diff --git a/VP/index-all.json b/VP/index-all.json new file mode 100644 index 0000000..627df90 --- /dev/null +++ b/VP/index-all.json @@ -0,0 +1,93 @@ +[ + { + "uuid": "8a38755f-e805-42a6-b872-5bb4c9df1a1d", + "clientUrl": "http://testbed.ejprd.semlab-leiden.nl:5000", + "state": "ACTIVE", + "registrationTime": "2024-02-13T10:48:35.596Z", + "modificationTime": "2024-10-15T11:34:03.062Z" + }, + { + "uuid": "cd65140d-27f6-45f3-afc0-84b3047ac0e0", + "clientUrl": "http://testbed.ejprd.semlab-leiden.nl:10000", + "state": "ACTIVE", + "registrationTime": "2024-02-27T15:53:06.198Z", + "modificationTime": "2024-10-15T11:34:02.970Z" + }, + { + "uuid": "67f26b17-bed5-4be5-a9d9-e6488923faf1", + "clientUrl": "http://152.228.212.152:9000", + "state": "ACTIVE", + "registrationTime": "2024-03-25T11:48:35.327Z", + "modificationTime": "2024-10-17T07:31:55.958Z" + }, + { + "uuid": "30874e87-2179-4101-a1a0-8451c5ed4d7f", + "clientUrl": "https://w3id.org/duchenne-fdp", + "state": "ACTIVE", + "registrationTime": "2024-05-24T11:03:06.503Z", + "modificationTime": "2024-10-18T11:37:18.262Z" + }, + { + "uuid": "33cfda82-ae8b-417a-a867-ae101132ade9", + "clientUrl": "https://w3id.org/bgv-fdp", + "state": "INACTIVE", + "registrationTime": "2024-06-01T12:27:23.645Z", + "modificationTime": "2024-10-03T05:43:10.141Z" + }, + { + "uuid": "7e435bb3-72e7-46b6-a4f6-64c0850f3eee", + "clientUrl": "https://w3id.org/ERKNet/fdp", + "state": "ACTIVE", + "registrationTime": "2024-08-13T10:12:41.598Z", + "modificationTime": "2024-10-17T10:12:41.517Z" + }, + { + "uuid": "a0f736d9-7d38-48fa-b241-c76b29d73d65", + "clientUrl": "https://w3id.org/ERKNet/fdp/", + "state": "INACTIVE", + "registrationTime": "2024-08-13T13:46:02.737Z", + "modificationTime": "2024-08-30T10:23:34.927Z" + }, + { + "uuid": "ecdc9b94-7084-4aea-9176-29251c35552f", + "clientUrl": "https://jbo.bgv.cbgp.upm.es", + "state": "INACTIVE", + "registrationTime": "2024-08-13T13:49:21.616Z", + "modificationTime": "2024-10-03T05:43:01.999Z" + }, + { + "uuid": "196ff4c1-efed-496e-b465-c0754ff418ad", + "clientUrl": "http://fairdatapointorphanet.info:7070/", + "state": "INACTIVE", + "registrationTime": "2024-08-30T09:33:53.970Z", + "modificationTime": "2024-10-03T05:42:59.333Z" + }, + { + "uuid": "38067156-fe30-4f1b-a234-84e6d53f0e42", + "clientUrl": "https://ostrails.github.io/sandbox/fdp.ttl", + "state": "ACTIVE", + "registrationTime": "2024-10-16T14:25:29.953Z", + "modificationTime": "2024-10-16T14:25:2* Connection #0 to host testbed.ejprd.semlab-leiden.nl left intact9.953Z" + }, + { + "uuid": "5abb940a-fdca-4ec0-b133-df252c2fe4cb", + "clientUrl": "https: //ostrails.github.io/sandbox/proxyfdp.ttl", + "state": "ACTIVE", + "registrationTime": "2024-10-18T11:46:18.829Z", + "modificationTime": "2024-10-18T11:46:18.829Z" + }, + { + "uuid": "88618abe-bfff-4289-bef9-a49f4fc01a0b", + "clientUrl": "https://ostrails.github.io/sandbox/proxyservice.ttl", + "state": "ACTIVE", + "registrationTime": "2024-10-18T14:37:32.592Z", + "modificationTime": "2024-10-18T14:37:32.592Z" + }, + { + "uuid": "98179f89-2cfa-4084-b1cd-f7cbb73cff70", + "clientUrl": "https://ostrails.github.io/sandbox/gobierno.ttl", + "state": "ACTIVE", + "registrationTime": "2024-10-19T12:03:27.685Z", + "modificationTime": "2024-10-19T12:03:27.685Z" + } +] \ No newline at end of file diff --git a/VP/vp-interface/Gemfile b/VP/vp-interface/Gemfile index a646401..a3653fb 100644 --- a/VP/vp-interface/Gemfile +++ b/VP/vp-interface/Gemfile @@ -1,60 +1,58 @@ # frozen_string_literal: false -source "https://rubygems.org" -#sinatra (2.2.4, 1.4.8) -#sinatra-cross_origin (0.4.0) -#sinatra-respond_to (0.9.0, 0.4.0) +source 'https://rubygems.org' gemspec -ruby "~> 3.3.0" -# gem 'activerecord', '~> 7', '>= 7', require: 'active_record' -gem "bcrypt" -gem "debase", git: "https://github.com/ruby-debug/debase.git", tag: "v0.2.5.beta2" -gem "linkeddata", "~> 3.2.0" -gem "metainspector", "~> 5-11-2" -gem "parseconfig", "~>1.1.2" -gem "pry" -gem "rake", "~> 13.0" -gem "rdf-raptor", "~> 3.1.0" -gem "require_all" -gem "rest-client", "~>2.1.0" -gem "rspec", "~> 3.11.0" -gem "rubocop" -gem "ruby-debug-ide" -gem "shotgun" -gem "sinatra", "~> 2.2" -#gem "sinatra", "~> 1.4.8" -gem "cgi", "~> 0.4.1" -gem "csv" -gem "fileutils", "~>1.5.0" -gem "json", "~> 2.7.1" -gem "json-canonicalization", "~> 1.0.0" -gem "openapi3_parser", "~> 0.10.0" -gem "securerandom" -gem "sinatra-cross_origin" -gem "swagger-blocks", "~> 3.0.0" -gem "tempfile" -gem "thin" -gem "tux" -gem "xml-simple", "~>1.1.8" +ruby '~> 3.3.0' +gem 'bcrypt' +gem 'debase', git: 'https://github.com/ruby-debug/debase.git', tag: 'v0.2.5.beta2' +gem 'linkeddata', '~> 3.2.0' +gem 'metainspector', '~> 5-11-2' +gem 'parseconfig', '~>1.1.2' +gem 'pry' +gem 'rake', '~> 13.0' +gem 'rdf-raptor', '~> 3.1.0' +gem 'require_all' +gem 'rest-client', '~>2.1.0' +gem 'rubocop' +gem 'ruby-debug-ide' +gem 'shotgun' +gem 'sinatra', '~> 2.2' +# gem "sinatra", "~> 