From: Xebar Saram <zeltakc@gmail.com>
To: John Kitchin <jkitchin@andrew.cmu.edu>
Cc: org mode <emacs-orgmode@gnu.org>
Subject: Re: helm-bibtex questions
Date: Sat, 27 Jun 2015 09:11:59 +0300 [thread overview]
Message-ID: <CAOQHXPoZt_3_R9qsoVeO5TKeNEStPUyKj3mR-8gKs=0o9KoVjQ@mail.gmail.com> (raw)
In-Reply-To: <m2ioaailwv.fsf@andrew.cmu.edu>
[-- Attachment #1: Type: text/plain, Size: 18304 bytes --]
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 <jkitchin@andrew.cmu.edu>
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 <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
> >>>
> >>
> >>
>
> --
> 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
>
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next prev parent reply other threads:[~2015-06-27 6:12 UTC|newest]
Thread overview: 26+ messages / expand[flat|nested] mbox.gz Atom feed top
[not found] <s7xudwyj5ehe8r98klrf3034.1435230561139@email.android.com>
2015-06-26 7:14 ` helm-bibtex questions Xebar Saram
2015-06-26 14:28 ` John Kitchin
2015-06-27 6:11 ` Xebar Saram [this message]
2015-06-27 11:44 ` John Kitchin
2015-06-30 9:15 ` Eric S Fraga
2015-06-30 13:19 ` John Kitchin
2015-06-30 13:44 ` Xebar Saram
2015-06-30 14:37 ` Eric S Fraga
2015-07-01 4:53 ` Xebar Saram
2015-06-17 18:08 Xebar Saram
2015-06-17 20:02 ` Titus von der Malsburg
2015-06-18 11:32 ` Xebar Saram
2015-06-18 18:38 ` Titus von der Malsburg
2015-06-19 10:56 ` Xebar Saram
2015-06-19 21:02 ` John Kitchin
2015-06-21 18:29 ` Titus von der Malsburg
2015-06-21 18:40 ` John Kitchin
2015-06-22 14:28 ` Xebar Saram
2015-06-22 15:12 ` Titus von der Malsburg
2015-06-24 19:54 ` Xebar Saram
2015-06-24 21:03 ` John Kitchin
2015-06-26 7:21 ` Xebar Saram
2015-06-26 17:21 ` Titus von der Malsburg
2015-06-26 17:35 ` Titus von der Malsburg
2015-06-26 17:54 ` John Kitchin
2015-06-19 21:08 ` John Kitchin
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