bibsync 0.0.1 → 0.0.2

data/lib/bibsync/bibliography.rb

@@ -3,16 +3,11 @@ module BibSync
     include Enumerable
 
     attr_reader :file
+    attr_accessor :save_hook
 
     def initialize(file = nil)
-      @entries, @file = {}, file
-      parse(File.read(@file)) if @file && File.exists?(@file)
-      @dirty = false
-      @save_hooks = []
-    end
-
-    def save_hook(hook)
-      @save_hooks << hook
+      @entries, @save_hook = {}, nil
+      load(file)
     end
 
     def dirty?
@@ -23,6 +18,14 @@ module BibSync
       @dirty = true
     end
 
+    def empty?
+      @entries.empty?
+    end
+
+    def size
+      @entries.size
+    end
+
     def [](key)
       @entries[key]
     end
@@ -35,10 +38,17 @@ module BibSync
       end
     end
 
+    def clear
+      unless @entries.empty?
+        @entries.clear
+        dirty!
+      end
+    end
+
     def relative_path(file)
       raise 'No filename given' unless @file
-      bibpath = Pathname.new(@file).realpath.parent
-      Pathname.new(file).realpath.relative_path_from(bibpath).to_s
+      bibpath = File.absolute_path(File.dirname(@file))
+      Pathname.new(file).realpath.relative_path_from(Pathname.new(bibpath)).to_s
     end
 
     def each(&block)
@@ -49,12 +59,12 @@ module BibSync
       if file
         @file = file
         @parent_path = nil
-        @dirty = true
+        dirty!
       end
 
       raise 'No filename given' unless @file
       if @dirty
-        @save_hooks.each {|hook| hook.call(self) }
+        @save_hook.call(self) if @save_hook
         File.open("#{@file}.tmp", 'w') {|f| f.write(self) }
         File.rename("#{@file}.tmp", @file)
         @dirty = false
@@ -65,11 +75,25 @@ module BibSync
     end
 
     def <<(entry)
+      raise 'Entry has no key' if !entry.key || entry.key.empty?
+      raise 'Entry is already existing' if @entries.include?(entry.key)
       entry.bibliography = self
       @entries[entry.key] = entry
       dirty!
     end
 
+    def load(file)
+      parse(File.read(file)) if file && File.exists?(file)
+      @file = file
+      @dirty = false
+    end
+
+    def load!(file)
+      parse(File.read(file))
+      @file = file
+      @dirty = false
+    end
+
     def parse(text)
       until text.empty?
         case text
@@ -94,21 +118,34 @@ module BibSync
     class Entry
       include Enumerable
 
-      attr_accessor :key, :type, :bibliography
+      attr_accessor :bibliography, :type
+      attr_reader :key
 
       def self.parse(text)
-        entry = Entry.new
-        entry.parse(text)
-        entry
+        Entry.new.tap {|e| e.parse(text) }
+      end
+
+      def initialize(fields = {})
+        self.key = fields.delete(:key) if fields.include?(:key)
+        self.type = fields.delete(:type) if fields.include?(:type)
+        @fields = fields
       end
 
-      def initialize
-        @fields = {}
+      def key=(key)
+        key = key.to_s
+        raise 'Key cannot be empty' if key.empty?
+        if bib = bibliography
+          bib.delete(self)
+          @key = key
+          bib << self
+        else
+          @key = key
+        end
       end
 
       def file=(file)
         raise 'No bibliography set' unless bibliography
-        file =~ /\.(\w+)$/
+        file =~ /\.(\w+)\Z/
         self[:file] = ":#{bibliography.relative_path(file)}:#{$1.upcase}" # JabRef file format "description:path:type"
         file
       end
@@ -116,9 +153,9 @@ module BibSync
       def file
         if self[:file]
           raise 'No bibliography set' unless bibliography
-          description, file, type = self[:file].split(':', 3)
-          path = (Pathname.new(bibliography.file).realpath.parent + file).to_s
-          { :name => File.basename(path), :type => type.upcase.to_sym, :path => path }
+          _, file, type = self[:file].split(':', 3)
+          path = File.join(File.absolute_path(File.dirname(bibliography.file)), file)
+          { name: File.basename(path), type: type.upcase.to_sym, path: path }
         end
       end
 