1.4.8" +gem 'cgi', '~> 0.4.1' +gem 'csv' +gem 'fileutils', '~>1.5.0' +gem 'json', '~> 2.7.1' +gem 'json-canonicalization', '~> 1.0.0' +gem 'openapi3_parser', '~> 0.10.0' +gem 'securerandom' +gem 'sinatra-cross_origin' +gem 'swagger-blocks', '~> 3.0.0' +gem 'tempfile' +gem 'thin' +gem 'tux' +gem 'xml-simple', '~>1.1.8' group :test do - gem "capybara" - gem "rack-test" - # gem 'database_cleaner', git: 'https://github.com/bmabey/database_cleaner.git' + gem 'capybara' + gem 'rack-test' + gem 'rspec', '~> 3.11.0' + gem 'rspec-core', '~> 3.11' + gem "rspec-openapi", "~> 0.18.3" + end -gem "dpop", "~> 0.1.3" +gem 'dpop', '~> 0.1.3' -gem "activesupport", "~> 7.0.3.1" +gem 'activesupport', '~> 7.0.3.1' -gem "erb", "~> 4.0" +gem 'erb', '~> 4.0' # gem "omniauth", "~> 1.1" # gem "omniauth-openid-connect", "~> 0.2.3" -gem "jwt", "~> 2.8" +gem 'jwt', '~> 2.8' +gem 'sinatra-respond_to', '~> 0.4.0' -gem "sinatra-respond_to", "~> 0.4.0" diff --git a/VP/vp-interface/Gemfile.lock b/VP/vp-interface/Gemfile.lock index 25b6a1e..c5778ef 100644 --- a/VP/vp-interface/Gemfile.lock +++ b/VP/vp-interface/Gemfile.lock @@ -14,6 +14,19 @@ PATH GEM remote: https://rubygems.org/ specs: + actionpack (7.0.3.1) + actionview (= 7.0.3.1) + activesupport (= 7.0.3.1) + rack (~> 2.0, >= 2.2.0) + rack-test (>= 0.6.3) + rails-dom-testing (~> 2.0) + rails-html-sanitizer (~> 1.0, >= 1.2.0) + actionview (7.0.3.1) + activesupport (= 7.0.3.1) + builder (~> 3.1) + erubi (~> 1.4) + rails-dom-testing (~> 2.0) + rails-html-sanitizer (~> 1.1, >= 1.2.0) activesupport (7.0.3.1) concurrent-ruby (~> 1.0, >= 1.0.2) i18n (>= 1.6, < 2) @@ -43,6 +56,7 @@ GEM commonmarker (1.1.5-x86_64-linux) concurrent-ruby (1.2.2) connection_pool (2.4.1) + crass (1.0.6) csv (3.2.8) daemons (1.4.1) debase-ruby_core_source (3.2.1) @@ -61,6 +75,7 @@ GEM unicode-types (~> 1.8) erb (4.0.4) cgi (>= 0.3.3) + erubi (1.13.0) eventmachine (1.2.7) faraday (2.7.10) faraday-net_http (>= 2.0, < 3.1) @@ -146,6 +161,9 @@ GEM sparql-client (~> 3.2, >= 3.2.2) yaml-ld (~> 0.0) logger (1.5.3) + loofah (2.22.0) + crass (~> 1.0.2) + nokogiri (>= 1.12.0) matrix (0.4.2) metainspector (5.15.0) addressable (~> 2.8.4) @@ -196,6 +214,13 @@ GEM rack rack-test (2.1.0) rack (>= 1.3) + rails-dom-testing (2.2.0) + activesupport (>= 5.0.0) + minitest + nokogiri (>= 1.6) + rails-html-sanitizer (1.6.0) + loofah (~> 2.21) + nokogiri (~> 1.14) rainbow (3.1.1) rake (13.0.6) rdf (3.3.1) @@ -293,6 +318,10 @@ GEM rspec-mocks (3.11.2) diff-lcs (>= 1.2.0, < 2.0) rspec-support (~> 3.11.0) + rspec-openapi (0.18.3) + actionpack (>= 5.2.0) + rails-dom-testing + rspec-core rspec-support (3.11.1) rubocop (1.54.2) json (~> 2.3) @@ -412,6 +441,8 @@ DEPENDENCIES require_all rest-client (~> 2.1.0) rspec (~> 3.11.0) + rspec-core (~> 3.11) + rspec-openapi (~> 0.18.3) rubocop ruby-debug-ide securerandom diff --git a/VP/vp-interface/app/controllers/application_controller.rb b/VP/vp-interface/app/controllers/application_controller.rb index 13c6b66..370cb16 100644 --- a/VP/vp-interface/app/controllers/application_controller.rb +++ b/VP/vp-interface/app/controllers/application_controller.rb @@ -1,61 +1,60 @@ # frozen_string_literal: false -require_relative "../../config/environment" # for docker -require "swagger/blocks" -require "sinatra" -require "sinatra/base" -require "json" -require "erb" +require_relative '../../config/environment' # for docker +require 'swagger/blocks' +require 'sinatra' +require 'sinatra/base' +require 'json' +require 'erb' # require 'omniauth' # require 'omniauth-openid-connect' require 'jwt' # DO NOT change the order of loading below. The files contain executable code that builds the overall configuration before this module starts -require_relative "../../lib/configuration" # VPConfig and FDPConfig -require_relative "models" -require_relative "routes" -require_relative "../../lib/cache" -require_relative "../../lib/fdp" -require_relative "../../lib/vp" -require_relative "../../lib/metadata_functions" -require_relative "../../lib/services" -require_relative "../../lib/wordcloud" - +require_relative '../../lib/configuration' # VPConfig and FDPConfig +require_relative 'models' +require_relative 'routes' +require_relative '../../lib/cache' +require_relative '../../lib/fdp' +require_relative '../../lib/vp' +require_relative '../../lib/metadata_functions' +require_relative '../../lib/services' +require_relative '../../lib/wordcloud' class ApplicationController < Sinatra::Application include Swagger::Blocks - set :bind, "0.0.0.0" + set :bind, '0.0.0.0' before do - response.headers["Access-Control-Allow-Origin"] = "*" + response.headers['Access-Control-Allow-Origin'] = '*' end configure do - set :public_folder, "public" - set :views, "app/views" + set :public_folder, 'public' + set :views, 'app/views' enable :cross_origin end # routes... - options "*" do - response.headers["Allow"] = "GET, PUT, POST, DELETE, OPTIONS" - response.headers["Access-Control-Allow-Headers"] = "Authorization, Content-Type, Accept, X-User-Email, X-Auth-Token" - response.headers["Access-Control-Allow-Origin"] = "*" + options '*' do + response.headers['Allow'] = 'GET, PUT, POST, DELETE, OPTIONS' + response.headers['Access-Control-Allow-Headers'] = 'Authorization, Content-Type, Accept, X-User-Email, X-Auth-Token' + response.headers['Access-Control-Allow-Origin'] = '*' 200 end swagger_root do - key :swagger, "2.0" + key :swagger, '2.0' info do - key :version, "1.0.0" - key :title, "FLAIR-GG Virtual Platform Server" - key :description, "Enables discovery of Germplasm resources" - key :termsOfService, "https://example.org" + key :version, '1.0.0' + key :title, 'FLAIR-GG Virtual Platform Server' + key :description, 'Enables discovery of Germplasm resources' + key :termsOfService, 'https://example.org' contact do - key :name, "Mark D. Wilkinson" + key :name, 'Mark D. Wilkinson' end license do - key :name, "MIT" + key :name, 'MIT' end end # tag do @@ -66,9 +65,9 @@ class ApplicationController < Sinatra::Application # key :url, 'https://fairdata.services/Champion/about' # end # end - key :schemes, ["http"] - key :host, ENV.fetch("HARVESTER", nil) - key :basePath, "/flair-gg-vp-server" + key :schemes, ['http'] + key :host, ENV.fetch('HARVESTER', nil) + key :basePath, '/flair-gg-vp-server' # key :consumes, ['application/json'] # key :produces, ['application/json'] end @@ -77,9 +76,8 @@ class ApplicationController < Sinatra::Application SWAGGERED_CLASSES = [ErrorModel, AllResourcesResponse, OntologySearchResponse, KeywordSearchResponse, self].freeze set_routes(classes: SWAGGERED_CLASSES) - - VP.new(config: VPConfig.new) # set up index and active sites) + + VP.new(config: VPConfig.new) # set up index and active sites) run! # if app_file == $PROGRAM_NAME end - diff --git a/VP/vp-interface/app/controllers/routes.rb b/VP/vp-interface/app/controllers/routes.rb index 6bc11c4..fa636e8 100644 --- a/VP/vp-interface/app/controllers/routes.rb +++ b/VP/vp-interface/app/controllers/routes.rb @@ -2,71 +2,71 @@ def set_routes(classes: allclasses) set :server_settings, timeout: 180 - set :public_folder, "public" + set :public_folder, 'public' - get "/" do - redirect "/flair-gg-vp-server/resources" + get '/' do + redirect '/flair-gg-vp-server/resources' end - get "/flair-gg-vp-server" do + get '/flair-gg-vp-server' do content_type :json response.body = JSON.dump(Swagger::Blocks.build_root_json(classes)) end - get "/flair-gg-vp-server/force-refresh" do - warn "initializing refresh in routes" - unless File.exist?("./cache/REFRESHING") # multiple browser calls are a problem! + get '/flair-gg-vp-server/force-refresh' do + warn 'initializing refresh in routes' + unless File.exist?('./cache/REFRESHING') # multiple browser calls are a problem! VP.restart - @discoverables = VP.current_vp.get_resources # "./lib/metadata_functions" - FileUtils.rm_f("./cache/servicetypes.json") # remove the cache + @discoverables = VP.current_vp.get_resources # "./lib/metadata_functions" + FileUtils.rm_f('./cache/servicetypes.json') # remove the cache @services = VP.current_vp.collect_data_services end - redirect "/flair-gg-vp-server/resources" # before do collect_data_services will be called, and this will refresh + redirect '/flair-gg-vp-server/resources' # before do collect_data_services will be called, and this will refresh end - get "/flair-gg-vp-server/resources" do - @discoverables = VP.current_vp.get_resources # "./lib/metadata_functions" - @message = "All Resources" + get '/flair-gg-vp-server/resources' do + @discoverables = VP.current_vp.get_resources # "./lib/metadata_functions" + @message = 'All Resources' request.accept.each do |type| case type.to_s - when "text/html" + when 'text/html' halt erb :discovered_layout - when "application/json" + when 'application/json' content_type :json halt @discoverables.to_json end end - error 406 # @message = "All Resources" + error 406 # @message = "All Resources" # erb :discovered_layout end - get "/flair-gg-vp-server/keyword-search" do - keyword = params["keyword"].strip + get '/flair-gg-vp-server/keyword-search' do + keyword = params['keyword'].strip @discoverables = VP.current_vp.keyword_search_shell(keyword: keyword) # "./lib/vp" - @message = "Keyword Search Results" + @message = 'Keyword Search Results' request.accept.each do |type| case type.to_s - when "text/html" + when 'text/html' halt erb :discovered_layout - when "application/json" + when 'application/json' content_type :json halt @discoverables.to_json end end - error 406 # @message = "All Resources" + error 406 # @message = "All Resources" # erb :discovered_layout end - post "/flair-gg-vp-server/keyword-search" do + post '/flair-gg-vp-server/keyword-search' do data = JSON.parse request.body.read.to_s - keyword = data["keyword"] ? data["keyword"].strip : "" + keyword = data['keyword'] ? data['keyword'].strip : '' @discoverables = VP.current_vp.keyword_search_shell(keyword: keyword) # "./lib/vp" - @message = "Keyword Search Results" + @message = 'Keyword Search Results' request.accept.each do |type| case type.to_s - when "text/html" + when 'text/html' halt erb :discovered_layout - when "application/json" + when 'application/json' content_type :json halt @discoverables.to_json end @@ -75,16 +75,16 @@ def set_routes(classes: allclasses) # erb :discovered_layout end - get "/flair-gg-vp-server/ontology-search" do - term = params["uri"].strip - term = term.gsub(/\S+:/, "") unless term =~ /^http/ + get '/flair-gg-vp-server/ontology-search' do + term = params['uri'].strip + term = term.gsub(/\S+:/, '') unless term =~ /^http/ @discoverables = VP.current_vp.ontology_search_shell(term: term) # "./lib/vp" - @message = "Ontology Search Results" + @message = 'Ontology Search Results' request.accept.each do |type| case type.to_s - when "text/html" + when 'text/html' halt erb :discovered_layout - when "application/json" + when 'application/json' content_type :json halt @discoverables.to_json end @@ -92,17 +92,17 @@ def set_routes(classes: allclasses) error 406 # erb :discovered_layout end - post "/flair-gg-vp-server/ontology-search" do + post '/flair-gg-vp-server/ontology-search' do data = JSON.parse request.body.read.to_s - term = data["uri"] ? data["uri"].strip : "" - term = term.gsub(/\S+:/, "") unless term =~ /^http/ + term = data['uri'] ? data['uri'].strip : '' + term = term.gsub(/\S+:/, '') unless term =~ /^http/ @discoverables = VP.current_vp.ontology_search_shell(term: term) # "./lib/vp" - @message = "Ontology Search Results" + @message = 'Ontology Search Results' request.accept.each do |type| case type.to_s - when "text/html" + when 'text/html' halt erb :discovered_layout - when "application/json" + when 'application/json' content_type :json halt @discoverables.to_json end @@ -116,15 +116,16 @@ def set_routes(classes: allclasses) # @servicecollection, @commongetparams, @commonpostparams = VP.current_vp.retrieve_sevices(termuri: termuri) # "./lib/vp" # erb :services_layout # end - get "/flair-gg-vp-server/retrieve-services" do - termuri = params["services"] + get '/flair-gg-vp-server/retrieve-services' do + termuri = params['services'] @servicecollection, @commongetparams, @commonpostparams = VP.current_vp.retrieve_sevices(termuri: termuri) # "./lib/vp" request.accept.each do |type| case type.to_s - when "text/html" + when 'text/html' halt erb :services_layout - when "application/json" - @minimized_collection = @servicecollection.minimize_service_collection( commongetparams: @commongetparams, commonpostparams: @commonpostparams) + when 'application/json' + @minimized_collection = @servicecollection.minimize_service_collection(commongetparams: @commongetparams, + commonpostparams: @commonpostparams) @servicecollection.vpgraph = nil content_type :json response = @minimized_collection.to_json @@ -134,50 +135,83 @@ def set_routes(classes: allclasses) error 406 end - post "/flair-gg-vp-server/execute-data-services" do - @servicelabel = params["servicelabel"].downcase.gsub(/\s+/, "_") # no spaces in service filenames - label leads to jupyter file - @location, @results = VP.current_vp.execute_data_services(params: params) - erb :execution_results_layout - end + post '/flair-gg-vp-server/execute-data-services' do + # three possibilities: + # 1) they send key/value pairs as params from form interface + # 2) they send _request_body from the form interfaces + # 3) they send JSON as the body + if request.content_type == 'application/json' + j = JSON.parse(request.body.read.to_s) + j = j.first if j.is_a? Array + # {uri: serviceuri, + # _request_body: {json: data}, + # service_list: [endpoint, endpoint, endpoint] + # } # this is passed to all services + _serviceuri = j['uri'].gsub(%r{.*[/\#](\S+)}, '\1') # take fragment only + servicelabel = @serviceuri.downcase.gsub(/\s+/, '_') + analytics = "https://wilkinsonlab.github.io/FLAIR-GG-Analytics/lab/index.html?path=FLAIR-GG%2F#{servicelabel}.ipynb" + location, results = VP.current_vp.execute_data_services_api(json: j) + request.accept.each do |type| + case type.to_s + when 'application/json' + content_type :json + halt({ 'key' => location, 'jupyter' => analytics, 'results' => results }.to_json) + end + end + else + @servicelabel = params['servicelabel'].downcase.gsub(/\s+/, '_') # no spaces in service filenames - label leads to jupyter file + @location, @results = VP.current_vp.execute_data_services(params: params) + request.accept.each do |type| + case type.to_s + when 'text/html' + halt erb :execution_results_layout + when 'application/json' + content_type :json + halt({ 'location' => location, 'jupyter' => @servicelabel }.to_json) + end + end + end + error 406 + end - get "/flair-gg-vp-server/wordcloud" do + get '/flair-gg-vp-server/wordcloud' do @freqs = Wordcloud.new.count_words # "./lib/wordcloud" erb :wordcloud end - get "/flair-gg-vp-server/wordcloud/force-refresh" do + get '/flair-gg-vp-server/wordcloud/force-refresh' do @discoverables = {} @freqs = {} - if File.exist?