unipept 2.2.2 → 3.0.2

checksums.yaml

@@ -1,7 +1,7 @@
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+  metadata.gz: b4684d01b8ed753c705e56cc82f59783cd8f4bdf2ebb6fd9d5ddc5e2cb6ff84b
+  data.tar.gz: 3ce7f3443ba3047aa4f54e09b9ad872b34a9f72df0a32d929c3967294a821ff7
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+  data.tar.gz: f4ccfaf31feac1b4a4547ae8f8b3d50ccf55462a883a04813983ff0c76744e3c7afeefc0921250b6ab13dff439964b7c16b56c62d9257a23ff0cd9368f7ba3c8

data/Gemfile

@@ -4,6 +4,9 @@ source 'http://rubygems.org'
 gem 'cri', '~>2.15.10'
 gem 'typhoeus', '~> 1.3.1'
 
+# this is not explicitly used, but an older incompatible version comes bundled with ruby
+gem 'psych', '~> 4.0.3'
+
 group :development do
   gem 'minitest', '~> 5.14'
   gem 'rake', '~> 13.0.1'

data/Gemfile.lock

@@ -16,7 +16,7 @@ GEM
       ruby2_keywords
     faraday-net_http (1.0.1)
     ffi (1.12.1)
-    git (1.8.1)
+    git (1.11.0)
       rchardet (~> 1.8)
     github_api (0.19.0)
       addressable (~> 2.4)
@@ -26,6 +26,7 @@ GEM
       oauth2 (~> 1.0)
     hashie (3.6.0)
     highline (2.0.3)
+    json (2.6.2)
     juwelier (2.4.9)
       builder
       bundler
@@ -42,11 +43,11 @@ GEM
     kamelcase (0.0.2)
       semver2 (~> 3)
     mini_portile2 (2.8.0)
-    minitest (5.15.0)
+    minitest (5.16.2)
     multi_json (1.15.0)
     multi_xml (0.6.0)
     multipart-post (2.1.1)
-    nokogiri (1.13.4)
+    nokogiri (1.13.6)
       mini_portile2 (~> 2.8.0)
       racc (~> 1.4)
     oauth2 (1.4.4)
@@ -56,39 +57,40 @@ GEM
       multi_xml (~> 0.5)
       rack (>= 1.2, < 3)
     parallel (1.22.1)
-    parser (3.1.1.0)
+    parser (3.1.2.0)
       ast (~> 2.4.1)
-    psych (4.0.3)
+    psych (4.0.4)
       stringio
     public_suffix (4.0.6)
     racc (1.6.0)
-    rack (2.2.3)
+    rack (2.2.3.1)
     rainbow (3.1.1)
     rake (13.0.6)
     rchardet (1.8.0)
     rdoc (6.4.0)
       psych (>= 4.0.0)
-    regexp_parser (2.3.0)
+    regexp_parser (2.5.0)
     rexml (3.2.5)
-    rubocop (1.27.0)
+    rubocop (1.31.2)
+      json (~> 2.3)
       parallel (~> 1.10)
       parser (>= 3.1.0.0)
       rainbow (>= 2.2.2, < 4.0)
       regexp_parser (>= 1.8, < 3.0)
-      rexml
-      rubocop-ast (>= 1.16.0, < 2.0)
+      rexml (>= 3.2.5, < 4.0)
+      rubocop-ast (>= 1.18.0, < 2.0)
       ruby-progressbar (~> 1.7)
       unicode-display_width (>= 1.4.0, < 3.0)
-    rubocop-ast (1.17.0)
+    rubocop-ast (1.18.0)
       parser (>= 3.1.1.0)
     ruby-progressbar (1.11.0)
     ruby2_keywords (0.0.4)
     semver2 (3.4.2)
-    stringio (3.0.1)
+    stringio (3.0.2)
     thread_safe (0.3.6)
     typhoeus (1.3.1)
       ethon (>= 0.9.0)
-    unicode-display_width (2.1.0)
+    unicode-display_width (2.2.0)
 
