bivy 0.0.5

data/lib/format/acs.rb

@@ -0,0 +1,88 @@
+
+# see: http://www.lib.berkeley.edu/CHEM/acsstyle.html
+
+# Article:
+# Basic Format:
+# Author, A. A; Author, B. B; Author, C. C. Title of Article. Journal Abbreviation (italics) [Online if online] Year (boldface), Volume (italics), Pagination.
+
+# Borman, S. Protein Sequencing For The Masses. Chem. Eng. News [Online] 2004, 82, pp 22-23.
+# Slunt, K. M.; Giancarlo, L. C. Student-Centered Learning: A Comparison of Two Different Methods of Instruction. J. Chem. Educ. 2004, 81, pp 985-988.
+# Takahaski, T. The Fate of Industrial Carbon Dioxide. Science [Online] 2004, 305, 352-353.
+#                                              {italics      }  {b}  {i}
+# (1) Washburn, M.P.; Wolters, D.; Yates, J.R. Nat. Biotechnol. 2001, 19, 242-7.
+#
+#
+# Book with Author(s)
+
+#Basic Format:
+#Author, A. A.; Author, B. B. Book Title (italics), Edition (if any); Publisher: Place of Publication, Year; Pagination.
+#
+#Dill, K. A.; Bromberg, S. Molecular Driving Forces: Statistical Thermodynamics in Chemistry and Biology; Garland Science: New York, 2003.
+#Engel, R; Cohen, J. I. Synthesis of Carbon-Phosphorus Bonds: New Methods of Exploration; CRC Press: Boca Raton, FL, 2004; pp 54-56.
+#Zumdahl, S. S. Chemical Principles, 4th ed.; Houghton Mifflin: Boston, MA, 2002; p 7.
+
+class Format::ACS
+  include Format
+  Format::Symbol_to_class_string[:acs] = 'ACS'
+
+=begin
+  def article(cit)
+    [author_list('.', ', ', '; '), i(journal_iso), b(year), [vol, pages].compact.join(', ')]
+  end
+
+  # needs to deal with journal or no journal
+  def article_to_be_submitted(cit)
+    [author_list('.'), i(journal_iso), i('Article to be submitted')]
+  end
+
+  def webpage(cit)
+    [periodize(b(title)), u(url), periodize("#{b(year)}, #{month} #{day}")].compact.join(' ')
+  end
+
+  # TODO: book
+
+=end
+
+ def article
+    vol_o_nil = 
+      if vol
+        "#{vol}"
+      else
+        nil
+      end
+    [author_list('.'), i(journal_iso), [b(year), i(vol), pages].compact.join(', ')]
+  end
+
+  def article_to_be_submitted
+    [author_list('.'), i(journal_iso), i('Article to be submitted')]
+  end
+
+# Webpage (2 examples):
+# ChemFinder.Com. http://chemfinder.cambridgesoft.com (accessed July 14, 2004).
+
+  # (accessed July 14, 2004)
+  def webpage
+    accessed_string = nil
+    if year
+      accessed_string = '(accessed '
+      if month
+        accessed_string << month.to_s
+        if day
+          accessed_string << " #{day}, "
+        else
+          accessed_string << " "
+        end
+      end
+      accessed_string << year.to_s << ')'
+    end
+
+    [periodize(title), url, accessed_string].compact.join(' ') << '.'
+  end
+
+  # TODO: book
+
+
+end
+
+
+

