nothing happens on clicking a cite link #787
Comments
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Can you post the contents of the org-file that causes the error? If you run M-x org-ref in that file, does it have any output? What happens when you try to open a pdf? |
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Hi! Yes, a message is printed to the messages buffer: Well, I go to helm-bibtex directly, stand on a source and hit TAB, then f2 |
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an update: helm-bibtex does work (for opening pdfs from its menu), but cite links still don't. |
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I am seeing a similar error on opening Traceback from opening the cite link: |
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can you send me a small org file and bib file that shows this issue? |
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The org file the bib file @book{ahrensHowTakeSmart2017,
title = {How to Take Smart Notes: One Simple Technique to Boost Writing, Learning and Thinking: For Students, Academics and Nonfiction Book Writers},
shorttitle = {How to Take Smart Notes},
author = {Ahrens, Sönke},
date = {2017},
publisher = {{CreateSpace}},
location = {{North Charleston, SC}},
file = {/Users/user/Zotero/storage/NZ6D82FC/Ahrens - 2017 - How to take smart notes one simple technique to b.pdf},
isbn = {978-1-5428-6650-7},
langid = {english},
pagetotal = {170}
}
@thesis{lynaghComputationalAnalysisProtein2010,
title = {Computational Analysis of Protein Structures: Data Visualization, Vector Quantization, and Spectral Clustering},
author = {Lynagh, Kevin},
date = {2010},
institution = {{Reed College}},
file = {/Users/user/Zotero/storage/CNU3NH74/beautiful.pdf},
keywords = {algorithms,beautiful,biology,chemistry,computer science,LaTeX,typography},
type = {Bachelor Thesis}
} |
jkitchin
pushed a commit
that referenced
this issue
Dec 30, 2020
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The @thesis entry is not recognized by bibtex as a valid type, so it cannot find that entry. In the BibTeX dialect you get: One way you can probably solve this is to run this:
If you update to the new commit, you should be able to fix this with a line like this at the top of your bib file % -- mode:bibtex; eval: (bibtex-set-dialect 'biblatex t); -- or these at the bottom: @comment Local Variables: |
It would also help to see the bibtex file. |
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Thanks for the shove! Sounds obvious in retrospect... I will go with the |
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@J0ns4 and @fleimgruber I have pushed a totally new |
Closed
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The new |
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Hi,
I don't get any more informative error message from the newer version, but
I have found something strange - when I hit enter over a cite link in
org-ref's manual the actions menu pops up like it should, but for my own
links I still get '''org-ref-cite-candidates: Wrong type argument: stringp,
nil'''.
Does this help to make sense of something?
Thanks!
…On Sat, 2 Jan 2021 at 19:54, John Kitchin ***@***.***> wrote:
Closed #787 <#787>.
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I don't get a buffer, just the message at the bottom of the screen: I checked the repo, and the last commit there is 7adb762 from Dec. 31... The following is the file (though I see the same behavior in all of my file): and this is the .bib file: |
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@jonathan-sahar-tau as you do not have a bibliography link in the .org file, e.g. Also, could you evaluate |
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Thanks for the quick response!
```
org-ref-default-bibliography is a variable defined in org-ref-core.el.
Value
"~/google_drive/.notes/.bibliography/references.bib"
```
the backtrace shows:
```
Debugger entered--Lisp error: (wrong-type-argument stringp nil)
insert-file-contents(nil)
org-ref-cite-candidates()
org-ref-cite-click-helm(nil)
funcall(org-ref-cite-click-helm nil)
(lambda (_) (funcall org-ref-cite-onclick-function
nil))("amir19_simul_thoug_measur_study_inter")
funcall((lambda (_) (funcall org-ref-cite-onclick-function nil))
"amir19_simul_thoug_measur_study_inter")
(condition-case nil (funcall (org-link-get-parameter type :follow) path
arg) (wrong-number-of-arguments (funcall (org-link-get-parameter type
:follow) path)))
(progn (condition-case nil (funcall (org-link-get-parameter type :follow)
path arg) (wrong-number-of-arguments (funcall (org-link-get-parameter type
:follow) path))))
(if (functionp f) (progn (condition-case nil (funcall
(org-link-get-parameter type :follow) path arg) (wrong-number-of-arguments
(funcall (org-link-get-parameter type :follow) path)))))
(let ((f (org-link-get-parameter type :follow))) (if (functionp f) (progn
(condition-case nil (funcall (org-link-get-parameter type :follow) path
arg) (wrong-number-of-arguments (funcall (org-link-get-parameter type
:follow) path))))))
(cond ((equal type (quote "file")) (let* ((option (org-element-property
:search-option link)) (path (if option (concat path "::" option) path)))
(org-link-open-as-file path (let* ((val (org-element-property :application
link))) (cond (arg arg) ((equal val ...) (quote emacs)) ((equal val ...)
