From mboxrd@z Thu Jan 1 00:00:00 1970 From: John Kitchin Subject: Re: jabref like orgmode based solution to bibliography management (not for latex) Date: Sat, 5 Dec 2015 08:05:51 -0500 Message-ID: References: <87r3py5b8f.fsf@posteo.de> <87h9qs67i9.fsf@posteo.de> Mime-Version: 1.0 Content-Type: multipart/alternative; boundary=047d7bae465c8bd16c05262648f5 Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:52782) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1a5CXC-0006fH-UJ for emacs-orgmode@gnu.org; Sat, 05 Dec 2015 08:05:56 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1a5CXA-0006ST-Sz for emacs-orgmode@gnu.org; Sat, 05 Dec 2015 08:05:54 -0500 Received: from mail-wm0-x22d.google.com ([2a00:1450:400c:c09::22d]:35376) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1a5CXA-0006SK-Ie for emacs-orgmode@gnu.org; Sat, 05 Dec 2015 08:05:52 -0500 Received: by wmuu63 with SMTP id u63so92087044wmu.0 for ; Sat, 05 Dec 2015 05:05:51 -0800 (PST) In-Reply-To: List-Id: "General discussions about Org-mode." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: emacs-orgmode-bounces+geo-emacs-orgmode=m.gmane.org@gnu.org Sender: emacs-orgmode-bounces+geo-emacs-orgmode=m.gmane.org@gnu.org To: Xebar Saram Cc: org mode , Titus von der Malsburg --047d7bae465c8bd16c05262648f5 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Try (untested) (defun helm-bibtex-ikloog-publications () "Search BibTeX entries authored by me" (interactive) (let ((helm-bibtex-bibliography "your special bibfile")) (helm :sources '(helm-source-bibtex) :full-frame t :input "kloog !unpublished !prep " :candidate-number-limit 500))) John ----------------------------------- Professor John Kitchin Doherty Hall A207F Department of Chemical Engineering Carnegie Mellon University Pittsburgh, PA 15213 412-268-7803 @johnkitchin http://kitchingroup.cheme.cmu.edu On Sat, Dec 5, 2015 at 7:17 AM, Xebar Saram wrote: > Hi again Titus and list > > so the semester is finally nearing the end which means i finally have som= e > time (and a life :)) to get back to what i partially started a few months > ago. > > i have a question regarding Predefined searches. i have a search that > works well for searching papers i authored. > i am thinking of moving towards 2 bib files instead of 1 big one, that is > one for my papers and one for the rest (any disadvantages of using 2 bib > files?). > i want to add in the Predefined search to only draw from my file (mypaper= .bib), > even though in the default helm-bibtex sources it will have 2 inputs. is > such a thing possible? > > this is how a current search i have looks like > > #+BEGIN_SRC emacs-lisp :results none > > ;; Define helm-search with predefined search expression: > (defun helm-bibtex-ikloog-publications () > "Search BibTeX entries authored by me" > (interactive) > (helm :sources '(helm-source-bibtex) > :full-frame t > :input "kloog !unpublished !prep " > :candidate-number-limit 500)) > #+END_SRC > > how does one add the specific .bib file filter? > > best > > Z > > On Sun, May 31, 2015 at 7:23 PM, Titus von der Malsburg < > malsburg@posteo.de> wrote: > >> >> On 2015-05-31 Sun 03:01, Xebar Saram wrote: >> > Thanks so much everyone for these great replies. i will investigate th= is >> > further today and let everyone know how im going with my transition :) >> > >> > thanks again >> > >> > PS: Titus, do you think that the helm-bibtex APA style reference list >> > could be user customizable in the future? >> >> Depends on what you mean by customizable. If you mean a customization >> option to allows you to replace the function for APA formatting with >> another function, then yes that would definitely make sense. >> >> Titus >> >> > >> > Z. >> > >> > On Sat, May 30, 2015 at 6:56 PM, John Kitchin >> > wrote: >> > >> >> >> >> >> >> On Saturday, May 30, 2015, Titus von der Malsburg >> >> wrote: >> >> >> >>> >> >>> On 2015-05-30 Sat 01:20, Xebar Saram wrote: >> >>> > Hi all >> >>> > >> >>> > i have been using jabref for the past 2-4 years in my academia wor= k >> to >> >>> > manage my reference library. i dont use latex (..its on my TODO >> >>> list...when >> >>> > (f ever) i have time..) so for now i just want something to manage >> my >> >>> > references. the key things i need to move over from jabref are: >> >>> >> >>> Author of helm-bibtex here. >> >>> >> >>> > 1. easy add references >> >>> >> >>> Helm-bibtex doesn=E2=80=99t deal with this because I prefer to edit = my BibTeX >> >>> file by hand. BibTeX retrieved from journals is almost always messy >> and >> >>> I need to edit it anyway. It=E2=80=99s not too hard, though: I clic= k on >> BibTeX >> >>> export on the journal page, the BibTeX file is opened in Emacs, I fi= x >> >>> it, and use a command that appends it to my bibliography. >> >>> >> >>> However, I think org-ref has tools that do more to support importing >> new >> >>> entries and org-ref combines well with helm-bibtex. >> >> >> >> >> >> Org-ref has doi-utils that let you add bibtex entries and download PD= Fs >> >> from a doi or crossref query. >> >> >> >> >> >>> >> >>> > 2. a way to quick filter references (helm bibtex seems like a good >> >>> solution) >> >>> >> >>> That=E2=80=99s what helm-bibtex was written to solve. >> >>> >> >>> > 3. filter lists based on tags/keywords (orgmode has that covered) >> >>> >> >>> In helm-bibtex you can also search for keywords and tags. >> >>> >> >>> > 4. this one is important: a way to quickly export selected >> references in >> >>> > word/odf/html based on a pre fixed style (ie Nature, Chicago etc) >> >>> >> >>> helm-bibtex can generate references in APA style but as far as I can >> see >> >>> Chicago style is very similar, so it shouldn=E2=80=99t be hard to ad= d support >> >>> for that. >> >>> >> >>> > anyone uses such a system in emacs/org and can recommend the way t= o >> >>> > go? >> >>> >> >>> For more details, see: https://github.com/tmalsburg/helm-bibtex >> >>> >> >>> Titus >> >>> >> >>> >> >> >> >> -- >> >> John >> >> >> >> ----------------------------------- >> >> Professor John Kitchin >> >> Doherty Hall A207F >> >> Department of Chemical Engineering >> >> Carnegie Mellon University >> >> Pittsburgh, PA 15213 >> >> 412-268-7803 >> >> @johnkitchin >> >> http://kitchingroup.cheme.cmu.edu >> >> >> >> >> >> >> >> > --047d7bae465c8bd16c05262648f5 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Try (untested)

