qa 0.10.1 → 0.10.2
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- checksums.yaml +4 -4
- data/Rakefile +12 -2
- data/app/controllers/qa/terms_controller.rb +14 -16
- data/app/models/qa/mesh_tree.rb +3 -5
- data/app/models/qa/subject_mesh_term.rb +15 -15
- data/config/routes.rb +1 -1
- data/lib/generators/qa/install/install_generator.rb +2 -3
- data/lib/generators/qa/local/tables/mysql/mysql_generator.rb +3 -5
- data/lib/generators/qa/local/tables/tables_generator.rb +4 -6
- data/lib/qa/authorities/assign_fast/generic_authority.rb +16 -19
- data/lib/qa/authorities/assign_fast_subauthority.rb +3 -5
- data/lib/qa/authorities/authority_with_sub_authority.rb +1 -2
- data/lib/qa/authorities/base.rb +2 -3
- data/lib/qa/authorities/geonames.rb +11 -12
- data/lib/qa/authorities/getty.rb +7 -8
- data/lib/qa/authorities/getty/aat.rb +11 -12
- data/lib/qa/authorities/getty/tgn.rb +15 -15
- data/lib/qa/authorities/getty/ulan.rb +15 -16
- data/lib/qa/authorities/loc/generic_authority.rb +32 -33
- data/lib/qa/authorities/loc_subauthority.rb +17 -20
- data/lib/qa/authorities/local.rb +41 -40
- data/lib/qa/authorities/local/file_based_authority.rb +18 -19
- data/lib/qa/authorities/local/mysql_table_based_authority.rb +8 -6
- data/lib/qa/authorities/local/registry.rb +5 -5
- data/lib/qa/authorities/local/table_based_authority.rb +26 -19
- data/lib/qa/authorities/mesh.rb +8 -16
- data/lib/qa/authorities/mesh_tools.rb +5 -5
- data/lib/qa/authorities/mesh_tools/mesh_data_parser.rb +4 -6
- data/lib/qa/authorities/mesh_tools/mesh_importer.rb +11 -13
- data/lib/qa/authorities/oclcts.rb +0 -1
- data/lib/qa/authorities/oclcts/generic_oclc_authority.rb +16 -16
- data/lib/qa/authorities/tgnlang.rb +7 -12
- data/lib/qa/version.rb +1 -1
- data/spec/controllers/terms_controller_spec.rb +44 -54
- data/spec/lib/authorities/assign_fast_spec.rb +25 -27
- data/spec/lib/authorities/file_based_authority_spec.rb +25 -26
- data/spec/lib/authorities/geonames_spec.rb +5 -6
- data/spec/lib/authorities/getty/aat_spec.rb +6 -10
- data/spec/lib/authorities/getty/tgn_spec.rb +6 -10
- data/spec/lib/authorities/getty/ulan_spec.rb +6 -10
- data/spec/lib/authorities/getty_spec.rb +4 -5
- data/spec/lib/authorities/loc_spec.rb +30 -36
- data/spec/lib/authorities/local_spec.rb +5 -7
- data/spec/lib/authorities/mesh_spec.rb +9 -9
- data/spec/lib/authorities/mysql_table_based_authority_spec.rb +13 -5
- data/spec/lib/authorities/oclcts_spec.rb +17 -21
- data/spec/lib/authorities/table_based_authority_spec.rb +21 -12
- data/spec/lib/authorities/tgnlang_spec.rb +4 -6
- data/spec/lib/authorities_loc_subauthorities.rb +50 -54
- data/spec/lib/mesh_data_parser_spec.rb +73 -79
- data/spec/lib/services/rdf_authority_parser_spec.rb +2 -7
- data/spec/lib/tasks/mesh.rake_spec.rb +16 -12
- data/spec/models/subject_mesh_term_spec.rb +4 -4
- data/spec/routing/route_spec.rb +13 -15
- data/spec/spec_helper.rb +3 -4
- data/spec/test_app_templates/lib/generators/test_app_generator.rb +0 -1
- metadata +45 -17
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require 'spec_helper'
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describe Qa::Authorities::MeshTools::MeshDataParser do
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it "parses a record correctly" do
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data = <<-EOS
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data = <<-EOS
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*NEWRECORD
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A = 45
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B = a = b = c = d
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B = more than one
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EOS
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mesh =
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mesh = described_class.new(StringIO.new(data))
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records = mesh.all_records
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expect(records.length).to eq(1)
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expect(records[0]).to eq(
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expect(records[0]).to eq('A' => ['45'], 'B' => ['a = b = c = d', 'more than one'])
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end
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it "handles two records" do
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print entry = test
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mesh =
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mesh = described_class.new(StringIO.new(data))
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records = mesh.all_records
