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helm-bibtex's Issues

Do not see any bibtex entries

Hi,

I tried helm bibtex with a test .bib file but I only get the fallback options and no search results. The bibtex file is validated and syntactically correct.
For helm-bibtex I tried the latest version from github as well as the package from melpa. I use helm version helm-20141226.1305.

No Error messages in the Messages Buffer

Thanks for any ideas on what could be wrong.

Bibtex file

@article{Siebert2010,
title = "Quantifying blue and green virtual water contents in global crop production as well as potential production losses without irrigation ",
journal = "Journal of Hydrology ",
volume = 384,
number = "3–4",
pages = "198 - 217",
year = 2010,
note = "Green-Blue Water Initiative (GBI) ",
issn = "0022-1694",
doi = "http://dx.doi.org/10.1016/j.jhydrol.2009.07.031",
url = "http://www.sciencedirect.com/science/article/pii/S0022169409004235",
author = "Stefan Siebert and Petra Döll",
keywords = "Crop water requirement",
keywords = "Global crop water model",
keywords = "Virtual water content",
keywords = "Irrigation water use",
keywords = "Crop production",
keywords = "Crop yield "
}

@article{Zwart2010WATPRO,
title = "WATPRO: A remote sensing based model for mapping water productivity of wheat ",
journal = "Agricultural Water Management ",
volume = 97,
number = 10,
pages = "1628 - 1636",
year = 2010,
issn = "0378-3774",
doi = "http://dx.doi.org/10.1016/j.agwat.2010.05.017",
url = "http://www.sciencedirect.com/science/article/pii/S037837741000185X",
author = "Sander J. Zwart and Wim G.M. Bastiaanssen and Charlotte de Fraiture and David J. Molden",
keywords = "Water productivity",
keywords = "Global modelling",
keywords = "Benchmarking",
keywords = "Wheat",
keywords = "Remote sensing "
}

Feature Request: Citation command.

Dear Titus,

I like the idea of replacing ebib with helm-bibtex. The only thing I would wish for is a way to specify the citation command to use ( \cite{}, \textcite{}, etc)

If there was a way to add an argument like in ebib:

 '(ebib-citation-commands (quote 
((any (("cite" "\\cite%<[%A]%>{%K}") 
("t" "\\textcite%<[%A]%>{%K}") 
("p" "\\parencite%<[%A]%>{%K}"))) 
(org-mode (("ebib" "[[ebib:%K][%D]]")))
(markdown-mode (("t" "@%K%< [%A]%>"))))))

That would be great!

Wish I could code up the elisp right now, but I am late on a couple of deadlines!

Thanks,

-Cyrus

unhelpful error if helm-bibtex-library-path is not set

Hello,
I stumbled over an odd error in helm-bibtex today. If the variable helm-bibtex-library-path is not set, which is the default, one gets the error

f-absolute?: Wrong type argument: stringp, nil

when pressing RET over an entry. Obviously, this is not very telling (to me at least). Just setting the variable to "~/" fixes the issue, even though there are no pdf's to be found under that path. I think a good default value would be the folder of the bib file?
Cheers,
Christian

Request for helm-bibtex-notes-file

Instead of storing my notes in a separate directory, which I think is what helm-bibtex proposes, I like to keep my notes in one org file, which looks something like this:

** Author (2013) Title
:PROPERTIES:
:Custom_ID: bibtex-key
:END:

So I was wondering if you could add "helm-bibtex-notes-file", which would be the equivalent of "helm-bibtex-notes-path". But instead of searching for the bibtex-key.org file, it would search for the bibtex-key in the file specified by the user, for example:

(setq helm-bibtex-notes-file "~/.emacs.d/annotation.org")

Allow to Insert citation in pandoc markdown format

Thank you for this nice mode. Really useful and fast to deal with references and documents.