data/lib/format/bioinformatics.rb

@@ -0,0 +1,33 @@
+
+# authors(initialed,comma'd,no spaces, using et al for 3 or more) (2007) *title* i(Journal_iso) *year*, i(vol(issue)), pages.
+# authors(initialed) \(year\). "title" u(Journal_medline) *vol*(issue): pages.
+class Format::Bioinformatics
+  include Format
+
+  def article
+    [ [periodize(author_list('.', ',',nil)), par(year), periodize(title), i(journal_iso)].compact.join(' '), b(vol), pages].compact.join(', ') << '.'
+  end
+
+  #def article_to_be_submitted
+  #  #[periodize(author_list('.')),  periodize(par(year)), "\"#{periodize(title)}\"", i(journal_medline), b(vol), par(issue), ": #{pages}"].compact.join(' ')
+  #  [author_list('.'), "\"#{periodize(title)}\"", u(journal_medline), i('Article to be submitted')].compact.join(' ') << '.'
+  #end
+
+  def article_in_review
+    [periodize(author_list('.', ',',nil)), par(year), periodize(title), i(journal_iso)].compact.join(' ') + ', ' + i('manuscript in review') << '.'
+  end
+
+  # shouldn't really be webpages in the references
+  def webpage
+    abort 'shouldnt be webpages in Bioinformatics journals!'
+  end
+
+  #def workshop
+  #  [periodize(author_list('.')),  periodize(par(year)), "\"#{periodize(title)}\"", u(name), "#{pages}"].compact.join(' ') << '.'
+  #end
+
+  # TODO: book
+
+end
+
+

data/lib/format/bmc.rb

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+
+class Format::BMC
+  include Format
+  Format::Symbol_to_class_string[:bmc] = 'BMC'
+
+ def article
+    issue_string =
+      if issue.nil?
+        ''
+      else
+        "(#{issue})"
+      end
+    vol_string = 
+      if vol.nil?
+        ''
+      else
+        vol
+      end
+
+    # This is the original:
+    "#{author_list('')}: #{b(periodize(title))} #{i(journal_medline)} #{year}, #{b(vol_string)}#{issue_string}:#{pages_full}."
+    #  ThIS IS NOT the BMC format:
+    # "#{author_list('.', ' ', ', ', '&', true)} (#{year}) #{title.gsub(/\.$/,'')}, #{periodize(i(journal_iso))} #{i(vol_string)}, #{pages}."
+  end
+
+# Webpage (2 examples):
+# b(Webpage Name) [http://chemfinder.cambridgesoft.com]
+
+  def webpage
+    [b(title), br(url)].compact.join(' ')
+  end
+
+  # TODO: book
+
+end
+
+
+

data/lib/format/jtp.rb

@@ -0,0 +1,30 @@
+
+# authors(initialed) *title* i(Journal_iso) *year*, i(vol(issue)), pages.
+class Format::JTP
+  include Format
+  Format::Symbol_to_class_string[:jtp] = 'JTP'
+
+  def article
+    vol_issue = 
+      if vol
+        "#{vol}#{par(issue)}"
+      else
+        nil
+      end
+    [author_list('.'), b(title), i(journal_iso), [b(year), vol_issue, pages].compact.join(', ')]
+  end
+
+  def article_to_be_submitted
+    [author_list('.'), i(journal_iso), i('Article to be submitted')]
+  end
+
+  def webpage
+    [periodize(b(title)), u(url), periodize("#{b(year)}, #{month} #{day}")].compact.join(' ')
+  end
+
+  # TODO: book
+  
+  
+end
+
+

