labimotion 2.1.0 → 2.2.0.rc5
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
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@@ -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: 5aa32269487161d9b1e5647154e1d55ec3fae34dc50082e538adae80679afdf9
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data.tar.gz: 5df8ec5d405a7c64ee0840cfffe1dd8a60537997447c898d2f1d8870b3910830
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SHA512:
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metadata.gz:
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data.tar.gz:
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metadata.gz: 68ebbb1d5ebbe512808bcab3f34b3452c9ee0dbeceebbed183db20904e433b0aa06cd533f66a0896e7d3824e615307d25edd669cb1de5c0f0415213c2f349e1f
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data.tar.gz: 14a545856a83b9d5778910eefd06c2cb4b865e696036c8e7e1901c18e2688726c6447aca3af8a65703e788d2fc95357acfe1fd5e6177706a3f0dc62b712e885d
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@@ -87,12 +87,13 @@ module Labimotion
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}
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element = Labimotion::Element.new(attributes)
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-
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all_coll = Collection.get_all_collection_for_user(current_user.id)
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element.collections << all_coll
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if params[:collection_id] && params[:collection_id] != all_coll.id
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collection = current_user.collections.find(params[:collection_id])
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element.collections << collection
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end
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all_coll = Collection.get_all_collection_for_user(current_user.id)
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element.collections << all_coll
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element.save!
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element.properties = update_sample_association(params[:properties], current_user, element)
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# element.properties = update_vocabularies(_properties, current_user, element)
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@@ -246,27 +247,21 @@ module Labimotion
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end
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def list_serialized_elements(params, current_user)
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if params[:collection_id]
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Collection
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.belongs_to_or_shared_by(current_user.id, current_user.group_ids)
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.find_by(id: params[:collection_id])&.id
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elsif params[:sync_collection_id]
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current_user
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.all_sync_in_collections_users
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.find_by(id: params[:sync_collection_id])&.collection&.id
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end
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scope = Labimotion::Element.none
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if params[:collection_id]
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begin
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collection = Collection.accessible_for(current_user).find(params[:collection_id])
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scope = collection.elements
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.joins(:element_klass)
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.where(element_klasses: { name: params[:el_type] })
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.includes(:tag)
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rescue ActiveRecord::RecordNotFound
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Labimotion::Element.none
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end
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else
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-
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# All collection of current_user
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scope = Labimotion::Element.for_user(current_user.id)
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end
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## TO DO: refactor labimotion
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@@ -12,7 +12,7 @@ module Labimotion
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end
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def self.elements_search(params, current_user, c_id, dl)
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collection = Collection.
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collection = Collection.accessible_for(current_user).find(c_id)
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element_scope = Labimotion::Element.joins(:collections_elements).where('collections_elements.collection_id = ?', collection.id).joins(:element_klass).where('element_klasses.id = elements.element_klass_id AND element_klasses.name = ?', params[:selection][:genericElName])
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element_scope = element_scope.where('elements.name like (?)', "%#{params[:selection][:searchName]}%") if params[:selection][:searchName].present?
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element_scope = element_scope.where('elements.short_label like (?)', "%#{params[:selection][:searchShowLabel]}%") if params[:selection][:searchShowLabel].present?
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@@ -97,7 +97,7 @@ module Labimotion
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def self.samples_search(c_id = @c_id)
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sqls = []
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sps = params[:selection][:searchProperties]
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collection = Collection.
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collection = Collection.accessible_for(current_user).find(c_id)
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element_scope = Sample.joins(:collections_samples).where('collections_samples.collection_id = ?', collection.id)
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return element_scope if sps.empty?
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data/lib/labimotion/version.rb
CHANGED
metadata
CHANGED
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@@ -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: 2.
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version: 2.2.0.rc5
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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: 2026-
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date: 2026-03-25 00:00:00.000000000 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: caxlsx
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@@ -98,7 +98,6 @@ files:
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- lib/labimotion/helpers/vocabulary_helpers.rb
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- lib/labimotion/libs/attachment_handler.rb
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- lib/labimotion/libs/converter.rb
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- lib/labimotion/libs/data/layer/StdDataset.json
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- lib/labimotion/libs/data/mapper/Chemwiki.json
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- lib/labimotion/libs/data/mapper/Source.json
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- lib/labimotion/libs/data/vocab/Standard.json
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@@ -183,9 +182,9 @@ required_ruby_version: !ruby/object:Gem::Requirement
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version: '3.4'
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required_rubygems_version: !ruby/object:Gem::Requirement
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requirements:
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- - "
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- - ">"
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- !ruby/object:Gem::Version
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version:
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version: 1.3.1
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requirements: []
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rubygems_version: 3.1.6
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signing_key:
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@@ -1,212 +0,0 @@
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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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"type": "text",
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"field": "time",
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"label": "starting time",
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"default": "",
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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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"type": "text",
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"field": "contributor",
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"label": "contributor",
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"position": 5,
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"sub_fields": [],
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"text_sub_fields": []
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},
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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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"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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"field": "operator",
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"label": "operator",
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"position": 7,
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"text_sub_fields": []
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},
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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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"sub_fields": [],
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"text_sub_fields": []
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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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"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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"position": 2,
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},
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"field": "amount",
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"label": "amount",
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"position": 3,
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},
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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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"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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197
|
-
"default": "",
|
|
198
|
-
"position": 5,
|
|
199
|
-
"required": false,
|
|
200
|
-
"sub_fields": [],
|
|
201
|
-
"text_sub_fields": []
|
|
202
|
-
}
|
|
203
|
-
],
|
|
204
|
-
"position": -1,
|
|
205
|
-
"timeRecord": "",
|
|
206
|
-
"wf_position": 0
|
|
207
|
-
}
|
|
208
|
-
},
|
|
209
|
-
"version": "0.1",
|
|
210
|
-
"select_options": {
|
|
211
|
-
}
|
|
212
|
-
}
|