RubyGems - unipept - Versions diffs - 2.2.0 → 3.0.0 - Mend

unipept 2.2.0 → 3.0.0

Files changed (41) hide show

checksums.yaml +4 -4
data/.github/dependabot.yml +9 -0
data/.github/workflows/ci.yml +6 -27
data/.rakeTasks +2 -2
data/.rubocop.yml +2 -0
data/.ruby-version +1 -1
data/CITATION.cff +30 -0
data/Gemfile +2 -2
data/Gemfile.lock +60 -41
data/README.md +2 -2
data/Rakefile +4 -4
data/VERSION +1 -1
data/lib/commands/prot2pept.rb +1 -2
data/lib/commands/unipept/api_runner.rb +8 -12
data/lib/commands/unipept/config.rb +1 -1
data/lib/commands/unipept/pept2taxa.rb +1 -5
data/lib/commands/unipept/taxa2tree.rb +3 -3
data/lib/commands/uniprot.rb +4 -5
data/lib/configuration.rb +6 -7
data/lib/formatters.rb +7 -7
data/lib/server_message.rb +3 -5
data/test/commands/unipept/test_api_runner.rb +9 -8
data/test/commands/unipept/test_config.rb +1 -1
data/test/commands/unipept/test_pept2ec.rb +2 -2
data/test/commands/unipept/test_pept2funct.rb +2 -2
data/test/commands/unipept/test_pept2go.rb +2 -2
data/test/commands/unipept/test_pept2interpro.rb +2 -2
data/test/commands/unipept/test_pept2lca.rb +2 -2
data/test/commands/unipept/test_pept2prot.rb +2 -2
data/test/commands/unipept/test_pept2taxa.rb +2 -4
data/test/commands/unipept/test_peptinfo.rb +2 -2
data/test/commands/unipept/test_taxa2lca.rb +2 -2
data/test/commands/unipept/test_taxa2tree.rb +2 -2
data/test/commands/unipept/test_taxonomy.rb +2 -2
data/test/support/api_stub.rb +4 -4
data/test/test_configuration.rb +1 -1
data/test/test_formatters.rb +5 -5
data/test/test_output_writer.rb +1 -1
data/test/test_server_message.rb +3 -3
data/unipept.gemspec +17 -21
metadata +11 -9

checksums.yaml CHANGED Viewed

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: ae8f504a45da4b1347a4dae8c3989d56051ece08b84b77ed5a7b07bd8fd7e389
-  data.tar.gz: b718c39e60d721878b539b4b1e80edfa9df66ed1b1f841b0c45a78946a9a2df5
+  metadata.gz: 1dfd4f81d97870e20ecaeea0cc3e047667a70e556d0ea3c1d39b729dcd6dd7b2
+  data.tar.gz: f2227172f0b5cfb7ec80d2ae00181749d7e00667ec88332fb43775be42e3c6fa
 SHA512:
-  metadata.gz: 852005f9d3c107a5dfef6eec2dbb2ec0a9800e48857eed1e043492efe7d8ac0532424eed809fc599b5b11d35b6972291bb4b6d3af06414edd36572bafb5b330e
-  data.tar.gz: 16a34b6be468f68572bb0c9cc09eb23142570ec01549df41fdd5d4b5413d65c77978717ea0db3af6701eb81e80a73c60c6d5760261b3831266b32dbef7e631e3
+  metadata.gz: 07f29c4d733ebe355d922ab199eaf092ad63b010cfe9aa079167f83384fc4c20255e7ca3caad619c8dabff5a4646a4aa742084eb6df25bb90b591435160a6473
+  data.tar.gz: 7f166594e85b531205ed3044125f2dc6782fdd461404feac059ea616ebc08a80887f991bbb39310aa75de248494c493454b937099558a2234fec666e9afba462

data/.github/dependabot.yml ADDED Viewed

@@ -0,0 +1,9 @@
+version: 2
+updates:
+- package-ecosystem: bundler
+  directory: "/"
+  schedule:
+    interval: monthly
+    time: "13:00"
+    timezone: Europe/Brussels
+  open-pull-requests-limit: 99

data/.github/workflows/ci.yml CHANGED Viewed

@@ -7,27 +7,16 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        ruby: ["2.4", "2.5", "2.6"]
+        ruby: ["2.7", "3.0", "3.1"]
       fail-fast: false
     name: Test Ruby ${{ matrix.ruby }}
     steps:
       - uses: actions/checkout@v1
       - name: Setup Ruby
-        uses: actions/setup-ruby@v1
+        uses: ruby/setup-ruby@v1
         with:
           ruby-version: ${{ matrix.ruby }}
-      - name: Cache Ruby dependencies
-        uses: actions/cache@v1
-        with:
-          path: vendor/bundle
-          key: ${{ runner.os }}-${{ matrix.ruby }}-gem-${{ hashFiles('**/Gemfile.lock') }}
-          restore-keys: |
-            ${{ runner.os }}-${{ matrix.ruby }}-gem-
-      - name: Install dependencies
-        run: |
-          gem install bundler:1.17.2
-          bundle config path vendor/bundle
-          bundle install --jobs 4 --retry 3
+          bundler-cache: true
       - name: Test
         run: |
           bundle exec rake test
@@ -37,19 +26,9 @@ jobs:
     steps:
       - uses: actions/checkout@v1
       - name: Setup Ruby
-        uses: actions/setup-ruby@v1
-      - name: Cache Ruby dependencies
-        uses: actions/cache@v1
+        uses: ruby/setup-ruby@v1
         with:
-          path: vendor/bundle
-          key: ${{ runner.os }}-${{ matrix.ruby }}-gem-${{ hashFiles('**/Gemfile.lock') }}
-          restore-keys: |
-            ${{ runner.os }}-${{ matrix.ruby }}-gem-
-      - name: Install dependencies
-        run: |
-          gem install bundler:1.17.2
-          bundle config path vendor/bundle
-          bundle install --jobs 4 --retry 3
+          bundler-cache: true
       - name: Test
         run: |
-          bundle exec rake test_style
+          bundle exec rake test_style

