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Author Topic: Using okular with Docear
Jay Dugger
Newbie
Posts: 1
Post Using okular with Docear
on: October 14, 2012, 11:27

don't forget to tell us your operating system (e.g. Windows 7, 64 Bit), your Java version (Java 6, 32 Bit) and let us know if you are using the latest Docear versio

Under Ubuntu 11.04, java-6-openjdk, one can use the pdf viewer Okular (http://okular.kde.org).

The command string below works for a manual pdf reader command definition (Tools, Preferences, PDF Management).

/usr/bin/okular*-p*$PAGE*$FILE

Unfortunately Okular manages annotations via a sort of private overlay kept outside the PDF file itself.

Thank you for your feedback. Please note that we - the Docear team - currently do not have the time to answer support questions. However, we encourage all Docear users to help each other.

Stefan-
[Docear]
Administrator
Posts: 969
Post Re: Using okular with Docear
on: October 15, 2012, 14:49

Hello Jay,

Unfortunately Okular manages annotations via a sort of private overlay kept outside the PDF file itself.

This is the reason why we have not added this pdf viewer to our list.

However, if you like, we can add the command string you have provided to our examples list. Evince - the default pdf viewer in Gnome - is mentioned there as well.

Best,
Stefan

Stefan Langer
Product Management & Research
Docear - The Academic Literature Suite
http://docear.org

Facebook: https://www.facebook.com/pages/Docear/137985949605902
Google+: https://plus.google.com/106965732112113749959/posts
Twitter: https://twitter.com/Docear_org

Maras
Newbie
Posts: 4
Post Re: Using okular with Docear
on: October 15, 2012, 21:36

And Evinece's notes can be imported into Docear very well. And Okular's notes and hihglights will be in the near future, as I can understand (recent changes in the Poppler enabled that).

Maras
Newbie
Posts: 4
Post Re: Using okular with Docear
on: October 16, 2012, 18:24

You can place these instructions for using Evince's notes with Docear: http://blogs.perl.org/users/cyocum/2011/10/annotating-pdfs-with-evince.html somewhere in your FAQ. Importing of such notes is working perfectly for me. It's a pity that Evince have not implemented highliht feature yet. But maybe in the future.

Stefan-
[Docear]
Administrator
Posts: 969
Post Re: Using okular with Docear
on: October 16, 2012, 23:29

Hello Maras,

the website states:

When you are done, you will need to save the PDF as a different file. I am not sure why this is but if I saved it on top of the old file, it didn’t take the annotations.

And that's why we don't want to support it officially in Docear. Users might think that it works as well as using the PDF-XChange Viewer or the Foxit Reader.
I am using Linux too, so I can totally understand that you want to use a native PDF viewer in Linux. I am not very happy about it, but using the PDF-XChange Viewer in WINE works much better than creating annotations with evince and entering a new filename every time.
Besides when using the PDF-XChange Viewer, Docear will be able to import not only bookmarks and notes but also highlighted text. Just install it using WINE and restart Docear. Docear will ask you if you want to use it.

Anyway, there is already a note about evince in Docear:
In "Tools" > "Preferences ..." > "PDF Management" please click the button "Manually define the pdf reader command"

A dialog will open which I have just created for users who want to use a different PDF viewer with Docear.
The last sample shows the command you might want to use in order to enable evince in Docear:

evince*-i*$PAGE*$FILE

Best regards,
Stefan

Stefan Langer
Product Management & Research
Docear - The Academic Literature Suite
http://docear.org

Facebook: https://www.facebook.com/pages/Docear/137985949605902
Google+: https://plus.google.com/106965732112113749959/posts
Twitter: https://twitter.com/Docear_org

Gustavo-
Olivares
Newbie
Posts: 1
Post Re: Using okular with Docear
on: April 11, 2013, 02:46

I know this post is a bit old but I thought of updating on Evince and comments.
(Fedora 18_64bit Docear Beta9 Evince 3.6.1)

I've been able to reliably import comments added with Evince into Docear and very happily open the PDF directly on my comment via Docear using the syntax

evince*-i*$PAGE*$FILE

The file is open correctly, I can add annotations and then when I save (File-Save Copy) I just overwrite the original file, close Evince and in Docear I select "import new annotations" and the magic happens!

