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add all MOD metadata to the submission model
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syphax-bouazzouni committed Feb 12, 2025
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Showing 1 changed file with 171 additions and 30 deletions.
201 changes: 171 additions & 30 deletions lib/ontologies_linked_data/models/ontology_submission.rb
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Original file line number Diff line number Diff line change
Expand Up @@ -13,52 +13,193 @@ module Models
class OntologySubmission < LinkedData::Models::Base

include LinkedData::Concerns::SubmissionProcessable
include LinkedData::Concerns::OntologySubmission::MetadataExtractor
include LinkedData::Concerns::OntologySubmission::Validators

FLAT_ROOTS_LIMIT = 1000

model :ontology_submission, name_with: lambda { |s| submission_id_generator(s) }
attribute :submissionId, enforce: [:integer, :existence]
model :ontology_submission, scheme: File.join(__dir__, '../../../config/schemes/ontology_submission.yml'),
name_with: ->(s) { submission_id_generator(s) }

attribute :submissionId, type: :integer, enforce: [:existence]

# Object description properties metadata
# Configurable properties for processing
attribute :prefLabelProperty, enforce: [:uri]
attribute :definitionProperty, enforce: [:uri]
attribute :synonymProperty, enforce: [:uri]
attribute :authorProperty, enforce: [:uri]
attribute :classType, enforce: [:uri]
attribute :hierarchyProperty, enforce: [:uri]
attribute :obsoleteProperty, enforce: [:uri]
attribute :obsoleteParent, enforce: [:uri]
attribute :prefLabelProperty, type: :uri, default: ->(s) { Goo.vocabulary(:skos)[:prefLabel] }
attribute :definitionProperty, type: :uri, default: ->(s) { Goo.vocabulary(:skos)[:definition] }
attribute :synonymProperty, type: :uri, default: ->(s) { Goo.vocabulary(:skos)[:altLabel] }
attribute :authorProperty, type: :uri, default: ->(s) { Goo.vocabulary(:dc)[:creator] }
attribute :classType, type: :uri
attribute :hierarchyProperty, type: :uri, default: ->(s) { default_hierarchy_property(s) }
attribute :obsoleteProperty, type: :uri, default: ->(s) { Goo.vocabulary(:owl)[:deprecated] }
attribute :obsoleteParent, type: :uri
attribute :createdProperty, type: :uri, default: ->(s) { Goo.vocabulary(:dc)[:created] }
attribute :modifiedProperty, type: :uri, default: ->(s) { Goo.vocabulary(:dc)[:modified] }

# Ontology metadata
attribute :hasOntologyLanguage, namespace: :omv, enforce: [:existence, :ontology_format]
attribute :homepage
attribute :publication
attribute :uri, namespace: :omv
attribute :naturalLanguage, namespace: :omv, enforce: [:list]
attribute :documentation, namespace: :omv
# General metadata
attribute :URI, namespace: :omv, type: :uri, enforce: %i[existence distinct_of_identifier], fuzzy_search: true
attribute :versionIRI, namespace: :owl, type: :uri, enforce: [:distinct_of_URI]
attribute :version, namespace: :omv
attribute :creationDate, namespace: :omv, enforce: [:date_time], default: lambda { |record| DateTime.now }
attribute :description, namespace: :omv
attribute :status, namespace: :omv
attribute :contact, enforce: [:existence, :contact, :list]
attribute :released, enforce: [:date_time, :existence]
attribute :status, namespace: :omv, enforce: %i[existence], default: ->(x) { 'production' }
attribute :deprecated, namespace: :owl, type: :boolean, default: ->(x) { false }
attribute :hasOntologyLanguage, namespace: :omv, type: :ontology_format, enforce: [:existence]
attribute :hasFormalityLevel, namespace: :omv, type: :uri
attribute :hasOntologySyntax, namespace: :omv, type: :uri, default: ->(s) { ontology_syntax_default(s) }
attribute :naturalLanguage, namespace: :omv, type: %i[list uri], enforce: [:lexvo_language]
attribute :isOfType, namespace: :omv, type: :uri
attribute :identifier, namespace: :dct, type: %i[list uri], enforce: [:distinct_of_URI]