 PLATFORMS
   ruby
@@ -97,6 +99,7 @@ DEPENDENCIES
   cri (~> 2.15.10)
   juwelier
   minitest (~> 5.14)
+  psych (~> 4.0.3)
   rake (~> 13.0.1)
   rubocop (~> 1.11)
   typhoeus (~> 1.3.1)

data/VERSION

@@ -1 +1 @@
-2.2.2
+3.0.2

data/lib/commands/unipept/api_runner.rb

@@ -10,7 +10,7 @@ module Unipept
 
       @host = host
       @user_agent = "Unipept CLI - unipept #{Unipept::VERSION}"
-      @url = "#{@host}/api/v1/#{cmd.name}.json"
+      @url = "#{@host}/api/v2/#{cmd.name}.json"
       @fasta = false
     end
 

data/lib/commands/unipept/taxa2tree.rb

@@ -14,7 +14,7 @@ module Unipept::Commands
 
       if options[:format] == 'html'
         # Overwrite the URL for this command, since it's possible that it uses HTML generated by the server.
-        @url = "#{@host}/api/v1/#{cmd.name}.html"
+        @url = "#{@host}/api/v2/#{cmd.name}.html"
       elsif args[:format] == 'url'
         @link = true
       end

data/lib/commands/uniprot.rb

@@ -60,7 +60,7 @@ module Unipept::Commands
         get_uniprot_entry(accession, 'fasta').lines.map(&:chomp)[1..].join
       else
         # other format has been specified, just download and output
-        resp = Typhoeus.get("https://www.uniprot.org/uniprot/#{accession}.#{format}")
+        resp = Typhoeus.get("https://rest.uniprot.org/uniprotkb/#{accession}.#{format}")
         resp.response_body if resp.success?
       end
     end

data/lib/server_message.rb

@@ -7,7 +7,7 @@ module Unipept
     attr_reader :message_url, :configuration
 
     def initialize(host)
-      @message_url = "#{host}/api/v1/messages.json"
+      @message_url = "#{host}/api/v2/messages.json"
       @configuration = Unipept::Configuration.new
     end
 

data/test/commands/unipept/test_api_runner.rb

@@ -13,7 +13,7 @@ module Unipept
       assert_equal('test_host', runner.options[:host])
       assert_equal(%w[a b c], runner.arguments)
       assert(!runner.configuration.nil?)
-      assert_equal('http://test_host/api/v1/test.json', runner.url)
+      assert_equal('http://test_host/api/v2/test.json', runner.url)
       assert(/Unipept CLI - unipept [0-9]*\.[0-9]*\.[0-9]*/.match runner.user_agent)
     end
 

data/test/support/api_stub.rb

@@ -15,7 +15,7 @@ class ApiStub
 
   def setup_endpoint(name)
     items = JSON.parse(File.read(File.join(File.dirname(__FILE__), "resources/#{name}.json")))
-    Typhoeus.stub("http://api.unipept.ugent.be/api/v1/#{name}.json").and_return do |req|
+    Typhoeus.stub("http://api.unipept.ugent.be/api/v2/#{name}.json").and_return do |req|
       peptides = req.options[:body][:input]
 
       filtered = items.select { |item| peptides.include? item['peptide'] }
@@ -25,7 +25,7 @@ class ApiStub
   end
 
   def setup_taxa2lca
-    Typhoeus.stub('http://api.unipept.ugent.be/api/v1/taxa2lca.json').and_return(
+    Typhoeus.stub('http://api.unipept.ugent.be/api/v2/taxa2lca.json').and_return(
       Typhoeus::Response.new(code: 200, body: '{
         "taxon_id": 1678,
         "taxon_name": "Bifidobacterium",
@@ -36,7 +36,7 @@ class ApiStub
 
   def setup_taxonomy
     items = JSON.parse(File.read(File.join(File.dirname(__FILE__), 'resources/taxonomy.json')))
-    Typhoeus.stub('http://api.unipept.ugent.be/api/v1/taxonomy.json').and_return do |req|
+    Typhoeus.stub('http://api.unipept.ugent.be/api/v2/taxonomy.json').and_return do |req|
       taxa = req.options[:body][:input].map(&:to_i)
 
       filtered = items.select { |item| taxa.include? item['taxon_id'] }
@@ -47,7 +47,7 @@ class ApiStub
 
