cirneco 0.9.16 → 0.9.17

data/resources/jats-1.1/standard-modules/xml.xsd

@@ -1,287 +0,0 @@
-<?xml version='1.0'?>
-<?xml-stylesheet href="../2008/09/xsd.xsl" type="text/xsl"?>
-<xs:schema targetNamespace="http://www.w3.org/XML/1998/namespace" 
-  xmlns:xs="http://www.w3.org/2001/XMLSchema" 
-  xmlns   ="http://www.w3.org/1999/xhtml"
-  xml:lang="en">
-
- <xs:annotation>
-  <xs:documentation>
-   <div>
-    <h1>About the XML namespace</h1>
-
-    <div class="bodytext">
-     <p>
-      This schema document describes the XML namespace, in a form
-      suitable for import by other schema documents.
-     </p>
-     <p>
-      See <a href="http://www.w3.org/XML/1998/namespace.html">
-      http://www.w3.org/XML/1998/namespace.html</a> and
-      <a href="http://www.w3.org/TR/REC-xml">
-      http://www.w3.org/TR/REC-xml</a> for information 
-      about this namespace.
-     </p>
-     <p>
-      Note that local names in this namespace are intended to be
-      defined only by the World Wide Web Consortium or its subgroups.
-      The names currently defined in this namespace are listed below.
-      They should not be used with conflicting semantics by any Working
-      Group, specification, or document instance.
-     </p>
-     <p>   
-      See further below in this document for more information about <a
-      href="#usage">how to refer to this schema document from your own
-      XSD schema documents</a> and about <a href="#nsversioning">the
-      namespace-versioning policy governing this schema document</a>.
-     </p>
-    </div>
-   </div>
-  </xs:documentation>
- </xs:annotation>
-
- <xs:attribute name="lang">
-  <xs:annotation>
-   <xs:documentation>
-    <div>
-     
-      <h3>lang (as an attribute name)</h3>
-      <p>
-       denotes an attribute whose value
-       is a language code for the natural language of the content of
-       any element; its value is inherited.  This name is reserved
-       by virtue of its definition in the XML specification.</p>
-     
-    </div>
-    <div>
-     <h4>Notes</h4>
-     <p>
-      Attempting to install the relevant ISO 2- and 3-letter
-      codes as the enumerated possible values is probably never
-      going to be a realistic possibility.  
-     </p>
-     <p>
-      See BCP 47 at <a href="http://www.rfc-editor.org/rfc/bcp/bcp47.txt">
-       http://www.rfc-editor.org/rfc/bcp/bcp47.txt</a>
-      and the IANA language subtag registry at
-      <a href="http://www.iana.org/assignments/language-subtag-registry">
-       http://www.iana.org/assignments/language-subtag-registry</a>
-      for further information.
-     </p>
-     <p>
-      The union allows for the 'un-declaration' of xml:lang with
-      the empty string.
-     </p>
-    </div>
-   </xs:documentation>
-  </xs:annotation>
-  <xs:simpleType>
-   <xs:union memberTypes="xs:language">
-    <xs:simpleType>    
-     <xs:restriction base="xs:string">
-      <xs:enumeration value=""/>
-     </xs:restriction>
-    </xs:simpleType>
-   </xs:union>
-  </xs:simpleType>
- </xs:attribute>
-
- <xs:attribute name="space">
-  <xs:annotation>
-   <xs:documentation>
-    <div>
-     
-      <h3>space (as an attribute name)</h3>
-      <p>
-       denotes an attribute whose
-       value is a keyword indicating what whitespace processing
-       discipline is intended for the content of the element; its
-       value is inherited.  This name is reserved by virtue of its
-       definition in the XML specification.</p>
-     
-    </div>
-   </xs:documentation>
-  </xs:annotation>
-  <xs:simpleType>
-   <xs:restriction base="xs:NCName">
-    <xs:enumeration value="default"/>
-    <xs:enumeration value="preserve"/>
-   </xs:restriction>
-  </xs:simpleType>
- </xs:attribute>
- 
- <xs:attribute name="base" type="xs:anyURI"> <xs:annotation>
-   <xs:documentation>
-    <div>
-     
-      <h3>base (as an attribute name)</h3>
-      <p>
-       denotes an attribute whose value
-       provides a URI to be used as the base for interpreting any
-       relative URIs in the scope of the element on which it
-       appears; its value is inherited.  This name is reserved
-       by virtue of its definition in the XML Base specification.</p>
-     
-     <p>
-      See <a
-      href="http://www.w3.org/TR/xmlbase/">http://www.w3.org/TR/xmlbase/</a>
-      for information about this attribute.