("./cache/WCREFRESHING") # multiple browser calls are a problem! + if File.exist?('./cache/WCREFRESHING') # multiple browser calls are a problem! erb :discovered_layout else - f = open("./cache/WCREFRESHING", "w") # multiple browser calls are a problem! - f.puts "WCREFRESHING" + f = open('./cache/WCREFRESHING', 'w') # multiple browser calls are a problem! + f.puts 'WCREFRESHING' f.close - warn "forced refresh" + warn 'forced refresh' wc = Wordcloud.new(refresh: true) @freqs = wc.count_words warn "received #{@freqs.length}" - FileUtils.rm_f("./cache/WCREFRESHING") + FileUtils.rm_f('./cache/WCREFRESHING') end erb :wordcloud end - get "/flair-gg-vp-server/refresh-servicetypes" do - FileUtils.rm_f("./cache/servicetypes.json") # remove the cache + get '/flair-gg-vp-server/refresh-servicetypes' do + FileUtils.rm_f('./cache/servicetypes.json') # remove the cache @services = VP.current_vp.collect_data_services # refresh - redirect "/flair-gg-vp-server/resources" # before do collect_data_services will be called, and this will refresh + redirect '/flair-gg-vp-server/resources' # before do collect_data_services will be called, and this will refresh end # API Only - get "/flair-gg-vp-server/servicetypes" do - FileUtils.rm_f("./cache/servicetypes.json") # remove the cache + get '/flair-gg-vp-server/servicetypes' do + FileUtils.rm_f('./cache/servicetypes.json') # remove the cache @services = VP.current_vp.collect_data_services # refresh request.accept.each do |type| case type.to_s - when "application/json" + when 'application/json' content_type :json halt @services.to_json end diff --git a/VP/vp-interface/app/models/openapi3.json b/VP/vp-interface/app/models/openapi3.json new file mode 100644 index 0000000..d9e2b3e --- /dev/null +++ b/VP/vp-interface/app/models/openapi3.json @@ -0,0 +1,229 @@ +{ + "openapi": "3.0.1", + "info": { + "title": "XXX & GRLC", + "description": "The FAIR Data Point grlc server for the XXXX Project", + "contact": { + "name": "Your Name Here", + "url": "https://my.organization.org" + }, + "version": "local" + }, + "servers": [ + { + "url": "//testbed.ejprd.semlab-leiden.nl:30001/api-local/" + } + ], + "paths": { + "/count": { + "get": { + "tags": [ + "Patient Count" + ], + "summary": "Returns the number of patients in the registry with the corresponding disease code", + "description": "\n\n```\n#+ summary: Returns the number of patients in the registry with the corresponding disease code\n#+ tags:\n#+ - Patient Count\n#+ defaults:\n#+ - type: http://www.orpha.net/ORDO/Orphanet_98896\n#+ endpoint_in_url: False\n\nPREFIX obo: \nPREFIX sio: \nPREFIX xsd: \nPREFIX ordo: \nPREFIX rdfs: \nPREFIX ofn: \n\nselect (COUNT(?disattribute) as ?count) where { \n?disprocess a ; # diagnostic process\n sio:SIO_000229 ?disoutput .\n?disoutput a ; # diagnosis code\n sio:SIO_000628 ?disattribute.\n?disattribute a ?_type_iri . # attribute is a orphacode\n}\n\n```", + "parameters": [ + { + "name": "type", + "in": "query", + "description": "A value of type string (iri) that will substitute ?_type_iri in the original query", + "required": true, + "schema": { + "type": "string", + "format": "iri", + "default": "http://www.orpha.net/ORDO/Orphanet_98896" + } + } + ], + "responses": { + "200": { + "description": "Query response", + "content": { + "text/csv": { + "schema": { + "type": "array", + "items": { + "type": "object", + "properties": {} + } + } + }, + "application/json": { + "schema": { + "type": "array", + "items": { + "type": "object", + "properties": {} + } + } + }, + "text/html": { + "schema": { + "type": "array", + "items": { + "type": "object", + "properties": {} + } + } + } + } + }, + "default": { + "description": "Unexpected error", + "content": { + "text/csv": { + "schema": { + "$ref": "#/components/schemas/Message" + } + }, + "application/json": { + "schema": { + "$ref": "#/components/schemas/Message" + } + }, + "text/html": { + "schema": { + "$ref": "#/components/schemas/Message" + } + } + } + } + } + } + }, + "/kpi-ttd": { + "get": { + "tags": [ + "KPI diagnosis-delay" + ], + "summary": "Returns the Key Performance Indicator of the delay between symptom onset and diagnosis. This data is aggregated by disease, and by year of diagnosis, and is measured in days.", + "description": "\n\n```\n#+ summary: Returns the Key Performance Indicator of the delay between symptom onset and diagnosis. This data is aggregated by disease, and by year of diagnosis, and is measured in days.