I have a working org-roam instance working which is absolutely fantastic. I am using org-roam-bibtex to insert citations and when I create a note for a bibtex entry it’s captured with citekey, author etc. All very nice.
The next thing I’m after is being able to open the pdf and have notes in noter (just like the youtube video).
When I run org-roam-bibtex (C-c ]) and selecting entry “2 open pdf” the buffer redirects to “/” root in dired, i.e. when I try to open a pdf it doesn’t find the pdf. This is with all entries so I’m pretty sure I’m doing something fundamentally wrong.
This is my init-orgroam.el file:
;; Roam Research Emacs
(use-package org-roam
:ensure t
:hook
(after-init . org-roam-mode)
:custom
(org-roam-directory "~/Org/slipbox/")
:bind (:map org-roam-mode-map
(("C-c n l" . org-roam)
("C-c n f" . org-roam-find-file)
("C-c n g" . org-roam-graph))
:map org-mode-map
(("C-c n i" . org-roam-insert))
(("C-c n I" . org-roam-insert-immediate))))
;; Allows for Org-roam to display in a web browser
(use-package org-roam-server
:ensure t
:config
(setq org-roam-server-host "127.0.0.1"
org-roam-server-port 8080
org-roam-server-authenticate nil
org-roam-server-export-inline-images t
org-roam-server-serve-files nil
org-roam-server-served-file-extensions '("pdf" "mp4" "ogv")
org-roam-server-network-poll t
org-roam-server-network-arrows nil
org-roam-server-network-label-truncate t
org-roam-server-network-label-truncate-length 60
org-roam-server-network-label-wrap-length 20))
;; Add bibliography and bibliographical notes to Org Roam
(use-package org-roam-bibtex
:ensure t
:hook (org-roam-mode . org-roam-bibtex-mode)
:bind (:map org-mode-map
(("C-c n a" . orb-note-actions)))
:config
(setq orb-preformat-keywords
'(("citekey" . "=key=") "title" "url" "file" "author-or-editor" "keywords"))
(setq orb-process-file-field t)
(setq orb-file-field-extensions "pdf")
(setq orb-templates
'(("r" "ref" plain (function org-roam-capture--get-point)
""
:file-name "literature/${citekey}"
:head "#+TITLE: ${citekey}: ${title}\n#+ROAM_KEY: ${ref}\n- tags ::\n- keywords :: ${keywords}\n* ${title}\n:PROPERTIES:\n:Custom_ID: ${citekey}\n:URL: ${url}\n:AUTHOR: ${author-or-editor}\n:NOTER_DOCUMENT: ${file}\n:NOTER_PAGE:\n:END:"))))
(use-package company-org-roam
:ensure t
:config
(push 'company-org-roam company-backends))
(provide 'init-orgroam)
Sorry, I would not be able to read all your config, but that’s what I notice.
I have written an article on PDF-Tools, Org-noter, and ORB. It was done on Windows; I believe it would be applicable if you are on a different OS.
Firstly, nobiot, thank you for your guides. I used it when I first started with org-roam and it was an invaluable resource. So thank you very much.
I replaced
":NOTER_DOCUMENT: ${file}\n"
with :NOTER_DOCUMENT: %(orb-process-file-field \"${citekey}\")
and still the same result.
Here is an bibtex entry I am trying to access @article{wolfmoon12,
title = {"{{The Moon}} over the {{Mountain}}": {{Stories}} by {{Atsushi Nakajima}} by {{Paul McCarthy}} and {{Nobuko Ochner}} (Review)},
shorttitle = {"{{The Moon}} over the {{Mountain}}"},
author = {Wolf, Charles De},
date = {2012},
journaltitle = {Monumenta Nipponica},
volume = {67},
pages = {371–374},
publisher = {{Sophia University}},
issn = {1880-1390},
doi = {10.1353/mni.2012.0021},
file = {files/1450/Wolf - 2012 - The Moon over the Mountain Stories by Atsushi N.pdf},
langid = {english},
number = {2}
}
EDIT:
#+TITLE: wolfmoon12: The Moon over the Mountain": Stories by Atsushi Nakajima by Paul McCarthy and Nobuko Ochner (review)
#+ROAM_KEY: cite:wolfmoon12
- tags ::
- keywords ::
* The Moon over the Mountain": Stories by Atsushi Nakajima by Paul McCarthy and Nobuko Ochner (review)
:PROPERTIES:
:Custom_ID: wolfmoon12
:URL:
:AUTHOR: Wolf, C. D.
