attach_ary = []
138
148
  att_ary = create_uploads(
139
- 'Element',
149
+ Labimotion::Prop::ELEMENT,
140
150
  params[:att_id],
141
151
  params[:elfiles],
142
152
  params[:elInfo],
@@ -146,7 +156,7 @@ module Labimotion
146
156
  (attach_ary << att_ary).flatten! unless att_ary&.empty?
147
157
 
148
158
  att_ary = create_uploads(
149
- 'Segment',
159
+ Labimotion::Prop::SEGMENT,
150
160
  params[:att_id],
151
161
  params[:sefiles],
152
162
  params[:seInfo],
@@ -195,7 +205,7 @@ module Labimotion
195
205
  layer, field = params[:sort_column].split('.')
196
206
 
197
207
  element_klass = Labimotion::ElementKlass.find_by(name: params[:el_type])
198
- allowed_fields = element_klass.properties_release.dig('layers', layer, 'fields')&.pluck('field') || []
208
+ allowed_fields = element_klass.properties_release.dig(Labimotion::Prop::LAYERS, layer, Labimotion::Prop::FIELDS)&.pluck('field') || []
199
209
 
200
210
  if field.in?(allowed_fields)
201
211
  query = ActiveRecord::Base.sanitize_sql(
@@ -258,7 +268,7 @@ module Labimotion
258
268
  layer, field = params[:sort_column].split('.')
259
269
 
260
270
  element_klass = Labimotion::ElementKlass.find_by(name: params[:el_type])
261
- allowed_fields = element_klass.properties_release.dig('layers', layer, 'fields')&.pluck('field') || []
271
+ allowed_fields = element_klass.properties_release.dig(Labimotion::Prop::LAYERS, layer, Labimotion::Prop::FIELDS)&.pluck('field') || []
262
272
 
263
273
  if field.in?(allowed_fields)
264
274
  query = ActiveRecord::Base.sanitize_sql(
@@ -107,9 +107,9 @@ module Labimotion
107
107
 
108
108
  def fetch_properties_uploads(properties)
109
109
  uploads = []
110
- properties['layers'].keys.each do |key|
111
- layer = properties['layers'][key]
112
- field_uploads = layer['fields'].select { |ss| ss['type'] == 'upload' }
110
+ properties[Labimotion::Prop::LAYERS].keys.each do |key|
111
+ layer = properties[Labimotion::Prop::LAYERS][key]
112
+ field_uploads = layer[Labimotion::Prop::FIELDS].select { |ss| ss['type'] == Labimotion::FieldType::UPLOAD }
113
113
  field_uploads.each do |field|
114
114
  ((field['value'] && field['value']['files']) || []).each do |file|
115
115
  uploads.push({ layer: key, field: field['field'], uid: file['uid'], filename: file['filename'] })
@@ -125,10 +125,10 @@ module Labimotion
125
125
  def update_properties_upload(element, properties, att, pa)
126
126
  return if pa.nil?
127
127
 
128
- idx = properties['layers'][pa[:layer]]['fields'].index { |fl| fl['field'] == pa[:field] }
129
- fidx = properties['layers'][pa[:layer]]['fields'][idx]['value']['files'].index { |fi| fi['uid'] == pa[:uid] }
130
- properties['layers'][pa[:layer]]['fields'][idx]['value']['files'][fidx]['aid'] = att.id
131
- properties['layers'][pa[:layer]]['fields'][idx]['value']['files'][fidx]['uid'] = att.identifier
128
+ idx = properties[Labimotion::Prop::LAYERS][pa[:layer]][Labimotion::Prop::FIELDS].index { |fl| fl['field'] == pa[:field] }
129
+ fidx = properties[Labimotion::Prop::LAYERS][pa[:layer]][Labimotion::Prop::FIELDS][idx]['value']['files'].index { |fi| fi['uid'] == pa[:uid] }
130
+ properties[Labimotion::Prop::LAYERS][pa[:layer]][Labimotion::Prop::FIELDS][idx]['value']['files'][fidx]['aid'] = att.id
131
+ properties[Labimotion::Prop::LAYERS][pa[:layer]][Labimotion::Prop::FIELDS][idx]['value']['files'][fidx]['uid'] = att.identifier
132
132
  element.update_columns(properties: properties)
133
133
  rescue StandardError => e
134
134
  Labimotion.log_exception(e, current_user)
@@ -143,9 +143,9 @@ module Labimotion
143
143
  map_info&.keys&.each do |key|
144
144
  next if map_info[key]['files'].empty?
145
145
 