Would be nice if it could insert citation in the pandoc-citeproc format. In this format (http://johnmacfarlane.net/pandoc/README.html#citations):

Citations go inside square brackets and are separated by semicolons. Each citation must have a key, composed of ‘@’ + the citation identifier from the database, and may optionally have a prefix, a locator, and a suffix. The citation key must begin with a letter or _, and may contain alphanumerics, _, and internal punctuation characters (:.#$%&-+?<>~/). Here are some examples:
Blah blah [see @doe99, pp. 33-35; also @smith04, ch. 1].
Blah blah [@doe99, pp. 33-35, 38-39 and passim].
Blah blah [@smith04; @doe99].
A minus sign (-) before the @ will suppress mention of the author in the citation. This can be useful when the author is already mentioned in the text:
Smith says blah [-@smith04].

File mode specification error

Hi Titus,

I am having an issue with a few items in my bibliography. I insert a citation, using the helm-bibtex function, but when I click on the link (to open the pdf, for example) I get the following in the message buffer:

File mode specification error: (invalid-function dbus-ignore-errors)
(No changes need to be saved)
File mode specification error: (invalid-function dbus-ignore-errors)
progn: Wrong type argument: stringp, nil
(No changes need to be saved)
File mode specification error: (invalid-function dbus-ignore-errors)
!!! No entry found !!!

This happens only with some references. Here is the bibtex entry for two of them, in case it is of any use:

@TechReport{Cameron2011,
Title = {EUSeaMap - Preparatory Action for development and assessment of a European broad-scale seabed habitat map final report},
Author = {Cameron, A., and Askew, N.},
Year = {2011},
Note = {Available at http://jncc.gov.uk/euseamap},
File = {:Cameron2011.pdf:PDF},
Timestamp = {2013.09.09}
}

@TechReport{EUSeaMap,
Title = {Technical Appendix No. 2: Wave base data and thresholds},
Author = {EUSeaMap},
File = {:EUSeaMap.pdf:PDF},
Owner = {julian},
Timestamp = {2015.05.22}
}

Let me know if you need any other information

All the best,

Julian

insert formatted references "leaves out" authors

Hi Titus

As requested im posting the issue on github. i have put an example below of a .bib entry i have

@article{abby-2015-prenat-early,
  author =   {Abby F. Fleisch, Heike Luttmann-Gibson, Wei Perng,
                  Sheryl L. Rifas-Shiman, Brent A. Coull,
                  Petros Koutrakis, Joel D. Schwartz, Antonella
                  Zanobetti, Christos S.  Mantzoros, Matthew
                  W. Gillman, , Diane R. Gold, , Emily Oken, },
  title =    {Prenatal and Early Life Exposure To Traffic
                  Pollution and Cardiometabolic Health in Childhood},
  journal =  {},
  year =     {2105},
  pubstate =     {prep},
  tags =     { },
}

and how org inserts the formatted references into emacs (only the 1st author is present as you can see:

- Abby F. Fleisch, H. L. (2015). Prenatal and early life exposure to
  traffic pollution and cardiometabolic health in childhood. , (), .

Maybe its my entry that isnt properly formatted (i use org-ref-clean for that)?

thx

Z

[Feature request] impact factor and cited number

Hi @tmalsburg

Do you have any idea that how to add the impact factor of general and cited number to helm-bibtex?

Because I have a lot of papers, I would like to choose paper with good impact factor and well cited number to read and cite first. Of course, I can do it manually by looking up in website or by memorizing the journals. However, it is still convenient to pick up papers if IF and cited number are there.

Thanks in advance.
llcc

Add resolution of cross-references

A request: it would be helpful if helm-bibtex used the crossref field, if available, to show the inherited auhtor and year fields for inbook, incollection, inproceeding entries.

Candidates not formatted on helm-bibtex call

Hey, first thanks for a really useful package!

Second, here's an issue I bumped into: when I open the helm buffer (calling helm-bibtex), candidates are not formatted which is a bit annoying with long title references as lines get wrapped: here

This issue goes away after I start filtering some candidates and even if I delete the pattern completely: this

I was thinking that a call to helm-bibtex-candidates-formatter just when the buffer is loaded should fix the issue. I played a bit with the helm-bibtex and helm source but I can't really figure out where this should go. If you can give me some pointers I'm happy to send a pull request.

"Loading bibliography ..." information when "helm-bibtex-library-path" is set

Hi,

Thanks for this powerful extension of Emacs first. I would like to report an issue on my Mac as described in the title.

