fix tests

.gitignore

@@ -27,3 +27,6 @@
 
 # Ignore master key for decrypting credentials and more.
 /config/master.key
+
+/coverage
+.idea/

Gemfile

@@ -43,6 +43,9 @@ group :development, :test do
   #Codecov for coverage processing
   gem 'simplecov'
   gem 'simplecov-cobertura'
+
+  # Mocking HTTP requests to third parties.
+  gem 'webmock'
 end
 
 group :development do

Gemfile.lock

@@ -85,6 +85,8 @@ GEM
       capistrano (~> 3.0)
       sshkit (~> 1.2)
     concurrent-ruby (1.2.2)
+    crack (0.4.5)
+      rexml
     crass (1.0.6)
     debug (1.6.2)
       irb (>= 1.3.6)
@@ -98,6 +100,7 @@ GEM
     faraday-net_http (3.0.0)
     globalid (1.1.0)
       activesupport (>= 5.0)
+    hashdiff (1.0.1)
     i18n (1.12.0)
       concurrent-ruby (~> 1.0)
     io-console (0.5.11)
@@ -236,6 +239,10 @@ GEM
     tzinfo (2.0.6)
       concurrent-ruby (~> 1.0)
     unicode-display_width (2.3.0)
+    webmock (3.19.1)
+      addressable (>= 2.8.0)
+      crack (>= 0.3.2)
+      hashdiff (>= 0.4.0, < 2.0.0)
     websocket-driver (0.7.5)
       websocket-extensions (>= 0.1.0)
     websocket-extensions (0.1.5)
@@ -266,6 +273,7 @@ DEPENDENCIES
   simplecov-cobertura
   stathat (~> 0.1.7)
   tzinfo-data
+  webmock
 
 RUBY VERSION
    ruby 3.1.2p20

app/controllers/api/api_controller.rb

@@ -70,18 +70,10 @@ def set_query
              end
   end
 
-  # prepares the sequences query
-  def set_sequences
-    rel_name = @equate_il ? :peptides : :original_peptides
-    @sequences = Sequence.joins(rel_name => :uniprot_entry)
-                         .where(sequence: @input)
-  end
-
   # Reorders the results according to the input order
   def filter_input_order
     @input_order.select! do |s|
-      key = @equate_il ? s.tr('I', 'L') : s
-      @result.key? key
+      @result.key? s
     end
   end
 

app/controllers/mpa/pept2data_controller.rb

@@ -1,13 +1,7 @@
 class Mpa::Pept2dataController < Mpa::MpaController
   include SuffixArrayHelper
 
-  def get_time
-    Process.clock_gettime(Process::CLOCK_MONOTONIC, :millisecond)
-  end
-
   def pept2data
-    start = get_time
-
     peptides = params[:peptides] || []
     missed = params[:missed].nil? ? false : params[:missed]
     equate_il = params[:equate_il].nil? ? true : params[:equate_il]
@@ -32,8 +26,5 @@ def pept2data
     Lineage.find(taxa).each do |lineage|
       @lineages[lineage.taxon_id] = lineage.to_a_idx
     end
-
-    @timings = Hash.new
-    @timings["total"] = get_time - start
   end
 end

app/controllers/private_api/proteins_controller.rb

@@ -19,6 +19,8 @@ def proteins
       return
     end
 
+    puts peptide
+
     # Request the suffix array search service
     search_result = search([ peptide ], equate_il).first
 
@@ -29,8 +31,6 @@ def proteins
       return
     end
 
-    puts search_result
-
     @lca = search_result["lca"]
     @proteins = UniprotEntry
       .includes(:taxon)
@@ -48,7 +48,6 @@ def proteins
 
     # Lineage van de lca ophalen
     lca_lineage = Lineage.find(@lca)
-    puts lca_lineage.inspect
     finished = (@lca == 1)
     while !finished && lca_lineage.has_next?
       next_rank = lca_lineage.next_t

app/views/api/pept2ec/pept2ec.json.jbuilder

@@ -1,8 +1,7 @@
 json.array! @input_order do |peptide|
-  seq_index = @equate_il ? peptide.tr('I', 'L') : peptide
-  if @result.key? seq_index
+  if @result.key? peptide
     json.peptide peptide
-    json.total_protein_count @result[seq_index][:total]
-    json.ec(@result[seq_index][:ec].sort_by { |v| -v[:protein_count] })
+    json.total_protein_count @result[peptide][:total]
+    json.ec(@result[peptide][:ec].sort_by { |v| -v[:protein_count] })
   end
 end