146
- if type == 'Segment'
146
+ if type == Labimotion::Prop::SEGMENT
147
147
  element = Labimotion::Segment.find_by(element_id: id, segment_klass_id: key)
148
- elsif type == 'Element'
148
+ elsif type == Labimotion::Prop::ELEMENT
149
149
  element = Labimotion::Element.find_by(id: id)
150
150
  end
151
151
  next if element.nil?
@@ -73,8 +73,7 @@ module Labimotion
73
73
  attributes['updated_by'] = current_user.id
74
74
  attributes['sync_by'] = current_user.id
75
75
  attributes['sync_time'] = DateTime.now
76
-
77
- element_klass = Labimotion::ElementKlass.find_by(identifier: response['element_klass']['identifier'])
76
+ element_klass = Labimotion::ElementKlass.find_by(identifier: response['element_klass']['identifier']) if response.dig('element_klass','identifier').present?
78
77
  element_klass = Labimotion::ElementKlass.find_by(name: response['element_klass']['name'], is_generic: false) if element_klass.nil?
79
78
  return { status: 'error', message: "The element [#{response['element_klass']['name']}] does not exist in this instance" } if element_klass.nil?
80
79
 
@@ -247,39 +247,38 @@ module Labimotion
247
247
  end
248
248
 
249
249
  def self.update_ds(dataset, dsr, current_user = nil) # rubocop: disable Metrics/PerceivedComplexity
250
- layers = dataset.properties['layers'] || {}
250
+ layers = dataset.properties[Labimotion::Prop::LAYERS] || {}
251
251
  new_prop = dataset.properties
252
252
  dsr.each do |ds|
253
253
  layer = layers[ds[:layer]]
254
- next if layer.nil? || layer['fields'].nil?
254
+ next if layer.nil? || layer[Labimotion::Prop::FIELDS].nil?
255
255
 
256
- fields = layer['fields'].select{ |f| f['field'] == ds[:field] }
256
+ fields = layer[Labimotion::Prop::FIELDS].select{ |f| f['field'] == ds[:field] }
257
257
  fi = fields&.first
258
- idx = layer['fields'].find_index(fi)
258
+ idx = layer[Labimotion::Prop::FIELDS].find_index(fi)
259
259
  fi['value'] = ds[:value]
260
260
  fi['device'] = ds[:device] || ds[:value]
261
- new_prop['layers'][ds[:layer]]['fields'][idx] = fi
261
+ new_prop[Labimotion::Prop::LAYERS][ds[:layer]][Labimotion::Prop::FIELDS][idx] = fi
262
262
  end
263
- new_prop.dig('layers', 'general', 'fields')&.each_with_index do |fi, idx|
263
+ new_prop.dig(Labimotion::Prop::LAYERS, 'general', Labimotion::Prop::FIELDS)&.each_with_index do |fi, idx|
264
264
  if fi['field'] == 'creator' && current_user.present?
265
- fi['label'] = fi['label']
266
265
  fi['value'] = current_user.name
267
266
  fi['system'] = current_user.name
268
- new_prop['layers']['general']['fields'][idx] = fi
267
+ new_prop[Labimotion::Prop::LAYERS]['general'][Labimotion::Prop::FIELDS][idx] = fi
269
268
  end
270
269
  end
271
270
  element = Container.find(dataset.element_id)&.root_element
272
- element.present? && element&.class&.name == 'Sample' && new_prop.dig('layers', 'sample_details', 'fields')&.each_with_index do |fi, idx|
271
+ element.present? && element&.class&.name == 'Sample' && new_prop.dig(Labimotion::Prop::LAYERS, 'sample_details', Labimotion::Prop::FIELDS)&.each_with_index do |fi, idx|
273
272
  if fi['field'] == 'id'
274
273
  fi['value'] = element.id
275
274
  fi['system'] = element.id
276
- new_prop['layers']['general']['fields'][idx] = fi
275
+ new_prop[Labimotion::Prop::LAYERS]['sample_details'][Labimotion::Prop::FIELDS][idx] = fi
277
276
  end
278
277
 
279
278
  if fi['field'] == 'label'
280
279
  fi['value'] = element.short_label
281
280
  fi['system'] = element.short_label
282
- new_prop['layers']['general']['fields'][idx] = fi
281
+ new_prop[Labimotion::Prop::LAYERS]['sample_details'][Labimotion::Prop::FIELDS][idx] = fi
283
282
  end
284
283
  end
285
284
  dataset.properties = new_prop
@@ -345,9 +344,9 @@ module Labimotion
345
344
 
