bolognese 0.11.3 → 0.11.4

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 3a474fc02c5cd6efde7e3281b2b028893ba95762eb76db7ea6292ca262104493
-  data.tar.gz: 2ddb4c167ce6fdf718ad17bb5802465291d500e8f660232b5649635191ced1e0
+  metadata.gz: 30348e9164a584a0cdd9bb4a80ab50907e78f10e56a8213d736c03052dbc81b9
+  data.tar.gz: 026581048dea86848ef44e43b04dc891b901f39cb554d24cce95c614b8a5f3d4
 SHA512:
-  metadata.gz: 180c4a1b2d5b68bde9f40b0e4b6e3710e5d698e06ce8c9d95b3b1e881992dced59b509b5dd50ca281de976b93ce7160ecd67b9f1b7c235e3d4bff7fc59018c0b
-  data.tar.gz: 5e7345b954368e38a3f168343f565ab6ecc92ca0fe69726c92416550644094ede0e201aff89bef492eac232b63a966f757aecf3d52ed45acf686115de798ca49
+  metadata.gz: cbb748a13ce8b8ea3daf1ee0f57458c9e2904b39c639a4959a5a48bfbde7f5c5c26e421f815a5a997cdba2465bc7a096f47abd8175f0d1b4f00325900d9c5185
+  data.tar.gz: e71415a8a4e291a6e87150f88d4e976a1f00d94b7b67d7bc7faa7b3ce97e08208e7aaa6c9283b07cbad86465c0b82ebd9ec85155e8f2567f1fb7d5c34c93a29b

data/Gemfile.lock

@@ -1,7 +1,7 @@
 PATH
   remote: .
   specs:
-    bolognese (0.11.3)
+    bolognese (0.11.4)
       activesupport (>= 4.2.5, < 6)
       benchmark_methods (~> 0.7)
       bibtex-ruby (~> 4.1)
@@ -78,7 +78,7 @@ GEM
     loofah (2.2.2)
       crass (~> 1.0.2)
       nokogiri (>= 1.5.9)
-    maremma (4.0.12)
+    maremma (4.1)
       activesupport (>= 4.2.5, < 6)
       addressable (>= 2.3.6)
       builder (~> 3.2, >= 3.2.2)

data/lib/bolognese/readers/datacite_reader.rb

@@ -45,8 +45,13 @@ module Bolognese
       end
 
       def read_datacite(string: nil, **options)
+        doc = Nokogiri::XML(string, nil, 'UTF-8', &:noblanks)
+        ns = doc.collect_namespaces.find { |k, v| v.start_with?("http://datacite.org/schema/kernel") }
+        schema_version = Array.wrap(ns).last || "http://datacite.org/schema/kernel-4"
+        doc.remove_namespaces!
+        string = doc.to_xml(:indent => 2)
+        
         meta = Maremma.from_xml(string).to_h.fetch("resource", {})
-        schema_version = meta.fetch("xmlns", nil)
 
         # validate only when option is set, as this step is expensive and
         # not needed if XML comes from DataCite MDS
@@ -69,7 +74,7 @@ module Bolognese
           if r.is_a?(String)
             sanitize(r)
           else
-            { "title_type" => r["titleType"], "lang" => r["xml:lang"], "text" => sanitize(r["__content__"]) }.compact
+            { "title_type" => r["titleType"], "lang" => r["lang"], "text" => sanitize(r["__content__"]) }.compact
           end
         end.unwrap
 

data/lib/bolognese/utils.rb

@@ -354,7 +354,7 @@ module Bolognese
         "ris"
       elsif options[:ext] == ".xml" && Maremma.from_xml(string).to_h.dig("doi_records", "doi_record", "crossref")
         "crossref"
-      elsif options[:ext] == ".xml" && Maremma.from_xml(string).to_h.dig("resource", "xmlns").to_s.start_with?("http://datacite.org/schema/kernel")
+      elsif options[:ext] == ".xml" && Nokogiri::XML(string, nil, 'UTF-8', &:noblanks).collect_namespaces.find { |k, v| v.start_with?("http://datacite.org/schema/kernel") }      
         "datacite"
       elsif options[:ext] == ".json" && Maremma.from_json(string).to_h.dig("ris_type")
         "crosscite"