(quote system)) (t nil)))))) ((member type (quote ("radio" "fuzzy"
"custom-id" "coderef"))) (if (run-hook-with-args-until-success (quote
org-open-link-functions) path) nil (if (not arg) (org-mark-ring-push)
(switch-to-buffer-other-window (org-link--buffer-for-internals))) (let
((destination (save-excursion (save-restriction ... ... ...)))) (if (and
(<= (point-min) destination) (>= (point-max) destination)) nil (widen))
(goto-char destination)))) (t (let ((f (org-link-get-parameter type
:follow))) (if (functionp f) (progn (condition-case nil (funcall
(org-link-get-parameter type :follow) path arg) (wrong-number-of-arguments
(funcall ... path))))))))
(let ((type (org-element-property :type link)) (path
(org-element-property :path link))) (cond ((equal type (quote "file"))
(let* ((option (org-element-property :search-option link)) (path (if option
(concat path "::" option) path))) (org-link-open-as-file path (let* ((val
...)) (cond (arg arg) (... ...) (... ...) (t nil)))))) ((member type (quote
("radio" "fuzzy" "custom-id" "coderef"))) (if
(run-hook-with-args-until-success (quote org-open-link-functions) path) nil
(if (not arg) (org-mark-ring-push) (switch-to-buffer-other-window
(org-link--buffer-for-internals))) (let ((destination (save-excursion
...))) (if (and (<= ... destination) (>= ... destination)) nil (widen))
(goto-char destination)))) (t (let ((f (org-link-get-parameter type
:follow))) (if (functionp f) (progn (condition-case nil (funcall ... path
arg) (wrong-number-of-arguments ...))))))))
org-link-open((link (:type "cite" :path
"amir19_simul_thoug_measur_study_inter" :format plain :raw-link
"cite:amir19_simul_thoug_measur_study_inter" :application nil
:search-option nil :begin 293 :end 335 :contents-begin nil :contents-end
nil :post-blank 0 :parent (paragraph (:begin 293 :end 335 :contents-begin
293 :contents-end 335 :post-blank 0 :post-affiliated 293 :parent nil))))
nil)
(cond ((not type) (user-error "No link found")) ((memq type (quote
(comment comment-block node-property keyword))) (call-interactively
(function org-open-at-point-global))) ((memq type (quote (headline
inlinetask))) (org-match-line org-complex-heading-regexp) (let ((tags-beg
(match-beginning 5)) (tags-end (match-end 5))) (if (and tags-beg (>=
(point) tags-beg) (< (point) tags-end)) (org-tags-view arg (save-excursion
(let* (... ...) (buffer-substring ... ...)))) (let* ((val
(org-offer-links-in-entry ... ... arg))) (if (consp val) (let* (...) (if
... ... ...)) nil))))) ((or (eq type (quote footnote-reference)) (and (eq
type (quote footnote-definition)) (save-excursion (skip-chars-forward "
\011") (let ((begin ...)) (if begin (< ... begin) (= ... ...))))))
(org-footnote-action)) ((and (eq type (quote planning)) (org-in-regexp
org-ts-regexp-both nil t)) (org-follow-timestamp-link)) ((and (eq type
(quote clock)) value (>= (point) (org-element-property :begin value)) (<=
(point) (org-element-property :end value))) (org-follow-timestamp-link))
((eq type (quote src-block)) (org-babel-open-src-block-result)) ((>=
(point) (save-excursion (goto-char (org-element-property :end context))
(skip-chars-backward " \011") (point))) (user-error "No link found")) ((eq
type (quote inline-src-block)) (org-babel-open-src-block-result)) ((eq type
(quote timestamp)) (org-follow-timestamp-link)) ((eq type (quote link))
(org-link-open context arg)) (t (user-error "No link found")))
(let* ((context (org-element-lineage (org-element-context) (quote (clock
comment comment-block footnote-definition footnote-reference headline
inline-src-block inlinetask keyword link node-property planning src-block
timestamp)) t)) (type (org-element-type context)) (value
(org-element-property :value context))) (cond ((not type) (user-error "No
link found")) ((memq type (quote (comment comment-block node-property
keyword))) (call-interactively (function org-open-at-point-global))) ((memq
type (quote (headline inlinetask))) (org-match-line
org-complex-heading-regexp) (let ((tags-beg (match-beginning 5)) (tags-end
(match-end 5))) (if (and tags-beg (>= (point) tags-beg) (< (point)
tags-end)) (org-tags-view arg (save-excursion (let* ... ...))) (let* ((val
...)) (if (consp val) (let* ... ...) nil))))) ((or (eq type (quote
footnote-reference)) (and (eq type (quote footnote-definition))
(save-excursion (skip-chars-forward " \011") (let (...) (if begin ...