data/lib/format/mla.rb

@@ -0,0 +1,50 @@
+
+# authors(initialed) *title* i(Journal_iso) *year*, i(vol(issue)), pages.
+# authors(initialed) \(year\). "title" u(Journal_medline) *vol*(issue): pages.
+class Format::MLA
+  include Format
+  Format::Symbol_to_class_string[:mla] = 'MLA'
+
+  def article
+    vol_issue = 
+      if vol
+        "#{b(vol)}#{par(issue)}"
+      else
+        nil
+      end
+    [periodize(author_list('.')),  periodize(par(year)), "\"#{periodize(title)}\"", u(journal_medline), "#{vol_issue}: #{pages}"].compact.join(' ') << '.'
+  end
+
+  def article_to_be_submitted
+    #[periodize(author_list('.')),  periodize(par(year)), "\"#{periodize(title)}\"", i(journal_medline), b(vol), par(issue), ": #{pages}"].compact.join(' ')
+    [author_list('.'), "\"#{periodize(title)}\"", u(journal_medline), i('Article to be submitted')].compact.join(' ') << '.'
+  end
+
+  def webpage
+    accessed_string = nil
+    if year
+      accessed_string = '(accessed '
+      if month
+        accessed_string << month.to_s
+        if day
+          accessed_string << " #{day}, "
+        else
+          accessed_string << " "
+        end
+      end
+      accessed_string << year.to_s << ')'
+    end
+
+    [periodize(title), url, accessed_string].compact.join(' ') << '.'
+  end
+
+  def workshop
+    [periodize(author_list('.')),  periodize(par(year)), "\"#{periodize(title)}\"", u(name), "#{pages}"].compact.join(' ') << '.'
+
+  end
+
+  # TODO: book
+  
+end
+
+

