sequencescape-client-api 0.4.2 → 0.6.0.pre.rc1
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- checksums.yaml +4 -4
- data/.github/workflows/ruby.yml +39 -0
- data/.gitignore +1 -0
- data/.rubocop.yml +16 -10
- data/.rubocop_todo.yml +58 -18
- data/README.markdown +11 -7
- data/lib/sequencescape-api/connection_factory.rb +5 -5
- data/lib/sequencescape-api/connection_factory/actions.rb +6 -6
- data/lib/sequencescape-api/finder_methods.rb +1 -3
- data/lib/sequencescape-api/rails.rb +5 -9
- data/lib/sequencescape-api/version.rb +1 -1
- data/lib/sequencescape/barcode_printer.rb +1 -1
- data/lib/sequencescape/order.rb +2 -1
- data/sequencescape-api.gemspec +15 -3
- data/spec/sequencescape-api/contracts/create-invalid-resource.txt +1 -1
- data/spec/sequencescape-api/contracts/create-model-c-has-many-inline-nested.txt +1 -1
- data/spec/sequencescape-api/contracts/create-model-c-has-many-inline.txt +1 -1
- data/spec/sequencescape-api/contracts/create-model-c-has-many.txt +1 -1
- data/spec/sequencescape-api/contracts/create-model-c.txt +1 -1
- data/spec/sequencescape-api/contracts/create-via-has-many.txt +1 -1
- data/spec/sequencescape-api/contracts/retrieve-belongs-to-association.txt +1 -1
- data/spec/sequencescape-api/contracts/retrieve-model.txt +1 -2
- data/spec/sequencescape-api/contracts/retrieve-results-page-1.txt +1 -1
- data/spec/sequencescape-api/contracts/retrieve-results-page-2.txt +1 -1
- data/spec/sequencescape-api/contracts/retrieve-results-page-3.txt +1 -1
- data/spec/sequencescape-api/contracts/retrieve-root-with-an-authorised-client.txt +1 -2
- data/spec/sequencescape-api/contracts/retrieve-root-with-an-unauthorised-client.txt +1 -2
- data/spec/sequencescape-api/contracts/retrieve-unauthorised-model-a-list.txt +1 -2
- data/spec/sequencescape-api/contracts/retrieve-unauthorised-model-b-list.txt +1 -2
- data/spec/sequencescape-api/contracts/retrieve-unauthorised-model-c-list.txt +1 -2
- data/spec/sequencescape-api/contracts/update-invalid-resource.txt +1 -1
- data/spec/sequencescape-api/contracts/update-model-c.txt +1 -1
- data/spec/sequencescape-api/root_spec.rb +3 -3
- data/spec/support/contract_helper.rb +3 -3
- metadata +40 -14
checksums.yaml
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metadata.gz:
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metadata.gz: 44f010fb9ed69aae5a2db7f07ae354c9c122ad86fb5d96c0a731cd0db7a7188e
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data.tar.gz: 3d4ddf33e18bcceb7c04634b2c7c753a47ab91ad3ae8280b75c9f7e47f5497e5
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data.tar.gz: 96d7dbd068dfbf42cc9425330c146f1d6a24abf7c5da19306b8d3ebaace8f0e3ca933f2037826f6a335390a0bcf05e8e598ca7993e0b49fcb597d6c006ed372c
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name: Ruby
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on:
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- push
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jobs:
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test:
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runs-on: ubuntu-latest
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strategy:
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matrix:
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ruby: ["2.5", "2.6", "2.7", "3.0"]
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name: Ruby Test ${{ matrix.ruby }}
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uses: ruby/setup-ruby@v1
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with:
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ruby-version: ${{ matrix.ruby }}
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true # Runs bundle install and caches gems. See the ruby_test.yml
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uses: ruby/setup-ruby@v1
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data/README.markdown
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Sequencescape Client API
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========================
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# Sequencescape Client API
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This is the Ruby client library for the Sequencescape API.
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Documentation can be found [on the wiki](https://github.com/sanger/sequencescape-client-api/wiki).
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Version Guides
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--------------
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## Version Guides
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- 0.2.x Supports older versions of Rails.
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- 0.3.x Supports Rails 3.2.x to 5.1.x
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- 0.4.x Supports Rails 5.0 and up
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- 0.5.x Supports Rails 5.0 and up, drops yajl in favour of multi-json
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- 0.6.x Removes usage of WTSISignOn cookie. Replaces with user specific api key,
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can be provided to Sequencescape::Api.new as user_api_key: or via
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`api_connection_options` in the controller.
