unipept 0.8.0 → 0.9.0
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- 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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1
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+
require_relative '../lib/server_message'
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2
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+
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3
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module Unipept
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4
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class ServerMessageTestCase < Unipept::TestCase
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5
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def test_init
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6
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assert_equal('http://test_host/api/v1/messages.json', ServerMessage.new('http://test_host').message_url)
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7
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end
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8
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9
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def test_fetch_server_message
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10
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server = ServerMessage.new('http://api.unipept.ugent.be')
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11
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assert(!server.fetch_server_message.nil?)
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12
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end
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13
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14
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def test_print_server_message
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15
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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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17
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server.stub(:fetch_server_message, 'message') do
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18
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out, _err = capture_io_while do
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19
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def $stdout.tty?
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20
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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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24
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assert_equal('message', out.chomp)
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25
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end
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26
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end
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27
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end
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28
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29
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def test_empty_print_server_message
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30
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server = ServerMessage.new('http://api.unipept.ugent.be')
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31
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server.stub(:recently_fetched?, false) do
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32
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server.stub(:fetch_server_message, '') do
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33
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out, _err = capture_io_while do
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34
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def $stdout.tty?
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35
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true
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36
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end
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37
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server.print
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38
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end
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39
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assert_equal('', out)
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40
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end
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41
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end
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42
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end
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43
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44
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def test_recent_print_server_message
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45
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server = ServerMessage.new('http://api.unipept.ugent.be')
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46
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server.stub(:recently_fetched?, true) do
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47
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+
server.stub(:fetch_server_message, 'message') do
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48
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out, _err = capture_io_while do
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49
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def $stdout.tty?
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50
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true
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51
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end
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52
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server.print
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53
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end
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54
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assert_equal('', out)
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55
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end
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56
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end
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57
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end
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58
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59
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def test_no_tty_print_server_message
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60
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server = ServerMessage.new('http://api.unipept.ugent.be')
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61
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server.stub(:recently_fetched?, false) do
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62
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server.stub(:fetch_server_message, 'message') do
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63
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out, _err = capture_io_while do
|
64
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def $stdout.tty?
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65
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false
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66
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end
|
67
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server.print
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68
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end
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69
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assert_equal('', out)
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70
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end
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71
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end
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72
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end
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73
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+
|
74
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def test_never_recently_fetched
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75
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server = ServerMessage.new('http://api.unipept.ugent.be')
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76
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server.configuration.delete('last_fetch_date')
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77
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assert(!server.recently_fetched?)
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78
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end
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79
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+
|
80
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def test_old_recently_fetched
|
81
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server = ServerMessage.new('http://api.unipept.ugent.be')
|
82
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server.configuration['last_fetch_date'] = Time.now - 60 * 60 * 25
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83
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assert(!server.recently_fetched?)
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84
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end
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85
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+
|
86
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def test_recently_recently_fetched
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87
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server = ServerMessage.new('http://api.unipept.ugent.be')
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88
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server.configuration['last_fetch_date'] = Time.now - 60 * 60 * 1
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89
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assert(server.recently_fetched?)
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90
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end
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91
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end
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92
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end
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data/unipept.gemspec
CHANGED
@@ -2,15 +2,15 @@
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2
2
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# DO NOT EDIT THIS FILE DIRECTLY
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3
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# Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
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4
4
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# -*- encoding: utf-8 -*-
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5
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-
# stub: unipept 0.
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5
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+
# stub: unipept 0.9.0 ruby lib
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6
6
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7
7
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Gem::Specification.new do |s|
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8
8
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s.name = "unipept"
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9
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-
s.version = "0.
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9
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+
s.version = "0.9.0"
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10
10
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11
11
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s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
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12
12
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s.authors = ["Toon Willems", "Bart Mesuere", "Tom Naessens"]
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13
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-
s.date = "2015-06-
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13
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+
s.date = "2015-06-21"
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14
14
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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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15
15
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s.email = "unipept@ugent.be"
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16
16
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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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48
48
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"lib/commands/uniprot.rb",
|
49
49
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"lib/configuration.rb",
|
50
50
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"lib/formatters.rb",
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51
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+
"lib/output_writer.rb",
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52
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+
"lib/server_message.rb",
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51
53
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"lib/version.rb",
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52
54
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"test/commands/test_peptfilter.rb",
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53
55
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"test/commands/test_prot2pept.rb",
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@@ -62,10 +64,11 @@ Gem::Specification.new do |s|
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62
64
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"test/commands/unipept/test_taxonomy.rb",
|
63
65
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"test/helper.rb",
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64
66
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"test/test_bach_order.rb",
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65
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-
"test/test_base.rb",
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66
67
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"test/test_batch_iterator.rb",
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67
68
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"test/test_configuration.rb",
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68
69
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"test/test_formatters.rb",
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70
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+
"test/test_output_writer.rb",
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71
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+
"test/test_server_message.rb",
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69
72
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"unipept.gemspec"
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70
73
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]
|
71
74
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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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1
1
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--- !ruby/object:Gem::Specification
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2
2
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name: unipept
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3
3
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version: !ruby/object:Gem::Version
|
4
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-
version: 0.
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4
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+
version: 0.9.0
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5
5
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platform: ruby
|
6
6
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authors:
|
7
7
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- Toon Willems
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@@ -10,7 +10,7 @@ authors:
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|
10
10
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autorequire:
|
11
11
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bindir: bin
|
12
12
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cert_chain: []
|
13
|
-
date: 2015-06-
|
13
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+
date: 2015-06-21 00:00:00.000000000 Z
|
14
14
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dependencies:
|
15
15
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- !ruby/object:Gem::Dependency
|
16
16
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name: cri
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@@ -154,6 +154,8 @@ files:
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|
154
154
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- lib/commands/uniprot.rb
|
155
155
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- lib/configuration.rb
|
156
156
|
- lib/formatters.rb
|
157
|
+
- lib/output_writer.rb
|
158
|
+
- lib/server_message.rb
|
157
159
|
- lib/version.rb
|
158
160
|
- test/commands/test_peptfilter.rb
|
159
161
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- test/commands/test_prot2pept.rb
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@@ -168,10 +170,11 @@ files:
|
|
168
170
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- test/commands/unipept/test_taxonomy.rb
|
169
171
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- test/helper.rb
|
170
172
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- test/test_bach_order.rb
|
171
|
-
- test/test_base.rb
|
172
173
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- test/test_batch_iterator.rb
|
173
174
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- test/test_configuration.rb
|
174
175
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- test/test_formatters.rb
|
176
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+
- test/test_output_writer.rb
|
177
|
+
- test/test_server_message.rb
|
175
178
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- unipept.gemspec
|
176
179
|
homepage: https://github.com/unipept/unipept-cli/
|
177
180
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licenses:
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