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inukshuk / bibtex-ruby

A BibTeX library, parser, and converter for Ruby.
http://inukshuk.github.com/bibtex-ruby
GNU General Public License v3.0
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Corruption of @comment fields used by BibDesk for library management #138

Open retrography opened 4 years ago

retrography commented 4 years ago

Loading a BibTeX file written by BibDesk and rewriting results in corruption and loss of library management settings that BibDesk encodes into comment fields in XML format. See before and after below.

It seems to me only linefeeds have been removed, which must not have any effect on parsing of the XML format, yet BibDesk can't find the script groups anymore. The only explanation I can come up with is that when all linefeeds are removed, the length of a comment field may become longer than the maximum line length conventionally supported by XML parsers. This limit is normally set to 32kb, while in my file the longest comment field is less than 14kb long. But still, the parser used in BibDesk may be over-sensitive or not standard-based.

Is there any way to prevent bibtex-ruby from reformatting these fields?

Before:


@comment{BibDesk Static Groups{
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE plist PUBLIC "-//Apple//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
<plist version="1.0">
<array>
    <dict>
        <key>group name</key>
        <string>--- Reading List ---</string>
        <key>keys</key>
        <string>Ahuja2012gdo,Tourish2019tnm</string>
    </dict>
    <dict>
        <key>group name</key>
        <string>Correct Metadata Examples</string>
        <key>keys</key>
        <string>Bardram2010wpd,Brandes2009nes,Moran1996VALUE-CREATION,Chen2008eph,Brin1995cdm,Sung1988tpr,Daniel2008neo,Zargar2013rrw,Kumar2010seo,Mukherjee2013dcn,Pinsker2018isr,Pinsker2018rbh,Pinsker2018bhs,Kuk2006sik,Bonaccorsi2006esu,MacCormack2006esc,CasadesusMasanell2006dmd,Baldwin2006apd,vonKrogh2006ms</string>
    </dict>
    <dict>
        <key>group name</key>
        <string>Course: Aaron - Computational Field Research</string>
        <key>keys</key>
        <string>Lounsbury2002sso,Evans2014caq,Borner2010mls,Kilduff2006ptf,Abbott1990psm,Adamic2003snc,Haythornthwaite1998sns,Laxman2006std,Watts2007tfc,Wilson2001apc,Epstein1999abc,Sabherwal1993eti,Gabadinho2011avs,Berger2011cll,Wilson1999csa,Ahuja2000cns,Howison2014cto,Watts2011Collective-dynamics,Fortunato2010cdg,Girvan2002css,Elzinga2010cct,Carley2001cas,Cederman2005cms,Carley2002cos,Al2009css,LaRosa2011cmp,Gaskin2011dtv,Sarkar2005dsn,Agarwal2008eoi,Monge2001ecn,Barabasi1999esr,Kane2014elc,Situngkir2003ees,Kossinets2006eae,Gray2008etr,Barabasi2002esn,Borgs2004ecs,Macy2002ffa,Feller2008fpp,Krackhardt1994gtd,Vaast2011gte,Backstrom2006gfl,Mislove2008gfs,Holland1989ipi,Ahonen2015ibd,Langley2010ipp,Lazer2009lnc,Molloy2011mit,FalkKrzesinski2011mra,Mislove2007mao,Abbott1990mrs,Zachariadis2013mic,Newman2006mcs,Gauthier2010msa,Contractor2011mnd,Borgatti2009nas,Goggins2010nat,Daniel2008neo,Ahuja1999nsv,Brandes2009nes,Viegas2004nca,Holme2006npt,Borgatti1992nps,Freelon2014idt,Pentland1994org,Clauset2009pld,Goel2010pcb,Choi2012ppw,Krackhardt1987qpt,Hubert1976qag,Silverman1998qrm,Palla2007qsg,Abbott2000sao,Abbott1995san,Walker1997scs,Fulk1993scc,Tichy1979sna,Haines1988sna,Catanzaro2004sng,OinasKukkonen2010sni,Obstfeld2005snt,Gulati1995ssa,Uzzi1997ssc,White1976ssf,Wu2000scs,Cressie1993ssd,Fombrun1982snr,Burt2004shg,Burt2001shn,Kumar2010seo,Brass2004tsn,Contractor2006tmm,Kleinberg2008cst,Aral2011dbt,Hummon1995ecs,Suh2011ivs,Burt2000nss,Ron1996pal,Milgram1967swp,Baker1993soc,PerrySmith2003ssc,Uzzi1996sce,Granovetter1973swt,Granovetter1983swt,Granovetter1978tmc,Balkundi2006tlt,Geiger2011tef,Cook1992tas,Palla2005uoc,Webb1979umo,Gasson2011ugt,McKenny2012uca,Howison2011viu,Buhlmann1999vlm,Lyytinen2009vcr,Shen2011wcw,vanderAalst2004wmd</string>
    </dict>
    <dict>
        <key>group name</key>
        <string>Digital Methods: Network</string>
        <key>keys</key>
        <string>Kilduff2010osn,Kivela2014mn,Padgett1993rar,Gould1991mnm,Brennecke2017fkn</string>
    </dict>
    <dict>
        <key>group name</key>
        <string>Digital Methods: Semantic</string>
        <key>keys</key>
        <string>Hannigan2019tmm,Blei2012ptm,Kaplan2015des,Croidieu2017lla,Tirunillai2014mmm</string>
    </dict>
    <dict>
        <key>group name</key>
        <string>Import</string>
        <key>keys</key>
        <string></string>
    </dict>
    <dict>
        <key>group name</key>
        <string>Knowledge Reuse</string>
        <key>keys</key>
        <string>Alavi2001rkm,Argote2000ktb,Kyriakou2017krc,Allen2010iqr,Markus2001ttk,Majchrzak2004kri,Grant1996pdc,Kogut1992kfc,Teece1986pft,Szulanski2000pkt,Argote1999olc,Nonaka1994dto,Swan2001kma,Thomke1998med,Gray2000ekm,Hargadon1997tbi,Zahra2019wdw</string>
    </dict>
    <dict>
        <key>group name</key>
        <string>Multiplexity</string>
        <key>keys</key>
        <string>Li2019ute</string>
    </dict>
    <dict>
        <key>group name</key>
        <string>Project: Anthropomorphism</string>
        <key>keys</key>
        <string>Chmielewski2019mcs</string>
    </dict>
    <dict>
        <key>group name</key>
        <string>Similarity</string>
        <key>keys</key>
        <string>Zadeh2012dis,Broder1997rcd</string>
    </dict>
    <dict>
        <key>group name</key>
        <string>Writing &amp; Reviewing</string>
        <key>keys</key>
        <string>Lee1995rmp,Lepak2009wig,Romanelli1996brl,Schwab198reb,Leblebici1996arb,Webster2002app</string>
    </dict>
</array>
</plist>
}}