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- master currently corresponds to 0.
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- master currently corresponds to 0.6.x
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Making a release
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## Making a release
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1. Update the version number in `lib/sequencescape-api/version.rb`
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major.minor.point-rcx
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major.minor.point
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4. Ensure everything is committed, and for non-pre-releases, make sure you are
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merged to master.
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```
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rake release
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``
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```
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def self.create(options)
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required_options = []
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required_options.push(:
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required_options.push(:user_api_key) if options[:authorisation].blank?
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required_options.push(:url) if default_url.blank?
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attr_reader :url, :
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private :url, :
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private :url, :user_api_key, :read_timeout
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def initialize(options)
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require '
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require 'multi_json'
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# PINCHED FROM https://gist.github.com/736721
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def create(url, body, handler)
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def create(url, body, handler)
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perform(:post, url, jsonify(body, action: :create)) do |response|
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case response
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when Net::HTTPCreated then handler.success(parse_json_from(response))
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def create_from_file(url, file, filename, content_type, handler)
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def create_from_file(url, file, filename, content_type, handler)
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perform_for_file(:post, url, file, filename, content_type) do |response|
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case response
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unless body.nil?
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request.content_type = 'application/json'
|
115
115
|
# request.body = body.to_json
|
116
|
-
request.body =
|
116
|
+
request.body = MultiJson.dump(body)
|
117
117
|
end
|
118
118
|
yield(connection.request(request))
|
119
119
|
end
|
@@ -146,12 +146,12 @@ module Sequencescape::Api::ConnectionFactory::Actions
|
|
146
146
|
def parse_json_from(response)
|
147
147
|
raise ServerError, 'server returned non-JSON content' unless response.content_type == 'application/json'
|
148
148
|
|
149
|
-
|
149
|
+
MultiJson.load(StringIO.new(response.body))
|
150
150
|
end
|
151
151
|
private :parse_json_from
|
152
152
|
|
153
153
|
def headers
|
154
|
-
{ 'Accept' => 'application/json', 'Cookie' => "
|
154
|
+
{ 'Accept' => 'application/json', 'Cookie' => "api_key=#{user_api_key}" }.tap do |standard|
|
155
155
|
standard.merge!('X-Sequencescape-Client-ID' => @authorisation) unless @authorisation.blank?
|
156
156
|
end
|
157
157
|
end
|
@@ -82,11 +82,9 @@ end
|
|
82
82
|
class Sequencescape::Api::PageOfResults
|
83
83
|
include Enumerable
|
84
84
|
|
85
|
-
attr_reader :api, :actions
|
85
|
+
attr_reader :api, :actions, :size
|
86
86
|
private :api, :actions
|
87
87
|
|
88
|
-
attr_reader :size
|
89
|
-
|
90
88
|
def initialize(api, json, &block)