data/.rakeTasks CHANGED Viewed

@@ -1,7 +1,7 @@
-<?xml version="1.0" encoding="UTF-8"?>
+<?xml version="1.0" encoding="UTF-8"?>
 <Settings><!--This file was automatically generated by Ruby plugin.
 You are allowed to:
 1. Remove rake task
 2. Add existing rake tasks
 To add existing rake tasks automatically delete this file and reload the project.
---><RakeGroup description="" fullCmd="" taksId="rake"><RakeTask description="Build gem into pkg/" fullCmd="build" taksId="build" /><RakeTask description="Remove any temporary products" fullCmd="clean" taksId="clean" /><RakeTask description="Remove any generated files" fullCmd="clobber" taksId="clobber" /><RakeTask description="Remove RDoc HTML files" fullCmd="clobber_rdoc" taksId="clobber_rdoc" /><RakeTask description="Start IRB with all runtime dependencies loaded" fullCmd="console[script]" taksId="console[script]" /><RakeGroup description="" fullCmd="" taksId="gemcutter"><RakeTask description="Release gem to Gemcutter" fullCmd="gemcutter:release" taksId="release" /></RakeGroup><RakeTask description="Generate and validate gemspec" fullCmd="gemspec" taksId="gemspec" /><RakeGroup description="" fullCmd="" taksId="gemspec"><RakeTask description="Display the gemspec for debugging purposes, as jeweler knows it (not from the filesystem)" fullCmd="gemspec:debug" taksId="debug" /><RakeTask description="Regenerate the gemspec on the filesystem" fullCmd="gemspec:generate" taksId="generate" /><RakeTask description="Regenerate and validate gemspec, and then commits and pushes to git" fullCmd="gemspec:release" taksId="release" /><RakeTask description="Validates the gemspec on the filesystem" fullCmd="gemspec:validate" taksId="validate" /></RakeGroup><RakeGroup description="" fullCmd="" taksId="git"><RakeTask description="Tag and push release to git" fullCmd="git:release" taksId="release" /></RakeGroup><RakeTask description="Build and install gem using `gem install`" fullCmd="install" taksId="install" /><RakeTask description="Build RDoc HTML files" fullCmd="rdoc" taksId="rdoc" /><RakeTask description="Release gem" fullCmd="release" taksId="release" /><RakeTask description="Rebuild RDoc HTML files" fullCmd="rerdoc" taksId="rerdoc" /><RakeTask description="Run RuboCop" fullCmd="test_style" taksId="test_style" /><RakeGroup description="" fullCmd="" taksId="test_style"><RakeTask description="Auto-correct RuboCop offenses" fullCmd="test_style:auto_correct" taksId="auto_correct" /></RakeGroup><RakeTask description="Displays the current version" fullCmd="version" taksId="version" /><RakeGroup description="" fullCmd="" taksId="version"><RakeGroup description="" fullCmd="" taksId="bump"><RakeTask description="Bump the major version by 1" fullCmd="version:bump:major" taksId="major" /><RakeTask description="Bump the a minor version by 1" fullCmd="version:bump:minor" taksId="minor" /><RakeTask description="Bump the patch version by 1" fullCmd="version:bump:patch" taksId="patch" /></RakeGroup><RakeTask description="Writes out an explicit version" fullCmd="version:write" taksId="write" /></RakeGroup><RakeTask description="" fullCmd="console" taksId="console" /><RakeTask description="" fullCmd="default" taksId="default" /><RakeTask description="" fullCmd="gemspec_required" taksId="gemspec_required" /><RakeTask description="" fullCmd="rdoc/created.rid" taksId="rdoc/created.rid" /><RakeTask description="" fullCmd="test" taksId="test" /><RakeTask description="" fullCmd="test_unit" taksId="test_unit" /><RakeTask description="" fullCmd="version_required" taksId="version_required" /></RakeGroup></Settings>
+--><RakeGroup description="" fullCmd="" taksId="rake"><RakeTask description="Build gem into pkg/" fullCmd="build" taksId="build" /><RakeTask description="Remove any temporary products" fullCmd="clean" taksId="clean" /><RakeTask description="Remove any generated files" fullCmd="clobber" taksId="clobber" /><RakeTask description="Remove RDoc HTML files" fullCmd="clobber_rdoc" taksId="clobber_rdoc" /><RakeTask description="Start IRB with all runtime dependencies loaded" fullCmd="console[script]" taksId="console[script]" /><RakeGroup description="" fullCmd="" taksId="gemcutter"><RakeTask description="Release gem to Gemcutter" fullCmd="gemcutter:release" taksId="release" /></RakeGroup><RakeTask description="Generate and validate gemspec" fullCmd="gemspec" taksId="gemspec" /><RakeGroup description="" fullCmd="" taksId="gemspec"><RakeTask description="Display the gemspec for debugging purposes, as juwelier knows it (not from the filesystem)" fullCmd="gemspec:debug" taksId="debug" /><RakeTask description="Regenerate the gemspec on the filesystem" fullCmd="gemspec:generate" taksId="generate" /><RakeTask description="Regenerate and validate gemspec, and then commits and pushes to git" fullCmd="gemspec:release" taksId="release" /><RakeTask description="Validates the gemspec on the filesystem" fullCmd="gemspec:validate" taksId="validate" /></RakeGroup><RakeGroup description="" fullCmd="" taksId="git"><RakeTask description="Tag and push release to git" fullCmd="git:release" taksId="release" /></RakeGroup><RakeTask description="Build and install gem using `gem install`" fullCmd="install" taksId="install" /><RakeTask description="Build RDoc HTML files" fullCmd="rdoc" taksId="rdoc" /><RakeTask description="Release gem" fullCmd="release" taksId="release" /><RakeTask description="Rebuild RDoc HTML files" fullCmd="rerdoc" taksId="rerdoc" /><RakeTask description="Run RuboCop" fullCmd="test_style" taksId="test_style" /><RakeGroup description="" fullCmd="" taksId="test_style"><RakeTask description="Auto-correct RuboCop offenses" fullCmd="test_style:auto_correct" taksId="auto_correct" /></RakeGroup><RakeTask description="Displays the current version" fullCmd="version" taksId="version" /><RakeGroup description="" fullCmd="" taksId="version"><RakeGroup description="" fullCmd="" taksId="bump"><RakeTask description="Bump the major version by 1" fullCmd="version:bump:major" taksId="major" /><RakeTask description="Bump the a minor version by 1" fullCmd="version:bump:minor" taksId="minor" /><RakeTask description="Bump the patch version by 1" fullCmd="version:bump:patch" taksId="patch" /></RakeGroup><RakeTask description="Writes out an explicit version" fullCmd="version:write" taksId="write" /></RakeGroup><RakeTask description="" fullCmd="console" taksId="console" /><RakeTask description="" fullCmd="default" taksId="default" /><RakeTask description="" fullCmd="gemspec_required" taksId="gemspec_required" /><RakeTask description="" fullCmd="rdoc/created.rid" taksId="rdoc/created.rid" /><RakeTask description="" fullCmd="test" taksId="test" /><RakeTask description="" fullCmd="test_unit" taksId="test_unit" /><RakeTask description="" fullCmd="version_required" taksId="version_required" /></RakeGroup></Settings>