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expect(records.length).to eq(2)
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expect(records[0]).to eq(
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expect(records[1]).to eq(
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expect(records[0]).to eq('A' => ['45'], 'B' => ['a = b = c = d'])
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expect(records[1]).to eq('A' => ['another field'], 'print entry' => ['test'])
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end
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it 'ignores bad input' do
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space at beginning of line and no =
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*NEWRECORD
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EOS
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mesh =
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mesh = described_class.new(StringIO.new(data))
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records = mesh.all_records
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expect(records.length).to eq(2)
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expect(records[0]).to eq(
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expect(records[0]).to eq('A' => ['45'])
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expect(records[1]).to eq({})
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end
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it 'parses a sample mesh file' do
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mesh =
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mesh = described_class.new(webmock_fixture('mesh.txt'))
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records = mesh.all_records
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expect(records.length).to eq(11)
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expect(records[0]).to eq(
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"DC" => ["1"],
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"DX" => ["19840101"],
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"UI" => ["D000001"]
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})
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expect(records[0]).to eq("RECTYPE" => ["D"],
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"MH" => ["Malaria"],
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"AQ" => ["BL CF CI CL CN CO DH DI DT EC EH EM EN EP ET GE HI IM ME MI MO NU PA PC PP PS PX RA RH RI RT SU TH TM UR US VE VI"],
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"PRINT ENTRY" => ["Marsh Fever|T047|NON|EQV|NLM (2006)|050114|abcdef",
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"Plasmodium Infections|T047|NON|EQV|UNK (19XX)|740330|PLASMODIUM INFECT|abcdefv",
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"Remittent Fever|T047|NON|EQV|NLM (2006)|050114|abcdef"],
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"ENTRY" => ["Infections, Plasmodium|T047|NON|EQV|NLM (1992)|911126|INFECT PLASMODIUM|abcdefv",
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"Paludism|T047|NON|EQV|NLM (2005)|040220|abcdef",
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"Fever, Marsh",
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"Fever, Remittent",
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"Infection, Plasmodium",
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"Plasmodium Infection"],
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"MN" => ["C03.752.530", "C23.996.660"],
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"FX" => ["Antimalarials"],
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"MH_TH" => ["NLM (1986)", "ORD (2010)"],
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"ST" => ["T047"],
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"AN" => ["GEN or unspecified; specify Plasmodium species IM if possible but note P. falciparum malaria = MALARIA, FALCIPARUM; P. vivax malaria = MALARIA, VIVAX; tertian malaria = MALARIA, VIVAX, quartan malaria: coord IM with PLASMODIUM MALARIAE (IM); malariotherapy = HYPERTHERMIA, INDUCED: do not confuse with MALARIA /ther; /drug ther: consider also ANTIMALARIALS"],
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"MS" => ["A protozoan disease caused in humans by four species of the PLASMODIUM genus: PLASMODIUM FALCIPARUM; PLASMODIUM VIVAX; PLASMODIUM OVALE; and PLASMODIUM MALARIAE; and transmitted by the bite of an infected female mosquito of the genus ANOPHELES. Malaria is endemic in parts of Asia, Africa, Central and South America, Oceania, and certain Caribbean islands. It is characterized by extreme exhaustion associated with paroxysms of high FEVER; SWEATING; shaking CHILLS; and ANEMIA. Malaria in ANIMALS is caused by other species of plasmodia."],
