identifiers 0.9.1 → 0.10.0

checksums.yaml

@@ -1,7 +1,7 @@
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data/CHANGELOG.md

@@ -2,6 +2,10 @@
 All notable changes to this project will be documented in this file. This
 project adheres to [Semantic Versioning](http://semver.org/).
 
+## [0.10.0] - 2017-12-20
+### Added
+- Extract PubMed IDs from URLs (e.g https://www.ncbi.nlm.nih.gov/pubmed/123456) and URIs with schemes `pmid:` and `info:pmid`
+
 ## [0.9.1] - 2017-08-01
 ### Fixed
 - Don't extract duplicate ISBN-10s from within ISBN-13s
@@ -63,3 +67,4 @@ project adheres to [Semantic Versioning](http://semver.org/).
 [0.8.1]: https://github.com/altmetric/identifiers/releases/tag/v0.8.1
 [0.9.0]: https://github.com/altmetric/identifiers/releases/tag/v0.9.0
 [0.9.1]: https://github.com/altmetric/identifiers/releases/tag/v0.9.1
+[0.10.0]: https://github.com/altmetric/identifiers/releases/tag/v0.10.0

data/lib/identifiers/isbn.rb

@@ -1,99 +1,99 @@
-module Identifiers
-  class ISBN
-    ISBN_13_REGEXP = /
-      \b
-      97[89]            # ISBN (GS1) Bookland prefix
-      [\p{Pd}\p{Zs}]?   # Optional hyphenation
-      (?:
-        \d              # Digit
-        [\p{Pd}\p{Zs}]? # Optional hyphenation
-      ){9}
-      \d                # Check digit
-      \b
-    /x
-    ISBN_10_REGEXP = /
-      (?<!              # Don't match a hyphenated or spaced ISBN-13
-        97[89]
-        [\p{Pd}\p{Zs}]
-      )
-      \b
-      (?:
-        \d              # Digit
-        [\p{Pd}\p{Zs}]? # Optional hyphenation
-      ){9}
-      [\dX]             # Check digit
-      \b
-    /x
-    ISBN_A_REGEXP = %r{
-      \b
-      (?<=10\.) # Directory indicator (always 10)
-      97[89]\.  # ISBN (GS1) Bookland prefix
-      \d{2,8}   # ISBN registration group element and publisher prefix
-      /         # Prefix/suffix divider
-      \d{1,7}   # ISBN title enumerator and check digit
-      \b
-    }x
-
-    def self.extract(str)
-      extract_isbn_as(str) + extract_thirteen_digit_isbns(str) + extract_ten_digit_isbns(str)
-    end
-
-    def self.extract_isbn_as(str)
-      extract_thirteen_digit_isbns(str.to_s.scan(ISBN_A_REGEXP).join("\n").tr('/.', ''))
-    end
-
-    def self.extract_thirteen_digit_isbns(str)
-      str
-        .to_s
-        .scan(ISBN_13_REGEXP)
-        .map { |isbn| isbn.gsub(/[\p{Pd}\p{Zs}]/, '') }
-        .select { |isbn| valid_isbn_13?(isbn) }
-    end
-
-    def self.extract_ten_digit_isbns(str)
-      str
-        .to_s
-        .scan(ISBN_10_REGEXP)
-        .map { |isbn| isbn.gsub(/[\p{Pd}\p{Zs}]/, '') }
-        .select { |isbn| valid_isbn_10?(isbn) }
-        .map { |isbn|
-          isbn.chop!
-          isbn.prepend('978')
-          isbn << isbn_13_check_digit(isbn).to_s
-
-          isbn
-        }
-    end
-
-    def self.isbn_13_check_digit(isbn)
-      sum = digits_of(isbn).zip([1, 3].cycle).map { |digit, weight| digit * weight }.reduce(:+)
-      check_digit = 10 - (sum % 10)
-
-      if check_digit == 10
-        0
-      else
-        check_digit
-      end
-    end
-
-    def self.valid_isbn_13?(isbn)
-      return false unless isbn =~ ISBN_13_REGEXP
-