@comment{BibDesk Smart Groups{
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE plist PUBLIC "-//Apple//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
<plist version="1.0">
<array>
    <dict>
        <key>conditions</key>
        <array>
            <dict>
                <key>comparison</key>
                <integer>4</integer>
                <key>key</key>
                <string>Journal</string>
                <key>value</key>
                <string></string>
                <key>version</key>
                <string>1</string>
            </dict>
            <dict>
                <key>comparison</key>
                <integer>4</integer>
                <key>key</key>
                <string>Journaltitle</string>
                <key>value</key>
                <string></string>
                <key>version</key>
                <string>1</string>
            </dict>
            <dict>
                <key>comparison</key>
                <integer>4</integer>
                <key>key</key>
                <string>Type</string>
                <key>value</key>
                <string>article</string>
                <key>version</key>
                <string>1</string>
            </dict>
        </array>
        <key>conjunction</key>
        <integer>0</integer>
        <key>group name</key>
        <string>Journalles Articles</string>
    </dict>
</array>
</plist>
}}

@comment{BibDesk Script Groups{
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE plist PUBLIC "-//Apple//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
<plist version="1.0">
<array>
    <dict>
        <key>group name</key>
        <string>-Journal of Applied Psychology</string>
        <key>script arguments</key>
        <string>https://psycnet.apa.org/journals/apl.rss</string>
        <key>script path</key>
        <string>/Users/mah/Library/Application Support/BibDesk/Group Scripts/RSS2BibTeX.py</string>
        <key>script type</key>
        <integer>0</integer>
    </dict>
    <dict>
        <key>group name</key>
        <string>-Journal of Business Ethics</string>
        <key>script arguments</key>
        <string>https://link.springer.com/search.rss?facet-content-type=Article&amp;facet-journal-id=10551&amp;channel-name=Journal+of+Business+Ethics</string>
        <key>script path</key>
        <string>/Users/mah/Library/Application Support/BibDesk/Group Scripts/RSS2BibTeX.py</string>
        <key>script type</key>
        <integer>0</integer>
    </dict>
    <dict>
        <key>group name</key>
        <string>-MISQ Executive</string>
        <key>script arguments</key>
        <string>https://aisel.aisnet.org/misqe/recent.rss</string>
        <key>script path</key>
        <string>/Users/mah/Library/Application Support/BibDesk/Group Scripts/RSS2BibTeX.py</string>
        <key>script type</key>
        <integer>0</integer>
    </dict>
    <dict>
        <key>group name</key>
        <string>Academy of Management Annals</string>
        <key>script arguments</key>
        <string>https://journals.aom.org/action/showFeed?jc=annals&amp;type=etoc&amp;feed=rss</string>
        <key>script path</key>
        <string>/Users/mah/Library/Application Support/BibDesk/Group Scripts/RSS2BibTeX.py</string>
        <key>script type</key>
        <integer>0</integer>
    </dict>
    <dict>
        <key>group name</key>
        <string>Academy of Management Discoveries</string>
        <key>script arguments</key>
        <string>https://journals.aom.org/action/showFeed?jc=amd&amp;type=etoc&amp;feed=rss</string>
        <key>script path</key>
        <string>/Users/mah/Library/Application Support/BibDesk/Group Scripts/RSS2BibTeX.py</string>
        <key>script type</key>
        <integer>0</integer>
    </dict>
    <dict>
        <key>group name</key>
        <string>Academy of Management Journal</string>
        <key>script arguments</key>
        <string>https://journals.aom.org/action/showFeed?jc=amj&amp;type=etoc&amp;feed=rss</string>
        <key>script path</key>
        <string>/Users/mah/Library/Application Support/BibDesk/Group Scripts/RSS2BibTeX.py</string>
        <key>script type</key>
        <integer>0</integer>
    </dict>
    <dict>
        <key>group name</key>