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"OL" => ["use MALARIA to search MALARIA CONTROL 1966"],
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"PM" => ["MALARIA CONTROL was heading 1963-66"],
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"HN" => ["MALARIA CONTROL was heading 1963-66"],
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"MED" => ["*1141", "1541"],
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"M90" => ["*2010", "2428"],
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"M85" => ["*2929", "3509"],
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"M80" => ["*2008", "2567"],
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"M75" => ["*1414", "1928"],
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"M66" => ["*2561", "3568"],
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"M94" => ["*1272", "1646"],
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"CATSH" => ["CAT LIST"],
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"MR" => ["20120703"],
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"DA" => ["19990101"],
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"DC" => ["1"],
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"UI" => ["D008288"])
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expect(records[1]).to eq("RECTYPE" => ["D"],
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"MH" => ["Calcimycin"],
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"AQ" => ["AA AD AE AG AI AN BI BL CF CH CL CS CT DU EC HI IM IP ME PD PK PO RE SD ST TO TU UR"],
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"ENTRY" => ["A-23187|T109|T195|LAB|NRW|NLM (1991)|900308|abbcdef",
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"A23187|T109|T195|LAB|NRW|UNK (19XX)|741111|abbcdef",
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"Antibiotic A23187|T109|T195|NON|NRW|NLM (1991)|900308|abbcdef",
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"A 23187",
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"A23187, Antibiotic"],
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"MN" => ["D03.438.221.173"],
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"PA" => ["Anti-Bacterial Agents", "Calcium Ionophores"],
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"MH_TH" => ["NLM (1975)"],
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"ST" => ["T109", "T195"],
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"N1" => ["4-Benzoxazolecarboxylic acid, 5-(methylamino)-2-((3,9,11-trimethyl-8-(1-methyl-2-oxo-2-(1H-pyrrol-2-yl)ethyl)-1,7-dioxaspiro(5.5)undec-2-yl)methyl)-, (6S-(6alpha(2S*,3S*),8beta(R*),9beta,11alpha))-"],
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"RN" => ["52665-69-7"],
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"PI" => ["Antibiotics (1973-1974)", "Carboxylic Acids (1973-1974)"],
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"MS" => ["An ionophorous, polyether antibiotic from Streptomyces chartreusensis. It binds and transports CALCIUM and other divalent cations across membranes and uncouples oxidative phosphorylation while inhibiting ATPase of rat liver mitochondria. The substance is used mostly as a biochemical tool to study the role of divalent cations in various biological systems."],
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"OL" => ["use CALCIMYCIN to search A 23187 1975-90"],
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"PM" => ["91; was A 23187 1975-90 (see under ANTIBIOTICS 1975-83)"],
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"HN" => ["91(75); was A 23187 1975-90 (see under ANTIBIOTICS 1975-83)"],
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"MED" => ["*62", "847"],
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"M90" => ["*299", "2405"],
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"M85" => ["*454", "2878"],
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"M80" => ["*316", "1601"],
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"M75" => ["*300", "823"],
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"M66" => ["*1", "3"],
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"M94" => ["*153", "1606"],
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"MR" => ["20110624"],
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"DA" => ["19741119"],
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"DC" => ["1"],
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"DX" => ["19840101"],
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"UI" => ["D000001"])
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end
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end
