Merge branch 'develop' into feature/test-action

unipept · Mar 14, 2023 · 3c0e018 · 3c0e018
2 parents 944cd94 + 4f861ca
commit 3c0e018
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Showing 14 changed files with 2 additions and 569 deletions.
diff --git a/app/controllers/api/api_controller.rb b/app/controllers/api/api_controller.rb
@@ -38,7 +38,7 @@ def pept2prot
       end
 
       ids = ids.uniq.compact.sort
-      UniprotEntry.includes(:taxon, :ec_cross_references, :go_cross_references, :refseq_cross_references, :embl_cross_references)
+      UniprotEntry.includes(:taxon, :ec_cross_references, :go_cross_references)
                   .where(id: ids).find_in_batches do |group|
         group.each do |uni|
           lookup[uni.id].each { |s| @result[s] << uni }

diff --git a/app/models/embl_cross_reference.rb b/app/models/embl_cross_reference.rb
diff --git a/app/models/proteome.rb b/app/models/proteome.rb
diff --git a/app/models/proteome_cache.rb b/app/models/proteome_cache.rb
diff --git a/app/models/proteome_cross_reference.rb b/app/models/proteome_cross_reference.rb
diff --git a/app/models/refseq_cross_reference.rb b/app/models/refseq_cross_reference.rb
diff --git a/app/models/uniprot_entry.rb b/app/models/uniprot_entry.rb
@@ -14,12 +14,9 @@
 class UniprotEntry < ApplicationRecord
   include ReadOnlyModel
 
-  has_many :refseq_cross_references
-  has_many :embl_cross_references
   has_many :ec_cross_references
   has_many :go_cross_references
   has_many :interpro_cross_references
-  has_many :proteome_cross_references
 
   has_many :peptides
   has_many :ec_numbers, through: :ec_cross_references

diff --git a/app/views/api/api/pept2prot.json.erb b/app/views/api/api/pept2prot.json.erb
@@ -11,11 +11,7 @@
           "taxon_id" => u.taxon_id,
           "taxon_name" => u.taxon.try(:name),
           "ec_references" => u.ec_cross_references.map(&:ec_number_code).join(" "),
-          "go_references" => u.go_cross_references.map(&:go_term_code).join(" "),
-          "refseq_ids" => u.refseq_cross_references.map(&:sequence_id).join(" "),
-          "refseq_protein_ids" => u.refseq_cross_references.map(&:protein_id).join(" "),
-          "insdc_ids" => u.embl_cross_references.map(&:sequence_id).join(" "),
-          "insdc_protein_ids" => u.embl_cross_references.map(&:protein_id).join(" "),
+          "go_references" => u.go_cross_references.map(&:go_term_code).join(" ")
         }
       end
     end.flatten).html_safe

diff --git a/test/controllers/api/api_controller_test.rb b/test/controllers/api/api_controller_test.rb
@@ -90,10 +90,6 @@ class Api::ApiControllerTest < ActionController::TestCase
     assert_not @response.body.include? '"taxon_name":null'
     assert @response.body.include? 'ec_references'
     assert @response.body.include? 'go_references'
-    assert @response.body.include? 'refseq_ids'
-    assert @response.body.include? 'refseq_protein_ids'
-    assert @response.body.include? 'insdc_ids'
-    assert @response.body.include? 'insdc_protein_ids'
     assert_not @response.body.include? '"uniprot_id":"nr2"'
   end
 
@@ -112,10 +108,6 @@ class Api::ApiControllerTest < ActionController::TestCase
     assert_not @response.body.include? '"taxon_name":null'
     assert @response.body.include? 'ec_references'
     assert @response.body.include? 'go_references'
-    assert @response.body.include? 'refseq_ids'
-    assert @response.body.include? 'refseq_protein_ids'
-    assert @response.body.include? 'insdc_ids'
-    assert @response.body.include? 'insdc_protein_ids'
     assert @response.body.include? '"uniprot_id":"nr2"'
   end
 

diff --git a/test/models/embl_cross_reference_test.rb b/test/models/embl_cross_reference_test.rb