Re: [EXT] Problem with org-ref

[John Kitchin]

thanks for the troubleshooting. I pushed a fix that should use the
customizable pdf filename function instead.

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 Wed, Mar 10, 2021 at 10:36 AM Marvin M. Doyley 
wrote:

> HI Kyle,
>
> This solved my problems
>
>  Thanks,
>
> M
>
>
>
>
> On Mar 9, 2021, at 11:49 PM, Kyle Meyer  wrote:
>
> Marvin M. Doyley writes:
>
> Hi there,
>
> When I use crossref-add-bibtex-entry it download the BibTeX entry but
> cannot download the associated pdf.
> I get the following error  (wrong-type-argument stringp
> ("/Users/doyley/Dropbox/Filing_Cabinet/B/refs/pdf/“))
>
> I configured org-ref as follows
>
> (setq org-ref-bibliography-notes
> '("/Users/doyley/Dropbox/Filing_Cabinet/B/refs/ref_notes.org")
>  org-ref-default-bibliography
> '("/Users/doyley/Dropbox/Filing_Cabinet/B/refs/ref.bib")
>  org-ref-pdf-directory
> '("/Users/doyley/Dropbox/Filing_Cabinet/B/refs/pdf/")
>   org-ref-notes-citation-link '("cite")
>  )
>
>
> [ Caveat: I've never used org-ref ]
>
> org-ref's 0383cc2 (support multiple pdf directories, 2016-06-10) updated
> org-ref-pdf-directory to accept a list value, so your value is valid,
> but...
>
> Debugger entered--Lisp error: (wrong-type-argument stringp
> ("/Users/doyley/Dropbox/Filing_Cabinet/B/refs/pdf/"))
>
>  file-name-as-directory(("/Users/doyley/Dropbox/Filing_Cabinet/B/refs/pdf/"))
>  doi-utils-get-bibtex-entry-pdf(nil)
>
>
> ... doi-utils-get-bibtex-entry-pdf wasn't updated for that (+cc the
> author of that commit and John Kitchin).
>
> It looks like org-ref-pdf-directory still supports a string, though, and
> you only have one item, so you should be able to work around the issue
> with
>
>  (setq org-ref-pdf-directory
> "/Users/doyley/Dropbox/Filing_Cabinet/B/refs/pdf/")
>
>
>

Re: [EXT] Problem with org-ref

[Marvin M. Doyley]

HI Kyle,

This solved my problems

 Thanks, 

M




> On Mar 9, 2021, at 11:49 PM, Kyle Meyer  wrote:
> 
> Marvin M. Doyley writes:
> 
>> Hi there,
>> 
>> When I use crossref-add-bibtex-entry it download the BibTeX entry but cannot 
>> download the associated pdf.
>> I get the following error  (wrong-type-argument stringp 
>> ("/Users/doyley/Dropbox/Filing_Cabinet/B/refs/pdf/“))
>> 
>> I configured org-ref as follows
>> 
>> (setq org-ref-bibliography-notes 
>> '("/Users/doyley/Dropbox/Filing_Cabinet/B/refs/ref_notes.org") 
>>  org-ref-default-bibliography 
>> '("/Users/doyley/Dropbox/Filing_Cabinet/B/refs/ref.bib") 
>>  org-ref-pdf-directory 
>> '("/Users/doyley/Dropbox/Filing_Cabinet/B/refs/pdf/")
>>org-ref-notes-citation-link '("cite")
>>  )
> 
> [ Caveat: I've never used org-ref ]
> 
> org-ref's 0383cc2 (support multiple pdf directories, 2016-06-10) updated
> org-ref-pdf-directory to accept a list value, so your value is valid,
> but...
> 
>> Debugger entered--Lisp error: (wrong-type-argument stringp 
>> ("/Users/doyley/Dropbox/Filing_Cabinet/B/refs/pdf/"))
>>  file-name-as-directory(("/Users/doyley/Dropbox/Filing_Cabinet/B/refs/pdf/"))
>>  doi-utils-get-bibtex-entry-pdf(nil)
> 
> ... doi-utils-get-bibtex-entry-pdf wasn't updated for that (+cc the
> author of that commit and John Kitchin).
> 
> It looks like org-ref-pdf-directory still supports a string, though, and
> you only have one item, so you should be able to work around the issue
> with
> 
>  (setq org-ref-pdf-directory 
> "/Users/doyley/Dropbox/Filing_Cabinet/B/refs/pdf/")

Re: Problem with org-ref

[Kyle Meyer]

Marvin M. Doyley writes:

> Hi there,
>
> When I use crossref-add-bibtex-entry it download the BibTeX entry but cannot 
> download the associated pdf.
> I get the following error  (wrong-type-argument stringp 
> ("/Users/doyley/Dropbox/Filing_Cabinet/B/refs/pdf/“))
>
> I configured org-ref as follows
>
> (setq org-ref-bibliography-notes 
> '("/Users/doyley/Dropbox/Filing_Cabinet/B/refs/ref_notes.org") 
>   org-ref-default-bibliography 
> '("/Users/doyley/Dropbox/Filing_Cabinet/B/refs/ref.bib") 
>   org-ref-pdf-directory 
> '("/Users/doyley/Dropbox/Filing_Cabinet/B/refs/pdf/")
> org-ref-notes-citation-link '("cite")
>   )

[ Caveat: I've never used org-ref ]

org-ref's 0383cc2 (support multiple pdf directories, 2016-06-10) updated
org-ref-pdf-directory to accept a list value, so your value is valid,
but...

> Debugger entered--Lisp error: (wrong-type-argument stringp 
> ("/Users/doyley/Dropbox/Filing_Cabinet/B/refs/pdf/"))
>   file-name-as-directory(("/Users/doyley/Dropbox/Filing_Cabinet/B/refs/pdf/"))
>   doi-utils-get-bibtex-entry-pdf(nil)

... doi-utils-get-bibtex-entry-pdf wasn't updated for that (+cc the
author of that commit and John Kitchin).

It looks like org-ref-pdf-directory still supports a string, though, and
you only have one item, so you should be able to work around the issue
with

  (setq org-ref-pdf-directory 
"/Users/doyley/Dropbox/Filing_Cabinet/B/refs/pdf/")

Problem with org-ref

[Marvin M. Doyley]

Hi there,

When I use crossref-add-bibtex-entry it download the BibTeX entry but cannot 
download the associated pdf.
I get the following error  (wrong-type-argument stringp 
("/Users/doyley/Dropbox/Filing_Cabinet/B/refs/pdf/“))

I configured org-ref as follows

(setq org-ref-bibliography-notes 
'("/Users/doyley/Dropbox/Filing_Cabinet/B/refs/ref_notes.org") 
  org-ref-default-bibliography 
'("/Users/doyley/Dropbox/Filing_Cabinet/B/refs/ref.bib") 
  org-ref-pdf-directory 
'("/Users/doyley/Dropbox/Filing_Cabinet/B/refs/pdf/")
  org-ref-notes-citation-link '("cite")
  )

(setq bibtex-completion-bibliography  
'("/Users/doyley/Dropbox/Filing_Cabinet/B/refs/ref.bib") 
  bibtex-completion-library-path '("~/Org-files/Notes/PDF"))

(setq bibtex-completion-notes-path "~/Org-files/Notes/ref_notes.org") 
(setq bibtex-completion-pdf-symbol "⌘")
(setq bibtex-completion-notes-symbol "✎")