-     </p>
-    </div>
-   </xs:documentation>
-  </xs:annotation>
- </xs:attribute>
- 
- <xs:attribute name="id" type="xs:ID">
-  <xs:annotation>
-   <xs:documentation>
-    <div>
-     
-      <h3>id (as an attribute name)</h3> 
-      <p>
-       denotes an attribute whose value
-       should be interpreted as if declared to be of type ID.
-       This name is reserved by virtue of its definition in the
-       xml:id specification.</p>
-     
-     <p>
-      See <a
-      href="http://www.w3.org/TR/xml-id/">http://www.w3.org/TR/xml-id/</a>
-      for information about this attribute.
-     </p>
-    </div>
-   </xs:documentation>
-  </xs:annotation>
- </xs:attribute>
-
- <xs:attributeGroup name="specialAttrs">
-  <xs:attribute ref="xml:base"/>
-  <xs:attribute ref="xml:lang"/>
-  <xs:attribute ref="xml:space"/>
-  <xs:attribute ref="xml:id"/>
- </xs:attributeGroup>
-
- <xs:annotation>
-  <xs:documentation>
-   <div>
-   
-    <h3>Father (in any context at all)</h3> 
-
-    <div class="bodytext">
-     <p>
-      denotes Jon Bosak, the chair of 
-      the original XML Working Group.  This name is reserved by 
-      the following decision of the W3C XML Plenary and 
-      XML Coordination groups:
-     </p>
-     <blockquote>
-       <p>
-	In appreciation for his vision, leadership and
-	dedication the W3C XML Plenary on this 10th day of
-	February, 2000, reserves for Jon Bosak in perpetuity
-	the XML name "xml:Father".
-       </p>
-     </blockquote>
-    </div>
-   </div>
-  </xs:documentation>
- </xs:annotation>
-
- <xs:annotation>
-  <xs:documentation>
-   <div xml:id="usage" id="usage">
-    <h2><a name="usage">About this schema document</a></h2>
-
-    <div class="bodytext">
-     <p>
-      This schema defines attributes and an attribute group suitable
-      for use by schemas wishing to allow <code>xml:base</code>,
-      <code>xml:lang</code>, <code>xml:space</code> or
-      <code>xml:id</code> attributes on elements they define.
-     </p>
-     <p>
-      To enable this, such a schema must import this schema for
-      the XML namespace, e.g. as follows:
-     </p>
-     <pre>
-          &lt;schema . . .>
-           . . .
-           &lt;import namespace="http://www.w3.org/XML/1998/namespace"
-                      schemaLocation="http://www.w3.org/2001/xml.xsd"/>
-     </pre>
-     <p>
-      or
-     </p>
-     <pre>
-           &lt;import namespace="http://www.w3.org/XML/1998/namespace"
-                      schemaLocation="http://www.w3.org/2009/01/xml.xsd"/>
-     </pre>
-     <p>
-      Subsequently, qualified reference to any of the attributes or the
-      group defined below will have the desired effect, e.g.
-     </p>
-     <pre>
-          &lt;type . . .>
-           . . .
-           &lt;attributeGroup ref="xml:specialAttrs"/>
-     </pre>
-     <p>
-      will define a type which will schema-validate an instance element
-      with any of those attributes.
-     </p>
-    </div>
-   </div>
-  </xs:documentation>
- </xs:annotation>
-
- <xs:annotation>
-  <xs:documentation>
-   <div id="nsversioning" xml:id="nsversioning">
-    <h2><a name="nsversioning">Versioning policy for this schema document</a></h2>
-    <div class="bodytext">
-     <p>
-      In keeping with the XML Schema WG's standard versioning
-      policy, this schema document will persist at
-      <a href="http://www.w3.org/2009/01/xml.xsd">
-       http://www.w3.org/2009/01/xml.xsd</a>.
