cirneco 0.8.6 → 0.8.7

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 6d25a0884369e841925bac38f6bbeb3b7790d48c
-  data.tar.gz: 6408f829c40940f06ce392354aec25ebc8e60585
+  metadata.gz: f31aa95c4a43e1374ff505a52fe6a812576f4b6e
+  data.tar.gz: 7ec6ab0d1ade494caf4e5844d1c6e3dcb033ea44
 SHA512:
-  metadata.gz: 1a750ad1c2f9396cc6eb200783d141159538e4fe815804a0ffdbcf2c8a279dda426d52997afb7e9d17d66ca56b699998e94f91e5d79537002a9348c38cb350cd
-  data.tar.gz: 485343087a69b16061854e02ceaab1f620a7f035c75d1b0a796056d03d48fd65b14cc43cacf091f0aa870a4c008272ebf15bde69a88adc52660dccd1d55fb1b9
+  metadata.gz: 4c02aabc718588da40567d5d7bf8a290e956e8ea2cc580e42aa7fbc93d8b5cf5c59f2b172ebae941a53f4dfcde3e49882704c236e180f5b8fbaaaa68523ecdad
+  data.tar.gz: 13362e8c0cc37c13725aa173bbc05ee83a68e05b63238b6b63557fd80ef7d77b5351c7b94f1dbfd19d2ee37a65d0d963ada43139d7d409faaa08b20ee33e2a3f

data/.travis.yml

@@ -6,9 +6,6 @@ before_install:
 - wget https://github.com/jgm/pandoc/releases/download/1.15.2/pandoc-1.15.2-1-amd64.deb
 - sudo dpkg -i pandoc-1.15.2-1-amd64.deb
 - rm pandoc-1.15.2-1-amd64.deb
-- sudo add-apt-repository ppa:kalakris/cmake -y
-- sudo apt-get update -q
-- sudo apt-get install cmake -y
 
 install:
 - travis_retry bundle install

data/Gemfile.lock

@@ -1,7 +1,7 @@
 PATH
   remote: .
   specs:
-    cirneco (0.8.6)
+    cirneco (0.8.7)
       activesupport (~> 4.2, >= 4.2.5)
       base32-crockford-checksum (~> 0.2.2)
       bergamasco (~> 0.3)
@@ -52,7 +52,7 @@ GEM
     json (1.8.3)
     loofah (2.0.3)
       nokogiri (>= 1.5.9)
-    maremma (3.1)
+    maremma (3.1.1)
       activesupport (~> 4.2, >= 4.2.5)
       builder (~> 3.2, >= 3.2.2)
       excon (~> 0.45.0)
@@ -122,4 +122,4 @@ DEPENDENCIES
   webmock (~> 1.22, >= 1.22.3)
 
 BUNDLED WITH
-   1.12.5
+   1.13.6

data/lib/cirneco/doi.rb

@@ -105,6 +105,8 @@ module Cirneco
     method_option :sitepath, :default => ENV['SITE_SITEPATH']
     method_option :authorpath, :default => ENV['SITE_AUTHORPATH']
     method_option :referencespath, :default => ENV['SITE_REFERENCESPATH']
+    method_option :source_dir
+    method_option :index_dir
     method_option :csl, :default => ENV['SITE_CSLPATH']
     method_option :number, :aliases => '-n'
     method_option :username, :default => ENV['MDS_USERNAME']
@@ -112,13 +114,7 @@ module Cirneco
     method_option :prefix, :default => ENV['PREFIX']
     method_option :sandbox, :type => :boolean, :force => false
     def mint(url)
-
-      if url.is_a?(Array)
-        response = mint_dois_for_all_urls(url, options)
-      else
-        response = mint_doi_for_url(url, options)
-      end
-
+      response = mint_dois_for_all_urls(url, options)
       puts response
     end
 