Also enclosed is the backtrace
Thanks for your help in resolving this issue 
M

Debugger entered--Lisp error: (wrong-type-argument stringp 
("/Users/doyley/Dropbox/Filing_Cabinet/B/refs/pdf/"))
  file-name-as-directory(("/Users/doyley/Dropbox/Filing_Cabinet/B/refs/pdf/"))
  doi-utils-get-bibtex-entry-pdf(nil)
  funcall-interactively(doi-utils-get-bibtex-entry-pdf nil)
  call-interactively(doi-utils-get-bibtex-entry-pdf record nil)
  command-execute(doi-utils-get-bibtex-entry-pdf record)
  helm-M-x-execute-command(doi-utils-get-bibtex-entry-pdf)
  helm-execute-selection-action-1()
  helm-execute-selection-action()
  helm-internalname . "Emacs Commands history") (candidates . 
#f(compiled-function () #)) (keymap keymap (keymap 
...) keymap (21 . helm-M-x-universal-argument) keymap (127 . 
delete-backward-char) (27 keymap ...) (C-return . helm-cr-empty-string) keymap 
(tab . helm-execute-persistent-action) (normal-state keymap "Auxiliary keymap 
for Normal stat..." ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 
... ... ... ... ... ...) (insert-state keymap "Auxiliary keymap for Insert 
stat..." ... ... ... ... ... ... ... ...) (\(insert\ normal\)-state keymap 
"Auxiliary keymap for (insert nor...") (26 . helm-select-action) (f13 lambda 
nil ... ...) (f12 lambda nil ... ...) (f11 lambda nil ... ...) (f10 lambda nil 
... ...) (f9 lambda nil ... ...) (f8 lambda nil ... ...) (f7 lambda nil ... 
...) (f6 lambda nil ... ...) (f5 lambda nil ... ...) (f4 lambda nil ... ...) 
(f3 lambda nil ... ...) (f2 lambda nil ... ...) (menu-bar keymap ...) (help 
keymap ...) (23 . #f(compiled-function () ... #)) (f1 
lambda nil ... ...) (8 keymap ... ... ... ... ...) ...) (action . 
helm-type-command-actions) (persistent-action . helm-M-x-persistent-action) 
(persistent-help . "Describe this command") (help-message . 
helm-M-x-help-message) (requires-pattern . 0) (filtered-candidate-transformer 
helm-M-x-transformer-no-sort helm-fuzzy-highlight-matches) (volatile . t) 
(match . identity) (redisplay . identity) (nomark . t) (coerce . 
helm-symbolify) (header-line . "C-j: Describe this command (keep...") 
(must-match . t) (group . helm-command) (match-dynamic . t)) ((name . "Emacs 
Commands") (candidates . #f(compiled-function () #)) 
(keymap keymap (keymap ...) keymap (21 . helm-M-x-universal-argument) keymap 
(127 . delete-backward-char) (27 keymap ...) (C-return . helm-cr-empty-string) 
keymap (tab . helm-execute-persistent-action) (normal-state keymap "Auxiliary 
keymap for Normal stat..." ... ... ... ... ... ... ... ... ... ... ... ... ... 
... ... ... ... ... ... ... ...) (insert-state keymap "Auxiliary keymap for 
Insert stat..." ... ... ... ... ... ... ... ...) (\(insert\ normal\)-state 
keymap "Auxiliary keymap for (insert nor...") (26 . helm-select-action) (f13 
lambda nil ... ...) (f12 lambda nil ... ...) (f11 lambda nil ... ...) (f10 
lambda nil ... ...) (f9 lambda nil ... ...) (f8 lambda nil ... ...) (f7 lambda 
nil ... ...) (f6 lambda nil ... ...) (f5 lambda nil ... ...) (f4 lambda nil ... 
...) (f3 lambda nil ... ...) (f2 lambda nil ... ...) (menu-bar keymap ...) 
(help keymap ...) (23 . #f(compiled-function () ... #)) (f1 lambda nil ... ...) (8 keymap ... ... ... ... ...) ...) 
(action . helm-type-command-actions) (persistent-action . 
helm-M-x-persistent-action) (persistent-help . "Describe this command") 
(help-message . helm-M-x-help-message) (requires-pattern . 0) 
(filtered-candidate-transformer helm-M-x-transformer-no-sort 
helm-fuzzy-highlight-matches) (volatile . t) (match . identity) (redisplay . 
identity) (nomark . t) (coerce . helm-symbolify) (header-line . "C-j: Describe 
this command (keep...") (must-match . t) (group . helm-command) (match-dynamic 
. t))) nil "M-x " nil nil "*helm M-x*" nil nil helm-M-x-input-history)
  apply(helm-internal name . "Emacs Commands history") (candidates . 
#f(compiled-function () #)) (keymap keymap (keymap 
...) keymap (21 . helm-M-x-universal-argument) keymap (127 . 
delete-backward-char) (27 keymap ...) (C-return . helm-cr-empty-string) keymap 
(tab 

Re: problem with org-ref

[John Kitchin]

This means the biblio package is not installed for some reason.

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 Mon, Jul 20, 2020 at 9:10 AM Johannes Brauer 
wrote:

> Hi!
> After having upgraded my packages I can activate org-ref anymore.
> (require 'org-ref) results in the error message:
> File error: Cannot open load file, No such file or directory, biblio
>
> Any hints what is going wrong?
>
> I am using
> org-ref-20200710.1516
> Aquamacs 3.5  GNU Emacs 25.3.50.1 (x86_64-apple-darwin16.7.0
> macOs 10.15.6
>
> Johannes
>
>
>

problem with org-ref

[Johannes Brauer]

Hi!
After having upgraded my packages I can activate org-ref anymore. 
(require 'org-ref) results in the error message:
File error: Cannot open load file, No such file or directory, biblio

Any hints what is going wrong?

I am using
org-ref-20200710.1516
Aquamacs 3.5  GNU Emacs 25.3.50.1 (x86_64-apple-darwin16.7.0
macOs 10.15.6

Johannes

Re: [O] problem with org-ref after upgrading org-mode from 8.3 to 9.0.5

[Johannes Brauer]

The problem was a corrupted let-plist package in my elpa folder. After 
reinstalling the package all works fine.

Johannes
Am 03.04.2017 um 20:05 schrieb John Kitchin 
>:

That looks like an issue with helm-Bibtex. You might try updating it and/or 
raise an issue with that package.


On Mon, Apr 3, 2017 at 11:03 AM Johannes Brauer 
> wrote:
that’s what I get executing (require 'org-ref):

Debugger entered--Lisp error: (error "Required feature ‘let-alist’ was not 
provided")
  require(let-alist)
  
byte-code("\300\301!\210\300\302!\210\300\303!\210\300\304!\210\300\305!\210\300\306!\210\300\307!\210\300\310!\210\300\311!\207"
 [require bibtex browse-url hl-line ido json url-queue dash let-alist seq] 2)
  require(biblio-core)
  
byte-code("\300\301!\210\300\302!\210\300\303!\210\300\304!\210\300\305!\210\300\306!\210\300\307!\210\300\310!\210\311\312!\207"
 [require biblio-core biblio-doi biblio-arxiv biblio-crossref biblio-dblp 
biblio-hal biblio-dissemin biblio-download provide biblio] 2)
  require(biblio)
  eval-buffer(# nil 
"/Users/johannes/Library/Preferences/Aquamacs 
Emacs/Packages/elpa/helm-bibtex-20170321.1306/bibtex-completion.el" nil t)  ; 
Reading at buffer position 1340
  load-with-code-conversion("/Users/johannes/Library/Preferences/Aquamacs 
Emacs/Packages/elpa/helm-bibtex-20170321.1306/bibtex-completion.el" 
"/Users/johannes/Library/Preferences/Aquamacs 
Emacs/Packages/elpa/helm-bibtex-20170321.1306/bibtex-completion.el" nil t)
  require(bibtex-completion)
  byte-code("\306\307!\210\306\310!\210\306\311!\210\306\312!\210\313 \314\211  
\314  :\203f
--
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

Re: [O] problem with org-ref after upgrading org-mode from 8.3 to 9.0.5

[John Kitchin]

That looks like an issue with helm-Bibtex. You might try updating it and/or
raise an issue with that package.