data/.rubocop.yml CHANGED Viewed

@@ -1,4 +1,6 @@
 AllCops:
+  TargetRubyVersion: 2.7
+  NewCops: enable
   Exclude:
     - 'unipept.gemspec'
     - 'vendor/**/*'

data/.ruby-version CHANGED Viewed

	@@ -1 +1 @@
1	- 2.6.6
1	+ 3.0.0

data/CITATION.cff ADDED Viewed

@@ -0,0 +1,30 @@
+cff-version: 1.2.0
+message: "If you use this software, please cite it as below."
+preferred-citation:
+  type: article
+  authors:
+  - family-names: "Verschaffelt"
+    given-names: "Pieter"
+  - family-names: "Van Thienen"
+    given-names: "Philippe"
+  - family-names: "Van Den Bossche"
+    given-names: "Tim"
+  - family-names: "Van der Jeugt"
+    given-names: "Felix"
+  - family-names: "De Tender"
+    given-names: "Caroline"
+  - family-names: "Martens"
+    given-names: "Lennart"
+  - family-names: "Dawyndt"
+    given-names: "Peter"
+  - family-names: "Mesuere"
+    given-names: "Bart"
+    orcid: "https://orcid.org/0000-0003-0610-3441"
+  doi: "10.1093/bioinformatics/btaa553"
+  journal: "Bioinformatics"
+  start: 4220
+  end: 4221
+  title: "Unipept CLI 2.0: adding support for visualizations and functional annotations"
+  issue: 14
+  volume: 36
+  year: 2020

data/Gemfile CHANGED Viewed

@@ -7,9 +7,9 @@ gem 'typhoeus', '~> 1.3.1'
 group :development do
   gem 'minitest', '~> 5.14'
   gem 'rake', '~> 13.0.1'
-  gem 'rubocop', '~>0.79.0'
+  gem 'rubocop', '~>1.11'
 end
 group :release do
-  gem 'jeweler'
+  gem 'juwelier'
 end

data/Gemfile.lock CHANGED Viewed

@@ -1,85 +1,104 @@
 GEM
   remote: http://rubygems.org/
   specs:
-    addressable (2.4.0)
-    ast (2.4.0)
+    addressable (2.8.0)
+      public_suffix (>= 2.0.2, < 5.0)
+    ast (2.4.2)
     builder (3.2.4)
-    cri (2.15.10)
+    cri (2.15.11)
     descendants_tracker (0.0.4)
       thread_safe (~> 0.3, >= 0.3.1)
     ethon (0.12.0)
       ffi (>= 1.3.0)
-    faraday (0.9.2)
+    faraday (1.3.0)
+      faraday-net_http (~> 1.0)
       multipart-post (>= 1.2, < 3)
+      ruby2_keywords
+    faraday-net_http (1.0.1)
     ffi (1.12.1)
-    git (1.5.0)
-    github_api (0.16.0)
-      addressable (~> 2.4.0)
+    git (1.8.1)
+      rchardet (~> 1.8)
+    github_api (0.19.0)
+      addressable (~> 2.4)
       descendants_tracker (~> 0.0.4)
-      faraday (~> 0.8, < 0.10)
-      hashie (>= 3.4)
-      mime-types (>= 1.16, < 3.0)
+      faraday (>= 0.8, < 2)
+      hashie (~> 3.5, >= 3.5.2)
       oauth2 (~> 1.0)
-    hashie (4.0.0)
+    hashie (3.6.0)
     highline (2.0.3)
-    jaro_winkler (1.5.4)
-    jeweler (2.3.9)
+    juwelier (2.4.9)
       builder
       bundler
-      git (>= 1.2.5)
-      github_api (~> 0.16.0)
-      highline (>= 1.6.15)
-      nokogiri (>= 1.5.10)
+      git
+      github_api
+      highline
+      kamelcase (~> 0)
+      nokogiri
       psych
       rake
       rdoc
       semver2
-    jwt (2.2.1)
-    mime-types (2.99.3)
-    mini_portile2 (2.4.0)
-    minitest (5.14.0)
-    multi_json (1.14.1)
+    jwt (2.2.2)
+    kamelcase (0.0.2)
+      semver2 (~> 3)
+    mini_portile2 (2.8.0)
+    minitest (5.15.0)
+    multi_json (1.15.0)
     multi_xml (0.6.0)
     multipart-post (2.1.1)
-    nokogiri (1.10.7)
-      mini_portile2 (~> 2.4.0)
-    oauth2 (1.4.2)
+    nokogiri (1.13.4)
+      mini_portile2 (~> 2.8.0)
+      racc (~> 1.4)
+    oauth2 (1.4.4)
       faraday (>= 0.8, < 2.0)
       jwt (>= 1.0, < 3.0)
       multi_json (~> 1.3)
       multi_xml (~> 0.5)
       rack (>= 1.2, < 3)
-    parallel (1.19.1)
-    parser (2.7.0.2)
-      ast (~> 2.4.0)
-    psych (3.1.0)
-    rack (2.1.1)
-    rainbow (3.0.0)
-    rake (13.0.1)
-    rdoc (6.2.1)
-    rubocop (0.79.0)
-      jaro_winkler (~> 1.5.1)
+    parallel (1.22.1)
+    parser (3.1.1.0)
+      ast (~> 2.4.1)
+    psych (4.0.3)
+      stringio
+    public_suffix (4.0.6)
+    racc (1.6.0)
+    rack (2.2.3)
+    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)
+    rexml (3.2.5)
+    rubocop (1.27.0)
       parallel (~> 1.10)
-      parser (>= 2.7.0.1)
+      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)
       ruby-progressbar (~> 1.7)
-      unicode-display_width (>= 1.4.0, < 1.7)
-    ruby-progressbar (1.10.1)
+      unicode-display_width (>= 1.4.0, < 3.0)
+    rubocop-ast (1.17.0)
+      parser (>= 3.1.1.0)
+    ruby-progressbar (1.11.0)
+    ruby2_keywords (0.0.4)
     semver2 (3.4.2)
+    stringio (3.0.1)
     thread_safe (0.3.6)
     typhoeus (1.3.1)
       ethon (>= 0.9.0)
-    unicode-display_width (1.6.1)
+    unicode-display_width (2.1.0)
 PLATFORMS
   ruby
 DEPENDENCIES
   cri (~> 2.15.10)
-  jeweler
+  juwelier
   minitest (~> 5.14)
   rake (~> 13.0.1)
-  rubocop (~> 0.79.0)
+  rubocop (~> 1.11)
   typhoeus (~> 1.3.1)
 BUNDLED WITH