@@ -126,6 +122,8 @@ module Cirneco
     method_option :sitepath, :default => ENV['SITE_SITEPATH']
     method_option :authorpath, :default => ENV['SITE_AUTHORPATH']
     method_option :referencespath, :default => ENV['SITE_REFERENCESPATH']
+    method_option :source_dir
+    method_option :index_dir
     method_option :csl, :default => ENV['SITE_CSLPATH']
     method_option :number, :aliases => '-n'
     method_option :username, :default => ENV['MDS_USERNAME']
@@ -133,13 +131,7 @@ module Cirneco
     method_option :prefix, :default => ENV['PREFIX']
     method_option :sandbox, :type => :boolean, :force => false
     def mint_and_hide(url)
-
-      if url.is_a?(Array)
-        response = mint_and_hide_dois_for_all_urls(url, options)
-      else
-        response = mint_and_hide_doi_for_url(url, options)
-      end
-
+      response = mint_and_hide_dois_for_all_urls(url, options)
       puts response
     end
 
@@ -147,19 +139,15 @@ module Cirneco
     method_option :sitepath, :default => ENV['SITE_SITEPATH']
     method_option :authorpath, :default => ENV['SITE_AUTHORPATH']
     method_option :referencespath, :default => ENV['SITE_REFERENCESPATH']
+    method_option :source_dir
+    method_option :index_dir
     method_option :csl, :default => ENV['SITE_CSLPATH']
     method_option :bibliography, :default => ENV['SITE_REFERENCESPATH']
     method_option :username, :default => ENV['MDS_USERNAME']
     method_option :password, :default => ENV['MDS_PASSWORD']
     method_option :sandbox, :type => :boolean, :force => false
     def hide(url)
-
-      if url.is_a?(Array)
-        response = hide_dois_for_all_urls(url, options)
-      else
-        response = hide_doi_for_url(url, options)
-      end
-
+      response = hide_dois_for_all_urls(url, options)
       puts response
     end
   end

data/lib/cirneco/utils.rb

@@ -103,68 +103,66 @@ module Cirneco
 
     # fetch schema.org metadata in JSON-LD format to mint DOI
     def mint_doi_for_url(url, options={})
-      filename = File.basename(url)
-      source_path = options[:source_path] || "/"
-      filepath = Dir.pwd + source_path + filename + ".md"
+      filename, build_path, source_path = filepath_from_url(url, options)
 
-      metadata = generate_metadata_for_work(url, options)
+      metadata = generate_metadata_for_work(build_path, options)
       return "DOI #{metadata["doi"]} not changed for #{filename}" if metadata["doi"] && metadata["date_issued"]
 
       response = post_metadata_for_work(metadata, options)
       return "Errors for DOI #{metadata["doi"]}: #{response.body['errors'].first['title']}\n" if response.body['errors']
 
-      new_metadata = Bergamasco::Markdown.update_file(filepath, "doi" => metadata["doi"], "published" => true)
+      new_metadata = Bergamasco::Markdown.update_file(source_path, "doi" => metadata["doi"], "published" => true)
       "DOI #{new_metadata["doi"]} minted for #{filename}"
     end
 
     # fetch schema.org metadata in JSON-LD format to mint DOI
     def mint_and_hide_doi_for_url(url, options={})
-      filename = File.basename(url)
-      source_path = options[:source_path] || "/"
-      filepath = Dir.pwd + source_path + filename + ".md"
+      filename, build_path, source_path = filepath_from_url(url, options)
 
-      metadata = generate_metadata_for_work(url, options)
+      metadata = generate_metadata_for_work(build_path, options)
       return "DOI #{metadata["doi"]} not changed for #{filename}" if metadata["doi"] && metadata["date_issued"]
 
       response = post_metadata_for_work(metadata, options)
       return "Errors for DOI #{metadata["doi"]}: #{response.body['errors'].first['title']}\n" if response.body['errors']
 
-      new_metadata = Bergamasco::Markdown.update_file(filepath, "doi" => metadata["doi"], "published" => false)
+      new_metadata = Bergamasco::Markdown.update_file(source_path, "doi" => metadata["doi"], "published" => false)
       "DOI #{new_metadata["doi"]} minted and hidden for #{filename}"
     end
 
