COIN-OR::LEMON - Graph Library

Ticket #184: 848db1b1cec6.patch

File 848db1b1cec6.patch, 39.0 KB (added by Alpar Juttner, 10 years ago)
  • CMakeLists.txt

    # HG changeset patch
    # User Alpar Juttner <alpar@cs.elte.hu>
    # Date 1253952949 -7200
    # Node ID 848db1b1cec6cd263772407c942f8347f1610965
    # Parent  0977046c60d27196e3b008fe9f65350180ec5362
    Bibtex References (#184)
    
    diff --git a/CMakeLists.txt b/CMakeLists.txt
    a b  
    3535CHECK_TYPE_SIZE("long long" LONG_LONG)
    3636SET(LEMON_HAVE_LONG_LONG ${HAVE_LONG_LONG})
    3737
     38INCLUDE(FindPythonInterp)
     39
    3840ENABLE_TESTING()
    3941
    4042ADD_SUBDIRECTORY(lemon)
  • configure.ac

    diff --git a/configure.ac b/configure.ac
    a b  
    4141AC_PROG_LIBTOOL
    4242
    4343AC_CHECK_PROG([doxygen_found],[doxygen],[yes],[no])
     44AC_CHECK_PROG([python_found],[python],[yes],[no])
    4445AC_CHECK_PROG([gs_found],[gs],[yes],[no])
    4546
    4647dnl Detect Intel compiler.
  • doc/CMakeLists.txt

    diff --git a/doc/CMakeLists.txt b/doc/CMakeLists.txt
    a b  
    99  @ONLY
    1010)
    1111
    12 IF(DOXYGEN_EXECUTABLE AND GHOSTSCRIPT_EXECUTABLE)
     12IF(DOXYGEN_EXECUTABLE AND PYTHONINTERP_FOUND AND GHOSTSCRIPT_EXECUTABLE)
    1313  FILE(MAKE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/html/)
    1414  SET(GHOSTSCRIPT_OPTIONS -dNOPAUSE -dBATCH -q -dEPSCrop -dTextAlphaBits=4 -dGraphicsAlphaBits=4 -sDEVICE=pngalpha)
    1515  ADD_CUSTOM_TARGET(html
     
    2828    COMMAND ${GHOSTSCRIPT_EXECUTABLE} ${GHOSTSCRIPT_OPTIONS} -r18 -sOutputFile=gen-images/nodeshape_4.png ${CMAKE_CURRENT_SOURCE_DIR}/images/nodeshape_4.eps
    2929    COMMAND ${GHOSTSCRIPT_EXECUTABLE} ${GHOSTSCRIPT_OPTIONS} -r18 -sOutputFile=gen-images/strongly_connected_components.png ${CMAKE_CURRENT_SOURCE_DIR}/images/strongly_connected_components.eps
    3030    COMMAND ${CMAKE_COMMAND} -E remove_directory html
     31    COMMAND ${PYTHON_EXECUTABLE} ${PROJECT_SOURCE_DIR}/scripts/bib2dox.py ${CMAKE_CURRENT_SOURCE_DIR}/references.bib >references.dox
    3132    COMMAND ${DOXYGEN_EXECUTABLE} Doxyfile
    3233    WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
    3334  )
  • doc/Doxyfile.in

    diff --git a/doc/Doxyfile.in b/doc/Doxyfile.in
    a b  
    9191                         "@abs_top_srcdir@/lemon/concepts" \
    9292                         "@abs_top_srcdir@/demo" \
    9393                         "@abs_top_srcdir@/tools" \
    94                          "@abs_top_srcdir@/test/test_tools.h"
     94                         "@abs_top_srcdir@/test/test_tools.h" \
     95                         "@abs_top_builddir@/doc/references.dox"
    9596INPUT_ENCODING         = UTF-8
    9697FILE_PATTERNS          = *.h \
    9798                         *.cc \
  • doc/Makefile.am

    diff --git a/doc/Makefile.am b/doc/Makefile.am
    a b  
    6666          exit 1; \
    6767        fi
    6868
    69 html-local: $(DOC_PNG_IMAGES)
     69references.dox: doc/references.bib
     70        if test ${python_found} = yes; then \
     71          cd doc; \
     72          python $(abs_top_srcdir)/scripts/bib2dox.py $(abs_top_builddir)/$< >$@; \
     73          cd ..; \
     74        else \
     75          echo; \
     76          echo "Python not found."; \
     77          echo; \
     78          exit 1; \
     79        fi
     80
     81html-local: $(DOC_PNG_IMAGES) references.dox
    7082        if test ${doxygen_found} = yes; then \
    7183          cd doc; \
    7284          doxygen Doxyfile; \
  • new file doc/references.bib

    diff --git a/doc/references.bib b/doc/references.bib
    new file mode 100644
    - +  
     1%%%%% Defining LEMON %%%%%
     2
     3@misc{lemon,
     4  key =          "LEMON",
     5  title =        "{LEMON -- Library for Efficient Modeling and
     6                  Optimization in Networks}",
     7  howpublished = "\url{http://lemon.cs.elte.hu/}",
     8  year =         2009
     9}
     10
     11@misc{egres,
     12  key =          "EGRES",
     13  title =        "{EGRES -- Egerv{\'a}ry Research Group on
     14                  Combinatorial Optimization}",
     15  howpublished = "\url{http://www.cs.elte.hu/egres/}",
     16  year =         2009
     17}
     18
     19@misc{coinor,
     20  key =          "COIN-OR",
     21  title =        "{COIN-OR -- Computational Infrastructure for
     22                  Operations Research}",
     23  howpublished = "\url{http://www.coin-or.org/}",
     24  year =         2009
     25}
     26
     27
     28%%%%% Other libraries %%%%%%
     29
     30@misc{boost,
     31  key =          "Boost",
     32  title =        "{Boost C++ Libraries}",
     33  howpublished = "\url{http://www.boost.org/}",
     34  year =         2009
     35}
     36
     37@book{bglbook,
     38  author =       "Jeremy G. Siek and Lee-Quan Lee and Andrew
     39                  Lumsdaine",
     40  title =        "{The Boost Graph Library}: User Guide and Reference
     41                  Manual",
     42  publisher =    "Addison-Wesley",
     43  year =         2002
     44}
     45
     46@misc{leda,
     47  key =          "LEDA",
     48  title =        "{LEDA -- Library of Efficient Data Types and
     49                  Algorithms}",
     50  howpublished = "\url{http://www.algorithmic-solutions.com/}",
     51  year =         2009
     52}
     53
     54@book{ledabook,
     55  author =       "Kurt Mehlhorn and Stefan N{\"a}her",
     56  title =        "{LEDA}: {A} platform for combinatorial and geometric
     57                  computing",
     58  isbn =         "0-521-56329-1",