data/README.md CHANGED Viewed

@@ -7,11 +7,11 @@ Documentation about the web service can be found at [http://unipept.ugent.be/api
 ## Installation
-To use the Unipept CLI, Ruby version 1.9.3 or higher needs to be installed. You can check this by running `ruby -v` on the commandline:
+To use the Unipept CLI, Ruby version 2.6 or higher needs to be installed. You can check this by running `ruby -v` on the commandline:
 ```
 $ ruby -v
-ruby 2.2.2p95 (2015-04-13 revision 50295) [x86_64-darwin14]
+ruby 3.0.0p0 (2020-12-25 revision 95aff21468) [arm64-darwin21]
 ```
 More information on installing Ruby can be found at https://www.ruby-lang.org/en/installation/

data/Rakefile CHANGED Viewed

@@ -11,8 +11,8 @@ require 'rake'
 require 'rake/testtask'
 require 'rubocop/rake_task'
 begin
-  require 'jeweler'
-  Jeweler::Tasks.new do |gem|
+  require 'juwelier'
+  Juwelier::Tasks.new do |gem|
     # gem is a Gem::Specification... see http://guides.rubygems.org/specification-reference/ for more options
     gem.name = 'unipept'
     gem.executables = %w[unipept prot2pept peptfilter uniprot]
@@ -26,9 +26,9 @@ begin
     EOS
     gem.email = 'unipept@ugent.be'
     gem.authors = ['Bart Mesuere', 'Pieter Verschaffelt', 'Toon Willems', 'Tom Naessens']
-    gem.required_ruby_version = '>= 2.0.0'
+    gem.required_ruby_version = '>= 2.6.0'
   end
-  Jeweler::RubygemsDotOrgTasks.new
+  Juwelier::RubygemsDotOrgTasks.new
 rescue LoadError
   # do nothing
 end

data/VERSION CHANGED Viewed

	@@ -1 +1 @@
1	- 2.2.0
1	+ 3.0.0

data/lib/commands/prot2pept.rb CHANGED Viewed

@@ -1,7 +1,6 @@
 module Unipept::Commands
   class Prot2pept
-    attr_reader :root_command
-    attr_reader :valid_formats
+    attr_reader :root_command, :valid_formats
     @root_command = Cri::Command.define do
       name 'prot2pept'

data/lib/commands/unipept/api_runner.rb CHANGED Viewed

@@ -2,19 +2,15 @@ require_relative '../../retryable_typhoeus'
 module Unipept
   class Commands::ApiRunner < Cri::CommandRunner
-    attr_reader :configuration
-    attr_reader :url
-    attr_reader :user_agent
+    attr_reader :configuration, :url, :user_agent
     def initialize(args, opts, cmd)
       super
       @configuration = Unipept::Configuration.new
       @host = host
-      @user_agent = 'Unipept CLI - unipept ' + Unipept::VERSION
-      @url = "#{@host}/api/v1/#{cmd.name}.json"
+      @user_agent = "Unipept CLI - unipept #{Unipept::VERSION}"
+      @url = "#{@host}/api/v2/#{cmd.name}.json"
       @fasta = false
     end
@@ -39,7 +35,7 @@ module Unipept
     # - if none of the previous are given, uses stdin
     def input_iterator
       return arguments.each unless arguments.empty?
-      return IO.foreach(options[:input]) if options[:input]
+      return File.foreach(options[:input]) if options[:input]
       $stdin.each_line
     end
@@ -148,7 +144,7 @@ module Unipept
     def save_error(message)
       path = error_file_path
       FileUtils.mkdir_p File.dirname(path)
-      File.open(path, 'w') { |f| f.write message }
+      File.write(path, message)
       warn "API request failed! log can be found in #{path}"
     end
@@ -173,7 +169,7 @@ module Unipept
       lambda do
         unless result.empty?
-          output_writer.write_line formatter.header(result, fasta_mapper) if batch_id.zero? && !options[:"no-header"]
+          output_writer.write_line formatter.header(result, fasta_mapper) if batch_id.zero? && !options[:'no-header']
           output_writer.write_line formatter.format(result, fasta_mapper, batch_id.zero?)
         end
       end
@@ -183,7 +179,7 @@ module Unipept
       if response.timed_out?
         -> { save_error('request timed out, continuing anyway, but results might be incomplete') }
       elsif response.code.zero?
-        -> { save_error('could not get an http response, continuing anyway, but results might be incomplete' + response.return_message) }
+        -> { save_error("could not get an http response, continuing anyway, but results might be incomplete#{response.return_message}") }
       else
         -> { save_error("Got #{response.code}: #{response.response_body}\nRequest headers: #{response.request.options}\nRequest body:\n#{response.request.encoded_body}\n\n") }
       end
@@ -212,7 +208,7 @@ module Unipept
           if %w[ec go ipr].include? k
             v.each do |item|
               item.each do |field_name, field_value|
-                new_field_name = %w[ec_number go_term ipr_code].include?(field_name) ? field_name : k + '_' + field_name
+                new_field_name = %w[ec_number go_term ipr_code].include?(field_name) ? field_name : "#{k}_#{field_name}"
                 output_row[new_field_name] = [] unless output_row.key? new_field_name
                 output_row[new_field_name] << field_value
               end

data/lib/commands/unipept/config.rb CHANGED Viewed

@@ -7,7 +7,7 @@ module Unipept
       if arguments.size == 2
         set_config(key, value)
-        puts key + ' was set to ' + value
+        puts "#{key} was set to #{value}"
       else
         puts get_config(key)
       end

data/lib/commands/unipept/pept2taxa.rb CHANGED Viewed

@@ -6,11 +6,7 @@ module Unipept::Commands
     end
     def default_batch_size
-      if options[:all]
-        5
-      else
-        10
-      end
+      5
     end
   end
 end

data/lib/commands/unipept/taxa2tree.rb CHANGED Viewed

@@ -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
@@ -34,7 +34,7 @@ module Unipept::Commands
     def input_iterator
       return arguments.each unless arguments.empty?
-      return IO.foreach(options[:input]) if options[:input]
+      return File.foreach(options[:input]) if options[:input]
       @stdin_contents.each
     end
@@ -57,7 +57,7 @@ module Unipept::Commands
           splitted[1] = splitted[1].to_i
           splitted
         end
-        data = Hash[data]
+        data = data.to_h
       else
         data = Hash.new 0
         input.each do |i|