I installed helm-bibtex via melpa with the newest version. My Emacs is Emacs 24.4 on Mac 10.10.2.

At first, I only have the following setting in my init.el:

(setq helm-bibtex-bibliography '("~/Documents/Work/Papers/MPC.bib"))

helm-bibtex works fine with this setting. However, if I add the following setting in init.el:

(setq helm-bibtex-library-path '("~/Documents/Work/Papers/MPC"))

Then when I ran helm-bibtex in Emacs, it will display "Loading bibliography ..." message in the echo area, which is similar to Issue #38.

So now I would just try the management function with helm-bibtex. Could you please help me with this? Thanks in advance.

helm-bibtex gets stuck on "Loading blbliography ... " with newest version from MELPA

Hi,
with the latest MELPA version of helm-bibtex (2015-02-13), I no longer get any results when trying to search for a string (even with a single character, such as "a"). Instead, the fallback menu is shown straight away, and when searching the message buffer displays only "Loading bibliography ...". However, helm-bibtex does have the correct path to the bibliography, and displays the fallback option "Create new entry in bibliography-name.bib", where bibliography-name.bib is the correct name of my bib file.

Any ideas what might be causing this to happen?

helm-bibtex-additional-search-fileds does not work properly

Hello,

thanks for this useful package. I tried to the helm-bibtex-additional-search-fields function for searching abstracts of my entries. This is the setup

(require 'helm-bibtex)
(setq helm-bibtex-bibliography "~/Documents/prova.bib")
(setq helm-bibtex-library-path "~/Dropbox/PDF")
(setq helm-bibtex-additional-search-fields '(abstract))

And this is a sample bib file

@article{Aron2007,
    file = {Aron2007},
    author = "Aron, Adam R",
    title = "The neural basis of inhibition in cognitive control.",
    DOI = "10.1177/1073858407299288",
    volume = "13",
    number = "3",
    year = "2007",
    journal = "Neuroscientist",
    pages = "214--228",
    abstract = "The concept of "inhibition" is widely used in synaptic, circuit, and systems neuroscience, where it has a clear meaning because it is clearly observable. The concept is also ubiquitous in psychology. One common use is to connote an active/willed process underlying cognitive control. Many authors claim that subjects execute cognitive control over unwanted stimuli, task sets, responses, memories, and emotions by inhibiting them, and that frontal lobe damage induces distractibility, impulsivity, and perseveration because of damage to an inhibitory mechanism. However, with the exception of the motor domain, the notion of an active inhibitory process underlying cognitive control has been heavily challenged. Alternative explanations have been provided that explain cognitive control without recourse to inhibition as concept, mechanism, or theory. This article examines the role that neuroscience can play when examining whether the psychological concept of active inhibition can be meaningfully applied in cognitive control research.",
    month = "June"
}


@Article{BertinMaghit2009,
    abstract = {L’elettrizzazione corrisponde all’insieme delle conseguenze derivanti dall’esposizione alla corrente elettrica. L’elettrocuzione è un arresto cardiaco indotto dalla corrente elettrica. La gravità immediata dei casi di elettrizzazione con corrente a bassa tensione, essenzialmente costituiti da incidenti domestici, è cardiovascolare, con il rischio di arresto cardiaco per fibrillazione ventricolare, di asfissia per tetania dei muscoli respiratori e di infarto miocardico. La corrente ad alta tensione provoca lesioni tissutali e viscerali tra i punti di entrata e di uscita, sedi di ustioni profonde. I bisogni idroelettrolitici iniziali sono maggiori di quelli che possono essere stimati sulla base delle sole ustioni visibili. Il trattamento chirurgico richiede interventi reiterati. La fulminazione nella sua forma grave richiede una gestione simile a quella dei casi di elettrizzazione da corrente ad alta tensione.},
    file = {Bertin2009.pdf},
    doi = {10.1016/S1286-9341(09)70016-X},
    url = {http://gen.lib.rus.ec/scimag/index.php?s=10.1016/S1286-9341(09)70016-X},
    number = {2},
    volume = {13},
    year = {2009},
    journal = {EMC - Urgenze},
    title = {Elettrizzazione, elettrocuzione, fulminazione},
    author = {Bertin-Maghit, M.}
}