     59  publisher =    "Cambridge University Press",
     60  address =      "New York, NY, USA",
     61  year =         1999
     62}
     63
     64
     65%%%%% Tools that LEMON depends on %%%%%
     66
     67@misc{cmake,
     68  key =          "CMake",
     69  title =        "{CMake -- Cross Platform Make}",
     70  howpublished = "\url{http://www.cmake.org/}",
     71  year =         2009
     72}
     73
     74@misc{doxygen,
     75  key =          "Doxygen",
     76  title =        "{Doxygen -- Source code documentation generator
     77                  tool}",
     78  howpublished = "\url{http://www.doxygen.org/}",
     79  year =         2009
     80}
     81
     82
     83%%%%% LP/MIP libraries %%%%%
     84
     85@misc{glpk,
     86  key =          "GLPK",
     87  title =        "{GLPK -- GNU Linear Programming Kit}",
     88  howpublished = "\url{http://www.gnu.org/software/glpk/}",
     89  year =         2009
     90}
     91
     92@misc{clp,
     93  key =          "Clp",
     94  title =        "{Clp -- Coin-Or Linear Programming}",
     95  howpublished = "\url{http://projects.coin-or.org/Clp/}",
     96  year =         2009
     97}
     98
     99@misc{cbc,
     100  key =          "Cbc",
     101  title =        "{Cbc -- Coin-Or Branch and Cut}",
     102  howpublished = "\url{http://projects.coin-or.org/Cbc/}",
     103  year =         2009
     104}
     105
     106@misc{cplex,
     107  key =          "CPLEX",
     108  title =        "{ILOG CPLEX}",
     109  howpublished = "\url{http://www.ilog.com/}",
     110  year =         2009
     111}
     112
     113@misc{soplex,
     114  key =          "SoPlex",
     115  title =        "{SoPlex -- The Sequential Object-Oriented Simplex}",
     116  howpublished = "\url{http://soplex.zib.de/}",
     117  year =         2009
     118}
     119
     120
     121%%%%% General books %%%%%
     122
     123@book{amo93networkflows,
     124  author =       "Ravindra K. Ahuja and Thomas L. Magnanti and James
     125                  B. Orlin",
     126  title =        "Network Flows: Theory, Algorithms, and Applications",
     127  publisher =    "Prentice-Hall, Inc.",
     128  year =         1993,
     129  month =        feb,
     130  isbn =         "978-0136175490"
     131}
     132
     133@book{schrijver03combinatorial,
     134  author =       "Alexander Schrijver",
     135  title =        "Combinatorial Optimization: Polyhedra and
     136                  Efficiency",
     137  publisher =    "Springer-Verlag",
     138  year =         2003,
     139  isbn =         "978-3540443896"
     140}
     141
     142@book{clrs01algorithms,
     143  author =       "Thomas H. Cormen and Charles E. Leiserson and Ronald
     144                  L. Rivest and Clifford Stein",
     145  title =        "Introduction to Algorithms",
     146  publisher =    "The MIT Press",
     147  year =         2001,
     148  edition =      "2nd",
     149}
     150
     151@book{stroustrup00cpp,
     152  author =       "Bjarne Stroustrup",
     153  title =        "The C++ Programming Language",
     154  edition =      "3rd",
     155  publisher =    "Addison-Wesley Professional",
     156  isbn =         0201700735,
     157  month =        "February",
     158  year =         2000
     159}
     160
     161
     162%%%%% Maximum flow algorithms %%%%%
     163
     164@inproceedings{goldberg86newapproach,
     165  author =       "Andrew V. Goldberg and Robert E. Tarjan",
     166  title =        "A new approach to the maximum flow problem",
     167  booktitle =    "STOC '86: Proceedings of the Eighteenth Annual ACM
     168                  Symposium on Theory of Computing",
     169  year =         1986,
     170  publisher =    "ACM Press",
     171  address =      "New York, NY",
     172  pages =        "136-146"
     173}
     174
     175@article{dinic70algorithm,
     176  author =       "E. A. Dinic",
     177  title =        "Algorithm for solution of a problem of maximum flow
     178                  in a network with power estimation",
     179  journal =      "Soviet Math. Doklady",
     180  year =         1970,
     181  volume =       11,
     182  pages =        "1277-1280"
     183}
     184
     185@article{goldberg08partial,
     186  author =       "Andrew V. Goldberg",
     187  title =        "The Partial Augment-Relabel Algorithm for the
     188                  Maximum Flow Problem",
     189  journal =      "16th Annual European Symposium on Algorithms",
     190  year =         2008,
     191  pages =        "466-477"
     192}
     193
     194@article{sleator83dynamic,
     195  author =       "Daniel D. Sleator and Robert E. Tarjan",
     196  title =        "A data structure for dynamic trees",
     197  journal =      "Journal of Computer and System Sciences",
     198  year =         1983,
     199  volume =       26,
     200  number =       3,
     201  pages =        "362-391"
     202}
     203
     204
     205%%%%% Minimum mean cycle algorithms %%%%%
     206
     207@article{karp78characterization,
     208  author =       "Richard M. Karp",
     209  title =        "A characterization of the minimum cycle mean in a
     210                  digraph",
     211  journal =      "Discrete Math.",
     212  year =         1978,
     213  volume =       23,
     214  pages =        "309-311"
     215}
     216
     217@article{dasdan98minmeancycle,
     218  author =       "Ali Dasdan and Rajesh K. Gupta",
     219  title =        "Faster Maximum and Minimum Mean Cycle Alogrithms for
     220                  System Performance Analysis",