On Mon, Apr 3, 2017 at 11:03 AM Johannes Brauer 
wrote:

> that’s what I get executing (require 'org-ref):
>
> Debugger entered--Lisp error: (error "Required feature ‘let-alist’ was not
> provided")
>   require(let-alist)
>
> byte-code("\300\301!\210\300\302!\210\300\303!\210\300\304!\210\300\305!\210\300\306!\210\300\307!\210\300\310!\210\300\311!\207"
> [require bibtex browse-url hl-line ido json url-queue dash let-alist seq] 2)
>   require(biblio-core)
>
> byte-code("\300\301!\210\300\302!\210\300\303!\210\300\304!\210\300\305!\210\300\306!\210\300\307!\210\300\310!\210\311\312!\207"
> [require biblio-core biblio-doi biblio-arxiv biblio-crossref biblio-dblp
> biblio-hal biblio-dissemin biblio-download provide biblio] 2)
>   require(biblio)
>   eval-buffer(# nil
> "/Users/johannes/Library/Preferences/Aquamacs
> Emacs/Packages/elpa/helm-bibtex-20170321.1306/bibtex-completion.el" nil t)
> ; Reading at buffer position 1340
>   load-with-code-conversion("/Users/johannes/Library/Preferences/Aquamacs
> Emacs/Packages/elpa/helm-bibtex-20170321.1306/bibtex-completion.el"
> "/Users/johannes/Library/Preferences/Aquamacs
> Emacs/Packages/elpa/helm-bibtex-20170321.1306/bibtex-completion.el" nil t)
>   require(bibtex-completion)
>   byte-code("\306\307!\210\306\310!\210\306\311!\210\306\312!\210\313
> \314\211  \314  :\203f

-- 
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

Re: [O] problem with org-ref after upgrading org-mode from 8.3 to 9.0.5

[Johannes Brauer]

that’s what I get executing (require 'org-ref):

Debugger entered--Lisp error: (error "Required feature ‘let-alist’ was not 
provided")
  require(let-alist)
  
byte-code("\300\301!\210\300\302!\210\300\303!\210\300\304!\210\300\305!\210\300\306!\210\300\307!\210\300\310!\210\300\311!\207"
 [require bibtex browse-url hl-line ido json url-queue dash let-alist seq] 2)
  require(biblio-core)
  
byte-code("\300\301!\210\300\302!\210\300\303!\210\300\304!\210\300\305!\210\300\306!\210\300\307!\210\300\310!\210\311\312!\207"
 [require biblio-core biblio-doi biblio-arxiv biblio-crossref biblio-dblp 
biblio-hal biblio-dissemin biblio-download provide biblio] 2)
  require(biblio)
  eval-buffer(# nil 
"/Users/johannes/Library/Preferences/Aquamacs 
Emacs/Packages/elpa/helm-bibtex-20170321.1306/bibtex-completion.el" nil t)  ; 
Reading at buffer position 1340
  load-with-code-conversion("/Users/johannes/Library/Preferences/Aquamacs 
Emacs/Packages/elpa/helm-bibtex-20170321.1306/bibtex-completion.el" 
"/Users/johannes/Library/Preferences/Aquamacs 
Emacs/Packages/elpa/helm-bibtex-20170321.1306/bibtex-completion.el" nil t)
  require(bibtex-completion)
  
byte-code("\306\307!\210\306\310!\210\306\311!\210\306\312!\210\313\314\211\314:\203f

Re: [O] problem with org-ref after upgrading org-mode from 8.3 to 9.0.5

[John Kitchin]

I have not seen that before. Was there a traceback that indicated where
the error came from?

Johannes Brauer writes:

> Hi,
> after the upgrade (require 'org-ref) results in the error message:
>  (error "Required feature ‘let-alist’ was not provided“)
>
> I am using Aquamacs 3.3  GNU Emacs 25.1.1. I looked for let-plist using 
> list-packages and found:
>   let-alist  1.0.4 built-in
>
>  What is going wrong?
>
> Johannes


--
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

[O] problem with org-ref after upgrading org-mode from 8.3 to 9.0.5

[Johannes Brauer]

Hi,
after the upgrade (require 'org-ref) results in the error message:
 (error "Required feature ‘let-alist’ was not provided“)

I am using Aquamacs 3.3  GNU Emacs 25.1.1. I looked for let-plist using 
list-packages and found:
  let-alist  1.0.4 built-in 

 What is going wrong?

Johannes

Re: [O] HTML Export problem with org-ref -- SOLVED

[Alan L Tyree]

On 10/02/17 10:23, Alan L Tyree wrote:
I'm trying to export a large document (about 600 printed a4 pages) to 
html. It contains a lot of references.


The export fails with this message:

byte-code: abl-8 chicago limit:t does not seem to exist

Because of the "chicago", I am presuming that the failure is in my 
setup of org-ref, but I can't seem to find any info on it.


What information can I provide to help track this down? any help 
greatly appreciated.


Cheers,

Alan

Org mode version 9.0.4 (9.0.4-elpaplus @ 
/home/alant/.emacs.d/elpa/org-plus-contrib-20170124/)


GNU Emacs 24.5.1 (x86_64-pc-linux-gnu, GTK+ Version 3.14.5) of 
2016-03-20 on trouble, modified by Debian


Debian Jessie installation.


Sorry for the noise. The problem was that I had some old (pre-org-ref I 
guess) bibliography stuff in the file. Commented out, but still picked 
up by org-ref. For the record:


# #+BIBLIOGRAPHY: abl-8 chicago limit:t
# #   \bibliographystyle{plain}
# #   \bibliography{refs,tyree}

Deleting from the file fixed everything.




--
Alan L Tyreehttp://www2.austlii.edu.au/~alan
Tel:  04 2748 6206  sip:typh...@iptel.org

Re: [O] HTML Export problem with org-ref

[Alan L Tyree]

On 10/02/17 10:23, Alan L Tyree wrote:
I'm trying to export a large document (about 600 printed a4 pages) to 
html. It contains a lot of references.


The export fails with this message:

byte-code: abl-8 chicago limit:t does not seem to exist

Because of the "chicago", I am presuming that the failure is in my 
setup of org-ref, but I can't seem to find any info on it.


What information can I provide to help track this down? any help 
greatly appreciated.


Cheers,

Alan

Org mode version 9.0.4 (9.0.4-elpaplus @ 
/home/alant/.emacs.d/elpa/org-plus-contrib-20170124/)


GNU Emacs 24.5.1 (x86_64-pc-linux-gnu, GTK+ Version 3.14.5) of 
2016-03-20 on trouble, modified by Debian


Debian Jessie installation.



More information:
I didn't notice before, but hovering over a citation gives this message:

Error running timer `org-ref-link-message': (error #("abl-8 chicago 
limit:t does not seem to exist" 0 21 (fontified nil)))






--
Alan L Tyreehttp://www2.austlii.edu.au/~alan
Tel:  04 2748 6206  sip:typh...@iptel.org

[O] HTML Export problem with org-ref

[Alan L Tyree]

I'm trying to export a large document (about 600 printed a4 pages) to 
html. It contains a lot of references.


The export fails with this message:

byte-code: abl-8 chicago limit:t does not seem to exist

Because of the "chicago", I am presuming that the failure is in my setup 
of org-ref, but I can't seem to find any info on it.


What information can I provide to help track this down? any help greatly 
appreciated.


Cheers,

Alan

Org mode version 9.0.4 (9.0.4-elpaplus @ 
/home/alant/.emacs.d/elpa/org-plus-contrib-20170124/)


GNU Emacs 24.5.1 (x86_64-pc-linux-gnu, GTK+ Version 3.14.5) of 
2016-03-20 on trouble, modified by Debian


Debian Jessie installation.


--
Alan L Tyreehttp://www2.austlii.edu.au/~alan
Tel:  04 2748 6206  sip:typh...@iptel.org

Re: [O] Problem with org-ref

[John Kitchin]

What about the value of org-ref-pdf-directory. This seems to be where your
error is coming from. Your debugger info suggests it is set to nil.

