labimotion 1.4.0.rc2 → 1.4.0.rc4
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- checksums.yaml +4 -4
- data/lib/labimotion/entities/element_revision_entity.rb +2 -2
- data/lib/labimotion/entities/eln_element_entity.rb +2 -2
- data/lib/labimotion/entities/properties_entity.rb +2 -2
- data/lib/labimotion/entities/segment_revision_entity.rb +2 -2
- data/lib/labimotion/helpers/segment_helpers.rb +2 -2
- data/lib/labimotion/libs/export_dataset.rb +5 -2
- data/lib/labimotion/utils/import_utils.rb +1 -1
- data/lib/labimotion/utils/serializer.rb +2 -2
- data/lib/labimotion/version.rb +1 -1
- 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:
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data.tar.gz:
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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:
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data.tar.gz:
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metadata.gz: e80ca22f7120c4d3f34b9eecc37baa2b40a83b7d34409b4598129bb939e1c473ed6fa7fe06c7c2396210dc25571238b1bc51733fafb373e8928c076aa8761fe2
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7
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data.tar.gz: 70ddf10ed69d7eea7ac3769e3a32dd59b38b3eed052ba232e9cdbadacaa2ef6bab9ea204537390c2abe71f06246ac9eeb650b2731b28d92ad8d1bc0d534d4b38
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@@ -23,7 +23,7 @@ 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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26
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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
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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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field_tables = object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS].select { |ss| ss['type'] == Labimotion::FieldType::TABLE }
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@@ -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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-
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
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@@ -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
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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
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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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@@ -88,7 +88,7 @@ module Labimotion
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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
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@@ -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
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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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field_sys_reactions = object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS].select { |ss| ss['type'] == Labimotion::FieldType::SYS_REACTION }
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@@ -69,7 +69,7 @@ module Labimotion
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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
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@@ -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
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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
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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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field_tables = object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS].select { |ss| ss['type'] == Labimotion::FieldType::TABLE }
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@@ -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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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
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@@ -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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rescue StandardError => e
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Labimotion.log_exception(e, current_user)
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raise e
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@@ -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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-
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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
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@@ -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
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def read
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@@ -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
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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?
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@@ -13,7 +13,7 @@ module Labimotion
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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
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@@ -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
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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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object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS][idx]['value']['el_decoupled'] = el.decoupled if %w[drag_sample].include?(field['type'])
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end
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data/lib/labimotion/version.rb
CHANGED
metadata
CHANGED
@@ -1,7 +1,7 @@
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--- !ruby/object:Gem::Specification
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name: labimotion
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version: !ruby/object:Gem::Version
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version: 1.4.0.
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version: 1.4.0.rc4
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platform: ruby
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authors:
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- Chia-Lin Lin
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@@ -9,7 +9,7 @@ authors:
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autorequire:
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bindir: bin
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cert_chain: []
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-
date: 2024-
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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
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name: rails
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