Scrivener->pandoc->DOCX rogue footnote problems

Scrivener->pandoc->DOCX rogue footnote problems

[AnnFran]

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Having spent an inordinate about of time working out a functional workflow 
from Scrivener to Word through pandoc with Zotero references, I am left 
with one weird problem that I have not been able to solve despite searching 
all relevant manuals and user forums. (Actually, I have a couple of other 
issues too, but first things first.) Since I really don't know whether this 
problem is more relevant to Scrivener or pandoc, I'm posting this to both 
forums and will share any answers I get.

To set the scene: 

1) I am using the most recent version of all three programs. 
2) I have used zotpick-pandoc_Scrivener to create citekey references in 
Scrivener.
3) I have created an export .bib file from Zotero using BetterBibLaTex.
4) I compile using an edited version of MultiMarkdown.
5) In case it matters, I prefer using free-floating footnote references (so 
I use a tilda as an anchor rather than a highlighted word.)
6) I do the pandoc conversion using the following command line in terminal: 
pandoc --bibliography=MY_Zotero_refs.bib -s MY_compiled_doc.txt -o 
output.docx --csl=chicago.csl -f markdown -t docx. (Note: I started 
figuring out to do this using the following web site, but I couldn't make 
the code work as it was described here: http://survivestatistics.com/scrivener- 
... mac-users/ 
<http://survivestatistics.com/scrivener-zotero-pandoc-integration-for-mac-users/>. 
Much googling later, I came up with this syntax, which seems to work fine.)
7) I have what seems to be an otherwise perfectly functional reference.docx 
in my .pandoc hidden folder.

My Problem: Rogue (and seemingly random) footnote errors

Most of my footnotes have been translated more or less perfectly (a total 
of 155 footnotes). (I'm sure there is always a bit of tweaking that will 
need to be done. But either the Multimarkdown compile format I am using or 
the pandoc translation (I have no idea which) is gagging on precisely 
seven, seemingly quite different types of Zotero references. I get no error 
when I run pandoc, but the footnote is empty, and then any subsequent 
citations of that reference have only a single digit, followed by a comma 
and the page range (which I entered manually into Scrivener). I have 
attached a PDF of the Word output file. (I stripped the text down to the 
minimum and added a second page with the bibliographic output for the 
affected citations creating using the "Create Bibliography from items" 
command directly from Zotero.) I've pasted the BetterBibLaTex output for 
these citations below my message. You can see that this file does turn up 
some error messages, but there is no logic to too them (similar error 
messages did not lead to problems with other citations), I did manage to 
fix a couple of similarly affected citations by tweaking the information in 
Zotero. (In one case, a title that started with a word in All-caps seemed 
to be the problem.) But I cannot figure out what is going on with the rest 
of them. 

Does anyone have any idea what might be going on here?

REFERENCES


@book{hirschfeldTransvestitenUntersuchungUeber1910,
  langid = {german},
  location = {{Berlin}},
  title = {Die Transvestiten: Eine Untersuchung \"uber den erotischen 
Verkleidungstrieb},
  publisher = {{Alfred Pulvermacher \& Co.}},
  date = {1910},
  author = {Hirschfeld, Magnus}
}

@book{doblerZwischenDuldungspolitikUnd2008,
  langid = {german},
  location = {{Frankfurt a.M.}},
  title = {Zwischen Duldungspolitik und Verbrechensbek\"ampfung: 
Homosexuellenverfolgung durch die Berliner Polizei von 1848 bis 1933},
  publisher = {{Verlag f\"ur Polizeiwissenschaft}},
  date = {2008},
  author = {Dobler, Jens}
}

@article{anon.SexOperationSelf1953,
  entrysubtype = {newspaper},
  location = {{San Francisco}},
  title = {Sex {{Operation}} on {{Self Fails XXX}} Check Publication},
  abstract = {full text attached in note},
  journaltitle = {San Francisco Examiner},
  date = {1953-08-19},
  author = {Anon.}
}
% == BibLateX quality report for anon.SexOperationSelf1953:
% Unexpected field 'location'