:NOTER_DOCUMENT: files/1450/Wolf - 2012 - The Moon over the Mountain Stories by Atsushi N.pdf
:NOTER_PAGE:
:END:
If not, I think your Emacs (org-ref, helm-bibtex, one of them) does not recognize the PDF stored in this path: file = {files/1450/Wolf - 2012 - The Moon over the Mountain Stories by Atsushi N.pdf},
My bibtex entry for the example above looks like this:
I’m on Windows, so yours may have “/” instead of “\” in the path. As you can see, it’s a full path to the corresponding PDF (and html) files.
Is your path reachable? files/1450/Wolf - 2012 - The Moon over the Mountain Stories by Atsushi N.pdf – I’m guessing this is supposed to be a relative path from… somewhere?
Maybe you could manually change it to its full absolute path manually and see if that would work (you may need to relaunch org-ref / helm-bibtex to get it parse .bib again (or relaunch Emacs altogether).
@nobiot, right. ORB has been recently updated to include a more user friendly option ${file} instead of more verbose %(orb-process-file-field \"${citekey}\").
The problem with @sinqbad’s config is that you set the wrong variable. You should put the template into orb-templates, because it replaces helm-bibtex note managing with its own. See examples of how to configure orb-templates in the README or search through this forum.
That can be an edge case. Under certain circumstances, bibtex-completion fails to retrieve the file name, for example if you have several file paths in the field, there may not be a space between them:
file = {path/to/file1.pdf;path/to/file2.pdf}
and not
file = {path/to/file1.pdf; path/to/file2.pdf}
Another thing to check is bibtex-completion-library-path - this is the variable bibtex-completion uses to look up the pdf files…
@singbad, right, I mean bibtex-completion-notes-template-multiple-files. Sorry, I didn’t see you had orb-templates set - one had to scroll the example to see it. I therefore thought you had the former set instead of the latter. That would explain it. Having both variables is redundant because bibtex-completion-notes-template-multiple-files does nothing when org-roam-bibtex-mode is active.
Anyway, it seems you’ve got your template capturing the file field value, right? If you opt for using ${file} instead of %(orb-process-file-field \"${citekey}\"), keep in mind that orb-preformat-keywords must contain "file" element and orb-process-file-keyword must be set to non-nil.
Then of course you must make sure that bibtex-completion can find your files.
@nobiot from what I can tell my bibtex-completion can “see” the pdf and even notes associated with it.
I changed my bibtex entry to be a absolute path: @article{wolfmoon12,
title = {"{{The Moon}} over the {{Mountain}}": {{Stories}} by {{Atsushi Nakajima}} by {{Paul McCarthy}} and {{Nobuko Ochner}} (Review)},
shorttitle = {"{{The Moon}} over the {{Mountain}}"},
author = {Wolf, Charles De},
date = {2012},
journaltitle = {Monumenta Nipponica},
volume = {67},
pages = {371–374},
publisher = {{Sophia University}},
issn = {1880-1390},
doi = {10.1353/mni.2012.0021},
file = {/home/solomon/Org/slipbox/bib/files/1450/Wolf - 2012 - The Moon over the Mountain Stories by Atsushi N.pdf},
langid = {english},
number = {2}
}
And after resetting emacs and reloading the bibtex file. When I try to open the pdf, it attempts to open in okular (a pdf viewer)
but will fail to open.
I can manually open the pdf in emacs with C-x C-f and it will open fine with pdf-tools.
I also got rid of the template bibtex-completion-notes-template-multiple-files
What’s the value of variable bibtex-completion-pdf-open-function?
I suspect for you somehow it’s set to open the external editor (Okular) you mention.
For me it’s set to ‘find-file’.
Or… Action 2 is set to some custom action, somehow somewhere.
The reason for my suspicion is that by all the changes you have made, the behaviour has changed.