-     </p>
-     <p>
-      At the date of issue it can also be found at
-      <a href="http://www.w3.org/2001/xml.xsd">
-       http://www.w3.org/2001/xml.xsd</a>.
-     </p>
-     <p>
-      The schema document at that URI may however change in the future,
-      in order to remain compatible with the latest version of XML
-      Schema itself, or with the XML namespace itself.  In other words,
-      if the XML Schema or XML namespaces change, the version of this
-      document at <a href="http://www.w3.org/2001/xml.xsd">
-       http://www.w3.org/2001/xml.xsd 
-      </a> 
-      will change accordingly; the version at 
-      <a href="http://www.w3.org/2009/01/xml.xsd">
-       http://www.w3.org/2009/01/xml.xsd 
-      </a> 
-      will not change.
-     </p>
-     <p>
-      Previous dated (and unchanging) versions of this schema 
-      document are at:
-     </p>
-     <ul>
-      <li><a href="http://www.w3.org/2009/01/xml.xsd">
-	http://www.w3.org/2009/01/xml.xsd</a></li>
-      <li><a href="http://www.w3.org/2007/08/xml.xsd">
-	http://www.w3.org/2007/08/xml.xsd</a></li>
-      <li><a href="http://www.w3.org/2004/10/xml.xsd">
-	http://www.w3.org/2004/10/xml.xsd</a></li>
-      <li><a href="http://www.w3.org/2001/03/xml.xsd">
-	http://www.w3.org/2001/03/xml.xsd</a></li>
-     </ul>
-    </div>
-   </div>
-  </xs:documentation>
- </xs:annotation>
-
-</xs:schema>
-

data/spec/file_utils_spec.rb

@@ -1,203 +0,0 @@
-require 'spec_helper'
-
-describe Cirneco::DataCenter, vcr: true, :order => :defined do
-  let(:prefix) { ENV['PREFIX'] }
-  let(:username) { ENV['MDS_USERNAME'] }
-  let(:password) { ENV['MDS_PASSWORD'] }
-  let(:source_dir) { "/spec/fixtures/" }
-  let(:bibliography) { "spec/fixtures/references.yaml" }
-  let(:options) { { username: username,
-                    password: password,
-                    sandbox: true,
-                    build_dir: source_dir,
-                    source_dir: source_dir } }
-
-  subject { Cirneco::DataCenter.new(prefix: prefix,
-                                    username: username,
-                                    password: password) }
-
-  context "accession_number" do
-    it 'should get existing' do
-      filepath = fixture_path + 'cool-dois.html.md'
-      response = subject.get_accession_number(filepath)
-      expect(response).to eq(123)
-    end
-
-    it 'should get existing for folder' do
-      response = subject.get_all_accession_numbers(fixture_path)
-      expect(response).to eq([123, 124])
-    end
-
-    it 'should update for file' do
-      filepath = fixture_path + 'cool-dois.html.md'
-      response = subject.update_accession_number(filepath)
-      expect(response).to eq("Accession number MS-123 not changed for cool-dois.html.md")
-    end
-
-    it 'should update for all files' do
-      response = subject.update_all_accession_numbers(fixture_path, opt_in: true)
-      expect(response).to eq(["Accession number MS-124 not changed for cool-dois-minted.html.md", "File cool-dois-no-accession-number.html.md ignored: no empty accession_number", "Accession number MS-123 not changed for cool-dois.html.md"])
-    end
-  end
-
-  context "mint and hide DOIs" do
-    it 'get urls for works' do
-      filepath = fixture_path + 'index.html'
-      response = subject.get_urls_for_works(filepath)
-      expect(response.length).to eq(2)
-    end
-
-    it 'should mint for url' do
-      filepath = fixture_path + 'cool-dois/index.html'
-      response = subject.mint_doi_for_url(filepath, options)
-      expect(response).to eq("DOI 10.5438/55e5-t5c0 minted for cool-dois.html.md")
-    end
-
-    it 'should hide for url' do