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require 'spec_helper'
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describe Qa::Services::RDFAuthorityParser do
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let(:source) {[File.join(fixture_path,'lexvo_snippet.rdf')] }
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let(:source) { [File.join(fixture_path, 'lexvo_snippet.rdf')] }
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let(:format) { 'rdfxml' }
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let(:predicate) { RDF::URI("http://www.w3.org/2008/05/skos#prefLabel") }
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let(:name) { 'language' }
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let(:ari_entry) { Qa::LocalAuthorityEntry.find_by(label: 'Ari') }
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describe "#import_rdf" do
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before
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blah = Qa::LocalAuthority.find_by_name(name)
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described_class.import_rdf(name, source, format: format, predicate: predicate)
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end
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before { described_class.import_rdf(name, source, format: format, predicate: predicate) }
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it "creates the authority and authority entries" do
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expect(Qa::LocalAuthority.count).to eq(1)
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expect(Qa::LocalAuthority.find_by(name: name)).not_to be_nil
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expect(Qa::LocalAuthorityEntry.count).to eq(2)
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expect(alum_entry).not_to be_nil
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expect(alum_entry.uri).to eq('http://lexvo.org/id/iso639-3/aab')
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expect(ari_entry).not_to be_nil
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expect(ari_entry.uri).to eq('http://lexvo.org/id/iso639-3/aac')
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end
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end
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@rake = Rake::Application.new
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Rake.application = @rake
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Rake.application.rake_require "mesh", ["#{Rails.root}/lib/tasks", "#{Rails.root}/../lib/tasks"], []
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Rake::Task.define_task(:environment)
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Rake::Task.define_task(:environment) # rspec has loaded rails
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end
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describe "mesh:import" do
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after :all do
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$stdout = STDOUT
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end
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it "
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it "has 'environment' as a prereq" do
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expect(@rake[@task_name].prerequisites).to include("environment")
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end
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it "
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it "requires $MESH_FILE to be set" do
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old_mesh_file = ENV.delete('MESH_FILE')
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@rake[@task_name].invoke
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@output.seek(0)
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expect(@output.read).to match(/Need to set \$MESH_FILE with path to file to ingest/)
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ENV['MESH_FILE'] = old_mesh_file
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end
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describe "create or update" do
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let(:input) { StringIO.new("*NEWRECORD\nUI = 5\nMH = test\n") }
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let(:term) { Qa::SubjectMeshTerm.find_by_term_id(5) }
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before do
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ENV['MESH_FILE'] = "dummy"
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allow(File).to receive(:open).with("dummy").and_yield(input)