@article{cauldwellPsychopathiaTransexualis2001,
  title = {Psychopathia {{Transexualis}}},
  volume = {5},
  abstract = {(Originally published in Sexology, vol. 16, 1949, pp. 
274-280. Copyright, 1949, by Sexology Magazine.)
http://www.iiav.nl/ezines/web/ijt/97-03/numbers/symposion/cauldwell\_02.htm},
  number = {2},
  journaltitle = {The International Journal of Transgenderism},
  date = {2001},
  author = {Cauldwell, David Oliver}
}
% == BibLateX quality report for cauldwellPsychopathiaTransexualis2001:
% ? Title looks like it was stored in title-case in Zotero

@online{anon.HarryBenjaminPart2012,
  title = {Harry {{Benjamin}}: Part 2 Rejuvenation},
  url = 
{https://zagria.blogspot.com/2012/10/harry-benjamin-part-2-rejuvenation_5.html},
  shorttitle = {Harry {{Benjamin}}},
  urldate = {2018-08-04},
  date = {2012-10-05},
  author = {Anon.}
}

@misc{strykerAleshiaBrevardCrenshaw1997,
  langid = {english},
  title = {Aleshia {{Brevard Crenshaw Interviews}}: {{First Interview}}, 
{{Watsonville}}, {{California}}},
  url = {http://www.glbthistory.org},
  abstract = {In Co-operation with Joanne Meyerowitz, University of 
Cincinnati and the Gay and Lesbian Historical Society of Northern 
California. Recorded at Lucas's home in San Francisco},
  urldate = {2016-05-05},
  date = {1997-08-02},
  editora = {Stryker, Susan},
  editoratype = {collaborator}
}
% == BibLateX quality report for strykerAleshiaBrevardCrenshaw1997:
% Unexpected field 'editora'
% Unexpected field 'editoratype'
% ? Title looks like it was stored in title-case in Zotero

@article{hirschfeldIntersexuelleKonstitution1923,
  langid = {german},
  title = {Die intersexuelle Konstitution},
  volume = {23},
  journaltitle = {Jahrbuch f\"ur sexuelle Zwischenstufen},
  date = {1923},
  pages = {3-27},
  author = {Hirschfeld, Magnus}
}




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Re: Scrivener->pandoc->DOCX rogue footnote problems

[John MacFarlane]

Can you try to prune things down to get a minimal
example?  That is, a _short_ markdown source + bib file
+ exact command line used to produce the output?

Then we can check it out and see better what might be
happening here.

AnnFran <aftimm-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org> writes:

> Having spent an inordinate about of time working out a functional workflow 
> from Scrivener to Word through pandoc with Zotero references, I am left 
> with one weird problem that I have not been able to solve despite searching 
> all relevant manuals and user forums. (Actually, I have a couple of other 
> issues too, but first things first.) Since I really don't know whether this 
> problem is more relevant to Scrivener or pandoc, I'm posting this to both 
> forums and will share any answers I get.
>
> To set the scene: 
>
> 1) I am using the most recent version of all three programs. 
> 2) I have used zotpick-pandoc_Scrivener to create citekey references in 
> Scrivener.
> 3) I have created an export .bib file from Zotero using BetterBibLaTex.
> 4) I compile using an edited version of MultiMarkdown.
> 5) In case it matters, I prefer using free-floating footnote references (so 
> I use a tilda as an anchor rather than a highlighted word.)
> 6) I do the pandoc conversion using the following command line in terminal: 
> pandoc --bibliography=MY_Zotero_refs.bib -s MY_compiled_doc.txt -o 
> output.docx --csl=chicago.csl -f markdown -t docx. (Note: I started 
> figuring out to do this using the following web site, but I couldn't make 
> the code work as it was described here: http://survivestatistics.com/scrivener- 
> ... mac-users/ 
> <http://survivestatistics.com/scrivener-zotero-pandoc-integration-for-mac-users/>. 
> Much googling later, I came up with this syntax, which seems to work fine.)
> 7) I have what seems to be an otherwise perfectly functional reference.docx 
> in my .pandoc hidden folder.
>
> My Problem: Rogue (and seemingly random) footnote errors
>
> Most of my footnotes have been translated more or less perfectly (a total 
> of 155 footnotes). (I'm sure there is always a bit of tweaking that will 
> need to be done. But either the Multimarkdown compile format I am using or 
> the pandoc translation (I have no idea which) is gagging on precisely 
> seven, seemingly quite different types of Zotero references. I get no error 
> when I run pandoc, but the footnote is empty, and then any subsequent 
> citations of that reference have only a single digit, followed by a comma 
> and the page range (which I entered manually into Scrivener). I have 
> attached a PDF of the Word output file. (I stripped the text down to the 
> minimum and added a second page with the bibliographic output for the 
> affected citations creating using the "Create Bibliography from items" 
> command directly from Zotero.) I've pasted the BetterBibLaTex output for 
> these citations below my message. You can see that this file does turn up 
> some error messages, but there is no logic to too them (similar error 
> messages did not lead to problems with other citations), I did manage to 
> fix a couple of similarly affected citations by tweaking the information in 
> Zotero. (In one case, a title that started with a word in All-caps seemed 
> to be the problem.) But I cannot figure out what is going on with the rest 
> of them. 
>
> Does anyone have any idea what might be going on here?
>
> REFERENCES
>
>
> @book{hirschfeldTransvestitenUntersuchungUeber1910,
>   langid = {german},
>   location = {{Berlin}},
>   title = {Die Transvestiten: Eine Untersuchung \"uber den erotischen 
> Verkleidungstrieb},
>   publisher = {{Alfred Pulvermacher \& Co.}},
>   date = {1910},
>   author = {Hirschfeld, Magnus}
> }
>
> @book{doblerZwischenDuldungspolitikUnd2008,
>   langid = {german},
>   location = {{Frankfurt a.M.}},
>   title = {Zwischen Duldungspolitik und Verbrechensbek\"ampfung: 
> Homosexuellenverfolgung durch die Berliner Polizei von 1848 bis 1933},
>   publisher = {{Verlag f\"ur Polizeiwissenschaft}},
>   date = {2008},
>   author = {Dobler, Jens}
> }
>
> @article{anon.SexOperationSelf1953,
>   entrysubtype = {newspaper},
>   location = {{San Francisco}},
>   title = {Sex {{Operation}} on {{Self Fails XXX}} Check Publication},
>   abstract = {full text attached in note},
>   journaltitle = {San Francisco Examiner},
>   date = {1953-08-19},
>   author = {Anon.}
> }
> % == BibLateX quality report for anon.SexOperationSelf1953:
> % Unexpected field 'location'
>
> @article{cauldwellPsychopathiaTransexualis2001,
>   title = {Psychopathia {{Transexualis}}},
>   volume = {5},
>   abstract = {(Originally published in Sexology, vol. 16, 1949, pp. 
> 274-280. Copyright, 1949, by Sexology Magazine.)
> http://www.iiav.nl/ezines/web/ijt/97-03/numbers/symposion/cauldwell\_02.htm},
>   number = {2},
>   journaltitle = {The International Journal of Transgenderism},
>   date = {2001},
>   author = {Cauldwell, David Oliver}
> }
> % == BibLateX quality report for cauldwellPsychopathiaTransexualis2001:
> % ? Title looks like it was stored in title-case in Zotero
>
> @online{anon.HarryBenjaminPart2012,
>   title = {Harry {{Benjamin}}: Part 2 Rejuvenation},
>   url = 
> {https://zagria.blogspot.com/2012/10/harry-benjamin-part-2-rejuvenation_5.html},
>   shorttitle = {Harry {{Benjamin}}},
>   urldate = {2018-08-04},
>   date = {2012-10-05},
>   author = {Anon.}
> }
>
> @misc{strykerAleshiaBrevardCrenshaw1997,
>   langid = {english},
>   title = {Aleshia {{Brevard Crenshaw Interviews}}: {{First Interview}}, 
> {{Watsonville}}, {{California}}},
>   url = {http://www.glbthistory.org},
>   abstract = {In Co-operation with Joanne Meyerowitz, University of 
> Cincinnati and the Gay and Lesbian Historical Society of Northern 
> California. Recorded at Lucas's home in San Francisco},
>   urldate = {2016-05-05},
>   date = {1997-08-02},
>   editora = {Stryker, Susan},
>   editoratype = {collaborator}
> }
> % == BibLateX quality report for strykerAleshiaBrevardCrenshaw1997:
> % Unexpected field 'editora'
> % Unexpected field 'editoratype'
> % ? Title looks like it was stored in title-case in Zotero
>
> @article{hirschfeldIntersexuelleKonstitution1923,
>   langid = {german},
>   title = {Die intersexuelle Konstitution},
>   volume = {23},
>   journaltitle = {Jahrbuch f\"ur sexuelle Zwischenstufen},
>   date = {1923},
>   pages = {3-27},
>   author = {Hirschfeld, Magnus}
> }
>
>
>
>
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Re: Scrivener->pandoc->DOCX rogue footnote problems