     221  journal =      "IEEE Transactions on Computer-Aided Design of
     222                  Integrated Circuits and Systems",
     223  year =         1998,
     224  volume =       17,
     225  number =       10,
     226  pages =        "889-899"
     227}
     228
     229
     230%%%%% Minimum cost flow algorithms %%%%%
     231
     232@article{klein67primal,
     233  author =       "Morton Klein",
     234  title =        "A primal method for minimal cost flows with
     235                  applications to the assignment and transportation
     236                  problems",
     237  journal =      "Management Science",
     238  year =         1967,
     239  volume =       14,
     240  pages =        "205-220"
     241}
     242
     243@inproceedings{goldberg88cyclecanceling,
     244  author =       "Andrew V. Goldberg and Robert E. Tarjan",
     245  title =        "Finding minimum-cost circulations by canceling
     246                  negative cycles",
     247  booktitle =    "STOC '88: Proceedings of the Twentieth Annual ACM
     248                  Symposium on Theory of Computing",
     249  year =         1988,
     250  publisher =    "ACM Press",
     251  address =      "New York, NY",
     252  pages =        "388-397"
     253}
     254
     255@article{edmondskarp72theoretical,
     256  author =       "Jack Edmonds and Richard M. Karp",
     257  title =        "Theoretical improvements in algorithmic efficiency
     258                  for network flow problems",
     259  journal =      "Journal of the ACM",
     260  year =         1972,
     261  volume =       19,
     262  number =       2,
     263  pages =        "248-264"
     264}
     265
     266@inproceedings{goldberg87approximation,
     267  author =       "Andrew V. Goldberg and Robert E. Tarjan",
     268  title =        "Solving minimum-cost flow problems by successive
     269                  approximation",
     270  booktitle =    "STOC '87: Proceedings of the Nineteenth Annual ACM
     271                  Symposium on Theory of Computing",
     272  year =         1987,
     273  publisher =    "ACM Press",
     274  address =      "New York, NY",
     275  pages =        "7-18"
     276}
     277
     278@article{goldberg90finding,
     279  author =       "Andrew V. Goldberg and Robert E. Tarjan",
     280  title =        "Finding Minimum-Cost Circulations by Successive
     281                  Approximation",
     282  journal =      "Mathematics of Operations Research",
     283  year =         1990,
     284  volume =       15,
     285  number =       3,
     286  pages =        "430-466"
     287}
     288
     289@article{goldberg97efficient,
     290  author =       "Andrew V. Goldberg",
     291  title =        "An Efficient Implementation of a Scaling
     292                  Minimum-Cost Flow Algorithm",
     293  journal =      "Journal of Algorithms",
     294  year =         1997,
     295  volume =       22,
     296  number =       1,
     297  pages =        "1-29"
     298}
     299
     300@article{bunnagel98efficient,
     301  author =       "Ursula {B\"unnagel} and Bernhard Korte and Jens
     302                  Vygen",
     303  title =        "Efficient implementation of the {Goldberg}-{Tarjan}
     304                  minimum-cost flow algorithm",
     305  journal =      "Optimization Methods and Software",
     306  year =         1998,
     307  volume =       10,
     308  pages =        "157-174"
     309}
     310
     311@mastersthesis{kellyoneill91netsimplex,
     312  author =       "Damian J. Kelly and Garrett M. O'Neill",
     313  title =        "The Minimum Cost Flow Problem and The Network
     314                  Simplex Method",
     315  school =       "University College",
     316  address =      "Dublin, Ireland",
     317  year =         1991,
     318  month =        sep,
     319}
     320
     321@techreport{lobel96networksimplex,
     322  author =       "Andreas {L\"obel}",
     323  title =        "Solving large-scale real-world minimum-cost flow
     324                  problems by a network simplex method",
     325  institution =  "Konrad-Zuse-Zentrum fur Informationstechnik Berlin
     326                  (ZIB)",
     327  address =      "Berlin, Germany",
     328  year =         1996,
     329  number =       "SC 96-7"
     330}
     331
     332@article{frangioni06computational,
     333  author =       "Antonio Frangioni and Antonio Manca",
     334  title =        "A Computational Study of Cost Reoptimization for
     335                  Min-Cost Flow Problems",
     336  journal =      "INFORMS Journal On Computing",
     337  year =         2006,
     338  volume =       18,
     339  number =       1,
     340  pages =        "61-70"
     341}
  • new file scripts/bib2dox.py

    diff --git a/scripts/bib2dox.py b/scripts/bib2dox.py
    new file mode 100644
    - +  
     1#!/usr/bin/env /usr/local/Python/bin/python2.1
     2"""
     3  Decoder for bibliographic data, BibTeX
     4  Usage: python bibtex2xml.py bibfile.bib > bibfile.xml
     5
     6  v.8
     7  (c)2002-06-23 Vidar Bronken Gundersen
     8  http://bibtexml.sf.net/
     9  Reuse approved as long as this notification is kept.
     10  Licence: GPL.
     11
     12  Contributions/thanks to:
     13  Egon Willighagen, http://sf.net/projects/jreferences/
     14  Richard Mahoney (for providing a test case)
     15
     16  Editted by Sara Sprenkle to be more robust and handle more bibtex features.  (c) 2003-01-15
     17  1.  Changed bibtex: tags to bibxml: tags.