@article{Biffl2009,
    author = "Biffl, Walter L and Kaups, Krista L and Cothren, C Clay and Brasel, Karen J and Dicker, Rochelle A and Bullard, M Kelley and Haan, James M and Jurkovich, Gregory J and Harrison, Paul and Moore, Forrest O and others",
    title = "Management of patients with anterior abdominal stab wounds: a Western Trauma Association multicenter trial",
    file = {Biffl2009.pdf},
    volume = "66",
    number = "5",
    year = "2009",
    journal = "Journal of Trauma and Acute Care Surgery",
    pages = "1294--1301",
    abstract = "The optimal managementof hemodynamically stable, asymptomaticpatients with anterior abdominal stabwounds (AASWs) remains controversial.The goal is to identify and treat injuries in asafe, cost-effective manner. Common evaluationstrategies include local wound exploration(LWE)/diagnostic peritoneal lavage(DPL), serial clinical assessments (SCAs),and computed tomography (CT) imaging.The purpose of this multicenter study was toevaluate the clinical course of patients managedby the various strategies, to determinewhether there are differences in associatednontherapeutic laparotomy (NONTHERLAP), emergency department (ED) discharge,or complication rates."
}

It seems that helm-bibtexlooks just in the default fields. It fails to show entries when I try to use words in abstract fields.

show bibkey in main view

Hi and thx for this great little helm addon.
is there anyway to have the main table show the bibkey alongside date and name?

thx!

Z

Feature request: opening files specified in "File" field.

(Disclaimer: I am new to helm-bibtex, so maybe I am missing something obvious).
I see we can redefine helm-bibtex-find-pdf. A use case that might not be that rare is when the name of the PDF has no clear relationship with the key, but is actually specified in the file field
File = {:home/ramon/a_directory/some_file_123.pdf:PDF},

But this might now always be the case, so some entries might follow the usual pattern (key.pdf). Is the reommended procedure to redefine helm-bibtex-find-pdf so we search both in the "File" field and the standard way? Or is there some easier procedure? (If the way to do it is by modifying the function, what is the best way to "get the file field" or similar ---elisp ignorant here, with just enough knowledge to modify elisp code by trial and error).

helm-bibtex doesn't propose the "search bibtext entries"

Hi,

When I do "M-x search-bibtex" the only things that it proposes to me is the "fallback options":

Search in Google Scholar
Search in Pubmed
Search in arXiv
Search in Bodleian Library
Search in Library of Congress
Search in Deutsche Nationalbibliothek
Search in British National Library
Search in Bibliothèque nationale de France
Search in Gallica Bibliothèque Numérique
Create new entry in test.bib

But nothing to search in my bib fil (test.bib).

I did something wrong?

Config:
(setq helm-bibtex-bibliography "/Users/Sam/Dropbox/Textes/test.bib")
mac OS10.9
emacs 24.3

Problem of presention - helm bibtex

I have two elements of configuration that are a problem for helm bibtex:
(global-visual-line-mode 1)
(set-fringe-mode 0)
As you can see above it breaks the lines and lead to a very bad presentation of helm bibtex
capture d ecran 2014-09-21 a 00 04 30
I do not know how I could manage to stop (global-visual-line-mode 1) and (set-fringe-mode 0) just when I am using helm-bibtex
Something like "add-hook" could be useful, I suppose. But don't know how to deal with that.

Quote key before using in re-search-forward.

Quote the key before using re-search-forward in helm-bibtex-get-entry,
because the key can contain regexp chars.

Use the same search algorithm in helm-bibtex-show-entry to find the
entry as in helm-bibtex-get-entry, because it can be possible to
have string entries which contain the key.

diff --git a/helm-bibtex.el b/helm-bibtex.el
index 237b047..98944b8 100644
--- a/helm-bibtex.el
+++ b/helm-bibtex.el
@@ -262,7 +262,7 @@ (defun helm-bibtex-get-entry (entry-key)
(goto-char (point-min))
(re-search-forward (concat "^@(" parsebib--bibtex-identifier
")[[:space:]][({][[:space:]]"

  •                           entry-key))
    
  •                           (regexp-quote entry-key)))
    
