Reference / citation managers for OBSD?

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Reference / citation managers for OBSD?

Michael L. Wilson
Dear OpenBSD users,

I've just acquired a Thinkpad x200 with the aim of transitioning into a full-time OpenBSD user. The 5.5 release with the Xfce desktop works flawlessly and I am very happy with this system.

Nearly all of my software needs have been quite satisfactorily met using the available packages. However, one minor niggle remains. I cannot seem to find a suitable reference/citation manager for academic work.

I am very fond of Zotero, but Firefox on OpenBSD seems to have issues with the Zotero plugin. The browser will not relaunch after it has been installed. Thus I am unable to use either Firefox or Zotero until the Zotero plugin is removed. I cannot either compile FireFox from ports due to space limitations on the current drive. Just for kicks I tried Zotero in a fresh install of FreeBSD and it does not have this issue.

I am aware that the problem appears to be more widespread: forums.zotero.org/discussion/32183?page=1#Item_12

None of the options listed on the Zotero forum worked for me. I even tried an online hack to get the Zotero plugin working in Seamonkey without success.

Jabref, the other alternative, is not available in the OpenBSD repository or in ports.

Ideally I would like a program that works well with LibreOffice. I have no qualms about learning something completely new until the Zotero issue is fixed. I am willing to wait patiently for a fix but in the meantime I need something to use. I would even be willing to explore a proprietary option as a last resort.

Any tips or suggestions would be very appreciated! I am willing to put in the time and effort to get this working so any suggestions will be taken very seriously.

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Re: Reference / citation managers for OBSD?

Zé Loff-2


> On 06/08/2014, at 07:13, "Michael L. Wilson" <[hidden email]> wrote:
>
> Dear OpenBSD users,
>
> I've just acquired a Thinkpad x200 with the aim of transitioning into a full-time OpenBSD user. The 5.5 release with the Xfce desktop works flawlessly and I am very happy with this system.
>
> Nearly all of my software needs have been quite satisfactorily met using the available packages. However, one minor niggle remains. I cannot seem to find a suitable reference/citation manager for academic work.
>
> I am very fond of Zotero, but Firefox on OpenBSD seems to have issues with the Zotero plugin. The browser will not relaunch after it has been installed. Thus I am unable to use either Firefox or Zotero until the Zotero plugin is removed. I cannot either compile FireFox from ports due to space limitations on the current drive. Just for kicks I tried Zotero in a fresh install of FreeBSD and it does not have this issue.
>
> I am aware that the problem appears to be more widespread: forums.zotero.org/discussion/32183?page=1#Item_12
>
> None of the options listed on the Zotero forum worked for me. I even tried an online hack to get the Zotero plugin working in Seamonkey without success.
>
> Jabref, the other alternative, is not available in the OpenBSD repository or in ports.
>
> Ideally I would like a program that works well with LibreOffice. I have no qualms about learning something completely new until the Zotero issue is fixed. I am willing to wait patiently for a fix but in the meantime I need something to use. I would even be willing to explore a proprietary option as a last resort.
>
> Any tips or suggestions would be very appreciated! I am willing to put in the time and effort to get this working so any suggestions will be taken very seriously.

I've been using JabRef for a couple of years (not with LibreOffice, though, just LaTeX). Just download the .jar file and run it with "java -jar ...".

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Re: Reference / citation managers for OBSD?

Landry Breuil-6
In reply to this post by Michael L. Wilson
On Wed, Aug 06, 2014 at 09:13:53AM +0300, Michael L. Wilson wrote:

> Dear OpenBSD users,
>
> I've just acquired a Thinkpad x200 with the aim of transitioning into a full-time OpenBSD user. The 5.5 release with the Xfce desktop works flawlessly and I am very happy with this system.
>
> Nearly all of my software needs have been quite satisfactorily met using the available packages. However, one minor niggle remains. I cannot seem to find a suitable reference/citation manager for academic work.
>
> I am very fond of Zotero, but Firefox on OpenBSD seems to have issues with the Zotero plugin. The browser will not relaunch after it has been installed. Thus I am unable to use either Firefox or Zotero until the Zotero plugin is removed. I cannot either compile FireFox from ports due to space limitations on the current drive. Just for kicks I tried Zotero in a fresh install of FreeBSD and it does not have this issue.
>
> I am aware that the problem appears to be more widespread: forums.zotero.org/discussion/32183?page=1#Item_12
>
> None of the options listed on the Zotero forum worked for me. I even tried an online hack to get the Zotero plugin working in Seamonkey without success.

I've already been asked about this last year, so i'll just copypaste
my reply:

=====
> After I install it into Firefox on OpenBSD, firefox does
> never fully load. There's running process but the application
> itself never appears. (Though it works under Linux.)
> Or... ktrace for debugging?

It tries to use pipes via mkfifo, then creates an empty sqlite
database... i see no binary component in the addon itself, so at least
it's not broken by design, but you'll have to debug it yourself with
upstream. They probably have debug options/knobs to make it more
verbose. And yes, ktrace too.
I'd say look into the xpi, unzip zotero.jar and start reading
content/zotero/xpcom/ipc.js.
=====

Also, for the record:
http://marc.info/?l=openbsd-cvs&m=133217901415880&w=2

I suppose you've tested the hack discussed in
https://forums.zotero.org/discussion/32183?page=1#Item_12 ?

> Jabref, the other alternative, is not available in the OpenBSD repository or in ports.

Jabref looks to be java, so you might want to try fetching the jar file
and run it directly. No need to make a port of it just to test it...