data/lib/commands/uniprot.rb CHANGED Viewed

@@ -2,8 +2,7 @@ require 'typhoeus'
 module Unipept::Commands
   class Uniprot
-    attr_reader :root_command
-    attr_reader :valid_formats
+    attr_reader :root_command, :valid_formats
     valid_formats = Set.new %w[fasta txt xml rdf gff sequence]
     @root_command = Cri::Command.define do
@@ -21,7 +20,7 @@ module Unipept::Commands
       The uniprot command yields just the protein sequences as a default, but can return several formats.
       EOS
-      required :f, :format, 'specify output format (available: ' + valid_formats.to_a.join(', ') + ') (default: sequence)'
+      required :f, :format, "specify output format (available: #{valid_formats.to_a.join(', ')}) (default: sequence)"
       flag :h, :help, 'show help for this command' do |_value, cmd|
         puts cmd.help
         exit 0
@@ -29,7 +28,7 @@ module Unipept::Commands
       run do |opts, args, _cmd|
         format = opts.fetch(:format, 'sequence')
         unless valid_formats.include? format
-          warn format + ' is not a valid output format. Available formats are: ' + valid_formats.to_a.join(', ')
+          warn "#{format} is not a valid output format. Available formats are: #{valid_formats.to_a.join(', ')}"
           exit 1
         end
         iterator = args.empty? ? $stdin.each_line : args
@@ -58,7 +57,7 @@ module Unipept::Commands
     # @return [String] The requested UniProt entry in the requested format
     def self.get_uniprot_entry(accession, format)
       if format == 'sequence'
-        get_uniprot_entry(accession, 'fasta').lines.map(&:chomp)[1..-1].join('')
+        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}")

data/lib/configuration.rb CHANGED Viewed

@@ -2,8 +2,7 @@ require 'yaml'
 module Unipept
   class Configuration
-    attr_reader :config
-    attr_reader :file_name
+    attr_reader :config, :file_name
     # Creates a new config object, based on a given YAML file. If no filename
     # given, '.unipeptrc' in the home dir of the user will be used.
@@ -14,17 +13,17 @@ module Unipept
     # config from
     def initialize(file = nil)
       @file_name = file || File.join(Dir.home, '.unipeptrc')
-      @config = if !File.exist? file_name
-                  {}
+      @config = if File.exist? file_name
+                  YAML.load_file file_name, permitted_classes: [Time]
                 else
-                  YAML.load_file file_name
+                  {}
                 end
     end
     # Saves the config to disk. If the file doesn't exist yet, a new one will be
     # created
     def save
-      File.open(file_name, 'w') { |f| f.write config.to_yaml }
+      File.write(file_name, config.to_yaml)
     end
     # Deletes a key
@@ -39,7 +38,7 @@ module Unipept
     # forwards =[] to the internal config hash
     def []=(*args)
-      config.[]=(*args)
+      config.[]=(*args) # rubocop:disable Layout/SpaceBeforeBrackets
     end
   end
 end

data/lib/formatters.rb CHANGED Viewed

@@ -156,7 +156,7 @@ module Unipept
     # @return [String] The converted input data in the JSON format
     def convert(data, first)
       output = data.map(&:to_json).join(',')
-      first ? output : ',' + output
+      first ? output : ",#{output}"
     end
   end
@@ -178,7 +178,7 @@ module Unipept
       # First we look for items for both ec numbers, go terms and ipr codes that are fully filled in.
       data.each do |row|
-        non_empty_items.keys.each do |annotation_type|
+        non_empty_items.each_key do |annotation_type|
           non_empty_items[annotation_type] = row if row[annotation_type] && !row[annotation_type].empty?
         end
       end
@@ -195,7 +195,7 @@ module Unipept
         idx = keys.index(annotation_type)
         keys.delete_at(idx)
-        keys.insert(idx, *non_empty_item[annotation_type].first.keys.map { |el| %w[ec_number go_term ipr_code].include?(el) ? el : annotation_type + '_' + el })
+        keys.insert(idx, *non_empty_item[annotation_type].first.keys.map { |el| %w[ec_number go_term ipr_code].include?(el) ? el : "#{annotation_type}_#{el}" })
         $keys_length = *non_empty_item[annotation_type].first.keys.length # rubocop:disable Style/GlobalVars
       end
@@ -243,8 +243,8 @@ module Unipept
           o.each do |k, v|
             if %w[ec go ipr].include? k
               if v && !v.empty?
-                v.first.keys.each do |key|
-                  row[key == 'protein_count' ? k + '_protein_count' : key] = (v.map { |el| el[key] }).join(' ').strip
+                v.first.each_key do |key|
+                  row[key == 'protein_count' ? "#{k}_protein_count" : key] = (v.map { |el| el[key] }).join(' ').strip
                 end
               else
                 row[k] = row.concat(Array.new($keys_length[0], nil)) # rubocop:disable Style/GlobalVars
@@ -304,7 +304,7 @@ module Unipept
     #
     # @return [String] The converted input data in the XML format
     def convert(data, _first)
-      data.map { |row| '<result>' + row.to_xml + '</result>' }.join('')
+      data.map { |row| "<result>#{row.to_xml}</result>" }.join
     end
   end
@@ -405,7 +405,7 @@ module Unipept
     #
     # @return [String] The converted input data in the Blast format
     def convert(data, _first)
-      data[0]['gist'].sub!('https://gist.github.com/', 'https://bl.ocks.org/') + "\n"
+      "#{data[0]['gist'].sub!('https://gist.github.com/', 'https://bl.ocks.org/')}\n"
     end
   end
 end

data/lib/server_message.rb CHANGED Viewed

@@ -4,12 +4,10 @@ require_relative 'configuration'
 module Unipept
   class ServerMessage
-    attr_reader :message_url
-    attr_reader :configuration
+    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
@@ -34,7 +32,7 @@ module Unipept
     # ago.
     def recently_fetched?
       last_fetched = @configuration['last_fetch_date']
-      !last_fetched.nil? && (last_fetched + 60 * 60 * 24) > Time.now
+      !last_fetched.nil? && (last_fetched + (60 * 60 * 24)) > Time.now
     end
     # Updates the last checked timestamp

