unipept 2.2.2 → 3.0.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: b8f3ce5867e19149483ab70e24d4cc5da97d8ba9e62e38491b714abc89078ee0
-  data.tar.gz: '09cfcdbc3608ee36a75825e7f7555add797b002e3abccc5caada703efc8d0b86'
+  metadata.gz: 1dfd4f81d97870e20ecaeea0cc3e047667a70e556d0ea3c1d39b729dcd6dd7b2
+  data.tar.gz: f2227172f0b5cfb7ec80d2ae00181749d7e00667ec88332fb43775be42e3c6fa
 SHA512:
-  metadata.gz: e29aa64adf5a502377c2fdedb63969d29fa6f8d517262d65ec0a99b40746bf0a1d3d5a26552dd25cd425008d0f8a0f4ed7bd69ec6786d77ef2c688ce0e5b7c5d
-  data.tar.gz: 9d6d08532a96fb85423a7843745df5fe75f125e6f7119f6ba2b76f525b75bd057aac7d27a0a5c1e6357df5aed0af42bb00a9fd260aa3be58f623dc75dc3da7b4
+  metadata.gz: 07f29c4d733ebe355d922ab199eaf092ad63b010cfe9aa079167f83384fc4c20255e7ca3caad619c8dabff5a4646a4aa742084eb6df25bb90b591435160a6473
+  data.tar.gz: 7f166594e85b531205ed3044125f2dc6782fdd461404feac059ea616ebc08a80887f991bbb39310aa75de248494c493454b937099558a2234fec666e9afba462

data/VERSION

@@ -1 +1 @@
-2.2.2
+3.0.0

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/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 3.0.0 ruby lib
 
 Gem::Specification.new do |s|
   s.name = "unipept".freeze
-  s.version = "2.2.2"
+  s.version = "3.0.0"
 
   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 = "2022-04-14"
   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]

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: unipept
 version: !ruby/object:Gem::Version
-  version: 2.2.2
+  version: 3.0.0
 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: 2022-04-14 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: cri