From mboxrd@z Thu Jan 1 00:00:00 1970 From: Xebar Saram Subject: Re: helm-bibtex questions Date: Fri, 26 Jun 2015 10:14:51 +0300 Message-ID: References: Mime-Version: 1.0 Content-Type: multipart/alternative; boundary=089e01493b94fee3c00519667e7c Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:54509) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1Z8Nqj-00052Z-Ks for emacs-orgmode@gnu.org; Fri, 26 Jun 2015 03:15:01 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1Z8Nqf-0005ud-PA for emacs-orgmode@gnu.org; Fri, 26 Jun 2015 03:14:57 -0400 Received: from mail-la0-x235.google.com ([2a00:1450:4010:c03::235]:32968) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1Z8Nqf-0005tN-4D for emacs-orgmode@gnu.org; Fri, 26 Jun 2015 03:14:53 -0400 Received: by laka10 with SMTP id a10so58296517lak.0 for ; Fri, 26 Jun 2015 00:14:51 -0700 (PDT) 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 , org mode --089e01493b94fee3c00519667e7c Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable thanks so much again John i did add this line (bibtex-set-dialect 'biblatex) in my init but that dosent seem to do much as i still get the "journal mandatory field missing" error. anything else i can try? best Z On Thu, Jun 25, 2015 at 2:09 PM, John Kitchin wrote: > I believe that is an emacs bibtex issue. You need some kind of line in > your bibtex file to specify it is the biblatex dialect. > > > On June 25, 2015, at 6:58 AM, Xebar Saram wrote: > > > Great, works well. one question though (and this may very well be due to > my inexperience). the jabref export i had used 'journaltitle' instead of > journal to be (to my understanding) compatible with the newer .bib files > used by biblatex (and biber). when i ran org-ref clean it gave an error o= n" > journal mandatory field missing". i had to replace all 'journaltitle' to > 'journal' to get it to work. > is this by design? does org-ref not support the new biblatex/biber .bib > file format? > > kind regards > > Itai > > On Thu, Jun 25, 2015 at 12:03 AM, John Kitchin > wrote: > >> yes, there is a way ;) >> >> First. Make sure you have a backup of the references. I like to keep >> mine in a local git repo so you can undo any mistakes that get made. >> >> I suggest you run these first: >> %% (bibtex-validate-globally) ; checks for duplicate keys >> %% (bibtex-validate) >> >> I also recommend you run bibtex-sort (it is easier to spot duplicates in >> a sorted list). >> >> and (org-ref-build-full-bibliography) <- makes a pdf of all references. >> >> to make sure everything is compliant and functional. >> >> Then, put this next line at the top of your bibtex file. The t argument = to >> org-ref-clean-bibtex-entry will preserve your existing keys. >> >> % (bibtex-map-entries (lambda (key start end) (org-ref-clean-bibtex-entr= y >> t))) >> >> Put your cursor at the end of that line, and type C-x C-e to run the >> function, and >> wait patiently. It took a few minutes on my 1300 entries, and I had to >> restart it once on some entry. >> >> when it is done, run (org-ref-build-full-bibliography) again to make >> sure it works and review the ~200 page pdf ;). fix errors and repeat >> until it builds ;) >> >> Note if you want to change title cases in all entries you can use >> >> % (bibtex-map-entries 'jmax-title-case-article) >> % (bibtex-map-entries 'jmax-sentence-case-article) >> >> I hope that helps! >> >> Xebar Saram writes: >> >> > John >> > >> > First of all thanks so much for the excellent org-ref-clean-bibtex-ent= ry >> > function i love it! >> > also your blog post on cleaning the bib file is a life saver >> > >> > i have 800 references, is there a way to auto >> > make org-ref-clean-bibtex-entry go thorough my whole bib file instead >> of me >> > going and cleaning it 1 by 1? >> > >> > kind regards >> > >> > Z. >> > >> > On Mon, Jun 22, 2015 at 6:12 PM, Titus von der Malsburg < >> malsburg@posteo.de> >> > wrote: >> > >> >> >> >> >> >> Here is my CV in org-mode: >> >> >> >> https://gist.github.com/tmalsburg/96084ba82281937c26b7 >> >> >> >> It=E2=80=99s a pretty straightforward org document except for one thi= ng: the >> key >> >> to making this work was biblatex which can be used to create several >> >> lists of references filtered according to keywords, author, etc. Thi= s >> >> allowed me to have separate sections for journal articles, conference >> >> presentations, etc. I store the relevant keywords in the tags field = of >> >> the BibTeX entries and since biblatex doesn=E2=80=99t know this field= , I copy >> >> the tags on-the-fly to the keywords field (see DeclareSourcemap in th= e >> >> LaTeX headers). >> >> >> >> Titus >> >> >> >> On 2015-06-22 Mon 07:28, Xebar Saram wrote: >> >> > Hi John >> >> > >> >> > a bit off topic, but do you also write your academic CV in orgmode = or >> >> > lateX? in anycase would you mind sharing your org/latex CV template= ? >> it >> >> > would be helpful as a starting point for me if thats possible. >> >> > >> >> > kind regards and thanks so much in advance >> >> > >> >> > Z >> >> > >> >> > On Sun, Jun 21, 2015 at 9:40 PM, John Kitchin < >> jkitchin@andrew.cmu.edu> >> >> > wrote: >> >> > >> >> >> sweet! I did not know you could do that! I will be refactoring >> org-ref >> >> >> soon to do that instead of redefining the commands! >> >> >> >> >> >> 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 Sun, Jun 21, 2015 at 2:29 PM, Titus von der Malsburg < >> >> >> malsburg@posteo.de> wrote: >> >> >> >> >> >>> >> >> >>> On 2015-06-19 Fri 03:56, Xebar Saram wrote: >> >> >>> > Hi again Titus >> >> >>> > >> >> >>> > 2 quick questions that arose from using helm-bitex today >> extensively: >> >> >>> > >> >> >>> > how does one exclude in the search items? for example i want to >> >> search >> >> >>> for >> >> >>> > xebar without keyword "progress" (I want to exclude in progress >> >> articles >> >> >>> > not published yet) >> >> >>> > >> >> >>> > is it possible to define default enter command in helm-bibtex ? >> >> >>> >> >> >>> Yes. Helm uses the first action as the default action. To move = an >> >> >>> action to the top of the list you can use the following code: >> >> >>> >> >> >>> (helm-delete-action-from-source "Insert BibTeX key" >> >> helm-source-bibtex) >> >> >>> (helm-add-action-to-source "Insert BibTeX key" >> >> 'helm-bibtex-insert-key >> >> >>> helm-source-bibtex 0) >> >> >>> >> >> >>> The second argument in the second line is the function that >> executes >> >> the >> >> >>> action. Here is a list of all actions and their functions: >> >> >>> >> >> >>> Open PDF file (if present): helm-bibtex-open-pdf >> >> >>> Open URL or DOI in browser: helm-bibtex-open-url-or-doi >> >> >>> Insert citation: helm-bibtex-insert-citation >> >> >>> Insert reference: helm-bibtex-insert-reference >> >> >>> Insert BibTeX key: helm-bibtex-insert-key >> >> >>> Insert BibTeX entry: helm-bibtex-insert-bibtex >> >> >>> Attach PDF to email: helm-bibtex-add-PDF-attachment >> >> >>> Edit notes: helm-bibtex-edit-notes >> >> >>> Show entry: helm-bibtex-show-entry >> >> >>> >> >> >>> Best, >> >> >>> >> >> >>> Titus >> >> >>> >> >> >>> > >> >> >>> > best >> >> >>> > >> >> >>> > Z >> >> >>> > >> >> >>> > On Thu, Jun 18, 2015 at 9:38 PM, Titus von der Malsburg < >> >> >>> malsburg@posteo.de> >> >> >>> > wrote: >> >> >>> > >> >> >>> >> >> >> >>> >> On 2015-06-18 Thu 04:32, Xebar Saram wrote: >> >> >>> >> > Hi Titus and thx so much for the answers! >> >> >>> >> > >> >> >>> >> > i will in the future use the github page to make requests. >> >> >>> >> > >> >> >>> >> > "The number of matches will be displayed in the mode line. " >> >> >>> >> > >> >> >>> >> > i see that now thx! :) the problem was(is) that its colored >> black >> >> on >> >> >>> my >> >> >>> >> > black modline BG which makes it invisible ;-) i assume