@@ -127,7 +164,7 @@ module BibSync
       end
 
       def []=(key, value)
-        if value then
+        if value
           key = convert_key(key)
           value = RawValue === value ? RawValue.new(value.to_s.strip) : value.to_s.strip
           if @fields[key] != value || @fields[key].class != value.class

data/lib/bibsync/command.rb

@@ -14,7 +14,7 @@ module BibSync
       process
       exit 0
     rescue Exception => ex
-      raise ex if Log.trace? || SystemExit === ex
+      raise ex if Log.trace || SystemExit === ex
       $stderr.print "#{ex.class}: " if ex.class != RuntimeError
       $stderr.puts ex.message
       $stderr.puts '  Use --trace for backtrace.'
@@ -63,11 +63,11 @@ module BibSync
       end
 
       opts.on('-V', '--verbose', 'Verbose output') do
-        Log.verbose!
+        Log.level = :debug
       end
 
       opts.on('--trace', 'Show a full traceback on error') do
-        Log.trace!
+        Log.trace = true
       end
 
       opts.on('-h', '--help', 'Display this help') do
@@ -90,16 +90,21 @@ module BibSync
 
       if @options[:bib]
         @options[:bib] = Bibliography.new(@options[:bib])
-        @options[:bib].save_hook(Transformer.new)
+        @options[:bib].save_hook = Transformer.new
       end
 
       actions = []
       actions << :FetchFromArXiv if @options[:fetch]
-      actions << :CheckVersions if @options[:check_versions] || @options[:update]
-      actions << :SynchronizeFiles << :SynchronizeMetadata if @options[:sync] || @options[:resync]
+      actions << :CheckArXivVersions if @options[:check_versions] || @options[:update]
+      actions << :SynchronizeFiles << :DetermineArXivDOI << :SynchronizeMetadata if @options[:sync] || @options[:resync]
       actions << :FindMyCitations if @options[:citedbyme]
-      actions << :Validate
-      actions << :JabrefFormat if @options[:jabref]
+      actions << :Validate if @options[:bib]
+      actions << :JabRefFormat if @options[:jabref]
+
+      if actions.empty?
+        puts "Please specify actions! See #{$0} --help"
+        exit
+      end
 
       actions.map {|a| Actions.const_get(a).new(@options) }.each {|a| a.run }
     end

data/lib/bibsync/log.rb

@@ -5,53 +5,55 @@ module BibSync
     Yellow = "\e[33m"
     Blue = "\e[36m"
 
-    def self.verbose?
-      @verbose
-    end
+    Level = {
+      debug:   nil,
+      info:    nil,
+      notice:  Blue,
+      warning: Yellow,
+      error:   Red,
+    }
 
-    def self.verbose!
-      @verbose = true
+    class << self
+      attr_accessor :level, :trace
     end
 
-    def self.trace?
-      @trace
-    end
-
-    def self.trace!
-      @trace = true
-    end
+    self.trace = false
+    self.level = :info
 
     def debug(message, opts = {})
-      info(message, opts) if Log.verbose?
+      log(:debug, message, opts)
     end
 
     def info(message, opts = {})
-      log(message, opts)
+      log(:info, message, opts)
     end
 
     def notice(message, opts = {})
-      log(message, opts.merge(:color => Blue))
+      log(:notice, message, opts)
     end
 
     def warning(message, opts = {})
-      log(message, opts.merge(:color => Yellow))
+      log(:warning, message, opts)
     end
 
     def error(message, opts = {})
-      log(message, opts.merge(:color => Red))
+      log(:error, message, opts)
     end
 
-    def log(message, opts = {})
+    def log(level, message, opts = {})
+      return if Level.keys.index(level) < Level.keys.index(Log.level)
       if ex = opts[:ex]
         message = "#{message} - #{ex.message}"
       end
-      message = "#{opts[:color]}#{message}#{Reset}" if opts[:color]
+      if color = Level[level]
+        message = "#{color}#{message}#{Reset}"
+      end
       if key = opts[:key]
         key = key.key if key.respond_to? :key
         message = "#{key} : #{message}"
       end
       puts(message)
-      if Log.trace? && ex = opts[:ex]
+      if Log.trace && ex = opts[:ex]
         puts(ex.backtrace.join("\n"))
       end
     end

data/lib/bibsync/transformer.rb

@@ -55,7 +55,7 @@ module BibSync
             entry[:shortjournal] = 'RMP'
           when /\ANew Journal of Physics\Z/i
             entry[:shortjournal] = 'NJP'
-          when /\A#{ArXivJournal}\Z/i
+          when /\AArXiv e-prints\Z/i
             entry[:shortjournal] = 'arXiv'
           when /\AEurophysics Letters\Z/i
             entry[:shortjournal] = 'EPL'

