labimotion 1.5.0.rc5 → 1.5.0.rc7
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +4 -4
- data/lib/labimotion/entities/dataset_entity.rb +74 -0
- data/lib/labimotion/entities/properties_entity.rb +48 -21
- data/lib/labimotion/entities/segment_entity.rb +1 -0
- data/lib/labimotion/entities/vocabulary_entity.rb +15 -1
- data/lib/labimotion/libs/data/vocab/Standard.json +25 -1
- data/lib/labimotion/libs/vocabulary_handler.rb +1 -1
- data/lib/labimotion/version.rb +1 -1
- metadata +2 -2
checksums.yaml
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metadata.gz: 933a7ef2942093d53c89df803dd802efeb4f0a0241193de7094d51c26fcfa8ff
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data.tar.gz: 5792273bc537ccf951ee3c7ab5ef575f23079b63acc8ce3f2d923fb445181d26
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metadata.gz: 2b50364418e278a654814ef2afa8c29bf2c9a2a1d4d134fb690573e317676b2fe9cdfa2afbc5cce8d65a5317fcf45a7f7a427791c36b19cc3f4d85a043055048
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data.tar.gz: 04a7949b73b943642f8c2e4e4541d4ee3695e27aded5fc447818c5bfaefd2ba8ced4626f9bd045eef9765fe75c7d5f42016f1afe2b202cd0454bcd5be89c94fe
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@@ -12,5 +12,79 @@ module Labimotion
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def klass_label
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object&.dataset_klass&.label
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end
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# def root_element
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# object&.element&.root_element
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# end
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# def properties
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# prop = object&.properties || {}
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# prop[Labimotion::Prop::LAYERS].keys.each do |key|
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# layer = prop[Labimotion::Prop::LAYERS][key] || {}
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# return prop if layer.empty? || layer[Labimotion::Prop::FIELDS].nil?
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# field_vocs = layer[Labimotion::Prop::FIELDS].select { |ss| ss['is_voc'] == true }
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# field_vocs.each do |field|
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# idx = prop[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS].index(field)
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# next if idx.nil?
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# case field['source']
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# when Labimotion::Prop::ELEMENT
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# if field['identifier'] == 'element.name'
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# # byebug
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# prop[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS][idx]['value'] = root_element&.name
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# # dic[field.identifier] = currentElement.name
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# end
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# when Labimotion::Prop::SEGMENT
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# segs = root_element&.segments&.select { |ss| field['source_id'] == ss.segment_klass&.identifier }
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# next if segs.empty? || field['layer_id'].blank? || field['field_id'].blank?
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# seg = segs&.first
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# seg_fields = seg.properties.dig(Labimotion::Prop::LAYERS, field['layer_id'], Labimotion::Prop::FIELDS).select { |ff| ff['field'] == field['field_id'] }
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# seg_field = seg_fields&.first
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# prop[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS][idx]['value'] = seg_field['value']
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# when Labimotion::Prop::DATASET
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# # byebug
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# dk = DatasetKlass.find_by(identifier: field["source_id"])
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# dk["ols_term_id"]
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# # byebug
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# # sel_ana = root_element.analyses.select { |ana| ana.extended_metadata["kind"].split("|")&.first&.strip == dk["ols_term_id"] }
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# anas = root_element.analyses.select { |ana| ana.extended_metadata["kind"].split("|")&.first&.strip == dk["ols_term_id"] }
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# anas.each do |ana|
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# cdss = ana.children
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# cdss.each do |cds|
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# next unless cds.dataset.present?
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# ds_prop = cds.dataset.properties
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# ds_fields = ds_prop.dig(Labimotion::Prop::LAYERS, field['layer_id'], Labimotion::Prop::FIELDS).select { |ff| ff['field'] == field['field_id'] }
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# ds_field = ds_fields&.first
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# # byebug
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# if prop[Labimotion::Prop::LAYERS][key].present? && ds_field['value'].present?
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# prop[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS][idx]['value'] = ds_field['value']
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# end
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# end
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# end
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# # sel_ana.dataset
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# # if root_element.analyses&.first&.extended_metadata["kind"].split("|")&.first&.strip == dk["ols_term_id"]
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# # byebug
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# # end
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# # root_element.analyses.select { |ss| ss.dataset_klass_id == dk.id }
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# end
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# end
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# # layer[Labimotion::Prop::FIELDS].each do |field|
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# # end
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# end
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# # byebug
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# # layers = properties['layers']
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# # properties['vocabularies'].each_with_object({}) do |v, h|
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# # h[v['name']] = v['value']
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# # end
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# prop
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# end
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end
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end
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@@ -7,27 +7,7 @@ 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[Labimotion::Prop::LAYERS]&.keys || []).each do |key|
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# field_vocabularies = object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS].select { |ss| ss['is_voc'] == true}
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# field_vocabularies.each do |field|
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# idx = object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS].index(field)
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# if field['identifier'] == '7c30cd4f-aef4-433a-946e-d0f81f8918f1'
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# if properties['klass'] == 'Dataset'
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# container = object&.element_type.constantize.find_by(id: object&.element_id)
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# element = container.root.containable
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# if field['source'] == 'Segment'
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# byebug
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# segments = element.segments.joins(:segment_klass).find_by('segment_klasses.identifier = ?', field['source_id'])
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# seg_prop = segments.properties
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# fields = seg_prop[Labimotion::Prop::LAYERS][field['layer_id']][Labimotion::Prop::FIELDS].select { |ss| ss['field'] == field['field_id'] }
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# val = fields.first['value']
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# object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS][idx]['value'] = val
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# end
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# end
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# # object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS][idx]['value'] = Time.now.strftime('%d/%m/%Y %H:%M')
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# end
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# end
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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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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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field_vocs = object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS].select { |ss| ss['is_voc'] == true }
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field_vocs.each do |field|
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idx = object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS].index(field)
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next if idx.nil?