     18  2.  Use xmlns:bibxml="http://bibtexml.sf.net/"
     19  3.  Allow spaces between @type and first {
     20  4.  "author" fields with multiple authors split by " and "
     21      are put in separate xml "bibxml:author" tags.
     22  5.  Option for Titles: words are capitalized
     23      only if first letter in title or capitalized inside braces
     24  6.  Removes braces from within field values
     25  7.  Ignores comments in bibtex file (including @comment{ or % )
     26  8.  Replaces some special latex tags, e.g., replaces ~ with '&#160;'
     27  9.  Handles bibtex @string abbreviations
     28        --> includes bibtex's default abbreviations for months
     29        --> does concatenation of abbr # " more " and " more " # abbr
     30  10. Handles @type( ... ) or @type{ ... }
     31  11. The keywords field is split on , or ; and put into separate xml
     32      "bibxml:keywords" tags
     33  12. Ignores @preamble
     34
     35  Known Limitations
     36  1.  Does not transform Latex encoding like math mode and special latex symbols.
     37  2.  Does not parse author fields into first and last names.
     38      E.g., It does not do anything special to an author whose name is in the form LAST_NAME, FIRST_NAME
     39      In "author" tag, will show up as <bibxml:author>LAST_NAME, FIRST_NAME</bibxml:author>
     40  3.  Does not handle "crossref" fields other than to print <bibxml:crossref>...</bibxml:crossref>
     41  4.  Does not inform user of the input's format errors.  You just won't be able to
     42      transform the file later with XSL
     43
     44  You will have to manually edit the XML output if you need to handle
     45  these (and unknown) limitations.
     46
     47"""
     48
     49import string, re
     50
     51# set of valid name characters
     52valid_name_chars = '[\w\-:]'
     53
     54#
     55# define global regular expression variables
     56#
     57author_rex = re.compile('\s+and\s+')
     58rembraces_rex = re.compile('[{}]')
     59capitalize_rex = re.compile('({\w*})')
     60
     61# used by bibtexkeywords(data)
     62keywords_rex = re.compile('[,;]')
     63
     64# used by concat_line(line)
     65concatsplit_rex = re.compile('\s*#\s*')
     66
     67# split on {, }, or " in verify_out_of_braces
     68delimiter_rex = re.compile('([{}"])',re.I)
     69
     70field_rex = re.compile('\s*(\w*)\s*=\s*(.*)')
     71data_rex = re.compile('\s*(\w*)\s*=\s*([^,]*),?')
     72
     73url_rex = re.compile('\\\url\{([^}]*)\}')
     74
     75
     76#
     77# return the string parameter without braces
     78#
     79def transformurls(str):
     80    return url_rex.sub(r'<a href="\1">\1</a>', str)
     81
     82#
     83# return the string parameter without braces
     84#
     85def removebraces(str):
     86    return rembraces_rex.sub('', str)
     87
     88#
     89# latex-specific replacements
     90# (do this after braces were removed)
     91#
     92def latexreplacements(line):
     93    line = string.replace(line, '~', '&nbsp;')
     94    line = string.replace(line, '\\\'a', '&aacute;')
     95    line = string.replace(line, '\\"a', '&auml;')
     96    line = string.replace(line, '\\\'e', '&eacute;')
     97    line = string.replace(line, '\\"e', '&euml;')
     98    line = string.replace(line, '\\\'i', '&iacute;')
     99    line = string.replace(line, '\\"i', '&iuml;')
     100    line = string.replace(line, '\\\'o', '&oacute;')
     101    line = string.replace(line, '\\"o', '&ouml;')
     102    line = string.replace(line, '\\\'u', '&uacute;')
     103    line = string.replace(line, '\\"u', '&uuml;')
     104    line = string.replace(line, '\\H o', '&otilde;')
     105    line = string.replace(line, '\\H u', '&uuml;')   # &utilde; does not exist
     106    line = string.replace(line, '\\\'A', '&Aacute;')
     107    line = string.replace(line, '\\"A', '&Auml;')
     108    line = string.replace(line, '\\\'E', '&Eacute;')
     109    line = string.replace(line, '\\"E', '&Euml;')
     110    line = string.replace(line, '\\\'I', '&Iacute;')
     111    line = string.replace(line, '\\"I', '&Iuml;')
     112    line = string.replace(line, '\\\'O', '&Oacute;')
     113    line = string.replace(line, '\\"O', '&Ouml;')
     114    line = string.replace(line, '\\\'U', '&Uacute;')
     115    line = string.replace(line, '\\"U', '&Uuml;')
     116    line = string.replace(line, '\\H O', '&Otilde;')
     117    line = string.replace(line, '\\H U', '&Uuml;')   # &Utilde; does not exist
     118
     119    return line
     120
     121#
     122# copy characters form a string decoding html expressions (&xyz;)
     123#
     124def copychars(str, ifrom, count):
     125    result = ''
     126    i = ifrom
     127    c = 0
     128    html_spec = False
     129    while (i < len(str)) and (c < count):
     130        if str[i] == '&':
     131            html_spec = True;
     132            if i+1 < len(str):
     133                result += str[i+1]
     134            c += 1
     135            i += 2
     136        else:
     137            if not html_spec:
     138                if ((str[i] >= 'A') and (str[i] <= 'Z')) or \
     139                   ((str[i] >= 'a') and (str[i] <= 'z')):
     140                    result += str[i]
     141                    c += 1
     142            elif str[i] == ';':
     143                html_spec = False;
     144            i += 1
     145   
     146    return result
     147
     148
     149#
     150# Handle a list of authors (separated by 'and').
