Zotero Viewer Plugin

cst · 08-22-2022, 06:56 AM

Hi!

I just finished developing a plugin that allows to efficiently browse PDF files stored in a Zotero library right on your E-Reader: zotero.koplugin

Feedback or bug reports are appreciated!

juliuss · 09-03-2022, 02:12 AM

This is great!

Would it be possible to support browsing the remote Zotero library through the API?

I frequently add items to my library and would like not to update it all the time!

cst · 09-15-2022, 04:27 AM

The way the plugin is currently written, it reads directly from Zotero's SQLite database. I had a quick glance at the API, but it does not seem to be possible to download the database. Therefore, integrating with the Web API would come with a substantial reimplementation effort.

If you are on linux and have ssh access to your E-Reader, you can easily script the update process to make it easier:

Code:

rsync -vrutU --delete ~/Zotero user@host:/mnt/us

aaaaa · 09-26-2022, 06:32 PM

In my current setup, I store PDFs in my Zotero library and primarily read them on my iPad. But I prefer the experience e-ink, so I'm considering picking up an ereader like the Onyx Boox.

Most of the guides for syncing Zotero and ereaders were written before Zotero 6 added a native PDF reader. The guides I've read recommend using ZotFile for sending and receiving PDFs between desktop and mobile. But I would rather find a solution that interfaces with Zotero in a more native way. Zotero's PDF reader allows me to #tag in-text highlights/annotations. I believe this tagging feature was purpose-built from the ground up for Zotero, so it's not part of any other standard PDF reader apps.

Does KOReader (or any other app) allow tagging like the native Zotero Reader? On iPad the official Zotero app uses their special annotation engine. If there's any e-ink device that uses the Zotero PDF engine I would abandon my iPad in a heartbeat — but until I find a workflow that supports it, I'm sticking with my iPad.

NiLuJe · 09-26-2022, 11:35 PM

If you value your sanity, you should avoid anything put out by Onyx.

(That's a very subtle hint, that, yes, any serious even semi-complex PDF workflow is probably best left to a serious tablet, and as much as it pains me to say that, because I hate iOS with a fiery passion, the iPad is just it).

cst · 09-27-2022, 09:18 AM

FYI, I am modifying the plugin to support the synchronization Web API from Zotero, making the intermediary step of copying the library unnecessary. (Partial) support for annotations is also planned.

You can watch the progress at the webapi branch.

Mat · 04-17-2023, 03:58 AM

Quote:

Originally Posted by cst

Hi!

I just finished developing a plugin that allows to efficiently browse PDF files stored in a Zotero library right on your E-Reader: zotero.koplugin

Feedback or bug reports are appreciated!

Hello,

Sorry for the stupid question, I'm a beginner.

In the attached procedure (see below), I can't find where to copy the zotero.sqlite files and the storage directory. The folders don't match between what I see on my computer with my Kobo USB and what I see on Koreader when setting the Zotero path under Search > Zotero > Settings.

Thank you for your help .

Installation Guide

Copy the files in this repository to <KOReader>/plugins/zotero.koplugin
Copy your Zotero directory to your E-Reader (strictly speaking, zotero.sqlite and the storage directory suffice)
Set the Zotero path under Search > Zotero > Settings
Browse your Zotero collection under Search > Zotero > Browse Database

cst · 04-17-2023, 12:12 PM

Technically, it should not matter where you put your zotero.sqlite and storage directory.
I do not know how the file system is organized on the Kobo, but you could for example put them alongside your normal ebook files.

Maybe someone who has a Kobo can chime in?

Quote:

Originally Posted by Mat

Hello,

Sorry for the stupid question, I'm a beginner.

In the attached procedure (see below), I can't find where to copy the zotero.sqlite files and the storage directory. The folders don't match between what I see on my computer with my Kobo USB and what I see on Koreader when setting the Zotero path under Search > Zotero > Settings.

Thank you for your help .

Installation Guide

Copy the files in this repository to <KOReader>/plugins/zotero.koplugin
Copy your Zotero directory to your E-Reader (strictly speaking, zotero.sqlite and the storage directory suffice)
Set the Zotero path under Search > Zotero > Settings
Browse your Zotero collection under Search > Zotero > Browse Database

Frenzie · 04-17-2023, 05:27 PM

We recommend installing KOReader in /mnt/onboard/.adds/koreader on Kobo.

Mat · 04-18-2023, 03:24 PM

Thank's a lot CST and Frenzie for your quick responses!

The problem is that on my computer "/mnt/onboard/" is displayed as the root directory (I can't see the "mnt" and the "onboard" folder.