data/test/commands/unipept/test_api_runner.rb CHANGED Viewed

@@ -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
@@ -67,8 +67,8 @@ module Unipept
     end
     def test_input_iterator_file
-      File.open('input_file', 'w') { |file| file.write(%w[a b c].join("\n")) }
-      runner = new_runner('test',  host: 'https://param_host', input: 'input_file')
+      File.write('input_file', %w[a b c].join("\n"))
+      runner = new_runner('test', host: 'https://param_host', input: 'input_file')
       output = []
       runner.input_iterator.each { |el| output << el.chomp }
       assert_equal(%w[a b c], output)
@@ -84,7 +84,7 @@ module Unipept
     end
     def test_input_iterator_arguments_priority
-      File.open('input_file', 'w') { |file| file.write(%w[1 2 3].join("\n")) }
+      File.write('input_file', %w[1 2 3].join("\n"))
       runner = new_runner('test', { host: 'https://param_host', input: 'input_file' }, %w[a b c])
       output = []
       _out, _err = capture_io_with_input(%w[1 2 3]) do
@@ -94,8 +94,8 @@ module Unipept
     end
     def test_input_iterator_file_priority
-      File.open('input_file', 'w') { |file| file.write(%w[a b c].join("\n")) }
-      runner = new_runner('test',  host: 'https://param_host', input: 'input_file')
+      File.write('input_file', %w[a b c].join("\n"))
+      runner = new_runner('test', host: 'https://param_host', input: 'input_file')
       output = []
       _out, _err = capture_io_with_input(%w[1 2 3]) do
         runner.input_iterator.each { |el| output << el.chomp }
@@ -280,7 +280,7 @@ module Unipept
           runner.save_error('error message')
         end
         assert(err.start_with?('API request failed! log can be found in'))
-        assert_equal('error message', IO.foreach('errordir/error.log').next.chomp)
+        assert_equal('error message', File.foreach('errordir/error.log').next.chomp)
       end
     end
@@ -319,7 +319,7 @@ module Unipept
     end
     def test_success_no_header_option_handle_response
-      runner = new_runner('test', Hash[:host, 'test', :'no-header', true])
+      runner = new_runner('test', { host: 'test', 'no-header': true })
       response = new_response(success: true, response_body: '[{"key1":"value1","key2":"value1"},{"key1":"value2","key2":"value2"}]')
       lambda = runner.handle_response(response, 0, nil)
       assert(lambda.lambda?)
@@ -409,6 +409,7 @@ module Unipept
     def new_response(values)
       response = Class.new do
         def initialize(values)
+          super()
           @values = values
         end

data/test/commands/unipept/test_config.rb CHANGED Viewed

@@ -44,7 +44,7 @@ module Unipept
       out, _err = capture_io_while do
         Commands::Unipept.run(['config', 'test', value])
       end
-      assert_equal('test was set to ' + value, out.chomp)
+      assert_equal("test was set to #{value}", out.chomp)
       assert_equal(value, Unipept::Configuration.new['test'])
     end

data/test/commands/unipept/test_pept2ec.rb CHANGED Viewed

@@ -87,7 +87,7 @@ module Unipept
       end
       lines = out.each_line
       assert_equal('', err)
-      output = lines.to_a.join('').chomp
+      output = lines.to_a.join.chomp
       assert(output.start_with?('['))
       assert(output.end_with?(']'))
       assert(!output.include?('}{'))
@@ -100,7 +100,7 @@ module Unipept
       end
       lines = out.each_line
       assert_equal('', err)
-      output = lines.to_a.join('').chomp
+      output = lines.to_a.join.chomp
       assert(output.start_with?('<results>'))
       assert(output.end_with?('</results>'))
       assert(output.include?('<fasta_header>'))

data/test/commands/unipept/test_pept2funct.rb CHANGED Viewed

@@ -87,7 +87,7 @@ module Unipept
       end
       lines = out.each_line
       assert_equal('', err)
-      output = lines.to_a.join('').chomp
+      output = lines.to_a.join.chomp
       assert(output.start_with?('['))
       assert(output.end_with?(']'))
       assert(!output.include?('}{'))
@@ -100,7 +100,7 @@ module Unipept
       end
       lines = out.each_line
       assert_equal('', err)
-      output = lines.to_a.join('').chomp
+      output = lines.to_a.join.chomp
       assert(output.start_with?('<results>'))
       assert(output.end_with?('</results>'))
       assert(output.include?('<fasta_header>'))

data/test/commands/unipept/test_pept2go.rb CHANGED Viewed

@@ -87,7 +87,7 @@ module Unipept
       end
       lines = out.each_line
       assert_equal('', err)
-      output = lines.to_a.join('').chomp
+      output = lines.to_a.join.chomp
       assert(output.start_with?('['))
       assert(output.end_with?(']'))
       assert(!output.include?('}{'))
@@ -100,7 +100,7 @@ module Unipept
       end
       lines = out.each_line
       assert_equal('', err)
-      output = lines.to_a.join('').chomp
+      output = lines.to_a.join.chomp
       assert(output.start_with?('<results>'))
       assert(output.end_with?('</results>'))
       assert(output.include?('<fasta_header>'))

data/test/commands/unipept/test_pept2interpro.rb CHANGED Viewed

@@ -87,7 +87,7 @@ module Unipept
       end
       lines = out.each_line
       assert_equal('', err)
-      output = lines.to_a.join('').chomp
+      output = lines.to_a.join.chomp
       assert(output.start_with?('['))
       assert(output.end_with?(']'))
       assert(!output.include?('}{'))
@@ -100,7 +100,7 @@ module Unipept
       end
       lines = out.each_line
       assert_equal('', err)
-      output = lines.to_a.join('').chomp
+      output = lines.to_a.join.chomp
       assert(output.start_with?('<results>'))
       assert(output.end_with?('</results>'))
       assert(output.include?('<fasta_header>'))

data/test/commands/unipept/test_pept2lca.rb CHANGED Viewed

@@ -87,7 +87,7 @@ module Unipept
       end
       lines = out.each_line
       assert_equal('', err)
-      output = lines.to_a.join('').chomp
+      output = lines.to_a.join.chomp
       assert(output.start_with?('['))
       assert(output.end_with?(']'))
       assert(!output.include?('}{'))
@@ -100,7 +100,7 @@ module Unipept
       end
       lines = out.each_line
       assert_equal('', err)
-      output = lines.to_a.join('').chomp
+      output = lines.to_a.join.chomp
       assert(output.start_with?('<results>'))
       assert(output.end_with?('</results>'))
       assert(output.include?('<fasta_header>'))

