serrano 0.5.0 → 1.0.0

checksums.yaml

@@ -1,7 +1,7 @@
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data/.github/workflows/ruby.yml

@@ -0,0 +1,30 @@
+name: Ruby
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+jobs:
+  test:
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ ubuntu-latest, macos-latest ]
+        ruby: [ 2.5, 2.6, 2.7 ]
+    runs-on: ${{ matrix.os }}
+    env:
+      CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+    steps:
+    - uses: actions/checkout@v2
+    - name: Setup Ruby
+      uses: ruby/setup-ruby@v1
+      with:
+        ruby-version: ${{ matrix.ruby }}
+    - name: Install dependencies
+      run: bundle install
+    - name: Run tests
+      run: |
+        bundle exec rake install
+        bundle exec rake test TESTOPTS="-v"

data/.gitignore

@@ -26,7 +26,7 @@ build/
 
 # for a library or gem, you might want to ignore these files since the code is
 # intended to run in multiple environments; otherwise, check them in:
-#Gemfile.lock
+Gemfile.lock
 .ruby-version
 .ruby-gemset
 
@@ -36,3 +36,5 @@ build/
 cache/
 
 lib/serrano/response.rb
+
+cursor_testing.rb

data/CHANGELOG.md

@@ -1,3 +1,29 @@
+## 1.0.0 (2020-10-19)
+
+* updated dependency versions
+
+## 0.6.2 (2020-05-29)
+
+* put documentation link back in rubygems page (#132)
+
+## 0.6.0 (2020-02-18)
+
+* query.title (`query_title` query filter as used here) has been removed; use `query_bibliographic` instead (#111)
+* bump `faraday` to version 0.17.1 from 0.17.0 (via dependabot) (#107)
+* bump `json` to version 2.3 from 2.2 (via dependabot) (#109)
+* bump `thor` minimum version (via dependabot) (#110)
+* better checking of filters; always check filters for proper formatting and acceptable types; improve filter tests; link to information on filters (#105) via PR from @beechnut
+
+## 0.5.4 (2019-11-27)
+
+* `Serrano.registration_agency` fixed: a change in an internal function caused this function to fail; tests added to prevent this in the future (#106)
+* bundle update, changes in gemfile.lock
+
+## 0.5.2 (2019-08-07)
+
+* fix url encoding (#51)
+* started using Rubocop; many styling changes (#52)
+
 ## 0.5.0 (2018-04-08)
 
 * Updated dependency versions

data/CODE_OF_CONDUCT.md

@@ -21,5 +21,5 @@ Instances of abusive, harassing, or otherwise unacceptable behavior may be repor
 opening an issue or contacting one or more of the project maintainers.
 
 This Code of Conduct is adapted from the Contributor Covenant
-(http:contributor-covenant.org), version 1.0.0, available at
-http://contributor-covenant.org/version/1/0/0/
+(https://contributor-covenant.org), version 1.0.0, available at
+https://contributor-covenant.org/version/1/0/0/

data/Gemfile

@@ -1,3 +1,5 @@
-source 'https://rubygems.org'
+# frozen_string_literal: true
+
+source "https://rubygems.org"
 
 gemspec

data/LICENSE

@@ -1,4 +1,4 @@
-Copyright (C) 2018 Scott Chamberlain
+Copyright (C) 2020 Scott Chamberlain
 
 Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
 

data/README.md

@@ -2,19 +2,22 @@ serrano
 =========
 
 [![gem version](https://img.shields.io/gem/v/serrano.svg)](https://rubygems.org/gems/serrano)
-[![Build Status](https://api.travis-ci.org/sckott/serrano.png)](https://travis-ci.org/sckott/serrano)
-[![codecov.io](http://codecov.io/github/sckott/serrano/coverage.svg?branch=master)](http://codecov.io/github/sckott/serrano?branch=master)
+[![Ruby](https://github.com/sckott/serrano/workflows/Ruby/badge.svg)](https://github.com/sckott/serrano/actions)
+[![codecov.io](https://codecov.io/github/sckott/serrano/coverage.svg?branch=master)](https://codecov.io/github/sckott/serrano?branch=master)
 [![DOI](https://zenodo.org/badge/2600/sckott/serrano.svg)](https://zenodo.org/badge/latestdoi/2600/sckott/serrano)
+[![Ruby Style Guide](https://img.shields.io/badge/code_style-standard-brightgreen.svg)](https://github.com/testdouble/standard)
 