# Description metadata
attribute :description, namespace: :omv, enforce: %i[concatenate existence], fuzzy_search: true
attribute :homepage, namespace: :foaf, type: :uri
attribute :documentation, namespace: :omv, type: :uri
attribute :notes, namespace: :omv, type: :list
attribute :keywords, namespace: :omv, type: :list
attribute :hiddenLabel, namespace: :skos, type: :list
attribute :alternative, namespace: :dct, type: :list
attribute :abstract, namespace: :dct
attribute :publication, type: %i[uri list]

# Licensing metadata
attribute :hasLicense, namespace: :omv, type: :uri
attribute :useGuidelines, namespace: :cc
attribute :morePermissions, namespace: :cc
# attribute :copyrightHolder, namespace: :schema, type: :Agent

# Date metadata
attribute :released, type: :date_time, enforce: [:existence]
attribute :valid, namespace: :dct, type: :date_time
attribute :curatedOn, namespace: :pav, type: %i[date_time list]
attribute :creationDate, namespace: :omv, type: :date_time, default: ->(x) { Date.today.to_datetime }
attribute :modificationDate, namespace: :omv, type: :date_time

# Person and organizations metadata
attribute :contact, type: %i[contact list], enforce: [:existence]
# attribute :hasCreator, namespace: :omv, type: %i[list Agent]
# attribute :hasContributor, namespace: :omv, type: %i[list Agent]
# attribute :curatedBy, namespace: :pav, type: %i[list Agent]
# attribute :publisher, namespace: :dct, type: %i[list Agent]
# attribute :fundedBy, namespace: :foaf, type: %i[list Agent]
# attribute :endorsedBy, namespace: :omv, type: %i[list Agent]
# attribute :translator, namespace: :schema, type: %i[list Agent]

# Community metadata
attribute :audience, namespace: :dct
attribute :repository, namespace: :doap, type: :uri
attribute :bugDatabase, namespace: :doap, type: :uri
attribute :mailingList, namespace: :doap
attribute :toDoList, namespace: :voaf, type: :list
attribute :award, namespace: :schema, type: :list

# Usage metadata
attribute :knownUsage, namespace: :omv, type: :list
attribute :designedForOntologyTask, namespace: :omv, type: %i[list uri]
attribute :hasDomain, namespace: :omv, type: :list, default: ->(s) { ontology_has_domain(s) }
attribute :coverage, namespace: :dct
attribute :example, namespace: :vann, type: :list

# Methodology metadata
attribute :conformsToKnowledgeRepresentationParadigm, namespace: :omv
attribute :usedOntologyEngineeringMethodology, namespace: :omv
attribute :usedOntologyEngineeringTool, namespace: :omv, type: %i[list]
attribute :accrualMethod, namespace: :dct, type: %i[list]
attribute :accrualPeriodicity, namespace: :dct
attribute :accrualPolicy, namespace: :dct
attribute :competencyQuestion, namespace: :mod, type: :list
attribute :wasGeneratedBy, namespace: :prov, type: :list
attribute :wasInvalidatedBy, namespace: :prov, type: :list

# Internal values for parsing - not definitive
# Links
attribute :pullLocation, type: :uri # URI for pulling ontology
attribute :isFormatOf, namespace: :dct, type: :uri
attribute :hasFormat, namespace: :dct, type: %i[uri list]
attribute :dataDump, namespace: :void, type: :uri, default: -> (s) { data_dump_default(s) }
attribute :csvDump, type: :uri, default: -> (s) { csv_dump_default(s) }
attribute :uriLookupEndpoint, namespace: :void, type: :uri, default: -> (s) { uri_lookup_default(s) }
attribute :openSearchDescription, namespace: :void, type: :uri, default: -> (s) { open_search_default(s) }
attribute :source, namespace: :dct, type: :list
attribute :endpoint, namespace: :sd, type: %i[uri list],
default: ->(s) { default_sparql_endpoint(s) }
attribute :includedInDataCatalog, namespace: :schema, type: %i[list uri]

