bolognese 1.3.23 → 1.4

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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+  data.tar.gz: 685185e34e72712a6223e9c84a928de5668e692a09f6304c4f3d0722c9e74417
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data/Gemfile.lock

@@ -1,7 +1,7 @@
 PATH
   remote: .
   specs:
-    bolognese (1.3.23)
+    bolognese (1.4)
       activesupport (>= 4.2.5, < 6)
       benchmark_methods (~> 0.7)
       bibtex-ruby (~> 4.1)
@@ -11,15 +11,17 @@ PATH
       concurrent-ruby (~> 1.0.5)
       csl-styles (~> 1.0, >= 1.0.1.8)
       edtf (~> 3.0, >= 3.0.4)
+      faraday (= 0.17.0)
       gender_detector (~> 0.1.2)
       iso8601 (~> 0.9.1)
       json-ld-preloaded (= 3.0.2)
-      jsonlint (~> 0.2.0)
+      jsonlint (~> 0.3.0)
       loofah (~> 2.0, >= 2.0.3)
       maremma (>= 4.3, < 5)
       namae (~> 1.0)
       nokogiri (~> 1.10.4)
-      oj (>= 2.8.3)
+      oj (~> 3.10)
+      oj_mimic_json (~> 1.0, >= 1.0.1)
       postrank-uri (~> 1.0, >= 1.0.18)
       rdf-rdfxml (~> 2.2)
       rdf-turtle (~> 3.0, >= 3.0.6)
@@ -28,7 +30,7 @@ PATH
 GEM
   remote: https://rubygems.org/
   specs:
-    activesupport (5.2.3)
+    activesupport (5.2.4)
       concurrent-ruby (~> 1.0, >= 1.0.2)
       i18n (>= 0.7, < 2)
       minitest (~> 5.1)
@@ -38,7 +40,7 @@ GEM
     benchmark_methods (0.7)
     bibtex-ruby (4.4.7)
       latex-decode (~> 0.0)
-    builder (3.2.3)
+    builder (3.2.4)
     citeproc (1.0.9)
       namae (~> 1.0)
     citeproc-ruby (1.1.10)
@@ -81,7 +83,7 @@ GEM
     i18n (1.7.0)
       concurrent-ruby (~> 1.0)
     iso8601 (0.9.1)
-    json (2.2.0)
+    json (2.3.0)
     json-ld (3.0.2)
       multi_json (~> 1.12)
       rdf (>= 2.2.8, < 4.0)
@@ -89,12 +91,12 @@ GEM
       json-ld (~> 3.0)
       multi_json (~> 1.12)
       rdf (~> 3.0)
-    jsonlint (0.2.0)
-      oj (~> 2)
-      trollop (~> 2)
+    jsonlint (0.3.0)
+      oj (~> 3)
+      optimist (~> 3)
     latex-decode (0.3.1)
     link_header (0.0.8)
-    loofah (2.3.0)
+    loofah (2.4.0)
       crass (~> 1.0.2)
       nokogiri (>= 1.5.9)
     maremma (4.4)
@@ -109,13 +111,15 @@ GEM
       nokogiri (~> 1.10.4)
       oj (>= 2.8.3)
     mini_portile2 (2.4.0)
-    minitest (5.12.2)
+    minitest (5.13.0)
     multi_json (1.14.1)
     multipart-post (2.1.1)
     namae (1.0.1)
-    nokogiri (1.10.4)
+    nokogiri (1.10.7)
       mini_portile2 (~> 2.4.0)
-    oj (2.18.5)
+    oj (3.10.0)
+    oj_mimic_json (1.0.1)
+    optimist (3.0.0)
     postrank-uri (1.0.24)
       addressable (>= 2.4.0)
       nokogiri (>= 1.8.0)
@@ -125,7 +129,7 @@ GEM
     rack-test (0.8.3)
       rack (>= 1.0, < 3)
     rake (12.3.3)
-    rdf (3.0.12)
+    rdf (3.0.13)
       hamster (~> 3.0)
       link_header (~> 0.0, >= 0.0.8)
     rdf-aggregate-repo (2.2.1)
@@ -174,7 +178,6 @@ GEM
     thor (0.20.3)
     thread_safe (0.3.6)
     tilt (2.0.10)
-    trollop (2.9.9)
     tzinfo (1.2.5)
       thread_safe (~> 0.1)
     unicode_utils (1.4.0)