        <string>Academy of Management Learning &amp; Education</string>
        <key>script arguments</key>
        <string>https://journals.aom.org/action/showFeed?jc=amle&amp;type=etoc&amp;feed=rss</string>
        <key>script path</key>
        <string>/Users/mah/Library/Application Support/BibDesk/Group Scripts/RSS2BibTeX.py</string>
        <key>script type</key>
        <integer>0</integer>
    </dict>
    <dict>
        <key>group name</key>
        <string>Academy of Management Perspectives</string>
        <key>script arguments</key>
        <string>https://journals.aom.org/action/showFeed?jc=amp&amp;type=etoc&amp;feed=rss</string>
        <key>script path</key>
        <string>/Users/mah/Library/Application Support/BibDesk/Group Scripts/RSS2BibTeX.py</string>
        <key>script type</key>
        <integer>0</integer>
    </dict>
    <dict>
        <key>group name</key>
        <string>Academy of Management Review</string>
        <key>script arguments</key>
        <string>https://journals.aom.org/action/showFeed?jc=amr&amp;type=etoc&amp;feed=rss</string>
        <key>script path</key>
        <string>/Users/mah/Library/Application Support/BibDesk/Group Scripts/RSS2BibTeX.py</string>
        <key>script type</key>
        <integer>0</integer>
    </dict>
    <dict>
        <key>group name</key>
        <string>Administrative Science Quarterly</string>
        <key>script arguments</key>
        <string>https://journals.sagepub.com/action/showFeed?jc=asqa&amp;type=etoc&amp;feed=rss</string>
        <key>script path</key>
        <string>/Users/mah/Library/Application Support/BibDesk/Group Scripts/RSS2BibTeX.py</string>
        <key>script type</key>
        <integer>0</integer>
    </dict>
    <dict>
        <key>group name</key>
        <string>American Journal of Sociology</string>
        <key>script arguments</key>
        <string>https://www.journals.uchicago.edu/action/showFeed?jc=ajs&amp;type=etoc&amp;feed=rss</string>
        <key>script path</key>
        <string>/Users/mah/Library/Application Support/BibDesk/Group Scripts/RSS2BibTeX.py</string>
        <key>script type</key>
        <integer>0</integer>
    </dict>
    <dict>
        <key>group name</key>
        <string>American Sociological Review</string>
        <key>script arguments</key>
        <string>https://journals.sagepub.com/action/showFeed?jc=asra&amp;type=etoc&amp;feed=rss</string>
        <key>script path</key>
        <string>/Users/mah/Library/Application Support/BibDesk/Group Scripts/RSS2BibTeX.py</string>
        <key>script type</key>
        <integer>0</integer>
    </dict>
    <dict>
        <key>group name</key>
        <string>Annual Review of Psychology</string>
        <key>script arguments</key>
        <string>https://www.annualreviews.org/action/showFeed?jc=psych&amp;type=etoc&amp;feed=rss</string>
        <key>script path</key>
        <string>/Users/mah/Library/Application Support/BibDesk/Group Scripts/RSS2BibTeX.py</string>
        <key>script type</key>
        <integer>0</integer>
    </dict>
    <dict>
        <key>group name</key>
        <string>Annual Review of Sociology</string>
        <key>script arguments</key>
        <string>https://www.annualreviews.org/action/showFeed?jc=soc&amp;type=etoc&amp;feed=rss</string>
        <key>script path</key>
        <string>/Users/mah/Library/Application Support/BibDesk/Group Scripts/RSS2BibTeX.py</string>
        <key>script type</key>
        <integer>0</integer>
    </dict>
    <dict>
        <key>group name</key>
        <string>Entrepreneurship Theory and Practice</string>
        <key>script arguments</key>
        <string>https://journals.sagepub.com/action/showFeed?jc=etpb&amp;type=etoc&amp;feed=rss</string>
        <key>script path</key>
        <string>/Users/mah/Library/Application Support/BibDesk/Group Scripts/RSS2BibTeX.py</string>
        <key>script type</key>
        <integer>0</integer>
    </dict>
    <dict>
        <key>group name</key>
        <string>Human Relations</string>
        <key>script arguments</key>
        <string>https://journals.sagepub.com/action/showFeed?jc=huma&amp;type=etoc&amp;feed=rss</string>
        <key>script path</key>
        <string>/Users/mah/Library/Application Support/BibDesk/Group Scripts/RSS2BibTeX.py</string>