thats >> an >> >> helm >> >> >>> >> config >> >> >>> >> > i need to change >> >> >>> >> > >> >> >>> >> > >> >> >>> >> > "If you don=E2=80=99t want to type these search expressions,= you could >> >> >>> create a >> >> >>> >> > command that invokes helm-bibtex with a default search >> expression >> >> and >> >> >>> >> that >> >> >>> >> > command could be bound to a keyboard shortcut." >> >> >>> >> > >> >> >>> >> > that would be prefect for me and a solution to my issue. >> would you >> >> >>> mind >> >> >>> >> > giving an example of such a code chunk. unfortunately i dont >> know >> >> >>> elisp >> >> >>> >> though >> >> >>> >> > as john recommended i will do my best this summer when the >> >> semester >> >> >>> ends >> >> >>> >> to >> >> >>> >> > try and pick it up :) >> >> >>> >> >> >> >>> >> Sure, here you go: >> >> >>> >> >> >> >>> >> #+BEGIN_SRC elisp >> >> >>> >> ;; Define helm-search with predefined search expression: >> >> >>> >> (defun helm-bibtex-my-publications () >> >> >>> >> "Search BibTeX entries authored by Xebar Saram." >> >> >>> >> (interactive) >> >> >>> >> (helm :sources '(helm-source-bibtex) >> >> >>> >> :full-frame t >> >> >>> >> :input "xebar saram" >> >> >>> >> :candidate-number-limit 500)) >> >> >>> >> >> >> >>> >> ;; Bind this search function to Ctrl-x p: >> >> >>> >> (global-set-key (kbd "C-x p") 'helm-bibtex-my-publications) >> >> >>> >> #+END_SRC >> >> >>> >> >> >> >>> >> > i will definitely use your tag system as you recommended, >> sounds >> >> >>> perfect >> >> >>> >> > for me >> >> >>> >> >> >> >>> >> The tag system also comes in handy when generating publication >> lists >> >> >>> for >> >> >>> >> CVs and web pages because BibTeX does not distinguish between >> >> >>> conference >> >> >>> >> papers, posters, and talks. If you have tags for that, it=E2= =80=99s >> >> relatively >> >> >>> >> easy to create separate sections for these types of publicatio= ns >> >> using >> >> >>> >> biblatex or bib2bib and bibtex2html in the case of web pages. >> >> >>> >> >> >> >>> >> > thanks again for your kind help and the amazing app ;-) >> >> >>> >> >> >> >>> >> You are welcome. >> >> >>> >> >> >> >>> >> Titus >> >> >>> >> >> >> >>> >> > >> >> >>> >> > best >> >> >>> >> > >> >> >>> >> > Z >> >> >>> >> > >> >> >>> >> > >> >> >>> >> > >> >> >>> >> > On Wed, Jun 17, 2015 at 11:02 PM, Titus von der Malsburg < >> >> >>> >> malsburg@posteo.de >> >> >>> >> >> wrote: >> >> >>> >> > >> >> >>> >> >> >> >> >>> >> >> On 2015-06-17 Wed 11:08, Xebar Saram wrote: >> >> >>> >> >> > Hi Titus >> >> >>> >> >> > >> >> >>> >> >> > I have been exploring helm-bibtex a bit today and have so= me >> >> >>> questions. >> >> >>> >> >> btw >> >> >>> >> >> > is this the preferred way to make requests/ask questions >> or is >> >> >>> >> >> > github preferred? >> >> >>> >> >> >> >> >>> >> >> Helm-bibtex is not part of org (although it tries to work >> well >> >> with >> >> >>> >> >> org). So I=E2=80=99m not sure whether this list is the bes= t place >> for >> >> >>> >> >> discussing it. For now the issue tracker on Github might b= e >> a >> >> >>> better >> >> >>> >> >> option: >> >> >>> >> >> >> >> >>> >> >> https://github.com/tmalsburg/helm-bibtex/issues >> >> >>> >> >> >> >> >>> >> >> > in any case i was wondering a few things: >> >> >>> >> >> > >> >> >>> >> >> > 1. is it possible to have custom sorting? i want all view= s >> to >> >> >>> sort by >> >> >>> >> >> > Author, year, month >> >> >>> >> >> >> >> >>> >> >> I prefer to see the entries in the (inverse) order in which >> they >> >> >>> appear >> >> >>> >> >> in the BibTeX file. This way, recent additions show up at >> the >> >> >>> >> >> top. However, I agree that sorting would be useful (see >> issues >> >> #5 >> >> >>> and >> >> >>> >> >> #21); it just doesn=E2=80=99t have high priority for me. P= ull >> requests >> >> >>> welcome. >> >> >>> >> >> >> >> >>> >> >> > 2. i would really like