data/lib/bibsync/utils.rb

@@ -1,10 +1,8 @@
 module BibSync
   module Utils
-    ArXivJournal = 'ArXiv e-prints'
-
-    def split_filename(file)
-      file =~ /^(.*?)\.(\w+)$/
-      return $1, $2.upcase
+    def name_without_ext(file)
+      file =~ /\A(.*?)\.\w+\Z/
+      $1
     end
 
     def fetch(url, headers = {})
@@ -17,7 +15,7 @@ module BibSync
 
     def arxiv_download(dir, id)
       url = "http://arxiv.org/pdf/#{id}"
-      file = File.join(dir, "#{arxiv_id(id, :version => true, :prefix => false)}.pdf")
+      file = File.join(dir, "#{arxiv_id(id, version: true, prefix: false)}.pdf")
       result = `curl --stderr - -S -s -L -o #{Shellwords.escape file} #{Shellwords.escape url}`
       raise result.chomp if $? != 0
     end
@@ -36,10 +34,10 @@ module BibSync
       raise unless opts.include?(:prefix) && opts.include?(:version)
       arxiv = arxiv[:arxiv] if Bibliography::Entry === arxiv
       if arxiv
-        arxiv = arxiv.sub(/^.*\//, '') unless opts[:prefix]
-        arxiv = arxiv.sub(/v\d+$/, '') unless opts[:version]
-        arxiv
+        arxiv = arxiv.sub(/\A.*\//, '') unless opts[:prefix]
+        arxiv = arxiv.sub(/v\d+\Z/, '') unless opts[:version]
       end
+      arxiv
     end
   end
 end

data/lib/bibsync/version.rb

@@ -1,3 +1,3 @@
 module BibSync
-  VERSION = '0.0.1'
+  VERSION = '0.0.2'
 end

data/test/actions/test_check_arxiv_versions.rb

@@ -0,0 +1,4 @@
+require 'helper'
+
+describe BibSync::Actions::CheckArXivVersions do
+end

data/test/actions/test_determine_arxiv_doi.rb

@@ -0,0 +1,61 @@
+require 'helper'
+
+describe BibSync::Actions::DetermineArXivDOI do
+  before do
+    @tmpfile = File.join(fixturedir, 'tmp.bib')
+  end
+
+  after do
+    File.unlink(@tmpfile) if File.exists?(@tmpfile)
+  end
+
+  let(:bib) do
+    BibSync::Bibliography.new(@tmpfile)
+  end
+
+  let(:fixturebib) do
+    BibSync::Bibliography.new(File.join(fixturedir, 'test.bib'))
+  end
+
+  let(:action) do
+    BibSync::Actions::DetermineArXivDOI.new(bib: bib)
+  end
+
+  it 'should find arXiv identifier in pdf file' do
+    entry = fixturebib['FileWithEmbeddedArXiv']
+    bib << entry
+    action.run
+    entry[:arxiv].must_equal '0911.2512v3'
+  end
+
+  it 'should find DOI identifier in file and add missing arXiv identifier' do
+    entry = fixturebib['FileWithEmbeddedDOI']
+    bib << entry
+    action.run
+    entry[:arxiv].must_equal '0911.2512v3'
+    entry[:doi].must_equal '10.1103/PhysRevLett.104.106404'
+  end
+
+  it 'should interpret file name as arXiv identifier' do
+    entry = fixturebib['0911.2512v3']
+    bib << entry
+    action.run
+    entry[:arxiv].must_equal '0911.2512v3'
+  end
+
+  it 'should interpret file name as DOI identifier and add missing arXiv identifier' do
+    entry = fixturebib['PhysRevLett.104.106404']
+    bib << entry
+    action.run
+    entry[:arxiv].must_equal '0911.2512v3'
+    entry[:doi].must_equal '10.1103/PhysRevLett.104.106404'
+  end
+
+  it 'should add missing arXiv identifier' do
+    entry = fixturebib['HasDOI']
+    bib << entry
+    entry[:doi].must_equal '10.1103/PhysRevLett.104.106404'
+    action.run
+    entry[:arxiv].must_equal '0911.2512v3'
+  end
+end

