biblicit 1.0

data/.gitignore

@@ -0,0 +1,3 @@
+perl/log/*
+perl/HeaderParseService/tmp/*
+Gemfile.lock

data/.rspec

@@ -0,0 +1 @@
+--require spec_helper --color

data/Gemfile

@@ -0,0 +1,6 @@
+# encoding: UTF-8
+
+source :rubygems
+
+# Specify your gem's dependencies in the gemspec
+gemspec

data/LICENSE.TXT

@@ -0,0 +1,176 @@
+                              Apache License
+                        Version 2.0, January 2004
+                     http://www.apache.org/licenses/
+
+TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
+1. Definitions.
+
+   "License" shall mean the terms and conditions for use, reproduction,
+   and distribution as defined by Sections 1 through 9 of this document.
+
+   "Licensor" shall mean the copyright owner or entity authorized by
+   the copyright owner that is granting the License.
+
+   "Legal Entity" shall mean the union of the acting entity and all
+   other entities that control, are controlled by, or are under common
+   control with that entity. For the purposes of this definition,
+   "control" means (i) the power, direct or indirect, to cause the
+   direction or management of such entity, whether by contract or
+   otherwise, or (ii) ownership of fifty percent (50%) or more of the
+   outstanding shares, or (iii) beneficial ownership of such entity.
+
+   "You" (or "Your") shall mean an individual or Legal Entity
+   exercising permissions granted by this License.
+
+   "Source" form shall mean the preferred form for making modifications,
+   including but not limited to software source code, documentation
+   source, and configuration files.
+
+   "Object" form shall mean any form resulting from mechanical
+   transformation or translation of a Source form, including but
+   not limited to compiled object code, generated documentation,
+   and conversions to other media types.
+
+   "Work" shall mean the work of authorship, whether in Source or
+   Object form, made available under the License, as indicated by a
+   copyright notice that is included in or attached to the work
+   (an example is provided in the Appendix below).
+
+   "Derivative Works" shall mean any work, whether in Source or Object
+   form, that is based on (or derived from) the Work and for which the
+   editorial revisions, annotations, elaborations, or other modifications
+   represent, as a whole, an original work of authorship. For the purposes
+   of this License, Derivative Works shall not include works that remain
+   separable from, or merely link (or bind by name) to the interfaces of,
+   the Work and Derivative Works thereof.
+
+   "Contribution" shall mean any work of authorship, including
+   the original version of the Work and any modifications or additions
+   to that Work or Derivative Works thereof, that is intentionally
+   submitted to Licensor for inclusion in the Work by the copyright owner
+   or by an individual or Legal Entity authorized to submit on behalf of
+   the copyright owner. For the purposes of this definition, "submitted"
+   means any form of electronic, verbal, or written communication sent
+   to the Licensor or its representatives, including but not limited to
+   communication on electronic mailing lists, source code control systems,
+   and issue tracking systems that are managed by, or on behalf of, the
+   Licensor for the purpose of discussing and improving the Work, but
+   excluding communication that is conspicuously marked or otherwise
+   designated in writing by the copyright owner as "Not a Contribution."
+
+   "Contributor" shall mean Licensor and any individual or Legal Entity
+   on behalf of whom a Contribution has been received by Licensor and
+   subsequently incorporated within the Work.
+
+2. Grant of Copyright License. Subject to the terms and conditions of
+   this License, each Contributor hereby grants to You a perpetual,
+   worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+   copyright license to reproduce, prepare Derivative Works of,
+   publicly display, publicly perform, sublicense, and distribute the
+   Work and such Derivative Works in Source or Object form.
+
+3. Grant of Patent License. Subject to the terms and conditions of
+   this License, each Contributor hereby grants to You a perpetual,
+   worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+   (except as stated in this section) patent license to make, have made,
+   use, offer to sell, sell, import, and otherwise transfer the Work,
+   where such license applies only to those patent claims licensable
+   by such Contributor that are necessarily infringed by their
+   Contribution(s) alone or by combination of their Contribution(s)
+   with the Work to which such Contribution(s) was submitted. If You
+   institute patent litigation against any entity (including a
+   cross-claim or counterclaim in a lawsuit) alleging that the Work
+   or a Contribution incorporated within the Work constitutes direct
+   or contributory patent infringement, then any patent licenses
+   granted to You under this License for that Work shall terminate