     # fetch schema.org metadata in JSON-LD format to mint DOI
     # DOIs are never deleted, but we can remove the metadata from the DataCite index
     def hide_doi_for_url(url, options={})
-      filename = File.basename(url)
-      source_path = options[:source_path] || "/"
-      filepath = Dir.pwd + source_path + filename + ".md"
+      filename, build_path, source_path = filepath_from_url(url, options)
 
-      metadata = generate_metadata_for_work(url, options)
-      return "DOI #{metadata["doi"]} not changed for #{filename}" unless metadata["doi"] && metadata["date_issued"]
+      metadata = generate_metadata_for_work(build_path, options)
+      return "No DOI for #{filename}" unless metadata["doi"]
+      return "DOI #{metadata["doi"]} not active for #{filename}" unless metadata["date_issued"]
 
       response = hide_metadata_for_work(metadata, options)
       return "Errors for DOI #{metadata["doi"]}: #{response.body['errors'].first['title']}\n" if response.body['errors']
 
-      new_metadata = Bergamasco::Markdown.update_file(filepath, "published" => false)
+      new_metadata = Bergamasco::Markdown.update_file(source_path, "published" => false)
       "DOI #{metadata["doi"]} hidden for #{filename}"
     end
 
-    def mint_dois_for_all_urls(urls, options={})
-      urls.map do |url|
-        mint_doi_for_url(url, options)
+    def mint_dois_for_all_urls(url, options={})
+      urls = get_urls_for_works(url)
+      urls.map do |u|
+        mint_doi_for_url(u, options)
       end.join("\n")
     end
 
-    def mint_and_hide_dois_for_all_urls(urls, options={})
-      urls.map do |url|
-        mint_and_hide_doi_for_url(url, options)
+    def mint_and_hide_dois_for_all_urls(url, options={})
+      urls = get_urls_for_works(url)
+      urls.map do |u|
+        mint_and_hide_doi_for_url(u, options)
       end.join("\n")
     end
 
-    def hide_dois_for_all_urls(urls, options={})
-      urls.map do |url|
-        hide_doi_for_url(url, options)
+    def hide_dois_for_all_urls(url, options={})
+      urls = get_urls_for_works(url)
+      urls.map do |u|
+        hide_doi_for_url(u, options)
       end.join("\n")
     end
 
@@ -331,6 +329,38 @@ module Cirneco
       end.select { |t| t[:related_identifier_type].present? }
     end
 
+    def filepath_from_url(url, options={})
+      if doi_from_url(url)
+        response = Maremma.head(url, limit: 0)
+        url = response.headers.fetch("Location", "")
+      end
+
+      uri = Addressable::URI.parse(url.gsub(/\/$/, ""))
+      filename = (File.basename(uri.path, ".html").presence || "index") + ".html"
+
+      if filename == "index.html"
+        index_dir = options[:index_dir].presence || "/"
+        build_path = Dir.pwd + index_dir + filename
+        source_path = build_path + ".erb"
+      else
+        source_dir = options[:source_dir].presence || "/"
+        build_path = Dir.pwd + source_dir + filename
+        source_path = build_path + ".md"
+      end
+      [filename, build_path, source_path]
+    end
+
+    def doi_from_url(url)
+      return nil unless url.present?
+
+      if /(http|https):\/\/(dx\.)?doi\.org\/(\w+)/.match(url)
+        uri = Addressable::URI.parse(url)
+        uri.path[1..-1].upcase
+      elsif url.starts_with?("doi:")
+        url[4..-1].upcase
+      end
+    end
+
     def orcid_from_url(url)
       return nil unless url.present?
 

