labimotion 1.4.0.rc2 → 1.4.0.rc4

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Files changed (11) hide show
  1. checksums.yaml +4 -4
  2. data/lib/labimotion/entities/element_revision_entity.rb +2 -2
  3. data/lib/labimotion/entities/eln_element_entity.rb +2 -2
  4. data/lib/labimotion/entities/properties_entity.rb +2 -2
  5. data/lib/labimotion/entities/segment_revision_entity.rb +2 -2
  6. data/lib/labimotion/helpers/segment_helpers.rb +2 -2
  7. data/lib/labimotion/libs/export_dataset.rb +5 -2
  8. data/lib/labimotion/utils/import_utils.rb +1 -1
  9. data/lib/labimotion/utils/serializer.rb +2 -2
  10. data/lib/labimotion/version.rb +1 -1
  11. metadata +2 -2
checksums.yaml CHANGED
@@ -1,7 +1,7 @@
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  ---
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  SHA256:
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- metadata.gz: 6f07e0d77afbb79bc2652b5f7edbc105133f727593a9a9cc236e17762d1b7e15
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- data.tar.gz: a6d9a86cd6363b5d81f1c141f56ac85974d6622c3cfd06dc21a3184610d5c76b
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+ metadata.gz: f38f255a309e305ddfe715e5382c0087acde8a05c42434a8c87c03640ad38772
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+ data.tar.gz: a3ed70fa27d008b51f416fbd4ac9a2ce70e1d3cc117bdfa37e31010a62301b98
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  SHA512:
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- metadata.gz: 68ab2a10825518b8c7b22e0ae47aeb48c867404f857e98957082f952f7d42983bc07c50f62ff0dd71be1e6c9bb4f0843fabecdcf7f9ef40f5ce0d253b12dc4f6
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- data.tar.gz: c45113c276c4954803005084733c1e4e13315e9888bb0da50663b3d68577badae0cf5278e2bf1ed4d9cc80002366b981dc80563aa40657cbebf892f34b97f8f7
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+ metadata.gz: e80ca22f7120c4d3f34b9eecc37baa2b40a83b7d34409b4598129bb939e1c473ed6fa7fe06c7c2396210dc25571238b1bc51733fafb373e8928c076aa8761fe2
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+ data.tar.gz: 70ddf10ed69d7eea7ac3769e3a32dd59b38b3eed052ba232e9cdbadacaa2ef6bab9ea204537390c2abe71f06246ac9eeb650b2731b28d92ad8d1bc0d534d4b38
data/lib/labimotion/entities/element_revision_entity.rb CHANGED
@@ -23,7 +23,7 @@ module Labimotion
23
23
 
24
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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
25
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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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+ 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 || 'nosvg')
27
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  end
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29
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  field_tables = object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS].select { |ss| ss['type'] == Labimotion::FieldType::TABLE }
@@ -41,7 +41,7 @@ module Labimotion
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  find_mol = Molecule.find_by(id: sub_value[col_id]['value']['el_id'])
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  next unless find_mol.present?
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43
 
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- sub_value[col_id]['value']['el_svg'] = File.join('/images', 'molecules', find_mol.molecule_svg_file)
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+ sub_value[col_id]['value']['el_svg'] = File.join('/images', 'molecules', find_mol.molecule_svg_file) if find_mol&.molecule_svg_file&.present?
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  sub_value[col_id]['value']['el_inchikey'] = find_mol.inchikey
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  sub_value[col_id]['value']['el_smiles'] = find_mol.cano_smiles
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  sub_value[col_id]['value']['el_iupac'] = find_mol.iupac_name
data/lib/labimotion/entities/eln_element_entity.rb CHANGED
@@ -47,7 +47,7 @@ module Labimotion
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  el.short_label
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  end
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  object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS][idx]['value']['el_svg'] =
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- field['type'] == Labimotion::FieldType::DRAG_SAMPLE ? el.get_svg_path : File.join('/images', 'molecules', el.molecule_svg_file)
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+ field['type'] == Labimotion::FieldType::DRAG_SAMPLE ? el.get_svg_path : File.join('/images', 'molecules', el&.molecule_svg_file || 'nosvg')
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  end
52
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  field_tables = object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS].select { |ss| ss['type'] == Labimotion::FieldType::TABLE }
@@ -88,7 +88,7 @@ module Labimotion
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88
 
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  case obj
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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_svg'] = File.join('/images', 'molecules', find_obj.molecule_svg_file) if find_obj&.molecule_svg_file&.present?
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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
data/lib/labimotion/entities/properties_entity.rb CHANGED
@@ -20,7 +20,7 @@ module Labimotion
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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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+ 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 || 'nosvg')
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  end
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26
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  field_sys_reactions = object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS].select { |ss| ss['type'] == Labimotion::FieldType::SYS_REACTION }
@@ -69,7 +69,7 @@ module Labimotion
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70
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  case obj
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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_svg'] = File.join('/images', 'molecules', find_obj.molecule_svg_file) if find_obj&.molecule_svg_file&.present?
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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
data/lib/labimotion/entities/segment_revision_entity.rb CHANGED
@@ -22,7 +22,7 @@ module Labimotion
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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
24
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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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+ 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 || 'nosvg')
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  end
27
27
 
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  field_tables = object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS].select { |ss| ss['type'] == Labimotion::FieldType::TABLE }
@@ -40,7 +40,7 @@ module Labimotion
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  find_mol = Molecule.find_by(id: sub_value[col_id]['value']['el_id'])
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  next unless find_mol.present?
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42
 