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@rake[@task_name].invoke
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end
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it "creates or update all records in the config file" do
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expect(term).not_to be_nil
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expect(term.term).to eq("test")
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end
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end
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end
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end
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require 'spec_helper'
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describe Qa::SubjectMeshTerm, :
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describe Qa::SubjectMeshTerm, type: :model do
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before(:all) do
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@term = Qa::SubjectMeshTerm.new
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@term.term_id = "ABCDEFG"
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it "saves a synonym list" do
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a = Qa::SubjectMeshTerm.new
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a.term_id = 'a'
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a.synonyms = ['b','c']
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a.synonyms = ['b', 'c']
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a.save
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expect(a.synonyms).to eq(['b', 'c'])
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end
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end
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it "returns parents"
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#do
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# do
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# SubjectMeshTerm.create(term_id: "1")
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# SubjectMeshTerm.create(term_id: "2")
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# SubjectMeshTerm.create(term_id: "3")
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@@ -45,5 +45,5 @@ describe Qa::SubjectMeshTerm, :type => :model do
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46
|
# @term.trees.should == ["D1.2.3", "D1.A.3"]
|
47
47
|
# @term.parents.map { |p| p.term_id }.should == ["1", "2", "3"]
|
48
|
-
#end
|
48
|
+
# end
|
49
49
|
end
|
data/spec/routing/route_spec.rb
CHANGED
@@ -1,34 +1,32 @@
|
|
1
1
|
require 'spec_helper'
|
2
2
|
|
3
|
-
describe "QA Routes", :
|
4
|
-
|
3
|
+
describe "QA Routes", type: :routing do
|
5
4
|
routes { Qa::Engine.routes }
|
6
5
|
|
7
6
|
context "listing terms" do
|
8
|
-
it "
|
9
|
-
expect(
|
7
|
+
it "routes to index with an authority" do
|
8
|
+
expect(get: '/terms/vocab').to route_to(controller: 'qa/terms', action: 'index', vocab: 'vocab')
|
10
9
|
end
|
11
|
-
it "
|
12
|
-
expect(
|
10
|
+
it "routes to index with an authority and a subauthority" do
|
11
|
+
expect(get: '/terms/vocab/sub').to route_to(controller: 'qa/terms', action: 'index', vocab: 'vocab', subauthority: 'sub')
|
13
12
|
end
|
14
13
|
end
|
15
14
|
|
16
15
|
context "searching for terms" do
|
17
|
-
it "
|
18
|
-
expect(
|
16
|
+
it "routes to searching for an authority" do
|
17
|
+
expect(get: '/search/vocab').to route_to(controller: 'qa/terms', action: 'search', vocab: 'vocab')
|
19
18
|
end
|
20
|
-
it "
|
21
|
-
expect(
|
19
|
+
it "routes to searching for an authority and a subauthority" do
|
20
|
+
expect(get: '/search/vocab/sub').to route_to(controller: 'qa/terms', action: 'search', vocab: 'vocab', subauthority: 'sub')
|
22
21
|
end
|
23
22
|
end
|
24
23
|
|
25
24
|
context "displaying a single term" do
|
26
|
-
it "
|
27
|
-
expect(
|
25
|
+
it "routes to an authority" do
|
26
|
+
expect(get: '/show/vocab/term_id').to route_to(controller: 'qa/terms', action: 'show', vocab: 'vocab', id: 'term_id')
|
28
27
|
end
|
29
|
-
it "
|
30
|
-
expect(
|
28
|
+
it "routes to an authority with a subauthority" do
|
29
|
+
expect(get: '/show/vocab/sub/term_id').to route_to(controller: 'qa/terms', action: 'show', vocab: 'vocab', subauthority: 'sub', id: 'term_id')
|
31
30
|
end
|
32
31
|
end
|
33
|
-
|
34
32
|
end
|
data/spec/spec_helper.rb
CHANGED
@@ -19,8 +19,7 @@ require 'webmock/rspec'
|
|
19
19
|
Dir[Rails.root.join("spec/support/**/*.rb")].each { |f| require f }
|
20
20
|
|
21
21
|
RSpec.configure do |config|
|
22
|
-
|
23
|
-
config.fixture_path = File.expand_path("../fixtures", __FILE__)
|
22
|
+
config.fixture_path = File.expand_path("../fixtures", __FILE__)
|
24
23
|
|
25