a way to have stored smart groups >> (like >> >> the >> >> >>> >> jabref >> >> >>> >> >> > dynamic groups if your aware of that). that is for exampl= e >> >> create >> >> >>> a >> >> >>> >> group >> >> >>> >> >> > that auto selects all publications i have (by my first/la= st >> >> name) >> >> >>> and >> >> >>> >> >> shows >> >> >>> >> >> > the count (in numbers) of these publications. >> >> >>> >> >> >> >> >>> >> >> I=E2=80=99m not familiar with smart groups but it seems tha= t all >> >> >>> helm-bibtex is >> >> >>> >> >> doing is giving you very flexible smart groups defined by >> your >> >> >>> search >> >> >>> >> >> expressions. For example, if you want a list of your >> >> publications, >> >> >>> you >> >> >>> >> >> can simple enter your name. And if you want a list of your >> >> >>> articles, >> >> >>> >> >> you can enter your name + =E2=80=9Carticle=E2=80=9D. If yo= u want all your >> >> articles >> >> >>> from >> >> >>> >> >> 2010, enter your name + =E2=80=9Carticles 2010=E2=80=9D. A= nd so on. The >> number >> >> of >> >> >>> >> >> matches will be displayed in the mode line. If you don=E2= =80=99t >> want to >> >> >>> type >> >> >>> >> >> these search expressions, you could create a command that >> invokes >> >> >>> >> >> helm-bibtex with a default search expression and that comma= nd >> >> could >> >> >>> be >> >> >>> >> >> bound to a keyboard shortcut. >> >> >>> >> >> >> >> >>> >> >> > Another example is a group to keep track of all the paper= s >> im >> >> >>> working >> >> >>> >> on >> >> >>> >> >> or >> >> >>> >> >> > invloved with by matching keyword author and prep/*other >> key >> >> word >> >> >>> >> >> >> >> >>> >> >> I use two BibTeX fields to tag entries: =E2=80=9Ckeywords= =E2=80=9D for >> keywords >> >> >>> >> >> describing the content of the paper (as usual) and =E2=80= =9Ctags=E2=80=9D for >> >> meta >> >> >>> >> >> data. Values that I use in tags are =E2=80=9Cown=E2=80=9D,= =E2=80=9Cmanuscript=E2=80=9D, >> >> =E2=80=9Cposter=E2=80=9D, >> >> >>> >> >> =E2=80=9Ctalk=E2=80=9D, =E2=80=A6 So if I want a list of al= l articles in progress, I >> >> search >> >> >>> for >> >> >>> >> >> =E2=80=9Cown manuscript=E2=80=9D. Since the tags field is = non-standard, it >> has >> >> to >> >> >>> be >> >> >>> >> >> added to `helm-bibtex-additional-search-fields`. >> >> >>> >> >> >> >> >>> >> >> Another solution would be to use the pubstate field and to >> search >> >> >>> for >> >> >>> >> >> your name and =E2=80=9Cforthcoming=E2=80=9D (add pubstate t= o >> >> >>> >> >> helm-bibtex-additional-search-fields for this to work). >> >> >>> >> >> >> >> >>> >> >> > 3.is it possible to ass an option to auto generate a >> bibkey >> >> for a >> >> >>> >> >> selected >> >> >>> >> >> > citation based on user criteria such as >> >> author(date)short-title? >> >> >>> >> >> >> >> >>> >> >> Maintaining the content of the BibTeX file not really in th= e >> >> scope >> >> >>> of >> >> >>> >> >> helm-bibtex (I prefer to write my BibTeX entries by hand). >> >> Perhaps >> >> >>> >> >> org-ref or ebib can help here? Once you have a function th= at >> >> >>> generates >> >> >>> >> >> a new key and inserts it in the BibTeX file, you can easily >> add >> >> it >> >> >>> to >> >> >>> >> >> the list of actions in helm-bibtex. >> >> >>> >> >> >> >> >>> >> >> Hope that helps. >> >> >>> >> >> >> >> >>> >> >> Titus >> >> >>> >> >> >> >> >>> >> >> > thx so much in advance, you and john have given me >> confidence >> >> to >> >> >>> >> finally >> >> >>> >> >> > dive into the whole latex/bibteX world >> >> >>> >> >> > >> >> >>> >> >> > best >> >> >>> >> >> > >> >> >>> >> >> > Z >> >> >>> >> >> >> >> >>> >> >> >> >> >>> >> >> >> >>> >> >> >> >>> >> >> >>> >> >> >> >> >> >> >> >> >> -- >> 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 >> > > --089e01493b94fee3c00519667e7c Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
thanks so much again John