-      result = digits_of(isbn).zip([1, 3].cycle).map { |digit, weight| digit * weight }.reduce(:+)
-
-      (result % 10).zero?
-    end
-
-    def self.valid_isbn_10?(isbn)
-      return false unless isbn =~ ISBN_10_REGEXP
-
-      result = digits_of(isbn).with_index.map { |digit, weight| digit * weight.succ }.reduce(:+)
-
-      (result % 11).zero?
-    end
-
-    def self.digits_of(isbn)
-      isbn.to_s.each_char.map { |char| char == 'X' ? 10 : Integer(char) }.to_enum
-    end
-  end
-end
+module Identifiers
+  class ISBN
+    ISBN_13_REGEXP = /
+      \b
+      97[89]            # ISBN (GS1) Bookland prefix
+      [\p{Pd}\p{Zs}]?   # Optional hyphenation
+      (?:
+        \d              # Digit
+        [\p{Pd}\p{Zs}]? # Optional hyphenation
+      ){9}
+      \d                # Check digit
+      \b
+    /x
+    ISBN_10_REGEXP = /
+      (?<!              # Don't match a hyphenated or spaced ISBN-13
+        97[89]
+        [\p{Pd}\p{Zs}]
+      )
+      \b
+      (?:
+        \d              # Digit
+        [\p{Pd}\p{Zs}]? # Optional hyphenation
+      ){9}
+      [\dX]             # Check digit
+      \b
+    /x
+    ISBN_A_REGEXP = %r{
+      \b
+      (?<=10\.) # Directory indicator (always 10)
+      97[89]\.  # ISBN (GS1) Bookland prefix
+      \d{2,8}   # ISBN registration group element and publisher prefix
+      /         # Prefix/suffix divider
+      \d{1,7}   # ISBN title enumerator and check digit
+      \b
+    }x
+
+    def self.extract(str)
+      extract_isbn_as(str) + extract_thirteen_digit_isbns(str) + extract_ten_digit_isbns(str)
+    end
+
+    def self.extract_isbn_as(str)
+      extract_thirteen_digit_isbns(str.to_s.scan(ISBN_A_REGEXP).join("\n").tr('/.', ''))
+    end
+
+    def self.extract_thirteen_digit_isbns(str)
+      str
+        .to_s
+        .scan(ISBN_13_REGEXP)
+        .map { |isbn| isbn.gsub(/[\p{Pd}\p{Zs}]/, '') }
+        .select { |isbn| valid_isbn_13?(isbn) }
+    end
+
+    def self.extract_ten_digit_isbns(str)
+      str
+        .to_s
+        .scan(ISBN_10_REGEXP)
+        .map { |isbn| isbn.gsub(/[\p{Pd}\p{Zs}]/, '') }
+        .select { |isbn| valid_isbn_10?(isbn) }
+        .map { |isbn|
+          isbn.chop!
+          isbn.prepend('978')
+          isbn << isbn_13_check_digit(isbn).to_s
+
+          isbn
+        }
+    end
+
+    def self.isbn_13_check_digit(isbn)
+      sum = digits_of(isbn).zip([1, 3].cycle).map { |digit, weight| digit * weight }.reduce(:+)
+      check_digit = 10 - (sum % 10)
+
+      if check_digit == 10
+        0
+      else
+        check_digit
+      end
+    end
+
+    def self.valid_isbn_13?(isbn)
+      return false unless isbn =~ ISBN_13_REGEXP
+
+      result = digits_of(isbn).zip([1, 3].cycle).map { |digit, weight| digit * weight }.reduce(:+)
+
+      (result % 10).zero?
+    end
+
+    def self.valid_isbn_10?(isbn)
+      return false unless isbn =~ ISBN_10_REGEXP
+
+      result = digits_of(isbn).with_index.map { |digit, weight| digit * weight.succ }.reduce(:+)
+
+      (result % 11).zero?
+    end
+
+    def self.digits_of(isbn)
+      isbn.to_s.each_char.map { |char| char == 'X' ? 10 : Integer(char) }.to_enum
+    end
+  end
+end

