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 <johnrkitchin@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 dialect.
>
>
> On June 25, 2015, at 6:58 AM, Xebar Saram <zeltakc@gmail.com> 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 <jkitchin@andrew.cmu.edu>
> 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 <
>> 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
>> >> >>> >> >>
>> >> >>> >> >>
>> >> >>> >>
>> >> >>> >>
>> >> >>>
>> >> >>>
>> >> >>
>> >>
>> >>
>>
>> --
>> 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
>>
>
>