labimotion 2.0.0 → 2.0.1
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/apis/labimotion_api.rb +3 -1
- data/lib/labimotion/apis/labimotion_hub_api.rb +83 -10
- data/lib/labimotion/apis/standard_api.rb +2 -1
- data/lib/labimotion/apis/standard_layer_api.rb +17 -4
- data/lib/labimotion/apis/vocabulary_api.rb +20 -6
- data/lib/labimotion/constants.rb +7 -0
- data/lib/labimotion/entities/dataset_entity.rb +1 -0
- data/lib/labimotion/entities/element_entity.rb +0 -1
- data/lib/labimotion/entities/klass_revision_entity.rb +5 -9
- data/lib/labimotion/entities/properties_entity.rb +41 -102
- data/lib/labimotion/entities/segment_entity.rb +2 -0
- data/lib/labimotion/entities/vocabulary_entity.rb +12 -3
- data/lib/labimotion/helpers/element_helpers.rb +1 -2
- data/lib/labimotion/helpers/generic_helpers.rb +1 -6
- data/lib/labimotion/helpers/param_helpers.rb +16 -0
- data/lib/labimotion/libs/converter.rb +1 -0
- data/lib/labimotion/libs/data/layer/StdDataset.json +212 -0
- data/lib/labimotion/libs/data/vocab/System.json +1 -1
- data/lib/labimotion/libs/export_dataset.rb +98 -343
- data/lib/labimotion/libs/nmr_mapper.rb +247 -204
- data/lib/labimotion/libs/template_hub.rb +28 -10
- data/lib/labimotion/models/concerns/generic_klass_revisions.rb +0 -1
- data/lib/labimotion/models/concerns/generic_revisions.rb +0 -3
- data/lib/labimotion/models/concerns/klass_revision.rb +23 -0
- data/lib/labimotion/models/dataset_klasses_revision.rb +4 -1
- data/lib/labimotion/models/element.rb +0 -3
- data/lib/labimotion/models/element_klasses_revision.rb +3 -2
- data/lib/labimotion/models/segment_klasses_revision.rb +4 -1
- data/lib/labimotion/models/template_submission.rb +52 -0
- data/lib/labimotion/utils/utils.rb +0 -21
- data/lib/labimotion/version.rb +1 -1
- data/lib/labimotion.rb +3 -3
- metadata +5 -6
- data/lib/labimotion/libs/data/mapper/Chemwiki.json +0 -236
- data/lib/labimotion/libs/data/mapper/Source.json +0 -78
- data/lib/labimotion/libs/dataset_builder.rb +0 -70
- data/lib/labimotion/utils/mapper_utils.rb +0 -169
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@@ -134,5 +134,21 @@ module Labimotion
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optional :select_options, type: Hash, desc: 'selections'
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optional :option_layers, type: String, desc: 'option'
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end
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# params :vocabulary_save do
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# requires :type, type: String, desc: 'type'
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# requires :field, type: String, desc: 'field'
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# optional :default, type: String, desc: 'default'
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# optional :description, type: String, desc: 'description'
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# optional :label, type: String, desc: 'label'
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# optional :position, type: Integer, desc: 'position'
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# optional :ontology, type: Hash, desc: 'ontology'
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# optional :required, type: Boolean, desc: 'is required?'