        <key>script type</key>
        <integer>0</integer>
    </dict>
    <dict>
        <key>group name</key>
        <string>Human Resource Management</string>
        <key>script arguments</key>
        <string>https://onlinelibrary.wiley.com/feed/1099050x/most-recent</string>
        <key>script path</key>
        <string>/Users/mah/Library/Application Support/BibDesk/Group Scripts/RSS2BibTeX.py</string>
        <key>script type</key>
        <integer>0</integer>
    </dict>
    <dict>
        <key>group name</key>
        <string>Information Systems Journal</string>
        <key>script arguments</key>
        <string>https://onlinelibrary.wiley.com/feed/13652575/most-recent</string>
        <key>script path</key>
        <string>/Users/mah/Library/Application Support/BibDesk/Group Scripts/RSS2BibTeX.py</string>
        <key>script type</key>
        <integer>0</integer>
    </dict>
    <dict>
        <key>group name</key>
        <string>Information Systems Research</string>
        <key>script arguments</key>
        <string>https://pubsonline.informs.org/action/showFeed?type=etoc&amp;feed=rss&amp;jc=isre</string>
        <key>script path</key>
        <string>/Users/mah/Library/Application Support/BibDesk/Group Scripts/RSS2BibTeX.py</string>
        <key>script type</key>
        <integer>0</integer>
    </dict>
    <dict>
        <key>group name</key>
        <string>Journal of Association for Information Systems</string>
        <key>script path</key>
        <string>/Users/mah/Library/Application Support/BibDesk/Group Scripts/JAIS.py</string>
    </dict>
    <dict>
        <key>group name</key>
        <string>Journal of International Business Studies</string>
        <key>script arguments</key>
        <string>https://link.springer.com/search.rss?facet-content-type=Article&amp;facet-journal-id=41267&amp;channel-name=Journal+of+International+Business+Studies "Journal of International Business Studies"</string>
        <key>script path</key>
        <string>/Users/mah/Library/Application Support/BibDesk/Group Scripts/RSS2BibTeX.py</string>
        <key>script type</key>
        <integer>0</integer>
    </dict>
    <dict>
        <key>group name</key>
        <string>Journal of Management</string>
        <key>script arguments</key>
        <string>https://journals.sagepub.com/action/showFeed?jc=joma&amp;type=etoc&amp;feed=rss</string>
        <key>script path</key>
        <string>/Users/mah/Library/Application Support/BibDesk/Group Scripts/RSS2BibTeX.py</string>
        <key>script type</key>
        <integer>0</integer>
    </dict>
    <dict>
        <key>group name</key>
        <string>Journal of Management Information Systems</string>
        <key>script arguments</key>
        <string>https://www.tandfonline.com/feed/rss/mmis20</string>
        <key>script path</key>
        <string>/Users/mah/Library/Application Support/BibDesk/Group Scripts/RSS2BibTeX.py</string>
        <key>script type</key>
        <integer>0</integer>
    </dict>
    <dict>
        <key>group name</key>
        <string>Journal of Management Inquiry</string>
        <key>script arguments</key>
        <string>https://journals.sagepub.com/action/showFeed?jc=jmia&amp;type=etoc&amp;feed=rss</string>
        <key>script path</key>
        <string>/Users/mah/Library/Application Support/BibDesk/Group Scripts/RSS2BibTeX.py</string>
        <key>script type</key>
        <integer>0</integer>
    </dict>
    <dict>
        <key>group name</key>
        <string>Journal of Management Studies</string>
        <key>script arguments</key>
        <string>https://onlinelibrary.wiley.com/feed/14676486/most-recent</string>
        <key>script path</key>
        <string>/Users/mah/Library/Application Support/BibDesk/Group Scripts/RSS2BibTeX.py</string>
        <key>script type</key>
        <integer>0</integer>
    </dict>
    <dict>
        <key>group name</key>
        <string>Management Science</string>
        <key>script arguments</key>
        <string>https://pubsonline.informs.org/action/showFeed?type=etoc&amp;feed=rss&amp;jc=mnsc</string>
        <key>script path</key>
        <string>/Users/mah/Library/Application Support/BibDesk/Group Scripts/RSS2BibTeX.py</string>
        <key>script type</key>
        <integer>0</integer>