data/bolognese.gemspec

@@ -17,6 +17,7 @@ Gem::Specification.new do |s|
 
   # Declary dependencies here, rather than in the Gemfile
   s.add_dependency 'maremma', '>= 4.3', '< 5'
+  s.add_dependency 'faraday', '0.17.0'
   s.add_dependency 'nokogiri', '~> 1.10.4'
   s.add_dependency 'loofah', '~> 2.0', '>= 2.0.3'
   s.add_dependency 'builder', '~> 3.2', '>= 3.2.2'
@@ -30,9 +31,10 @@ Gem::Specification.new do |s|
   s.add_dependency 'csl-styles', '~> 1.0', '>= 1.0.1.8'
   s.add_dependency 'iso8601', '~> 0.9.1'
   s.add_dependency 'postrank-uri', '~> 1.0', '>= 1.0.18'
-  s.add_dependency 'json-ld-preloaded', '= 3.0.2'
-  s.add_dependency 'jsonlint', '~> 0.2.0'
-  s.add_dependency 'oj', '>= 2.8.3'
+  s.add_dependency 'json-ld-preloaded', '3.0.2'
+  s.add_dependency 'jsonlint', '~> 0.3.0'
+  s.add_dependency 'oj', '~> 3.10'
+  s.add_dependency "oj_mimic_json", "~> 1.0", ">= 1.0.1"
   s.add_dependency 'rdf-turtle', '~> 3.0', '>= 3.0.6'
   s.add_dependency 'rdf-rdfxml', '~> 2.2'
   s.add_dependency 'benchmark_methods', '~> 0.7'

data/lib/bolognese/metadata_utils.rb

@@ -121,7 +121,7 @@ module Bolognese
     end
 
     def graph
-      RDF::Graph.new << JSON::LD::API.toRdf(schema_hsh)
+      RDF::Graph.new << ::JSON::LD::API.toRdf(schema_hsh)
     end
 
     def citeproc_hsh

data/lib/bolognese/readers/npm_reader.rb

@@ -3,6 +3,15 @@
 module Bolognese
   module Readers
     module NpmReader
+      def get_npm(id: nil, **options)
+        return { "string" => nil, "state" => "not_found" } unless id.present?
+        id = normalize_id(id)
+        response = Maremma.get(id, accept: "json", raw: true)
+        string = response.body.fetch("data", nil)
+
+        { "string" => string }
+      end
+
       def read_npm(string: nil, **options)
         if string.present?
           errors = jsonlint(string)

data/lib/bolognese/utils.rb

@@ -342,6 +342,8 @@ module Bolognese
         %w(DataCite Crossref mEDRA KISTI JaLC OP).include?(ra) ? ra.downcase : nil
       elsif /\A(?:(http|https):\/(\/)?orcid\.org\/)?(\d{4}-\d{4}-\d{4}-\d{3}[0-9X]+)\z/.match(id)
         "orcid"
+      elsif /\A(http|https):\/(\/)?github\.com\/(.+)\/package.json\z/.match(id)
+        "npm"
       elsif /\A(http|https):\/(\/)?github\.com\/(.+)\z/.match(id)
         "codemeta"
       else

data/lib/bolognese/version.rb

@@ -1,3 +1,3 @@
 module Bolognese
-  VERSION = "1.3.23"
+  VERSION = "1.4"
 end

data/package.json

@@ -0,0 +1,12 @@
+{
+  "name": "edam-browser",
+  "description": "The EDAM Browser is a client-side web-based visualization javascript widget. Its goals are to help describing bio-related resources and service with EDAM, and to facilitate and foster community contributions to EDAM.",
+  "author": "Bryan Brancotte",
+  "version": "1.0.0",
+  "scripts": {
+    "test": "jshint js/*js"
+  },
+  "devDependencies": {
+    "jshint": "^2.9.5"
+  }
+}

data/spec/find_from_format_spec.rb

@@ -44,6 +44,11 @@ describe Bolognese::CLI do
       expect(subject.find_from_format_by_id(id)).to eq("codemeta")
     end
 