[AnnFran]

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Darn. I'm sorry. I really thought I had parsed things down. But here are 
examples on the basis of just two references:


*The Markdown Source for two references (one repeated and one with text in 
the note):*
arguments about diversity.[^fn1] 

interwar Berlin.[^fn2] 

in a 1949 article [^fn3]

[^fn1]: @hirschfeldTransvestitenUntersuchungUeber1910.

[^fn2]: @hirschfeldTransvestitenUntersuchungUeber1910, 4-5.

[^fn3]: @cauldwellPsychopathiaTransexualis1949. Lorem ipsum dolor sit amet, 
consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et 
dolore magna aliqua.

*The .BIB source for these two citations:*

@book{hirschfeldTransvestitenUntersuchungUeber1910,
  langid = {german},
  location = {{Berlin}},
  title = {Die Transvestiten: Eine Untersuchung \"uber den erotischen 
Verkleidungstrieb},
  publisher = {{Alfred Pulvermacher \& Co.}},
  date = {1910},
  author = {Hirschfeld, Magnus}
}

@article{cauldwellPsychopathiaTransexualis2001,
  title = {Psychopathia {{Transexualis}}},
  volume = {5},
  abstract = {(Originally published in Sexology, vol. 16, 1949, pp. 
274-280. Copyright, 1949, by Sexology Magazine.)
http://www.iiav.nl/ezines/web/ijt/97-03/numbers/symposion/cauldwell\_02.htm},
  number = {2},
  journaltitle = {The International Journal of Transgenderism},
  date = {2001},
  author = {Cauldwell, David Oliver}
}
% == BibLateX quality report for cauldwellPsychopathiaTransexualis2001:
% ? Title looks like it was stored in title-case in Zotero

*The precise command line I used in terminal: *

pandoc --bibliography=MY_Zotero_refs.bib -s MY_compiled_doc.txt -o 
output.docx --csl=chicago.csl -f markdown -t docx

The Word output in the footnotes (with brackets to denote superscript. Line 
starting with the 6. is what was generated for FN 3):

 [1]
 [2]    
 [3]  1, 4-5.
 
6.    Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do 
eiusmod tempor incididunt ut labore et dolore magna aliqua. Dictum at 
tempor commodo ullamcorper. Nibh venenatis cras sed felis eget velit. Orci 
phasellus egestas tellus rutrum tellus pellentesque eu tincidunt tortor.

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Re: Scrivener->pandoc->DOCX rogue footnote problems

[John MacFarlane]

OK, I think I see what's happening here!

If you don't know about it, look in the manual for
pandoc's example list syntax.  Here's a numbered
example list:

@foo. first item.
@bar. second item.

You can refer back to it like this: in item @bar, blah
blah.

So, I suspect that what's happening in your case is
that

@hirschfeldTransvestitenUntersuchungUeber1910.

and

@cauldwellPsychopathiaTransexualis1949.

are being parsed as example lists.  This causes
the other occurrence of

@hirschfeldTransvestitenUntersuchungUeber1910,

to be parsed as a reference back to the example list.

(The syntax overlap is unfortunate.)

Try disabling example lists (-f
markdown-example_lists), or, if you need them,
backslash-escape the periods to prevent these from
being interpreted as list markers.