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- sub_value[col_id]['value']['el_svg'] = File.join('/images', 'molecules', find_mol.molecule_svg_file)
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+ sub_value[col_id]['value']['el_svg'] = File.join('/images', 'molecules', find_mol.molecule_svg_file) if find_mol&.molecule_svg_file&.present?
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  sub_value[col_id]['value']['el_inchikey'] = find_mol.inchikey
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  sub_value[col_id]['value']['el_smiles'] = find_mol.cano_smiles
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  sub_value[col_id]['value']['el_iupac'] = find_mol.iupac_name
data/lib/labimotion/helpers/segment_helpers.rb CHANGED
@@ -107,9 +107,9 @@ 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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- attr_klass = response.dig('element_klass', {}) # response['element_klass']
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+ attr_klass = response['element_klass'] ## response.dig('element_klass', {}) # response['element_klass']
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  validate_klass(attributes, attr_klass)
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-
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+
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  rescue StandardError => e
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  Labimotion.log_exception(e, current_user)
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  raise e
data/lib/labimotion/libs/export_dataset.rb CHANGED
@@ -97,7 +97,10 @@ module Labimotion
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  type = "#{field['type']}-#{field['option_layers']}" if field['type'] == Labimotion::FieldType::SELECT || field['type'] == Labimotion::FieldType::SYSTEM_DEFINED
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  show_value = field['value'] =~ /\A\d+,\d+\z/ ? field['value']&.gsub(',', '.') : field['value']
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- sheet.add_row([' ', field['label'], nil, field['value_system'], field['field'], type, from_device, field['dkey'], nil].freeze)
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+ ols_short_form = (field['ontology'] && field['ontology']['short_form']) || ''
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+ ols_label = (field['ontology'] && field['ontology']['label']) || ''
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+ ols_iri = (field['ontology'] && field['ontology']['iri']) || ''
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+ sheet.add_row([' ', field['label'], nil, field['value_system'], field['field'], type, from_device, field['dkey'], nil, ols_short_form, ols_label, ols_iri].freeze)
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  case field['type']
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  when Labimotion::FieldType::SELECT
@@ -166,7 +169,7 @@ module Labimotion
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  end
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  def header
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- ['Layer Label', 'Field Label', 'Value', 'Unit', 'Name', 'Type', 'Source?', 'Source identifier', 'Source data'].freeze
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+ ['Layer Label', 'Field Label', 'Value', 'Unit', 'Name', 'Type', 'Source?', 'Source identifier', 'Source data', 'Ontology', 'Ontology Label', 'iri'].freeze
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  end
171
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  def read
data/lib/labimotion/utils/import_utils.rb CHANGED
@@ -24,7 +24,7 @@ module Labimotion
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  value['el_id'] = molecule.id
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  value['el_tip'] = "#{molecule.inchikey}@@#{molecule.cano_smiles}"
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  value['el_label'] = molecule.iupac_name
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- value['el_svg'] = File.join('/images', 'molecules', molecule.molecule_svg_file)
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+ value['el_svg'] = File.join('/images', 'molecules', molecule&.molecule_svg_file) if molecule&.molecule_svg_file.present?
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  value['el_inchikey'] = molecule.inchikey
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  value['el_smiles'] = molecule.cano_smiles
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  value['el_type'] = 'molecule' if value['el_type'].nil?
data/lib/labimotion/utils/serializer.rb CHANGED
@@ -13,7 +13,7 @@ module Labimotion
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13
 
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  case obj
15
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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_svg'] = File.join('/images', 'molecules', find_obj.molecule_svg_file) if find_obj&.molecule_svg_file&.present?
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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
@@ -56,7 +56,7 @@ module Labimotion
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  object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS][idx]['value']['el_tip'] = el.short_label if %w[drag_sample].include?(field['type'])
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  object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS][idx]['value']['el_tip'] = "#{el.element_klass&.label}@@#{el.name}" if %w[drag_element].include?(field['type'])
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  object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS][idx]['value']['icon_name'] = el.element_klass&.icon_name || '' if %w[drag_element].include?(field['type'])
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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) if Labimotion::FieldType::DRAG_MS.include?(field['type'])
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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 || 'nosvg') if Labimotion::FieldType::DRAG_MS.include?(field['type'])
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60
  object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS][idx]['value']['el_decoupled'] = el.decoupled if %w[drag_sample].include?(field['type'])
61
61
  end
62
62
 
data/lib/labimotion/version.rb CHANGED
@@ -2,5 +2,5 @@
2
2
 
3
3
  ## Labimotion Version
4
4
  module Labimotion
5
- VERSION = '1.4.0.rc2'
5
+ VERSION = '1.4.0.rc4'
6
6
  end
metadata CHANGED
@@ -1,7 +1,7 @@
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  --- !ruby/object:Gem::Specification
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  name: labimotion
3
3
  version: !ruby/object:Gem::Version
4
- version: 1.4.0.rc2
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+ version: 1.4.0.rc4
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5
  platform: ruby
6
6
  authors:
7
7
  - Chia-Lin Lin
@@ -9,7 +9,7 @@ authors:
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9
  autorequire:
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10
  bindir: bin
11
11
  cert_chain: []
12
- date: 2024-05-29 00:00:00.000000000 Z
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+ date: 2024-06-25 00:00:00.000000000 Z
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  dependencies:
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  - !ruby/object:Gem::Dependency
15
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  name: rails