...))))) (org-footnote-action)) ((and (eq type (quote planning))
(org-in-regexp org-ts-regexp-both nil t)) (org-follow-timestamp-link))
((and (eq type (quote clock)) value (>= (point) (org-element-property
:begin value)) (<= (point) (org-element-property :end value)))
(org-follow-timestamp-link)) ((eq type (quote src-block))
(org-babel-open-src-block-result)) ((>= (point) (save-excursion (goto-char
(org-element-property :end context)) (skip-chars-backward " \011")
(point))) (user-error "No link found")) ((eq type (quote inline-src-block))
(org-babel-open-src-block-result)) ((eq type (quote timestamp))
(org-follow-timestamp-link)) ((eq type (quote link)) (org-link-open context
arg)) (t (user-error "No link found"))))
(if (run-hook-with-args-until-success (quote
org-open-at-point-functions)) nil (let* ((context (org-element-lineage
(org-element-context) (quote (clock comment comment-block
footnote-definition footnote-reference headline inline-src-block inlinetask
keyword link node-property planning src-block timestamp)) t)) (type
(org-element-type context)) (value (org-element-property :value context)))
(cond ((not type) (user-error "No link found")) ((memq type (quote (comment
comment-block node-property keyword))) (call-interactively (function
org-open-at-point-global))) ((memq type (quote (headline inlinetask)))
(org-match-line org-complex-heading-regexp) (let ((tags-beg
(match-beginning 5)) (tags-end (match-end 5))) (if (and tags-beg (>= ...
tags-beg) (< ... tags-end)) (org-tags-view arg (save-excursion ...)) (let*
(...) (if ... ... nil))))) ((or (eq type (quote footnote-reference)) (and
(eq type (quote footnote-definition)) (save-excursion (skip-chars-forward "
\011") (let ... ...)))) (org-footnote-action)) ((and (eq type (quote
planning)) (org-in-regexp org-ts-regexp-both nil t))
(org-follow-timestamp-link)) ((and (eq type (quote clock)) value (>=
(point) (org-element-property :begin value)) (<= (point)
(org-element-property :end value))) (org-follow-timestamp-link)) ((eq type
(quote src-block)) (org-babel-open-src-block-result)) ((>= (point)
(save-excursion (goto-char (org-element-property :end context))
(skip-chars-backward " \011") (point))) (user-error "No link found")) ((eq
type (quote inline-src-block)) (org-babel-open-src-block-result)) ((eq type
(quote timestamp)) (org-follow-timestamp-link)) ((eq type (quote link))
(org-link-open context arg)) (t (user-error "No link found")))))
org-open-at-point(nil)
```
…On Mon, 4 Jan 2021 at 13:47, fleimgruber ***@***.***> wrote:
@jonathan-sahar-tau <https://github.com/jonathan-sahar-tau> as you do not
have a bibliography link in the .org file, e.g. bibliography:library.bib,
the first question would probably be whether org-ref picks up the .bib file
you want. What is the value of org-ref-default-bibliography?
Also, could you evaluate (setq debug-on-error t) and provide the contents
of the *Backtrace* buffer to see where the error comes from within org-ref
?
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(which is the correct value) |
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It should be a list, as in ("~/google_drive/.notes/.bibliography/references.bib") and not a string. That is most likely the problem. |
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Amazing, it works!
Thank you so much for your patience - apologies for the uninspiring
underlying problem :))
…On Mon, 4 Jan 2021 at 15:23, John Kitchin ***@***.***> wrote:
It should be a list, as in
("~/google_drive/.notes/.bibliography/references.bib") and not a string.
That is most likely the problem.
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I apologize for opening an issue for this, but I'm really stuck and I can't get ahead..
I can insert bibliography links with org-ref-insert -link, but when hitting 'return' with the point on a link I get a message saying: "wrong type argument stringp, nil", with no reference to the function that throws the error, so I don't even know where to begin investigating... querying what 'return' does in that context only gives the general "org-dwim at point".
An additional problem which may be related, is that I can't get helm-bibtex to open the related pdf in emacs (something which used to work for me and broke somehow)
These are the relevant lines from my config (relating to org-ref and helm bibtex) :
I'd appreciate any help, thanks!
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