   # Expects to be called with taxa "78", "57", "89", "28" and "67"
   def setup_taxa2tree
-    Typhoeus.stub('http://api.unipept.ugent.be/api/v1/taxa2tree.json').and_return do |_|
+    Typhoeus.stub('http://api.unipept.ugent.be/api/v2/taxa2tree.json').and_return do |_|
       link = req.options[:body][:link] == 'true'
       if link
         Typhoeus::Response.new(code: 200, body: JSON.dump(gist: 'https://gist.github.com/8837824df7ef9831a9b4216f3fb547ee'))

data/test/test_server_message.rb

@@ -3,7 +3,7 @@ require_relative '../lib/server_message'
 module Unipept
   class ServerMessageTestCase < Unipept::TestCase
     def test_init
-      assert_equal('http://test_host/api/v1/messages.json', ServerMessage.new('http://test_host').message_url)
+      assert_equal('http://test_host/api/v2/messages.json', ServerMessage.new('http://test_host').message_url)
     end
 
     def test_fetch_server_message

data/unipept.gemspec

@@ -2,16 +2,16 @@
 # DO NOT EDIT THIS FILE DIRECTLY
 # Instead, edit Juwelier::Tasks in Rakefile, and run 'rake gemspec'
 # -*- encoding: utf-8 -*-
-# stub: unipept 2.2.2 ruby lib
+# stub: unipept 3.0.2 ruby lib
 
 Gem::Specification.new do |s|
   s.name = "unipept".freeze
-  s.version = "2.2.2"
+  s.version = "3.0.2"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0".freeze) if s.respond_to? :required_rubygems_version=
   s.require_paths = ["lib".freeze]
   s.authors = ["Bart Mesuere".freeze, "Pieter Verschaffelt".freeze, "Toon Willems".freeze, "Tom Naessens".freeze]
-  s.date = "2022-04-13"
+  s.date = "2022-07-08"
   s.description = "    Command line interface to the Unipept (http://unipept.ugent.be) web services\n    (pept2lca, taxa2lca, pept2taxa, pept2prot and taxonomy) and some utility\n    commands for handling proteins using the command line.\n".freeze
   s.email = "unipept@ugent.be".freeze
   s.executables = ["unipept".freeze, "prot2pept".freeze, "peptfilter".freeze, "uniprot".freeze]
@@ -105,7 +105,7 @@ Gem::Specification.new do |s|
   s.homepage = "http://unipept.ugent.be".freeze
   s.licenses = ["MIT".freeze]
   s.required_ruby_version = Gem::Requirement.new(">= 2.6.0".freeze)
-  s.rubygems_version = "3.1.4".freeze
+  s.rubygems_version = "3.3.7".freeze
   s.summary = "Command line interface to Unipept web services.".freeze
 
   if s.respond_to? :specification_version then
@@ -115,12 +115,14 @@ Gem::Specification.new do |s|
   if s.respond_to? :add_runtime_dependency then
     s.add_runtime_dependency(%q<cri>.freeze, ["~> 2.15.10"])
     s.add_runtime_dependency(%q<typhoeus>.freeze, ["~> 1.3.1"])
+    s.add_runtime_dependency(%q<psych>.freeze, ["~> 4.0.3"])
     s.add_development_dependency(%q<minitest>.freeze, ["~> 5.14"])
     s.add_development_dependency(%q<rake>.freeze, ["~> 13.0.1"])
     s.add_development_dependency(%q<rubocop>.freeze, ["~> 1.11"])
   else
     s.add_dependency(%q<cri>.freeze, ["~> 2.15.10"])
     s.add_dependency(%q<typhoeus>.freeze, ["~> 1.3.1"])
+    s.add_dependency(%q<psych>.freeze, ["~> 4.0.3"])
     s.add_dependency(%q<minitest>.freeze, ["~> 5.14"])
     s.add_dependency(%q<rake>.freeze, ["~> 13.0.1"])
     s.add_dependency(%q<rubocop>.freeze, ["~> 1.11"])

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: unipept
 version: !ruby/object:Gem::Version
-  version: 2.2.2
+  version: 3.0.2
 platform: ruby
 authors:
 - Bart Mesuere
@@ -11,7 +11,7 @@ authors:
 autorequire:
 bindir: bin
 cert_chain: []
-date: 2022-04-13 00:00:00.000000000 Z
+date: 2022-07-08 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: cri
@@ -41,6 +41,20 @@ dependencies:
     - - "~>"
       - !ruby/object:Gem::Version
         version: 1.3.1
+- !ruby/object:Gem::Dependency
+  name: psych
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 4.0.3
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 4.0.3
 - !ruby/object:Gem::Dependency
   name: minitest
   requirement: !ruby/object:Gem::Requirement
@@ -198,7 +212,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.1.4
+rubygems_version: 3.3.7
 signing_key:
 specification_version: 4
 summary: Command line interface to Unipept web services.