    (let ((entry-type (match-string 1)))
    (helm-bibtex-prep-entry (parsebib-read-entry entry-type)))))

@@ -494,7 +494,10 @@ (defun helm-bibtex-show-entry (key)
(let ((buf (helm-bibtex-buffer-visiting bibtex-file)))
(find-file bibtex-file)
(goto-char (point-min))

  •    (if (search-forward key nil t)
    
  •    (if (re-search-forward
    
  •         (concat "^@\(" parsebib--bibtex-identifier
    
  •                 "\)[[:space:]]_[({][[:space:]]_"
    
  •                 (regexp-quote key)) nil t)
         (throw 'break t)
       (unless buf
         (kill-buffer)))))))
    

```helm-bibtex-show-entry``` fails for single file.

You probably need to add a conditional for the case where there is only one bibtex file and not a list, e.g.,

(if (listp helm-bibtex-bibliography)
                helm-bibtex-bibliography
              (list helm-bibtex-bibliography)) 

PS. Great job on all the new features! I love what you are doing here...

Feature request: make fallback options helm actions

The current implementation adds the fallbacks as another helm source and therefore requires navigating in the helm buffer to select a fallback. If these were actions instead, a user could hit tab and use helm filtering again to more quickly get to the fallback they wanted.

Feature request: Option to auto-populate orgmode notes file

First off, helm-bibtex is AWESOME. I'm not sure I've yet come down from my high from learning about this to help with my research.

I use the orgmode notes option a great deal. I find I start all my note files the same way: by converting key parts of the bibtex entry into org tags. For example, starting my notes file:

#+TITLE: [[http://books.google.com/books?id%3Dy8GiAwAAQBAJ][Event Cognition]] (2014)
#+AUTHOR: Radvansky, G.A. and Zacks, J.M.

from:

@book{radvansky2014event,
  publisher = {Oxford University Press},
  year = {2014},
  url = {http://books.google.com/books?id=y8GiAwAAQBAJ},
  isbn = {9780199898145},
  author = {Radvansky, G.A. and Zacks, J.M.},
  title = {Event Cognition},
}

It would be nice if there were a function/variable to do this automatically if the notes are not yet created, since I'm visiting them via selection of a bibtex entry anyway.

Add tags/categories to items

In the long term, it would be amazing to have a tagging mechanism for candidates. This allows:

  1. work planning: mark papers as read/unread/favorite/indexed/reviewed etc.
  2. content indexing: group papers which are relevant to a certain concept

The index could be stored as a separate file (in the same path as the .bib file) which has a mapping from keys to a list of tags. For content indexing tags should be hierarchical, with 1 or 2 levels of nesting.

helm-bibtex would let users:

  1. search based on tag using some simple syntax e.g.:
    • simple :read - entries matching the read tag
    • hierarchy :conjugate gradient.sparse - the conjugate gradient -> sparse hierarchy
    • union :conjugate gradient|:sparse - either conjugate gradient or sparse
    • intersection :conjugate gradient&:sparse - matching both
  2. edit candidate tags via an extra option in the candidate menu
  3. generate a text version of its index (markdown would be easy)

An example markdown index:

% Paper Index

# Conjugate gradient
* Dense [@lopes2008high]
* Sparse [@chow2014efficient]

What do you think?

auto create orgnote if not present?

Hi :)

i would like to suggest that (if possible) helm-bitex would offer to create a note (or org file) and move to it if not present for a bibtex entry. as far as i can tell currently it only says:

Non-existent agenda file ~/org/files/Uni/papers/bib/notes/_(sub)_ChronicEffectsTemperature.org. [R]emove from list or [A]bort?

thx!

z

Issues with parsebib in version 20141214.1529

Hi,

Thanks for your continuous work, I really like your extension! Too bad that the latest version does not work for me anymore (using emacs 24.4.1 on ubuntu). First, there is some weird issue with the parsebib.el dependency. When I run helm-bibtex, it does not show any entries. Turning on debugging-on-error does not return any error and (require 'parsebib) does not help either. While debugging, I discovered that evaluating some parsebib functions manually, or calling (load "parsebib.el") fixes the issue in so far as the bibtex items are displayed in helm-bibtex again. With this, however, opening pdfs and note files from helm-bibtex does not work (the filenames are wrong, although they are correct when deciding whether or not to draw the corresponding icons).
