labimotion 1.1.3 → 1.2.0.0
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- checksums.yaml +4 -4
- data/lib/labimotion/apis/generic_element_api.rb +32 -38
- data/lib/labimotion/collection/export.rb +45 -84
- data/lib/labimotion/collection/import.rb +60 -54
- data/lib/labimotion/entities/element_revision_entity.rb +10 -10
- data/lib/labimotion/entities/eln_element_entity.rb +23 -23
- data/lib/labimotion/entities/properties_entity.rb +18 -19
- data/lib/labimotion/entities/segment_revision_entity.rb +11 -11
- data/lib/labimotion/helpers/element_helpers.rb +14 -4
- data/lib/labimotion/helpers/generic_helpers.rb +9 -9
- data/lib/labimotion/helpers/segment_helpers.rb +1 -2
- data/lib/labimotion/libs/converter.rb +12 -13
- data/lib/labimotion/libs/export_dataset.rb +32 -6
- data/lib/labimotion/libs/nmr_mapper.rb +27 -27
- data/lib/labimotion/libs/properties_handler.rb +95 -0
- data/lib/labimotion/libs/sample_association.rb +15 -15
- data/lib/labimotion/models/concerns/generic_klass_revisions.rb +1 -1
- data/lib/labimotion/models/concerns/generic_revisions.rb +3 -3
- data/lib/labimotion/models/concerns/linked_properties.rb +18 -0
- data/lib/labimotion/models/concerns/segmentable.rb +17 -12
- data/lib/labimotion/models/element.rb +26 -17
- data/lib/labimotion/utils/export_utils.rb +196 -0
- data/lib/labimotion/utils/field_type.rb +23 -0
- data/lib/labimotion/utils/import_utils.rb +244 -59
- data/lib/labimotion/utils/prop.rb +27 -0
- data/lib/labimotion/utils/search.rb +2 -2
- data/lib/labimotion/utils/serializer.rb +22 -22
- data/lib/labimotion/version.rb +1 -1
- data/lib/labimotion.rb +4 -1
- metadata +7 -2
@@ -6,39 +6,38 @@ module Labimotion
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# TODO: Refactor this method to something more readable/understandable
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def properties
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(object&.properties.is_a?(Hash) && object.properties[
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(object&.properties.is_a?(Hash) && object.properties[Labimotion::Prop::LAYERS]&.keys || []).each do |key|
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# layer = object.properties[key]
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field_sample_molecules = object.properties[
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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 }
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field_sample_molecules.each do |field|
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idx = object.properties[
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idx = object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS].index(field)
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sid = field.dig('value', 'el_id')
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next unless sid.present?
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el = field['type'] ==
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el = field['type'] == Labimotion::FieldType::DRAG_SAMPLE ? Sample.find_by(id: sid) : Molecule.find_by(id: sid)
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next unless el.present?
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next unless object.properties.dig(
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next unless object.properties.dig(Labimotion::Prop::LAYERS, key, Labimotion::Prop::FIELDS, idx, 'value').present?
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object.properties[
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object.properties[
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object.properties[
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object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS][idx]['value']['el_label'] = el.short_label if field['type'] == Labimotion::FieldType::DRAG_SAMPLE
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object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS][idx]['value']['el_tip'] = el.short_label if field['type'] == Labimotion::FieldType::DRAG_SAMPLE
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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)
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end
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field_tables = object.properties[
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field_tables = object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS].select { |ss| ss['type'] == Labimotion::FieldType::TABLE }
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field_tables.each do |field|
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idx = object.properties[
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next unless field['sub_values'].present? && field[
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idx = object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS].index(field)
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next unless field['sub_values'].present? && field[Labimotion::Prop::SUBFIELDS].present?
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field_table_molecules = field[
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object.properties[
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field_table_molecules = field[Labimotion::Prop::SUBFIELDS].select { |ss| ss['type'] == Labimotion::FieldType::DRAG_MOLECULE }
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object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS][idx] = set_table(field, field_table_molecules, Labimotion::Prop::MOLECULE) if field_table_molecules.present?
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field_table_samples = field[
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object.properties[
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field_table_samples = field[Labimotion::Prop::SUBFIELDS].select { |ss| ss['type'] == Labimotion::FieldType::DRAG_SAMPLE }
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object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS][idx] = set_table(field, field_table_samples, Labimotion::Prop::SAMPLE) if field_table_samples.present?