data/test/commands/unipept/test_pept2prot.rb CHANGED Viewed

@@ -88,7 +88,7 @@ module Unipept
       end
       lines = out.each_line
       assert_equal('', err)
-      output = lines.to_a.join('').chomp
+      output = lines.to_a.join.chomp
       assert(output.start_with?('['))
       assert(output.end_with?(']'))
       assert(!output.include?('}{'))
@@ -101,7 +101,7 @@ module Unipept
       end
       lines = out.each_line
       assert_equal('', err)
-      output = lines.to_a.join('').chomp
+      output = lines.to_a.join.chomp
       assert(output.start_with?('<results>'))
       assert(output.end_with?('</results>'))
       assert(output.include?('<fasta_header>'))

data/test/commands/unipept/test_pept2taxa.rb CHANGED Viewed

@@ -5,8 +5,6 @@ module Unipept
     def test_default_batch_size
       command = Cri::Command.define { name 'pept2taxa' }
       pept2taxa = Commands::Pept2taxa.new({ host: 'http://api.unipept.ugent.be' }, [], command)
-      assert_equal(10, pept2taxa.default_batch_size)
-      pept2taxa.options[:all] = true
       assert_equal(5, pept2taxa.default_batch_size)
     end
@@ -72,7 +70,7 @@ module Unipept
       end
       lines = out.each_line
       assert_equal('', err)
-      output = lines.to_a.join('').chomp
+      output = lines.to_a.join.chomp
       assert(output.start_with?('['))
       assert(output.end_with?(']'))
       assert(!output.include?('}{'))
@@ -85,7 +83,7 @@ module Unipept
       end
       lines = out.each_line
       assert_equal('', err)
-      output = lines.to_a.join('').chomp
+      output = lines.to_a.join.chomp
       assert(output.start_with?('<results>'))
       assert(output.end_with?('</results>'))
       assert(output.include?('<fasta_header>'))

data/test/commands/unipept/test_peptinfo.rb CHANGED Viewed

@@ -87,7 +87,7 @@ module Unipept
       end
       lines = out.each_line
       assert_equal('', err)
-      output = lines.to_a.join('').chomp
+      output = lines.to_a.join.chomp
       assert(output.start_with?('['))
       assert(output.end_with?(']'))
       assert(!output.include?('}{'))
@@ -100,7 +100,7 @@ module Unipept
       end
       lines = out.each_line
       assert_equal('', err)
-      output = lines.to_a.join('').chomp
+      output = lines.to_a.join.chomp
       assert(output.start_with?('<results>'))
       assert(output.end_with?('</results>'))
       assert(output.include?('<fasta_header>'))

data/test/commands/unipept/test_taxa2lca.rb CHANGED Viewed

@@ -47,7 +47,7 @@ module Unipept
         Commands::Unipept.run(%w[taxa2lca --host http://api.unipept.ugent.be --format xml 216816 1680])
       end
       lines = out.each_line
-      output = lines.to_a.join('').chomp
+      output = lines.to_a.join.chomp
       assert_equal('', err)
       assert(output.start_with?('<results>'))
       assert(output.end_with?('</results>'))
@@ -58,7 +58,7 @@ module Unipept
         Commands::Unipept.run(%w[taxa2lca --host http://api.unipept.ugent.be --format json 216816 1680])
       end
       lines = out.each_line
-      output = lines.to_a.join('').chomp
+      output = lines.to_a.join.chomp
       assert_equal('', err)
       assert(output.start_with?('['))
       assert(output.end_with?(']'))

data/test/commands/unipept/test_taxa2tree.rb CHANGED Viewed

@@ -36,7 +36,7 @@ module Unipept
       Commands::Unipept.run(%w[taxa2tree --host http://api.unipept.ugent.be 78 57 89 28 67])
     end
     lines = out.each_line
-    output = lines.to_a.join('').chomp
+    output = lines.to_a.join.chomp
     assert_equal('', err)
     assert(output.start_with?('{'))
@@ -60,7 +60,7 @@ module Unipept
     end
     lines = out.each_line
     assert_equal('', err)
-    output = lines.to_a.join('').chomp
+    output = lines.to_a.join.chomp
     assert(output.start_with?('<!DOCTYPE html>'))
     assert(output.end_with?('</html>'))
     assert(output.include?('</body>'))

data/test/commands/unipept/test_taxonomy.rb CHANGED Viewed

@@ -70,7 +70,7 @@ module Unipept
       end
       lines = out.each_line
       assert_equal('', err)
-      output = lines.to_a.join('').chomp
+      output = lines.to_a.join.chomp
       assert(output.start_with?('['))
       assert(output.end_with?(']'))
       assert(!output.include?('}{'))
@@ -83,7 +83,7 @@ module Unipept
       end
       lines = out.each_line
       assert_equal('', err)
-      output = lines.to_a.join('').chomp
+      output = lines.to_a.join.chomp
       assert(output.start_with?('<results>'))
       assert(output.end_with?('</results>'))
       assert(output.include?('<fasta_header>'))

data/test/support/api_stub.rb CHANGED Viewed

@@ -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_configuration.rb CHANGED Viewed

@@ -9,7 +9,7 @@ module Unipept
     def test_load_with_file
       hash = { 'key' => 'value' }
-      File.open('new_file', 'w') { |f| f.write hash.to_yaml }
+      File.write('new_file', hash.to_yaml)
       config = Configuration.new('new_file')
       assert_equal(hash, config.config)
     end

data/test/test_formatters.rb CHANGED Viewed

@@ -114,7 +114,7 @@ module Unipept
     def test_convert
       assert_equal(TestObject.as_json, formatter.convert([TestObject.test_object], true))
-      assert_equal(',' + TestObject.as_json, formatter.convert([TestObject.test_object], false))
+      assert_equal(",#{TestObject.as_json}", formatter.convert([TestObject.test_object], false))
     end
     def test_format_with_fasta
@@ -159,7 +159,7 @@ module Unipept
       fasta = [['peptide', '>test']]
       object = [TestObject.test_object, TestObject.test_object]
       assert_equal(TestObject.as_csv_header, formatter.header(object))
-      assert_equal('fasta_header,' + TestObject.as_csv_header, formatter.header(object, fasta))
+      assert_equal("fasta_header,#{TestObject.as_csv_header}", formatter.header(object, fasta))
     end
     def test_footer
@@ -180,7 +180,7 @@ module Unipept
     def test_format_with_fasta
       fasta = [['>test', '5']]
       object = [TestObject.test_object, TestObject.test_object]
-      csv = ['>test,' + TestObject.as_csv, '>test,' + TestObject.as_csv, ''].join("\n")
+      csv = [">test,#{TestObject.as_csv}", ">test,#{TestObject.as_csv}", ''].join("\n")
       assert_equal(csv, formatter.format(object, fasta, false))
     end
   end
@@ -203,7 +203,7 @@ module Unipept
     end
     def test_convert
-      xml = '<result>' + TestObject.as_xml + '</result>'
+      xml = "<result>#{TestObject.as_xml}</result>"
       assert_equal(xml, formatter.convert([TestObject.test_object], true))
       assert_equal(xml, formatter.convert([TestObject.test_object], false))
     end
@@ -211,7 +211,7 @@ module Unipept
     def test_format_with_fasta
       fasta = [['>test', '5']]
       output = formatter.format([TestObject.test_object], fasta, false)
-      xml = '<result><fasta_header>>test</fasta_header>' + TestObject.as_xml + '</result>'
+      xml = "<result><fasta_header>>test</fasta_header>#{TestObject.as_xml}</result>"
       assert_equal(xml, output)
     end
   end