346
345
  def self.metadata(id)
347
346
  att = Attachment.find(id)
348
- return if att.nil? || att.attachable_id.nil? || att.attachable_type != 'Container'
347
+ return if att.nil? || att.attachable_id.nil? || att.attachable_type != Labimotion::Prop::CONTAINER
349
348
 
350
- ds = Labimotion::Dataset.find_by(element_type: 'Container', element_id: att.attachable_id)
349
+ ds = Labimotion::Dataset.find_by(element_type: Labimotion::Prop::CONTAINER, element_id: att.attachable_id)
351
350
  att.update_column(:con_state, Labimotion::ConState::COMPLETED) if ds.present?
352
351
  process_ds(att.id) if ds.nil?
353
352
  end
@@ -18,6 +18,8 @@ module Labimotion
18
18
  element_name = Container.find(id)&.root_element&.short_label
19
19
  ols = ols_name(id)
20
20
  "#{element_name}_#{ols.gsub(' ', '_')}.xlsx"
21
+ rescue StandardError => e
22
+ Labimotion.log_exception(e)
21
23
  end
22
24
 
23
25
  def ols_name(id)
@@ -32,6 +34,9 @@ module Labimotion
32
34
  name = '1H NMR' if ds.dataset_klass.ols_term_id == 'CHMO:0000593'
33
35
  name = '13C NMR' if ds.dataset_klass.ols_term_id == 'CHMO:0000595'
34
36
  name.slice(0, 26)
37
+ rescue StandardError => e
38
+ Labimotion.log_exception(e)
39
+ 'ols_name'
35
40
  end
36
41
 
37
42
  def description(ds, id)
@@ -56,6 +61,8 @@ module Labimotion
56
61
  sheet.add_row(['Source data', 'The data from Device or Chemotion, cannot be modified once a generic dataset is created'])
57
62
  sheet.add_row([''])
58
63
  sheet.add_row([''])
64
+ rescue StandardError => e
65
+ Labimotion.log_exception(e)
59
66
  end
60
67
 
61
68
  def export(id)
@@ -74,26 +81,32 @@ module Labimotion
74
81
  layer_style = sheet.styles.add_style(b: true, bg_color: 'CEECF5')
75
82
  sheet.add_row(header, style: header_style)
76
83
 
77
- layers = ds.properties['layers'] || {}
84
+ layers = ds.properties[Labimotion::Prop::LAYERS] || {}
85
+ options = ds.properties[Labimotion::Prop::SEL_OPTIONS]
78
86
  layer_keys = layers.keys.sort_by { |key| layers[key]['position'] }
79
87
  layer_keys.each do |key|
80
88
  layer = layers[key]
81
89
  sheet.add_row([layer['label'], ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' '], style: layer_style)
82
- sorted_fields = layer['fields'].sort_by { |obj| obj['position'] }
90
+ sorted_fields = layer[Labimotion::Prop::FIELDS].sort_by { |obj| obj['position'] }
83
91
  sorted_fields.each do |field|
84
92
  next if field['type'] == 'dummy'
85
93
 
86
94
  type = field['type']
87
95
  from_device = field['device'].present? ? 'Device' : ''
88
96
  from_device = field['system'].present? ? 'Chemotion' : from_device
89
- type = "#{field['type']}-#{field['option_layers']}" if field['type'] == 'select' || field['type'] == 'system-defined'
97
+ type = "#{field['type']}-#{field['option_layers']}" if field['type'] == Labimotion::FieldType::SELECT || field['type'] == Labimotion::FieldType::SYSTEM_DEFINED
90
98
 
91
99
  show_value = field['value'] =~ /\A\d+,\d+\z/ ? field['value']&.gsub(',', '.') : field['value']
92
100
  sheet.add_row([' ', field['label'], nil, field['value_system'], field['field'], type, from_device, field['dkey'], nil].freeze)
93
101
 