-      filepath = fixture_path + 'cool-dois-minted/index.html'
-      response = subject.hide_doi_for_url(filepath, options)
-      expect(response).to eq("DOI 10.5438/55e5-t5c0 hidden for cool-dois-minted.html.md")
-    end
-
-    it 'should mint and hide for url' do
-      filepath = fixture_path + 'cool-dois/index.html'
-      response = subject.mint_and_hide_doi_for_url(filepath, options)
-      expect(response).to eq("DOI 10.5438/55e5-t5c0 minted and hidden for cool-dois.html.md")
-    end
-
-    it 'should mint for all urls' do
-      filepath = fixture_path + 'index.html'
-      response = subject.mint_dois_for_all_urls(filepath, options)
-      expect(response).to eq("DOI 10.5438/55e5-t5c0 minted for cool-dois.html.md\nDOI 10.5438/0007-nw90 minted for index.html.erb")
-    end
-
-    it 'should hide for all urls' do
-      filepath = fixture_path + 'index-minted.html'
-      response = subject.hide_dois_for_all_urls(filepath, options)
-      expect(response).to eq("No DOI for cool-dois.html.md\nErrors for DOI 10.5438/0000-nw90: Not found\n")
-    end
-
-    it 'should mint and hide for all urls' do
-      filepath = fixture_path + 'index.html'
-      response = subject.mint_and_hide_dois_for_all_urls(filepath, options)
-      expect(response).to eq("DOI 10.5438/55e5-t5c0 minted and hidden for cool-dois.html.md\nDOI 10.5438/0000-00ss minted and hidden for index.html.erb")
-    end
-
-    it 'should get_json_ld_from_work' do
-      filepath = fixture_path + 'cool-dois/index.html'
-      json = subject.get_json_ld_from_work(filepath)
-      metadata = JSON.parse(json)
-      expect(metadata["url"]).to eq("https://blog.datacite.org/cool-dois/")
-      expect(metadata["author"]).to eq([{"@type"=>"Person", "@id"=>"http://orcid.org/0000-0003-1419-2405", "givenName"=>"Martin", "familyName"=>"Fenner", "name"=>"Martin Fenner"}])
-      expect(metadata["description"]).to eq("In 1998 Tim Berners-Lee coined the term cool URIs (1998), that is URIs that don’t change. We know that URLs referenced in the scholarly literature are often not cool, leading to link rot (Klein et al., 2014) and making it hard or impossible to find...")
-      expect(metadata["citation"]).to eq([{"@type"=>"CreativeWork",
-                                           "@id"=>"https://www.w3.org/Provider/Style/URI"},
-                                          {"@type"=>"CreativeWork",
-                                           "@id"=>"https://doi.org/10.1371/journal.pone.0115253"}])
-      expect(metadata["isPartOf"]).to eq("@type"=>"Blog", "@id"=>"https://blog.datacite.org", "name"=>"DataCite Blog")
-    end
-
-    it 'should post_metadata_for_work' do
-      filepath = fixture_path + 'cool-dois/index.html'
-      json = subject.get_json_ld_from_work(filepath)
-      response = subject.post_metadata_for_work(json, options)
-      expect(response.body["data"]).to eq("OK")
-      expect(response.status).to eq(201)
-    end
-
-    it 'should hide_metadata_for_work' do
-      filepath = fixture_path + 'cool-dois/index.html'
-      json = subject.get_json_ld_from_work(filepath)
-      response = subject.hide_metadata_for_work(json, options)
-      expect(response.body["data"]).to eq("OK")
-      expect(response.status).to eq(200)
-    end
-  end
-
-  context "jats" do
-    it 'should generate metadata for jats' do
-      filepath = fixture_path + 'cool-dois/index.html'
-      metadata = subject.generate_metadata_for_jats(filepath)
-      expect(metadata["author"]).to eq([{"given_name"=>"Martin", "family_name"=>"Fenner", "orcid"=>"0000-0003-1419-2405"}])
-      expect(metadata["license_url"]).to eq("https://creativecommons.org/licenses/by/4.0/")
-    end
-