    </dict>
    <dict>
        <key>group name</key>
        <string>Nature Human Behavior</string>
        <key>script arguments</key>
        <string>http://feeds.nature.com/nathumbehav/rss/current</string>
        <key>script path</key>
        <string>/Users/mah/Library/Application Support/BibDesk/Group Scripts/RSS2BibTeX.py</string>
        <key>script type</key>
        <integer>0</integer>
    </dict>
    <dict>
        <key>group name</key>
        <string>Organization</string>
        <key>script arguments</key>
        <string>https://journals.sagepub.com/action/showFeed?jc=orga&amp;type=etoc&amp;feed=rss</string>
        <key>script path</key>
        <string>/Users/mah/Library/Application Support/BibDesk/Group Scripts/RSS2BibTeX.py</string>
        <key>script type</key>
        <integer>0</integer>
    </dict>
    <dict>
        <key>group name</key>
        <string>Organization Science</string>
        <key>script arguments</key>
        <string>https://pubsonline.informs.org/action/showFeed?type=etoc&amp;feed=rss&amp;jc=orsc</string>
        <key>script path</key>
        <string>/Users/mah/Library/Application Support/BibDesk/Group Scripts/RSS2BibTeX.py</string>
        <key>script type</key>
        <integer>0</integer>
    </dict>
    <dict>
        <key>group name</key>
        <string>Organization Studies</string>
        <key>script arguments</key>
        <string>https://journals.sagepub.com/action/showFeed?jc=ossa&amp;type=etoc&amp;feed=rss</string>
        <key>script path</key>
        <string>/Users/mah/Library/Application Support/BibDesk/Group Scripts/RSS2BibTeX.py</string>
        <key>script type</key>
        <integer>0</integer>
    </dict>
    <dict>
        <key>group name</key>
        <string>Organizational Research Methods</string>
        <key>script arguments</key>
        <string>https://journals.sagepub.com/action/showFeed?jc=orma&amp;type=etoc&amp;feed=rss</string>
        <key>script path</key>
        <string>/Users/mah/Library/Application Support/BibDesk/Group Scripts/RSS2BibTeX.py</string>
        <key>script type</key>
        <integer>0</integer>
    </dict>
    <dict>
        <key>group name</key>
        <string>Social Forces</string>
        <key>script arguments</key>
        <string>https://academic.oup.com/rss/site_5513/3374.xml "Social Forces"</string>
        <key>script path</key>
        <string>/Users/mah/Library/Application Support/BibDesk/Group Scripts/RSS2BibTeX.py</string>
        <key>script type</key>
        <integer>0</integer>
    </dict>
    <dict>
        <key>group name</key>
        <string>Strategic Entrepreneurship Journal</string>
        <key>script arguments</key>
        <string>https://onlinelibrary.wiley.com/feed/1932443x/most-recent</string>
        <key>script path</key>
        <string>/Users/mah/Library/Application Support/BibDesk/Group Scripts/RSS2BibTeX.py</string>
        <key>script type</key>
        <integer>0</integer>
    </dict>
    <dict>
        <key>group name</key>
        <string>Strategic Management Journal</string>
        <key>script arguments</key>
        <string>https://onlinelibrary.wiley.com/feed/10970266/most-recent</string>
        <key>script path</key>
        <string>/Users/mah/Library/Application Support/BibDesk/Group Scripts/RSS2BibTeX.py</string>
        <key>script type</key>
        <integer>0</integer>
    </dict>
    <dict>
        <key>group name</key>
        <string>Strategic Organization</string>
        <key>script arguments</key>
        <string>https://journals.sagepub.com/action/showFeed?jc=soqa&amp;type=etoc&amp;feed=rss</string>
        <key>script path</key>
        <string>/Users/mah/Library/Application Support/BibDesk/Group Scripts/RSS2BibTeX.py</string>
        <key>script type</key>
        <integer>0</integer>
    </dict>
</array>
</plist>
}}

After:

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inukshuk commented 4 years ago

Interesting! A quick look reveals that printing out comments is slightly problematic, because there are extra spaces around the outer braces. The parser does not seem to care about line-breaks at all for comments -- so it's probably the lexer that swallows the breaks.

It's probably the chop here in the lexer that removes the line-breaks.