 `serrano` is a low level client for Crossref APIs
 
-Docs: http://www.rubydoc.info/gems/serrano
+Docs: https://www.rubydoc.info/gems/serrano
 
 Other Crossref API clients:
 
 - Python: [habanero](https://github.com/sckott/habanero)
 - R: [rcrossref](https://github.com/ropensci/rcrossref)
 
+Crossref's API issue tracker: https://gitlab.com/crossref/issues
+
 ## Changes
 
 For changes see the [Changelog][changelog]
@@ -44,7 +47,7 @@ Other methods:
 
 Note about searching:
 
-You are using the Crossref search API described at https://github.com/CrossRef/rest-api-doc/blob/master/rest_api.md. When you search with query terms, on Crossref servers they are not searching full text, or even abstracts of articles, but only what is available in the data that is returned to you. That is, they search article titles, authors, etc. For some discussion on this, see https://github.com/CrossRef/rest-api-doc/issues/101
+You are using the Crossref search API described at https://github.com/CrossRef/rest-api-doc When you search with query terms, on Crossref servers they are not searching full text, or even abstracts of articles, but only what is available in the data that is returned to you. That is, they search article titles, authors, etc. For some discussion on this, see https://gitlab.com/crossref/issues/issues/101
 
 Rate limits:
 
@@ -60,6 +63,11 @@ To get in the polite pool it's a good idea now to include a `mailto` email
 address. See docs for more information. TLDR: set your email in an env var `CROSSREF_EMAIL`.
 
 
+URL Encoding:
+
+We do URL encoding of DOIs for you for all methods except `Serrano.citation_count` which doesn't work if you encode DOIs beforehand. We use `ERB::Util.url_encode` to encode.
+
+
 ## Install
 
 ### Release version
@@ -115,6 +123,12 @@ Search works by query string
 Serrano.works(query: "ecology")
 ```
 
+Search works using metadata filters. See [CrossRef filter docs](https://github.com/CrossRef/rest-api-doc#filter-names).
+
+```ruby
+Serrano.works(query: "ecology", filter: { has_abstract: true })
+```
+
 Search journals by publisher name
 
 ```ruby
@@ -181,8 +195,8 @@ Commands:
 * License: MIT
 
 [crapi]: https://github.com/CrossRef/rest-api-doc/blob/master/rest_api.md
-[cn]: http://www.crosscite.org/cn/
-[tdm]: http://www.crossref.org/tdm/
-[ccount]: http://labs.crossref.org/openurl/
+[cn]: https://citation.crosscite.org/docs.html
+[tdm]: https://www.crossref.org/education/retrieve-metadata/rest-api/text-and-data-mining/
+[ccount]: https://labs.crossref.org/openurl/
 [csl]: https://github.com/citation-style-language/styles
 [changelog]: https://github.com/sckott/serrano/blob/master/CHANGELOG.md

data/Rakefile

@@ -1,19 +1,23 @@
+# frozen_string_literal: true
+
 require "bundler/gem_tasks"
-require 'rake/testtask'
+require "rake/testtask"
+require "standard"
+require "standard/rake"
 
 Rake::TestTask.new do |t|
   t.libs << "test"
-  t.test_files = FileList['test/test-*.rb']
+  t.test_files = FileList["test/test_*.rb"]
   t.verbose = true
   t.warning = false
 end
 
 desc "Run tests"
-task :default => :test
+task default: :test
 
 desc "Build serrano docs"
 task :docs do
-	system "yardoc"
+  system "yardoc"
 end
 
 desc "bundle install"
@@ -28,15 +32,15 @@ end
 
 desc "Build serrano"
 task :build do
-	system "gem build serrano.gemspec"
+  system "gem build serrano.gemspec"
 end
 
 desc "Install serrano"
-task :install => [:bundle, :build] do
-	system "gem install serrano-#{Serrano::VERSION}.gem"
+task install: %i[bundle build] do
+  system "gem install serrano-#{Serrano::VERSION}.gem"
 end
 
 desc "Release to Rubygems"
-task :release => :build do
+task release: :build do
   system "gem push serrano-#{Serrano::VERSION}.gem"
 end

data/bin/serrano

@@ -1,14 +1,15 @@
 #!/usr/bin/env ruby
+# frozen_string_literal: true
 
-require "thor"
-require "serrano"
-require "multi_json"
+require 'thor'
+require 'serrano'
+require 'multi_json'
 
 class Sr < Thor
   include Thor::Actions
   # class_option :json, :type => :boolean, :default => false
 
