unipept 0.8.0 → 0.9.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +4 -4
- data/.travis.yml +2 -0
- data/README.md +4 -4
- data/VERSION +1 -1
- data/lib/commands/unipept/api_runner.rb +64 -70
- data/lib/commands/unipept/pept2lca.rb +1 -1
- data/lib/commands/unipept/pept2prot.rb +1 -1
- data/lib/commands/unipept/pept2taxa.rb +1 -1
- data/lib/commands/unipept/taxa2lca.rb +1 -1
- data/lib/commands/unipept/taxonomy.rb +1 -1
- data/lib/commands/unipept.rb +6 -2
- data/lib/formatters.rb +91 -86
- data/lib/output_writer.rb +13 -0
- data/lib/server_message.rb +45 -0
- data/test/commands/unipept/test_api_runner.rb +28 -122
- data/test/commands/unipept/test_pept2lca.rb +52 -2
- data/test/commands/unipept/test_pept2prot.rb +40 -3
- data/test/commands/unipept/test_pept2taxa.rb +40 -3
- data/test/commands/unipept/test_taxa2lca.rb +26 -2
- data/test/commands/unipept/test_taxonomy.rb +39 -2
- data/test/test_formatters.rb +83 -13
- data/test/test_output_writer.rb +29 -0
- data/test/test_server_message.rb +92 -0
- data/unipept.gemspec +7 -4
- metadata +6 -3
- data/test/test_base.rb +0 -6
@@ -0,0 +1,92 @@
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require_relative '../lib/server_message'
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module Unipept
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class ServerMessageTestCase < Unipept::TestCase
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def test_init
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assert_equal('http://test_host/api/v1/messages.json', ServerMessage.new('http://test_host').message_url)
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end
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def test_fetch_server_message
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server = ServerMessage.new('http://api.unipept.ugent.be')
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assert(!server.fetch_server_message.nil?)
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end
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def test_print_server_message
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server = ServerMessage.new('http://api.unipept.ugent.be')
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server.stub(:recently_fetched?, false) do
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server.stub(:fetch_server_message, 'message') do
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out, _err = capture_io_while do
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def $stdout.tty?
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true
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end
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server.print
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end
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assert_equal('message', out.chomp)
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end
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end
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end
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def test_empty_print_server_message
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server = ServerMessage.new('http://api.unipept.ugent.be')
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server.stub(:recently_fetched?, false) do
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server.stub(:fetch_server_message, '') do
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out, _err = capture_io_while do
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def $stdout.tty?
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true
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end
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server.print
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end
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assert_equal('', out)
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end
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end
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end
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def test_recent_print_server_message
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server = ServerMessage.new('http://api.unipept.ugent.be')
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server.stub(:recently_fetched?, true) do
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server.stub(:fetch_server_message, 'message') do
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out, _err = capture_io_while do
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def $stdout.tty?
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true
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end
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server.print
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end
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assert_equal('', out)
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end
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end
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end
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def test_no_tty_print_server_message
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server = ServerMessage.new('http://api.unipept.ugent.be')
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server.stub(:recently_fetched?, false) do
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server.stub(:fetch_server_message, 'message') do
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out, _err = capture_io_while do
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def $stdout.tty?
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false
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end
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server.print
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end
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assert_equal('', out)
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end
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end
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end
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def test_never_recently_fetched
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server = ServerMessage.new('http://api.unipept.ugent.be')
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server.configuration.delete('last_fetch_date')
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assert(!server.recently_fetched?)
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end
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def test_old_recently_fetched
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server = ServerMessage.new('http://api.unipept.ugent.be')
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server.configuration['last_fetch_date'] = Time.now - 60 * 60 * 25
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assert(!server.recently_fetched?)
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end
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def test_recently_recently_fetched
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server = ServerMessage.new('http://api.unipept.ugent.be')
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server.configuration['last_fetch_date'] = Time.now - 60 * 60 * 1
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assert(server.recently_fetched?)
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end
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end
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end
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data/unipept.gemspec
CHANGED
@@ -2,15 +2,15 @@
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# DO NOT EDIT THIS FILE DIRECTLY
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# Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
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# -*- encoding: utf-8 -*-
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# stub: unipept 0.
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# stub: unipept 0.9.0 ruby lib
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Gem::Specification.new do |s|
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s.name = "unipept"
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s.version = "0.
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s.version = "0.9.0"
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s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
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s.authors = ["Toon Willems", "Bart Mesuere", "Tom Naessens"]
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s.date = "2015-06-
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s.date = "2015-06-21"
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s.description = " Command line interface to the Unipept (http://unipept.ugent.be) web services\n (pept2lca, taxa2lca, pept2taxa and taxonomy) and some utility commands for\n handling proteins using the command line.\n"
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s.email = "unipept@ugent.be"
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s.executables = ["unipept", "prot2pept", "peptfilter", "uniprot"]
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@@ -48,6 +48,8 @@ Gem::Specification.new do |s|
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"lib/commands/uniprot.rb",
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"lib/configuration.rb",
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"lib/formatters.rb",
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"lib/output_writer.rb",
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"lib/server_message.rb",
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"lib/version.rb",
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"test/commands/test_peptfilter.rb",
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"test/commands/test_prot2pept.rb",
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"test/commands/unipept/test_taxonomy.rb",
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"test/helper.rb",
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"test/test_bach_order.rb",
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"test/test_base.rb",
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"test/test_batch_iterator.rb",
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"test/test_configuration.rb",
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"test/test_formatters.rb",
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"test/test_output_writer.rb",
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"test/test_server_message.rb",
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"unipept.gemspec"
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]
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s.homepage = "https://github.com/unipept/unipept-cli/"
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metadata
CHANGED
@@ -1,7 +1,7 @@
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--- !ruby/object:Gem::Specification
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name: unipept
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version: !ruby/object:Gem::Version
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version: 0.
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version: 0.9.0
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platform: ruby
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authors:
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- Toon Willems
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autorequire:
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bindir: bin
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cert_chain: []
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date: 2015-06-
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date: 2015-06-21 00:00:00.000000000 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: cri
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@@ -154,6 +154,8 @@ files:
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- lib/commands/uniprot.rb
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- lib/configuration.rb
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- lib/formatters.rb
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- lib/output_writer.rb
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- lib/server_message.rb
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- lib/version.rb
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- test/commands/test_peptfilter.rb
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- test/commands/test_prot2pept.rb
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@@ -168,10 +170,11 @@ files:
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- test/commands/unipept/test_taxonomy.rb
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- test/helper.rb
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- test/test_bach_order.rb
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- test/test_base.rb
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- test/test_batch_iterator.rb
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- test/test_configuration.rb
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- test/test_formatters.rb
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- test/test_output_writer.rb
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- test/test_server_message.rb
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- unipept.gemspec
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homepage: https://github.com/unipept/unipept-cli/
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licenses:
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