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end
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end
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object.properties
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end
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def set_table(field, field_table_objs, obj)
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col_ids = field_table_objs.map { |x| x.values[0] }
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col_ids.each do |col_id|
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@@ -46,16 +45,16 @@ module Labimotion
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next unless sub_value[col_id].present? && sub_value[col_id]['value'].present? && sub_value[col_id]['value']['el_id'].present?
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find_obj = obj.constantize.find_by(id: sub_value[col_id]['value']['el_id'])
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next
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next if find_obj.blank?
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case obj
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when
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when Labimotion::Prop::MOLECULE
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sub_value[col_id]['value']['el_svg'] = File.join('/images', 'molecules', find_obj.molecule_svg_file)
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sub_value[col_id]['value']['el_inchikey'] = find_obj.inchikey
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sub_value[col_id]['value']['el_smiles'] = find_obj.cano_smiles
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sub_value[col_id]['value']['el_iupac'] = find_obj.iupac_name
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sub_value[col_id]['value']['el_molecular_weight'] = find_obj.molecular_weight
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when
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when Labimotion::Prop::SAMPLE
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sub_value[col_id]['value']['el_svg'] = find_obj.get_svg_path
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sub_value[col_id]['value']['el_label'] = find_obj.short_label
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sub_value[col_id]['value']['el_short_label'] = find_obj.short_label
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@@ -9,27 +9,27 @@ module Labimotion
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end
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def properties
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object.properties[
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field_sample_molecules = object.properties[
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object.properties[Labimotion::Prop::LAYERS]&.keys.each do |key|
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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 }
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field_sample_molecules.each do |field|
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idx = object.properties[
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idx = object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS].index(field)
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sid = field.dig('value', 'el_id')
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next unless sid.present?
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el = field['type'] ==
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el = field['type'] == Labimotion::FieldType::DRAG_SAMPLE ? Sample.find_by(id: sid) : Molecule.find_by(id: sid)
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next unless el.present?
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next unless object.properties.dig(
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next unless object.properties.dig(Labimotion::Prop::LAYERS, key, Labimotion::Prop::FIELDS, idx, 'value').present?
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object.properties[
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object.properties[
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object.properties[
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object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS][idx]['value']['el_label'] = el.short_label if field['type'] == Labimotion::FieldType::DRAG_SAMPLE
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object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS][idx]['value']['el_tip'] = el.short_label if field['type'] == Labimotion::FieldType::DRAG_SAMPLE
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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)
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end
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field_tables = object.properties[
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field_tables = object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS].select { |ss| ss['type'] == Labimotion::FieldType::TABLE }
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field_tables.each do |field|
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next unless field['sub_values'].present? && field[
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next unless field['sub_values'].present? && field[Labimotion::Prop::SUBFIELDS].present?
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field_table_molecules = field[
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field_table_molecules = field[Labimotion::Prop::SUBFIELDS].select { |ss| ss['type'] == Labimotion::FieldType::DRAG_MOLECULE }
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next unless field_table_molecules.present?
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col_ids = field_table_molecules.map { |x| x.values[0] }
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@@ -133,10 +133,20 @@ module Labimotion
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raise e
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end
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def split_elements(ui_state, current_user)
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col_id = ui_state[:currentCollectionId] || 0
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element_ids = Labimotion::Element.for_user(current_user.id).for_ui_state_with_collection(ui_state[:element], Labimotion::CollectionsElement, col_id)
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klass_id = Labimotion::ElementKlass.find_by(name: ui_state[:element][:name])&.id
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Labimotion::Element.where(id: element_ids, element_klass_id: klass_id).each do |element|
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element.split(current_user, col_id)
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end
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{}
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end
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def upload_generics_files(current_user, params)
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attach_ary = []
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att_ary = create_uploads(
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Labimotion::Prop::ELEMENT,
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params[:att_id],
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params[:elfiles],
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params[:elInfo],
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@@ -146,7 +156,7 @@ module Labimotion
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(attach_ary << att_ary).flatten! unless att_ary&.empty?
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att_ary = create_uploads(
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Labimotion::Prop::SEGMENT,
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params[:att_id],
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params[:sefiles],
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params[:seInfo],
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@@ -195,7 +205,7 @@ module Labimotion
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layer, field = params[:sort_column].split('.')
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element_klass = Labimotion::ElementKlass.find_by(name: params[:el_type])
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allowed_fields = element_klass.properties_release.dig(
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allowed_fields = element_klass.properties_release.dig(Labimotion::Prop::LAYERS, layer, Labimotion::Prop::FIELDS)&.pluck('field') || []
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if field.in?(allowed_fields)
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query = ActiveRecord::Base.sanitize_sql(
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@@ -258,7 +268,7 @@ module Labimotion
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layer, field = params[:sort_column].split('.')
