Re: [O] Fwd: Citation processing via Zotero + zotxt

[Richard Lawrence]

Hi Matt and all,

Matt Lundin  writes:

> One question (based on complete ignorance of either zotero or zotxt) is
> whether those of us who maintain bibtex databases solely in emacs would
> have to interact with the zotero GUI.

My goal would be that you wouldn't need to interact with it at all.
(You would need to have Firefox running in the background, but that's it
-- no need to actually interact with the window as a user.)

> Let's say I have a bib file and an org document containing
> citations. Would everything place transparently in the background
> without ever having to interact with zotero? Can zotero query a bib
> file without requiring the user manually to import/export the
> database?

I do not know of a way to do this at the moment.  But it may already
exist somewhere, and if it doesn't, I don't think it will be too hard to
build.  (If anyone knows better, please let me know!)
 
Best,
Richard

Re: [O] Fwd: Citation processing via Zotero + zotxt

[Matt Lundin]

Matt Price  writes:

> On Sat, Nov 28, 2015 at 3:16 PM, Richard Lawrence
>  wrote:

> I know that many people (perhaps especially the `power users' who
> have been active in the citations discussion so far) prefer to
> maintain their reference database without the aid of a GUI
> reference manager like Zotero. I still think Zotero + zotxt is the
> best option for non-LaTeX citation processing, even for these
> folks. The ease of installation (and removal) of the required
> programs alone makes it worth it, even if you never actually
> populate a Zotero database. So given what I know at the moment, I
> think our efforts would best be directed at making the in-progress
> org-cite library communicate with Zotero via zotxt. What do you
> think?
>
> Best,
> Richard
>
> [1] https://www.zotero.org/
> [2] https://gitlab.com/egh/zotxt/
> [3] See the bibliographyEndpoint function in:
> https://gitlab.com/egh/zotxt/blob/master/extension/bootstrap.js
> [4] https://gitlab.com/egh/zotxt-emacs
>
> I love Zotxt. my only concern is for those people who run a remote
> Emacs. If, say, you run emacs on a server that you access by ssh, it
> will not be possible to process your citations with org. 
>
> I personally don't use this method, though I have occasionally had to
> work off of a server via some randome computer when my laptop breaks
> down. For me, this is a veyr rare case. Is there anyone on the list
> who might actually be negatively affected by this? 

I do have a remote emacs installation that I use occasionally, but not
enough to make this a concern.

One question (based on complete ignorance of either zotero or zotxt) is
whether those of us who maintain bibtex databases solely in emacs would
have to interact with the zotero GUI. Let's say I have a bib file and an
org document containing citations. Would everything place transparently
in the background without ever having to interact with zotero? Can
zotero query a bib file without requiring the user manually to
import/export the database?

Thanks,
Matt

Re: [O] Fwd: Citation processing via Zotero + zotxt

[Matt Price]

On Tue, Dec 1, 2015 at 10:51 AM, Richard Lawrence <
richard.lawre...@berkeley.edu> wrote:

> Hi Eric and all,
>
> Eric S Fraga  writes:
>
> > On Tuesday,  1 Dec 2015 at 07:12, Matt Price wrote:
> >> I love Zotxt. my only concern is for those people who run a remote
> Emacs.
> >> If, say, you run emacs on a server that you access by ssh, it will not
> be
> >> possible to process your citations with org.
> >
> > I'm not sure I understand this.
> >
> > Is the implication that one will need to be connected to the Internet to
> > be able to export citations?  If so, this is not good.
>
> No, you should not need to be connected to the Internet.  As I envision
> things, Emacs will just speak to the Zotero installation on the local
> machine.  That's what zotxt does now.  So, there should be no problem as
> long as Firefox, Zotero and zotxt are running on the same machine that
> is running Emacs.
>
> I suppose the concern is that someone running a remote Emacs is likely
> doing so on a machine that does not have a GUI...and hence may not have
> Firefox installed, and consequently won't have Zotero or zotxt.  In that
> case, citation processing would have to go another route.
>

This is the scenario I was envisioning, thank you both for clarifying.

>
> Are there a lot of people in that situation?
>

... and this is precisely the question I meant to ask.

>
> Best,
> Richard
>

Re: [O] Fwd: Citation processing via Zotero + zotxt

[Eric S Fraga]

On Tuesday,  1 Dec 2015 at 07:12, Matt Price wrote:
> I love Zotxt. my only concern is for those people who run a remote Emacs.
> If, say, you run emacs on a server that you access by ssh, it will not be
> possible to process your citations with org.

I'm not sure I understand this.

Is the implication that one will need to be connected to the Internet to
be able to export citations?  If so, this is not good.  I do much, often
most, of my writing while off-line (long train journeys every day).  It
would be quite intrusive to my writing habits to have to ensure that I
can connect to prepare actual exported documents.

For most, this may not be an issue so obviously my concern should not
derail any progress etc. but I am probably not alone...  Clarification,
in any case, would be welcome.

thanks,
eric
-- 
: Eric S Fraga (0xFFFCF67D), Emacs 25.0.50.2, Org release_8.3.2-355-g18f083

Re: [O] Fwd: Citation processing via Zotero + zotxt

[Richard Lawrence]

Hi Eric and all,

Eric S Fraga  writes:

> On Tuesday,  1 Dec 2015 at 07:12, Matt Price wrote:
>> I love Zotxt. my only concern is for those people who run a remote Emacs.
>> If, say, you run emacs on a server that you access by ssh, it will not be
>> possible to process your citations with org.
>
> I'm not sure I understand this.
>
> Is the implication that one will need to be connected to the Internet to
> be able to export citations?  If so, this is not good.