app/views/api/pept2funct/pept2funct.json.jbuilder

@@ -1,10 +1,9 @@
 json.array! @input_order do |peptide|
-  seq_index = @equate_il ? peptide.tr('I', 'L') : peptide
-  if @result.key? seq_index
+  if @result.key? peptide
     json.peptide peptide
-    json.total_protein_count @result[seq_index][:total]
-    json.ec(@result[seq_index][:ec].sort_by { |value| -value[:protein_count] })
-    json.partial! partial: 'api/pept2go', locals: { data: @result[seq_index][:go] }
-    json.partial! partial: 'api/pept2interpro', locals: { data: @result[seq_index][:ipr] }
+    json.total_protein_count @result[peptide][:total]
+    json.ec(@result[peptide][:ec].sort_by { |value| -value[:protein_count] })
+    json.partial! partial: 'api/pept2go', locals: { data: @result[peptide][:go] }
+    json.partial! partial: 'api/pept2interpro', locals: { data: @result[peptide][:ipr] }
   end
 end

app/views/api/pept2go/pept2go.json.jbuilder

@@ -1,8 +1,7 @@
 json.array! @input_order do |peptide|
-  seq_index = @equate_il ? peptide.tr('I', 'L') : peptide
-  if @result.key? seq_index
+  if @result.key? peptide
     json.peptide peptide
-    json.total_protein_count @result[seq_index][:total]
-    json.partial! partial: 'api/pept2go', locals: { data: @result[seq_index][:go] }
+    json.total_protein_count @result[peptide][:total]
+    json.partial! partial: 'api/pept2go', locals: { data: @result[peptide][:go] }
   end
 end

app/views/api/pept2interpro/pept2interpro.json.jbuilder

@@ -1,8 +1,7 @@
 json.array! @input_order do |peptide|
-  seq_index = @equate_il ? peptide.tr('I', 'L') : peptide
-  if @result.key? seq_index
+  if @result.key? peptide
     json.peptide peptide
-    json.total_protein_count @result[seq_index][:total]
-    json.partial! partial: 'api/pept2interpro', locals: { data: @result[seq_index][:ipr] }
+    json.total_protein_count @result[peptide][:total]
+    json.partial! partial: 'api/pept2interpro', locals: { data: @result[peptide][:ipr] }
   end
 end

app/views/api/pept2lca/pept2lca.json.jbuilder

@@ -1,7 +1,6 @@
 json.array! @input_order do |peptide|
-  seq_index = @equate_il ? peptide.tr('I', 'L') : peptide
-  if @result.key? seq_index
+  if @result.key? peptide
     json.peptide peptide
-    json.partial! partial: 'api/pept2lca', locals: { data: @result[seq_index] }
+    json.partial! partial: 'api/pept2lca', locals: { data: @result[peptide] }
   end
 end

app/views/api/pept2taxa/pept2taxa.json.erb

@@ -1,10 +1,9 @@
 <%=
   Oj.dump(
-    @input_order.map do |k|
-      seq_index = @equate_il ? k.gsub(/I/,'L') : k
-      v = @result[seq_index]
+    @input_order.map do |peptide|
+      v = @result[peptide]
       v.map do |p|
-        res = { "peptide" => k,
+        res = { "peptide" => peptide,
                 "taxon_id" => p.id,
                 "taxon_name" => p.name,
                 "taxon_rank" => p.rank,

app/views/api/peptinfo/peptinfo.json.jbuilder

@@ -1,11 +1,10 @@
 json.array! @input_order do |peptide|
-  seq_index = @equate_il ? peptide.tr('I', 'L') : peptide
-  if @result.key? seq_index
+  if @result.key? peptide
     json.peptide peptide
-    json.total_protein_count @result[seq_index][:total]
-    json.ec(@result[seq_index][:ec].sort_by { |value| -value[:protein_count] })
-    json.partial! partial: 'api/pept2go', locals: { data: @result[seq_index][:go] }
-    json.partial! partial: 'api/pept2interpro', locals: { data: @result[seq_index][:ipr] }
-    json.partial! partial: 'api/pept2lca', locals: { data: @result[seq_index][:lca] }
+    json.total_protein_count @result[peptide][:total]
+    json.ec(@result[peptide][:ec].sort_by { |value| -value[:protein_count] })
+    json.partial! partial: 'api/pept2go', locals: { data: @result[peptide][:go] }
+    json.partial! partial: 'api/pept2interpro', locals: { data: @result[peptide][:ipr] }
+    json.partial! partial: 'api/pept2lca', locals: { data: @result[peptide][:lca] }
   end
 end

app/views/mpa/pept2data/pept2data.json.jbuilder

@@ -7,4 +7,3 @@ json.peptides @response do |peptide|
     json.data peptide["fa"]["data"]
   end
 end
-json.timings @timings

