From mboxrd@z Thu Jan 1 00:00:00 1970 From: John Kitchin Subject: Re: helm-bibtex questions Date: Sat, 27 Jun 2015 07:44:24 -0400 Message-ID: References: Mime-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:57357) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1Z8oXA-0001Mj-3S for emacs-orgmode@gnu.org; Sat, 27 Jun 2015 07:44:34 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1Z8oX6-0006F4-Oi for emacs-orgmode@gnu.org; Sat, 27 Jun 2015 07:44:32 -0400 Received: from mail-qk0-x231.google.com ([2607:f8b0:400d:c09::231]:33215) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1Z8oX6-0006F0-Hk for emacs-orgmode@gnu.org; Sat, 27 Jun 2015 07:44:28 -0400 Received: by qkhu186 with SMTP id u186so68949112qkh.0 for ; Sat, 27 Jun 2015 04:44:28 -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: Xebar Saram Cc: org mode You need: % -*- mode:bibtex; eval: (bibtex-set-dialect 'biblatex); -*- You probably have to close and reopen the file, and you will probably be prompted for running local variables (or use C-x C-e after the command above it With this, it works fine for me. This isn't really an org-ref problem, it is happening in bibtex-clean-entry. it might be better to move it to github. I just noticed a similar issue already there: https://github.com/jkitchin/org-ref/issues/40 ;) Xebar Saram writes: > hmm strange still dosent work for me. here is the top section of my bib f= ile > > -*- mode:bibtex; eval: (bibtex-set-dialect 'biblatex); -*- > > @article{ackerman-1998-discr-clear, > author =3D {Ackerman, {S.A.} and Strabala, {K.I.} and Menzel, > {W.P.} and Frey, {R.A.} and Moeller, {C.C.} and > Gumley, {L.E.}}, > title =3D {Discriminating Clear Sky From Clouds With Modis}, > journal =3D {Journal of Geophysical Research}, > volume =3D 103, > number =3D {D24}, > pages =3D {32,141--32,157}, > year =3D 1998, > shorttitle =3D {Discriminating clear sky from clouds with {MODIS}}, > } > > > when i use the org ref clean i still get > > bibtex-format-entry: Mandatory field `journal' is missing > > > also in the emacs menu the entry type is still bibtex. i tried restarting > emacs and still no go. > > any clue? also do you prefer I continue this discussion on the github > org-ref site? > > best! > > Z > > > On Fri, Jun 26, 2015 at 5:28 PM, John Kitchin > wrote: > >> >> http://tex.stackexchange.com/questions/78455/does-emacs-support-editing-= bibliography-files-for-biblatex >> >> I think you need this in your bibtex file: >> >> -*- mode:bibtex; eval: (bibtex-set-dialect 'biblatex); -*- >> >> >> Xebar Saram writes: >> >> > 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 fi= les >> >> 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 'journaltitle' >> to >> >> 'journal' to get it to work. >> >> is this by design? does org-ref not support the new biblatex/biber .b= ib >> >> 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 referenc= es. >> >>> >> >>> 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-entry >> >>> 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-entry >> >>> > 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 inst= ead >> >>> 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= thing: the >> >>> key >> >>> >> to making this work was biblatex which can be used to create seve= ral >> >>> >> lists of references filtered according to keywords, author, etc. >> This >> >>> >> 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 f= ield, I >> copy >> >>> >> the tags on-the-fly to the keywords field (see DeclareSourcemap in >> the >> >>> >> 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-bibt= ex >> ? >> >>> >> >>> >> >>> >> >>> 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 request= s. >> >>> >> >>> >> > >> >>> >> >>> >> > "The number of matches will be displayed in the mode lin= e. >> " >> >>> >> >>> >> > >> >>> >> >>> >> > i see that now thx! :) the problem was(is) that its colo= red >> >>> 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 expressi= ons, 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 t= he >> >>> >> 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 betw= een >> >>> >> >>> 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 >> publications >> >>> >> using >> >>> >> >>> >> biblatex or bib2bib and bibtex2html in the case of web pag= es. >> >>> >> >>> >> >> >>> >> >>> >> > 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 >> some >> >>> >> >>> questions. >> >>> >> >>> >> >> btw >> >>> >> >>> >> >> > is this the preferred way to make requests/ask questi= ons >> >>> or is >> >>> >> >>> >> >> > github preferred? >> >>> >> >>> >> >> >> >>> >> >>> >> >> Helm-bibtex is not part of org (although it tries to wo= rk >> >>> well >> >>> >> with >> >>> >> >>> >> >> org). So I=E2=80=99m not sure whether this list is the= best place >> >>> for >> >>> >> >>> >> >> discussing it. For now the issue tracker on Github mig= ht >> be >> >>> 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 >> 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. 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= . Pull >> >>> requests >> >>> >> >>> welcome. >> >>> >> >>> >> >> >> >>> >> >>> >> >> > 2. i would really like a way to have stored smart gro= ups >> >>> (like >> >>> >> the >> >>> >> >>> >> jabref >> >>> >> >>> >> >> > dynamic groups if your aware of that). that is for >> example >> >>> >> create >> >>> >> >>> a >> >>> >> >>> >> group >> >>> >> >>> >> >> > that auto selects all publications i have (by my >> first/last >> >>> >> name) >> >>> >> >>> and >> >>> >> >>> >> >> shows >> >>> >> >>> >> >> > the count (in numbers) of these publications. >> >>> >> >>> >> >> >> >>> >> >>> >> >> I=E2=80=99m not familiar with smart groups but it seems= that 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. I= f you want all your >> >>> >> articles >> >>> >> >>> from >> >>> >> >>> >> >> 2010, enter your name + =E2=80=9Carticles 2010=E2=80=9D= . And 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 th= at >> >>> invokes >> >>> >> >>> >> >> helm-bibtex with a default search expression 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 keyword author and prep/*ot= her >> >>> key >> >>> >> word >> >>> >> >>> >> >> >> >>> >> >>> >> >> I use two BibTeX fields to tag entries: =E2=80=9Ckeywor= ds=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 o= f all 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 pubsta= te to >> >>> >> >>> >> >> 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 >> the >> >>> >> scope >> >>> >> >>> of >> >>> >> >>> >> >> helm-bibtex (I prefer to write my BibTeX entries by han= d). >> >>> >> Perhaps >> >>> >> >>> >> >> org-ref or ebib can help here? Once you have a function >> that >> >>> >> >>> 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 >> >>> >> >> >> >> >> >> -- >> 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 >> -- 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