     151# It gives back an array of the follwing values:
     152#  - num: the number of authors,
     153#  - list: the list of the author names,
     154#  - text: the bibtex text (separated by commas and/or 'and')
     155#  - abbrev: abbreviation that can be used for indicate the
     156#    bibliography entries
     157#
     158def bibtexauthor(data):
     159    result = {}
     160    bibtex = ''
     161    result['list'] = author_rex.split(data)
     162    result['num'] = len(result['list'])
     163    for i, author in enumerate(result['list']):
     164        # general transformations
     165        author = latexreplacements(removebraces(author.strip()))
     166        # transform "Xyz, A. B." to "A. B. Xyz"
     167        pos = author.find(',')
     168        if pos != -1:
     169            author = author[pos+1:].strip() + ' ' + author[:pos].strip()
     170        result['list'][i] = author
     171        bibtex += author + '#'
     172    bibtex = bibtex[:-1]
     173    if result['num'] > 1:
     174        ix = bibtex.rfind('#')
     175        if result['num'] == 2:
     176            bibtex = bibtex[:ix] + ' and ' + bibtex[ix+1:]
     177        else:
     178            bibtex = bibtex[:ix] + ', and ' + bibtex[ix+1:]
     179    bibtex = bibtex.replace('#', ', ')
     180    result['text'] = bibtex
     181   
     182    result['abbrev'] = ''
     183    for author in result['list']:
     184        pos = author.rfind(' ') + 1
     185        count = 1
     186        if result['num'] == 1:
     187            count = 3
     188        result['abbrev'] += copychars(author, pos, count)
     189
     190    return result
     191
     192
     193#
     194# data = title string
     195# @return the capitalized title (first letter is capitalized), rest are capitalized
     196# only if capitalized inside braces
     197#
     198def capitalizetitle(data):
     199    title_list = capitalize_rex.split(data)
     200    title = ''
     201    count = 0
     202    for phrase in title_list:
     203         check = string.lstrip(phrase)
     204
     205         # keep phrase's capitalization the same
     206         if check.find('{') == 0:
     207              title += removebraces(phrase)
     208         else:
     209         # first word --> capitalize first letter (after spaces)
     210              if count == 0:
     211                  title += check.capitalize()
     212              else:
     213                  title += phrase.lower()
     214         count = count + 1
     215
     216    return title
     217
     218
     219#
     220# @return the bibtex for the title
     221# @param data --> title string
     222# braces are removed from title
     223#
     224def bibtextitle(data, entrytype):
     225    if entrytype in ('book', 'inbook'):
     226        title = removebraces(data.strip())
     227    else:
     228        title = removebraces(capitalizetitle(data.strip()))
     229    bibtex = title
     230    return bibtex
     231
     232
     233#
     234# function to compare entry lists
     235#
     236def entry_cmp(x, y):
     237    return cmp(x[0], y[0])
     238
     239
     240#
     241# print the XML for the transformed "filecont_source"
     242#
     243def bibtexdecoder(filecont_source):
     244    filecont = []
     245    file = []
     246   
     247    # want @<alphanumeric chars><spaces>{<spaces><any chars>,
     248    pubtype_rex = re.compile('@(\w*)\s*{\s*(.*),')
     249    endtype_rex = re.compile('}\s*$')
     250    endtag_rex = re.compile('^\s*}\s*$')
     251
     252    bracefield_rex = re.compile('\s*(\w*)\s*=\s*(.*)')
     253    bracedata_rex = re.compile('\s*(\w*)\s*=\s*{(.*)},?')
     254
     255    quotefield_rex = re.compile('\s*(\w*)\s*=\s*(.*)')
     256    quotedata_rex = re.compile('\s*(\w*)\s*=\s*"(.*)",?')
     257
     258    for line in filecont_source:
     259        line = line[:-1]
     260
     261        # encode character entities
     262        line = string.replace(line, '&', '&amp;')
     263        line = string.replace(line, '<', '&lt;')
     264        line = string.replace(line, '>', '&gt;')
     265
     266        # start entry: publication type (store for later use)
     267        if pubtype_rex.match(line):
     268        # want @<alphanumeric chars><spaces>{<spaces><any chars>,
     269            entrycont = {}
     270            entry = []
     271            entrytype = pubtype_rex.sub('\g<1>',line)
     272            entrytype = string.lower(entrytype)
     273            # entryid   = pubtype_rex.sub('\g<2>', line)
     274
     275        # end entry if just a }
     276        elif endtype_rex.match(line):
     277            # generate doxygen code for the entry
     278
     279            # enty type related formattings
     280            if entrytype in ('book', 'inbook'):
     281                entrycont['title'] = '<em>' + entrycont['title'] + '</em>'
     282                if not entrycont.has_key('author'):
     283                    entrycont['author'] = entrycont['editor']
     284                    entrycont['author']['text'] += ', editors'
     285            elif entrytype == 'article':
     286                entrycont['journal'] = '<em>' + entrycont['journal'] + '</em>'
     287            elif entrytype in ('inproceedings', 'incollection', 'conference'):
     288                entrycont['booktitle'] = '<em>' + entrycont['booktitle'] + '</em>'
     289            elif entrytype == 'techreport':
     290                if not entrycont.has_key('type'):
     291                    entrycont['type'] = 'Technical report'
     292            elif entrytype == 'mastersthesis':
     293                entrycont['type'] = 'Master\'s thesis'
     294            elif entrytype == 'phdthesis':
     295                entrycont['type'] = 'PhD thesis'
     296
     297            for eline in entrycont:
     298                if eline != '':
     299                    eline = latexreplacements(eline)
     300
     301            if entrycont.has_key('pages') and (entrycont['pages'] != ''):
     302                entrycont['pages'] = string.replace(entrycont['pages'], '--', '-')
     303
     304            if entrycont.has_key('author') and (entrycont['author'] != ''):
     305                entry.append(entrycont['author']['text'] + '.')
