From mboxrd@z Thu Jan 1 00:00:00 1970 From: John Kitchin Subject: Re: helm-bibtex questions Date: Fri, 26 Jun 2015 10:28:32 -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]:50585) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1Z8UcR-0005Ww-MM for emacs-orgmode@gnu.org; Fri, 26 Jun 2015 10:28:42 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1Z8UcN-0007VI-Hl for emacs-orgmode@gnu.org; Fri, 26 Jun 2015 10:28:39 -0400 Received: from mail-qk0-x234.google.com ([2607:f8b0:400d:c09::234]:36531) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1Z8UcN-0007V8-C1 for emacs-orgmode@gnu.org; Fri, 26 Jun 2015 10:28:35 -0400 Received: by qkei195 with SMTP id i195so17474992qke.3 for ; Fri, 26 Jun 2015 07:28:35 -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 http://tex.stackexchange.com/questions/78455/does-emacs-support-editing-bib= liography-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 files >> used by biblatex (and biber). when i ran org-ref clean it gave an error = 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 .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-ent= ry >>> 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-en= try >>> > 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 th= ing: the >>> key >>> >> to making this work was biblatex which can be used to create several >>> >> lists of references filtered according to keywords, author, etc. Th= is >>> >> 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 fiel= d, I copy >>> >> the tags on-the-fly to the keywords field (see DeclareSourcemap in t= he >>> >> 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 templat= e? >>> 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 publicati= ons >>> >> 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 s= ome >>> >> >>> 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 be= st place >>> for >>> >> >>> >> >> discussing it. For now the issue tracker on Github might = 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 vie= ws >>> 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 groups >>> (like >>> >> the >>> >> >>> >> jabref >>> >> >>> >> >> > dynamic groups if your aware of that). that is for examp= le >>> >> create >>> >> >>> a >>> >> >>> >> group >>> >> >>> >> >> > that auto selects all publications i have (by my first/l= ast >>> >> name) >>> >> >>> and >>> >> >>> >> >> shows >>> >> >>> >> >> > the count (in numbers) of these publications. >>> >> >>> >> >> >>> >> >>> >> >> I=E2=80=99m not familiar with smart groups but it seems th= at 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 y= ou 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 that >>> invokes >>> >> >>> >> >> helm-bibtex with a default search expression and that comm= and >>> >> could >>> >> >>> be >>> >> >>> >> >> bound to a keyboard shortcut. >>> >> >>> >> >> >>> >> >>> >> >> > Another example is a group to keep track of all the pape= rs >>> 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 a= ll 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 = 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 t= he >>> >> 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 t= hat >>> >> >>> 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