unipept 3.0.1 → 3.1.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
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-  data.tar.gz: 9964dc3d83bb794673a067a9aac45cd638b6248230972c2ea02a13dab4beaba4
+  metadata.gz: 91451cf1d23535a5698b259a004df798959fb0116a0dc8ba11c17e2c4bbdcf23
+  data.tar.gz: 2b68c81a3d284b50e2d20f51cc2655dac736a649fbe1f743062bb32d38fce903
 SHA512:
-  metadata.gz: de2af48a091dc98dc745c451433fa91fcb95ba056fe0fda4520a455568de93f7b60125e9e5c4bb4c27fc97c35d8464daf3c09c371b19e6bcb51f516af9b6eff9
-  data.tar.gz: 3952e4ec06d8f64a0c536f3cb02fba11d6470fc63b0aaa6d4ba3dcbdb2c0f77ed02857559962ea2458f7642f59c2bb67276e7c5a0915745eda1ec0f445a1b1e9
+  metadata.gz: b7dfc8ec5d8d16ab448a2935eb8697252b360aa675021624a52383147ba07c93ef76a4396935bdee3e06a5ed968bf7c6afa180d2513ab0b118ace98af855c108
+  data.tar.gz: 616446c5da67f407c78cac0b051042c61dc7c25a15fd03c44656f1f347d3eabf841c4a4e80e0e17c4d2d54b1b4698578ca1a5d074fcbf0bf69d170abd8b503a5

data/.devcontainer/devcontainer.json

@@ -0,0 +1,18 @@
+// For format details, see https://aka.ms/devcontainer.json. For config options, see the
+// README at: https://github.com/devcontainers/templates/tree/main/src/ruby
+{
+	"name": "Ruby",
+	// Or use a Dockerfile or Docker Compose file. More info: https://containers.dev/guide/dockerfile
+	"image": "mcr.microsoft.com/devcontainers/ruby:1-3.2-bookworm",
+	// Features to add to the dev container. More info: https://containers.dev/features.
+	// "features": {},
+	// Use 'forwardPorts' to make a list of ports inside the container available locally.
+	// "forwardPorts": [],
+	// Use 'postCreateCommand' to run commands after the container is created.
+	"postCreateCommand": "ruby --version",
+	"postStartCommand": "bundle install"
+	// Configure tool-specific properties.
+	// "customizations": {},
+	// Uncomment to connect as root instead. More info: https://aka.ms/dev-containers-non-root.
+	// "remoteUser": "root"
+}

data/.github/workflows/ci.yml

@@ -7,7 +7,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        ruby: ["2.7", "3.0", "3.1"]
+        ruby: ["2.7", "3.0", "3.1", "3.2"]
       fail-fast: false
     name: Test Ruby ${{ matrix.ruby }}
     steps:

data/.rubocop.yml

@@ -15,6 +15,8 @@ Style/FrozenStringLiteralComment:
 # disable for now
 Lint/NestedMethodDefinition:
   Enabled: false
+Lint/Lint/RedundantStringCoercion:
+  Enabled: false
 Style/ClassVars:
   Enabled: false
 Style/Documentation:

data/.vscode/tasks.json

@@ -0,0 +1,28 @@
+{
+	"version": "2.0.0",
+	"tasks": [
+		{
+			"type": "rake",
+			"task": "test_style:autocorrect_all",
+			"group": "test",
+			"problemMatcher": [],
+			"label": "rake: test_style:autocorrect_all"
+		},
+		{
+			"type": "rake",
+			"task": "test",
+			"group": {
+				"kind": "test",
+				"isDefault": true
+			},
+			"problemMatcher": [],
+			"label": "rake: test"
+		},
+		{
+			"type": "shell",
+			"command": "bundle exec rake gemspec",
+			"label": "generate gemspec",
+			"problemMatcher": []
+		}
+	]
+}

data/Gemfile

@@ -2,15 +2,15 @@ source 'http://rubygems.org'
 # Add dependencies required to use your gem here.
 