data/lib/identifiers/pubmed_id.rb

@@ -1,7 +1,11 @@
-module Identifiers
-  class PubmedId
-    def self.extract(str)
-      str.to_s.scan(/(?<=^|[[:space:]])0*(?!0)(\d+)(?=$|[[:space:]])/).flatten
-    end
-  end
-end
+module Identifiers
+  class PubmedId
+    ZERO_PADDED_NUMBER = %r{(?<=^|[[:space:]])0*(?!0)(\d+)(?=$|[[:space:]])}
+    PUBMED_URL = %r{(?:https?://(?:www\.)?ncbi\.nlm\.nih\.gov/(?:m/)?pubmed/|pmid:|info:pmid/)0*(\d+)}i
+
+    def self.extract(str)
+      str = str.to_s
+      str.scan(ZERO_PADDED_NUMBER).flatten | str.scan(PUBMED_URL).flatten
+    end
+  end
+end

data/spec/identifiers/isbn_spec.rb

@@ -1,97 +1,97 @@
-require 'identifiers/isbn'
-
-RSpec.describe Identifiers::ISBN do
-  it 'extracts a ISBN' do
-    expect(described_class.extract('ISBN: 9780805069099')).to contain_exactly('9780805069099')
-  end
-
-  it 'extracts ISBNs when given as a number' do
-    isbn = 9780805069099
-
-    expect(described_class.extract(isbn)).to contain_exactly('9780805069099')
-  end
-
-  it 'normalizes 13-digit ISBNs' do
-    str = "978-0-80-506909-9\n978-0-67-187919-8"
-
-    expect(described_class.extract(str)).to contain_exactly('9780805069099', '9780671879198')
-  end
-
-  it 'extracts multiple ISBN-13s separated by a space' do
-    str = '978-0-80-506909-9 978-0-67-187919-8'
-
-    expect(described_class.extract(str)).to contain_exactly('9780805069099', '9780671879198')
-  end
-
-  it 'extracts ISBNs with hyphens' do
-    expect(described_class.extract('ISBN: 978-0-80-506909-9')).to contain_exactly('9780805069099')
-  end
-
-  it 'extracts ISBNs with Unicode dashes' do
-    expect(described_class.extract('ISBN: 978–0–80–506909–9')).to contain_exactly('9780805069099')
-  end
-
-  it 'extracts ISBNs with spaces' do
-    expect(described_class.extract('ISBN: 978 0 80 506909 9')).to contain_exactly('9780805069099')
-  end
-
-  it 'extracts ISBNs with Unicode spaces' do
-    expect(described_class.extract('ISBN: 978 0 80 506909 9')).to contain_exactly('9780805069099')
-  end
-
-  it 'extracts ISBN-13s from ISBN-As' do
-    expect(described_class.extract('10.978.8898392/315')).to contain_exactly('9788898392315')
-  end
-
-  it 'does not extract invalid ISBNs from ISBN-As' do
-    expect(described_class.extract('10.978.8898392/316')).to be_empty
-  end
-
-  it 'normalizes 10-digit ISBNs' do
-    str = "0-8050-6909-7 \n 2-7594-0269-X"
-
-    expect(described_class.extract(str)).to contain_exactly('9780805069099', '9782759402694')
-  end
-
-  it 'extracts multiple 10-digit ISBNs separated by a space' do
-    str = '0-8050-6909-7 2-7594-0269-X'
-
-    expect(described_class.extract(str)).to contain_exactly('9780805069099', '9782759402694')
-  end
-
-  it 'normalizes 10-digit ISBNs with Unicode dashes' do
-    expect(described_class.extract('0–8050–6909–7')).to contain_exactly('9780805069099')
-  end
-
-  it 'normalizes 10-digit ISBNs with a check digit of 10' do
-    expect(described_class.extract('4423272350')).to contain_exactly('9784423272350')
-  end
-
-  it 'normalizes 10-digit ISBNs with spaces' do
-    expect(described_class.extract('0 8050 6909 7')).to contain_exactly('9780805069099')
-  end
-
-  it 'normalizes 10-digit ISBNs with Unicode spaces' do
-    expect(described_class.extract('0 8050 6909 7')).to contain_exactly('9780805069099')
-  end
-
-  it 'normalizes 10-digit ISBNs with spaces and a check digit of X' do
-    expect(described_class.extract('2 7594 0269 X')).to contain_exactly('9782759402694')
-  end
-
-  it 'does not extract invalid 13-digit ISBNs' do
-    expect(described_class.extract('9783319217280')).to be_empty
-  end
-
-  it 'does not extract invalid 10-digit ISBNs' do
-    expect(described_class.extract('3319217280')).to be_empty
-  end
-
