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 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’s a pretty straightforward org document except for one thing: the key
> to making this work was biblatex which can be used to create several
> 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’t know this field, 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-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’t 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’s
> relatively
> >>> >> easy to create separate sections for these types of publications
> 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 some
> >>> 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’m not sure whether this list is the best 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 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’t 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 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’m 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 + “article”.  If you want all your
> articles
> >>> from
> >>> >> >> 2010, enter your name + “articles 2010”.  And so on.  The number
> of
> >>> >> >> matches will be displayed in the mode line.  If you don’t 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.
> >>> >> >>
> >>> >> >> > Another example is a group to keep track of all the papers im
> >>> working
> >>> >> on
> >>> >> >> or
> >>> >> >> > invloved with by matching keyword author and prep/*other key
> word
> >>> >> >>
> >>> >> >> I use two BibTeX fields to tag entries: “keywords” for keywords
> >>> >> >> describing the content of the paper (as usual) and “tags” for
> meta
> >>> >> >> data.  Values that I use in tags are “own”, “manuscript”,
> “poster”,
> >>> >> >> “talk”, … So if I want a list of all articles in progress, I
> search
> >>> for
> >>> >> >> “own manuscript”.  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 “forthcoming” (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 the
> 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 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
> >>> >> >>
> >>> >> >>
> >>> >>
> >>> >>
> >>>
> >>>
> >>
>
>