\n#+ tags:\n#+ - KPI diagnosis-delay\n#+ defaults:\n#+ \n#+ endpoint_in_url: False\n\n################################################################\n# list diagnosis and time from onset to diagnosis\n################################################################\n\nPREFIX obo: \nPREFIX sio: \nPREFIX xsd: \nPREFIX ordo: \nPREFIX rdfs: \nPREFIX ofn: \n\n# date of symptom onset is the value (output) of its own model, date of diagnosis is in the context of the diagnosis model\n#SELECT DISTINCT ?pid ?onsetvalue ?diagnosisdate ?ORDO ?yearOfDiagnosis (xsd:integer(ROUND(AVG(?timeOnsetToDiagnosis))) as ?avgoffset)\nSELECT DISTINCT ?ORDO ?yearOfDiagnosis (xsd:integer(ROUND(AVG(?timeOnsetToDiagnosis))) as ?avgoffset)\nWHERE {\n BIND(xsd:integer(ofn:asDays(?diagnosisdate - ?onsetvalue )) AS ?timeOnsetToDiagnosis)\n BIND(SUBSTR(str(?diagnosisdate), 1,4) AS ?yearOfDiagnosis)\n \n\t\tGRAPH ?diseasegraph {\n ?disperson sio:SIO_000228 ?disrole . # person has role role\n ?disrole sio:SIO_000356 ?disprocess ; # is realized in process\n a sio:SIO_000016 .\n ?disprocess a ; # diagnostic process\n sio:SIO_000229 ?disoutput .\n ?disoutput a ; # diagnosis code\n sio:SIO_000628 ?disattribute.\n ?disattribute a ?ORDO.\n FILTER(!(?ORDO = sio:SIO_000614))\n }\n ?diseasegraph a obo:NCIT_C62143 ; # encounter\n \t\t\tsio:SIO_000068 ?diseasetimeline, ?diseaseevent ; # is part of\n \t\t\tsio:SIO_000680 ?diseasestartdate . # start date\n \t?diseasestartdate sio:SIO_000300 ?diagnosisdate . # need the has value property\n\n ?diseasetimeline a obo:NCIT_C54576, sio:SIO_000417; \n \tsio:SIO_000332 ?diseaseindividual .\n ?diseaseindividual sio:SIO_000671 ?diseaseindividual_identifier .\n ?diseaseindividual_identifier sio:SIO_000300 ?pid .\n\n\n# date of symptom onset is the value (output) of its own model, date of diagnosis is in the context of the diagnosis model\n GRAPH ?onsetg {\n ?onsetrole sio:SIO_000356 ?onsetprocess ; \n a sio:SIO_000016 .\n ?onsetprocess a sio:SIO_000006 , ?onsetprocess_type ; \n sio:SIO_000229 ?onsetoutput .\n ?onsetoutput a sio:SIO_000015, ?onsetoutput_type; \n sio:SIO_000628 ?onsetattribute.\n ?onsetattribute a .\n \t\n ?onsetoutput sio:SIO_000300 ?onsetvalue .\n }\n ?onsetg a obo:NCIT_C62143 ; # encounter\n\t sio:SIO_000068 ?onsettimeline, ?onsetevent . # is part of\n\n ?onsettimeline a obo:NCIT_C54576, sio:SIO_000417; \n \t sio:SIO_000332 ?onsetindividual .\n ?onsetindividual sio:SIO_000671 ?onsetindividual_identifier .\n ?onsetindividual_identifier sio:SIO_000300 ?pid . # close the join around PID\n \n} group by ?ORDO ?yearOfDiagnosis order by ?yearOfDiagnosis ?ORDO \n```", + "responses": { + "200": { + "description": "Query response", + "content": { + "text/csv": { + "schema": { + "type": "array", + "items": { + "type": "object", + "properties": {} + } + } + }, + "application/json": { + "schema": { + "type": "array", + "items": { + "type": "object", + "properties": {} + } + } + }, + "text/html": { + "schema": { + "type": "array", + "items": { + "type": "object", + "properties": {} + } + } + } + } + }, + "default": { + "description": "Unexpected error", + "content": { + "text/csv": { + "schema": { + "$ref": "#/components/schemas/Message" + } + }, + "application/json": { + "schema": { + "$ref": "#/components/schemas/Message" + } + }, + "text/html": { + "schema": { + "$ref": "#/components/schemas/Message" + } + } + } + } + } + } + }, + "/phenotype-frequencies": { + "get": { + "tags": [ + "Phenotype frequency" + ], + "summary": "Returns the number of patients in the registry that have had a phenotype code at any time", + "description": "\n\n```\n#+ summary: Returns the number of patients in the registry that have had a phenotype code at any time\n#+ tags:\n#+ - Phenotype frequency\n#+ defaults:\n#+ \n#+ endpoint_in_url: False\n\nPREFIX obo: \nPREFIX sio: \nPREFIX xsd: \nPREFIX ordo: \nPREFIX rdfs: \nPREFIX ofn: \n\n\nselect ?pheno (count(?pheno) as ?frequency) where {\n select distinct ?p ?pheno where {\n\t\tGRAPH ?diseasegraph {\n ?disprocess a ; # diagnostic process\n sio:SIO_000229 ?disoutput .\n ?disoutput a ; # diagnosis code\n sio:SIO_000628 ?disattribute.\n ?disattribute a ?pheno .\n FILTER(!(?pheno = sio:SIO_000614))\n\n\t\t}\n ?diseasegraph a obo:NCIT_C62143 ; # encounter\n \t\t\tsio:SIO_000068 ?diseasetimeline, ?diseaseevent . # is part of\n\n\t ?diseasetimeline a obo:NCIT_C54576, sio:SIO_000417; \n \tsio:SIO_000332 ?diseaseindividual .\n\t ?diseaseindividual sio:SIO_000671 ?diseaseindividual_identifier .\n \t?diseaseindividual_identifier sio:SIO_000300 ?p .\n }\n} group by ?pheno order by desc(?frequency)\n```", + "responses": { + "200": { + "description": "Query response", + "content": { + "text/csv": { + "schema": { + "type": "array", + "items": { + "type": "object", + "properties": {} + } + } + }, + "application/json": { + "schema": { + "type": "array", + "items": { + "type": "object", + "properties": {} + } + } + }, + "text/html": { + "schema": { + "type": "array", + "items": { + "type": "object", + "properties": {} + } + } + } + } + }, + "default": { + "description": "Unexpected error", + "content": { + "text/csv": { + "schema": { + "$ref": "#/components/schemas/Message" + } + }, + "application/json": { + "schema": { + "$ref": "#/components/schemas/Message" + } + }, + "text/html": { + "schema": { + "$ref": "#/components/schemas/Message" + } + } + } + } + } + } + } + }, + "components": { + "schemas": { + "Message": { + "type": "string" + } + } + }, + "x-original-swagger-version": "2.0" +} \ No newline at end of file diff --git a/VP/vp-interface/app/views/_sidebar.erb b/VP/vp-interface/app/views/_sidebar.erb index 92a0f12..c280173 100644 --- a/VP/vp-interface/app/views/_sidebar.erb +++ b/VP/vp-interface/app/views/_sidebar.erb @@ -1,10 +1,10 @@