-  it 'does not extract ISBN-10s from hyphenated ISBN-13s' do
-    expect(described_class.extract('978-0-309-57079-4')).to contain_exactly('9780309570794')
-  end
-
-  it 'does not extract ISBN-10s from space-separated ISBN-13s' do
-    expect(described_class.extract('978 0 309 57079 4')).to contain_exactly('9780309570794')
-  end
-end
+require 'identifiers/isbn'
+
+RSpec.describe Identifiers::ISBN do
+  it 'extracts a ISBN' do
+    expect(described_class.extract('ISBN: 9780805069099')).to contain_exactly('9780805069099')
+  end
+
+  it 'extracts ISBNs when given as a number' do
+    isbn = 9780805069099
+
+    expect(described_class.extract(isbn)).to contain_exactly('9780805069099')
+  end
+
+  it 'normalizes 13-digit ISBNs' do
+    str = "978-0-80-506909-9\n978-0-67-187919-8"
+
+    expect(described_class.extract(str)).to contain_exactly('9780805069099', '9780671879198')
+  end
+
+  it 'extracts multiple ISBN-13s separated by a space' do
+    str = '978-0-80-506909-9 978-0-67-187919-8'
+
+    expect(described_class.extract(str)).to contain_exactly('9780805069099', '9780671879198')
+  end
+
+  it 'extracts ISBNs with hyphens' do
+    expect(described_class.extract('ISBN: 978-0-80-506909-9')).to contain_exactly('9780805069099')
+  end
+
+  it 'extracts ISBNs with Unicode dashes' do
+    expect(described_class.extract('ISBN: 978–0–80–506909–9')).to contain_exactly('9780805069099')
+  end
+
+  it 'extracts ISBNs with spaces' do
+    expect(described_class.extract('ISBN: 978 0 80 506909 9')).to contain_exactly('9780805069099')
+  end
+
+  it 'extracts ISBNs with Unicode spaces' do
+    expect(described_class.extract('ISBN: 978 0 80 506909 9')).to contain_exactly('9780805069099')
+  end
+
+  it 'extracts ISBN-13s from ISBN-As' do
+    expect(described_class.extract('10.978.8898392/315')).to contain_exactly('9788898392315')
+  end
+
+  it 'does not extract invalid ISBNs from ISBN-As' do
+    expect(described_class.extract('10.978.8898392/316')).to be_empty
+  end
+
+  it 'normalizes 10-digit ISBNs' do
+    str = "0-8050-6909-7 \n 2-7594-0269-X"
+
+    expect(described_class.extract(str)).to contain_exactly('9780805069099', '9782759402694')
+  end
+
+  it 'extracts multiple 10-digit ISBNs separated by a space' do
+    str = '0-8050-6909-7 2-7594-0269-X'
+
+    expect(described_class.extract(str)).to contain_exactly('9780805069099', '9782759402694')
+  end
+
+  it 'normalizes 10-digit ISBNs with Unicode dashes' do
+    expect(described_class.extract('0–8050–6909–7')).to contain_exactly('9780805069099')
+  end
+
+  it 'normalizes 10-digit ISBNs with a check digit of 10' do
+    expect(described_class.extract('4423272350')).to contain_exactly('9784423272350')
+  end
+
+  it 'normalizes 10-digit ISBNs with spaces' do
+    expect(described_class.extract('0 8050 6909 7')).to contain_exactly('9780805069099')
+  end
+
+  it 'normalizes 10-digit ISBNs with Unicode spaces' do
+    expect(described_class.extract('0 8050 6909 7')).to contain_exactly('9780805069099')
+  end
+
+  it 'normalizes 10-digit ISBNs with spaces and a check digit of X' do
+    expect(described_class.extract('2 7594 0269 X')).to contain_exactly('9782759402694')
+  end
+
+  it 'does not extract invalid 13-digit ISBNs' do
+    expect(described_class.extract('9783319217280')).to be_empty
+  end
+
+  it 'does not extract invalid 10-digit ISBNs' do
+    expect(described_class.extract('3319217280')).to be_empty
+  end
+
+  it 'does not extract ISBN-10s from hyphenated ISBN-13s' do
+    expect(described_class.extract('978-0-309-57079-4')).to contain_exactly('9780309570794')
+  end
+
+  it 'does not extract ISBN-10s from space-separated ISBN-13s' do
+    expect(described_class.extract('978 0 309 57079 4')).to contain_exactly('9780309570794')
+  end
+end