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# optional :sub_fields, type: Array, desc: 'sub_fields'
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# optional :text_sub_fields, type: Array, desc: 'text_sub_fields'
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# optional :source_type, type: String, desc: 'source type'
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# optional :source_id, type: String, desc: 'source id'
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# optional :layer_id, type: String, desc: 'layer id'
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# end
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end
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end
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@@ -123,6 +123,7 @@ module Labimotion
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tmp_file.write(response.parsed_response)
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tmp_file.rewind
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# name = response&.headers && response&.headers['content-disposition']&.split('=')&.last
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filename = oat.filename
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name = "#{File.basename(filename, '.*')}.zip"
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att = Attachment.new(
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@@ -0,0 +1,212 @@
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{
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"layers": {
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"std_general": {
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"wf": false,
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"key": "std_general",
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"std": true,
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"cols": 4,
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"color": "default",
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"label": "Standard General description",
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"style": "panel_generic_heading",
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"fields": [
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{
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"type": "text",
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"field": "title",
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"label": "title",
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"default": "",
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"ontology": {
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"id": "afo:class:http://purl.allotrope.org/ontologies/result#AFR_0001080",
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"iri": "http://purl.allotrope.org/ontologies/result#AFR_0001080",
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"type": "class",
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"label": "title",
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"obo_id": "AFR:0001080",
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"short_form": "AFR_0001080",
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"description": [
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"A title is a prefix or suffix added to a personal name. A title can be a title of honor, that is a title bestowed as an award, a honorary title (academic), that is a recognition of contributions by a non-employee or employee, a hereditary title, that is a title that remains in a family or a job title, that is a designation of a person's position in an organization. [Wikipedia]"
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],
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"ontology_name": "afo",
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"ontology_prefix": "AFO"
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},
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"position": 1,
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"required": false,
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"sub_fields": [],
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"text_sub_fields": []
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},
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{
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"type": "text",
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"field": "data_type",
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"label": "Type of the data ",
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"default": "",
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"readonly": true,
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"position": 2,
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"required": false,
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"sub_fields": [],
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"description": "Ontologies!!!! type of entity",
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"placeholder": "e.g. sample or reaction analysis",
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"text_sub_fields": []
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},
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{
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"type": "text",
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"field": "date",
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"label": "date",
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"default": "",
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"position": 3,
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"required": false,
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"sub_fields": [],
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"text_sub_fields": []
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},
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{
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"type": "text",
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"field": "time",
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"label": "starting time",
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"default": "",
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"position": 4,
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"required": false,
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"sub_fields": [],
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"text_sub_fields": []
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},
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{
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"type": "text",
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"field": "contributor",
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"label": "contributor",
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"default": "",
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"position": 5,
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"required": false,
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"sub_fields": [],
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"description": "",
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"text_sub_fields": []
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},
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{
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"type": "text",
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"field": "creator",
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"label": "creator",
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"default": "",
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"position": 6,
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"required": false,
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"sub_fields": [],
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"description": "the person who upload the analysis",
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"text_sub_fields": []
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},
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{
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"type": "text",
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"field": "operator",
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"label": "operator",
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"default": "",
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"position": 7,
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"required": false,
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"sub_fields": [],
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"text_sub_fields": []
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},
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{
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"type": "text",
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"field": "comments",
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"label": "comments",
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"default": "",
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"position": 8,
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"required": false,
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"sub_fields": [],
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"text_sub_fields": []
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},
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{
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"opid": 8,
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"type": "text",
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"field": "Producer",
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"label": "Producer of the sample",
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"is_voc": true,
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"source": "Segment",
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"default": "",
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"field_id": "Producer",
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"layer_id": "bsi",
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"ontology": {
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"id": "schema:property:https://schema.org/producer",
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"iri": "https://schema.org/producer",
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"type": "property",
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"label": "producer",
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"obo_id": "schema:producer",
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"short_form": "schema_producer",
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"description": [
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"The person or organization who produced the work (e.g. music album, movie, TV/radio series etc.)."
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],
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"ontology_name": "schema",
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"ontology_prefix": "schema"
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},
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"position": 9,
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"source_id": "dce363d5-56d0-4324-9914-0476be999016",
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"identifier": "357b7cd3-ca47-49e0-be47-154d907c2cf5",
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"sub_fields": [],
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"text_sub_fields": []
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}
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],
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"position": -2,
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"condition": "",
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"wf_position": 0
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},
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"std_sample_details": {
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"wf": false,
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"key": "std_sample_details",
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"cols": 3,
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"std": true,
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"color": "none",
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"label": "Standard Sample details",
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"style": "panel_generic_heading",
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"fields": [
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{
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"type": "text",
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"field": "label",
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"label": "label",
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"default": "",
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"position": 1,
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"required": false,
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"sub_fields": [],
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"text_sub_fields": []
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},
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{
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"type": "text",
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"field": "id",
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"label": "id",
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"default": "",
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"position": 2,
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"required": false,
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"sub_fields": [],
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"text_sub_fields": []
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},
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{
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"type": "text",
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"field": "amount",
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"label": "amount",
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"default": "",
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"position": 3,
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"required": false,
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"sub_fields": [],
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"text_sub_fields": []
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},
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{
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"type": "text",
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"field": "volume",
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"label": "volume",
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"default": "",
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"position": 4,
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"required": false,
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"sub_fields": [],
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"text_sub_fields": []
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},
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{
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"type": "text",
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"field": "size",
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"label": "size",
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"default": "",
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"position": 5,
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"required": false,
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"sub_fields": [],
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"text_sub_fields": []
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}
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],
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"position": -1,
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"timeRecord": "",
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"wf_position": 0
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}
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},
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"version": "0.1",
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"select_options": {
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}
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}
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