And at the opposite, I can't find the ".add" folder on Koreader because it's a hidden folder.,

I have copied the files to root directory and set the Zotero Path to mnt/onboard/ and is has find the directory

!

I have now an other porblem, When I Browse my Zotero collection under Search > Zotero > Browse Database, it doesn't work and it shows an error message (see photo). Can someone help me again. Thanx a lot and have a nice day

Mat · 05-02-2023, 05:00 AM

Hello,

I would like to ask you again: does anyone have a solution to propose to me to make my pluggin work? I still have the same error screen (see picture above)

Thank you for your help

Quote:

Originally Posted by Mat

Thank's a lot CST and Frenzie for your quick responses!

The problem is that on my computer "/mnt/onboard/" is displayed as the root directory (I can't see the "mnt" and the "onboard" folder.

And at the opposite, I can't find the ".add" folder on Koreader because it's a hidden folder.,

I have copied the files to root directory and set the Zotero Path to mnt/onboard/ and is has find the directory

!

I have now an other porblem, When I Browse my Zotero collection under Search > Zotero > Browse Database, it doesn't work and it shows an error message (see photo). Can someone help me again. Thanx a lot and have a nice day

Frenzie · 05-02-2023, 03:28 PM

Did you try the latest version? https://github.com/stelzch/zotero.ko...15da93d75193d2 sounds suspiciously relevant

Mat · 05-16-2023, 03:46 AM

Hello Frenzie,

Thank you for your answer and your help.

Of course I tried that before writing. And it didn't work.

It was the right solution though. I only had to not download the three plugin files individually (which I had done) but download them as .zip, remove the "master" extension and drop the whole folder under <KOReader>/plugins/zotero.koplugin

Now it works. Hopefully this can help others.

Have a nice day

ryanwwest · 05-24-2023, 03:53 PM

Hey, this looks cool and it caught my attention that you mention PDF annotation support. However, I see a Feb 24 commit labeled 'drop buggy annotation support' and can only assume that you ran into some challenges trying to go between Zotero and KOReader annotations? I'd love to hear what the challenges were and whether you think it's still viable to pursue - I'm trying to figure out and maybe develop a way to store and sync PDF/EPUB/HTML annotations across different apps (like some sort of universal file) and was planning to initially use KOReader's .sdr Lua file storage as the 'annotation file type' that other apps can read from (see https://www.ryanwwest.com/pkm-annotation/ for a related post I wrote).

cst · 05-26-2023, 03:29 AM

Hi Ryan,

IIRC one problem with annotations was to get it to synchronize properly. Since annotations are not uniquely identified, I tried to match the bounding boxes but this is tricky, because they might differ in size.
Secondly, the annotation format of KOReader is a bit opaque and not really documented. There even are multiple versions of how something can be done.
Also, annotations for PDFs are stored twice: once in the .sdr folder as metadata and optionally in the PDF file itself.
I definitely think it is possible to integrate and synchronize external annotations into KOReader, but because there is no API for this and because the annotation format is underspecified it would be an unpleasant developer experience and take some time

09-15-2022, 04:27 AM	#3
cst Junior Member Posts: 5 Karma: 9970 Join Date: Aug 2022 Device: KT3	The way the plugin is currently written, it reads directly from Zotero's SQLite database. I had a quick glance at the API, but it does not seem to be possible to download the database. Therefore, integrating with the Web API would come with a substantial reimplementation effort. If you are on linux and have ssh access to your E-Reader, you can easily script the update process to make it easier: Code: rsync -vrutU --delete ~/Zotero user@host:/mnt/us

04-18-2023, 03:24 PM	#10
Mat Junior Member Posts: 4 Karma: 10 Join Date: Apr 2023 Device: Kobo	Thank's a lot CST and Frenzie for your quick responses! The problem is that on my computer "/mnt/onboard/" is displayed as the root directory (I can't see the "mnt" and the "onboard" folder. And at the opposite, I can't find the ".add" folder on Koreader because it's a hidden folder., I have copied the files to root directory and set the Zotero Path to mnt/onboard/ and is has find the directory ! I have now an other porblem, When I Browse my Zotero collection under Search > Zotero > Browse Database, it doesn't work and it shows an error message (see photo). Can someone help me again. Thanx a lot and have a nice day Attached Thumbnails

05-16-2023, 03:46 AM	#13
Mat Junior Member Posts: 4 Karma: 10 Join Date: Apr 2023 Device: Kobo	Thank you Hello Frenzie, Thank you for your answer and your help. Of course I tried that before writing. And it didn't work. It was the right solution though. I only had to not download the three plugin files individually (which I had done) but download them as .zip, remove the "master" extension and drop the whole folder under <KOReader>/plugins/zotero.koplugin Now it works. Hopefully this can help others. Have a nice day

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09-03-2022, 02:12 AM	#2
juliuss Member Posts: 12 Karma: 10 Join Date: Jan 2022 Device: Kindle	This is great! Would it be possible to support browsing the remote Zotero library through the API? I frequently add items to my library and would like not to update it all the time!