Debugger entered--Lisp error: (wrong-type-argument stringp nil)
  file-name-as-directory(nil)
  org-ref-open-bibtex-notes()
  doi-utils-insert-bibtex-entry-fr

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 Thu, Dec 24, 2015 at 10:16 PM, Andreas Kiermeier <
andreas.kierme...@gmail.com> wrote:

> I've set the HOME environment variable to "C:/Users/andre_000/Documents"
> and hence need the .. to get into the Dropbox folder.
>
> Executing (find-file org-ref-bibliography-notes) does find and open the
> correct notes file.
>
> Using an absolute path, as in:
>
> (setq org-ref-bibliography-notes
> "C:/Users/andre_000/Dropbox/_biblio/org-ref/bibnotes.org"
>   org-ref-default-bibliography
> '("C:/Users/andre_000/Dropbox/_biblio/refs.bib"))
>
> results in the same error.
>
> After dropping a PDF file into the .bib file I end up with the following
> additional entry (for example) in the bibnotes.org file. I thought I'd
> include it just to ensure that nothing gets chopped of - this entry
> correctly reflect the PDF.
>
> ** TODO 2007 - Taenia Saginata in Europe
>  :PROPERTIES:
>   :Custom_ID: dorny_2007
>   :AUTHOR: Dorny \& Praet
>   :JOURNAL: Veterinary Parasitology
>   :YEAR: 2007
>   :VOLUME: 149
>   :PAGES: 22-24
>   :DOI: 10.1016/j.vetpar.2007.07.004
>   :URL: http://dx.doi.org/10.1016/j.vetpar.2007.07.004
>  :END:
>
> Does the notes file need a specific set up in terms of headers etc?
>
>
> --
> Dr Andreas Kiermeier | Director
> Statistical Process Improvement Consulting and Training Pty Ltd
> Mbl: +61 (4)23 028 565 | Email: andreas.kierme...@gmail.com
> Australia
>
> On 25 December 2015 at 13:17, John Kitchin 
> wrote:
>
>> That is an odd looking path. On Mac that would expand to something like
>>
>> /Users/Dropbox/_biblio/org-ref/bibnotes.org
>>
>> and on linux
>>
>> /home/Dropbox/_biblio/org-ref/bibnotes.org
>>
>> usually you should not have permission for that, and neither make sense
>> to me.
>>
>> Does (file-exists-p org-ref-bibliography-notes) return true?
>>
>> or alternatively does (find-file org-ref-bibliography-notes) actually
>> open a writable file?
>>
>> I would think this is what you want (unless you have some unusual setup
>> and permissions):
>>
>> (setq org-ref-bibliography-notes "~/Dropbox/_biblio/org-ref/bibnotes.org"
>>org-ref-default-bibliography '("~/Dropbox/_biblio/refs.bib"))
>>
>> i.e. no .. in the path.
>>
>> Andreas Kiermeier writes:
>>
>> > Hi John,
>> >
>> > I've set it at follows (based on your setup) in my init.el file:
>> >
>> > (setq org-ref-bibliography-notes "~/../Dropbox/_biblio/org-ref/
>> bibnotes.org"
>> >   org-ref-default-bibliography '("~/../Dropbox/_biblio/refs.bib"))
>> >
>> > So, non-nil.
>> >
>> > Andreas
>> >
>> > On 25 December 2015 at 00:45, John Kitchin 
>> wrote:
>> >
>> >>
>> >> On Thu, Dec 24, 2015 at 1:04 AM, Andreas Kiermeier <
>> >> andreas.kierme...@gmail.com> wrote:
>> >>
>> >>> org-ref-open-bibtex-notes()
>> >>
>> >>
>> >> That looks like a different error that occurs in
>> org-ref-open-bibtex-notes().
>> >> Up to that point everything looks normal.
>> >>
>> >> What do you have your org-ref-bibliography-notes variable set to? The
>> >> default value is nil which would cause that error.
>> >>
>> >>
>> >>
>> >> 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
>> >>
>> >>
>>
>> --
>> 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
>>
>
>

Re: [O] Problem with org-ref

[Andreas Kiermeier]

Thanks John.

Yes, that was the case, because I had no intention of downloading the pdfs.
So I had set

(setq doi-utils-download-pdf nil)

and left org-ref-pdf-directory nil. Setting it to a valid directory gets
rid of the error. Thanks.

I would find it useful (given that I've disabled auto-download) if I was
prompted for the location of the pdf. That way I could either (a) provide a
link to the pdf wherever I've stored it, or (b) not provide a link (yet).
Just a thought.

Thanks again for all your help.

Andreas

On 26 December 2015 at 00:37, John Kitchin  wrote:

> What about the value of org-ref-pdf-directory. This seems to be where your
> error is coming from. Your debugger info suggests it is set to nil.
>
> Debugger entered--Lisp error: (wrong-type-argument stringp nil)
>   file-name-as-directory(nil)
>   org-ref-open-bibtex-notes()
>   doi-utils-insert-bibtex-entry-fr
>
> 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 Thu, Dec 24, 2015 at 10:16 PM, Andreas Kiermeier <
> andreas.kierme...@gmail.com> wrote:
>
>> I've set the HOME environment variable to "C:/Users/andre_000/Documents"
>> and hence need the .. to get into the Dropbox folder.
>>
>> Executing (find-file org-ref-bibliography-notes) does find and open the
>> correct notes file.
>>
>> Using an absolute path, as in:
>>
>> (setq org-ref-bibliography-notes
>> "C:/Users/andre_000/Dropbox/_biblio/org-ref/bibnotes.org"
>>   org-ref-default-bibliography
>> '("C:/Users/andre_000/Dropbox/_biblio/refs.bib"))
>>
>> results in the same error.
>>
>> After dropping a PDF file into the .bib file I end up with the following
>> additional entry (for example) in the bibnotes.org file. I thought I'd
>> include it just to ensure that nothing gets chopped of - this entry
>> correctly reflect the PDF.
>>
>> ** TODO 2007 - Taenia Saginata in Europe
>>  :PROPERTIES:
>>   :Custom_ID: dorny_2007
>>   :AUTHOR: Dorny \& Praet
>>   :JOURNAL: Veterinary Parasitology
>>   :YEAR: 2007
>>   :VOLUME: 149
>>   :PAGES: 22-24
>>   :DOI: 10.1016/j.vetpar.2007.07.004
>>   :URL: http://dx.doi.org/10.1016/j.vetpar.2007.07.004
>>  :END:
>>
>> Does the notes file need a specific set up in terms of headers etc?
>>
>>
>> --
>> Dr Andreas Kiermeier | Director
>> Statistical Process Improvement Consulting and Training Pty Ltd
>> Mbl: +61 (4)23 028 565 | Email: andreas.kierme...@gmail.com
>> Australia
>>
>> On 25 December 2015 at 13:17, John Kitchin 
>> wrote:
>>
>>> That is an odd looking path. On Mac that would expand to something like
>>>
>>> /Users/Dropbox/_biblio/org-ref/bibnotes.org
>>>
>>> and on linux
>>>
>>> /home/Dropbox/_biblio/org-ref/bibnotes.org
>>>
>>> usually you should not have permission for that, and neither make sense
>>> to me.
>>>
>>> Does (file-exists-p org-ref-bibliography-notes) return true?
>>>
>>> or alternatively does (find-file org-ref-bibliography-notes) actually
>>> open a writable file?
>>>
>>> I would think this is what you want (unless you have some unusual setup
>>> and permissions):
>>>
>>> (setq org-ref-bibliography-notes "~/Dropbox/_biblio/org-ref/bibnotes.org
>>> "
>>>org-ref-default-bibliography '("~/Dropbox/_biblio/refs.bib"))
>>>
>>> i.e. no .. in the path.
>>>
>>> Andreas Kiermeier writes:
>>>
>>> > Hi John,
>>> >
>>> > I've set it at follows (based on your setup) in my init.el file:
>>> >
>>> > (setq org-ref-bibliography-notes "~/../Dropbox/_biblio/org-ref/
>>> bibnotes.org"
>>> >   org-ref-default-bibliography '("~/../Dropbox/_biblio/refs.bib"))
>>> >
>>> > So, non-nil.
>>> >
>>> > Andreas
>>> >
>>> > On 25 December 2015 at 00:45, John Kitchin 
>>> wrote:
>>> >
>>> >>
>>> >> On Thu, Dec 24, 2015 at 1:04 AM, Andreas Kiermeier <
>>> >> andreas.kierme...@gmail.com> wrote:
>>> >>
>>> >>> org-ref-open-bibtex-notes()
>>> >>
>>> >>
>>> >> That looks like a different error that occurs in
>>> org-ref-open-bibtex-notes().
>>> >> Up to that point everything looks normal.
>>> >>
>>> >> What do you have your org-ref-bibliography-notes variable set to? The
>>> >> default value is nil which would cause that error.
>>> >>
>>> >>
>>> >>
>>> >> 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
>>> >>
>>> >>
>>>
>>> --
>>> 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
>>>
>>
>>
>

Re: [O] Problem with org-ref

[Andreas Kiermeier]

Magic!
Thanks a lot, John.

