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 20:28:26 +0200 Message-ID: References: <87r3py5b8f.fsf@posteo.de> <87h9qs67i9.fsf@posteo.de> <87zixowz4r.fsf@posteo.de> Mime-Version: 1.0 Content-Type: multipart/alternative; boundary=001a11492e483432df05262aca82 Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:48925) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1a5HZN-0008IA-Ac for emacs-orgmode@gnu.org; Sat, 05 Dec 2015 13:28:31 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1a5HZL-0005Uj-81 for emacs-orgmode@gnu.org; Sat, 05 Dec 2015 13:28:29 -0500 Received: from mail-yk0-x229.google.com ([2607:f8b0:4002:c07::229]:34624) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1a5HZL-0005Ud-14 for emacs-orgmode@gnu.org; Sat, 05 Dec 2015 13:28:27 -0500 Received: by ykfs79 with SMTP id s79so157331630ykf.1 for ; Sat, 05 Dec 2015 10:28:26 -0800 (PST) In-Reply-To: <87zixowz4r.fsf@posteo.de> 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: Titus von der Malsburg Cc: org mode , John Kitchin --001a11492e483432df05262aca82 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Hi Guys I have no clue why i had the issue before but after an emacs restart Johns code snippet does work :D thanks again guys, really appreciate your help as always kind regards Z On Sat, Dec 5, 2015 at 8:04 PM, Titus von der Malsburg wrote: > > John=E2=80=99s code should do the trick. I don=E2=80=99t see how this co= uld possibly > cause your problems with the action menu. The change should be > completely transparent for Helm. > > Regarding your other question: I don=E2=80=99t see any disadvantages of u= sing > several BibTeX files but I also don=E2=80=99t see an advantage because > helm-bibtex gives you all you need to select your own publications with > just a few key strokes. If helm-bibtex=E2=80=99 search does not work wel= l in > your case (perhaps another author has the same name as you), I would > suggest using tags to mark your own publications: > > https://github.com/tmalsburg/helm-bibtex#tagging-publications > > Titus > > > On 2015-12-05 Sat 05:31, John Kitchin wrote: > > I cannot reproduce that, and it shouldn't have any effect. Maybe > > something else is going on. > > > >> > >> Thanks for the quick answer. this does seem to work but as a side effe= ct > >> 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) > >>> > >>> > >>> > >>> > >>> > >>> 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 hav= e > >>>> 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 tha= t > >>>> 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 investiga= te > >>>>> 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 > 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 wit= h > >>>>> another function, then yes that would definitely make sense. > >>>>> > >>>>> 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 academi= a > >>>>> work to > >>>>> >>> > manage my reference library. i dont use latex (..its on my TO= DO > >>>>> >>> 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 ar= e: > >>>>> >>> > >>>>> >>> 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= 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 > importing > >>>>> new > >>>>> >>> entries and org-ref combines well with helm-bibtex. > >>>>> >> > >>>>> >> > >>>>> >> Org-ref has doi-utils that let you add bibtex entries and downlo= ad > >>>>> PDFs > >>>>> >> 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 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/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 > >>>>> >> > >>>>> >> > >>>>> >> > >>>>> > >>>>> > >>>> > >>> > > --001a11492e483432df05262aca82 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Hi Guys

I have no clue why i had the is= sue before but after an emacs restart Johns code snippet does work :D
=

thanks again guys, really appreciate your help as alway= s

kind regards

Z

On Sat, Dec 5,= 2015 at 8:04 PM, Titus von der Malsburg <malsburg@posteo.de> wrote:

John=E2=80=99s code should do the trick.=C2=A0 I don=E2=80=99t see how this= could possibly
cause your problems with the action menu.=C2=A0 The change should be
completely transparent for Helm.