So, the only thing missing now is highlight support.

Regards
El Gus

Stefan-
[Docear]
Administrator
Posts: 969
Post Re: Using okular with Docear
on: April 11, 2013, 12:20

Hello Gustavo,

I am very glad it works out for you. (that's the reason I have implemented the manual PDF reader definition) 🙂

It works the same way on my system (Debian/sid 64bit) - however I still prefer to use the PDF X-Change-Viewer in WINE, since I can import highlighted text with it.

Cheers and thanks for your feedback. 🙂
Stefan

Stefan Langer
Product Management & Research
Docear - The Academic Literature Suite
http://docear.org

Facebook: https://www.facebook.com/pages/Docear/137985949605902
Google+: https://plus.google.com/106965732112113749959/posts
Twitter: https://twitter.com/Docear_org

Laura
Newbie
Posts: 3
Post Re: Using okular with Docear
on: September 22, 2013, 15:14

Just an FYI, the newest versions of Okular store the annotations within the PDF. I'm very happy about this, because I want to use Okular + Zotero + Docear on my Linux machine (yay open source!). Once (and if) I get everything up and running, I'll post an update.

Stefan-
[Docear]
Administrator
Posts: 969
Post Re: Using okular with Docear
on: September 23, 2013, 12:38

Hello Laura,

if you could send the reader definition string (like: "evince*-i*$PAGE*$FILE") for Okular, I will happily update the examples in the dialog!

Thanks for your help! 🙂
Cheers,
Stefan

Stefan Langer
Product Management & Research
Docear - The Academic Literature Suite
http://docear.org

Facebook: https://www.facebook.com/pages/Docear/137985949605902
Google+: https://plus.google.com/106965732112113749959/posts
Twitter: https://twitter.com/Docear_org

Dominic-
Hosler
Newbie
Posts: 5
Post Re: Using okular with Docear
on: October 15, 2013, 14:10

Hi,

I just started using Okular as well, the definition string that I'm using is "okular*-p*$PAGE*$FILE".

It successfully imported the pdf and the comment annotations (both pop-up comments and permanently visible comments).

It did not collect the highlighted text because it doesn't appear with a pop-up of that text.

It's plenty good enough for me because I far prefer software that respects freedom, I will not use the proprietary PDF X-Change.

Thanks,

Dom

Dominic-
Hosler
Newbie
Posts: 5
Post Re: Using okular with Docear
on: October 15, 2013, 14:15

Just to add, it also successfully opened the pdf in Okular (when clicking on the pdf link), and opened the pdf to the top of the page that included the appropriate comment (when clicking on the comment link).

I'm really excited to start using this as my main organization for literature.

Stefan-
[Docear]
Administrator
Posts: 969
Post Re: Using okular with Docear
on: October 21, 2013, 15:13

Hello Dominic,

I am glad that Okular works for you.

But I have some questions:
I am using GNOME and Evince: When I open a PDF file on a specific page using Evince and then click on another annotation on Docear, Evince will jump to right the page without starting a new instance. In contrast if I do that using Okular, a new instance of Okular is started.
Can you confirm that?

Another questions is regarding some error reports we were receiving from some Windows users. They complained that Docear does not remember the PDF viewer they have manually defined. They had to define the command every time they started Docear. For me it works perfectly though.
How about your system?

Best regards and thanks for your help! 🙂
Stefan

Stefan Langer
Product Management & Research
Docear - The Academic Literature Suite
http://docear.org

Facebook: https://www.facebook.com/pages/Docear/137985949605902
Google+: https://plus.google.com/106965732112113749959/posts
Twitter: https://twitter.com/Docear_org

Dominic-
Hosler
Newbie
Posts: 5
Post Re: Using okular with Docear
on: October 21, 2013, 16:31

Hi Stefan,

Yes I can confirm that each time it opens a new instance of Okular. I don't know how to prevent that. For me Okular is still the best setup to use.

Docear remembers my custom command for the pdf reader, (my system is Arch Linux on x86_64, running KDE 4.11.2, and jre7-openjdk v. 7.u40_2.4.2).