data/lib/cirneco/version.rb

@@ -1,3 +1,3 @@
 module Cirneco
-  VERSION = "0.8.6"
+  VERSION = "0.8.7"
 end

data/spec/api_spec.rb

@@ -66,7 +66,7 @@ describe Cirneco::Work, vcr: true, :order => :defined do
       it 'should get all dois' do
         response = subject.get_dois(options)
         dois = response.body["data"]
-        expect(dois.length).to eq(504)
+        expect(dois.length).to eq(516)
         expect(dois.first).to eq("10.23725/0000-03VC")
       end
 

data/spec/doi_spec.rb

@@ -17,7 +17,7 @@ describe Cirneco::Doi do
   let(:csl) { "spec/fixtures/apa.csl" }
   let(:bibliography) { "spec/fixtures/bibliography.yaml" }
   let(:api_options) { { username: username, password: password, sandbox: true } }
-  let(:mint_options) { { username: username, password: password, sandbox: true, source_path: "/spec/fixtures/", csl: csl, bibliography: bibliography } }
+  let(:mint_options) { { username: username, password: password, sandbox: true, source_dir: "/spec/fixtures/", index_dir: "/spec/fixtures/", csl: csl, bibliography: bibliography } }
 
   describe "MDS DOI API", vcr: true, :order => :defined do
     context "put" do
@@ -105,20 +105,21 @@ describe Cirneco::Doi do
     end
 
     it 'mints dois for list of urls' do
+      filepath = fixture_path + 'index.html'
       subject.options = mint_options
-      expect { subject.mint [filepath] }.to output("DOI 10.5072/0000-03VC minted for #{filename}\n").to_stdout
+      expect { subject.mint filepath }.to output("DOI 10.5072/0000-03VC minted for cool-dois.html\nDOI 10.5072/0000-00SS minted for index.html\n").to_stdout
     end
 
     it 'hides dois for list of urls' do
-      filename = 'cool-dois-minted.html'
-      filepath = fixture_path + filename
-      subject.options = mint_options.merge(filepath: filepath)
-      expect { subject.hide [filepath] }.to output("DOI 10.5072/0000-03WD hidden for #{filename}\n").to_stdout
+      filepath = fixture_path + 'index.html'
+      subject.options = mint_options
+      expect { subject.hide filepath }.to output("No DOI for cool-dois.html\nNo DOI for index.html\n").to_stdout
     end
 
     it 'mints and hides dois for list of urls' do
+      filepath = fixture_path + 'index.html'
       subject.options = mint_options
-      expect { subject.mint_and_hide [filepath] }.to output("DOI 10.5072/0000-03VC minted and hidden for #{filename}\n").to_stdout
+      expect { subject.mint_and_hide filepath }.to output("DOI 10.5072/0000-03VC minted and hidden for cool-dois.html\nDOI 10.5072/0000-00SS minted and hidden for index.html\n").to_stdout
     end
   end
 end