24
|
config.use_transactional_fixtures = true
|
26
25
|
|
@@ -41,8 +40,8 @@ RSpec.configure do |config|
|
|
41
40
|
config.infer_spec_type_from_file_location!
|
42
41
|
end
|
43
42
|
|
44
|
-
def webmock_fixture
|
45
|
-
File.new File.expand_path(File.join("../fixtures", fixture),
|
43
|
+
def webmock_fixture(fixture)
|
44
|
+
File.new File.expand_path(File.join("../fixtures", fixture), __FILE__)
|
46
45
|
end
|
47
46
|
|
48
47
|
# returns the file contents
|
metadata
CHANGED
@@ -1,7 +1,7 @@
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
2
2
|
name: qa
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
version: 0.10.
|
4
|
+
version: 0.10.2
|
5
5
|
platform: ruby
|
6
6
|
authors:
|
7
7
|
- Stephen Anderson
|
@@ -15,7 +15,7 @@ authors:
|
|
15
15
|
autorequire:
|
16
16
|
bindir: bin
|
17
17
|
cert_chain: []
|
18
|
-
date: 2016-
|
18
|
+
date: 2016-10-25 00:00:00.000000000 Z
|
19
19
|
dependencies:
|
20
20
|
- !ruby/object:Gem::Dependency
|
21
21
|
name: rails
|
@@ -94,7 +94,7 @@ dependencies:
|
|
94
94
|
- !ruby/object:Gem::Version
|
95
95
|
version: '0'
|
96
96
|
- !ruby/object:Gem::Dependency
|
97
|
-
name:
|
97
|
+
name: byebug
|
98
98
|
requirement: !ruby/object:Gem::Requirement
|
99
99
|
requirements:
|
100
100
|
- - ">="
|
@@ -108,7 +108,21 @@ dependencies:
|
|
108
108
|
- !ruby/object:Gem::Version
|
109
109
|
version: '0'
|
110
110
|
- !ruby/object:Gem::Dependency
|
111
|
-
name:
|
111
|
+
name: engine_cart
|
112
|
+
requirement: !ruby/object:Gem::Requirement
|
113
|
+
requirements:
|
114
|
+
- - "~>"
|
115
|
+
- !ruby/object:Gem::Version
|
116
|
+
version: '0.8'
|
117
|
+
type: :development
|
118
|
+
prerelease: false
|
119
|
+
version_requirements: !ruby/object:Gem::Requirement
|
120
|
+
requirements:
|
121
|
+
- - "~>"
|
122
|
+
- !ruby/object:Gem::Version
|
123
|
+
version: '0.8'
|
124
|
+
- !ruby/object:Gem::Dependency
|
125
|
+
name: linkeddata
|
112
126
|
requirement: !ruby/object:Gem::Requirement
|
113
127
|
requirements:
|
114
128
|
- - ">="
|
@@ -122,7 +136,7 @@ dependencies:
|
|
122
136
|
- !ruby/object:Gem::Version
|
123
137
|
version: '0'
|
124
138
|
- !ruby/object:Gem::Dependency
|
125
|
-
name:
|
139
|
+
name: rspec-rails
|
126
140
|
requirement: !ruby/object:Gem::Requirement
|
127
141
|
requirements:
|
128
142
|
- - ">="
|
@@ -150,21 +164,21 @@ dependencies:
|
|
150
164
|
- !ruby/object:Gem::Version
|
151
165
|
version: '0'
|
152
166
|
- !ruby/object:Gem::Dependency
|
153
|
-
name:
|
167
|
+
name: sqlite3
|
154
168
|
requirement: !ruby/object:Gem::Requirement
|
155
169
|
requirements:
|
156
|
-
- - "
|
170
|
+
- - ">="
|
157
171
|
- !ruby/object:Gem::Version
|
158
|
-
version: '0
|
172
|
+
version: '0'
|
159
173
|
type: :development
|
160
174
|
prerelease: false
|
161
175
|
version_requirements: !ruby/object:Gem::Requirement
|
162
176
|
requirements:
|
163
|
-
- - "
|
177
|
+
- - ">="
|
164
178
|
- !ruby/object:Gem::Version
|
165
|
-
version: '0
|
179
|
+
version: '0'
|
166
180
|
- !ruby/object:Gem::Dependency
|
167
|
-
name:
|
181
|
+
name: webmock
|
168
182
|
requirement: !ruby/object:Gem::Requirement
|
169
183
|
requirements:
|
170
184
|
- - ">="
|
@@ -178,19 +192,33 @@ dependencies:
|
|
178
192
|
- !ruby/object:Gem::Version
|
179
193
|
version: '0'
|
180
194
|
- !ruby/object:Gem::Dependency
|
181
|
-
name:
|
195
|
+
name: rubocop
|
182
196
|
requirement: !ruby/object:Gem::Requirement
|
183
197
|
requirements:
|
184
|
-
- - "
|
198
|
+
- - "~>"
|
185
199
|
- !ruby/object:Gem::Version
|
186
|
-
version:
|
200
|
+
version: 0.42.0
|
187
201
|
type: :development
|
188
202
|
prerelease: false
|
189
203
|
version_requirements: !ruby/object:Gem::Requirement
|
190
204
|
requirements:
|
191
|
-
- - "
|
205
|
+
- - "~>"
|
192
206
|
- !ruby/object:Gem::Version
|
193
|
-
version:
|
207
|
+
version: 0.42.0
|
208
|
+
- !ruby/object:Gem::Dependency
|
209
|
+
name: rubocop-rspec
|
210
|
+
requirement: !ruby/object:Gem::Requirement
|
211
|
+
requirements:
|
212
|
+
- - "~>"
|
213
|
+
- !ruby/object:Gem::Version
|
214
|
+
version: '1.5'
|
215
|
+
type: :development
|
216
|
+
prerelease: false
|
217
|
+
version_requirements: !ruby/object:Gem::Requirement
|
218
|
+
requirements:
|
219
|
+
- - "~>"
|
220
|
+
- !ruby/object:Gem::Version
|
221
|
+
version: '1.5'
|
194
222
|
description: Provides a set of uniform RESTful routes to query any controlled vocabulary
|
195
223
|
or set of authority terms.
|
196
224
|
email:
|
@@ -331,7 +359,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
|
|
331
359
|
version: '0'
|
332
360
|
requirements: []
|
333
361
|
rubyforge_project:
|
334
|
-
rubygems_version: 2.
|
362
|
+
rubygems_version: 2.6.4
|
335
363
|
signing_key:
|
336
364
|
specification_version: 4
|
337
365
|
summary: You should question your authorities.
|