data/test/actions/test_fetch_from_arxiv.rb

@@ -0,0 +1,4 @@
+require 'helper'
+
+describe BibSync::Actions::FetchFromArXiv do
+end

data/test/actions/test_find_my_citations.rb

@@ -0,0 +1,4 @@
+require 'helper'
+
+describe BibSync::Actions::FindMyCitations do
+end

data/test/actions/test_jabref_format.rb

@@ -0,0 +1,4 @@
+require 'helper'
+
+describe BibSync::Actions::JabRefFormat do
+end

data/test/actions/test_synchronize_files.rb

@@ -0,0 +1,4 @@
+require 'helper'
+
+describe BibSync::Actions::SynchronizeFiles do
+end

data/test/actions/test_synchronize_metadata.rb

@@ -0,0 +1,34 @@
+require 'helper'
+
+describe BibSync::Actions::SynchronizeMetadata do
+  before do
+    @tmpfile = File.join(fixturedir, 'tmp.bib')
+  end
+
+  after do
+    File.unlink(@tmpfile) if File.exists?(@tmpfile)
+  end
+
+  let(:bib) do
+    BibSync::Bibliography.new(@tmpfile)
+  end
+
+  let(:fixturebib) do
+    BibSync::Bibliography.new(File.join(fixturedir, 'test.bib'))
+  end
+
+  let(:action) do
+    BibSync::Actions::SynchronizeMetadata.new(bib: bib)
+  end
+
+  it 'should download metadata' do
+    entry = fixturebib['HasArXiv']
+    bib << entry
+    action.run
+    entry[:title].must_equal 'Chirality Induced Tilted-Hill Giant Nernst Signal'
+    entry[:journal].must_equal 'Physical Review Letters'
+    entry[:doi].must_equal '10.1103/PhysRevLett.104.106404'
+    entry[:arxiv].must_equal '0911.2512v3'
+    entry[:url].must_match(/dx\.doi\.org/)
+  end
+end

data/test/actions/test_validate.rb

@@ -0,0 +1,4 @@
+require 'helper'
+
+describe BibSync::Actions::Validate do
+end

data/test/fixture/FileWithEmbeddedArXiv.tex

@@ -0,0 +1,7 @@
+\documentclass{article}
+
+\begin{document}
+
+arXiv: 0911.2512v3
+
+\end{document}

data/test/fixture/FileWithEmbeddedDOI.tex

@@ -0,0 +1,7 @@
+\documentclass{article}
+
+\begin{document}
+
+doi: 10.1103/PhysRevLett.104.106404
+
+\end{document}

data/test/fixture/entry.bib

@@ -0,0 +1,8 @@
+@BOOK{TestBook,
+  title = {BookTitle},
+  publisher = {BookPublisher},
+  year = {2000},
+  month = jan,
+  author = {BookAuthor},
+  volume = {BookVolume}
+}

data/test/fixture/test.bib

@@ -0,0 +1,34 @@
+@BOOK{TestBook,
+  title = {BookTitle},
+  publisher = {BookPublisher},
+  year = {2000},
+  month = jan,
+  author = {BookAuthor},
+  volume = {BookVolume}
+}
+
+@ARTICLE{FileWithEmbeddedArXiv,
+  file = {:FileWithEmbeddedArXiv.pdf:PDF}
+}
+
+@ARTICLE{FileWithEmbeddedDOI,
+  file = {:FileWithEmbeddedDOI.pdf:PDF}
+}
+
+@ARTICLE{HasArXiv,
+  arxiv = {0911.2512v3}
+}
+
+@ARTICLE{HasDOI,
+  doi = {10.1103/PhysRevLett.104.106404}
+}
+
+@ARTICLE{0911.2512v3,
+  file = {:0911.2512v3.txt:TXT}
+}
+
+@ARTICLE{PhysRevLett.104.106404,
+  file = {:PhysRevLett.104.106404.txt:TXT}
+}
+
+@COMMENT{TestComment}

data/test/helper.rb

@@ -0,0 +1,21 @@
+require 'minitest/spec'
+require 'minitest/autorun'
+require 'bibsync'
+require 'fileutils'
+
+BibSync::Log.level = :error
+BibSync::Log.trace = true
+
+module Helper
+  def fixturedir
+    File.join(File.dirname(__FILE__), 'fixture')
+  end
+end
+
+class MiniTest::Spec
+  include Helper
+
+  after do
+    FileUtils.rm_rf(File.join(File.dirname(__FILE__), 'tmp'))
+  end
+end