Let me know if you have any idea what my problem could be...

Thanks
Peter

Sort order

Ebib sorts the bib file alphabetically (a-z), but helm-bibtex reverses the order (z-a). Any idea how to fix this?

Insert reference generates "Wrong type argument"

Hi,

I was trying the helm-bibtex-insert-reference command today using the most recent helm-bibtex on melpa and noticed that any entry with the author field containing "Lastname, Firstname" generated wrong type argument. Author fields containing "Firstname Lastname" were fine. I didn't try any with multiple authors. The error pops up within helm-bibtex-apa-format-authors.

Thanks in advance, if you can get a chance to confirm and/or fix it.

Scott

Request for new action: insert link to pdf and title

Hi Titus,
Sorry if this is a very personalized request. When I was using RefTex, I had customized an "citation" option that inserted an org link to the pdf and the title of the selected reference. I used this quite a bit to prepare lists of bilbiography to read for particular projects. When using this option, I would get something like this:

** [[/home/julian/Documents/Refs/Lurton2015.pdf][Lurton2015]] Backscatter measurements by seafloor-mapping sonars

It seems that it should be relatively simple to create a new function to do this. But my emacs lisp knowledge is very limited. I started with this:

(defun helm-bibtex-insert-link-to-pdf-and-title (_)
"Insert link to pdf and title at point."
(let ((keys (helm-marked-candidates :with-wildcard t)))
(with-helm-current-buffer
(insert
(concat "**[["
helm-bibtex-library-path
(funcall 'helm-bibtex-format-citation-default keys)
".pdf]["
(funcall 'helm-bibtex-format-citation-default keys)
"]]"
)))))

But obviously does not work (I get a "Wrong type argument: characterp" error), and I am not sure how to get the title in. Whenever you have the chance, could you give me a hand?
Many thanks,

Julian

Add open-notes/pdf-at-point?

Hi, thanks for the tool once again!

Recently I needed to do lookups of notes or pdfs given a bibtex key. This is easy with the functions bellow:

(defun open-notes-at-point ()
  "Open notes corresponding to the citation key at point"
  (interactive)
  (find-file (format "%s/%s%s" helm-bibtex-notes-path (word-at-point) helm-bibtex-notes-extension)))

(defun open-pdf-at-point ()
  "Open pdf corresponding to the citation key at point"
  (interactive)
  (find-file 
   (format "%s/%s.pdf" helm-bibtex-library-path (word-at-point))))

Maybe helm-bibtex already has these functions and I missed them somehow?

If not and unless I am missing something, I think it might be convenient to include them since:

  1. (IMHO) these type of lookups are common (e.g. when revising material, writing surveys etc.)
  2. the configuration is already in place

Highlighted and clickable pandoc citations

Hello,

First of all sorry about my lack of emacs knowledge to achieve what I'm asking here.

Would there be any way of making an inserted pandoc citation a link highlighted and clickable?

As you know a typical pandoc citation is like this [@mycitation]

I would like @mycitation to become an active link in emacs. When clicked, it should take the person to the related entry in helm-bibtex.

Thanks in advance,

Steve

helm-bibtex-additional-search-fields with repeated fields

If one exports a bibtex file from Zotero one can have multiple annote fields per entry. If one has

(setq helm-bibtex-additional-search-field '(annote))`

only the contents of the last annote are searched. Is there a way to have it search in all annotes of every entry?

Request for multiple directories in helm-bibtex-library-path

I'm trying helm-bibtex for the first time and am very impressed. I have my PDF files in several directories, including one for papers and one for books. I'd therefore like helm-bibtex-library-path to support a list of directories, in the same way that helm-bibtex-bibliography supports a list of bib-files.

I suppose some people might also want the option to search all subdirectories of a given path, though that wouldn't meet my present need.

Possibility of star system

Hi @tmalsburg

Is it possible to give a star function to helm-bibtex, then it can be easier to find some important bibliographies marked before? or think in another way, like i can add priority to any single org-mode headline in org-mode, then let helm-bibtex recognize it? Does this can come true?

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