From mboxrd@z Thu Jan 1 00:00:00 1970 From: Xebar Saram Subject: Re: jabref like orgmode based solution to bibliography management (not for latex) Date: Sat, 5 Dec 2015 15:17:10 +0200 Message-ID: References: <87r3py5b8f.fsf@posteo.de> <87h9qs67i9.fsf@posteo.de> Mime-Version: 1.0 Content-Type: multipart/alternative; boundary=001a1140bb060c4dc00526267123 Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:54114) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1a5Ci9-0000Y9-U3 for emacs-orgmode@gnu.org; Sat, 05 Dec 2015 08:17:16 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1a5Ci7-0000d8-E4 for emacs-orgmode@gnu.org; Sat, 05 Dec 2015 08:17:13 -0500 Received: from mail-yk0-x22d.google.com ([2607:f8b0:4002:c07::22d]:35752) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1a5Ci7-0000ch-8R for emacs-orgmode@gnu.org; Sat, 05 Dec 2015 08:17:11 -0500 Received: by ykba77 with SMTP id a77so151423788ykb.2 for ; Sat, 05 Dec 2015 05:17:10 -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: John Kitchin Cc: org mode , Titus von der Malsburg --001a1140bb060c4dc00526267123 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Hi John Thanks for the quick answer. this does seem to work but as a side effect seems to break the TAB key to select action the message window shows: helm-select-nth-action: Nothing is selected No Actions available [8 times] thx again Z On Sat, Dec 5, 2015 at 3:05 PM, John Kitchin wrote: > 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unpublished !prep " 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 >> some 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 i= s >> 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 (mypape= r.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 >>> this >>> > 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 lis= t >>> > 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 >>> work 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 manag= e >>> 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 mess= y >>> and >>> >>> I need to edit it anyway. It=E2=80=99s not too hard, though: I cli= ck on >>> BibTeX >>> >>> export on the journal page, the BibTeX file is opened in Emacs, I f= ix >>> >>> it, and use a command that appends it to my bibliography. >>> >>> >>> >>> However, I think org-ref has tools that do more to support importin= g >>> 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 like a goo= d >>> >>> 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 ca= n >>> see >>> >>> Chicago style is very similar, so it shouldn=E2=80=99t be hard to a= dd 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/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 >>> >> >>> >> >>> >> >>> >>> >> > --001a1140bb060c4dc00526267123 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Hi John

Thanks for the quick answer. th= is does seem to work but as a side effect seems to break the TAB key to sel= ect action
the message window shows:

helm-select-nth-action: Nothing is selected
No Actions availabl= e [8 times]

thx again

Z

O= n Sat, Dec 5, 2015 at 3:05 PM, John Kitchin <jkitchin@andrew.cmu.e= du> wrote:
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-bibliograp= hy "your special bibfile"))
=C2=A0 =C2=A0(helm :sources '(helm-source-bibtex)
<= div style=3D"font-size:13px">=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0:full-frame = t
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0:inp= ut "kloog=C2=A0!unpublished !prep "
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0:candidate-number-limit 500)= ))



John

-----------------------------------
Professor Joh= n Kitchin=C2=A0
Doherty Hall A207F
Department of Chemical Engineering=
Carnegie Mellon University
Pittsburgh, PA 15213
412-268-7803
=

On Sat, Dec 5,= 2015 at 7:17 AM, Xebar Saram <zeltakc@gmail.com> wrote:
=
Hi again Titus and list
so the semester is finally nearing the end which means i fi= nally have some time (and a life :)) to get back to what i partially starte= d a few months ago.

i have a question regarding=C2= =A0Predefined searches. i have a search that works well for searching paper= s i authored.=C2=A0
i am thinking of moving towards 2 bib files i= nstead of 1 big one, that is one for my papers and one for the rest (any di= sadvantages of using 2 bib files?).
i want to add in the=C2=A0Pre= defined search to only draw from my file (mypaper.bib), even t= hough 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 predefined search expression:
=C2=A0(defun helm-bibtex-ikloog-publications = ()
=C2=A0 =C2=A0"Search BibTeX entries authored= by me"
=C2=A0 =C2=A0(interactive)
=C2=A0 =C2=A0(h= elm :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 !unpublished !prep "
= =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0:candidate-number-limit 500))
#= +END_SRC

how does one add t= he specific .bib file filter?

best

<= /div>
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
>>
>>
>>




--001a1140bb060c4dc00526267123--