data/lib/formatter.rb

@@ -0,0 +1,276 @@
+require 'citation'
+require 'pubmed'
+require 'set'
+require 'ooffice'
+
+class Formatter
+
+  FindStartCitation = '#['
+  FindEndCitation = ']'
+  SplitCitations = ','
+  StartNumbering = 1
+  ReplaceWith = 'X'
+
+
+  # later we can figure out the little trick to do this on the fly
+  # the letter for the entry being added
+  ArSizeToLetter = {
+    1 => 'b',
+    2 => 'c',
+    3 => 'd',
+    4 => 'e',
+    5 => 'f',
+    6 => 'g',
+    7 => 'h',
+    8 => 'i',
+    9 => 'j',
+    10 => 'k',
+  }
+
+  # outputs an html string and modifies the document (only .odt files
+  # currently)
+  # biblio is a yaml file
+  # creates .cit.odt file with citations replaced
+  def create_bibliography(document, biblio, options={})
+    bib = Bibliography.from_yaml(biblio)
+    new_document = document.sub(/\.odt$/, '.cit.odt')
+
+    ordered_cit_ids = nil
+    if options[:bib] == :mla
+      OpenOffice.new.modify_content(document, new_document) do |xml| 
+        if cp = options[:cit_pos]
+          xml = reposition_citations(xml, cp)
+        end
+        # this may actually change the year on some bibs
+        (new_xml, ordered_cit_ids) = replace_citations_mla(xml, bib)
+        new_xml
+      end
+      unless ordered_cit_ids ; abort "Couldn't get citations" end
+      bib.select_by_id!(ordered_cit_ids)
+    else
+      OpenOffice.new.modify_content(document, new_document) do |xml| 
+        if cp = options[:cit_pos]
+          xml = reposition_citations(xml, cp)
+        end
+        if options[:bracket]
+          (new_xml, ordered_cit_ids) = replace_citations_numerically(xml, FindStartCitation, FindEndCitation, SplitCitations, StartNumbering, ' [X]')
+          # (string, find_start_citation='#[', find_end_citation=']', split_citations=',', start_numbering=1, replace_with='X')
+        else
+          (new_xml, ordered_cit_ids) = replace_citations_numerically(xml)
+        end
+        new_xml
+      end
+      unless ordered_cit_ids ; abort "Couldn't get citations" end
+      bib.select_by_id!(ordered_cit_ids)
+    end
+    bib
+  end
+
+  # moves all citations following '.' or ',' to desired position
+  # position = :before or :after
+  #
+  def reposition_citations(xml, position)
+    # search<text:span text:style-name="T29">#[Keller2002]</text:span>,
+    # --> search,<text:span text:style-name="T29">#[Keller2002]</text:span>
+    #  human samples<text:span text:style-name="T29">#[Qian2005]</text:span>.
+    # -->  human samples.<text:span text:style-name="T29">#[Qian2005]</text:span>
+    #  OR human samples#[Qian2005].
+    # -->  human samples.#[Qian2005]
+    case position
+    when :after
+      xml = xml.gsub(/(#\[.*?\])([\.\,])/) do |md|
+        $2 + $1
+      end
+      xml.gsub(/(<[^\/][^<]+>)(#\[.*?\])(<\/.*?>)([\.\,])/) do |md|
+        $4 + $1 + $2 + $3
+      end
+    when :before
+      xml = xml.gsub(/([\.\,])(#\[.*?\])/) do |md|
+        $2 + $1
+      end
+      xml.gsub(/([\.\,])(<[^\/][^<]+>)(#\[.*?\])(<\/.*?>)/) do |md|
+        $2 + $3 + $4 + $1
+      end
+
+    end
+  end
+
+  def to_mla_ref(citation)
+    if citation.bibtype == :webpage
+      citation.title
+    else
+      author_bit = 
+        if citation.authors.is_a? String  # just use first listed thing for now
+          citation.authors.split(/\s+/).first
+        else # assuming array
+          aa = citation.authors
+          case aa.size
+          when 1 
+            aa[0].last
+          when 2 
+            aa[0].last + ' and ' + aa[1].last
+            #aa[0].last + ' &amp; ' + aa[1].last   ## using an ampersand
+          else
+            aa[0].last + ' et al.'
+          end
+        end
+      author_bit + ', ' + "#{citation.year}"
+    end
+  end
+
+  # order can be :alphabetical or :as_is
+  # warning: may change the year on some bib citations!
+  def replace_citations_mla(string, bib, start_citation='#[', end_citation=']', split_citations=',', order=:alphabetical)
+    regex_string = Regexp.escape(start_citation) + '(.*?)' + Regexp.escape(end_citation)
+    id_to_cit = {}
+    bib.citations.each do |cit|
+      id_to_cit[cit.ident] = cit
+    end
+
+    # This is a hash that helps to distinguish between citations with the same
+    # mla_ref.
+    mla_ref_to_cits = Hash.new {|h,k| h[k] = [] }
+    id_to_mla_ref = {}  # from the citation id to the mla_ref
+    # First pass to determine if some author/year combos are duplicated
+    # in which case they will be yeara and yearb and so on (2004a).
+    string.scan(/#{regex_string}/) do
+      refs = $1.split(split_citations)
+      refs.each do |ref|
+        unless id_to_cit.key?(ref)
+          puts "*************************************"
+          puts "* No citation for: #{ref}"
+          puts "*************************************"
+          exit
+        end
+        citation = id_to_cit[ref]