On 26 December 2015 at 12:06, John Kitchin  wrote:

> That sounds ok. I pushed a change that sort of does what you ask for. If
> the "calculated" pdf doesn't exist then you should get prompted for a pdf,
> and pressing enter for the default (no pdf) should not add a pdf link.
>
> 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 Fri, Dec 25, 2015 at 7:03 PM, Andreas Kiermeier <
> andreas.kierme...@gmail.com> wrote:
>
>> Thanks John.
>>
>> Yes, that was the case, because I had no intention of downloading the
>> pdfs. So I had set
>>
>> (setq doi-utils-download-pdf nil)
>>
>> and left org-ref-pdf-directory nil. Setting it to a valid directory gets
>> rid of the error. Thanks.
>>
>> I would find it useful (given that I've disabled auto-download) if I was
>> prompted for the location of the pdf. That way I could either (a) provide a
>> link to the pdf wherever I've stored it, or (b) not provide a link (yet).
>> Just a thought.
>>
>> Thanks again for all your help.
>>
>> Andreas
>>
>> On 26 December 2015 at 00:37, John Kitchin 
>> wrote:
>>
>>> What about the value of org-ref-pdf-directory. This seems to be where
>>> your error is coming from. Your debugger info suggests it is set to nil.
>>>
>>> Debugger entered--Lisp error: (wrong-type-argument stringp nil)
>>>   file-name-as-directory(nil)
>>>   org-ref-open-bibtex-notes()
>>>   doi-utils-insert-bibtex-entry-fr
>>>
>>> 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 Thu, Dec 24, 2015 at 10:16 PM, Andreas Kiermeier <
>>> andreas.kierme...@gmail.com> wrote:
>>>
 I've set the HOME environment variable to
 "C:/Users/andre_000/Documents" and hence need the .. to get into the
 Dropbox folder.

 Executing (find-file org-ref-bibliography-notes) does find and open
 the correct notes file.

 Using an absolute path, as in:

 (setq org-ref-bibliography-notes
 "C:/Users/andre_000/Dropbox/_biblio/org-ref/bibnotes.org"
   org-ref-default-bibliography
 '("C:/Users/andre_000/Dropbox/_biblio/refs.bib"))

 results in the same error.

 After dropping a PDF file into the .bib file I end up with the
 following additional entry (for example) in the bibnotes.org file. I
 thought I'd include it just to ensure that nothing gets chopped of - this
 entry correctly reflect the PDF.

 ** TODO 2007 - Taenia Saginata in Europe
  :PROPERTIES:
   :Custom_ID: dorny_2007
   :AUTHOR: Dorny \& Praet
   :JOURNAL: Veterinary Parasitology
   :YEAR: 2007
   :VOLUME: 149
   :PAGES: 22-24
   :DOI: 10.1016/j.vetpar.2007.07.004
   :URL: http://dx.doi.org/10.1016/j.vetpar.2007.07.004
  :END:

 Does the notes file need a specific set up in terms of headers etc?


 --
 Dr Andreas Kiermeier | Director
 Statistical Process Improvement Consulting and Training Pty Ltd
 Mbl: +61 (4)23 028 565 | Email: andreas.kierme...@gmail.com
 Australia

 On 25 December 2015 at 13:17, John Kitchin 
 wrote:

> That is an odd looking path. On Mac that would expand to something like
>
> /Users/Dropbox/_biblio/org-ref/bibnotes.org
>
> and on linux
>
> /home/Dropbox/_biblio/org-ref/bibnotes.org
>
> usually you should not have permission for that, and neither make sense
> to me.
>
> Does (file-exists-p org-ref-bibliography-notes) return true?
>
> or alternatively does (find-file org-ref-bibliography-notes) actually
> open a writable file?
>
> I would think this is what you want (unless you have some unusual setup
> and permissions):
>
> (setq org-ref-bibliography-notes "~/Dropbox/_biblio/org-ref/
> bibnotes.org"
>org-ref-default-bibliography '("~/Dropbox/_biblio/refs.bib"))
>
> i.e. no .. in the path.
>
> Andreas Kiermeier writes:
>
> > Hi John,
> >
> > I've set it at follows (based on your setup) in my init.el file:
> >
> > (setq org-ref-bibliography-notes "~/../Dropbox/_biblio/org-ref/
> bibnotes.org"
> >   org-ref-default-bibliography
> '("~/../Dropbox/_biblio/refs.bib"))
> >
> > So, non-nil.
> >
> > Andreas
> >
> > On 25 December 2015 at 00:45, John Kitchin 
> wrote:
> >
> >>
> >> On Thu, Dec 24, 2015 at 1:04 AM, Andreas Kiermeier <
> >> andreas.kierme...@gmail.com> wrote:
> >>
> >>> 

Re: [O] Problem with org-ref

[John Kitchin]

That sounds ok. I pushed a change that sort of does what you ask for. If
the "calculated" pdf doesn't exist then you should get prompted for a pdf,
and pressing enter for the default (no pdf) should not add a pdf link.

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 Fri, Dec 25, 2015 at 7:03 PM, Andreas Kiermeier <
andreas.kierme...@gmail.com> wrote:

> Thanks John.
>
> Yes, that was the case, because I had no intention of downloading the
> pdfs. So I had set
>
> (setq doi-utils-download-pdf nil)
>
> and left org-ref-pdf-directory nil. Setting it to a valid directory gets
> rid of the error. Thanks.
>
> I would find it useful (given that I've disabled auto-download) if I was
> prompted for the location of the pdf. That way I could either (a) provide a
> link to the pdf wherever I've stored it, or (b) not provide a link (yet).
> Just a thought.
>
> Thanks again for all your help.
>
> Andreas
>
> On 26 December 2015 at 00:37, John Kitchin 
> wrote:
>
>> What about the value of org-ref-pdf-directory. This seems to be where
>> your error is coming from. Your debugger info suggests it is set to nil.
>>
>> Debugger entered--Lisp error: (wrong-type-argument stringp nil)
>>   file-name-as-directory(nil)
>>   org-ref-open-bibtex-notes()
>>   doi-utils-insert-bibtex-entry-fr
>>
>> 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 Thu, Dec 24, 2015 at 10:16 PM, Andreas Kiermeier <
>> andreas.kierme...@gmail.com> wrote:
>>
>>> I've set the HOME environment variable to "C:/Users/andre_000/Documents"
>>> and hence need the .. to get into the Dropbox folder.
>>>
>>> Executing (find-file org-ref-bibliography-notes) does find and open the
>>> correct notes file.
>>>
>>> Using an absolute path, as in:
>>>
>>> (setq org-ref-bibliography-notes
>>> "C:/Users/andre_000/Dropbox/_biblio/org-ref/bibnotes.org"
>>>   org-ref-default-bibliography
>>> '("C:/Users/andre_000/Dropbox/_biblio/refs.bib"))
>>>
>>> results in the same error.
>>>
>>> After dropping a PDF file into the .bib file I end up with the following
>>> additional entry (for example) in the bibnotes.org file. I thought I'd
>>> include it just to ensure that nothing gets chopped of - this entry
>>> correctly reflect the PDF.
>>>
>>> ** TODO 2007 - Taenia Saginata in Europe
>>>  :PROPERTIES:
>>>   :Custom_ID: dorny_2007
>>>   :AUTHOR: Dorny \& Praet
>>>   :JOURNAL: Veterinary Parasitology
>>>   :YEAR: 2007
>>>   :VOLUME: 149
>>>   :PAGES: 22-24
>>>   :DOI: 10.1016/j.vetpar.2007.07.004
>>>   :URL: http://dx.doi.org/10.1016/j.vetpar.2007.07.004
>>>  :END:
>>>
>>> Does the notes file need a specific set up in terms of headers etc?
>>>
>>>
>>> --
>>> Dr Andreas Kiermeier | Director
>>> Statistical Process Improvement Consulting and Training Pty Ltd
>>> Mbl: +61 (4)23 028 565 | Email: andreas.kierme...@gmail.com
>>> Australia
>>>
>>> On 25 December 2015 at 13:17, John Kitchin 
>>> wrote:
>>>
 That is an odd looking path. On Mac that would expand to something like

 /Users/Dropbox/_biblio/org-ref/bibnotes.org

 and on linux

 /home/Dropbox/_biblio/org-ref/bibnotes.org

 usually you should not have permission for that, and neither make sense
 to me.