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element_klass = Labimotion::ElementKlass.find_by(name: params[:el_type])
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allowed_fields = element_klass.properties_release.dig(
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allowed_fields = element_klass.properties_release.dig(Labimotion::Prop::LAYERS, layer, Labimotion::Prop::FIELDS)&.pluck('field') || []
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if field.in?(allowed_fields)
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query = ActiveRecord::Base.sanitize_sql(
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@@ -107,9 +107,9 @@ module Labimotion
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def fetch_properties_uploads(properties)
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uploads = []
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properties[
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layer = properties[
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field_uploads = layer[
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properties[Labimotion::Prop::LAYERS].keys.each do |key|
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layer = properties[Labimotion::Prop::LAYERS][key]
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field_uploads = layer[Labimotion::Prop::FIELDS].select { |ss| ss['type'] == Labimotion::FieldType::UPLOAD }
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field_uploads.each do |field|
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((field['value'] && field['value']['files']) || []).each do |file|
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uploads.push({ layer: key, field: field['field'], uid: file['uid'], filename: file['filename'] })
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@@ -125,10 +125,10 @@ module Labimotion
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def update_properties_upload(element, properties, att, pa)
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return if pa.nil?
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idx = properties[
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fidx = properties[
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properties[
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properties[
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idx = properties[Labimotion::Prop::LAYERS][pa[:layer]][Labimotion::Prop::FIELDS].index { |fl| fl['field'] == pa[:field] }
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fidx = properties[Labimotion::Prop::LAYERS][pa[:layer]][Labimotion::Prop::FIELDS][idx]['value']['files'].index { |fi| fi['uid'] == pa[:uid] }
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properties[Labimotion::Prop::LAYERS][pa[:layer]][Labimotion::Prop::FIELDS][idx]['value']['files'][fidx]['aid'] = att.id
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properties[Labimotion::Prop::LAYERS][pa[:layer]][Labimotion::Prop::FIELDS][idx]['value']['files'][fidx]['uid'] = att.identifier
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element.update_columns(properties: properties)
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rescue StandardError => e
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Labimotion.log_exception(e, current_user)
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@@ -143,9 +143,9 @@ module Labimotion
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map_info&.keys&.each do |key|
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next if map_info[key]['files'].empty?
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if type ==
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if type == Labimotion::Prop::SEGMENT
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element = Labimotion::Segment.find_by(element_id: id, segment_klass_id: key)
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elsif type ==
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elsif type == Labimotion::Prop::ELEMENT
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element = Labimotion::Element.find_by(id: id)
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end
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next if element.nil?
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@@ -73,8 +73,7 @@ module Labimotion
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attributes['updated_by'] = current_user.id
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attributes['sync_by'] = current_user.id
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attributes['sync_time'] = DateTime.now
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element_klass = Labimotion::ElementKlass.find_by(identifier: response['element_klass']['identifier'])
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element_klass = Labimotion::ElementKlass.find_by(identifier: response['element_klass']['identifier']) if response.dig('element_klass','identifier').present?
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element_klass = Labimotion::ElementKlass.find_by(name: response['element_klass']['name'], is_generic: false) if element_klass.nil?
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return { status: 'error', message: "The element [#{response['element_klass']['name']}] does not exist in this instance" } if element_klass.nil?
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@@ -247,39 +247,38 @@ module Labimotion
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end
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def self.update_ds(dataset, dsr, current_user = nil) # rubocop: disable Metrics/PerceivedComplexity
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layers = dataset.properties[
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layers = dataset.properties[Labimotion::Prop::LAYERS] || {}
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new_prop = dataset.properties
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dsr.each do |ds|
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layer = layers[ds[:layer]]
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next if layer.nil? || layer[
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next if layer.nil? || layer[Labimotion::Prop::FIELDS].nil?
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fields = layer[
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fields = layer[Labimotion::Prop::FIELDS].select{ |f| f['field'] == ds[:field] }
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fi = fields&.first
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idx = layer[
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idx = layer[Labimotion::Prop::FIELDS].find_index(fi)
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fi['value'] = ds[:value]
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fi['device'] = ds[:device] || ds[:value]
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new_prop[
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new_prop[Labimotion::Prop::LAYERS][ds[:layer]][Labimotion::Prop::FIELDS][idx] = fi
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end
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new_prop.dig(
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new_prop.dig(Labimotion::Prop::LAYERS, 'general', Labimotion::Prop::FIELDS)&.each_with_index do |fi, idx|
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if fi['field'] == 'creator' && current_user.present?