data/spec/fixtures/index-minted.html

@@ -0,0 +1,271 @@
+
+<!DOCTYPE html>
+  <html>
+    <head>
+    <meta charset="utf-8">
+    <!-- (1) Optimize for mobile versions: http://goo.gl/EOpFl -->
+    <meta name="viewport" content="width=device-width, initial-scale=1.0">
+    <!-- (1) force latest IE rendering engine: bit.ly/1c8EiC9 -->
+    <meta http-equiv="X-UA-Compatible" content="IE=edge">
+
+
+    <title>DataCite Blog</title>
+    <meta name="description" content="The DataCite Blog" />
+
+    <meta name="HandheldFriendly" content="True" />
+    <meta name="MobileOptimized" content="320" />
+    <meta name="apple-mobile-web-app-capable" content="yes">
+    <meta name="apple-mobile-web-app-status-bar-style" content="black-translucent">
+
+    <!-- DublinCore Metadata -->
+    <meta property="dc:title" content="DataCite Blog" />
+    <meta property="dc:format" content="text/html" />
+    <meta property="dc:language" content="en" />
+    <meta property="dc:rights" content="CC-BY" />
+    <meta property="dc:source" content="DataCite Blog" />
+    <meta property="dc:subject" content="Scholarly Communication" />
+    <meta property="dc:type" content="website" />
+
+
+    <meta property="og:site_name" content="DataCite Blog" />
+    <meta property="og:description" content="The DataCite Blog" />
+    <meta property="og:image" content="/images/datacite.png" />
+    <meta property="og:type" content="blog" />
+
+    <link href="//fonts.googleapis.com/css?family=Libre+Baskerville:400,400i,700" rel="stylesheet">
+    <link href='//fonts.googleapis.com/css?family=Raleway:400,600,400italic,600italic' rel='stylesheet' type='text/css'>
+    <link href="//maxcdn.bootstrapcdn.com/font-awesome/4.6.1/css/font-awesome.min.css" rel="stylesheet" type='text/css'>
+    <link href="//assets.datacite.org/stylesheets/datacite.css" rel='stylesheet' type='text/css'>
+
+    <link href="/images/favicon.ico" rel="icon" type="image/ico" />
+
+      <script
+        src="//d2wy8f7a9ursnm.cloudfront.net/bugsnag-2.min.js"
+        data-apikey="c37a5861967091a9b42a1a77e235114a">
+      </script>
+
+    <script type="application/ld+json">
+      {"@context":"http://schema.org","@type":"Blog","@id":"https://doi.org/10.5072/0000-NW90","name":"DataCite Blog","alternateName":"MS-25-1785","url":"https://blog.datacite.org/","author":[{"@type":"Person","@id":"http://orcid.org/0000-0002-9300-5278","givenName":"Patricia","familyName":"Cruse","name":"Trisha Cruse"},{"@type":"Person","@id":"http://orcid.org/0000-0001-5952-7630","givenName":"Laura","familyName":"Rueda","name":"Laura Rueda"},{"@type":"Person","@id":"http://orcid.org/0000-0003-3484-6875","givenName":"Kristian","familyName":"Garza","name":"Kristian Garza"},{"@type":"Person","@id":"http://orcid.org/0000-0003-1419-2405","givenName":"Martin","familyName":"Fenner","name":"Martin Fenner"}],"publisher":{"@type":"Organization","name":"DataCite"},"dateCreated":"2015-08-03","datePublished":"2015-08-03","dateModified":"2015-08-03","version":"1.0","description":"The DataCite blog.","license":"https://creativecommons.org/licenses/by/4.0/","hasPart":[{"@type":"BlogPosting","@id":"https://doi.org/10.5438/55E5-T5C0","name":"Cool DOI's","datePublished":"2016-12-15"}]}
+    </script>
+  </head>
+  <body>
+
+<!-- header start -->
+
+<div class="header" id="navtop">
+  <div class="navbar navbar-default navbar-static-top" role="navigation">
+    <div class="container-fluid">
+      <div class="navbar-header"
+        <button type="button" class="navbar-toggle" data-toggle="collapse" data-target=".navbar-collapse">
+          <span class="sr-only">Toggle navigation</span>
+          <span class="icon-bar"></span>
+          <span class="icon-bar"></span>
+          <span class="icon-bar"></span>
+        </button>
+        <a class="navbar-brand" href="/">DataCite Blog</a>
+      </div>
+      <div class="navbar-collapse collapse">
+        <ul class="nav navbar-nav navbar-right">
+          <li class="dropdown">
+            <a href="#" class="dropdown-toggle" data-toggle="dropdown" id="support">Support <span class="caret"></a>
+            <ul class="dropdown-menu" role="menu">
+              <li><a href="mailto:support@datacite.org">Email</a></li>
+              <li><a href="https://github.com/datacite/blog">Source Code</a></li>
+            </ul>
+          </li>
+          <li class="dropdown">
+            <a href="#" class="dropdown-toggle" data-toggle="dropdown" id="sites"><i class='fa fa-th'></i> <span class="caret"></span></a>
+            <ul class="dropdown-menu" role="menu">