     306            if entrycont.has_key('title') and (entrycont['title'] != ''):
     307                entry.append(entrycont['title'] + '.')
     308            if entrycont.has_key('journal') and (entrycont['journal'] != ''):
     309                entry.append(entrycont['journal'] + ',')
     310            if entrycont.has_key('booktitle') and (entrycont['booktitle'] != ''):
     311                entry.append('In ' + entrycont['booktitle'] + ',')
     312            if entrycont.has_key('type') and (entrycont['type'] != ''):
     313                eline = entrycont['type']
     314                if entrycont.has_key('number') and (entrycont['number'] != ''):
     315                    eline += ' ' + entrycont['number']
     316                eline += ','
     317                entry.append(eline)
     318            if entrycont.has_key('institution') and (entrycont['institution'] != ''):
     319                entry.append(entrycont['institution'] + ',')
     320            if entrycont.has_key('publisher') and (entrycont['publisher'] != ''):
     321                entry.append(entrycont['publisher'] + ',')
     322            if entrycont.has_key('school') and (entrycont['school'] != ''):
     323                entry.append(entrycont['school'] + ',')
     324            if entrycont.has_key('address') and (entrycont['address'] != ''):
     325                entry.append(entrycont['address'] + ',')
     326            if entrycont.has_key('edition') and (entrycont['edition'] != ''):
     327                entry.append(entrycont['edition'] + ' edition,')
     328            if entrycont.has_key('howpublished') and (entrycont['howpublished'] != ''):
     329                entry.append(entrycont['howpublished'] + ',')
     330            if entrycont.has_key('volume') and (entrycont['volume'] != ''):
     331                eline = entrycont['volume'];
     332                if entrycont.has_key('number') and (entrycont['number'] != ''):
     333                    eline += '(' + entrycont['number'] + ')'
     334                if entrycont.has_key('pages') and (entrycont['pages'] != ''):
     335                    eline += ':' + entrycont['pages']
     336                eline += ','
     337                entry.append(eline)
     338            else:
     339                if entrycont.has_key('pages') and (entrycont['pages'] != ''):
     340                    entry.append('pages ' + entrycont['pages'] + ',')
     341            if entrycont.has_key('year') and (entrycont['year'] != ''):
     342                if entrycont.has_key('month') and (entrycont['month'] != ''):
     343                    entry.append(entrycont['month'] + ' ' + entrycont['year'] + '.')
     344                else:
     345                    entry.append(entrycont['year'] + '.')
     346            if entrycont.has_key('note') and (entrycont['note'] != ''):
     347                entry.append(entrycont['note'] + '.')
     348
     349            # generate keys for sorting and for the output
     350            sortkey = ''
     351            bibkey = ''
     352            if entrycont.has_key('author'):
     353                for author in entrycont['author']['list']:
     354                    sortkey += copychars(author, author.rfind(' ')+1, len(author))
     355                bibkey = entrycont['author']['abbrev']
     356            else:
     357                bibkey = 'x'
     358            if entrycont.has_key('year'):
     359                sortkey += entrycont['year']
     360                bibkey += entrycont['year'][-2:]
     361            if entrycont.has_key('title'):
     362                sortkey += entrycont['title']
     363            if entrycont.has_key('key'):
     364                sortkey = entrycont['key'] + sortkey
     365                bibkey = entrycont['key']
     366            entry.insert(0, sortkey)
     367            entry.insert(1, bibkey)
     368           
     369            # add the entry to the file contents
     370            filecont.append(entry)
     371
     372        else:
     373            # field, publication info
     374            field = ''
     375            data = ''
     376           
     377            # field = {data} entries
     378            if bracedata_rex.match(line):
     379                field = bracefield_rex.sub('\g<1>', line)
     380                field = string.lower(field)
     381                data =  bracedata_rex.sub('\g<2>', line)
     382
     383            # field = "data" entries
     384            elif quotedata_rex.match(line):
     385                field = quotefield_rex.sub('\g<1>', line)
     386                field = string.lower(field)
     387                data =  quotedata_rex.sub('\g<2>', line)
     388
     389            # field = data entries
     390            elif data_rex.match(line):
     391                field = field_rex.sub('\g<1>', line)
     392                field = string.lower(field)
     393                data =  data_rex.sub('\g<2>', line)
     394           
     395            if field in ('author', 'editor'):
     396                entrycont[field] = bibtexauthor(data)
     397                line = ''
     398            elif field == 'title':
     399                line = bibtextitle(data, entrytype)
     400            elif field != '':
     401                line = removebraces(transformurls(data.strip()))
     402
     403            if line != '':
     404                line = latexreplacements(line)
     405                entrycont[field] = line
     406
     407
     408    # sort entries
     409    filecont.sort(entry_cmp)
     410   
     411    # count the bibtex keys
     412    keytable = {}
     413    counttable = {}
     414    for entry in filecont:
     415        bibkey = entry[1]
     416        if not keytable.has_key(bibkey):
     417            keytable[bibkey] = 1
     418        else:
     419            keytable[bibkey] += 1
     420
     421    for bibkey in keytable.keys():
     422        counttable[bibkey] = 0
     423   
     424    # generate output
     425    for entry in filecont:
     426        # generate output key form the bibtex key
     427        bibkey = entry[1]
     428        if keytable[bibkey] == 1:
     429            outkey = bibkey
     430        else:
     431            outkey = bibkey + chr(97 + counttable[bibkey])
     432        counttable[bibkey] += 1
     433       
     434        # append the entry code to the output
     435        file.append('<tr valign="top">\n' + \
     436                    '<td>[' + outkey + ']</td>')
     437        file.append('<td>')
     438        file.append('\\anchor ' + outkey)
     439        for line in entry[2:]:
     440            file.append(line)
     441        file.append('</td>\n</tr>')
     442        file.append('')
     443
     444    return file
     445
     446
     447#
     448# return 1 iff abbr is in line but not inside braces or quotes
     449# assumes that abbr appears only once on the line (out of braces and quotes)
     450#
     451def verify_out_of_braces(line, abbr):
     452
     453    phrase_split = delimiter_rex.split(line)
     454
     455    abbr_rex = re.compile( '\\b' + abbr + '\\b', re.I)
     456
     457    open_brace = 0
     458    open_quote = 0
     459
     460    for phrase in phrase_split:
     461        if phrase == "{":
     462            open_brace = open_brace + 1
     463        elif phrase == "}":
     464            open_brace = open_brace - 1
     465        elif phrase == '"':
     466            if open_quote == 1:
     467                open_quote = 0
     468            else:
     469                open_quote = 1
     470        elif abbr_rex.search(phrase):
     471            if open_brace == 0 and open_quote == 0:
     472                return 1
     473
     474    return 0
     475
     476
     477#
     478# a line in the form phrase1 # phrase2 # ... # phrasen
     479# is returned as phrase1 phrase2 ... phrasen
     480# with the correct punctuation
     481# Bug: Doesn't always work with multiple abbreviations plugged in
     482#
     483def concat_line(line):
     484    # only look at part after equals
     485    field = field_rex.sub('\g<1>',line)
     486    rest = field_rex.sub('\g<2>',line)
     487
     488    concat_line = field + ' ='
     489
     490    pound_split = concatsplit_rex.split(rest)
     491
     492    phrase_count = 0
     493    length = len(pound_split)
     494
     495    for phrase in pound_split:
     496        phrase = phrase.strip()
     497        if phrase_count != 0:
     498            if phrase.startswith('"') or phrase.startswith('{'):
     499                phrase = phrase[1:]
     500        elif phrase.startswith('"'):
     501            phrase = phrase.replace('"','{',1)
     502
     503        if phrase_count != length-1:
     504            if phrase.endswith('"') or phrase.endswith('}'):
     505                phrase = phrase[:-1]
     506        else:
     507            if phrase.endswith('"'):
     508                phrase = phrase[:-1]
     509                phrase = phrase + "}"
     510            elif phrase.endswith('",'):
     511                phrase = phrase[:-2]
     512                phrase = phrase + "},"
     513
     514        # if phrase did have \#, add the \# back
     515        if phrase.endswith('\\'):
     516            phrase = phrase + "#"
     517        concat_line = concat_line + ' ' + phrase
     518
     519        phrase_count = phrase_count + 1
     520
     521    return concat_line
     522
     523
     524#
     525# substitute abbreviations into filecont
     526# @param filecont_source - string of data from file
     527#
     528def bibtex_replace_abbreviations(filecont_source):
     529    filecont = filecont_source.splitlines()
     530
     531    #  These are defined in bibtex, so we'll define them too
     532    abbr_list = ['jan','feb','mar','apr','may','jun',
     533                 'jul','aug','sep','oct','nov','dec']
     534    value_list = ['January','February','March','April',
     535                  'May','June','July','August','September',
     536                  'October','November','December']
     537
     538    abbr_rex = []
     539    total_abbr_count = 0
     540
     541    front = '\\b'
     542    back = '(,?)\\b'
     543
     544    for x in abbr_list:
     545        abbr_rex.append( re.compile( front + abbr_list[total_abbr_count] + back, re.I ) )
     546        total_abbr_count = total_abbr_count + 1
     547
     548
     549    abbrdef_rex = re.compile('\s*@string\s*{\s*('+ valid_name_chars +'*)\s*=(.*)',
     550                             re.I)
     551
     552    comment_rex = re.compile('@comment\s*{',re.I)
     553    preamble_rex = re.compile('@preamble\s*{',re.I)
     554
     555    waiting_for_end_string = 0
     556    i = 0
     557    filecont2 = ''
     558
     559    for line in filecont:
     560        if line == ' ' or line == '':
     561            continue
     562
     563        if waiting_for_end_string:
     564            if re.search('}',line):
     565                waiting_for_end_string = 0
     566                continue
     567
     568        if abbrdef_rex.search(line):
     569            abbr = abbrdef_rex.sub('\g<1>', line)
     570
     571            if abbr_list.count(abbr) == 0:
     572                val = abbrdef_rex.sub('\g<2>', line)
     573                abbr_list.append(abbr)
     574                value_list.append(string.strip(val))
     575                abbr_rex.append( re.compile( front + abbr_list[total_abbr_count] + back, re.I ) )
     576                total_abbr_count = total_abbr_count + 1
     577            waiting_for_end_string = 1
     578            continue
     579
     580        if comment_rex.search(line):
     581            waiting_for_end_string = 1
     582            continue
     583
     584        if preamble_rex.search(line):
     585            waiting_for_end_string = 1
     586            continue
     587
     588
     589        # replace subsequent abbreviations with the value
     590        abbr_count = 0
     591
     592        for x in abbr_list:
     593
     594            if abbr_rex[abbr_count].search(line):
     595                if verify_out_of_braces(line,abbr_list[abbr_count]) == 1:
     596                    line = abbr_rex[abbr_count].sub( value_list[abbr_count] + '\g<1>', line)
     597                # Check for # concatenations
     598                if concatsplit_rex.search(line):
     599                    line = concat_line(line)
     600            abbr_count = abbr_count + 1
     601
