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Merge pull request #39 from ontoportal-lirmm/feature/add-agent-crud-e…
…ndpoint Feature: Add agent crud endpoints
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,145 @@ | ||
| class AgentsController < ApplicationController | ||
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| %w[/agents /Agents].each do |namespace| | ||
| namespace namespace do | ||
| # Display all agents | ||
| get do | ||
| check_last_modified_collection(LinkedData::Models::Agent) | ||
| query = LinkedData::Models::Agent.where | ||
| query = apply_filters(LinkedData::Models::Agent, query) | ||
| query = query.include(LinkedData::Models::Agent.goo_attrs_to_load(includes_param)) | ||
| if page? | ||
| page, size = page_params | ||
| agents = query.page(page, size).all | ||
| else | ||
| agents = query.to_a | ||
| end | ||
| reply agents | ||
| end | ||
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| # Display a single agent | ||
| get '/:id' do | ||
| check_last_modified_collection(LinkedData::Models::Agent) | ||
| id = params["id"] | ||
| agent = LinkedData::Models::Agent.find(id).include(LinkedData::Models::Agent.goo_attrs_to_load(includes_param)).first | ||
| error 404, "Agent #{id} not found" if agent.nil? | ||
| reply 200, agent | ||
| end | ||
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| # Create a agent with the given acronym | ||
| post do | ||
| reply 201, create_new_agent | ||
| end | ||
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| # Create a agent with the given acronym | ||
| put '/:acronym' do | ||
| reply 201, create_new_agent | ||
| end | ||
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| # Update an existing submission of a agent | ||
| patch '/:id' do | ||
| acronym = params["id"] | ||
| agent = LinkedData::Models::Agent.find(acronym).include(LinkedData::Models::Agent.attributes).first | ||
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| if agent.nil? | ||
| error 400, "Agent does not exist, please create using HTTP PUT before modifying" | ||
| else | ||
| agent = update_agent(agent, params) | ||
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| error 400, agent.errors unless agent.errors.empty? | ||
| end | ||
| halt 204 | ||
| end | ||
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| # Delete a agent | ||
| delete '/:id' do | ||
| agent = LinkedData::Models::Agent.find(params["id"]).first | ||
| agent.delete | ||
| halt 204 | ||
| end | ||
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| private | ||
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| def update_identifiers(identifiers) | ||
| Array(identifiers).map do |i| | ||
| next nil if i.empty? | ||
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| id = i["id"] || LinkedData::Models::AgentIdentifier.generate_identifier(i['notation'], i['schemaAgency']) | ||
| identifier = LinkedData::Models::AgentIdentifier.find(RDF::URI.new(id)).first | ||
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| if identifier | ||
| identifier.bring_remaining | ||
| else | ||
| identifier = LinkedData::Models::AgentIdentifier.new | ||
| end | ||
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| i.delete "id" | ||
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| next identifier if i.keys.size.zero? | ||
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| populate_from_params(identifier, i) | ||
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| if identifier.valid? | ||
| identifier.save | ||
| else | ||
| error 400, identifier.errors | ||
| end | ||
| identifier | ||
| end.compact | ||
| end | ||
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| def update_affiliations(affiliations) | ||
| Array(affiliations).map do |aff| | ||
| affiliation = aff["id"] ? LinkedData::Models::Agent.find(RDF::URI.new(aff["id"])).first : nil | ||
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| if affiliation | ||
| affiliation.bring_remaining | ||
| affiliation.identifiers.each{|i| i.bring_remaining} | ||
| end | ||
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| next affiliation if aff.keys.size.eql?(1) && aff["id"] | ||
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| if affiliation | ||
| affiliation = update_agent(affiliation, aff) | ||
| else | ||
| affiliation = create_new_agent(aff["id"], aff) | ||
| end | ||
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| error 400, affiliation.errors unless affiliation.errors.empty? | ||
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| affiliation | ||
| end | ||
| end | ||
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| def create_new_agent (id = @params['id'], params = @params) | ||
