Re: [O] helm-bibtex questions

[John Kitchin]

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 file
>
> -*- mode:bibtex; eval: (bibtex-set-dialect 'biblatex); -*-
>
> @article{ackerman-1998-discr-clear,
>   author = {Ackerman, {S.A.} and Strabala, {K.I.} and Menzel,
>                   {W.P.} and Frey, {R.A.} and Moeller, {C.C.} and
>                   Gumley, {L.E.}},
>   title = {Discriminating Clear Sky From Clouds With Modis},
>   journal = {Journal of Geophysical Research},
>   volume = 103,
>   number = {D24},
>   pages = {32,141--32,157},
>   year = 1998,
>   shorttitle = {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 <address@hidden>
> 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 <address@hidden>
>> > 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 <address@hidden> 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 <address@hidden
>> >
>> >> 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-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 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 <
>> >>> address@hidden>
>> >>> > 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 <
>> >>> address@hidden>
>> >>> >> > 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 <
>> >>> >> >> address@hidden> 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 <
>> >>> >> >>> address@hidden>
>> >>> >> >>> > 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 <
>> >>> >> >>> >> address@hidden
>> >>> >> >>> >> >> 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
>> >>> >> >>> >> >>
>> >>> >> >>> >> >>
>> >>> >> >>> >>
>> >>> >> >>> >>
>> >>> >> >>>
>> >>> >> >>>
>> >>> >> >>
>> >>> >>
>> >>> >>
>> >>>
>> >>> --
>> >>> 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