|
91
89
|
@api = api
|
92
90
|
@ctor = block
|
@@ -1,7 +1,6 @@
|
|
1
1
|
module Sequencescape::Api::Rails
|
2
2
|
# Including this module into your Rails ApplicationController adds a before filter that will
|
3
|
-
# provide a
|
4
|
-
# use, accessible through `api`.
|
3
|
+
# provide a Sequencescape::Api instance to use, accessible through `api`.
|
5
4
|
module ApplicationController
|
6
5
|
def self.included(base) # rubocop:todo Metrics/MethodLength
|
7
6
|
base.class_eval do
|
@@ -20,32 +19,29 @@ module Sequencescape::Api::Rails
|
|
20
19
|
end
|
21
20
|
end
|
22
21
|
|
22
|
+
private
|
23
|
+
|
23
24
|
def api_class
|
24
25
|
::Sequencescape::Api
|
25
26
|
end
|
26
|
-
private :api_class
|
27
27
|
|
28
28
|
def configure_api
|
29
|
-
@api = api_class.new(
|
29
|
+
@api = api_class.new(api_connection_options)
|
30
30
|
end
|
31
|
-
private :configure_api
|
32
31
|
|
33
32
|
def api_connection_options
|
34
|
-
{}
|
33
|
+
raise Sequencescape::Api::Error, "api_connection_options not implemented for #{self.class}"
|
35
34
|
end
|
36
|
-
private :api_connection_options
|
37
35
|
|
38
36
|
def sequencescape_api_error_handler(exception)
|
39
37
|
Rails.logger.error "#{exception}, #{exception.backtrace}"
|
40
38
|
raise StandardError, "There is an issue with the API connection to Sequencescape (#{exception.message})"
|
41
39
|
end
|
42
|
-
private :sequencescape_api_error_handler
|
43
40
|
|
44
41
|
def sequencescape_api_unauthenticated_handler(exception)
|
45
42
|
Rails.logger.error "#{exception}, #{exception.backtrace}"
|
46
43
|
raise StandardError, 'You are not authenticated; please visit the WTSI login page'
|
47
44
|
end
|
48
|
-
private :sequencescape_api_unauthenticated_handler
|
49
45
|
end
|
50
46
|
|
51
47
|
# Including this module into your Rails model indicates that the model is associated with
|
data/lib/sequencescape/order.rb
CHANGED
data/sequencescape-api.gemspec
CHANGED
@@ -10,6 +10,7 @@ Gem::Specification.new do |s|
|
|
10
10
|
s.homepage = ''
|
11
11
|
s.summary = 'Gem for the client side of the Sequencescape API'
|
12
12
|
s.description = 'Provides all of the necessary code for interacting with the Sequencescape API'
|
13
|
+
s.required_ruby_version = '> 2.4'
|
13
14
|
|
14
15
|
s.rubyforge_project = 'sequencescape-client-api'
|
15
16
|
|
@@ -18,16 +19,27 @@ Gem::Specification.new do |s|
|
|
18
19
|
s.executables = `git ls-files -- bin/*`.split("\n").map { |f| File.basename(f) }
|
19
20
|
s.require_paths = ['lib']
|
20
21
|
|
22
|
+
s.post_install_message = <<~POST_INSTALL
|
23
|
+
sequencescape-client-api has dropped 'yajl-ruby' in favour of 'multi_json',
|
24
|
+
https://rubygems.org/gems/multi_json. This will automatically pick the
|
25
|
+
fastest json encoder in your Gemfile, falling back to the default encoder.
|
26
|
+
|
27
|
+
For best performance you are strongly encouraged to add a custom json
|
28
|
+
encoder to your project. eg. bundle install oj.
|
29
|
+
POST_INSTALL
|
30
|
+
|
21
31
|
s.add_dependency('activemodel', '>= 5.0.0')
|
22
|
-
s.add_dependency('activesupport', '>= 5.0.0')
|
32
|
+
s.add_dependency('activesupport', '>= 5.0.0', '< 6.1.0')
|
23
33
|
s.add_dependency('i18n')
|
24
|
-
s.add_dependency('
|
34
|
+
s.add_dependency('multi_json')
|
25
35
|
|
26
36
|
s.add_development_dependency('pry')
|
27
37
|
s.add_development_dependency('rake')
|
28
38
|
s.add_development_dependency('redcarpet')
|
29
39
|
s.add_development_dependency('rspec', '~> 2.11.0')
|
30
|
-
s.add_development_dependency('rubocop', '~>
|
40
|
+
s.add_development_dependency('rubocop', '~> 1.3.1')
|
31
41
|
s.add_development_dependency('webmock')
|
32
42
|
s.add_development_dependency('yard')
|
43
|
+
# Add a json encoder for development
|
44
|
+
s.add_development_dependency('oj')
|
33
45
|
end
|
@@ -5,7 +5,7 @@ require 'spec_helper'
|
|
5
5
|
describe 'Handling authentication issues' do
|
6
6
|
stub_request_from('retrieve-root-with-an-unauthorised-client') { response('client-fails-authentication') }
|
7
7
|
|
8
|
-
subject { Sequencescape::Api.new(url: 'http://localhost:3000/',
|
8
|
+
subject { Sequencescape::Api.new(url: 'http://localhost:3000/', user_api_key: 'single-sign-on-cookie') }
|
9
9
|
|
10
10
|
it 'raises an exception' do
|
11
11
|
-> { subject }.should raise_error(Sequencescape::Api::UnauthenticatedError)
|
@@ -17,7 +17,7 @@ describe 'Retrieving the root URL' do
|
|
17
17
|
is_working_as_an_unauthorised_client
|
18
18
|
|
19
19
|
context 'with no namespace' do
|
20
|
-
subject { Sequencescape::Api.new(url: 'http://localhost:3000/',
|
20
|
+
subject { Sequencescape::Api.new(url: 'http://localhost:3000/', user_api_key: 'single-sign-on-cookie') }