No, you should not need to be connected to the Internet.  As I envision
things, Emacs will just speak to the Zotero installation on the local
machine.  That's what zotxt does now.  So, there should be no problem as
long as Firefox, Zotero and zotxt are running on the same machine that
is running Emacs.

I suppose the concern is that someone running a remote Emacs is likely
doing so on a machine that does not have a GUI...and hence may not have
Firefox installed, and consequently won't have Zotero or zotxt.  In that
case, citation processing would have to go another route.

Are there a lot of people in that situation?
 
Best,
Richard

[O] Fwd: Citation processing via Zotero + zotxt

[Matt Price]

On Sat, Nov 28, 2015 at 3:16 PM, Richard Lawrence <
richard.lawre...@berkeley.edu> wrote:

> Hi everyone,
>
> For the past few days, I've been looking more closely at using the
> combination of Zotero [1] with Erik Hetzner's zotxt plugin [2] as a
> means of processing citations when exporting to non-LaTeX backends.  I
> am now thinking that this is probably our best option, but I'd like to
> know what other people think before I sink a lot of work into it.
>
> Here are the reasons I think this is the best option:
>
> 1) It is really easy for users.
>
> For those unfamiliar, Zotero is a reference manager, and zotxt is a
> Zotero plugin that makes it easier to work with Zotero from plain text
> documents.  Both are Firefox plugins, which means they can be installed
> by a non-technical user with a couple of clicks.  It also means that
> users get updates automatically.  I think this is *really* important.
>
> Pretty much all the other options we have talked about seem like they
> will require multi-step, non-trivial installation procedures ("First
> install {Node.js/Haskell/JVM ...}, then install
> {citeproc-node/pandoc-citeproc/citeproc-java...}, then install our
> wrapper script...").  Updating could require other manual operations of
> similar complexity.  Avoiding that kind of procedure will make citations
> a lot more usable from Org for everyone.
>
> Also, unlike the other options, Zotero is a full-featured reference
> manager, not just a batch processor.  So we as users get a useful piece
> of software with a simple installation procedure; the other options
> require a complex installation procedure for a less-useful program.
>
> 2) It is quite complete.
>
> Previously, I thought that it would be a similar amount of work to
> communicate with Zotero from Emacs as any of the other CSL
> implementations out there.  However, after looking at zotxt a bit more
> closely, I discovered that it has an (undocumented) API endpoint [3]
> that pretty much does exactly what we need: it accepts a list of
> citation objects, and returns a list of formatted citations and a
> formatted bibliography, which can be inserted into the exported
> document.
>
> This endpoint still needs a little bit of work, to generalize it and
> make it easier to get the data in the format we need.  (That is probably
> why it is undocumented in the README.) But it requires much less work
> than I thought it would, and much less work than it would be to get a
> full-featured setup with something like citeproc-node.
>
> Erik has also written a package for communicating with zotxt from Emacs,
> zotxt-emacs [4], which is available on MELPA.  This package already
> contains a lot of useful functions for querying the Zotero database and
> inserting reference data into documents, including links in Org
> documents.  I think it would be pretty straightforward to extend this
> package to provide a nice UI for writers who are inserting citations
> into Org documents, including search-based lookups of keys, etc.
> Perhaps org-ref could also be taught to communicate with zotxt (with or
> without zotxt-emacs) without too much work.
>
> 3) It uses citeproc-js.
>
> In previous discussions, I think we agreed that it would be best for us
> to use citeproc-js as a CSL processor, since it is the `canonical' CSL
> implementation, as opposed to pandoc-citeproc or citeproc-java.  Zotero
> just uses citeproc-js internally to process citations, so it meets this
> requirement.
>
>
> I know that many people (perhaps especially the `power users' who have
> been active in the citations discussion so far) prefer to maintain their
> reference database without the aid of a GUI reference manager like
> Zotero.  I still think Zotero + zotxt is the best option for non-LaTeX
> citation processing, even for these folks.  The ease of installation
> (and removal) of the required programs alone makes it worth it, even if
> you never actually populate a Zotero database.  So given what I know at
> the moment, I think our efforts would best be directed at making the
> in-progress org-cite library communicate with Zotero via zotxt.  What do
> you think?
>
> Best,
> Richard
>
> [1] https://www.zotero.org/
> [2] https://gitlab.com/egh/zotxt/
> [3] See the bibliographyEndpoint function in:
> https://gitlab.com/egh/zotxt/blob/master/extension/bootstrap.js
> [4] https://gitlab.com/egh/zotxt-emacs
>
> I love Zotxt. my only concern is for those people who run a remote Emacs.
If, say, you run emacs on a server that you access by ssh, it will not be
possible to process your citations with org.

I personally don't use this method, though I have occasionally had to work
off of a server via some randome computer when my laptop breaks down.  For
me, this is a veyr rare case. Is there anyone on the list who might
actually be negatively affected by this?