Upgrade StorageConversion problem with Betterbibtex and Pandoc (Using Zotero with Ulysses)
Hi there,
TL;DR: Generating Zotero citekeys with Better Bibtex, using Ulysses to write in markdown. adding citekeys. Converting citekeys to citations and bibliography in a word-document with an automated script/program utilizing Pandoc. Final citations end up as Author (Year), instead of (Author, Year). No problem with bibliography.
Markdown/Ulysses and Zotero
Recently I have gotten fond of doing my writing in markdown, which has complicated my process slightly in regards of citations. As a work-around I have been drafting with Ulysses, and still done most of the writing in Word, entering all the citations using the Zotero add-on. It is a pain in the ass and I just want to do all my writing in Ulysses, so I have been looking for a better way of doing this. And then I found this guide (for anyone using Ulysses to write, this tutorial is a gem*): http://raphaelkabo.com/blog/posts/markdown-to-word
The first time I saw it, I was a bit put off as I'm not much of a coder, but today I decided to give it a go. Things have gone remarkably well. Now I can even add citations to Ulysses through the same kind of Zotero dialogue as for the Word add-on. Though I have problems with the final conversion from markdown to docx. It is not turning out like I would like it to.
The problem
Following the guide I have made a tiny little program that is supposed to automate the Pandoc conversion, and after some tweaking it actually works. Running through the script I get a docx document where the citekeys are citations and the bibliography is perfect, but there is a huge problem: The year shows up inside the parenthesis, whereas the author's names show up outside.
For example:
@holmquist1998 =
Holmquist, Schmidt-Gengenbach, & Yoshioka (1998), instead of
(Holmquist, Schmidt-Gengenbach, & Yoshioka, 1998)
First I thought it would have to be the style-sheet I was using that was the culprit, but now I have tried two different apa style sheets, and one Chicago author date style, and the results are the same. I'm starting to wonder whether it can have something to do with the citekeys themselves, or probably rather how I have set up betterbibtext.
I'm not really sure whether this forum is the right place to ask, but there seems to be a bunch of people around here that really knows what they are doing, so I thought I'd give it a try.
An overview of my settings:
Zotero settings/export: Better BibTeX Citation Key Quick Copy
Zotero settings/Better Bibtex/Citation keys:
Citation key format: [auth:lower][year]
Force citation key to plain text - checked
QuickCopy format: LaTex
Anything here that looks off? If things look fine here, any ideas why the author name shows up outside the parenthesis? Really appreciate it if anyone has the time to help me out with this. I'd be super happy if I can finally be able to do all my writing in markdown.
*Following the guide, I had no problems until the last bit, where you can make a little program that automates the conversion so that you can send your text directly from Ulysses to word and get everything converted. It seems like the code doesn't really work with the newer version of Pandoc, so I did some slight tweaks, and now it kind of works. This is the code I'm using at the moment: https://ibb.co/iJxMCw (which paths you need to change, you can see in the original code in the tutorial).
TL;DR: Generating Zotero citekeys with Better Bibtex, using Ulysses to write in markdown. adding citekeys. Converting citekeys to citations and bibliography in a word-document with an automated script/program utilizing Pandoc. Final citations end up as Author (Year), instead of (Author, Year). No problem with bibliography.
Markdown/Ulysses and Zotero
Recently I have gotten fond of doing my writing in markdown, which has complicated my process slightly in regards of citations. As a work-around I have been drafting with Ulysses, and still done most of the writing in Word, entering all the citations using the Zotero add-on. It is a pain in the ass and I just want to do all my writing in Ulysses, so I have been looking for a better way of doing this. And then I found this guide (for anyone using Ulysses to write, this tutorial is a gem*): http://raphaelkabo.com/blog/posts/markdown-to-word
The first time I saw it, I was a bit put off as I'm not much of a coder, but today I decided to give it a go. Things have gone remarkably well. Now I can even add citations to Ulysses through the same kind of Zotero dialogue as for the Word add-on. Though I have problems with the final conversion from markdown to docx. It is not turning out like I would like it to.
The problem
Following the guide I have made a tiny little program that is supposed to automate the Pandoc conversion, and after some tweaking it actually works. Running through the script I get a docx document where the citekeys are citations and the bibliography is perfect, but there is a huge problem: The year shows up inside the parenthesis, whereas the author's names show up outside.
For example:
@holmquist1998 =
Holmquist, Schmidt-Gengenbach, & Yoshioka (1998), instead of
(Holmquist, Schmidt-Gengenbach, & Yoshioka, 1998)
First I thought it would have to be the style-sheet I was using that was the culprit, but now I have tried two different apa style sheets, and one Chicago author date style, and the results are the same. I'm starting to wonder whether it can have something to do with the citekeys themselves, or probably rather how I have set up betterbibtext.
I'm not really sure whether this forum is the right place to ask, but there seems to be a bunch of people around here that really knows what they are doing, so I thought I'd give it a try.
An overview of my settings:
Zotero settings/export: Better BibTeX Citation Key Quick Copy
Zotero settings/Better Bibtex/Citation keys:
Citation key format: [auth:lower][year]
Force citation key to plain text - checked
QuickCopy format: LaTex
Anything here that looks off? If things look fine here, any ideas why the author name shows up outside the parenthesis? Really appreciate it if anyone has the time to help me out with this. I'd be super happy if I can finally be able to do all my writing in markdown.
*Following the guide, I had no problems until the last bit, where you can make a little program that automates the conversion so that you can send your text directly from Ulysses to word and get everything converted. It seems like the code doesn't really work with the newer version of Pandoc, so I did some slight tweaks, and now it kind of works. This is the code I'm using at the moment: https://ibb.co/iJxMCw (which paths you need to change, you can see in the original code in the tutorial).