- Keyword Search:
+ Keyword Search:
- Ontology URI:
+ Ontology URI:
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Run `rake db:migrate` to resolve the issue.' # end -run ApplicationController +# run ApplicationController diff --git a/VP/vp-interface/lib/comon_queries.rb b/VP/vp-interface/lib/common_queries.rb similarity index 76% rename from VP/vp-interface/lib/comon_queries.rb rename to VP/vp-interface/lib/common_queries.rb index fdf2bf8..751ffca 100644 --- a/VP/vp-interface/lib/comon_queries.rb +++ b/VP/vp-interface/lib/common_queries.rb @@ -11,8 +11,8 @@ class VP VPDISCOVERABLE = "ejpnew:VPDiscoverable".freeze VPANNOTATION = "dcat:theme".freeze - def find_discoverables_query(graph:) - SPARQL.parse(" + def find_discoverables_query(graph:) + vpd = SPARQL.parse(" #{NAMESPACES} SELECT DISTINCT ?s ?t ?title ?contact ?servicetype WHERE { @@ -29,13 +29,13 @@ def find_discoverables_query(graph:) } ") - graph.query(vpd) - end + graph.query(vpd) + end - def keyword_search_query(graph:, keyword:) - vpd = SPARQL.parse(" + def keyword_search_query(graph:, keyword:) + vpd = SPARQL.parse(" #{NAMESPACES} - + SELECT DISTINCT ?s ?t ?title ?contact WHERE { VALUES ?connection { #{VPCONNECTION} } @@ -46,27 +46,26 @@ def keyword_search_query(graph:, keyword:) OPTIONAL{?s dcat:contactPoint ?c . ?c ?contact } . { - VALUES ?searchfields { dc:title dc:description dc:keyword } + VALUES ?searchfields { dc:title dc:description dc:keyword dcat:keyword } ?s ?searchfields ?kw FILTER(CONTAINS(lcase(?kw), '#{keyword}')) } }") - # warn "keyword search query #{vpd.to_sparql}" - # warn "graph is #{@graph.size}" - graph.query(vpd) - - end + # warn "keyword search query #{vpd.to_sparql}" + # warn "graph is #{@graph.size}" + graph.query(vpd) + end - def ontology_search_query(graph:, uri:) - vpd = SPARQL.parse(" + def ontology_search_query(graph:, uri:) + vpd = SPARQL.parse(" #{NAMESPACES} - + SELECT DISTINCT ?s ?t ?title ?contact WHERE { VALUES ?connection { #{VPCONNECTION} } VALUES ?discoverable { #{VPDISCOVERABLE} } - + ?s ?connection ?discoverable ; dc:title ?title ; a ?t . @@ -77,34 +76,33 @@ def ontology_search_query(graph:, uri:) FILTER(CONTAINS(str(?theme), '#{uri}')) } }") - - graph.query(vpd) - end - def verbose_annotations_query(graph:) - # TODO: This does not respect vpdiscoverable... - vpd = SPARQL.parse(" + graph.query(vpd) + end + + def verbose_annotations_query(graph:) + # TODO: This does not respect vpdiscoverable... + vpd = SPARQL.parse(" #{NAMESPACES} SELECT DISTINCT ?annot WHERE { VALUES ?annotation { dcat:theme dcat:themeTaxonomy } ?s ?annotation ?annot . }") - graph.query(vpd) - end + graph.query(vpd) + end - def keyword_annotations_query(graph:) - vpd = SPARQL.parse(" + def keyword_annotations_query(graph:) + vpd = SPARQL.parse(" #{NAMESPACES} select DISTINCT ?kw WHERE - { VALUES ?searchfields { dc:keyword } + { VALUES ?searchfields { dc:keyword dcat:keyword } ?s ?searchfields ?kw . }") - graph.query(vpd) - - end + graph.query(vpd) + end - def collect_data_services_query(graph:) - vpd = SPARQL.parse(" + def collect_data_services_query(graph:) + vpd = SPARQL.parse(" #{NAMESPACES} @@ -119,6 +117,6 @@ def collect_data_services_query(graph:) ?s dc:type ?type . } }") - graph.query(vpd) - end - \ No newline at end of file + graph.query(vpd) + end +end diff --git a/VP/vp-interface/lib/configuration.rb b/VP/vp-interface/lib/configuration.rb index 47e18b7..1f088a9 100644 --- a/VP/vp-interface/lib/configuration.rb +++ b/VP/vp-interface/lib/configuration.rb @@ -21,8 +21,9 @@ def get_active_sites(api:) :headers => { accept: "application/json" }, :verify_ssl => false ) - sites = JSON.parse(r.body).map { |s| s["clientUrl"] if s["state"] == "ACTIVE" } + sites = JSON.parse(r.body).map { |s| s["clientUrl"] if ["ACTIVE"].include? s["state"] } sites.compact! + warn "FOUND SITES #{sites}" sites end # { diff --git a/VP/vp-interface/lib/services.rb b/VP/vp-interface/lib/services.rb index ef5d074..1c439a9 100644 --- a/VP/vp-interface/lib/services.rb +++ b/VP/vp-interface/lib/services.rb @@ -177,7 +177,7 @@ def retrieve_endpoint(openapi:) j = JSON.parse(resp) j["servers"].each do |s| s["url"].gsub!(%r{/$}, "") - s["url"].gsub!(%r{^//}, "https://") + s["url"].gsub!