-    it 'should generate jats xml' do
-      filepath = fixture_path + 'cool-dois/index.html'
-      expect(subject.generate_jats_for_url(filepath, options.merge(bibliography: bibliography))).to eq("JATS XML written for cool-dois.html.md")
-    end
-
-    it 'should generate jats for all urls' do
-      filepath = fixture_path + 'index.html'
-      response = subject.generate_jats_for_all_urls(filepath, options)
-      expect(response).to eq("JATS XML written for cool-dois.html.md\nJATS XML written for index.html.erb")
-    end
-
-    # it 'should validate jats xml' do
-    #   filepath = fixture_path + 'cool-dois/index.html'
-    #   expect(subject.generate_jats_for_url(filepath, options.merge(bibliography: bibliography))).to eq("JATS XML written for cool-dois.html.md")
-    #   xml = IO.read(fixture_path + 'cool-dois/cool-dois.xml')
-    #   expect(subject.validate_jats(xml).body["errors"]).to be_empty
-    # end
-  end
-
-  context "get_related_identifiers" do
-    it 'isPartOf' do
-      metadata = { "isPartOf" => {
-        "@type" => "Blog",
-        "@id" => "https://blog.datacite.org",
-        "name" => "DataCite Blog" } }
-      expect(subject.get_related_identifiers(metadata)).to eq([{:value=>"https://blog.datacite.org/", :related_identifier_type=>"URL", :relation_type=>"IsPartOf"}])
-    end
-  end
-
-  context "filepath from url" do
-    it 'https://blog.datacite.org/' do
-      url = 'https://blog.datacite.org/'
-      filename, build_path, source_path = subject.filepath_from_url(url, build_dir: source_dir, source_dir: source_dir)
-      expect(filename).to eq("index.html.erb")
-      expect(source_path).to eq(fixture_path + "index.html.erb")
-      expect(build_path).to eq(fixture_path + "index.html")
-    end
-
-    it 'https://blog.datacite.org' do
-      url = 'https://blog.datacite.org'
-      filename, build_path, source_path = subject.filepath_from_url(url, build_dir: source_dir, source_dir: source_dir)
-      expect(filename).to eq("index.html.erb")
-      expect(source_path).to eq(fixture_path + "index.html.erb")
-      expect(build_path).to eq(fixture_path + "index.html")
-    end
-
-    it 'index.html' do
-      url = fixture_path + 'index.html'
-      filename, build_path, source_path = subject.filepath_from_url(url, build_dir: source_dir, source_dir: source_dir)
-      expect(filename).to eq("index.html.erb")
-      expect(source_path).to eq(fixture_path + "index.html.erb")
-      expect(build_path).to eq(fixture_path + "index.html")
-    end
-
-    it 'index.html basename' do
-      url = 'index.html'
-      filename, build_path, source_path = subject.filepath_from_url(url, build_dir: source_dir, source_dir: source_dir)
-      expect(filename).to eq("index.html.erb")
-      expect(source_path).to eq(fixture_path + "index.html.erb")
-      expect(build_path).to eq(fixture_path + "index.html")
-    end
-
-    it 'cool-dois.html' do
-      url = fixture_path + 'cool-dois.html'
-      filename, build_path, source_path = subject.filepath_from_url(url, build_dir: source_dir, source_dir: source_dir)
-      expect(filename).to eq("cool-dois.html.md")
-      expect(source_path).to eq(fixture_path + "cool-dois.html.md")
-      expect(build_path).to eq(fixture_path + "cool-dois/index.html")
-    end
-
-    it 'cool-dois.html basename' do
-      url = 'cool-dois.html'
-      filename, build_path, source_path = subject.filepath_from_url(url, build_dir: source_dir, source_dir: source_dir)
-      expect(filename).to eq("cool-dois.html.md")
-      expect(source_path).to eq(fixture_path + "cool-dois.html.md")
-      expect(build_path).to eq(fixture_path + "cool-dois/index.html")
-    end
-  end
-end