data/test/test_output_writer.rb CHANGED Viewed

@@ -23,7 +23,7 @@ module Unipept
         writer.output.flush
       end
       assert_equal('', out)
-      assert_equal('hello world', IO.foreach('output_file').next.chomp)
+      assert_equal('hello world', File.foreach('output_file').next.chomp)
     end
   end
 end

data/test/test_server_message.rb CHANGED Viewed

@@ -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
@@ -79,13 +79,13 @@ module Unipept
     def test_old_recently_fetched
       server = ServerMessage.new('http://api.unipept.ugent.be')
-      server.configuration['last_fetch_date'] = Time.now - 60 * 60 * 25
+      server.configuration['last_fetch_date'] = Time.now - (60 * 60 * 25)
       assert(!server.recently_fetched?)
     end
     def test_recently_recently_fetched
       server = ServerMessage.new('http://api.unipept.ugent.be')
-      server.configuration['last_fetch_date'] = Time.now - 60 * 60 * 1
+      server.configuration['last_fetch_date'] = Time.now - (60 * 60 * 1)
       assert(server.recently_fetched?)
     end
   end

data/unipept.gemspec CHANGED Viewed

@@ -1,17 +1,17 @@
-# Generated by jeweler
+# Generated by juwelier
 # DO NOT EDIT THIS FILE DIRECTLY
-# Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
+# Instead, edit Juwelier::Tasks in Rakefile, and run 'rake gemspec'
 # -*- encoding: utf-8 -*-
-# stub: unipept 2.2.0 ruby lib
+# stub: unipept 3.0.0 ruby lib
 Gem::Specification.new do |s|
   s.name = "unipept".freeze
-  s.version = "2.2.0"
+  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 = "2020-04-27"
+  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]
@@ -21,10 +21,12 @@ Gem::Specification.new do |s|
   ]
   s.files = [
     ".document",
+    ".github/dependabot.yml",
     ".github/workflows/ci.yml",
     ".rakeTasks",
     ".rubocop.yml",
     ".ruby-version",
+    "CITATION.cff",
     "Gemfile",
     "Gemfile.lock",
     "LICENSE.txt",
@@ -102,32 +104,26 @@ Gem::Specification.new do |s|
   ]
   s.homepage = "http://unipept.ugent.be".freeze
   s.licenses = ["MIT".freeze]
-  s.required_ruby_version = Gem::Requirement.new(">= 2.0.0".freeze)
-  s.rubygems_version = "3.0.3".freeze
+  s.required_ruby_version = Gem::Requirement.new(">= 2.6.0".freeze)
+  s.rubygems_version = "3.1.4".freeze
   s.summary = "Command line interface to Unipept web services.".freeze
   if s.respond_to? :specification_version then
     s.specification_version = 4
+  end
-    if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
-      s.add_runtime_dependency(%q<cri>.freeze, ["~> 2.15.10"])
-      s.add_runtime_dependency(%q<typhoeus>.freeze, ["~> 1.3.1"])
-      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, ["~> 0.79.0"])
-    else
-      s.add_dependency(%q<cri>.freeze, ["~> 2.15.10"])
-      s.add_dependency(%q<typhoeus>.freeze, ["~> 1.3.1"])
-      s.add_dependency(%q<minitest>.freeze, ["~> 5.14"])
-      s.add_dependency(%q<rake>.freeze, ["~> 13.0.1"])
-      s.add_dependency(%q<rubocop>.freeze, ["~> 0.79.0"])
-    end
+  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_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<minitest>.freeze, ["~> 5.14"])
     s.add_dependency(%q<rake>.freeze, ["~> 13.0.1"])
-    s.add_dependency(%q<rubocop>.freeze, ["~> 0.79.0"])
+    s.add_dependency(%q<rubocop>.freeze, ["~> 1.11"])
   end
 end

metadata CHANGED Viewed

@@ -1,17 +1,17 @@
 --- !ruby/object:Gem::Specification
 name: unipept
 version: !ruby/object:Gem::Version
-  version: 2.2.0
+  version: 3.0.0
 platform: ruby
 authors:
 - Bart Mesuere
 - Pieter Verschaffelt
 - Toon Willems
 - Tom Naessens
-autorequire:
+autorequire:
 bindir: bin
 cert_chain: []
-date: 2020-04-27 00:00:00.000000000 Z
+date: 2022-04-14 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: cri
@@ -75,14 +75,14 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 0.79.0
+        version: '1.11'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 0.79.0
+        version: '1.11'
 description: |2
       Command line interface to the Unipept (http://unipept.ugent.be) web services
       (pept2lca, taxa2lca, pept2taxa, pept2prot and taxonomy) and some utility
@@ -99,10 +99,12 @@ extra_rdoc_files:
 - README.md
 files:
 - ".document"
+- ".github/dependabot.yml"
 - ".github/workflows/ci.yml"
 - ".rakeTasks"
 - ".rubocop.yml"
 - ".ruby-version"
+- CITATION.cff
 - Gemfile
 - Gemfile.lock
 - LICENSE.txt
@@ -181,7 +183,7 @@ homepage: http://unipept.ugent.be
 licenses:
 - MIT
 metadata: {}
-post_install_message:
+post_install_message:
 rdoc_options: []
 require_paths:
 - lib
@@ -189,15 +191,15 @@ required_ruby_version: !ruby/object:Gem::Requirement
   requirements:
   - - ">="
     - !ruby/object:Gem::Version
-      version: 2.0.0
+      version: 2.6.0
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
   - - ">="
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.0.3
-signing_key:
+rubygems_version: 3.1.4
+signing_key:
 specification_version: 4
 summary: Command line interface to Unipept web services.
 test_files: []