94
- if %w[system-defined integer].include? field['type']
95
- sheet.rows.last.cells[2].type = :integer
96
- sheet.rows.last.cells[8].type = :integer
102
+ case field['type']
103
+ when Labimotion::FieldType::SELECT
104
+ sheet.rows.last.cells[2].type = :string
105
+ sheet.rows.last.cells[8].type = :string
106
+ show_value = opt_value(field, options) if show_value.present?
107
+ when Labimotion::FieldType::SYSTEM_DEFINED, Labimotion::FieldType::INTEGER
108
+ sheet.rows.last.cells[2].type = :float
109
+ sheet.rows.last.cells[8].type = :float
97
110
  else
98
111
  sheet.rows.last.cells[2].type = :string
99
112
  sheet.rows.last.cells[8].type = :string
@@ -105,6 +118,19 @@ module Labimotion
105
118
  end
106
119
  # sheet.column_widths nil, nil, nil, nil, 0, 0, 0, 0, 0
107
120
  end
121
+ rescue StandardError => e
122
+ Labimotion.log_exception(e)
123
+ end
124
+
125
+ def opt_value(field, options)
126
+ return nil if field.nil? || options.nil? || field['value']&.empty? || field['option_layers']&.empty?
127
+ return nil unless opts = options.fetch(field['option_layers'], nil)&.fetch('options', nil)
128
+
129
+ selected = opts&.find { |ss| ss['key'] == field['value'] }
130
+ selected&.fetch('label', nil) || field['value']
131
+ rescue StandardError => e
132
+ Labimotion.log_exception(e)
133
+ field['value']
108
134
  end
109
135
 
110
136
  def spectra(id)
@@ -109,7 +109,7 @@ module Labimotion
109
109
  return if field['field'] != field_name || value&.empty?
110
110
 
111
111
  field['value'] = value
112
- prop['layers'][layer_name]['fields'][idx] = field
112
+ prop[Labimotion::Prop::LAYERS][layer_name][Labimotion::Prop::FIELDS][idx] = field
113
113
  prop
114
114
  end
115
115
 
@@ -117,14 +117,14 @@ module Labimotion
117
117
  dataset = obj[:dataset]
118
118
  metadata = obj[:metadata]
119
119
  new_prop = dataset.properties
120
- new_prop.dig('layers', 'general', 'fields')&.each_with_index do |fi, idx|
120
+ new_prop.dig(Labimotion::Prop::LAYERS, 'general', Labimotion::Prop::FIELDS)&.each_with_index do |fi, idx|
121
121
  # new_prop = set_data(new_prop, fi, idx, 'general', 'title', metadata['NAME'])
122
122
  if fi['field'] == 'title' && metadata['NAME'].present?
123
123
  ## fi['label'] = fi['label']
124
124
  fi['value'] = metadata['NAME']
125
125
  fi['device'] = metadata['NAME']
126
126
  fi['dkey'] = 'NAME'
127
- new_prop['layers']['general']['fields'][idx] = fi
127
+ new_prop[Labimotion::Prop::LAYERS]['general'][Labimotion::Prop::FIELDS][idx] = fi
128
128
  end
129
129
 
130
130
  if fi['field'] == 'date' && metadata['Date_'].present?
@@ -132,7 +132,7 @@ module Labimotion
132
132
  fi['value'] = metadata['Date_']
133
133
  fi['device'] = metadata['Date_']
134
134
  fi['dkey'] = 'Date_'
135
- new_prop['layers']['general']['fields'][idx] = fi
135
+ new_prop[Labimotion::Prop::LAYERS]['general'][Labimotion::Prop::FIELDS][idx] = fi
136
136
  end
137
137
 
138
138
  if fi['field'] == 'time' && metadata['Time'].present?
@@ -140,130 +140,130 @@ module Labimotion
140
140
  fi['value'] = metadata['Time']
141
141
  fi['device'] = metadata['Time']
142
142
  fi['dkey'] = 'Time'
143
- new_prop['layers']['general']['fields'][idx] = fi
143
+ new_prop[Labimotion::Prop::LAYERS]['general'][Labimotion::Prop::FIELDS][idx] = fi
144
144
  end
145
145
 