config/database.yml

@@ -17,6 +17,7 @@ development:
 # Do not set this db to the same as development or production.
 test:
   <<: *default
+  username: unipept
   database: unipept_test
   url: <%= ENV['TEST_DATABASE_URL'] || ENV['DATABASE_URL'] %>
 

test/controllers/api/pept2ec_controller_test.rb

@@ -4,6 +4,8 @@ class Api::Pept2ecControllerTest < ActionController::TestCase
   teardown :assert_success
 
   test 'should get pept2ec' do
+    stub_http_request! 'test/fixtures/index/response.json'
+
     @expected = '[
       {"peptide":"AAIER","total_protein_count":3,"ec":[]},
       {"peptide":"AAILER","total_protein_count":1,"ec":[{"ec_number":"4.2.1.11","protein_count":1}]}
@@ -13,6 +15,8 @@ class Api::Pept2ecControllerTest < ActionController::TestCase
   end
 
   test 'should get pept2ec with il' do
+    stub_http_request! 'test/fixtures/index/response_equate.json'
+
     @expected = '[
       {"peptide":"AAIER","total_protein_count":22,"ec":[{"ec_number":"2.7.11.1","protein_count":4}]},
       {"peptide":"AAILER","total_protein_count":0,"ec":[]}
@@ -22,6 +26,8 @@ class Api::Pept2ecControllerTest < ActionController::TestCase
   end
 
   test 'should get pept2ec with extra' do
+    stub_http_request! 'test/fixtures/index/response.json'
+
     @expected = '[
       {"peptide":"AAIER","total_protein_count":3,"ec":[]},
       {"peptide":"AAILER","total_protein_count":1,"ec":[{"ec_number":"4.2.1.11","protein_count":1,"name":"Some Enzyme3"}]}
@@ -31,6 +37,8 @@ class Api::Pept2ecControllerTest < ActionController::TestCase
   end
 
   test 'should get pept2ec with extra and il' do
+    stub_http_request! 'test/fixtures/index/response_equate.json'
+
     @expected = '[
       {"peptide":"AAIER","total_protein_count":22,"ec":[{"ec_number":"2.7.11.1","protein_count":4,"name":"Some Enzyme2"}]},
       {"peptide":"AAILER","total_protein_count":0,"ec":[]}

test/controllers/api/pept2funct_controller_test.rb

@@ -4,6 +4,8 @@ class Api::Pept2functControllerTest < ActionController::TestCase
   teardown :assert_success
 
   test 'should get pept2funct' do
+    stub_http_request! 'test/fixtures/index/response.json'
+
     @expected = '[
       {"peptide":"AAIER","total_protein_count":3,"ec":[],"go":[{"go_term":"GO:0051301","protein_count":3},{"go_term":"GO:0005525","protein_count":3},{"go_term":"GO:0046872","protein_count":3},{"go_term":"GO:0007049","protein_count":3}],"ipr":[]},
       {"peptide":"AAILER","total_protein_count":1,"ec":[{"ec_number":"4.2.1.11","protein_count":1}],"go":[{"go_term":"GO:0005576","protein_count":1},{"go_term":"GO:0000287","protein_count":1},{"go_term":"GO:0004634","protein_count":1},{"go_term":"GO:0000015","protein_count":1},{"go_term":"GO:0006096","protein_count":1},{"go_term":"GO:0009986","protein_count":1}],"ipr":[{"code":"IPR000169","protein_count":1}]}
@@ -13,6 +15,8 @@ class Api::Pept2functControllerTest < ActionController::TestCase
   end
 
   test 'should get pept2funct with il' do
+    stub_http_request! 'test/fixtures/index/response_equate.json'
+
     @expected = '[
       {"peptide":"AAIER","total_protein_count":22,"ec":[{"ec_number":"2.7.11.1","protein_count":4}],"go":[{"go_term":"GO:0004674","protein_count":1},{"go_term":"GO:0005634","protein_count":1},{"go_term":"GO:0005524","protein_count":1},{"go_term":"GO:0016301","protein_count":1}],"ipr":[{"code":"IPR000169","protein_count":1}]},
       {"peptide":"AAILER","total_protein_count":0,"ec":[],"go":[],"ipr":[]}
@@ -22,6 +26,8 @@ class Api::Pept2functControllerTest < ActionController::TestCase
   end
 