 Does (file-exists-p org-ref-bibliography-notes) return true?

 or alternatively does (find-file org-ref-bibliography-notes) actually
 open a writable file?

 I would think this is what you want (unless you have some unusual setup
 and permissions):

 (setq org-ref-bibliography-notes "~/Dropbox/_biblio/org-ref/
 bibnotes.org"
org-ref-default-bibliography '("~/Dropbox/_biblio/refs.bib"))

 i.e. no .. in the path.

 Andreas Kiermeier writes:

 > Hi John,
 >
 > I've set it at follows (based on your setup) in my init.el file:
 >
 > (setq org-ref-bibliography-notes "~/../Dropbox/_biblio/org-ref/
 bibnotes.org"
 >   org-ref-default-bibliography '("~/../Dropbox/_biblio/refs.bib"))
 >
 > So, non-nil.
 >
 > Andreas
 >
 > On 25 December 2015 at 00:45, John Kitchin 
 wrote:
 >
 >>
 >> On Thu, Dec 24, 2015 at 1:04 AM, Andreas Kiermeier <
 >> andreas.kierme...@gmail.com> wrote:
 >>
 >>> org-ref-open-bibtex-notes()
 >>
 >>
 >> That looks like a different error that occurs in
 org-ref-open-bibtex-notes().
 >> Up to that point everything looks normal.
 >>
 >> What do you have your org-ref-bibliography-notes variable set to? The
 >> default value 

Re: [O] Problem with org-ref

[John Kitchin]

That is an odd looking path. On Mac that would expand to something like

/Users/Dropbox/_biblio/org-ref/bibnotes.org

and on linux

/home/Dropbox/_biblio/org-ref/bibnotes.org

usually you should not have permission for that, and neither make sense
to me.

Does (file-exists-p org-ref-bibliography-notes) return true?

or alternatively does (find-file org-ref-bibliography-notes) actually
open a writable file?

I would think this is what you want (unless you have some unusual setup
and permissions):

(setq org-ref-bibliography-notes "~/Dropbox/_biblio/org-ref/bibnotes.org"
   org-ref-default-bibliography '("~/Dropbox/_biblio/refs.bib"))

i.e. no .. in the path.

Andreas Kiermeier writes:

> Hi John,
>
> I've set it at follows (based on your setup) in my init.el file:
>
> (setq org-ref-bibliography-notes "~/../Dropbox/_biblio/org-ref/bibnotes.org"
>   org-ref-default-bibliography '("~/../Dropbox/_biblio/refs.bib"))
>
> So, non-nil.
>
> Andreas
>
> On 25 December 2015 at 00:45, John Kitchin  wrote:
>
>>
>> On Thu, Dec 24, 2015 at 1:04 AM, Andreas Kiermeier <
>> andreas.kierme...@gmail.com> wrote:
>>
>>> org-ref-open-bibtex-notes()
>>
>>
>> That looks like a different error that occurs in  
>> org-ref-open-bibtex-notes().
>> Up to that point everything looks normal.
>>
>> What do you have your org-ref-bibliography-notes variable set to? The
>> default value is nil which would cause that error.
>>
>>
>>
>> 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
>>
>>

--
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

Re: [O] Problem with org-ref

[Andreas Kiermeier]

I've set the HOME environment variable to "C:/Users/andre_000/Documents"
and hence need the .. to get into the Dropbox folder.

Executing (find-file org-ref-bibliography-notes) does find and open the
correct notes file.

Using an absolute path, as in:

(setq org-ref-bibliography-notes
"C:/Users/andre_000/Dropbox/_biblio/org-ref/bibnotes.org"
  org-ref-default-bibliography
'("C:/Users/andre_000/Dropbox/_biblio/refs.bib"))

results in the same error.

After dropping a PDF file into the .bib file I end up with the following
additional entry (for example) in the bibnotes.org file. I thought I'd
include it just to ensure that nothing gets chopped of - this entry
correctly reflect the PDF.

** TODO 2007 - Taenia Saginata in Europe
 :PROPERTIES:
  :Custom_ID: dorny_2007
  :AUTHOR: Dorny \& Praet
  :JOURNAL: Veterinary Parasitology
  :YEAR: 2007
  :VOLUME: 149
  :PAGES: 22-24
  :DOI: 10.1016/j.vetpar.2007.07.004
  :URL: http://dx.doi.org/10.1016/j.vetpar.2007.07.004
 :END:

Does the notes file need a specific set up in terms of headers etc?


-- 
Dr Andreas Kiermeier | Director
Statistical Process Improvement Consulting and Training Pty Ltd
Mbl: +61 (4)23 028 565 | Email: andreas.kierme...@gmail.com
Australia

On 25 December 2015 at 13:17, John Kitchin  wrote:

> That is an odd looking path. On Mac that would expand to something like
>
> /Users/Dropbox/_biblio/org-ref/bibnotes.org
>
> and on linux
>
> /home/Dropbox/_biblio/org-ref/bibnotes.org
>
> usually you should not have permission for that, and neither make sense
> to me.
>
> Does (file-exists-p org-ref-bibliography-notes) return true?
>
> or alternatively does (find-file org-ref-bibliography-notes) actually
> open a writable file?
>
> I would think this is what you want (unless you have some unusual setup
> and permissions):
>
> (setq org-ref-bibliography-notes "~/Dropbox/_biblio/org-ref/bibnotes.org"
>org-ref-default-bibliography '("~/Dropbox/_biblio/refs.bib"))
>
> i.e. no .. in the path.
>
> Andreas Kiermeier writes:
>
> > Hi John,
> >
> > I've set it at follows (based on your setup) in my init.el file:
> >
> > (setq org-ref-bibliography-notes "~/../Dropbox/_biblio/org-ref/
> bibnotes.org"
> >   org-ref-default-bibliography '("~/../Dropbox/_biblio/refs.bib"))
> >
> > So, non-nil.
> >
> > Andreas
> >
> > On 25 December 2015 at 00:45, John Kitchin 
> wrote:
> >
> >>
> >> On Thu, Dec 24, 2015 at 1:04 AM, Andreas Kiermeier <
> >> andreas.kierme...@gmail.com> wrote:
> >>
> >>> org-ref-open-bibtex-notes()
> >>
> >>
> >> That looks like a different error that occurs in
> org-ref-open-bibtex-notes().
> >> Up to that point everything looks normal.
> >>
> >> What do you have your org-ref-bibliography-notes variable set to? The
> >> default value is nil which would cause that error.
> >>
> >>
> >>
> >> 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
> >>
> >>
>
> --
> 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
>

Re: [O] Problem with org-ref

[Andreas Kiermeier]

Hi John,

I've set it at follows (based on your setup) in my init.el file:

(setq org-ref-bibliography-notes "~/../Dropbox/_biblio/org-ref/bibnotes.org"
  org-ref-default-bibliography '("~/../Dropbox/_biblio/refs.bib"))

So, non-nil.

Andreas​

On 25 December 2015 at 00:45, John Kitchin  wrote:

>
> On Thu, Dec 24, 2015 at 1:04 AM, Andreas Kiermeier <
> andreas.kierme...@gmail.com> wrote:
>
>> org-ref-open-bibtex-notes()
>
>
> That looks like a different error that occurs in  org-ref-open-bibtex-notes().
> Up to that point everything looks normal.
>
> What do you have your org-ref-bibliography-notes variable set to? The
> default value is nil which would cause that error.
>
>
>
> 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
>
>

Re: [O] Problem with org-ref

[John Kitchin]

On Thu, Dec 24, 2015 at 1:04 AM, Andreas Kiermeier <
andreas.kierme...@gmail.com> wrote:

> org-ref-open-bibtex-notes()


That looks like a different error that occurs in  org-ref-open-bibtex-notes().
Up to that point everything looks normal.

What do you have your org-ref-bibliography-notes variable set to? The
default value is nil which would cause that error.