146
146
  if fi['field'] == 'creator' && current_user.present?
147
147
  ## fi['label'] = fi['label']
148
148
  fi['value'] = current_user.name
149
- new_prop['layers']['general']['fields'][idx] = fi
149
+ new_prop[Labimotion::Prop::LAYERS]['general'][Labimotion::Prop::FIELDS][idx] = fi
150
150
  end
151
151
  end
152
152
  element = Container.find(id)&.root_element
153
- element.present? && element&.class&.name == 'Sample' && new_prop.dig('layers', 'sample_details',
154
- 'fields')&.each_with_index do |fi, idx|
153
+ element.present? && element&.class&.name == 'Sample' && new_prop.dig(Labimotion::Prop::LAYERS, 'sample_details',
154
+ Labimotion::Prop::FIELDS)&.each_with_index do |fi, idx|
155
155
  if fi['field'] == 'label'
156
156
  fi['value'] = element.short_label
157
- new_prop['layers']['sample_details']['fields'][idx] = fi
157
+ new_prop[Labimotion::Prop::LAYERS]['sample_details'][Labimotion::Prop::FIELDS][idx] = fi
158
158
  end
159
159
  if fi['field'] == 'id'
160
160
  fi['value'] = element.id
161
- new_prop['layers']['sample_details']['fields'][idx] = fi
161
+ new_prop[Labimotion::Prop::LAYERS]['sample_details'][Labimotion::Prop::FIELDS][idx] = fi
162
162
  end
163
163
  end
164
164
 
165
- new_prop.dig('layers', 'instrument', 'fields')&.each_with_index do |fi, idx|
165
+ new_prop.dig(Labimotion::Prop::LAYERS, 'instrument', Labimotion::Prop::FIELDS)&.each_with_index do |fi, idx|
166
166
  if fi['field'] == 'instrument' && metadata['INSTRUM'].present?
167
167
  ## fi['label'] = fi['label']
168
168
  fi['value'] = metadata['INSTRUM']
169
169
  fi['device'] = metadata['INSTRUM']
170
170
  fi['dkey'] = 'INSTRUM'
171
- new_prop['layers']['instrument']['fields'][idx] = fi
171
+ new_prop[Labimotion::Prop::LAYERS]['instrument'][Labimotion::Prop::FIELDS][idx] = fi
172
172
  end
173
173
  end
174
174
 
175
- new_prop.dig('layers', 'equipment', 'fields')&.each_with_index do |fi, idx|
175
+ new_prop.dig(Labimotion::Prop::LAYERS, 'equipment', Labimotion::Prop::FIELDS)&.each_with_index do |fi, idx|
176
176
  if fi['field'] == 'probehead' && metadata['PROBHD'].present?
177
177
  ## fi['label'] = fi['label']
178
178
  fi['value'] = metadata['PROBHD']
179
179
  fi['device'] = metadata['PROBHD']
180
180
  fi['dkey'] = 'PROBHD'
181
- new_prop['layers']['equipment']['fields'][idx] = fi
181
+ new_prop[Labimotion::Prop::LAYERS]['equipment'][Labimotion::Prop::FIELDS][idx] = fi
182
182
  end
183
183
  end
184
184
 
185
- new_prop.dig('layers', 'sample_preparation', 'fields')&.each_with_index do |fi, idx|
185
+ new_prop.dig(Labimotion::Prop::LAYERS, 'sample_preparation', Labimotion::Prop::FIELDS)&.each_with_index do |fi, idx|
186
186
  if fi['field'] == 'solvent' && metadata['SOLVENT'].present?
187
187
  ## fi['label'] = fi['label']
188
188
  fi['value'] = metadata['SOLVENT']
189
189
  fi['device'] = metadata['SOLVENT']
190
190
  fi['dkey'] = 'SOLVENT'
191
191
  fi['value'] = 'chloroform-D1 (CDCl3)' if metadata['SOLVENT'] == 'CDCl3'
192
- new_prop['layers']['sample_preparation']['fields'][idx] = fi
192
+ new_prop[Labimotion::Prop::LAYERS]['sample_preparation'][Labimotion::Prop::FIELDS][idx] = fi
193
193
  end
194
194
  end
195
195
 