=C2=A0(defun=C2=A0helm-bibtex-ikloog-publications ()
=C2=A0 =C2=A0"Search=C2=A0BibTeX=C2=A0entries auth= ored by me"
=C2=A0 =C2=A0(interacti= ve)
(let ((helm-bibtex-bibliography &quo= t;your special bibfile"))
=C2=A0 = =C2=A0(helm :sources '(helm-source-bibtex)
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0:full-frame t
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0:input "kloog=C2=A0!u= npublished !prep "
=C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0:candidate-number-limit 500)))



John
-----------------------------------
Professor John Kitchin=C2=A0Doherty Hall A207F
Department of Chemical Engineering
Carnegie Mello= n University
Pittsburgh, PA 15213
412-268-7803
<= /div>
On Sat, Dec 5, 2015 at 7:17 AM, Xebar Saram = <zeltakc@gmail.com> wrote:
Hi again Titus and list

so the semeste= r is finally nearing the end which means i finally have some time (and a li= fe :)) to get back to what i partially started a few months ago.
=
i have a question regarding=C2=A0Predefined searches. i have= a search that works well for searching papers i authored.=C2=A0
= i am thinking of moving towards 2 bib files instead of 1 big one, that is o= ne for my papers and one for the rest (any disadvantages of using 2 bib fil= es?).
i want to add in the=C2=A0Predefined search to only draw fr= om my file (mypaper.bib), even though in the default helm-bibtex sources it will have 2 inputs. is such a thing possible?