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case object.class.name
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when Labimotion::Prop::L_ELEMENT
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root_element = object
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when Labimotion::Prop::L_SEGMENT
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root_element = object&.element
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when Labimotion::Prop::L_DATASET
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root_element = object&.element&.root_element
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end
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case field['source']
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when Labimotion::Prop::ELEMENT
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if field['identifier'] == 'element.name'
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object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS][idx]['value'] = root_element&.name
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end
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when Labimotion::Prop::SEGMENT
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segs = root_element&.segments&.select { |ss| field['source_id'] == ss.segment_klass&.identifier }
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next if segs.empty? || field['layer_id'].blank? || field['field_id'].blank?
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seg = segs&.first
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seg_fields = seg.properties.dig(Labimotion::Prop::LAYERS, field['layer_id'], Labimotion::Prop::FIELDS).select { |ff| ff['field'] == field['field_id'] }
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seg_field = seg_fields&.first
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object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS][idx]['value'] = seg_field['value']
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when Labimotion::Prop::DATASET
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dk = DatasetKlass.find_by(identifier: field["source_id"])
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dk["ols_term_id"]
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anas = root_element.analyses.select { |ana| ana.extended_metadata["kind"].split("|")&.first&.strip == dk["ols_term_id"] }
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anas.each do |ana|
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cdss = ana.children
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cdss.each do |cds|
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next unless cds.dataset.present?
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ds_prop = cds.dataset.properties
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ds_fields = ds_prop.dig(Labimotion::Prop::LAYERS, field['layer_id'], Labimotion::Prop::FIELDS).select { |ff| ff['field'] == field['field_id'] }
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ds_field = ds_fields&.first
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if object.properties[Labimotion::Prop::LAYERS][key].present? && ds_field['value'].present?
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object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS][idx]['value'] = ds_field['value']
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end
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end
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end
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end
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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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# end
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expose :voc do |obj|
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-
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## byebug
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voc = (obj[:properties] && obj[:properties]['voc']) || {}
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case voc['source']
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when Labimotion::Prop::ELEMENT
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if voc['identifier'] == 'element.name'
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# byebug
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# voc['source_name'] = ElementKlass.find_by(identifier: voc['source_id'])&.name
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end
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when Labimotion::Prop::SEGMENT
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voc['source_name'] = SegmentKlass.find_by(identifier: voc['source_id'])&.label
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when Labimotion::Prop::DATASET
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voc['source_name'] = DatasetKlass.find_by(identifier: voc['source_id'])&.label
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end
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voc
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end
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expose :ontology do |obj|
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(obj[:properties] && obj[:properties]['ontology']) || {}
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"name": "Solvent",
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"label": "NMR Solvent",
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"field_type": "text",
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"opid":
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"opid": 0,
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"term_id": "NMR:1000330",
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"ontology": {
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"id": "nmrcv:class:http://nmrML.org/nmrCV#NMR:1000330",
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"iri": "http://nmrML.org/nmrCV#NMR:1000330",
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"short_form": "NMR:1000330",
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"label": "NMR solvent",
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"description": [
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"Use Chebi entities here."
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],
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"ontology_name": "nmrcv",
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"ontology_prefix": "NMRCV",
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"type": "class"
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},
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"source": "Standard"
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},
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{
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"field_type": "text",
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"opid": 0,
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"term_id": "NMR:1400025",
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"ontology": {
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"id": "nmrcv:class:http://nmrML.org/nmrCV#NMR:1400025",
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"iri": "http://nmrML.org/nmrCV#NMR:1400025",
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"short_form": "NMR:1400025",
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"label": "sample temperature in magnet",
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"description": [
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"def: The temperature of an NMR sample whilst in the magnet of an NMR instrument."
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],
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"ontology_name": "nmrcv",
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"ontology_prefix": "NMRCV",
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"type": "class"
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},
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"source": "Standard"
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}
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]
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fields = seg_prop[Labimotion::Prop::LAYERS][field['layer_id']][Labimotion::Prop::FIELDS].select { |ss| ss['field'] == field['field_id'] }
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val = fields.first['value']
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when 'Dataset'
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-
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# byebug
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end
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# case field['identifier']
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# when 'dateTime.now'
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data/lib/labimotion/version.rb
CHANGED
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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: 1.5.0.
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version: 1.5.0.rc7
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platform: ruby
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authors:
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- Chia-Lin Lin
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autorequire:
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bindir: bin
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cert_chain: []
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date: 2024-10-
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date: 2024-10-11 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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