data/spec/identifiers/pubmed_id_spec.rb

@@ -1,29 +1,99 @@
-require 'identifiers/pubmed_id'
-
-RSpec.describe Identifiers::PubmedId do
-  it 'extracts PubMed IDs' do
-    expect(described_class.extract("123\n456")).to contain_exactly('123', '456')
-  end
-
-  it 'does not return outputs with PubMed IDs in DOIs' do
-    str = "10.1038/nplants.2015.3\n10.1126/science.286.5445.1679e"
-
-    expect(described_class.extract(str)).to be_empty
-  end
-
-  it 'strips leading 0s' do
-    expect(described_class.extract("0000010203\n000456000")).to contain_exactly('10203', '456000')
-  end
-
-  it 'does not consider 0 as a valid Pubmed ID' do
-    expect(described_class.extract("00000000")).to be_empty
-  end
-
-  it 'extracts PubMed IDs separated by Unicode whitespace' do
-    expect(described_class.extract('123 456')).to contain_exactly('123', '456')
-  end
-
-  it 'considers Fixnum as potential PubmedIds too' do
-    expect(described_class.extract(123)).to contain_exactly('123')
-  end
-end
+require 'identifiers/pubmed_id'
+
+RSpec.describe Identifiers::PubmedId do
+  it 'extracts PubMed IDs' do
+    expect(described_class.extract("123\n456")).to contain_exactly('123', '456')
+  end
+
+  it 'extracts PubMed IDs from a PubMed URL with www' do
+    url = 'http://www.ncbi.nlm.nih.gov/pubmed/123456'
+
+    expect(described_class.extract(url)).to contain_exactly('123456')
+  end
+
+  it 'extracts PubMed IDs from a PubMed URL with www and https' do
+    url = 'https://www.ncbi.nlm.nih.gov/pubmed/123456'
+
+    expect(described_class.extract(url)).to contain_exactly('123456')
+  end
+
+  it 'extracts PubMed IDs from a PubMed URL without www' do
+    url = 'http://ncbi.nlm.nih.gov/pubmed/123456'
+
+    expect(described_class.extract(url)).to contain_exactly('123456')
+  end
+
+  it 'extracts PubMed IDs from a PubMed URL without www but with https' do
+    url = 'https://ncbi.nlm.nih.gov/pubmed/123456'
+
+    expect(described_class.extract(url)).to contain_exactly('123456')
+  end
+
+  it 'extracts PubMed IDs from a PubMed mobile URL' do
+    url = 'https://www.ncbi.nlm.nih.gov/m/pubmed/123456'
+
+    expect(described_class.extract(url)).to contain_exactly('123456')
+  end
+
+  it 'extracts PubMed IDs from a PubMed URL with hash parameters' do
+    url = 'https://www.ncbi.nlm.nih.gov/pubmed/123456#cm6191871_69589'
+
+    expect(described_class.extract(url)).to contain_exactly('123456')
+  end
+
+  it 'extracts PubMed IDs from a PubMed URL with query parameters' do
+    url = 'https://www.ncbi.nlm.nih.gov/pubmed/123456?hi=hello&goodbye=bye'
+
+    expect(described_class.extract(url)).to contain_exactly('123456')
+  end
+
+  it 'extracts zero leading PubMed IDs from a PubMed URL with query parameters' do
+    url = 'https://www.ncbi.nlm.nih.gov/pubmed/00123456?hi=hello&goodbye=bye'
+
+    expect(described_class.extract(url)).to contain_exactly('123456')
+  end
+
+  it 'extracts both number and URLs PubMed IDs' do
+    url = 'PubMed ID: 112233 another: https://www.ncbi.nlm.nih.gov/pubmed/123456'
+
+    expect(described_class.extract(url)).to contain_exactly('112233', '123456')
+  end
+
+  it 'does not return outputs with PubMed IDs in DOIs' do
+    str = "10.1038/nplants.2015.3\n10.1126/science.286.5445.1679e"
+
+    expect(described_class.extract(str)).to be_empty
+  end
+
+  it 'strips leading 0s' do
+    expect(described_class.extract("0000010203\n000456000")).to contain_exactly('10203', '456000')
+  end
+
+  it 'does not consider 0 as a valid PubMed ID' do
+    expect(described_class.extract('00000000')).to be_empty
+  end
+
+  it 'extracts PubMed IDs separated by Unicode whitespace' do
+    expect(described_class.extract('123 456')).to contain_exactly('123', '456')
+  end
+
+  it 'considers Fixnum as potential PubMed IDs too' do
+    expect(described_class.extract(123)).to contain_exactly('123')
+  end
+
+  it 'extracts PubMed IDs with pmid scheme' do
+    expect(described_class.extract('pmid:123')).to contain_exactly('123')
+  end
+
+  it 'strips leading zeroes from pmid scheme' do
+    expect(described_class.extract('pmid:000123')).to contain_exactly('123')
+  end
+
+  it 'extracts PubMed IDs with info pmid scheme' do
+    expect(described_class.extract('info:pmid/123')).to contain_exactly('123')
+  end
+
+  it 'strips leading zeroes from info pmid scheme' do
+    expect(described_class.extract('info:pmid/000123')).to contain_exactly('123')
+  end
+end