 gem 'cri', '~>2.15.10'
-gem 'typhoeus', '~> 1.3.1'
+gem 'typhoeus', '~> 1.4.0'
 
 # this is not explicitly used, but an older incompatible version comes bundled with ruby
-gem 'psych', '~> 4.0.3'
+gem 'psych', '~> 5.1.0'
 
 group :development do
-  gem 'minitest', '~> 5.14'
+  gem 'minitest', '~> 5.18'
   gem 'rake', '~> 13.0.1'
-  gem 'rubocop', '~>1.11'
+  gem 'rubocop', '~>1.50'
 end
 
 group :release do

data/Gemfile.lock

@@ -8,15 +8,16 @@ GEM
     cri (2.15.11)
     descendants_tracker (0.0.4)
       thread_safe (~> 0.3, >= 0.3.1)
-    ethon (0.12.0)
-      ffi (>= 1.3.0)
+    ethon (0.16.0)
+      ffi (>= 1.15.0)
     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 (1.8.1)
+    ffi (1.15.5)
+    git (1.18.0)
+      addressable (~> 2.8)
       rchardet (~> 1.8)
     github_api (0.19.0)
       addressable (~> 2.4)
@@ -26,6 +27,7 @@ GEM
       oauth2 (~> 1.0)
     hashie (3.6.0)
     highline (2.0.3)
+    json (2.6.3)
     juwelier (2.4.9)
       builder
       bundler
@@ -42,53 +44,54 @@ GEM
     kamelcase (0.0.2)
       semver2 (~> 3)
     mini_portile2 (2.8.0)
-    minitest (5.15.0)
+    minitest (5.18.1)
     multi_json (1.15.0)
     multi_xml (0.6.0)
     multipart-post (2.1.1)
-    nokogiri (1.13.4)
+    nokogiri (1.13.10)
       mini_portile2 (~> 2.8.0)
       racc (~> 1.4)
-    oauth2 (1.4.4)
-      faraday (>= 0.8, < 2.0)
+    oauth2 (1.4.11)
+      faraday (>= 0.17.3, < 3.0)
       jwt (>= 1.0, < 3.0)
       multi_json (~> 1.3)
       multi_xml (~> 0.5)
-      rack (>= 1.2, < 3)
-    parallel (1.22.1)
-    parser (3.1.1.0)
+      rack (>= 1.2, < 4)
+    parallel (1.23.0)
+    parser (3.2.2.1)
       ast (~> 2.4.1)
-    psych (4.0.3)
+    psych (5.1.0)
       stringio
     public_suffix (4.0.6)
-    racc (1.6.0)
-    rack (2.2.3)
+    racc (1.6.1)
+    rack (3.0.7)
     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 (2.8.0)
     rexml (3.2.5)
-    rubocop (1.27.0)
+    rubocop (1.50.2)
+      json (~> 2.3)
       parallel (~> 1.10)
-      parser (>= 3.1.0.0)
+      parser (>= 3.2.0.0)
       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 (>= 1.28.0, < 2.0)
       ruby-progressbar (~> 1.7)
-      unicode-display_width (>= 1.4.0, < 3.0)
-    rubocop-ast (1.17.0)
-      parser (>= 3.1.1.0)
-    ruby-progressbar (1.11.0)
+      unicode-display_width (>= 2.4.0, < 3.0)
+    rubocop-ast (1.28.0)
+      parser (>= 3.2.1.0)
+    ruby-progressbar (1.13.0)
     ruby2_keywords (0.0.4)
     semver2 (3.4.2)
-    stringio (3.0.1)
+    stringio (3.0.6)
     thread_safe (0.3.6)
-    typhoeus (1.3.1)
+    typhoeus (1.4.0)
       ethon (>= 0.9.0)
-    unicode-display_width (2.1.0)
+    unicode-display_width (2.4.2)
 