Regarding your other question: I don=E2=80=99t see any disadvantages of usi= ng
several BibTeX files but I also don=E2=80=99t see an advantage because
helm-bibtex gives you all you need to select your own publications with
just a few key strokes.=C2=A0 If helm-bibtex=E2=80=99 search does not work = well in
your case (perhaps another author has the same name as you), I would
suggest using tags to mark your own publications:

=C2=A0 https://github.com/tmalsburg/hel= m-bibtex#tagging-publications

Titus


On 2015-12-05 Sat 05:31, John Kitchin wrote:
> I cannot reproduce that, and it shouldn't have any effect. Maybe > something else is going on.
>
>>
>> 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 <jkitchin@andrew.cmu.edu>
>> wrote:
>>
>>> Try (untested)
>>>
>>>
>>>
>>>
>>>
>>> John
>>>
>>> -----------------------------------
>>> Professor John Kitchin
>>> Doherty Hall A207F
>>> Department of Chemical Engineering
>>> Carnegie Mellon University
>>> Pittsburgh, PA 15213
>>> 412-268-78= 03
>>> @johnkitchin
>>> http://kitchingroup.cheme.cmu.edu
>>>
>>>
>>> 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 f= inally 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 b= ig 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 m= y file (mypaper.bib),
>>>> even though in the default helm-bibtex sources it will hav= e 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 express= ion:
>>>>=C2=A0 (defun helm-bibtex-ikloog-publications ()
>>>>=C2=A0 =C2=A0 "Search BibTeX entries authored by me&qu= ot;
>>>>=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-frame t
>>>>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 :input "kloog !unpu= blished !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 &l= t;
>>>> 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=C2=A0 that the helm-bibte= x APA style reference list
>>>>> > could be user customizable in the future?
>>>>>
>>>>> Depends on what you mean by customizable.=C2=A0 If you= mean a customization
>>>>> option to allows you to replace the function for APA f= ormatting with
>>>>> another function, then yes that would definitely make = sense.
>>>>>
>>>>>=C2=A0 =C2=A0Titus
>>>>>
>>>>> >
>>>>> > 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 Mals= burg <malsburg@posteo.de
>>>>> >
>>>>> >> wrote:
>>>>> >>
>>>>> >>>
>>>>> >>> On 2015-05-30 Sat 01:20, Xebar Saram wrot= e:
>>>>> >>> > Hi all
>>>>> >>> >
>>>>> >>> > i have been using jabref for the pas= t 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 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 thi= s because I prefer to edit my BibTeX
>>>>> >>> file by hand.=C2=A0 BibTeX retrieved from= journals is almost always messy
>>>>> and
>>>>> >>> I need to edit it anyway.=C2=A0 It=E2=80= =99s not too hard, though: I click on
>>>>> BibTeX
>>>>> >>> export on the journal page, the BibTeX fi= le 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 d= o more to support importing
>>>>> new
>>>>> >>> entries and org-ref combines well with he= lm-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 good
>>>>> >>> solution)
>>>>> >>>
>>>>> >>> That=E2=80=99s what helm-bibtex was writt= en to solve.
>>>>> >>>
>>>>> >>> > 3. filter lists based on tags/keywor= ds (orgmode has that covered)
>>>>> >>>
>>>>> >>> In helm-bibtex you can also search for ke= ywords and tags.
>>>>> >>>
>>>>> >>> > 4. this one is important: a way to q= uickly export selected
>>>>> references in
>>>>> >>> > word/odf/html based on a pre fixed s= tyle (ie=C2=A0 Nature, Chicago etc)
>>>>> >>>
>>>>> >>> helm-bibtex can generate references in AP= A style but as far as I can
>>>>> see
>>>>> >>> Chicago style is very similar, so it shou= ldn=E2=80=99t be hard to add support
>>>>> >>> for that.
>>>>> >>>
>>>>> >>> > anyone uses such a system in emacs/o= rg and can recommend the way to
>>>>> >>> > go?
>>>>> >>>
>>>>> >>> For more details, see: htt= ps://github.com/tmalsburg/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=
>>>>> >>
>>>>> >>
>>>>> >>
>>>>>
>>>>>
>>>>
>>>


--001a11492e483432df05262aca82--