# Relations
attribute :hasPriorVersion, namespace: :omv, type: :uri
attribute :hasPart, namespace: :dct, type: %i[uri list]
attribute :ontologyRelatedTo, namespace: :door, type: %i[list uri]
attribute :similarTo, namespace: :door, type: %i[list uri]
attribute :comesFromTheSameDomain, namespace: :door, type: %i[list uri]
attribute :isAlignedTo, namespace: :door, type: %i[list uri]
attribute :isBackwardCompatibleWith, namespace: :omv, type: %i[list uri]
attribute :isIncompatibleWith, namespace: :omv, type: %i[list uri]
attribute :hasDisparateModelling, namespace: :door, type: %i[list uri]
attribute :hasDisjunctionsWith, namespace: :voaf, type: %i[uri list]
attribute :generalizes, namespace: :voaf, type: %i[list uri]
attribute :explanationEvolution, namespace: :door, type: %i[list uri]
attribute :useImports, namespace: :omv, type: %i[list uri]
attribute :usedBy, namespace: :voaf, type: %i[uri list]
attribute :workTranslation, namespace: :schema, type: %i[uri list]
attribute :translationOfWork, namespace: :schema, type: %i[uri list]

# Content metadata
attribute :uriRegexPattern, namespace: :void
attribute :preferredNamespaceUri, namespace: :vann, type: :uri
attribute :preferredNamespacePrefix, namespace: :vann
attribute :exampleIdentifier, namespace: :idot
attribute :keyClasses, namespace: :omv, type: %i[list]
attribute :metadataVoc, namespace: :voaf, type: %i[uri list]
attribute :uploadFilePath
attribute :diffFilePath
attribute :masterFileName
attribute :submissionStatus, enforce: [:submission_status, :list], default: lambda { |record| [LinkedData::Models::SubmissionStatus.find("UPLOADED").first] }
attribute :missingImports, enforce: [:list]

# URI for pulling ontology
attribute :pullLocation, enforce: [:uri]
# Media metadata
attribute :associatedMedia, namespace: :schema, type: %i[uri list]
attribute :depiction, namespace: :foaf, type: %i[uri list]
attribute :logo, namespace: :foaf, type: :uri

# Metrics metadata
attribute :metrics, type: :metrics

# Configuration metadata

# Internal values for parsing - not definitive
attribute :submissionStatus, type: %i[submission_status list], default: ->(record) { [LinkedData::Models::SubmissionStatus.find("UPLOADED").first] }
attribute :missingImports, type: :list

# Link to ontology
attribute :ontology, enforce: [:existence, :ontology]
attribute :ontology, type: :ontology, enforce: [:existence]

def self.agents_attrs
return [] #TODO implement agent separately
%i[hasCreator publisher copyrightHolder hasContributor
translator endorsedBy fundedBy curatedBy]
end

# Hypermedia settings
embed *%i[contact ontology metrics] + agents_attrs

def self.embed_values_hash
out = {
submissionStatus: [:code], hasOntologyLanguage: [:acronym]
}

# TODO implement agents separately
# agent_attributes = LinkedData::Models::Agent.goo_attrs_to_load +
# [identifiers: LinkedData::Models::AgentIdentifier.goo_attrs_to_load, affiliations: LinkedData::Models::Agent.goo_attrs_to_load]
#
# agents_attrs.each { |k| out[k] = agent_attributes }
out
end

embed_values self.embed_values_hash

serialize_default :contact, :ontology, :hasOntologyLanguage, :released, :creationDate, :homepage,
:publication, :documentation, :version, :description, :status, :submissionId

# Links
links_load :submissionId, ontology: [:acronym]
link_to LinkedData::Hypermedia::Link.new("metrics", ->(s) { "#{self.ontology_link(s)}/submissions/#{s.submissionId}/metrics" }, self.type_uri)
LinkedData::Hypermedia::Link.new("download", ->(s) { "#{self.ontology_link(s)}/submissions/#{s.submissionId}/download" }, self.type_uri)

#Link to metrics
attribute :metrics, enforce: [:metrics]

# Hypermedia settings
embed :contact, :ontology
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