+   as of the date such litigation is filed.
+
+4. Redistribution. You may reproduce and distribute copies of the
+   Work or Derivative Works thereof in any medium, with or without
+   modifications, and in Source or Object form, provided that You
+   meet the following conditions:
+
+   (a) You must give any other recipients of the Work or
+       Derivative Works a copy of this License; and
+
+   (b) You must cause any modified files to carry prominent notices
+       stating that You changed the files; and
+
+   (c) You must retain, in the Source form of any Derivative Works
+       that You distribute, all copyright, patent, trademark, and
+       attribution notices from the Source form of the Work,
+       excluding those notices that do not pertain to any part of
+       the Derivative Works; and
+
+   (d) If the Work includes a "NOTICE" text file as part of its
+       distribution, then any Derivative Works that You distribute must
+       include a readable copy of the attribution notices contained
+       within such NOTICE file, excluding those notices that do not
+       pertain to any part of the Derivative Works, in at least one
+       of the following places: within a NOTICE text file distributed
+       as part of the Derivative Works; within the Source form or
+       documentation, if provided along with the Derivative Works; or,
+       within a display generated by the Derivative Works, if and
+       wherever such third-party notices normally appear. The contents
+       of the NOTICE file are for informational purposes only and
+       do not modify the License. You may add Your own attribution
+       notices within Derivative Works that You distribute, alongside
+       or as an addendum to the NOTICE text from the Work, provided
+       that such additional attribution notices cannot be construed
+       as modifying the License.
+
+   You may add Your own copyright statement to Your modifications and
+   may provide additional or different license terms and conditions
+   for use, reproduction, or distribution of Your modifications, or
+   for any such Derivative Works as a whole, provided Your use,
+   reproduction, and distribution of the Work otherwise complies with
+   the conditions stated in this License.
+
+5. Submission of Contributions. Unless You explicitly state otherwise,
+   any Contribution intentionally submitted for inclusion in the Work
+   by You to the Licensor shall be under the terms and conditions of
+   this License, without any additional terms or conditions.
+   Notwithstanding the above, nothing herein shall supersede or modify
+   the terms of any separate license agreement you may have executed
+   with Licensor regarding such Contributions.
+
+6. Trademarks. This License does not grant permission to use the trade
+   names, trademarks, service marks, or product names of the Licensor,
+   except as required for reasonable and customary use in describing the
+   origin of the Work and reproducing the content of the NOTICE file.
+
+7. Disclaimer of Warranty. Unless required by applicable law or
+   agreed to in writing, Licensor provides the Work (and each
+   Contributor provides its Contributions) on an "AS IS" BASIS,
+   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
+   implied, including, without limitation, any warranties or conditions
+   of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A
+   PARTICULAR PURPOSE. You are solely responsible for determining the
+   appropriateness of using or redistributing the Work and assume any
+   risks associated with Your exercise of permissions under this License.
+
+8. Limitation of Liability. In no event and under no legal theory,
+   whether in tort (including negligence), contract, or otherwise,
+   unless required by applicable law (such as deliberate and grossly
+   negligent acts) or agreed to in writing, shall any Contributor be
+   liable to You for damages, including any direct, indirect, special,
+   incidental, or consequential damages of any character arising as a
+   result of this License or out of the use or inability to use the
+   Work (including but not limited to damages for loss of goodwill,
+   work stoppage, computer failure or malfunction, or any and all
+   other commercial damages or losses), even if such Contributor
+   has been advised of the possibility of such damages.
+
+9. Accepting Warranty or Additional Liability. While redistributing
+   the Work or Derivative Works thereof, You may choose to offer,
+   and charge a fee for, acceptance of support, warranty, indemnity,
+   or other liability obligations and/or rights consistent with this
+   License. However, in accepting such obligations, You may act only
+   on Your own behalf and on Your sole responsibility, not on behalf
+   of any other Contributor, and only if You agree to indemnify,
+   defend, and hold each Contributor harmless for any liability
+   incurred by, or claims asserted against, such Contributor by reason
+   of your accepting any such warranty or additional liability.
+
+END OF TERMS AND CONDITIONS