Thanks,
Dom

Stefan-
[Docear]
Administrator
Posts: 969
Post Re: Using okular with Docear
on: October 21, 2013, 16:45

Hello Dominic,

thanks for letting me know! 🙂

Best,
Stefan

Stefan Langer
Product Management & Research
Docear - The Academic Literature Suite
http://docear.org

Facebook: https://www.facebook.com/pages/Docear/137985949605902
Google+: https://plus.google.com/106965732112113749959/posts
Twitter: https://twitter.com/Docear_org

Alexmogave-
ro
Newbie
Posts: 2
Post Re: Using okular with Docear
on: January 21, 2014, 20:44

Hi all,
I would like to report that Okular works fine form me as well.
The only problem is that Docear imports only the highlight annotations (if commented), for instance rectangles are not imported even if I add comments on it.

Is this confirmed? Maybe I did something wrong?

Thank you very much
Alessandro

Stefan-
[Docear]
Administrator
Posts: 969
Post Re: Using okular with Docear
on: January 27, 2014, 11:27

Hello Alessandro,

The only problem is that Docear imports only the highlight annotations (if commented), for instance rectangles are not imported even if I add comments on it.

I can confirm this. Docear can only import bookmarks and notes, not highlighted text. There are however some PDF viewers out there which can automatically create notes from highlighted text. That's why we usually recommend our users to use the "PDF X-Change Viewer" (Please note: the PDF X-Change Editor is NOT supported by Docear right now.)

While it's simple to write a prototype that can import highlighted text from PDF documents, there are a lot of differences in the way how text or highlights are stored in PDF files. This leads to a lot of annoying exceptions and we decided not to implement native highlighted text import for now.

I am using Debian/sid and use WINE to run the "PDF X-Change viewer". It works fine on my computer and the computers of a lot of other users out there. If you need help with this, please let me know.

If you don't want to use PDFXCV, you need to copy the content of highlighted text into annotations manually. :/

Please read more about this topic here: http://www.docear.org/support/user-manual/#PDF_Editors

I am sorry for the inconveniences.

Best,
Stefan

Stefan Langer
Product Management & Research
Docear - The Academic Literature Suite
http://docear.org

Facebook: https://www.facebook.com/pages/Docear/137985949605902
Google+: https://plus.google.com/106965732112113749959/posts
Twitter: https://twitter.com/Docear_org

Alexmogave-
ro
Newbie
Posts: 2
Post Re: Using okular with Docear
on: March 10, 2014, 19:52

Hi Stefan,
thanks for the reply. I have just installed PDF X-Change Viewer, it works, but I still cannot import annotations on graphical elements such as squares or circles. Is it normal?

Kind regards
Alessandro

Stefan-
[Docear]
Administrator
Posts: 969
Post Re: Using okular with Docear
on: March 14, 2014, 15:15

Hello Alessandro,

import is only available for highlighted text (i.e. select a text, right-click, highlight).
What the PDFXCV does is to automatically create real annotations (comments) from text you highlight, so Docear can import them.

This, however, does not work for squares, circles, etc.

Best regards,
Stefan

Stefan Langer
Product Management & Research
Docear - The Academic Literature Suite
http://docear.org

Facebook: https://www.facebook.com/pages/Docear/137985949605902
Google+: https://plus.google.com/106965732112113749959/posts
Twitter: https://twitter.com/Docear_org

John
Newbie
Posts: 2
Post Re: Using okular with Docear
on: April 3, 2015, 16:42

For users who may build Okular from source code, adding a few lines will allow highlights to be written to the pop-up and imported in Docear without additional work for every highlight.

https://github.com/jsqliu/okular/commit/ee9a8f5272c1ea4b20648fe57b52c726751073aa

Also it's worth noting that Okular is less limited than PDF Xchange when it comes to annotating secured pdf files.

wrptsy
Newbie
Posts: 1
Post Re: Using okular with Docear
on: July 14, 2015, 15:32

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pti
Newbie
Posts: 12
Post Re: Using okular with Docear
on: February 8, 2016, 12:19

Yes, @John . I also just discovered jsqliu\'s addition that you link to. It is really great & solves a lot of things! I\'ve also assembled the instructions on how to build jsqliu\'s version of Okular here (as personally I would need that help 🙂 ): http://superuser.com/questions/673917/modify-okular-highlight-to-automatically-copy-highlighted-text-into-comment/1036573#1036573 . It\'s possible that it will take a while before the feature will be included as Okular standard.

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