|
21
21
|
|
22
22
|
Unauthorised::MODELS_THROUGH_API.each do |model|
|
23
23
|
it "provides the #{model} through the API instance" do
|
@@ -25,7 +25,7 @@ describe 'Retrieving the root URL' do
|
|
25
25
|
end
|
26
26
|
|
27
27
|
it "errors because Sequencescape::#{model.to_s.classify} is not defined" do
|
28
|
-
#
|
28
|
+
# NOTE: Using a regex as > Ruby 2.3 'DidYouMean' changes the error message slightly.
|
29
29
|
lambda {
|
30
30
|
subject.send(model.to_sym)
|
31
31
|
}.should raise_error(NameError,
|
@@ -35,7 +35,7 @@ module ContractHelper
|
|
35
35
|
@url = "http://localhost:3000#{match[:path]}"
|
36
36
|
@conditions = {}
|
37
37
|
@conditions[:headers] = Hash[*match[:headers].split(/\r?\n/).map { |l| l.split(':') }.flatten.map(&:strip)]
|
38
|
-
@conditions[:body] =
|
38
|
+
@conditions[:body] = MultiJson.dump(MultiJson.load(match[:body])) unless match[:body].blank?
|
39
39
|
end
|
40
40
|
end
|
41
41
|
|
@@ -96,7 +96,7 @@ module ContractHelper
|
|
96
96
|
end
|
97
97
|
let(:api) do
|
98
98
|
Sequencescape::Api.new(
|
99
|
-
url: 'http://localhost:3000/',
|
99
|
+
url: 'http://localhost:3000/', user_api_key: 'single-sign-on-cookie',
|
100
100
|
namespace: Unauthorised
|
101
101
|
)
|
102
102
|
end
|
@@ -107,7 +107,7 @@ module ContractHelper
|
|
107
107
|
|
108
108
|
let(:api) do
|
109
109
|
Sequencescape::Api.new(
|
110
|
-
url: 'http://localhost:3000/',
|
110
|
+
url: 'http://localhost:3000/', user_api_key: 'single-sign-on-cookie',
|
111
111
|
authorisation: 'authorised!', namespace: Authenticated
|
112
112
|
)
|
113
113
|
end
|
metadata
CHANGED
@@ -1,7 +1,7 @@
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
2
2
|
name: sequencescape-client-api
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
version: 0.
|
4
|
+
version: 0.6.0.pre.rc1
|
5
5
|
platform: ruby
|
6
6
|
authors:
|
7
7
|
- Matthew Denner
|
@@ -10,7 +10,7 @@ authors:
|
|
10
10
|
autorequire:
|
11
11
|
bindir: bin
|
12
12
|
cert_chain: []
|
13
|
-
date:
|
13
|
+
date: 2021-07-28 00:00:00.000000000 Z
|
14
14
|
dependencies:
|
15
15
|
- !ruby/object:Gem::Dependency
|
16
16
|
name: activemodel
|
@@ -33,6 +33,9 @@ dependencies:
|
|
33
33
|
- - ">="
|
34
34
|
- !ruby/object:Gem::Version
|
35
35
|
version: 5.0.0
|
36
|
+
- - "<"
|
37
|
+
- !ruby/object:Gem::Version
|
38
|
+
version: 6.1.0
|
36
39
|
type: :runtime
|
37
40
|
prerelease: false
|
38
41
|
version_requirements: !ruby/object:Gem::Requirement
|
@@ -40,6 +43,9 @@ dependencies:
|
|
40
43
|
- - ">="
|
41
44
|
- !ruby/object:Gem::Version
|
42
45
|
version: 5.0.0
|
46
|
+
- - "<"
|
47
|
+
- !ruby/object:Gem::Version
|
48
|
+
version: 6.1.0
|
43
49
|
- !ruby/object:Gem::Dependency
|
44
50
|
name: i18n
|
45
51
|
requirement: !ruby/object:Gem::Requirement
|
@@ -55,19 +61,19 @@ dependencies:
|
|
55
61
|
- !ruby/object:Gem::Version
|
56
62
|
version: '0'
|
57
63
|
- !ruby/object:Gem::Dependency
|
58
|
-
name:
|
64
|
+
name: multi_json
|
59
65
|
requirement: !ruby/object:Gem::Requirement
|
60
66
|
requirements:
|
61
67
|
- - ">="
|
62
68
|
- !ruby/object:Gem::Version
|
63
|
-
version:
|
69
|
+
version: '0'
|
64
70
|
type: :runtime
|
65
71
|