Landry

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Re: Reference / citation managers for OBSD?

Gregor Best
> [...]
> > Jabref, the other alternative, is not available in the OpenBSD repository or in ports.
>
> Jabref looks to be java, so you might want to try fetching the jar file
> and run it directly. No need to make a port of it just to test it...
> [...]

That should work. I've used Jabref for my thesis and a few papers and never had a problem.

--
        Gregor Best

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Re: Reference / citation managers for OBSD?

Amit Kulkarni-5
In reply to this post by Zé Loff-2
+1.

JabRef works just fine with bibtex or with importing your original citation
records from Endnote or some such Windows only software.


On Wed, Aug 6, 2014 at 2:59 AM, Zé Loff <[hidden email]> wrote:

>
>
> > On 06/08/2014, at 07:13, "Michael L. Wilson" <[hidden email]>
> wrote:
> >
> > Dear OpenBSD users,
> >
> > I've just acquired a Thinkpad x200 with the aim of transitioning into a
> full-time OpenBSD user. The 5.5 release with the Xfce desktop works
> flawlessly and I am very happy with this system.
> >
> > Nearly all of my software needs have been quite satisfactorily met using
> the available packages. However, one minor niggle remains. I cannot seem to
> find a suitable reference/citation manager for academic work.
> >
> > I am very fond of Zotero, but Firefox on OpenBSD seems to have issues
> with the Zotero plugin. The browser will not relaunch after it has been
> installed. Thus I am unable to use either Firefox or Zotero until the
> Zotero plugin is removed. I cannot either compile FireFox from ports due to
> space limitations on the current drive. Just for kicks I tried Zotero in a
> fresh install of FreeBSD and it does not have this issue.
> >
> > I am aware that the problem appears to be more widespread:
> forums.zotero.org/discussion/32183?page=1#Item_12
> >
> > None of the options listed on the Zotero forum worked for me. I even
> tried an online hack to get the Zotero plugin working in Seamonkey without
> success.
> >
> > Jabref, the other alternative, is not available in the OpenBSD
> repository or in ports.
> >
> > Ideally I would like a program that works well with LibreOffice. I have
> no qualms about learning something completely new until the Zotero issue is
> fixed. I am willing to wait patiently for a fix but in the meantime I need
> something to use. I would even be willing to explore a proprietary option
> as a last resort.
> >
> > Any tips or suggestions would be very appreciated! I am willing to put
> in the time and effort to get this working so any suggestions will be taken
> very seriously.
>
> I've been using JabRef for a couple of years (not with LibreOffice,
> though, just LaTeX). Just download the .jar file and run it with "java -jar
> ...".
>
>
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Re: Reference / citation managers for OBSD?

Michael L. Wilson
@ Zé, Todd, Landry, Gregor and Amit,

Thank you very much for your replies concerning my email about reference managers for OpenBSD. I have had a chance to sit down and work a bit with JabRef and indeed it does work quite nicely in OpenBSD when launched as follows:

/usr/local/jdk-1.7.0/bin/java -jar JabRef-2.10.jar

This was the last step to OpenBSD being a complete work replacement for my Linux-based OS.

Thanks again.

On 08/06/2014 04:18 PM, Amit Kulkarni wrote:

> +1.
>
> JabRef works just fine with bibtex or with importing your original citation
> records from Endnote or some such Windows only software.
>
>
> On Wed, Aug 6, 2014 at 2:59 AM, Zé Loff <[hidden email]> wrote:
>
>>
>>
>>> On 06/08/2014, at 07:13, "Michael L. Wilson" <[hidden email]>
>> wrote:
>>>
>>> Dear OpenBSD users,
>>>
>>> I've just acquired a Thinkpad x200 with the aim of transitioning into a
>> full-time OpenBSD user. The 5.5 release with the Xfce desktop works
>> flawlessly and I am very happy with this system.
>>>
>>> Nearly all of my software needs have been quite satisfactorily met using
>> the available packages. However, one minor niggle remains. I cannot seem to
>> find a suitable reference/citation manager for academic work.
>>>
>>> I am very fond of Zotero, but Firefox on OpenBSD seems to have issues
>> with the Zotero plugin. The browser will not relaunch after it has been
>> installed. Thus I am unable to use either Firefox or Zotero until the
>> Zotero plugin is removed. I cannot either compile FireFox from ports due to
>> space limitations on the current drive. Just for kicks I tried Zotero in a
>> fresh install of FreeBSD and it does not have this issue.
>>>
>>> I am aware that the problem appears to be more widespread:
>> forums.zotero.org/discussion/32183?page=1#Item_12
>>>
>>> None of the options listed on the Zotero forum worked for me. I even
>> tried an online hack to get the Zotero plugin working in Seamonkey without
>> success.
>>>
>>> Jabref, the other alternative, is not available in the OpenBSD
>> repository or in ports.
>>>
>>> Ideally I would like a program that works well with LibreOffice. I have
>> no qualms about learning something completely new until the Zotero issue is
>> fixed. I am willing to wait patiently for a fix but in the meantime I need
>> something to use. I would even be willing to explore a proprietary option
>> as a last resort.
>>>
>>> Any tips or suggestions would be very appreciated! I am willing to put
>> in the time and effort to get this working so any suggestions will be taken
>> very seriously.
>>
>> I've been using JabRef for a couple of years (not with LibreOffice,
>> though, just LaTeX). Just download the .jar file and run it with "java -jar
>> ...".
>>
>>