196
- new_prop.dig('layers', 'set', 'fields')&.each_with_index do |fi, idx|
196
+ new_prop.dig(Labimotion::Prop::LAYERS, 'set', Labimotion::Prop::FIELDS)&.each_with_index do |fi, idx|
197
197
  if fi['field'] == 'temperature' && metadata['TE'].present?
198
198
  ## fi['label'] = fi['label']
199
199
  fi['value'] = metadata['TE'].split(/\s+/).first
200
200
  fi['device'] = metadata['TE']
201
201
  fi['dkey'] = 'TE'
202
202
  fi['value_system'] = metadata['TE'].split(/\s+/).last
203
- new_prop['layers']['set']['fields'][idx] = fi
203
+ new_prop[Labimotion::Prop::LAYERS]['set'][Labimotion::Prop::FIELDS][idx] = fi
204
204
  end
205
205
  if fi['field'] == 'ns' && metadata['NS'].present?
206
206
  ## fi['label'] = fi['label']
207
207
  fi['value'] = metadata['NS']
208
208
  fi['device'] = metadata['NS']
209
209
  fi['dkey'] = 'NS'
210
- new_prop['layers']['set']['fields'][idx] = fi
210
+ new_prop[Labimotion::Prop::LAYERS]['set'][Labimotion::Prop::FIELDS][idx] = fi
211
211
  end
212
212
  if fi['field'] == 'PULPROG' && metadata['PULPROG'].present?
213
213
  ## fi['label'] = fi['label']
214
214
  fi['value'] = metadata['PULPROG']
215
215
  fi['device'] = metadata['PULPROG']
216
216
  fi['dkey'] = 'PULPROG'
217
- new_prop['layers']['set']['fields'][idx] = fi
217
+ new_prop[Labimotion::Prop::LAYERS]['set'][Labimotion::Prop::FIELDS][idx] = fi
218
218
  end
219
219
  if fi['field'] == 'td' && metadata['TD'].present?
220
220
  ## fi['label'] = fi['label']
221
221
  fi['value'] = metadata['TD']
222
222
  fi['device'] = metadata['TD']
223
223
  fi['dkey'] = 'TD'
224
- new_prop['layers']['set']['fields'][idx] = fi
224
+ new_prop[Labimotion::Prop::LAYERS]['set'][Labimotion::Prop::FIELDS][idx] = fi
225
225
  end
226
226
  if fi['field'] == 'done' && metadata['D1'].present?
227
227
  ## fi['label'] = fi['label']
228
228
  fi['value'] = metadata['D1']
229
229
  fi['device'] = metadata['D1']
230
230
  fi['dkey'] = 'D1'
231
- new_prop['layers']['set']['fields'][idx] = fi
231
+ new_prop[Labimotion::Prop::LAYERS]['set'][Labimotion::Prop::FIELDS][idx] = fi
232
232
  end
233
233
  if fi['field'] == 'sf' && metadata['SF'].present?
234
234
  ## fi['label'] = fi['label']
235
235
  fi['value'] = metadata['SF']
236
236
  fi['device'] = metadata['SF']
237
237
  fi['dkey'] = 'SF'
238
- new_prop['layers']['set']['fields'][idx] = fi
238
+ new_prop[Labimotion::Prop::LAYERS]['set'][Labimotion::Prop::FIELDS][idx] = fi
239
239
  end
240
240
  if fi['field'] == 'sfoone' && metadata['SFO1'].present?
241
241
  ## fi['label'] = fi['label']
242
242
  fi['value'] = metadata['SFO1']
243
243
  fi['device'] = metadata['SFO1']
244
244
  fi['dkey'] = 'SFO1'
245
- new_prop['layers']['set']['fields'][idx] = fi
245
+ new_prop[Labimotion::Prop::LAYERS]['set'][Labimotion::Prop::FIELDS][idx] = fi
246
246
  end
247
247
  if fi['field'] == 'sfotwo' && metadata['SFO2'].present?
248
248
  ## fi['label'] = fi['label']
249
249
  fi['value'] = metadata['SFO2']
250
250
  fi['device'] = metadata['SFO2']
251
251
  fi['dkey'] = 'SFO2'
252
- new_prop['layers']['set']['fields'][idx] = fi
252
+ new_prop[Labimotion::Prop::LAYERS]['set'][Labimotion::Prop::FIELDS][idx] = fi
253
253
  end
254
254
  if fi['field'] == 'nucone' && metadata['NUC1'].present?
255
255
  ## fi['label'] = fi['label']
256
256
  fi['value'] = metadata['NUC1']
257
257
  fi['device'] = metadata['NUC1']
258
258
  fi['dkey'] = 'NUC1'
259
- new_prop['layers']['set']['fields'][idx] = fi
259
+ new_prop[Labimotion::Prop::LAYERS]['set'][Labimotion::Prop::FIELDS][idx] = fi
260
260
  end
261
261
  if fi['field'] == 'nuctwo' && metadata['NUC2'].present?
262
262
  ## fi['label'] = fi['label']
263
263
  fi['value'] = metadata['NUC2']
264
264
  fi['device'] = metadata['NUC2']
265
265
  fi['dkey'] = 'NUC2'
266
- new_prop['layers']['set']['fields'][idx] = fi
266
+ new_prop[Labimotion::Prop::LAYERS]['set'][Labimotion::Prop::FIELDS][idx] = fi
267
267
  end
268
268
  end
269
269
  dataset.properties = new_prop