 PLATFORMS
   ruby
@@ -96,11 +99,11 @@ PLATFORMS
 DEPENDENCIES
   cri (~> 2.15.10)
   juwelier
-  minitest (~> 5.14)
-  psych (~> 4.0.3)
+  minitest (~> 5.18)
+  psych (~> 5.1.0)
   rake (~> 13.0.1)
-  rubocop (~> 1.11)
-  typhoeus (~> 1.3.1)
+  rubocop (~> 1.50)
+  typhoeus (~> 1.4.0)
 
 BUNDLED WITH
-   1.17.2
+   2.4.12

data/README.md

@@ -7,7 +7,7 @@ Documentation about the web service can be found at [http://unipept.ugent.be/api
 
 ## Installation
 
-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:
+To use the Unipept CLI, Ruby version 2.7 or higher needs to be installed. You can check this by running `ruby -v` on the commandline:
 
 ```
 $ ruby -v

data/Rakefile

@@ -25,8 +25,8 @@ begin
     commands for handling proteins using the command line.
     EOS
     gem.email = 'unipept@ugent.be'
-    gem.authors = ['Bart Mesuere', 'Pieter Verschaffelt', 'Toon Willems', 'Tom Naessens']
-    gem.required_ruby_version = '>= 2.6.0'
+    gem.authors = ['Bart Mesuere', 'Pieter Verschaffelt', 'Tibo Vande Moortele', 'Toon Willems', 'Tom Naessens']
+    gem.required_ruby_version = '>= 2.7.0'
   end
   Juwelier::RubygemsDotOrgTasks.new
 rescue LoadError

data/VERSION

@@ -1 +1 @@
-3.0.1
+3.1.0

data/lib/commands/unipept/protinfo.rb

@@ -0,0 +1,12 @@
+require_relative 'api_runner'
+module Unipept::Commands
+  class Protinfo < ApiRunner
+    def required_fields
+      ['protein']
+    end
+
+    def default_batch_size
+      1000
+    end
+  end
+end

data/lib/commands/unipept.rb

@@ -17,6 +17,7 @@ require_relative 'unipept/pept2lca'
 require_relative 'unipept/pept2prot'
 require_relative 'unipept/pept2taxa'
 require_relative 'unipept/peptinfo'
+require_relative 'unipept/protinfo'
 require_relative 'unipept/taxa2lca'
 require_relative 'unipept/taxonomy'
 require_relative 'unipept/taxa2tree'
@@ -33,6 +34,7 @@ module Unipept
       add_pept2interpro_command
       add_pept2lca_command
       add_peptinfo_command
+      add_protinfo_command
       add_taxa2lca_command
       add_pept2prot_command
       add_taxonomy_command
@@ -271,6 +273,28 @@ module Unipept
       end
     end
 
+    def add_protinfo_command
+      @root_command.define_command('protinfo') do
+        usage 'protinfo [options]'
+        summary 'Fetch functional and taxonomic information of UniProt ids'
+        description <<-EOS
+        For each UniProt id the unipept protinfo command retrieves from Unipept the functional information and the NCBI id. The command expects a list of UniProt ids that are passed
+
+         - as separate command line arguments
+
+         - in a text file that is passed as an argument to the -i option
+
+         - to standard input
+
+        The command will give priority to the first way tryptic peptides are passed, in the order as listed above. Text files and standard input should have one tryptic peptide per line.
+        EOS
+
+        option :s, :select, 'select the information fields to return. Selected fields are passed as a comma separated list of field names. Multiple -s (or --select) options may be used.', argument: :required, multiple: true
+
+        runner Commands::Protinfo
+      end
+    end
+
     def add_taxa2lca_command
       @root_command.define_command('taxa2lca') do
         usage 'taxa2lca [options]'

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/test/commands/unipept/test_protinfo.rb

@@ -0,0 +1,45 @@