-  desc "works [DOIs]", "Get works by DOIs"
+  desc 'works [DOIs]', 'Get works by DOIs'
   long_desc <<-LONGDESC
     `serrano works` accepts one or more DOIs to search for works
 
@@ -47,17 +48,17 @@ class Sr < Thor
     \x5"http://orcid.org/0000-0003-4087-8021"
     \x5"http://orcid.org/0000-0002-2076-5452"
   LONGDESC
-  option :json, :type => :boolean, :default => false
-  option :filter, :type => :hash, :default => nil
-  option :limit, :type => :numeric, :default => nil
-  def works(ids=nil)
-    if ids.nil?
-      out = Serrano.works(filter: options[:filter], limit: options[:limit])
-    else
-      out = Serrano.works(ids: ids.split(","), filter: options[:filter])
-    end
+  option :json, type: :boolean, default: false
+  option :filter, type: :hash, default: nil
+  option :limit, type: :numeric, default: nil
+  def works(ids = nil)
+    out = if ids.nil?
+            Serrano.works(filter: options[:filter], limit: options[:limit])
+          else
+            Serrano.works(ids: ids.split(','), filter: options[:filter])
+          end
     if !options[:json]
-      out = out.collect { |x| x['message'].select { |k,v| k[/DOI|type|title/] } }
+      out = out.collect { |x| x['message'].select { |k, _v| k[/DOI|type|title/] } }
       out.each do |x|
         puts 'DOI: ' + x['DOI'].to_s
         puts 'type: ' + x['type']
@@ -69,7 +70,7 @@ class Sr < Thor
     end
   end
 
-  desc "members [member IDs]", "Get members by id"
+  desc 'members [member IDs]', 'Get members by id'
   long_desc <<-LONGDESC
     `serrano members` accepts one or more Crossref member IDs
 
@@ -96,26 +97,26 @@ class Sr < Thor
 
     24 7 45 31 22 67 72 17 53 75 0 68 12 16 50 79 40 18 40 195
   LONGDESC
-  option :json, :type => :boolean, :default => false
-  option :query, :type => :string, :default => nil
-  option :limit, :type => :numeric, :default => nil
-  option :works, :type => :boolean, :default => false
-  def members(ids=nil)
+  option :json, type: :boolean, default: false
+  option :query, type: :string, default: nil
+  option :limit, type: :numeric, default: nil
+  option :works, type: :boolean, default: false
+  def members(ids = nil)
     if ids.nil?
       out = Serrano.members(query: options[:query], limit: options[:limit],
-        works: options[:works])
+                            works: options[:works])
     else
-      out = Serrano.members(ids: ids.split(","), query: options[:query], limit: options[:limit],
-        works: options[:works])
+      out = Serrano.members(ids: ids.split(','), query: options[:query], limit: options[:limit],
+                            works: options[:works])
     end
 
     if !options[:json]
       if !options[:works]
-        if out.class == Hash
-          out = out['message']['items']
-        else
-          out = out.collect { |x| x['message'] }
-        end
+        out = if out.class == Hash
+                out['message']['items']
+              else
+                out.collect { |x| x['message'] }
+              end
 
         # out = out.collect { |x| x['message'].select { |k,v| k[/id|primary-name/] } }
         out.each do |x|
@@ -131,8 +132,7 @@ class Sr < Thor
     end
   end
 
-
-  desc "prefixes [DOI prefixes]", "Search for prefixes by DOI prefix"
+  desc 'prefixes [DOI prefixes]', 'Search for prefixes by DOI prefix'
   long_desc <<-LONGDESC
     `serrano prefixes` accepts one or more Crossref member IDs
 