   test 'should get pept2funct with extra' do
+    stub_http_request! 'test/fixtures/index/response.json'
+
     @expected = '[
       {"peptide":"AAIER","total_protein_count":3,"ec":[],"go":[{"go_term":"GO:0051301","protein_count":3,"name":"some function 9"},{"go_term":"GO:0005525","protein_count":3,"name":"some function 10"},{"go_term":"GO:0046872","protein_count":3,"name":"some function 11"},{"go_term":"GO:0007049","protein_count":3,"name":"some function 12"}],"ipr":[]},
       {"peptide":"AAILER","total_protein_count":1,"ec":[{"ec_number":"4.2.1.11","protein_count":1,"name":"Some Enzyme3"}],"go":[{"go_term":"GO:0005576","protein_count":1,"name":"some function 16"},{"go_term":"GO:0000287","protein_count":1,"name":"some function 17"},{"go_term":"GO:0004634","protein_count":1,"name":"some function 18"},{"go_term":"GO:0000015","protein_count":1,"name":"some function 19"},{"go_term":"GO:0006096","protein_count":1,"name":"some function 20"},{"go_term":"GO:0009986","protein_count":1,"name":"some function 21"}],"ipr":[{"code":"IPR000169","protein_count":1,"name":"Cysteine peptidase, cysteine active site","type":"Active_site"}]}
@@ -31,6 +37,8 @@ class Api::Pept2functControllerTest < ActionController::TestCase
   end
 
   test 'should get pept2funct with domains' do
+    stub_http_request! 'test/fixtures/index/response.json'
+
     @expected = '[
       {"peptide":"AAIER","total_protein_count":3,"ec":[],"go":[{"molecular function":[{"go_term":"GO:0051301","protein_count":3},{"go_term":"GO:0007049","protein_count":3}]},{"cellular component":[{"go_term":"GO:0005525","protein_count":3}]},{"biological process":[{"go_term":"GO:0046872","protein_count":3}]}],"ipr":[]},
       {"peptide":"AAILER","total_protein_count":1,"ec":[{"ec_number":"4.2.1.11","protein_count":1}],"go":[{"cellular component":[{"go_term":"GO:0005576","protein_count":1},{"go_term":"GO:0009986","protein_count":1}]},{"molecular function":[{"go_term":"GO:0000287","protein_count":1},{"go_term":"GO:0000015","protein_count":1}]},{"biological process":[{"go_term":"GO:0004634","protein_count":1},{"go_term":"GO:0006096","protein_count":1}]}],"ipr":[{"Active_site":[{"code":"IPR000169","protein_count":1}]}]}
@@ -40,6 +48,8 @@ class Api::Pept2functControllerTest < ActionController::TestCase
   end
 
   test 'should get pept2funct with extra and domains' do
+    stub_http_request! 'test/fixtures/index/response.json'
+
     @expected = '[
       {"peptide":"AAIER","total_protein_count":3,"ec":[],"go":[{"molecular function":[{"go_term":"GO:0051301","protein_count":3,"name":"some function 9"},{"go_term":"GO:0007049","protein_count":3,"name":"some function 12"}]},{"cellular component":[{"go_term":"GO:0005525","protein_count":3,"name":"some function 10"}]},{"biological process":[{"go_term":"GO:0046872","protein_count":3,"name":"some function 11"}]}],"ipr":[]},
       {"peptide":"AAILER","total_protein_count":1,"ec":[{"ec_number":"4.2.1.11","protein_count":1,"name":"Some Enzyme3"}],"go":[{"cellular component":[{"go_term":"GO:0005576","protein_count":1,"name":"some function 16"},{"go_term":"GO:0009986","protein_count":1,"name":"some function 21"}]},{"molecular function":[{"go_term":"GO:0000287","protein_count":1,"name":"some function 17"},{"go_term":"GO:0000015","protein_count":1,"name":"some function 19"}]},{"biological process":[{"go_term":"GO:0004634","protein_count":1,"name":"some function 18"},{"go_term":"GO:0006096","protein_count":1,"name":"some function 20"}]}],"ipr":[{"Active_site":[{"code":"IPR000169","protein_count":1,"name":"Cysteine peptidase, cysteine active site"}]}]}
@@ -49,6 +59,8 @@ class Api::Pept2functControllerTest < ActionController::TestCase
   end
 
   test 'should get pept2funct with extra and domains and il' do
+    stub_http_request! 'test/fixtures/index/response_equate.json'
+
     @expected = '[
       {"peptide":"AAIER","total_protein_count":22,"ec":[{"ec_number":"2.7.11.1","protein_count":4,"name":"Some Enzyme2"}],"go":[{"biological process":[{"go_term":"GO:0004674","protein_count":1,"name":"some function 5"},{"go_term":"GO:0016301","protein_count":1,"name":"some function 8"}]},{"molecular function":[{"go_term":"GO:0005634","protein_count":1,"name":"some function 6"}]},{"cellular component":[{"go_term":"GO:0005524","protein_count":1,"name":"some function 7"}]}],"ipr":[{"Active_site":[{"code":"IPR000169","protein_count":1,"name":"Cysteine peptidase, cysteine active site"}]}]},
       {"peptide":"AAILER","total_protein_count":0,"ec":[],"go":[],"ipr":[]}