+        mla_ref = to_mla_ref(citation)
+        ## alter mla_ref if necessary
+        if mla_ref_to_cits.key?(mla_ref)
+          if id_to_mla_ref.key?(citation.ident)
+            # this reference already has already been seen, do nothing
+          else  # conflict
+            ar = mla_ref_to_cits[mla_ref]
+            if ar.size == 1
+              # change mla_ref
+              id_to_mla_ref[ar[0].ident] = mla_ref + 'a' # new mla_ref
+              # change the citation year for bibliography
+              id_to_cit[ar[0].ident].year << 'a'
+            end
+            letter = ArSizeToLetter[ar.size]
+            new_mla_ref = mla_ref + letter
+            # put in a modified mla_ref
+            id_to_mla_ref[citation.ident] = new_mla_ref
+            # change the year in bib
+            id_to_cit[citation.ident].year << letter
+            mla_ref_to_cits[mla_ref].push(citation)
+          end
+        else # first mla_ref of its kind
+          mla_ref_to_cits[mla_ref].push(citation)
+          id_to_mla_ref[ref] = mla_ref
+        end
+      end
+    end
+
+    # second pass to create actual citation with updated mla_refs
+    new_string = string.gsub(/#{regex_string}/) do
+      refs = $1.split(split_citations)
+      mla_refs = refs.map do |ref|
+        id_to_mla_ref[id_to_cit[ref].ident]
+      end
+      to_mla_citation_string(mla_refs)
+    end
+
+    # final list of citations will be ordered by ordering the mla_ref_to_cits
+    # keys (the years are already ordered a,b,c... if necessary)
+    
+    ordered_cit_ids = []
+    sorted_mla_refs = mla_ref_to_cits.keys.sort_by {|k| k.downcase }
+
+    sorted_mla_refs.each do |mla_ref|
+      cits = mla_ref_to_cits[mla_ref]
+      ordered_cit_ids.push( *(cits.map {|cit| cit.ident }) )
+    end
+    [new_string, ordered_cit_ids]
+  end
+
+  # takes a string of mla_refs and spits out the final guy
+  def to_mla_citation_string(mla_refs)
+    " (#{mla_refs.join('; ')})"
+  end
+
+
+  # replace citations will take any string and replace any references
+  # according to find_start_citation, find_end_citation and split_citations
+  # returns [string, citation_hash]
+  # string is the substituted string, hash is hashed by reference and gives
+  # replace_with uses the formatting of the string given to format the
+  # citation.  The 'X' is the numeric citation.  So, X is just the number and
+  # '[X]' would be a bracketed number.
+  # the citation number
+  # (see tests for examples) 
+  def replace_citations_numerically(string, find_start_citation=FindStartCitation, find_end_citation=FindEndCitation, split_citations=SplitCitations, start_numbering=StartNumbering, replace_with=ReplaceWith)
+    (before_X, after_X) = replace_with.split('X').map(&:to_s)
+    before_X ||= ''
+    after_X ||= ''
+    cits = {}
+    regex_string = Regexp.escape(find_start_citation) + '(.*?)' + Regexp.escape(find_end_citation)
+
+    ref_cnt = start_numbering
+    new_string = string.gsub(/#{regex_string}/) do
+      refs = $1.split(split_citations)
+      cit_list = refs.map do |ref|
+        unless cits.key? ref 
+          cits[ref] = ref_cnt
+          ref_cnt += 1
+        end
+        cits[ref]  # <- no formatting at this point
+      end
+      before_X + cit_string(cit_list) + after_X
+    end
+    ordered_cits = cits.map {|k,v| [v,k]}.sort.map {|ar| ar[1] }
+    [new_string, ordered_cits]
+  end
+
+  # given an array of citations, generate the string for their citation
+  # 
+  # e.g. if [10, 11, 12], string should be '10-12'
+  # e.g. if [4, 13, 12, 17] string should be '4,12-13,17' 
+  def cit_string(cit_num_array)
+    # Single citation:
+    if cit_num_array.size == 0
+      return ''
+    elsif cit_num_array.size == 1
+      return cit_num_array.first.to_s
+    end
+    # Multiple citations:
+    cit_num_array.sort!
+    #memo = [previous, running, size_cnt, string]
+    tracker = nil
+    cit_num_array.inject([nil,false,1,'']) do |memo,num|
+      ## not in a run:
+      if (num - 1) != memo[0] # not in a run:
+        if memo[1]            # finish a run
+          memo[3] << "-#{memo[0]},#{num}"
+        else                  # wasn't running before:
+          if memo[0]          # if there is a previous
+            memo[3] << ",#{num}"
+          else                # the start
+            memo[3] << "#{num}"
+          end
+        end
+        memo[1] = false       # state that we are not in a run
+      else                    # in a run 
+        if memo[2] == cit_num_array.size  # the last item (in a run)
+          memo[3] << "-#{num}"
+        end
+        memo[1] = true        # state that we are running
+      end
+      memo[2] += 1            # keep track of the size
+      memo[0] = num           # set previous number
+      tracker = memo
+      memo
+    end
+    tracker[3]
+  end
+
+end