prerelease: false
|
66
72
|
version_requirements: !ruby/object:Gem::Requirement
|
67
73
|
requirements:
|
68
74
|
- - ">="
|
69
75
|
- !ruby/object:Gem::Version
|
70
|
-
version:
|
76
|
+
version: '0'
|
71
77
|
- !ruby/object:Gem::Dependency
|
72
78
|
name: pry
|
73
79
|
requirement: !ruby/object:Gem::Requirement
|
@@ -130,14 +136,14 @@ dependencies:
|
|
130
136
|
requirements:
|
131
137
|
- - "~>"
|
132
138
|
- !ruby/object:Gem::Version
|
133
|
-
version:
|
139
|
+
version: 1.3.1
|
134
140
|
type: :development
|
135
141
|
prerelease: false
|
136
142
|
version_requirements: !ruby/object:Gem::Requirement
|
137
143
|
requirements:
|
138
144
|
- - "~>"
|
139
145
|
- !ruby/object:Gem::Version
|
140
|
-
version:
|
146
|
+
version: 1.3.1
|
141
147
|
- !ruby/object:Gem::Dependency
|
142
148
|
name: webmock
|
143
149
|
requirement: !ruby/object:Gem::Requirement
|
@@ -166,6 +172,20 @@ dependencies:
|
|
166
172
|
- - ">="
|
167
173
|
- !ruby/object:Gem::Version
|
168
174
|
version: '0'
|
175
|
+
- !ruby/object:Gem::Dependency
|
176
|
+
name: oj
|
177
|
+
requirement: !ruby/object:Gem::Requirement
|
178
|
+
requirements:
|
179
|
+
- - ">="
|
180
|
+
- !ruby/object:Gem::Version
|
181
|
+
version: '0'
|
182
|
+
type: :development
|
183
|
+
prerelease: false
|
184
|
+
version_requirements: !ruby/object:Gem::Requirement
|
185
|
+
requirements:
|
186
|
+
- - ">="
|
187
|
+
- !ruby/object:Gem::Version
|
188
|
+
version: '0'
|
169
189
|
description: Provides all of the necessary code for interacting with the Sequencescape
|
170
190
|
API
|
171
191
|
email:
|
@@ -176,6 +196,7 @@ executables: []
|
|
176
196
|
extensions: []
|
177
197
|
extra_rdoc_files: []
|
178
198
|
files:
|
199
|
+
- ".github/workflows/ruby.yml"
|
179
200
|
- ".gitignore"
|
180
201
|
- ".rspec"
|
181
202
|
- ".rubocop.yml"
|
@@ -493,23 +514,28 @@ files:
|
|
493
514
|
homepage: ''
|
494
515
|
licenses: []
|
495
516
|
metadata: {}
|
496
|
-
post_install_message:
|
517
|
+
post_install_message: |
|
518
|
+
sequencescape-client-api has dropped 'yajl-ruby' in favour of 'multi_json',
|
519
|
+
https://rubygems.org/gems/multi_json. This will automatically pick the
|
520
|
+
fastest json encoder in your Gemfile, falling back to the default encoder.
|
521
|
+
|
522
|
+
For best performance you are strongly encouraged to add a custom json
|
523
|
+
encoder to your project. eg. bundle install oj.
|
497
524
|
rdoc_options: []
|
498
525
|
require_paths:
|
499
526
|
- lib
|
500
527
|
required_ruby_version: !ruby/object:Gem::Requirement
|
501
528
|
requirements:
|
502
|
-
- - "
|
529
|
+
- - ">"
|
503
530
|
- !ruby/object:Gem::Version
|
504
|
-
version: '
|
531
|
+
version: '2.4'
|
505
532
|
required_rubygems_version: !ruby/object:Gem::Requirement
|
506
533
|
requirements:
|
507
|
-
- - "
|
534
|
+
- - ">"
|
508
535
|
- !ruby/object:Gem::Version
|
509
|
-
version:
|
536
|
+
version: 1.3.1
|
510
537
|
requirements: []
|
511
|
-
|
512
|
-
rubygems_version: 2.7.6.2
|
538
|
+
rubygems_version: 3.1.4
|
513
539
|
signing_key:
|
514
540
|
specification_version: 4
|
515
541
|
summary: Gem for the client side of the Sequencescape API
|