+    it "npm" do
+      id = "https://github.com/datacite/bracco/blob/master/package.json"
+      expect(subject.find_from_format_by_id(id)).to eq("npm")
+    end
+
     it "schema_org" do
       id = "https://dataverse.harvard.edu/dataset.xhtml?persistentId=doi:10.7910/DVN/GAOC03"
       expect(subject.find_from_format_by_id(id)).to eq("schema_org")

data/spec/metadata_spec.rb

@@ -153,7 +153,7 @@ describe Bolognese::Metadata, vcr: true do
     it "missing_comma" do
       json = IO.read(fixture_path + "datacite_software_missing_comma.json")
       response = subject.jsonlint(json)
-      expect(response).to eq(["expected comma, not a string at line 4, column 11 [parse.c:381]"])
+      expect(response).to eq(["expected comma, not a string (doi) at line 4, column 11 [parse.c:373]"])
     end
 
     it "overlapping_keys" do

data/spec/readers/datacite_json_reader_spec.rb

@@ -46,7 +46,7 @@ describe Bolognese::Metadata, vcr: true do
       input = fixture_path + "datacite_software_missing_comma.json"
       subject = Bolognese::Metadata.new(input: input, from: "datacite_json", show_errors: true)
       expect(subject.valid?).to be false
-      expect(subject.errors).to eq(["expected comma, not a string at line 4, column 11 [parse.c:381]"])
+      expect(subject.errors).to eq(["expected comma, not a string (doi) at line 4, column 11 [parse.c:373]"])
       expect(subject.codemeta).to be_nil
     end
 

data/spec/readers/schema_org_reader_spec.rb

@@ -66,8 +66,7 @@ describe Bolognese::Metadata, vcr: true do
       input = "https://www.zenodo.org/record/1196821"
       subject = Bolognese::Metadata.new(input: input, from: "schema_org")
       expect(subject.valid?).to be false
-      expect(subject.errors.size).to eq(2)
-      expect(subject.errors.first).to eq("49:0: ERROR: Element '{http://datacite.org/schema/kernel-4}publisher': [facet 'minLength'] The value has a length of '0'; this underruns the allowed minimum length of '1'.")
+      expect(subject.errors).to eq("49:0: ERROR: Element '{http://datacite.org/schema/kernel-4}publisher': [facet 'minLength'] The value has a length of '0'; this underruns the allowed minimum length of '1'.")
       expect(subject.identifiers).to eq([{"identifier"=>"https://doi.org/10.5281/zenodo.1196821", "identifierType"=>"DOI"}])
       expect(subject.doi).to eq("10.5281/zenodo.1196821")
       expect(subject.url).to eq("https://zenodo.org/record/1196821")

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bolognese
 version: !ruby/object:Gem::Version
-  version: 1.3.23
+  version: '1.4'
 platform: ruby
 authors:
 - Martin Fenner
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2019-10-16 00:00:00.000000000 Z
+date: 2019-12-15 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: maremma
@@ -30,6 +30,20 @@ dependencies:
     - - "<"
       - !ruby/object:Gem::Version
         version: '5'
+- !ruby/object:Gem::Dependency
+  name: faraday
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 0.17.0
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 0.17.0
 - !ruby/object:Gem::Dependency
   name: nokogiri
   requirement: !ruby/object:Gem::Requirement
@@ -274,28 +288,48 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 0.2.0
+        version: 0.3.0
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 0.2.0
+        version: 0.3.0
 - !ruby/object:Gem::Dependency
   name: oj
   requirement: !ruby/object:Gem::Requirement
     requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.10'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.10'
+- !ruby/object:Gem::Dependency
+  name: oj_mimic_json
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.0'
     - - ">="
       - !ruby/object:Gem::Version
-        version: 2.8.3
+        version: 1.0.1
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.0'
     - - ">="
       - !ruby/object:Gem::Version
-        version: 2.8.3
+        version: 1.0.1
 - !ruby/object:Gem::Dependency
   name: rdf-turtle
   requirement: !ruby/object:Gem::Requirement
@@ -592,6 +626,7 @@ files:
 - lib/bolognese/writers/ris_writer.rb
 - lib/bolognese/writers/schema_org_writer.rb
 - lib/bolognese/writers/turtle_writer.rb
+- package.json
 - resources/2008/09/xsd.xsl
 - resources/datacite-contributorType-v4.xsd
 - resources/datacite-dateType-v4.xsd