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

Re: [O] Problem with org-ref

[marvin doyley]

Hi John,I am using a Mac too, and pdftotext seem to be working, well for an ocr file (see below) if I run pdftotext on the original pdf I get nothing.cheers,MPS I am using brew poppler, which includes pdftotext On Dec 23, 2015, at 4:30 PM, John Kitchin  wrote:Thanks! Do you know if you have pdftotext working on your machine? The pdf drag-n-drop works by converting the pdf to text, and than matching a pattern to find a doi. If none is found, you get the message you noted. The url dnd works similarly, but there are a bunch of recipes for what to match depending on the base of the url.I did that on a Mac, and I haven't tested it on a windows or Linux machine. JohnO~

This is an open access article published under an ACS Authorchoice License 
which permits
copyingand redistribution ofthe article or any adaptations 
fornon-commercialpurposes.

ACS
rditers' Choice

r

e

pubs.acs.org/acscatalysis

Examples of Effective Data Sharing in Scientific Publishing
John R. Kitchin*
Department of Chemical Engineering, Carnegie Mellon University, 5000 Forbes 
Avenue, Pittsburgh, Pennsylvania 15213,
United States

6 Supporting Information
ABSTRACT: We present a perspective on an approach to data sharing in scientific 
publications we have been developing in our group.
The essence of the approach is that data can be embedded in a human-readable 
and machine-addressable way within the traditional
publishing environment. We show this by example for both computational and 
experimental data. We articulate a need for new authoring
tools to facilitate data sharing, and we discuss the tools we have been 
developing for this purpose. With these tools, data generation,
analysis, and manuscript preparation can be deeply integrated, resulting in 
easier and better data sharing in scientific publications.

1. INTRODUCTION

a)Q

Data sharing and m anagement plans are becoming an
increasingly important requirement for scientific research. The
1
National Science Foundation requires a data management plan
for all proposals and has a formal statement on data sharing.
The Department of Energy is beginning to require this in some
proposals and has issued a formal statement on data management. Th e N ational 
Institutes of Health has a formal data
sharing policy.4 These mandates do not usually say how the data
management plan must be implemented, simply that there must
be one that is appropriate for the data being generated and
consistent with the needs of the scientific field.
There are several challenges to meeting these requirements.
Data is a generic term that refers to a broad range of information that varies 
in size and complexity. There is no single
solution that fits all data. The tools we use to write manuscripts,
which has been the primary mode of data sharing for decades
typically only include graphical or tabular data. Those data
are usually not machine readable nor are they easy to reuse. We
believe that progress in data sharing will require the development of new tools 
and social expectations about scientific data.
T hese tools will have to i n tegrate data directly into t h e
manuscripts and into the manuscript preparation workflow,
so that by the time one finishes writing the manuscript, the data
is already integrated and ready to share with no further work
required. When this is possible, data will be shared much more
frequently.
In this Viewpoint, we illustrate an example of a method we
have been developing that enables data, analysis, and code
sharing within the traditional publishing environment. We have
published several papers this way already including experimental
5
6
work, combined computational and experimental work, and
computational work. ' T hese manuscripts in published form
are indistinguishable from other manuscripts in those journals.
However, the Supporting Information files are very difFerent.
Although, at first glance, the Supporting Information files are
simple PDF files that provide additional information, there
are actually data files embedded (see Figure I a ) in those
PDFs which can be extracted and reused. The data is human
readable in most cases, and machine addressable, enabling
reuse and sharing. We will provide an example of this for a

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An embeddedfi
le
in the PDF

Figure 1. (a) The attachments in the Supporting Information of ref 11.
There are two attachments. (b) A single attachment in the PDF file.
Double-clicking on the thumbtack(in the Supporting Information file)
will open the attached file.

paper we recently published in ACS Catalysis on "Estimating
Bulk-Composition-Dependent Hz Adsorption Energies on
Cu„Pd, „Alloy (111) Surfaces"."
The Supporting Information file for that article is available for
free.' When opened in a 

Re: [O] Problem with org-ref

[Andreas Kiermeier]

Hi John,
similar doi problem here.
My configuration is:

   - Windows 10
   - GNU Emacs 24.5.1 (i686-pc-mingw32) of 2015-04-11 on LEG570
   - Miktex (up-to-date) with pdftotext v0.32..0
   - org-ref v 0.5.0 (from melpa)

Running pdftotext from the command line works and produces a text file with
doi info.
Let me know what I can do to help to test things.
Thanks.
Andreas
PS: Thank you for org-ref ... an awesome Xmas present!


On 24 December 2015 at 08:00, John Kitchin  wrote:

> Thanks! Do you know if you have pdftotext working on your machine? The pdf
> drag-n-drop works by converting the pdf to text, and than matching a
> pattern to find a doi. If none is found, you get the message you noted. The
> url dnd works similarly, but there are a bunch of recipes for what to match
> depending on the base of the url.
>
> I did that on a Mac, and I haven't tested it on a windows or Linux
> machine.
>
> 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 Wed, Dec 23, 2015 at 4:22 PM, marvin doyley 
> wrote:
>
>> Hi John,
>>
>> I am playing with org-ref,  the melpa version.
>>
>> Everything works fine except, one thing.  When I drag a pdf to an empty
>> bibtex file it doesn’t extract the doi ( no doi found in the file:///).
>> I tried it pdf you used  in your video (Examples of Effective Data Sharing
>> in Scientific Publishing), but I got the same error. Dragging the url to
>> the bibtex file also doesn’t works for me.
>>
>> cheers,
>> M
>>
>> PS by the way, your video was excellent :)
>>
>
>

Re: [O] Problem with org-ref

[John Kitchin]

I tested part of this on Windows in a git bash shell:

$ pdftotext -v
pdftotext version 0.14.5
Copyright 2005-2010 The Poppler Developers - http://poppler.freedesktop.org
Copyright 1996-2004 Glyph & Cog, LLC

and then this works:
$ pdftotext.exe kitchin-2015-examp.pdf - | grep DOI
ACS Catal., Just Accepted Manuscript • DOI: 10.1021/acscatal.5b00538 •
Publicati
on Date (Web): 11 May 2015
readers and citable by the Digital Object Identifier (DOI®). “Just
Accepted” is
an optional service offered
sharing site which assigned the data set a DOI. 19 An alternative data
repositor
y could be an
institutional data repository which also provides a DOI for citing. It
remains t
o be seen if
stores that provide a citable DOI for the data set. The point is that this
appro
ach is very

However, I see that in emacs, it appears another pdftotext is getting used,
which does not work.
~/Desktop $ pdftotext -v
pdftotext version 2.03
Copyright 1996-2003 Glyph & Cog, LLC

that is the same version that runs in a cmd shell.

The version that seems to work for me is at "C:\Program Files
(x86)\Git\bin\pdftotext".

I added a variable to set the location of this program, and then rely on
the executable path. It was a little tricky to set this right, note the
escaped quotes.

#+BEGIN_SRC emacs-lisp
(setq pdftotext-executable "\"C:/Program Files (x86)/Git/bin/pdftotext\"")
#+END_SRC


It turned out there was another issue with the uri in the drag-n-drop
needing to be unescaped on windows because of the : in the path, which is
also done now.

I pushed these out. hopefully that makes some progress for you! or at least
gives some hints on where to look for the problem.

Merry Xmas!

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 Wed, Dec 23, 2015 at 6:56 PM, Andreas Kiermeier <
andreas.kierme...@gmail.com> wrote:

> Hi John,
> similar doi problem here.
> My configuration is:
>
>- Windows 10
>- GNU Emacs 24.5.1 (i686-pc-mingw32) of 2015-04-11 on LEG570
>- Miktex (up-to-date) with pdftotext v0.32..0
>- org-ref v 0.5.0 (from melpa)
>
> Running pdftotext from the command line works and produces a text file
> with doi info.
> Let me know what I can do to help to test things.
> Thanks.
> Andreas
> PS: Thank you for org-ref ... an awesome Xmas present!
>
>
> On 24 December 2015 at 08:00, John Kitchin 
> wrote:
>
>> Thanks! Do you know if you have pdftotext working on your machine? The
>> pdf drag-n-drop works by converting the pdf to text, and than matching a
>> pattern to find a doi. If none is found, you get the message you noted. The
>> url dnd works similarly, but there are a bunch of recipes for what to match
>> depending on the base of the url.
>>
>> I did that on a Mac, and I haven't tested it on a windows or Linux
>> machine.
>>
>> 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 Wed, Dec 23, 2015 at 4:22 PM, marvin doyley 
>> wrote:
>>
>>> Hi John,
>>>
>>> I am playing with org-ref,  the melpa version.
>>>
>>> Everything works fine except, one thing.  When I drag a pdf to an empty
>>> bibtex file it doesn’t extract the doi ( no doi found in the file:///).
>>> I tried it pdf you used  in your video (Examples of Effective Data Sharing
>>> in Scientific Publishing), but I got the same error. Dragging the url to
>>> the bibtex file also doesn’t works for me.
>>>
>>> cheers,
>>> M
>>>
>>> PS by the way, your video was excellent :)
>>>
>>
>>
>