+require_relative '../../../lib/commands'
+
+module Unipept
+  class UnipeptProtinfoTestCase < Unipept::TestCase
+    def test_default_batch_size
+      command = Cri::Command.define { name 'protinfo' }
+      protinfo = Commands::Protinfo.new({ host: 'http://api.unipept.ugent.be' }, [], command)
+      assert_equal(1000, protinfo.default_batch_size)
+    end
+
+    def test_required_fields
+      command = Cri::Command.define { name 'protinfo' }
+      protinfo = Commands::Protinfo.new({ host: 'http://api.unipept.ugent.be' }, [], command)
+      assert_equal(['protein'], protinfo.required_fields)
+    end
+
+    def test_argument_batch_size
+      command = Cri::Command.define { name 'protinfo' }
+      protinfo = Commands::Protinfo.new({ host: 'http://api.unipept.ugent.be', batch: '123' }, [], command)
+      assert_equal(123, protinfo.batch_size)
+    end
+
+    def test_batch_size
+      command = Cri::Command.define { name 'protinfo' }
+      protinfo = Commands::Protinfo.new({ host: 'http://api.unipept.ugent.be' }, [], command)
+      assert_equal(1000, protinfo.batch_size)
+    end
+
+    def test_help
+      out, _err = capture_io_while do
+        assert_raises SystemExit do
+          Commands::Unipept.run(%w[protinfo -h])
+        end
+      end
+      assert(out.include?('show help for this command'))
+
+      out, _err = capture_io_while do
+        assert_raises SystemExit do
+          Commands::Unipept.run(%w[protinfo --help])
+        end
+      end
+      assert(out.include?('show help for this command'))
+    end
+  end
+end

data/test/helper.rb

@@ -85,4 +85,4 @@ module Unipept
 end
 
 # Unexpected system exit is unexpected
-::MiniTest::Unit::TestCase::PASSTHROUGH_EXCEPTIONS.delete(SystemExit)
+MiniTest::Unit::TestCase::PASSTHROUGH_EXCEPTIONS.delete(SystemExit)

data/unipept.gemspec

@@ -1,17 +1,17 @@
 # Generated by juwelier
 # DO NOT EDIT THIS FILE DIRECTLY
-# Instead, edit Juwelier::Tasks in Rakefile, and run 'rake gemspec'
+# Instead, edit Juwelier::Tasks in rakefile, and run 'rake gemspec'
 # -*- encoding: utf-8 -*-
-# stub: unipept 3.0.1 ruby lib
+# stub: unipept 3.1.0 ruby lib
 
 Gem::Specification.new do |s|
   s.name = "unipept".freeze
-  s.version = "3.0.1"
+  s.version = "3.1.0"
 
   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 = "2022-04-27"
+  s.date = "2023-07-24"
   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]
@@ -20,12 +20,14 @@ Gem::Specification.new do |s|
     "README.md"
   ]
   s.files = [
+    ".devcontainer/devcontainer.json",
     ".document",
     ".github/dependabot.yml",
     ".github/workflows/ci.yml",
     ".rakeTasks",
     ".rubocop.yml",
     ".ruby-version",
+    ".vscode/tasks.json",
     "CITATION.cff",
     "Gemfile",
     "Gemfile.lock",
@@ -53,6 +55,7 @@ Gem::Specification.new do |s|
     "lib/commands/unipept/pept2prot.rb",
     "lib/commands/unipept/pept2taxa.rb",
     "lib/commands/unipept/peptinfo.rb",
+    "lib/commands/unipept/protinfo.rb",
     "lib/commands/unipept/taxa2lca.rb",
     "lib/commands/unipept/taxa2tree.rb",
     "lib/commands/unipept/taxonomy.rb",
@@ -78,6 +81,7 @@ Gem::Specification.new do |s|
     "test/commands/unipept/test_pept2prot.rb",
     "test/commands/unipept/test_pept2taxa.rb",
     "test/commands/unipept/test_peptinfo.rb",
+    "test/commands/unipept/test_protinfo.rb",
     "test/commands/unipept/test_taxa2lca.rb",