Originally, it was this:
When I run org-roam-bibtex (C-c ]) and selecting entry “2 open pdf” the buffer redirects to “/” root in dired, i.e. when I try to open a pdf it doesn’t find the pdf.
Now it’s this:
And after resetting emacs and reloading the bibtex file. When I try to open the pdf, it attempts to open in okular (a pdf viewer) but will fail to open.
So I think you are touching the right part of the configuration.
Now I suggest you look into why your Emacs tries to open the external PDF viewer.
EDIT:
See the excerpt from the documentation for the variable bibtex-completion-pdf-open-function below.
I think you have helm-open-file-with-default-tool, which then tries to use your system’s default viewer (which I suspect to be Okular). If so, change it to find-file (or remove the customization, so that it will be default back to find-file.
I don’t know where and how this value is set, though… It says the default is find-file.
Documentation:
The function used for opening PDF files.
This can be an arbitrary function that takes one argument: the
path to the PDF file. The default is ‘find-file’ which opens the
PDF in Emacs (either with docview or, if installed, the much
superior pdf-tools. When set to
‘helm-open-file-with-default-tool’, the systems default viewer
for PDFs is used.
@sinqbad, I don’t know if you are up for this, but I’d put edebug-defun for function bibtex-completion-open-pdf and run the action as normal. That should bring up a debugging session like I see below. You should be able to press space to evaluate one line by line, and see what bibtex-completion-pdf-open-function variable evaluates to. Here in my session, after choosing a PDF file, the variable evaluates to find-file.
If the debugger does not open a debegging session, that probably means that the action is not using this function (meaning, some other config maps the action number 2 to do something else).
If your case also evaluates to find-file, maybe it’s advised by some other function like this (visible in C-h f (I made this up this function):
And/or launch Emacs as vanilla with emacs -q and load minimum packages, put minimum config and see if opening pdf works. If it does, there is something to fix in your config (it could be outside of .el files you have been looking at…).
Look, there are three different packages developed independently by different people: Org Ref, Helm BibTeX and Org Roam BibTeX. They are interconnected in certain ways but that it is. It may look like a mess (and it is to some extent) but this is what we have.
So, Helm BibTeX lets you search through your bibliorgaphy: you run helm-bibtex, a window popups and you can perform some actions on entries in you .bib file using a user friendly Helm interface.
Org Ref allows for cite:citekey style links, it is a third-party solution for currently missing Org Mode citation links. Org Ref links are clickable and you can perform some actions on that. Most of the actions have nothing to do with Helm BibTeX because Org Ref has native implementation for them, although it could also use Helm BibTeX (and does so in some cases).
Org Roam BibTeX makes Org Roam note-taking machinery become aware of BibTeX. It does so by relying on bibtex-completion (the same library that powers Helm BibTeX). It also shadows native note-taking facilities of Org Ref and Helm BibTeX, allowing one to use Org Roam instead. So with Org Roam BibTeX you can access your Org Roam notes from both Helm BibTeX and Org Ref.
If you cannot open an org-ref link, then that’s a problem with Org Ref configuration, which is unfortunately a very common thing, but it has nothing to do with ORB nor with Helm BibTeX.
OK, I’ve looked at how Org Ref opens PDF files from a cite:link.
It calls a function specified in org-ref-open-pdf-function, which defaults to org-ref-open-pdf-at-point
org-ref-open-pdf-at-point then calls a function specified in org-ref-get-pdf-filename-function, which defaults to org-ref-get-pdf-filename
org-ref-get-pdf-filenameexpects the filename to be of format citekey.pdf. For a citekey citekey, when you click on a cite:citekey link, Org Ref will look for “citekey.pdf” in org-ref-pdf-directory.
Fortunately, there is a variable org-ref-get-pdf-filename-function that can be set to function org-ref-get-pdf-filename-helm-bibtex, which will use Helm BibTeX to retrieve the filename. Helm BibTeX’ logic of filename retrieval is more complex: it looks at the file field (this is what you want) among a few other things.
I bet (setq org-ref-get-pdf-filename-function #'org-ref-get-pdf-filename-helm-bibtex) will solve your problem with cite: links.