this is how a current search i have looks like
=

#+BEGIN_SRC emacs-lisp := results none

=C2=A0;; Define helm-search with pred= efined search expression:
=C2=A0(defun helm-bi= btex-ikloog-publications ()
=C2=A0 =C2=A0&quo= t;Search BibTeX entries authored by me"
=C2=A0 = =C2=A0(interactive)
=C2=A0 =C2=A0(helm :sources '(helm-source= -bibtex)
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0:full-fra= me t
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0:input "kloog !unpublished !prep "
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0:candidate-number-limit 500))
#+END_SRC
=

how does one add the specific .bib file filter?

best

Z

On Sun, May 31, 2015 at 7:23 PM, Titus von der Malsburg <malsburg@posteo.de> wrote:

On 2015-05-31 Sun 03:01, Xebar Saram wrote:
> Thanks so much everyone for these great replies. i will investigate th= is
> further today and let everyone know how im going with my transition :)=
>
> thanks again
>
> PS: Titus, do you think=C2=A0 that the helm-bibtex APA style reference= list
> could be user customizable in the future?

Depends on what you mean by customizable.=C2=A0 If you mean a custom= ization
option to allows you to replace the function for APA formatting with
another function, then yes that would definitely make sense.

=C2=A0 Titus

>
> Z.
>
> On Sat, May 30, 2015 at 6:56 PM, John Kitchin <jkitchin@andrew.cmu.edu> > wrote:
>
>>
>>
>> On Saturday, May 30, 2015, Titus von der Malsburg <malsburg@posteo.de>
>> wrote:
>>
>>>
>>> On 2015-05-30 Sat 01:20, Xebar Saram wrote:
>>> > Hi all
>>> >
>>> > i have been using jabref for the past 2-4 years in my aca= demia work to
>>> > manage my reference library. i dont use latex (..its on m= y TODO
>>> list...when
>>> > (f ever) i have time..) so for now i just want something = to manage my
>>> > references. the key things i need to move over from jabre= f are:
>>>
>>> Author of helm-bibtex here.
>>>
>>> > 1. easy add references
>>>
>>> Helm-bibtex doesn=E2=80=99t deal with this because I prefer to= edit my BibTeX
>>> file by hand.=C2=A0 BibTeX retrieved from journals is almost a= lways messy and
>>> I need to edit it anyway.=C2=A0 It=E2=80=99s not too hard, tho= ugh: I click on BibTeX
>>> export on the journal page, the BibTeX file is opened in Emacs= , I fix
>>> it, and use a command that appends it to my bibliography.
>>>
>>> However, I think org-ref has tools that do more to support imp= orting new
>>> entries and org-ref combines well with helm-bibtex.
>>
>>
>> Org-ref has doi-utils that let you add bibtex entries and download= PDFs
>> from a doi or crossref query.
>>
>>
>>>
>>> > 2. a way to quick filter references (helm bibtex seems li= ke a good
>>> solution)
>>>
>>> That=E2=80=99s what helm-bibtex was written to solve.
>>>
>>> > 3. filter lists based on tags/keywords (orgmode has that = covered)
>>>
>>> In helm-bibtex you can also search for keywords and tags.
>>>
>>> > 4. this one is important: a way to quickly export selecte= d references in
>>> > word/odf/html based on a pre fixed style (ie=C2=A0 Nature= , Chicago etc)
>>>
>>> helm-bibtex can generate references in APA style but as far as= I can see
>>> Chicago style is very similar, so it shouldn=E2=80=99t be hard= to add support
>>> for that.
>>>
>>> > anyone uses such a system in emacs/org and can recommend = the way to
>>> > go?
>>>
>>> For more details, see: https://github.com/tmals= burg/helm-bibtex
>>>
>>>=C2=A0 =C2=A0Titus
>>>
>>>
>>
>> --
>> John
>>
>> -----------------------------------
>> Professor John Kitchin
>> Doherty Hall A207F
>> Department of Chemical Engineering
>> Carnegie Mellon University
>> Pittsburgh, PA 15213
>> 412-268-7803
>> @johnkitchin
>> http://kitchingroup.cheme.cmu.edu
>>
>>
>>



--047d7bae465c8bd16c05262648f5--