i did add thi= s line=C2=A0
(bibtex-set-dialect 'biblatex)
in = my init but that dosent seem to do much as i still get the "journal mandatory field missing" er= ror. anything else i can try?

best

Z


On Thu, Jun 25, 2015 at 2:09 PM, John Kitchin = <johnrkitchi= n@gmail.com> wrote:

I believe that is an emacs bibtex issue. You= need some kind of line in your bibtex file to specify it is the biblatex d= ialect.



On June 25, 2015, at 6:58 AM, Xebar Saram <zeltakc@gmail.com> wrote:

<= br>
Great, works well. one question though (and this may very well be due t= o my inexperience). the jabref export i had used 'journaltitle' ins= tead of journal to be (to my understanding) compatible with the newer .bib = files used by biblatex (and biber). when i ran org-ref clean it gave an err= or on" journal mandatory field missing". i had to replace all=C2= =A0'journaltitle'=C2=A0 to 'journal' to get it to work.=C2= =A0
is this by design? does org-ref not support the new biblatex/biber = .bib file format?

kind regards

Itai

On Thu, Jun 25, 2015 at 12:03 AM, John Kitchin <<= a href=3D"mailto:jkitchin@andrew.cmu.edu" target=3D"_blank">jkitchin@andrew= .cmu.edu> wrote:
yes, the= re is a way ;)

First. Make sure you have a backup of the references. I like to keep
mine in a local git repo so you can undo any mistakes that get made.

I suggest you run these first:
%% (bibtex-validate-globally)=C2=A0 =C2=A0; checks for duplicate keys
%% (bibtex-validate)

I also recommend you run bibtex-sort (it is easier to spot duplicates in a sorted list).

and (org-ref-build-full-bibliography) <- makes a pdf of all references.<= br>
to make sure everything is compliant and functional.

Then, put this next line at the top of your bibtex file. The t argument to<= br> org-ref-clean-bibtex-entry will preserve your existing keys.

% (bibtex-map-entries (lambda (key start end) (org-ref-clean-bibtex-entry t= )))

Put your cursor at the end of that line, and type C-x C-e to run the functi= on, and
wait patiently. It took a few minutes on my 1300 entries, and I had to
restart it once on some entry.

when it is done, run (org-ref-build-full-bibliography) again to make
sure it works and review the ~200 page pdf ;). fix errors and repeat until = it builds ;)

Note if you want to change title cases in all entries you can use

% (bibtex-map-entries 'jmax-title-case-article)
% (bibtex-map-entries 'jmax-sentence-case-article)

I hope that helps!

Xebar Saram writes:

> John
>
> First of all thanks so much for the excellent org-ref-clean-bibtex-ent= ry
> function i love it!
> also your blog post on cleaning the bib file is a life saver
>
> i have 800 references, is there a way to auto
> make org-ref-clean-bibtex-entry go thorough my whole bib file instead = of me
> going and cleaning it 1 by 1?
>
> kind regards
>
> Z.
>
> On Mon, Jun 22, 2015 at 6:12 PM, Titus von der Malsburg <malsburg@posteo.de> > wrote:
>
>>
>>
>> Here is my CV in org-mode:
>>
>>=C2=A0 =C2=A0https://gist.github.com/t= malsburg/96084ba82281937c26b7
>>
>> It=E2=80=99s a pretty straightforward org document except for one = thing: the key
>> to making this work was biblatex which can be used to create sever= al
>> lists of references filtered according to keywords, author, etc.= =C2=A0 This
>> allowed me to have separate sections for journal articles, confere= nce
>> presentations, etc.=C2=A0 I store the relevant keywords in the tag= s field of
>> the BibTeX entries and since biblatex doesn=E2=80=99t know this fi= eld, I copy
>> the tags on-the-fly to the keywords field (see DeclareSourcemap in= the
>> LaTeX headers).
>>
>>=C2=A0 =C2=A0Titus
>>
>> On 2015-06-22 Mon 07:28, Xebar Saram wrote:
>> > Hi John
>> >
>> > a bit off topic, but do you also write your academic CV in or= gmode or
>> > lateX? in anycase would you mind sharing your org/latex CV te= mplate? it
>> > would be helpful as a starting point for me if thats possible= .
>> >
>> > kind regards and thanks so much in advance
>> >
>> > Z
>> >
>> > On Sun, Jun 21, 2015 at 9:40 PM, John Kitchin <jkitchin@andrew.cmu.edu>
>> > wrote:
>> >
>> >> sweet! I did not know you could do that! I will be refact= oring org-ref
>> >> soon to do that instead of redefining the commands!
>> >>
>> >> 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 Sun, Jun 21, 2015 at 2:29 PM, Titus von der Malsburg &= lt;
>> >> m= alsburg@posteo.de> wrote:
>> >>
>> >>>
>> >>> On 2015-06-19 Fri 03:56, Xebar Saram wrote:
>> >>> > Hi again Titus
>> >>> >
>> >>> > 2 quick questions that arose from using helm-bit= ex today extensively:
>> >>> >
>> >>> > how does one exclude in the search items? for ex= ample i want to
>> search
>> >>> for
>> >>> > xebar without keyword "progress" (I wa= nt to exclude in progress
>> articles
>> >>> > not published yet)
>> >>> >
>> >>> > is it possible to define default enter command i= n helm-bibtex ?
>> >>>
>> >>> Yes.=C2=A0 Helm uses the first action as the default = action.=C2=A0 To move an
>> >>> action to the top of the list you can use the followi= ng code:
>> >>>
>> >>>=C2=A0 =C2=A0(helm-delete-action-from-source "Ins= ert BibTeX key"
>> helm-source-bibtex)
>> >>>=C2=A0 =C2=A0(helm-add-action-to-source "Insert B= ibTeX key"
>> 'helm-bibtex-insert-key
>> >>> helm-source-bibtex 0)
>> >>>
>> >>> The second argument in the second line is the functio= n that executes
>> the
>> >>> action.=C2=A0 Here is a list of all actions and their= functions:
>> >>>
>> >>>=C2=A0 =C2=A0Open PDF file (if present): helm-bibtex-o= pen-pdf
>> >>>=C2=A0 =C2=A0Open URL or DOI in browser: helm-bibtex-o= pen-url-or-doi
>> >>>=C2=A0 =C2=A0Insert citation: helm-bibtex-insert-citat= ion
>> >>>=C2=A0 =C2=A0Insert reference: helm-bibtex-insert-refe= rence
>> >>>=C2=A0 =C2=A0Insert BibTeX key: helm-bibtex-insert-key=
>> >>>=C2=A0 =C2=A0Insert BibTeX entry: helm-bibtex-insert-b= ibtex
>> >>>=C2=A0 =C2=A0Attach PDF to email: helm-bibtex-add-PDF-= attachment
>> >>>=C2=A0 =C2=A0Edit notes: helm-bibtex-edit-notes
>> >>>=C2=A0 =C2=A0Show entry: helm-bibtex-show-entry
>> >>>
>> >>> Best,
>> >>>
>> >>>=C2=A0 =C2=A0Titus
>> >>>
>> >>> >
>> >>> > best
>> >>> >
>> >>> > Z
>> >>> >
>> >>> > On Thu, Jun 18, 2015 at 9:38 PM, Titus von der M= alsburg <
>> >>> malsburg@posteo.de>
>> >>> > wrote:
>> >>> >
>> >>> >>
>> >>> >> On 2015-06-18 Thu 04:32, Xebar Saram wrote:<= br> >> >>> >> > Hi Titus and thx so much for the answer= s!