data/lib/bolognese/version.rb

@@ -1,3 +1,3 @@
 module Bolognese
-  VERSION = "0.11.3"
+  VERSION = "0.11.4"
 end

data/spec/fixtures/ns0.xml

@@ -0,0 +1,2 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<ns0:resource xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:ns0="http://datacite.org/schema/kernel-2.2" xsi:schemaLocation="http://datacite.org/schema/kernel-2.2 http://schema.datacite.org/meta/kernel-2.2/metadata.xsd"><ns0:identifier identifierType="DOI">10.4231/D38G8FK8B</ns0:identifier><ns0:creators><ns0:creator>	<ns0:creatorName>Patiño, Carlos</ns0:creatorName></ns0:creator><ns0:creator>	<ns0:creatorName>Alzate-Vargas, Lorena</ns0:creatorName></ns0:creator><ns0:creator>	<ns0:creatorName>Li, Chunyu</ns0:creatorName></ns0:creator><ns0:creator>	<ns0:creatorName>Haley, Benjamin</ns0:creatorName></ns0:creator><ns0:creator>	<ns0:creatorName>Strachan, Alejandro</ns0:creatorName></ns0:creator></ns0:creators><ns0:titles>	<ns0:title>LAMMPS Data-File Generator</ns0:title></ns0:titles><ns0:publisher>nanoHUB</ns0:publisher><ns0:publicationYear>2018</ns0:publicationYear><ns0:dates>	<ns0:date dateType="Valid">2018-07-18</ns0:date>	<ns0:date dateType="Accepted">2018-07-18</ns0:date></ns0:dates><ns0:language>en</ns0:language><ns0:resourceType resourceTypeGeneral="Software">Simulation Tool</ns0:resourceType><ns0:version>1.5.2</ns0:version><ns0:descriptions>	<ns0:description descriptionType="Other">This tool generates all necessary input files for LAMMPS simulations of molecular systems starting with an atomistic structure.</ns0:description></ns0:descriptions></ns0:resource>

data/spec/readers/datacite_reader_spec.rb

@@ -354,6 +354,24 @@ describe Bolognese::Metadata, vcr: true do
       expect(subject.service_provider).to eq("DataCite")
     end
 
+    it "namespaced xml from string" do
+      input = fixture_path + "ns0.xml"
+      subject = Bolognese::Metadata.new(input: input)
+      expect(subject.valid?).to be true
+      expect(subject.identifier).to eq("https://doi.org/10.4231/d38g8fk8b")
+      expect(subject.type).to eq("SoftwareSourceCode")
+      expect(subject.additional_type).to eq("Simulation Tool")
+      expect(subject.resource_type_general).to eq("Software")
+      expect(subject.author.length).to eq(5)
+      expect(subject.author.first).to eq("type"=>"Person", "name"=>"Carlos PatiñO", "givenName"=>"Carlos", "familyName"=>"PatiñO")
+      expect(subject.title).to eq("LAMMPS Data-File Generator")
+      expect(subject.date_published).to eq("2018")
+      expect(subject.publication_year).to eq(2018)
+      expect(subject.publisher).to eq("nanoHUB")
+      expect(subject.service_provider).to eq("DataCite")
+      expect(subject.schema_version).to eq("http://datacite.org/schema/kernel-2.2")
+    end
+
     it "doi with + sign" do
       input = "10.5067/terra+aqua/ceres/cldtyphist_l3.004"
       subject = Bolognese::Metadata.new(input: input)

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bolognese
 version: !ruby/object:Gem::Version
-  version: 0.11.3
+  version: 0.11.4
 platform: ruby
 authors:
 - Martin Fenner
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2018-07-23 00:00:00.000000000 Z
+date: 2018-07-28 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: maremma
@@ -606,6 +606,7 @@ files:
 - spec/fixtures/datacite_software_overlapping_keys.json
 - spec/fixtures/gtex.xml
 - spec/fixtures/maremma/codemeta.json
+- spec/fixtures/ns0.xml
 - spec/fixtures/pure.bib
 - spec/fixtures/pure.ris
 - spec/fixtures/schema_org.json