@@ -162,24 +162,24 @@ class Sr < Thor
     \x5"Co-Action Publishing"
     \x5"Oxford University Press (OUP)"
   LONGDESC
-  option :json, :type => :boolean, :default => false
-  option :limit, :type => :numeric, :default => nil
-  option :works, :type => :boolean, :default => false
-  def prefixes(ids=nil)
-    if ids.nil?
-      out = Serrano.prefixes(limit: options[:limit], works: options[:works])
-    else
-      out = Serrano.prefixes(ids: ids.split(","), limit: options[:limit],
-        works: options[:works])
-    end
+  option :json, type: :boolean, default: false
+  option :limit, type: :numeric, default: nil
+  option :works, type: :boolean, default: false
+  def prefixes(ids = nil)
+    out = if ids.nil?
+            Serrano.prefixes(limit: options[:limit], works: options[:works])
+          else
+            Serrano.prefixes(ids: ids.split(','), limit: options[:limit],
+                             works: options[:works])
+          end
 
     if !options[:json]
       if !options[:works]
-        if out.class == Hash
-          out = out['message']['items']
-        else
-          out = out.collect { |x| x['message'] }
-        end
+        out = if out.class == Hash
+                out['message']['items']
+              else
+                out.collect { |x| x['message'] }
+              end
 
         out.each do |x|
           puts 'member: ' + x['member']
@@ -195,7 +195,7 @@ class Sr < Thor
     end
   end
 
-  desc "funders [funder IDs]", "Search for funders by DOI prefix"
+  desc 'funders [funder IDs]', 'Search for funders by DOI prefix'
   long_desc <<-LONGDESC
     `serrano funders` accepts one or more Crossref funder IDs
 
@@ -226,26 +226,26 @@ class Sr < Thor
 
     $ serrano funders 10.13039/100000001 --works=true --limit=2
   LONGDESC
-  option :json, :type => :boolean, :default => false
-  option :query, :type => :string, :default => nil
-  option :limit, :type => :numeric, :default => nil
-  option :works, :type => :boolean, :default => false
-  def funders(ids=nil)
+  option :json, type: :boolean, default: false
+  option :query, type: :string, default: nil
+  option :limit, type: :numeric, default: nil
+  option :works, type: :boolean, default: false
+  def funders(ids = nil)
     if ids.nil?
       out = Serrano.funders(query: options[:query], limit: options[:limit],
-        works: options[:works])
+                            works: options[:works])
     else
-      out = Serrano.funders(ids: ids.split(","), query: options[:query], limit: options[:limit],
-        works: options[:works])
+      out = Serrano.funders(ids: ids.split(','), query: options[:query], limit: options[:limit],
+                            works: options[:works])
     end
 
     if !options[:json]
       if !options[:works]
-        if out.class == Hash
-          out = out['message']['items']
-        else
-          out = out.collect { |x| x['message'] }
-        end
+        out = if out.class == Hash
+                out['message']['items']
+              else
+                out.collect { |x| x['message'] }
+              end
 
         out.each do |x|
           puts 'id: ' + x['id']
@@ -261,8 +261,7 @@ class Sr < Thor
     end
   end
 
-
-  desc "journals [journal ISSNs]", "Search for journals by ISSNs"
+  desc 'journals [journal ISSNs]', 'Search for journals by ISSNs'
   long_desc <<-LONGDESC
     `serrano journals` accepts one or more journal ISSNs
 
@@ -293,26 +292,26 @@ class Sr < Thor
 
     $ serrano journals 2167-8359 --query=ecology --works=true --limit=2
   LONGDESC
-  option :json, :type => :boolean, :default => false
-  option :query, :type => :string, :default => nil
-  option :limit, :type => :numeric, :default => nil
-  option :works, :type => :boolean, :default => false
-  def journals(ids=nil)
+  option :json, type: :boolean, default: false
+  option :query, type: :string, default: nil
+  option :limit, type: :numeric, default: nil
+  option :works, type: :boolean, default: false
+  def journals(ids = nil)
     if ids.nil?
       out = Serrano.journals(query: options[:query], limit: options[:limit],
-        works: options[:works])
+                             works: options[:works])
     else
-      out = Serrano.journals(ids: ids.split(","), query: options[:query], limit: options[:limit],
-        works: options[:works])
+      out = Serrano.journals(ids: ids.split(','), query: options[:query], limit: options[:limit],
+                             works: options[:works])
     end
 