...is an important finding [@holmquist1998]. -->...is an important finding (Holmquist, Schmidt-Gengenbach, & Yoshioka, 1998).
without brackets give you citations with authors in the text:
as @holmquist1998 say--> as Holmquist, Schmidt-Gengenbach, & Yoshioka (1998) say.
With the square brackets everything's working great. Thanks for the help :)
@aastals: Are you still using the code that you posted for the last step of the guide? I get the following warning in Ulysses when I try with your code:
„[WARNING] Deprecated: —latexmathml, —asciimathml, -m pandoc: Cannote decode byte ‚/xba‘:Data.Text.Internal.Encosing.decodeUtf8: Invalid UTF-8 stream
Any suggestions would be very much appreciated!
I'm attempting to set up the workflow found at http://raphaelkabo.com/blog/posts/markdown-to-word
but I am encountering trouble with the zotpick-pandoc applescript. I've set up the service module in Automator and the key command in system preferences. However, when using the key command, I get the error: The action “Run AppleScript” encountered an error: “The operation couldn’t be completed. (com.apple.Automator error -212.)”
In the automator workflow, I get the syntax error: Expected end of line, etc. but found “<”.
Any thoughts about troubleshooting the applescript?
I have set it up and have got it functioning well. I do have one more thing to fix though:
When I enter a citation 'as is' from the search, it is entered as [#citekey][].
The # must be then changed (manually) before running my export to [@citekey][]. Where do I go to change the symbol just before the citekey, or indeed where do I go to make the workflow look for the # instead!!
Thanks
Alistaur
Here it is in full, could you point me to the right bit please?
title=$(basename "$@" .md)
echo -e "\n\n# Bibliography" >> "$@"
/usr/local/bin/pandoc -s -smart --filter=/usr/local/bin/pandoc-citeproc --bibliography "/Users/awuni/Dropbox/_UNI/04. Library/_REF.MGMT/aw1.bib" --csl "/Users/awuni/Dropbox/_UNI/04. Library/_REF.MGMT/Harvard-ISO-690-Lboro.csl" --reference-doc "/Users/awuni/Dropbox/_UNI/04. Library/_REF.MGMT/reference.docx" -f markdown-smart -t docx -o /Users/awuni/Desktop/Output/"$title".docx "$@"
set theReference to do shell script "/usr/bin/curl 'http://localhost:23119/better-bibtex/cayw?format=pandoc' 2>/dev/null; exit 0"
and it worked fine. Thanks
I'm experiencing a citation formating issue. I followed Raphael Kalbo workflow and it works perfectly. However, in the word document generated, my citation numbers in the text appear with quotes "(1)" instead of the traditional (1). How could I get rid of the quotes ? (also i m no expert in apple script)
Thanks in advance,
Julien
sure. Here it is :
...performed as previously described[@dimastromatteo2018a]. ==> ......performed as previously described"(1)".
and here are my settings :
Zotero settings/export: Better BibTeX Citation Key Quick Copy
Zotero settings/Better Bibtex/Citation keys:
Citation key format: [auth:lower][year]
Force citation key to plain text - checked
QuickCopy format: Pandoc
Surround Pandoc citations with brackets - checked
Ok. Will do. Thanks for your help.
Now, my problem is that the headers and bibliographical notices in the final docx appears between brackets as :
[Bibliography]
[Arnstein Sherry R., 1969, « A Ladder Of Citizen Participation », Journal of the American Institute of Planners, vol. 35, n° 4 : 216‑224.]
Weird !
When I drag and drop my items into a text box, they show up as expected:
[@marcuse1969]
[@lowy2001]
[@takiguchi1939]
However, when I use zotpick, I get the following results:
@MARCuse1969
@LOWY2001
@TAKIGUChi1939
My settings are the same as Juleind73 above, ie:
Citation key format: [auth:lower][year]
Force citation key to plain text - checked
QuickCopy format: Pandoc
Surround Pandoc citations with brackets - checked
Does anyone have any idea about why this might be happening?
2. The various zotpick applescripts all request a specific format, we'd have to know which you are using.
1. I understand, these are separate actions.
2. I have copied the contents of zotpick-pandoc.applescript into the service that I am running through Automator. See below:
else if zotRunning is "ready" then
set theReference to do shell script "/usr/bin/curl 'http://localhost:23119/better-bibtex/cayw?format=pandoc' 2>/dev/null; exit 0"
&brackets=trueto the URLcurl 'http://localhost:23119/better-bibtex/cayw?format=pandoc'from the shell, what do you get?
I ran
curl 'http://localhost:23119/better-bibtex/cayw?format=pandoc&brackets=true'from Terminal, using the example of a book by Lowy from 2001, page 12, and got the following:[@lowy2001, p. 12]This is correct.
When I use a text editor, I can try citing the same book and page number repeatedly and I get different results one after another:
[@lowy2001, P. 12]
[@lOWY2001< P. 12]
[@lowy2001< P. 12]
[@lowy2001, p. 12}
[@loWY2001, p. 12]
This happens in a few different programs (DevonThink, Notes, TextMate). Here is the sequence when I used this window:
[@lowy2001, P. 12}[@lowy2001, p. 12]
[@lowy2001, p. 12]
What do you use for processing these documents? Pandoc?Pandoc. I may have something for you later today.}) is correctible. The 4th would be complex.Does it make any difference if you paste the information rather than perform it as keystrokes?
Now I'm going to hop over to the thread about generating live citations in Word, because if that is possible it would open up a whole new world!