(%r{^//}, "http://") end resp = j.to_json # back to json for the openapi3 begin @@ -190,12 +190,16 @@ def retrieve_endpoint(openapi:) # we are now scanning for the endpoint that was referenced in the FDP. # if we don't find it, we fail! (politely!) + # need to deal with http vs https, since they get messed up in the openAPI3 conversion + endpointsuffix = @endpoint.to_s.gsub(/https?:/, "") + api.paths.each do |path, pathitem| warn "path #{path}" base = pathitem.servers.first.url fullpath = base + path - warn "testing #{fullpath} against #{@endpoint}|" - unless fullpath == @endpoint # compare it to the endpoint that was in the FDP + fullpathsuffix = fullpath.gsub(/https?:/, "") + warn "testing #{fullpathsuffix} against #{endpointsuffix}|" + unless fullpathsuffix == endpointsuffix # compare it to the endpoint that was in the FDP warn "TEST FAILED" next end diff --git a/VP/vp-interface/lib/vp.rb b/VP/vp-interface/lib/vp.rb index e1a952a..f48fb92 100644 --- a/VP/vp-interface/lib/vp.rb +++ b/VP/vp-interface/lib/vp.rb @@ -78,7 +78,7 @@ def find_discoverables results = find_discoverables_query(graph: networkgraph) discoverables = build_from_results(results: results) - warn discoverables + warn "DISCOVERABLES", discoverables discoverables end @@ -180,6 +180,24 @@ def execute_data_services(params:) [downloadlocation, results] end + def execute_data_services_api(json:) + # {uri: serviceuri, + # _request_body: {json: data}, + # service_list: [endpoint, endpoint, endpoint] + # } # this is passed to all services + results = {} + json["service_list"].each do |ep| + endpoint = ep + if json["_request_body"] + result = Service::execute_post(endpoint: endpoint, body: params) + end + results[endpoint] = result.body if result + end + downloadlocation = process_and_upload_output(results: results) # in serviceoutput_processors/general.rb + [downloadlocation, results] + end + + def match_type_to_icon(type:) t = type.match(%r{[\#/](\w+?)$})[1].downcase.to_sym # anchor to end to capture last / or # warn "matching #{t}\n\n" diff --git a/VP/vp-interface/public/images/drug.png b/VP/vp-interface/public/images/drug copy.png similarity index 100% rename from VP/vp-interface/public/images/drug.png rename to VP/vp-interface/public/images/drug copy.png diff --git a/VP/vp-interface/public/images/flair-gg-logo copy.png b/VP/vp-interface/public/images/flair-gg-logo copy.png new file mode 100644 index 0000000..7b747f1 Binary files /dev/null and b/VP/vp-interface/public/images/flair-gg-logo copy.png differ diff --git a/VP/vp-interface/spec/application_controller_spec.rb b/VP/vp-interface/spec/application_controller_spec.rb index d57710e..aa73a81 100644 --- a/VP/vp-interface/spec/application_controller_spec.rb +++ b/VP/vp-interface/spec/application_controller_spec.rb @@ -1,13 +1,15 @@ -require_relative "spec_helper" +# frozen_string_literal: false -def app - ApplicationController -end +require_relative 'spec_helper' # this will load the app + +RSpec.describe 'ApplicationController', type: :request do + include Rack::Test::Methods + def app + ApplicationController + end -describe ApplicationController do - it "responds with a welcome message" do - get '/' - expect(last_response.status).to eq(200) - expect(last_response.body).to include("Welcome to the Sinatra Template!") + it 'returns a list of all known resources' do + get '/flair-gg-vp-server/resources' + expect(last_response.status).to eq(406) end end diff --git a/VP/vp-interface/spec/spec_helper.rb b/VP/vp-interface/spec/spec_helper.rb index b686a1e..534ffa0 100644 --- a/VP/vp-interface/spec/spec_helper.rb +++ b/VP/vp-interface/spec/spec_helper.rb @@ -1,36 +1,52 @@ ENV["SINATRA_ENV"] = "test" +ENV['RACK_ENV'] = "test" require_relative '../config/environment' +require 'rspec' require 'rack/test' -require 'capybara/rspec' -require 'capybara/dsl' +# require 'capybara/rspec' +# require 'capybara/dsl' -if ActiveRecord::Migrator.needs_migration? - raise 'Migrations are pending. Run `rake db:migrate SINATRA_ENV=test` to resolve the issue.' -end -ActiveRecord::Base.logger = nil +set :environment, :test +set :run, false +set :raise_errors, true +set :logging, false + +module RSpecMixin + def app + ApplicationController + + # App.new + end +end RSpec.configure do |config| - config.run_all_when_everything_filtered = true - config.filter_run :focus + config.tty = true + config.formatter = :documentation config.include Rack::Test::Methods - config.include Capybara::DSL - DatabaseCleaner.strategy = :truncation + config.include RSpecMixin +end +# RSpec.configure do |config| +# config.run_all_when_everything_filtered = true +# config.filter_run :focus +# config.include Rack::Test::Methods +# config.include Capybara::DSL +# DatabaseCleaner.strategy = :truncation - config.before do - DatabaseCleaner.clean - end +# config.before do +# DatabaseCleaner.clean +# end - config.after do - DatabaseCleaner.clean - end +# config.after do +# DatabaseCleaner.clean +# end - config.order = 'default' -end +# config.order = 'default' +# end def app Rack::Builder.parse_file('config.ru').first end -Capybara.app = app +# Capybara.app = app