+                  <li>
+                    <a href='https://api.datacite.org'>
+                      <i class='fa fa-cogs fa-fw'></i>
+                      API
+                    </a>
+                  </li>
+                  <li>
+                    <a href='https://blog.datacite.org'>
+                      <i class='fa fa-rss fa-fw'></i>
+                      Blog
+                    </a>
+                  </li>
+                  <li>
+                    <a href='http://citation.crosscite.org'>
+                      <i class='fa fa-file-text-o fa-fw'></i>
+                      Citation Formatter
+                    </a>
+                  </li>
+                  <li>
+                    <a href='https://data.datacite.org'>
+                      <i class='fa fa-repeat fa-fw'></i>
+                      Content Resolver
+                    </a>
+                  </li>
+                  <li>
+                    <a href='https://www.datacite.org'>
+                      <i class='fa fa-globe fa-fw'></i>
+                      Homepage
+                    </a>
+                  </li>
+                  <li>
+                    <a href='https://mds.datacite.org'>
+                      <i class='fa fa-database fa-fw'></i>
+                      MDS
+                    </a>
+                  </li>
+                  <li>
+                    <a href='https://oai.datacite.org'>
+                      <i class='fa fa-table fa-fw'></i>
+                      OAI-PMH
+                    </a>
+                  </li>
+                  <li>
+                    <a href='https://profiles.datacite.org'>
+                      <i class='fa fa-user fa-fw'></i>
+                      Profiles
+                    </a>
+                  </li>
+                  <li>
+                    <a href='https://schema.datacite.org'>
+                      <i class='fa fa-file-code-o fa-fw'></i>
+                      Schema
+                    </a>
+                  </li>
+                  <li>
+                    <a href='https://search.datacite.org'>
+                      <i class='fa fa-search fa-fw'></i>
+                      Search
+                    </a>
+                  </li>
+                  <li>
+                    <a href='https://stats.datacite.org'>
+                      <i class='fa fa-bar-chart fa-fw'></i>
+                      Statistics
+                    </a>
+                  </li>
+                  <li>
+                    <a href='http://status.datacite.org'>
+                      <i class='fa fa-calendar-check-o fa-fw'></i>
+                      Status
+                    </a>
+                  </li>
+            </ul>
+          </li>
+        </ul>
+      </div>
+    </div>
+  </div>
+</div>
+
+<!-- header end -->
+
+    <div class="container-fluid">
+  <div class="row">
+    <div class='col-md-8'>
+      <div class="search-wide">
+        <form action="/index.html" method="get" id="search-form" class="form-horizontal" role="form" data-site-url="https://blog.datacite.org" data-search-url="https://api.datacite.org">
+          <div class="input-group">
+            <input type="text" id="query" name="query" placeholder="Search blog" class="form-control">
+            <div class="input-group-btn">
+              <button type="submit" class="btn btn-primary hidden-xs">Search</button>
+            </div>
+          </div>
+        </form>
+      </div>
+    </div>
+  </div>
+  <div id="content"></div>
+  <div class="row">
+    <div class='col-md-4 post-list' id="left-col">
+    </div>
+    <div class='col-md-4 post-list' id="right-col">
+    </div>
+    <div class='col-md-3 col-md-offset-1'>
+      <div id="tags"/>
+    </div>
+  </div></div>
+  <div class="row">
+    <div class='col-md-8' id="pager"></div>
+  </div>
+</div>
+
+    <!-- footer start -->
+
+<footer class='row footer'>
+  <div class="container-fluid">
+    <div class='col-md-3 col-sm-4'>
+      <h4>About DataCite</h4>
+      <ul>
+        <li><a href="https://www.datacite.org/mission.html">What we do</a></a></li>
+        <li><a href="https://www.datacite.org/board.html">Board</a></a></li>
+        <li><a href="https://www.datacite.org/steering.html">Steering groups</a></a></li>
+        <li><a href="https://www.datacite.org/staff.html">Staff</a></a></li>
+        <li><a href="https://www.datacite.org/jobopportunities.html">Job opportunities</a></a></li>
+      </ul>
+    </div>
+    <div class='col-md-3 col-sm-4'>
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