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fi['label'] = fi['label']
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fi['value'] = current_user.name
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fi['system'] = current_user.name
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new_prop[
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new_prop[Labimotion::Prop::LAYERS]['general'][Labimotion::Prop::FIELDS][idx] = fi
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end
|
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end
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element = Container.find(dataset.element_id)&.root_element
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element.present? && element&.class&.name == 'Sample' && new_prop.dig(
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element.present? && element&.class&.name == 'Sample' && new_prop.dig(Labimotion::Prop::LAYERS, 'sample_details', Labimotion::Prop::FIELDS)&.each_with_index do |fi, idx|
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if fi['field'] == 'id'
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fi['value'] = element.id
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fi['system'] = element.id
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new_prop[
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new_prop[Labimotion::Prop::LAYERS]['sample_details'][Labimotion::Prop::FIELDS][idx] = fi
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end
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if fi['field'] == 'label'
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fi['value'] = element.short_label
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fi['system'] = element.short_label
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new_prop[
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new_prop[Labimotion::Prop::LAYERS]['sample_details'][Labimotion::Prop::FIELDS][idx] = fi
|
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end
|
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end
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dataset.properties = new_prop
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@@ -345,9 +344,9 @@ module Labimotion
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def self.metadata(id)
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att = Attachment.find(id)
|
348
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-
return if att.nil? || att.attachable_id.nil? || att.attachable_type !=
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347
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+
return if att.nil? || att.attachable_id.nil? || att.attachable_type != Labimotion::Prop::CONTAINER
|
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348
|
|
350
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-
ds = Labimotion::Dataset.find_by(element_type:
|
349
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+
ds = Labimotion::Dataset.find_by(element_type: Labimotion::Prop::CONTAINER, element_id: att.attachable_id)
|
351
350
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att.update_column(:con_state, Labimotion::ConState::COMPLETED) if ds.present?
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352
351
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process_ds(att.id) if ds.nil?
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352
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end
|
@@ -18,6 +18,8 @@ module Labimotion
|
|
18
18
|
element_name = Container.find(id)&.root_element&.short_label
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19
19
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ols = ols_name(id)
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20
20
|
"#{element_name}_#{ols.gsub(' ', '_')}.xlsx"
|
21
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+
rescue StandardError => e
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22
|
+
Labimotion.log_exception(e)
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21
23
|
end
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22
24
|
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23
25
|
def ols_name(id)
|
@@ -32,6 +34,9 @@ module Labimotion
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32
34
|
name = '1H NMR' if ds.dataset_klass.ols_term_id == 'CHMO:0000593'
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33
35
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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'
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35
40
|
end
|
36
41
|
|
37
42
|
def description(ds, id)
|
@@ -56,6 +61,8 @@ module Labimotion
|
|
56
61
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sheet.add_row(['Source data', 'The data from Device or Chemotion, cannot be modified once a generic dataset is created'])
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57
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sheet.add_row([''])
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58
63
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sheet.add_row([''])
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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')
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75
82
|
sheet.add_row(header, style: header_style)
|
76
83
|
|
77
|
-
layers = ds.properties[
|
84
|
+
layers = ds.properties[Labimotion::Prop::LAYERS] || {}
|
85
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+
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
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|
layer = layers[key]
|
81
89
|
sheet.add_row([layer['label'], ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' '], style: layer_style)
|
82
|
-
sorted_fields = layer[
|
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'] ==
|
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
|
-
|
95
|
-
|
96
|
-
sheet.rows.last.cells[
|
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[
|
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(
|
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[
|
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[
|
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[
|
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[
|
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(
|
154
|
-
|
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[
|
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[
|
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(
|
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[
|
171
|
+
new_prop[Labimotion::Prop::LAYERS]['instrument'][Labimotion::Prop::FIELDS][idx] = fi
|
172
172
|
end
|
173
173
|
end
|
174
174
|
|
175
|
-
new_prop.dig(
|
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[
|
181
|
+
new_prop[Labimotion::Prop::LAYERS]['equipment'][Labimotion::Prop::FIELDS][idx] = fi
|
182
182
|
end
|
183
183
|
end
|
184
184
|
|
185
|
-
new_prop.dig(
|
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[
|
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(
|
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[
|
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[
|
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[
|
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[
|
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[
|
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[
|
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[
|
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[
|
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[
|
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[
|
266
|
+
new_prop[Labimotion::Prop::LAYERS]['set'][Labimotion::Prop::FIELDS][idx] = fi
|
267
267
|
end
|
268
268
|
end
|
269
269
|
dataset.properties = new_prop
|