data/README.md

@@ -0,0 +1,120 @@
+biblicit
+=============
+
+Extract citations from PDFs.
+
+## Usage
+
+```ruby
+  # Extract metadata from a file using the code from CiteSeerX
+  Biblicit.extract(file: "myfile.pdf", tool: :citeseer)
+
+  # Extract metadata from the contents of a PDF using cb2bib
+  Biblicit.extract(contents: IO.read("myfile.pdf"), tool: :cb2bib, remote: true)
+```
+
+## Algorithms
+
+### CiteSeer (default)
+
+Wrapper around Perl code extracted from [CiteSeerX](http://citeseer.ist.psu.edu/). 
+
+Uses [Apache PDFBox](http://pdfbox.apache.org/) to extract text from the PDF, uses a model trained with the [svm-light](http://svmlight.joachims.org/) Support Vector Machine library to extract citation data for the PDF itself, and then uses [ParsCit](http://aye.comp.nus.edu.sg/parsCit/)'s model trained with the [CRF++](http://code.google.com/p/crfpp/) Conditional Random Fields library to parse citations from the PDF's bibliography, if any.
+
+### cb2Bib
+
+Wrapper around [cb2Bib](http://www.molspaces.com/cb2bib/) in command-line mode.
+
+Uses pdf2text from [Xpdf](http://www.foolabs.com/xpdf/download.html) to extract text from the PDF, uses an apparently less-sophisticated parsing algorithm than the CiteSeerX code to parse metadata, but then, if :remote=true, scrapes one of a large number of journal or public repository websites for a structured version of the citation data.
+
+## Requirements
+
+### CRF++
+ 
+##### From source
+
+    wget http://crfpp.googlecode.com/files/CRF%2B%2B-0.57.tar.gz
+    tar xvzf CRF++-0.57.tar.gz
+    cd CRF++-0.57
+    ./configure 
+    make
+    sudo make install
+
+##### On Debian/Ubuntu
+
+    sudo apt-add-repository 'deb http://cl.naist.jp/~eric-n/ubuntu-nlp oneiric all'
+    sudo apt-get update
+    sudo apt-get install libcrf++
+
+##### On OS X with Homebrew
+
+    brew install crf++
+
+### svm-light
+
+The included model requires version 5, not the current version.
+
+##### From source
+
+    mkdir svm_light5
+    cd svm_light5
+    wget http://download.joachims.org/svm_light/v5.00/svm_light.tar.gz
+    tar -xzf svm_light.tar.gz
+    make
+    sudo ln -s $(readlink -f "$(dirname svm_classify)/$(basename svm_classify)") /usr/bin/svm_classify5
+    sudo ln -s $(readlink -f "$(dirname svm_learn)/$(basename svm_learn)") /usr/bin/svm_learn5
+
+Note: On OS X you'll need to use greadlink instead of readlink if you have coreutils installed, or another workaround for the absence of `-f`.
+
+### Perl modules
+
+##### From CPAN
+
+    sudo cpan install DBI
+    sudo cpan install Digest::SHA1
+    sudo cpan install Log::Log4perl
+    sudo cpan install Log::Dispatch
+    sudo cpan install String::Approx
+
+### cb2bib
+
+##### From source (Linux)
+
+    wget http://www.molspaces.com/dl/progs/cb2bib-1.4.9.tar.gz
+    tar -xzvf cb2bib-1.4.9.tar.gz
+    cd cb2bib-1.4.9
+    ./configure --prefix /usr/local
+    make
+    sudo make install
+
+##### From source (OS X)
+
+Requires Qt & X11, unfortunately, and still requires a hack to work on recent versions of OS X.
+
+    wget http://www.molspaces.com/dl/progs/cb2bib-1.4.9.tar.gz
+    tar -xzvf cb2bib-1.4.9.tar.gz
+    cd cb2bib-1.4.9
+    ./configure --prefix /Applications/cb2Bib
+    make # fails first time...
+    mv src/Makefile src/Makefile.old
+    sed 's|-lX11 -framework QtWebKit|-lX11 -L/usr/X11/lib -I/usr/X11/include -framework QtWebKit|' src/Makefile.old > src/Makefile
+    make # should succeed now
+    sudo make install
+
+##### On Debian/Ubuntu
+
+    sudo apt-get install cb2bib
+
+### Other
+
+##### On Debian/Ubuntu
+
+    sudo apt-get install libicu-dev
+
+## Copying
+
+Copyright Academia.edu or the original author(s).
+
+Apache licensed (see LICENSE.TXT).
+
+Please note svm-light is in general free only for non-commercial use, but can be used in this gem by permission of the author. For conditions on additional uses see [the website](http://svmlight.joachims.org/).