     602
     603        filecont2 = filecont2 + line + '\n'
     604        i = i+1
     605
     606
     607    # Do one final pass over file
     608
     609    # make sure that didn't end up with {" or }" after the substitution
     610    filecont2 = filecont2.replace('{"','{{')
     611    filecont2 = filecont2.replace('"}','}}')
     612
     613    afterquotevalue_rex = re.compile('"\s*,\s*')
     614    afterbrace_rex = re.compile('"\s*}')
     615    afterbracevalue_rex = re.compile('(=\s*{[^=]*)},\s*')
     616
     617    # add new lines to data that changed because of abbreviation substitutions
     618    filecont2 = afterquotevalue_rex.sub('",\n', filecont2)
     619    filecont2 = afterbrace_rex.sub('"\n}', filecont2)
     620    filecont2 = afterbracevalue_rex.sub('\g<1>},\n', filecont2)
     621
     622    return filecont2
     623
     624#
     625# convert @type( ... ) to @type{ ... }
     626#
     627def no_outer_parens(filecont):
     628
     629    # do checking for open parens
     630    # will convert to braces
     631    paren_split = re.split('([(){}])',filecont)
     632
     633    open_paren_count = 0
     634    open_type = 0
     635    look_next = 0
     636
     637    # rebuild filecont
     638    filecont = ''
     639
     640    at_rex = re.compile('@\w*')
     641
     642    for phrase in paren_split:
     643        if look_next == 1:
     644            if phrase == '(':
     645                phrase = '{'
     646                open_paren_count = open_paren_count + 1
     647            else:
     648                open_type = 0
     649            look_next = 0
     650
     651        if phrase == '(':
     652            open_paren_count = open_paren_count + 1
     653
     654        elif phrase == ')':
     655            open_paren_count = open_paren_count - 1
     656            if open_type == 1 and open_paren_count == 0:
     657                phrase = '}'
     658                open_type = 0
     659
     660        elif at_rex.search( phrase ):
     661            open_type = 1
     662            look_next = 1
     663
     664        filecont = filecont + phrase
     665
     666    return filecont
     667
     668
     669#
     670# make all whitespace into just one space
     671# format the bibtex file into a usable form.
     672#
     673def bibtexwasher(filecont_source):
     674
     675    space_rex = re.compile('\s+')
     676    comment_rex = re.compile('\s*%')
     677
     678    filecont = []
     679
     680    # remove trailing and excessive whitespace
     681    # ignore comments
     682    for line in filecont_source:
     683        line = string.strip(line)
     684        line = space_rex.sub(' ', line)
     685        # ignore comments
     686        if not comment_rex.match(line) and line != '':
     687            filecont.append(' '+ line)
     688
     689    filecont = string.join(filecont, '')
     690
     691    # the file is in one long string
     692
     693    filecont = no_outer_parens(filecont)
     694
     695    #
     696    # split lines according to preferred syntax scheme
     697    #
     698    filecont = re.sub('(=\s*{[^=]*)},', '\g<1>},\n', filecont)
     699
     700    # add new lines after commas that are after values
     701    filecont = re.sub('"\s*,', '",\n', filecont)
     702    filecont = re.sub('=\s*([\w\d]+)\s*,', '= \g<1>,\n', filecont)
     703    filecont = re.sub('(@\w*)\s*({(\s*)[^,\s]*)\s*,',
     704                          '\n\n\g<1>\g<2>,\n', filecont)
     705
     706    # add new lines after }
     707    filecont = re.sub('"\s*}','"\n}\n', filecont)
     708    filecont = re.sub('}\s*,','},\n', filecont)
     709
     710
     711    filecont = re.sub('@(\w*)', '\n@\g<1>', filecont)
     712
     713    # character encoding, reserved latex characters
     714    filecont = re.sub('{\\\&}', '&', filecont)
     715    filecont = re.sub('\\\&', '&', filecont)
     716
     717    # do checking for open braces to get format correct
     718    open_brace_count = 0
     719    brace_split = re.split('([{}])',filecont)
     720
     721    # rebuild filecont
     722    filecont = ''
     723
     724    for phrase in brace_split:
     725        if phrase == '{':
     726            open_brace_count = open_brace_count + 1
     727        elif phrase == '}':
     728            open_brace_count = open_brace_count - 1
     729            if open_brace_count == 0:
     730                filecont = filecont + '\n'
     731
     732        filecont = filecont + phrase
     733
     734    filecont2 = bibtex_replace_abbreviations(filecont)
     735
     736    # gather
     737    filecont = filecont2.splitlines()
     738    i=0
     739    j=0         # count the number of blank lines
     740    for line in filecont:
     741        # ignore blank lines
     742        if line == '' or line == ' ':
     743            j = j+1
     744            continue
     745        filecont[i] = line + '\n'
     746        i = i+1
     747
     748    # get rid of the extra stuff at the end of the array
     749    # (The extra stuff are duplicates that are in the array because
     750    # blank lines were removed.)
     751    length = len( filecont)
     752    filecont[length-j:length] = []
     753
     754    return filecont
     755
     756
     757def filehandler(filepath):
     758    try:
     759        fd = open(filepath, 'r')
     760        filecont_source = fd.readlines()
     761        fd.close()
     762    except:
     763        print 'Could not open file:', filepath
     764    washeddata = bibtexwasher(filecont_source)
     765    outdata = bibtexdecoder(washeddata)
     766    print '/**'
     767    print '\page references References'
     768    print
     769    print '<table border="0" cellspacing="5px" width="100%">'
     770    print
     771    for line in outdata:
     772        print line
     773    print '</table>'
     774    print
     775    print '*/'
     776
     777
     778# main program
     779
     780def main():
     781    import sys
     782    if sys.argv[1:]:
     783        filepath = sys.argv[1]
     784    else:
     785        print "No input file"
     786        sys.exit()
     787    filehandler(filepath)
     788
     789if __name__ == "__main__": main()
     790
     791
     792# end python script