     if !options[:json]
       if !options[:works]
-        if out.class == Hash
-          out = out['message']['items']
-        else
-          out = out.collect { |x| x['message'] }
-        end
+        out = if out.class == Hash
+                out['message']['items']
+              else
+                out.collect { |x| x['message'] }
+              end
 
         out.each do |x|
           puts 'ISSN: ' + x['ISSN'][0]
@@ -328,7 +327,7 @@ class Sr < Thor
     end
   end
 
-  desc "types [type name]", "Search for types by name"
+  desc 'types [type name]', 'Search for types by name'
   long_desc <<-LONGDESC
     `serrano types` accepts one or more type names
 
@@ -359,20 +358,20 @@ class Sr < Thor
 
     $ serrano types dissertation --works --limit=2
   LONGDESC
-  option :json, :type => :boolean, :default => false
-  option :works, :type => :boolean, :default => false
-  option :limit, :type => :numeric, :default => nil
+  option :json, type: :boolean, default: false
+  option :works, type: :boolean, default: false
+  option :limit, type: :numeric, default: nil
   def types(*ids)
     out = Serrano.types(ids: ids, limit: options[:limit],
-      works: options[:works])
+                        works: options[:works])
 
     if !options[:json]
       if !options[:works]
-        if out.class == Hash
-          out = out['message']['items']
-        else
-          out = out.collect { |x| x['message'] }
-        end
+        out = if out.class == Hash
+                out['message']['items']
+              else
+                out.collect { |x| x['message'] }
+              end
 
         out.each do |x|
           puts 'id: ' + x['id']
@@ -387,7 +386,7 @@ class Sr < Thor
     end
   end
 
-  desc "licenses", "Search for licenses by name"
+  desc 'licenses', 'Search for licenses by name'
   long_desc <<-LONGDESC
     `serrano licenses` accepts one or more type names
 
@@ -416,8 +415,8 @@ class Sr < Thor
     "National Science Foundation"
     \x5"U.S. Department of Energy"
   LONGDESC
-  option :json, :type => :boolean, :default => false
-  option :query, :type => :string, :default => nil
+  option :json, type: :boolean, default: false
+  option :query, type: :string, default: nil
   def licenses
     out = Serrano.licenses(query: options[:query])
     if !options[:json]
@@ -432,7 +431,7 @@ class Sr < Thor
     end
   end
 
-  desc "contneg", "Content negotiation"
+  desc 'contneg', 'Content negotiation'
   long_desc <<-LONGDESC
     `serrano contneg` accepts a DOI
 
@@ -444,15 +443,15 @@ class Sr < Thor
 
     Murtaugh PA (2014).  In defense of P values . Ecology 95: 611–617.
   LONGDESC
-  option :format, :type => :string, :default => "text"
-  option :style, :type => :string, :default => "apa"
-  option :locale, :type => :string, :default => "en-US"
+  option :format, type: :string, default: 'text'
+  option :style, type: :string, default: 'apa'
+  option :locale, type: :string, default: 'en-US'
   def contneg(ids)
     puts Serrano.content_negotiation(ids: ids, format: options[:format], style:
       options[:style], locale: options[:locale])
   end
 
-  desc "version", "Get serrano version"
+  desc 'version', 'Get serrano version'
   def version
     puts Serrano::VERSION
   end
@@ -460,11 +459,11 @@ class Sr < Thor
   private
 
   def print_works(data)
-    if data.is_a? Array
-      data = data[0]['message']['items']
-    else
-      data = data.collect { |x| x['message'].select { |k,v| k[/DOI|type|title/] } }
-    end
+    data = if data.is_a? Array
+             data[0]['message']['items']
+           else
+             data.collect { |x| x['message'].select { |k, _v| k[/DOI|type|title/] } }
+           end
     data.each do |x|
       puts 'DOI: ' + x['DOI']
       puts 'type: ' + x['type']
@@ -472,7 +471,6 @@ class Sr < Thor
       puts
     end
   end
-
 end
 
 Sr.start(ARGV)