     "test/commands/unipept/test_taxa2tree.rb",
     "test/commands/unipept/test_taxonomy.rb",
@@ -105,27 +109,16 @@ 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 = "3.2.15".freeze
+  s.rubygems_version = "3.4.10".freeze
   s.summary = "Command line interface to Unipept web services.".freeze
 
-  if s.respond_to? :specification_version then
-    s.specification_version = 4
-  end
+  s.specification_version = 4
 
-  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"])
-  end
+  s.add_runtime_dependency(%q<cri>.freeze, ["~> 2.15.10"])
+  s.add_runtime_dependency(%q<typhoeus>.freeze, ["~> 1.4.0"])
+  s.add_runtime_dependency(%q<psych>.freeze, ["~> 5.1.0"])
+  s.add_development_dependency(%q<minitest>.freeze, ["~> 5.18"])
+  s.add_development_dependency(%q<rake>.freeze, ["~> 13.0.1"])
+  s.add_development_dependency(%q<rubocop>.freeze, ["~> 1.50"])
 end
 

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: unipept
 version: !ruby/object:Gem::Version
-  version: 3.0.1
+  version: 3.1.0
 platform: ruby
 authors:
 - Bart Mesuere
@@ -11,7 +11,7 @@ authors:
 autorequire:
 bindir: bin
 cert_chain: []
-date: 2022-04-27 00:00:00.000000000 Z
+date: 2023-07-24 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: cri
@@ -33,42 +33,42 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 1.3.1
+        version: 1.4.0
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 1.3.1
+        version: 1.4.0
 - !ruby/object:Gem::Dependency
   name: psych
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 4.0.3
+        version: 5.1.0
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 4.0.3
+        version: 5.1.0
 - !ruby/object:Gem::Dependency
   name: minitest
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '5.14'
+        version: '5.18'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '5.14'
+        version: '5.18'
 - !ruby/object:Gem::Dependency
   name: rake
   requirement: !ruby/object:Gem::Requirement
@@ -89,14 +89,14 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.11'
+        version: '1.50'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.11'
+        version: '1.50'
 description: |2
       Command line interface to the Unipept (http://unipept.ugent.be) web services
       (pept2lca, taxa2lca, pept2taxa, pept2prot and taxonomy) and some utility
@@ -112,12 +112,14 @@ extra_rdoc_files:
 - LICENSE.txt
 - README.md
 files:
+- ".devcontainer/devcontainer.json"
 - ".document"
 - ".github/dependabot.yml"
 - ".github/workflows/ci.yml"
 - ".rakeTasks"
 - ".rubocop.yml"
 - ".ruby-version"
+- ".vscode/tasks.json"
 - CITATION.cff
 - Gemfile
 - Gemfile.lock
@@ -145,6 +147,7 @@ files:
 - lib/commands/unipept/pept2prot.rb
 - lib/commands/unipept/pept2taxa.rb
 - lib/commands/unipept/peptinfo.rb
+- lib/commands/unipept/protinfo.rb
 - lib/commands/unipept/taxa2lca.rb
 - lib/commands/unipept/taxa2tree.rb
 - lib/commands/unipept/taxonomy.rb
@@ -170,6 +173,7 @@ files:
 - test/commands/unipept/test_pept2prot.rb
 - test/commands/unipept/test_pept2taxa.rb
 - test/commands/unipept/test_peptinfo.rb
+- test/commands/unipept/test_protinfo.rb
 - test/commands/unipept/test_taxa2lca.rb
 - test/commands/unipept/test_taxa2tree.rb
 - test/commands/unipept/test_taxonomy.rb
@@ -212,7 +216,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.2.15
+rubygems_version: 3.4.10
 signing_key:
 specification_version: 4
 summary: Command line interface to Unipept web services.