09-26-2022, 06:32 PM	#4
aaaaa Junior Member Posts: 1 Karma: 10 Join Date: Sep 2022 Device: Kindle, Boox	In my current setup, I store PDFs in my Zotero library and primarily read them on my iPad. But I prefer the experience e-ink, so I'm considering picking up an ereader like the Onyx Boox. Most of the guides for syncing Zotero and ereaders were written before Zotero 6 added a native PDF reader. The guides I've read recommend using ZotFile for sending and receiving PDFs between desktop and mobile. But I would rather find a solution that interfaces with Zotero in a more native way. Zotero's PDF reader allows me to #tag in-text highlights/annotations. I believe this tagging feature was purpose-built from the ground up for Zotero, so it's not part of any other standard PDF reader apps. Does KOReader (or any other app) allow tagging like the native Zotero Reader? On iPad the official Zotero app uses their special annotation engine. If there's any e-ink device that uses the Zotero PDF engine I would abandon my iPad in a heartbeat — but until I find a workflow that supports it, I'm sticking with my iPad.

09-26-2022, 11:35 PM	#5
NiLuJe BLAM! Posts: 13,492 Karma: 26017324 Join Date: Jun 2010 Location: Paris, France Device: Kindle 2i, 3g, 4, 5w, PW, PW2, PW5; Kobo H2O, Forma, Elipsa, Sage, C2E	If you value your sanity, you should avoid anything put out by Onyx. (That's a very subtle hint, that, yes, any serious even semi-complex PDF workflow is probably best left to a serious tablet, and as much as it pains me to say that, because I hate iOS with a fiery passion, the iPad is just it).

09-27-2022, 09:18 AM	#6
cst Junior Member Posts: 5 Karma: 9970 Join Date: Aug 2022 Device: KT3	FYI, I am modifying the plugin to support the synchronization Web API from Zotero, making the intermediary step of copying the library unnecessary. (Partial) support for annotations is also planned. You can watch the progress at the webapi branch.

04-17-2023, 05:27 PM	#9
Frenzie Wizard Posts: 1,649 Karma: 730583 Join Date: Oct 2014 Location: Antwerp Device: Kobo Aura H2O	We recommend installing KOReader in /mnt/onboard/.adds/koreader on Kobo.

05-02-2023, 03:28 PM	#12
Frenzie Wizard Posts: 1,649 Karma: 730583 Join Date: Oct 2014 Location: Antwerp Device: Kobo Aura H2O	Did you try the latest version? https://github.com/stelzch/zotero.ko...15da93d75193d2 sounds suspiciously relevant

05-24-2023, 03:53 PM	#14
ryanwwest Junior Member Posts: 6 Karma: 10 Join Date: Apr 2023 Device: Boox Max Lumi, Leaf 2	Hey, this looks cool and it caught my attention that you mention PDF annotation support. However, I see a Feb 24 commit labeled 'drop buggy annotation support' and can only assume that you ran into some challenges trying to go between Zotero and KOReader annotations? I'd love to hear what the challenges were and whether you think it's still viable to pursue - I'm trying to figure out and maybe develop a way to store and sync PDF/EPUB/HTML annotations across different apps (like some sort of universal file) and was planning to initially use KOReader's .sdr Lua file storage as the 'annotation file type' that other apps can read from (see https://www.ryanwwest.com/pkm-annotation/ for a related post I wrote).

05-26-2023, 03:29 AM	#15
cst Junior Member Posts: 5 Karma: 9970 Join Date: Aug 2022 Device: KT3	Hi Ryan, IIRC one problem with annotations was to get it to synchronize properly. Since annotations are not uniquely identified, I tried to match the bounding boxes but this is tricky, because they might differ in size. Secondly, the annotation format of KOReader is a bit opaque and not really documented. There even are multiple versions of how something can be done. Also, annotations for PDFs are stored twice: once in the .sdr folder as metadata and optionally in the PDF file itself. I definitely think it is possible to integrate and synchronize external annotations into KOReader, but because there is no API for this and because the annotation format is underspecified it would be an unpleasant developer experience and take some time

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