data/Rakefile

@@ -0,0 +1,8 @@
+# encoding: UTF-8
+
+require 'rake'
+require 'bundler/gem_tasks'
+require 'rspec/core/rake_task'
+require 'biblicit'
+
+RSpec::Core::RakeTask.new :spec

data/biblicit.gemspec

@@ -0,0 +1,33 @@
+# encoding: UTF-8
+
+lib = File.expand_path('../lib', __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+
+Gem::Specification.new do |gem|
+  gem.name          = "biblicit"
+  gem.version       = "1.0"
+  gem.authors       = ["David Judd"]
+  gem.email         = ["david@academia.edu"]
+  gem.description   = %q{Extract citations from PDFs.}
+  gem.summary       = %q{Extract citations from PDFs.}
+  gem.homepage      = "http://github.com/academia-edu/biblicit"
+
+  gem.files         = `git ls-files`.split("\n")
+  gem.executables   = gem.files.grep(%r{^bin/}).map{ |f| File.basename(f) }
+  gem.test_files    = gem.files.grep(%r{^spec/})
+  gem.require_paths = ["lib"]
+
+  gem.add_dependency 'activesupport'
+  gem.add_dependency 'nokogiri'
+
+  gem.add_development_dependency 'rake'
+  gem.add_development_dependency 'rspec'
+  gem.add_development_dependency 'pry'
+  gem.add_development_dependency 'pry-debugger'
+
+  gem.requirements << 'java'
+  gem.requirements << 'perl'
+  gem.requirements << 'for the :citeseer algorithm, the CRF++ Conditional Random Fields library (try "which crf_test")'
+  gem.requirements << 'for the :cb2bib algorithm, the cb2bib citation extraction tool'
+
+end