>> >>> >> >
>> >>> >> > i will in the future use the github pag= e to make requests.
>> >>> >> >
>> >>> >> > "The number of matches will be dis= played in the mode line. "
>> >>> >> >
>> >>> >> > i see that now thx! :) the problem was(= is) that its colored black
>> on
>> >>> my
>> >>> >> > black modline BG which makes it invisib= le ;-) i assume thats an
>> helm
>> >>> >> config
>> >>> >> > i need to change
>> >>> >> >
>> >>> >> >
>> >>> >> > "If you don=E2=80=99t want to type= these search expressions, you could
>> >>> create a
>> >>> >> > command that invokes helm-bibtex with a= default search expression
>> and
>> >>> >> that
>> >>> >> > command could be bound to a keyboard sh= ortcut."
>> >>> >> >
>> >>> >> > that would be prefect for me and a solu= tion to my issue. would you
>> >>> mind
>> >>> >> > giving an example of such a code chunk.= unfortunately i dont know
>> >>> elisp
>> >>> >> though
>> >>> >> > as john recommended i will do my best t= his summer when the
>> semester
>> >>> ends
>> >>> >> to
>> >>> >> > try and pick it up :)
>> >>> >>
>> >>> >> Sure, here you go:
>> >>> >>
>> >>> >> #+BEGIN_SRC elisp
>> >>> >> ;; Define helm-search with predefined search= expression:
>> >>> >> (defun helm-bibtex-my-publications ()
>> >>> >>=C2=A0 =C2=A0"Search BibTeX entries auth= ored by Xebar Saram."
>> >>> >>=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 &quo= t;xebar saram"
>> >>> >>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0:candidate-= number-limit 500))
>> >>> >>
>> >>> >> ;; Bind this search function to Ctrl-x p: >> >>> >> (global-set-key (kbd "C-x p") '= ;helm-bibtex-my-publications)
>> >>> >> #+END_SRC
>> >>> >>
>> >>> >> > i will definitely use your tag system a= s you recommended, sounds
>> >>> perfect
>> >>> >> > for me
>> >>> >>
>> >>> >> The tag system also comes in handy when gene= rating publication lists
>> >>> for
>> >>> >> CVs and web pages because BibTeX does not di= stinguish between
>> >>> conference
>> >>> >> papers, posters, and talks.=C2=A0 If you hav= e tags for that, it=E2=80=99s
>> relatively
>> >>> >> easy to create separate sections for these t= ypes of publications
>> using
>> >>> >> biblatex or bib2bib and bibtex2html in the c= ase of web pages.
>> >>> >>
>> >>> >> > thanks again for your kind help and the= amazing app ;-)
>> >>> >>
>> >>> >> You are welcome.
>> >>> >>
>> >>> >>=C2=A0 =C2=A0Titus
>> >>> >>
>> >>> >> >
>> >>> >> > best
>> >>> >> >
>> >>> >> > Z
>> >>> >> >
>> >>> >> >
>> >>> >> >
>> >>> >> > On Wed, Jun 17, 2015 at 11:02 PM, Titus= von der Malsburg <
>> >>> >> malsburg@posteo.de
>> >>> >> >> wrote:
>> >>> >> >
>> >>> >> >>
>> >>> >> >> On 2015-06-17 Wed 11:08, Xebar Sara= m wrote:
>> >>> >> >> > Hi Titus
>> >>> >> >> >
>> >>> >> >> > I have been exploring helm-bib= tex a bit today and have some
>> >>> questions.
>> >>> >> >> btw
>> >>> >> >> > is this the preferred way to m= ake requests/ask questions or is
>> >>> >> >> > github preferred?
>> >>> >> >>
>> >>> >> >> Helm-bibtex is not part of org (alt= hough it tries to work well
>> with
>> >>> >> >> org).=C2=A0 So I=E2=80=99m not sure= whether this list is the best place for
>> >>> >> >> discussing it.=C2=A0 For now the is= sue tracker on Github might be a
>> >>> better
>> >>> >> >> option:
>> >>> >> >>
>> >>> >> >>=C2=A0 =C2=A0h= ttps://github.com/tmalsburg/helm-bibtex/issues
>> >>> >> >>
>> >>> >> >> > in any case i was wondering a = few things:
>> >>> >> >> >
>> >>> >> >> > 1. is it possible to have cust= om sorting? i want all views to
>> >>> sort by
>> >>> >> >> > Author, year, month
>> >>> >> >>
>> >>> >> >> I prefer to see the entries in the = (inverse) order in which they
>> >>> appear
>> >>> >> >> in the BibTeX file.=C2=A0 This way,= recent additions show up at the
>> >>> >> >> top.=C2=A0 However, I agree that so= rting would be useful (see issues
>> #5
>> >>> and
