https://github.com/novoid/extract_pdf_annotations_to_orgmode
Extracting RepliGo PDF annotations to a Org-mode format snippet (unmaintained!)
https://github.com/novoid/extract_pdf_annotations_to_orgmode
orgdown orgmode pdf pdf-document shellscript
Last synced: 6 months ago
JSON representation
Extracting RepliGo PDF annotations to a Org-mode format snippet (unmaintained!)
- Host: GitHub
- URL: https://github.com/novoid/extract_pdf_annotations_to_orgmode
- Owner: novoid
- Created: 2012-03-06T13:20:19.000Z (over 13 years ago)
- Default Branch: master
- Last Pushed: 2015-11-12T11:38:23.000Z (almost 10 years ago)
- Last Synced: 2025-03-26T12:11:52.125Z (6 months ago)
- Topics: orgdown, orgmode, pdf, pdf-document, shellscript
- Language: Shell
- Homepage: http://karl-voit.at/2015/12/26/reference-management-with-orgmode/
- Size: 98.6 KB
- Stars: 28
- Watchers: 4
- Forks: 4
- Open Issues: 0
-
Metadata Files:
- Readme: README.org
Awesome Lists containing this project
README
* Extracting RepliGo PDF annotations to a Org-mode format snippet
I annotate PDF research paper files on my tablet using
[[http://www.cerience.com/products/reader/android][RepliGo Reader for Android]]. Because I am managing my research papers
within [[http://orgmode.org][Org-mode]] similar to [[http://tincman.wordpress.com/2011/01/04/research-paper-management-with-emacs-org-mode-and-reftex/][this description]] I want to get the PDF
annotations back out from the PDF files and into my Org-mode files.
Since RepliGo stores its annotations very parser-friendly (it's text!)
and Org-mode is just text, I can add something like this into Org-mode:
: #+begin_src sh :results output
: ${HOME}/bin/vkextract_annotations_to_orgmode_snippet.sh Qian2008
: #+end_src
When I execute this in Org-mode (using [[http://orgmode.org/org.html#Evaluating-code-blocks][babel: C-c C-c]]) its text output
gets back into Org-mode like this example demonstrates:
: #+results:
: #+begin_example
: ---- HIGHLIGHTS: ---
: Manage Radiologic Portable Document Format \(PDF\) Files Using iTunes
: In this article, we explain how to use the hidden function of iTunes \(Apple Computer\) to manage PDF documents as easily as managing music fles.
: PDF
:
: #+end_example
:
: Sticky Notes:
: #+begin_example
: ---- NOTES: ---
: This paper seems to be very relevant to my PIM study!
: #+end_example
This method works with GNU Linux. Adaptations of paths and so forth
are necessary in the script!
* Be aware of special characters and German umlauts
RepliGo does create «easy to extract» annotations under normal
circumstances. But when you
- highlight special characters such as [[http://en.wikipedia.org/wiki/Germanic_umlaut#German_orthography][German umlauts]],
- OR add sticky notes or text information containing non-[[http://en.wikipedia.org/wiki/Ascii#ASCII_printable_characters][ASCII]] characters,
RepliGo Reader Android switches to an UTF encoding. PDF files with
annotations stored as UTF can not extracted with this simple method
presented here. In this case you'll notice (only) funny characters in
the output of this script.
* Bonus: .emacs setup
These lines are part of my configuration. "C-c )" shows the reftex
citation menu and with "j" I can insert a snippet for inserting
annotations.
The rest might be helpful for your setup as well.
: ;;add a custom reftex cite format to insert links
: (reftex-set-cite-format
: '((?b . "[[bib:%l][%l.bib]]")
: (?r . "[[ref:%l][%l]]")
: (?p . "[[pdf:%l][%l.pdf]]")
: (?h . (concat "** %l - %t\n:PROPERTIES:\n:CREATED: "
: "<" (substring (format-time-string (org-time-stamp-format t t)) 1 -1) ">"
: "\n:ID: %l\n:END:\n[[bib:%l][%l.bib]]\n[[papers:%l][%l.pdf]]\n\n"))
: (?n . (concat "*** PDF Annotations: [[%l-notes.pdf][%l-notes.pdf]]\n:PROPERTIES:\n:CREATED: "
: "<" (substring (format-time-string (org-time-stamp-format t t)) 1 -1) ">"
: "\n:ID: %l-annotations\n:END:\n\n"
: "\#+begin_src sh :results output\n"
: "${HOME}/bin/vkextract_annotations_to_orgmode_snippet.sh %l\n"
: "#+end_src\n\n"))
: ))))
:
: ;; define shortcut for inserting references:
: (define-key org-mode-map (kbd "C-c )") 'reftex-citation)
:
: ;; define my own links for e.g. "[[pdf:Voit2012]]" -> "~/archive/papers_from_web/Voit2012.pdf"
: (setq org-link-abbrev-alist
: '(
: ("bib" . "~/archive/papers_from_web/references.bib::%s")
: ("ref" . "~/share/all/org-mode/references.org::/%s/")
: ("pdf" . "~/archive/papers_from_web/%s.pdf")
: ("notes" . "~/archive/papers_from_web/%s-notes.pdf")
: ))
* License
This documentation is licensed under a [[http://creativecommons.org/licenses/by-nc-sa/3.0/][Creative Commons
Attribution-NonCommercial-ShareAlike 3.0 Unported License]].
The script file is licenced under [[http://www.gnu.org/copyleft/gpl.html][GPL v3 or newer]].
* Example
This is an example entry of one paper in my «references.org» file:
** DONE Voit2011 - TagTree: storing and Re-Finding Files Using Tags :prioritized:to_read:
CLOSED: [2011-11-20 Sun 23:19]
:PROPERTIES:
:CREATED: <2011-11-20 Sun 23:19>
:ID: Voit2011
:END:
[[bib:Voit2011][Voit2011.bib]]
[[pdf:Voit2011][Voit2011.pdf]]
ISBN-13: 978-3-642-25363-8
ISBN-10: 3-642-25363-6
http://www.meduni-graz.at/imi/usab2011/
24-26 Nov 2011, Graz, Austria
http://www.springerlink.com/content/978-3-642-25363-8
- acceptance rate USAB2011: 18%
- this paper got recommended by [[contact:John Smith][John Smith]] on CHI2012
*** PDF Annotations: [[notes:Voit2011][Voit2011-notes.pdf]]
:PROPERTIES:
:CREATED: <2012-03-19 Mon 20:36>
:ID: Voit2011-notes
:END:
#+begin_src sh :results output
${HOME}/bin/vkextract_annotations_to_orgmode_snippet.sh Voit2011
#+end_src
#+RESULTS:
#+begin_example
---- HIGHLIGHTS: ---
navigation through folder hierarchies is
still the dominant mode of information access
strict hierarchy of folders
This paper describes TagTree, a new concept for storing and retrieving
files and folders using tagging and automatically maintained
navigational hierarchies.
compatible with all currently prevalent
software
implementation called tagstore
provides a flexible framework for experimentation and a testbed for both
usability studies and longer term field tests.
[...]
#+end_example
Annotations:
#+begin_example
---- Annotations: ---
this paper seems relevant to me
the authors seem to have achieved clever system integration
#+end_example
* Alternatives
Matt published
[[http://matt.hackinghistory.ca/2015/11/11/note-taking-with-pdf-tools/][a very
similar method on his blog]]. You might as well check it out.