data/lib/biblicit/cb2bib.rb

@@ -0,0 +1,83 @@
+# encoding: UTF-8
+
+require 'tempfile'
+
+module Cb2Bib
+
+  def self.extract(file, opts)
+    ParseOperation.new(file, opts)
+  end
+
+  class ParseOperation
+
+    def initialize(file, opts)
+      extract_from_file(file, opts[:remote] || false, opts[:sloppy] || true)
+    end
+
+    def header
+      @result
+    end
+
+  private
+
+    def extract_from_file(pdf, remote=false, sloppy=true)
+      bib = Tempfile.new(['out','.bib'])
+      conf = Tempfile.new(['cb2bib','.conf']) # we'll put our custom configuration here, and then cb2bib will fill in the rest with its defaults
+
+      begin
+        conf.write(cb2bib_config(remote))
+        conf.open # not clear why we have to do this, but otherwise cb2bib doesn't read it
+        `cb2bib #{sloppy ? '--sloppy' : ''} --doc2bib #{pdf.shellescape} #{bib.path} --conf #{conf.path}`
+        bibtext = bib.read
+      ensure
+        conf.close!
+        bib.close!
+      end
+
+      @result = {}
+
+      if defined?(bibtext) && !bibtext.blank?
+        bibtext.split("\n").each do |line|
+          if (m = line.match /^(\w+)\s+= \{?(.+)\},?$/)
+            field = cleaned_field(m[1])
+            value = cleaned_value(field, m[2])
+            @result[field] = value
+          end
+        end
+      end
+
+      @result[:valid] = !@result[:title].blank?
+    end
+
+    def cb2bib_config(remote)
+      "[cb2Bib]\nAutomaticQuery=#{!!remote}"
+    end
+
+    def cleaned_field(field)
+      cleaned = field.to_sym
+      if cleaned == :author
+        :authors
+      else
+        cleaned
+      end
+    end
+
+    def cleaned_value(field, value)
+      value.strip!
+      if (m = value.match /^\{(.+)\}$/)
+        value = m[1]
+        value.strip!
+      end
+
+      if field == :authors
+        value.split(' and ').map(&:strip)
+      elsif value.match /^\d+$/
+        value.to_i
+      else
+        value
+      end
+    end
+
+  end
+
+end

data/lib/biblicit/citeseer.rb

@@ -0,0 +1,53 @@
+# encoding: UTF-8
+
+require 'tmpdir'
+require 'shellwords'
+require 'nokogiri'
+
+module CiteSeer
+
+  PERL_DIR = "#{File.dirname(__FILE__)}/../../perl"
+
+  def self.extract(in_file, opts)
+    ParseOperation.new(in_file)
+  end
+
+  class ParseOperation
+
+    def initialize(in_file)
+      Dir.mktmpdir do |out_dir|
+        `#{PERL_DIR}/extract.pl #{in_file.shellescape} #{out_dir}`
+        @header_xml = IO.read("#{out_dir}/out.header")
+        @citations_xml = IO.read("#{out_dir}/out.parscit")
+      end
+    end
+
+    def header
+      @header ||= get_header
+    end
+
+    def citations
+      @citations ||= get_citations
+    end
+
+  private
+
+    def get_header
+      parsed = Nokogiri::XML @header_xml
+
+      {
+        title: parsed.css('title').text,
+        authors: parsed.css('author > name').map { |n| n.text },
+        abstract: parsed.css('abstract').text,
+        valid: parsed.css('validHeader').first.text == '1',
+      }
+    end
+
+    def get_citations
+      # TODO
+      []
+    end
+
+  end
+
+end

data/lib/biblicit/extractor.rb

@@ -0,0 +1,37 @@
+# encoding: UTF-8
+
+require 'biblicit/cb2bib'
+require 'biblicit/citeseer'
+
+require 'tempfile'
+
+module Biblicit
+
+  def self.extract(opts)
+    if (content = opts.delete(:content))
+      Tempfile.open(['in','.pdf']) do |pdf|
+        pdf.write(content)
+        extract_from_file pdf.path, opts
+      end
+    elsif (file = opts.delete(:file))
+      extract_from_file file, opts
+    else
+      raise 'Either file or content is required'
+    end
+  end
+
+private
+
+  def self.extract_from_file(file, opts)
+    tool = opts.delete(:tool) || :citeseer
+
+    if tool == :citeseer
+      CiteSeer.extract(file, opts)
+    elsif tool == :cb2bib
+      Cb2Bib.extract(file, opts)
+    else
+      raise "Unknown tool #{tool}"
+    end
+  end
+
+end

data/lib/biblicit.rb

@@ -0,0 +1,6 @@
+# encoding: UTF-8
+
+require 'active_support/core_ext/object'
+require 'active_support/core_ext/string'
+
+require 'biblicit/extractor'