AnnFran <aftimm-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org> writes:

> Darn. I'm sorry. I really thought I had parsed things down. But here are 
> examples on the basis of just two references:
>
>
> *The Markdown Source for two references (one repeated and one with text in 
> the note):*
> arguments about diversity.[^fn1] 
>
> interwar Berlin.[^fn2] 
>
> in a 1949 article [^fn3]
>
> [^fn1]: @hirschfeldTransvestitenUntersuchungUeber1910.
>
> [^fn2]: @hirschfeldTransvestitenUntersuchungUeber1910, 4-5.
>
> [^fn3]: @cauldwellPsychopathiaTransexualis1949. Lorem ipsum dolor sit amet, 
> consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et 
> dolore magna aliqua.
>
> *The .BIB source for these two citations:*
>
> @book{hirschfeldTransvestitenUntersuchungUeber1910,
>   langid = {german},
>   location = {{Berlin}},
>   title = {Die Transvestiten: Eine Untersuchung \"uber den erotischen 
> Verkleidungstrieb},
>   publisher = {{Alfred Pulvermacher \& Co.}},
>   date = {1910},
>   author = {Hirschfeld, Magnus}
> }
>
> @article{cauldwellPsychopathiaTransexualis2001,
>   title = {Psychopathia {{Transexualis}}},
>   volume = {5},
>   abstract = {(Originally published in Sexology, vol. 16, 1949, pp. 
> 274-280. Copyright, 1949, by Sexology Magazine.)
> http://www.iiav.nl/ezines/web/ijt/97-03/numbers/symposion/cauldwell\_02.htm},
>   number = {2},
>   journaltitle = {The International Journal of Transgenderism},
>   date = {2001},
>   author = {Cauldwell, David Oliver}
> }
> % == BibLateX quality report for cauldwellPsychopathiaTransexualis2001:
> % ? Title looks like it was stored in title-case in Zotero
>
> *The precise command line I used in terminal: *
>
> pandoc --bibliography=MY_Zotero_refs.bib -s MY_compiled_doc.txt -o 
> output.docx --csl=chicago.csl -f markdown -t docx
>
> The Word output in the footnotes (with brackets to denote superscript. Line 
> starting with the 6. is what was generated for FN 3):
>
>  [1]
>  [2]    
>  [3]  1, 4-5.
>  
> 6.    Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do 
> eiusmod tempor incididunt ut labore et dolore magna aliqua. Dictum at 
> tempor commodo ullamcorper. Nibh venenatis cras sed felis eget velit. Orci 
> phasellus egestas tellus rutrum tellus pellentesque eu tincidunt tortor.
>
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Re: Scrivener->pandoc->DOCX rogue footnote problems

[AnnFran]

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No love. I entered the following command:

pandoc --bibliography=Trans.bib -s Intimacy.txt -o output.docx -f 
markdown-example_lists --csl=chicago.csl -t docx

This produced the following error messages in terminal:

pandoc-citeproc: reference hirschfeldTransvestitenUntersuchungUber1910 not 
found
pandoc-citeproc: reference hirschfeldTransvestitenUntersuchungUber1910 not 
found
pandoc-citeproc: reference hirschfeldmagnusIntersexuelleKonstitution1923 
not found
pandoc-citeproc: reference cauldwellPsychopathiaTransexualis1949 not found

And in the Word output, I now get two bolded question marks with a period 
where the citation should be. (At least the weird extra space and list 
formatting is gone though!)

But this did, mysteriously, fix one of the seven references I'm having 
trouble with. The .bib output for that one looks like this:

@book{doblerZwischenDuldungspolitikUnd2008,
  langid = {german},
  location = {{Frankfurt a.M.}},
  title = {Zwischen Duldungspolitik und Verbrechensbek\"ampfung: 
Homosexuellenverfolgung durch die Berliner Polizei von 1848 bis 1933},
  publisher = {{Verlag f\"ur Polizeiwissenschaft}},
  date = {2008},
  author = {Dobler, Jens}

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Re: Scrivener->pandoc->DOCX rogue footnote problems

[John MacFarlane]

Check your bib file and make sure you have records for
each of these citation ids.  The one you gave me above
doesn't contain a reference for
cauldwellPsychopathiaTransexualis1949.
It has, instead, cauldwellPsychopathiaTransexualis2001.

When I fix your sample input (above) to reflect this,
it gives correct results for the minimal sample with
-f markdown-example_lists.

If you are still having problems, please, again, post
a minimal example to reproduce them.

Re: Scrivener->pandoc->DOCX rogue footnote problems

[AnnFran]

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Just to end this thread, the solution you gave me did actually work. I was 
making some other mistakes. Thanks very much for your help!

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