Re: [O] Problem with org-ref

[marvin doyley]

Hi John,
Its now working, it turns out the version of pdftotext that I was using wasn’t 
working well. I found different version (http://macappstore.org/pdftotext/ 
) that did the trick

cheers,
M

> On Dec 23, 2015, at 4:30 PM, John Kitchin  wrote:
> 
> Thanks! Do you know if you have pdftotext working on your machine? The pdf 
> drag-n-drop works by converting the pdf to text, and than matching a pattern 
> to find a doi. If none is found, you get the message you noted. The url dnd 
> works similarly, but there are a bunch of recipes for what to match depending 
> on the base of the url.
> 
> I did that on a Mac, and I haven't tested it on a windows or Linux machine. 
> 
> 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 Wed, Dec 23, 2015 at 4:22 PM, marvin doyley  > wrote:
> Hi John,
> 
> I am playing with org-ref,  the melpa version.
> 
> Everything works fine except, one thing.  When I drag a pdf to an empty 
> bibtex file it doesn’t extract the doi ( no doi found in the file:/// <>). I 
> tried it pdf you used  in your video (Examples of Effective Data Sharing in 
> Scientific Publishing), but I got the same error. Dragging the url to the 
> bibtex file also doesn’t works for me.
> 
> cheers,
> M
> 
> PS by the way, your video was excellent :)
> 

Re: [O] Problem with org-ref

[John Kitchin]

Thanks! Do you know if you have pdftotext working on your machine? The pdf
drag-n-drop works by converting the pdf to text, and than matching a
pattern to find a doi. If none is found, you get the message you noted. The
url dnd works similarly, but there are a bunch of recipes for what to match
depending on the base of the url.

I did that on a Mac, and I haven't tested it on a windows or Linux machine.

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 Wed, Dec 23, 2015 at 4:22 PM, marvin doyley  wrote:

> Hi John,
>
> I am playing with org-ref,  the melpa version.
>
> Everything works fine except, one thing.  When I drag a pdf to an empty
> bibtex file it doesn’t extract the doi ( no doi found in the file:///). I
> tried it pdf you used  in your video (Examples of Effective Data Sharing in
> Scientific Publishing), but I got the same error. Dragging the url to the
> bibtex file also doesn’t works for me.
>
> cheers,
> M
>
> PS by the way, your video was excellent :)
>

[O] Problem with org-ref

[marvin doyley]

Hi John,

I am playing with org-ref,  the melpa version.

Everything works fine except, one thing.  When I drag a pdf to an empty bibtex 
file it doesn’t extract the doi ( no doi found in the file:/// ). I 
tried it pdf you used  in your video (Examples of Effective Data Sharing in 
Scientific Publishing), but I got the same error. Dragging the url to the 
bibtex file also doesn’t works for me.

cheers,
M

PS by the way, your video was excellent :)

Re: [O] Problem with org-ref

[Andreas Kiermeier]

Hi John,

thanks for the quick feedback and fix. Yes, the version that comes with
GitHub (on Windows) works when set this way, though I had to specify
slightly differently (i.e quotes & backslashes):

(setq pdftotext-executable
"C:/Users/andre_000/AppData/Local/GitHub/PortableGit_c7e0cbde92ba565cb218a521411d0e854079a28c/mingw32/bin/pdftotext.exe")

But now the following error occurs, after inserting the new bibtex entry
and creating a new note (in the notes file):

org-ref-open-bibtex-notes: Wrong type argument: stringp, nil

Turning debugging on yields the following:

Debugger entered--Lisp error: (wrong-type-argument stringp nil)
  file-name-as-directory(nil)
  org-ref-open-bibtex-notes()
  doi-utils-insert-bibtex-entry-from-doi("10.1016/j.vetpar.2010.10.058")
  doi-utils-add-bibtex-entry-from-doi("10.1016/j.vetpar.2010.10.058"
"c:/Users/andre_000/Dropbox/_biblio/refs.bib")

org-ref-pdf-dnd-protocol("file:C%3A/Users/andre_000/Dropbox/Consulting/Projects/RedMeat/MLA_Beef_Measles-C_bovis/literature/VetPara_McFadden_2011.pdf"
private)
  byte-code(" \306 \211 \203%

Looks like something is still not quite right with the ":" in the pathname.

​Cheers,

Andreas​

On 24 December 2015 at 12:03, John Kitchin  wrote:

> I tested part of this on Windows in a git bash shell:
>
> $ pdftotext -v
> pdftotext version 0.14.5
> Copyright 2005-2010 The Poppler Developers -
> http://poppler.freedesktop.org
> Copyright 1996-2004 Glyph & Cog, LLC
>
> and then this works:
> $ pdftotext.exe kitchin-2015-examp.pdf - | grep DOI
> ACS Catal., Just Accepted Manuscript • DOI: 10.1021/acscatal.5b00538 •
> Publicati
> on Date (Web): 11 May 2015
> readers and citable by the Digital Object Identifier (DOI®). “Just
> Accepted” is
> an optional service offered
> sharing site which assigned the data set a DOI. 19 An alternative data
> repositor
> y could be an
> institutional data repository which also provides a DOI for citing. It
> remains t
> o be seen if
> stores that provide a citable DOI for the data set. The point is that this
> appro
> ach is very
>
> However, I see that in emacs, it appears another pdftotext is getting
> used, which does not work.
> ~/Desktop $ pdftotext -v
> pdftotext version 2.03
> Copyright 1996-2003 Glyph & Cog, LLC
>
> that is the same version that runs in a cmd shell.
>
> The version that seems to work for me is at "C:\Program Files
> (x86)\Git\bin\pdftotext".
>
> I added a variable to set the location of this program, and then rely on
> the executable path. It was a little tricky to set this right, note the
> escaped quotes.
>
> #+BEGIN_SRC emacs-lisp
> (setq pdftotext-executable "\"C:/Program Files (x86)/Git/bin/pdftotext\"")
> #+END_SRC
>
>
> It turned out there was another issue with the uri in the drag-n-drop
> needing to be unescaped on windows because of the : in the path, which is
> also done now.
>
> I pushed these out. hopefully that makes some progress for you! or at
> least gives some hints on where to look for the problem.
>
> Merry Xmas!
>
> 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 Wed, Dec 23, 2015 at 6:56 PM, Andreas Kiermeier <
> andreas.kierme...@gmail.com> wrote:
>
>> Hi John,
>> similar doi problem here.
>> My configuration is:
>>
>>- Windows 10
>>- GNU Emacs 24.5.1 (i686-pc-mingw32) of 2015-04-11 on LEG570
>>- Miktex (up-to-date) with pdftotext v0.32..0
>>- org-ref v 0.5.0 (from melpa)
>>
>> Running pdftotext from the command line works and produces a text file
>> with doi info.
>> Let me know what I can do to help to test things.
>> Thanks.
>> Andreas
>> PS: Thank you for org-ref ... an awesome Xmas present!
>>
>>
>> On 24 December 2015 at 08:00, John Kitchin 
>> wrote:
>>
>>> Thanks! Do you know if you have pdftotext working on your machine? The
>>> pdf drag-n-drop works by converting the pdf to text, and than matching a
>>> pattern to find a doi. If none is found, you get the message you noted. The
>>> url dnd works similarly, but there are a bunch of recipes for what to match
>>> depending on the base of the url.
>>>
>>> I did that on a Mac, and I haven't tested it on a windows or Linux
>>> machine.
>>>
>>> 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 Wed, Dec 23, 2015 at 4:22 PM, marvin doyley 
>>> wrote:
>>>
 Hi John,

 I am playing with org-ref,  the melpa version.

 Everything works fine except, one thing.  When I drag a pdf to an empty
 bibtex file it doesn’t extract the doi ( no doi found in the file:///).
 I tried it pdf