data/spec/spec_helper.rb

@@ -1,18 +1,18 @@
-RSpec.configure do |config|
-  config.filter_run :focus
-  config.run_all_when_everything_filtered = true
-  config.example_status_persistence_file_path = "spec/examples.txt"
-  config.disable_monkey_patching!
-  config.warnings = true
-  config.order = :random
-  config.default_formatter = 'doc' if config.files_to_run.one?
-  Kernel.srand config.seed
-
-  config.expect_with :rspec do |expectations|
-    expectations.include_chain_clauses_in_custom_matcher_descriptions = true
-  end
-
-  config.mock_with :rspec do |mocks|
-    mocks.verify_partial_doubles = true
-  end
-end
+RSpec.configure do |config|
+  config.filter_run :focus
+  config.run_all_when_everything_filtered = true
+  config.example_status_persistence_file_path = "spec/examples.txt"
+  config.disable_monkey_patching!
+  config.warnings = true
+  config.order = :random
+  config.default_formatter = 'doc' if config.files_to_run.one?
+  Kernel.srand config.seed
+
+  config.expect_with :rspec do |expectations|
+    expectations.include_chain_clauses_in_custom_matcher_descriptions = true
+  end
+
+  config.mock_with :rspec do |mocks|
+    mocks.verify_partial_doubles = true
+  end
+end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: identifiers
 version: !ruby/object:Gem::Version
-  version: 0.9.1
+  version: 0.10.0
 platform: ruby
 authors:
 - Jonathan Hernandez
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: exe
 cert_chain: []
-date: 2017-08-01 00:00:00.000000000 Z
+date: 2017-12-20 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: urn
@@ -119,7 +119,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.5.1
+rubygems_version: 2.6.13
 signing_key: 
 specification_version: 4
 summary: Utilities library for various scholarly identifiers used by Altmetric