| agent = nil | ||
| agent = LinkedData::Models::Agent.find(id).include(LinkedData::Models::Agent.goo_attrs_to_load(includes_param)).first if id | ||
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| if agent.nil? | ||
| agent = update_agent(LinkedData::Models::Agent.new, params) | ||
| error 400, agent.errors unless agent.errors.empty? | ||
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| return agent | ||
| else | ||
| error 400, "Agent exists, please use HTTP PATCH to update" | ||
| end | ||
| end | ||
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| def update_agent(agent, params) | ||
| return agent unless agent | ||
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| identifiers = params.delete "identifiers" | ||
| affiliations = params.delete "affiliations" | ||
| params.delete "id" | ||
| populate_from_params(agent, params) | ||
| agent.identifiers = update_identifiers(identifiers) | ||
| agent.affiliations = update_affiliations(affiliations) | ||
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| agent.save if agent.valid? | ||
| return agent | ||
| end | ||
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| end | ||
| end | ||
|
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| end |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,68 @@ | ||
| require 'sinatra/base' | ||
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| module Sinatra | ||
| module Helpers | ||
| module SubmissionHelper | ||
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| def submission_attributes_all | ||
| out = [LinkedData::Models::OntologySubmission.embed_values_hash] | ||
| out << {:contact=>[:name, :email]} | ||
| out << {:ontology=>[:acronym, :name, :administeredBy, :group, :viewingRestriction, :doNotUpdate, :flat, | ||
| :hasDomain, :summaryOnly, :acl, :viewOf, :ontologyType]} | ||
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| out | ||
| end | ||
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| def retrieve_submissions(options) | ||
| status = (options[:status] || "RDF").to_s.upcase | ||
| status = "RDF" if status.eql?("READY") | ||
| any = status.eql?("ANY") | ||
| include_views = options[:also_include_views] || false | ||
| includes, page, size, order_by, _ = settings_params(LinkedData::Models::OntologySubmission) | ||
| includes << :submissionStatus unless includes.include?(:submissionStatus) | ||
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| submissions_query = LinkedData::Models::OntologySubmission | ||
| if any | ||
| submissions_query = submissions_query.where | ||
| else | ||
| submissions_query = submissions_query.where({ submissionStatus: [code: status] }) | ||
| end | ||
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| submissions_query = apply_submission_filters(submissions_query) | ||
| submissions_query = submissions_query.filter(Goo::Filter.new(ontology: [:viewOf]).unbound) unless include_views | ||
| submissions_query = submissions_query.filter(filter) if filter? | ||
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| # When asking to display all metadata, we are using bring_remaining on each submission. Slower but best way to retrieve all attrs | ||
| if includes_param.first == :all | ||
| includes = [:submissionId, { :contact => [:name, :email], | ||
| :ontology => [:administeredBy, :acronym, :name, :summaryOnly, :ontologyType, :viewingRestriction, :acl, | ||
| :group, :hasDomain, :views, :viewOf, :flat, :notes, :reviews, :projects], | ||
| :submissionStatus => [:code], :hasOntologyLanguage => [:acronym], :metrics => [:classes, :individuals, :properties] }, | ||
| :submissionStatus] | ||
| else | ||
| if includes.find { |v| v.is_a?(Hash) && v.keys.include?(:ontology) } | ||
| includes << { :ontology => [:administeredBy, :acronym, :name, :viewingRestriction, :group, :hasDomain, :notes, :reviews, :projects, :acl, :viewOf] } | ||
| end | ||
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| if includes.find { |v| v.is_a?(Hash) && v.keys.include?(:contact) } | ||
| includes << { :contact => [:name, :email] } | ||
| end | ||
| end | ||
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| submissions = submissions_query.include(includes) | ||
| if page? | ||
| submissions.page(page, size).all | ||
| else | ||
| submissions.to_a | ||
| end | ||
| end | ||
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| def include_ready?(options) | ||
| options[:status] && options[:status].to_s.upcase.eql?("READY") | ||
| end | ||
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| end | ||
| end | ||
| end | ||
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| helpers Sinatra::Helpers::SubmissionHelper |
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