>> >>> >> >> #21); it just doesn=E2=80=99t have = high priority for me.=C2=A0 Pull requests
>> >>> welcome.
>> >>> >> >>
>> >>> >> >> > 2. i would really like a way t= o have stored smart groups (like
>> the
>> >>> >> jabref
>> >>> >> >> > dynamic groups if your aware o= f that). that is for example
>> create
>> >>> a
>> >>> >> group
>> >>> >> >> > that auto selects all publicat= ions i have (by my first/last
>> name)
>> >>> and
>> >>> >> >> shows
>> >>> >> >> > the count (in numbers) of thes= e publications.
>> >>> >> >>
>> >>> >> >> I=E2=80=99m not familiar with smart= groups but it seems that all
>> >>> helm-bibtex is
>> >>> >> >> doing is giving you very flexible s= mart groups defined by your
>> >>> search
>> >>> >> >> expressions.=C2=A0 For example, if = you want a list of your
>> publications,
>> >>> you
>> >>> >> >> can simple enter your name.=C2=A0 A= nd if you want a list of your
>> >>> articles,
>> >>> >> >> you can enter your name + =E2=80=9C= article=E2=80=9D.=C2=A0 If you want all your
>> articles
>> >>> from
>> >>> >> >> 2010, enter your name + =E2=80=9Car= ticles 2010=E2=80=9D.=C2=A0 And so on.=C2=A0 The number
>> of
>> >>> >> >> matches will be displayed in the mo= de line.=C2=A0 If you don=E2=80=99t want to
>> >>> type
>> >>> >> >> these search expressions, you could= create a command that invokes
>> >>> >> >> helm-bibtex with a default search e= xpression and that command
>> could
>> >>> be
>> >>> >> >> bound to a keyboard shortcut.
>> >>> >> >>
>> >>> >> >> > Another example is a group to = keep track of all the papers im
>> >>> working
>> >>> >> on
>> >>> >> >> or
>> >>> >> >> > invloved with by matching keyw= ord author and prep/*other key
>> word
>> >>> >> >>
>> >>> >> >> I use two BibTeX fields to tag entr= ies: =E2=80=9Ckeywords=E2=80=9D for keywords
>> >>> >> >> describing the content of the paper= (as usual) and =E2=80=9Ctags=E2=80=9D for
>> meta
>> >>> >> >> data.=C2=A0 Values that I use in ta= gs are =E2=80=9Cown=E2=80=9D, =E2=80=9Cmanuscript=E2=80=9D,
>> =E2=80=9Cposter=E2=80=9D,
>> >>> >> >> =E2=80=9Ctalk=E2=80=9D, =E2=80=A6 S= o if I want a list of all articles in progress, I
>> search
>> >>> for
>> >>> >> >> =E2=80=9Cown manuscript=E2=80=9D.= =C2=A0 Since the tags field is non-standard, it has
>> to
>> >>> be
>> >>> >> >> added to `helm-bibtex-additional-se= arch-fields`.
>> >>> >> >>
>> >>> >> >> Another solution would be to use th= e pubstate field and to search
>> >>> for
>> >>> >> >> your name and =E2=80=9Cforthcoming= =E2=80=9D (add pubstate to
>> >>> >> >> helm-bibtex-additional-search-field= s for this to work).
>> >>> >> >>
>> >>> >> >> > 3.is it possible to ass an option to aut= o generate a bibkey
>> for a
>> >>> >> >> selected
>> >>> >> >> > citation based on user criteri= a such as
>> author(date)short-title?
>> >>> >> >>
>> >>> >> >> Maintaining the content of the BibT= eX file not really in the
>> scope
>> >>> of
>> >>> >> >> helm-bibtex (I prefer to write my B= ibTeX entries by hand).
>> Perhaps
>> >>> >> >> org-ref or ebib can help here?=C2= =A0 Once you have a function that
>> >>> generates
>> >>> >> >> a new key and inserts it in the Bib= TeX file, you can easily add
>> it
>> >>> to
>> >>> >> >> the list of actions in helm-bibtex.=
>> >>> >> >>
>> >>> >> >> Hope that helps.
>> >>> >> >>
>> >>> >> >>=C2=A0 =C2=A0Titus
>> >>> >> >>
>> >>> >> >> > thx so much in advance, you an= d john have given me confidence
>> to
>> >>> >> finally
>> >>> >> >> > dive into the whole latex/bibt= eX world
>> >>> >> >> >
>> >>> >> >> > best
>> >>> >> >> >
>> >>> >> >> > Z
>> >>> >> >>
>> >>> >> >>
>> >>> >>
>> >>> >>
>> >>>
>> >>>
>> >>
>>
>>

--
Professor John Kitchin
Doherty Hall A207F
Department of Chemical Engineering
Carnegie Mellon University
Pittsburgh, PA 15213
412-2= 68-7803
@johnkitchin
http://kitchingroup.cheme.cmu.edu


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