data/perl/DocFilter/lib/CSXUtil/SafeText.pm

@@ -0,0 +1,140 @@
+#
+# Copyright 2007 Penn State University
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#     http://www.apache.org/licenses/LICENSE-2.0
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+package CSXUtil::SafeText;
+##
+##  Methods for stripping bad (XML unsafe) characters
+##  from strings and performing basic HTML entity
+##  translations.  Also contains a utility (stripArtifacts)
+##  for getting rid of crazy control characters and
+##  other things that probably aren't proper text.
+##
+##  Isaac Councill, 12/06/06
+##
+#######################################################
+##
+use strict;
+use utf8;
+require Exporter;
+
+our ($VERSION, @ISA, @EXPORT, @EXPORT_OK, %EXPORT_TAGS);
+
+$VERSION = 1.00;
+
+@ISA = qw(Exporter);
+@EXPORT_OK = qw(@badChars %htmlSpecialChars
+		%htmlCharEntities &stripBadChars
+		&encodeHTMLSpecialChars
+		&decodeHTMLSpecialChars
+		&cleanXML &cleanAll &stripArtifacts);
+
+
+##
+#######################################################
+##
+##  Sharable encoding data.
+##
+
+##  Hex codes for characters that should never be put into
+##  XML - or else parsers will barf.
+our @badChars = qw(\x00 \x01 \x02 \x03 \x04 \x05 \x06 \x07
+		   \x08 \x0B \x0C \x0E \x0F \x10 \x11 \x12
+		   \x13 \x14 \x15 \x16 \x17 \x18 \x19 \x1A
+		   \x1B \x1C \x1D \x1E \x1F \x7F);
+
+##  Subset of HTML characters that could be problematic
+##  for XML.  This is not a complete list of HTML
+##  special characters, but more mappings can be added
+##  as needed.
+our %htmlSpecialCharEncodings = ("&" => "&",
+				 ">" => ">",
+				 "<" => "&lt;",
+				 "\"" => "&quot;"
+				 );
+
+##  The reverse map.
+our %htmlSpecialCharDecodings;
+foreach my $key (keys %htmlSpecialCharEncodings) {
+    my $val = $htmlSpecialCharEncodings{$key};
+    $htmlSpecialCharDecodings{$val} = $key;
+}
+
+
+##
+#######################################################
+##
+##  Subroutines
+##
+
+##  Delete all occurences of bad characters in text,
+##  returns a new string that is clean.
+sub stripBadChars {
+    my $rtext = shift;
+    foreach my $char (@badChars) {
+	$$rtext =~ s/$char//g;
+    }
+}
+
+
+##  Encodes special characters into HTML equivalents
+##  and returns the encoded string.
+sub encodeHTMLSpecialChars {
+    my $rtext = shift;
+    foreach my $char (keys %htmlSpecialCharEncodings) {
+	my $code = $htmlSpecialCharEncodings{$char};
+	$$rtext =~ s/$char/$code/g;
+    }
+}
+
+
+##  Decodes a HTML entities in the supplied string
+##  into non-HTML character equivalents and returns
+##  the decoded string.
+sub decodeHTMLSpecialChars {
+    my $rtext = shift;
+    foreach my $code (keys %htmlSpecialCharDecodings) {
+	my $char = $htmlSpecialCharDecodings{$code};
+	$$rtext =~ s/$code/$char/g;
+    }
+}
+
+
+##  Strip out any characters that don't look like they
+##  belong in a proper, readable text string.
+##
+sub stripArtifacts {
+    my $rtext = shift;
+    $$rtext =~ s/[^\p{IsAlnum}\p{IsPunct}\p{IsSpace}\p{IsS}]//g;
+}
+
+
+##  Convenience routine for executing both XML safety
+##  routines in a single call.
+##
+sub cleanXML {
+    my $rtext = shift;
+    stripBadChars($rtext);
+    encodeHTMLSpecialChars($rtext);
+}
+
+
+##  Clean for XML and also strip out strange characters.
+##
+sub cleanAll {
+    my $rtext = shift;
+    stripBadChars($rtext);
+    stripArtifacts($rtext);
+    encodeHTMLSpecialChars($rtext);
+}
+
+
+1;