zot2sioyek 0.4.1

Script with managing utils of zotero database fratures to sioyek PDF reader.

Zotero to Sioyek Highlights Manager

---

Python script to embed zotero highlights to sioyek, and other utils.

• 🐍 Python sqlite3 and pyzotero Based Script

[!WARNING] Tested only in linux

📖 Contents

• ✨ Features
• 📚 Requirements
  • 🐍 Conda
• 📦 Installation
• 🔧 Configuration
  • 🎨 Colors
• 💻 Client
• 📝 TODO
• 🤝 Contributing
• 💓 Aknowledgements

✨ Features

• Embed zotero highlights to the sioyek database:

python zot2sioyek.py --insert-highlights "/path/to/file.pdf"

• Print in terminal the text of all the highlights from a zotero file, colored with the highlight color

python zot2sioyek.py --print-annotation-text "/path/to/file.pdf"

• To see all available commands:

python zot2sioyek.py --help

[!NOTE] If installed through pip, you can run only zot2sioyek instead of python zot2sioyek.py.

• For testing the package through pytest

python -m pytest --doctest-modules tests/test.py src/zot2sioyek/zot2sioyek.py

📚 Requirements

Requirements are automatic installed when this script is installed with pip

• pyzotero

• pymupdf

• PyQt5

• regex

• sqlite3

python -m pip install pyzotero pymupdf PyQt5 regex sqlite3

🐍 Conda

If wanted, requirements may be installed with conda, to run this script in a conda environment.

Inside this repo, run:

conda env create --file env.yml

📦 Installation

To run the script without installation, simply clone the repo or download /src/zot2sioyek/zot2sioyek.py and run it directly.

Default installation is done by

python -m pip install zot2sioyek

Being possible after install to run the comman with zot2sioyek in terminal.

Other possible approach to install is cloning the repo and installing locally

git clone https://github.com/eduardotlc/zot2sioyek
cd zot2sioyek
python -m pip install -e .

🔧 Configuration

To use this script define the variables in zot2sioyek.py:

• SIOYEK_PATH: Sioyek binary path.

• SIOYEK_LOCAL_DATABASE_FILE_PATH: Sioyek .db local database file path.

• SIOYEK_SHARED_DATABASE_FILE_PATH: Sioyek .db shared database file path.

• ZOTERO_LIBRARY_ID: Your personal library ID available Here, in the section Your userID for use in API calls.

• ZOTERO_API_KEY: Api key, you can obtain Here.

• ZOTERO_LIBRARY_TYPE: Zotero library type, can be 'user' or 'group'.

• ZOTERO_LOCAL_DIR: Zotero local storage folder, like /home/user/Zotero/storage.

• ZOTERO_TO_SIOYEK_COLORS: Sioyek highlight type letter associated to each zotero highlight color (Optional).

[!NOTE] The variables can also be defined as envrinoment variables (at your .zshrc/.bashrc etc...), with the exact same names as the script variables above, and ZOTERO_TO_SIOYEK_COLORS if defined should be defined as a string like: export ZOTERO_TO_SIOYEK_COLORS='{ "#5fb236": "h", "#a28ae5": "i", "#e56eee": "i", "#2ea8e5": "d", "#ff6666": "e", "#f19837": "r", "#ffd400": "s"}'

🎨 Colors

• This script defines ZOTERO_TO_SIOYEK_COLORS variable based on the most close colors of default sioyek config, to the zotero highlight colors. The conversion looks like the following (Zotero colors in the upper row, sioyek colors in the lower row):

• If you want to have the exact same colors of zotero highlights in sioyek, add the following to your sioyek prefs_user.config:

highlight_color_g 0.37 0.70 0.21
highlight_color_a 0.63 0.54 0.90
highlight_color_p 0.90 0.43 0.93
highlight_color_b 0.18 0.66 0.90
highlight_color_r 1.00 0.40 0.40
highlight_color_o 0.95 0.60 0.22
highlight_color_y 1.00 0.83 0.00

• Or to any highlight letter you want, since the defined letter on prefs_user.config and the script variable ZOTERO_TO_SIOYEK_COLORS match.

💻 Client

The following commands are available through:

In a local folder after downloading the script, cd in /src/zot2sioyek and run

python zot2sioyek.py [FLAG] [ARGS]

If installed through pip or through cloning or with pip install -e . in the repo root, the 2 following commands are available

python -m zot2sioyek.zot2sioyek [FLAG] [ARGS]

zot2sioyek [FLAG] [ARGS]

FLAGS                              ARGUMENTS
=====                              ==========


Script general utils.
----------------------

-h, --help                         
Print this script help.
If a Group name is passed after --help, the help to this specific group is printted
only. Available groups are: general, zotero, sioyek.         

Zotero Managing Commands.
--------------------------

-g, --get-highlights               [file_name_or_path]
Print all highlights from a given zotero file.
-p, --print-annotation-text        [file_name_or_path]
print all highlighted text for a given zotero PDF local file.
-T, --zotero-tags                  [file_name_or_path]
Prints a zotero PDF attachment parent item existing arguments.
-A, --add-zotero-tag               [file_name_or_path], [tag_str_to_add]
Add a tag to a zotero PDF attachment parent item. Takes arguments file name or
path, and tag str to add.         
-R, --remove-zotero-tag            [file_name_or_path], [tag_str_to_remove]
Remove a tag from a zotero PDF attachment parent item. Takes arguments file name or
path, and tag str to remove.         

Sioyek Main Commands.
----------------------

-f, --list-sioyek-files            
Print all files in sioyek local database
-H, --list-sioyek-hash             [file_name_or_path]
print a sioyek database pdf file md5sum hash.
-l, --print-sioyek-attributes      [file_name_or_path]
Print all Attributes and values in a sioyek database PDF file.
-i, --insert-highlight             [file_name_or_path]
Insert highlights in a sioyek database PDF file, importing this highlights from this
PDF file zotero attachment highlight.         
-d, --insert-dated-highlight       [datetime.datetime]
Insert highlights in multiple sioyek database PDF files, importing this highlights from this
based on the passed arguments of a datetime.datetime date, to start from to search
for highlights, limit_number_items, that sets the maximum of items to retrieve, and
sort method that organize the order of the retrieved items.         
-S, --list-all-sioyek-highlights   
Print all sioyek highlights
-k, --citation_key                 [file_name_or_path]
Print zotero PDF file parent citation key.

Extra options flags.
---------------------

--sort                             [pyzotero_sort_strategy]
Pyzotero items sorting method. Requires to have passed --insert-dated-highlight.

If an argument passed after a flag contain blank spaces, remember to quote wrap it,
while not being necessary case inputted after through prompted option.

Author: [e-mail]

[!NOTE] The --help flag, or not passing any flag, prints the above help. This help includes terminal colored lines and other formatters, if desired, the -h flag also print a help function, but in plain format.

Zotero Commands

The here examples to the zotero group command flags, were runned considering a local PDF file, that is also added to the zotero database, containing 3 differenct color highlights, that where added through zotero app.

Get Highlights

-g --get-highlights

zot2sioyek -g "/home/eduardotc/Zotero/storage/E5M6X2IH/green ultrafast one-pot mechanochemical bio catalyst encapsulation in MO.pdf"

1
-----
Text: water-based conditions to maintain enzymatic activity due to the inherent fragility
Color: #f19837
Relative Page: 2
Doc Page: 2
Creation Date: 2024-09-08 05:56:08
Modification Date: 2024-09-08 05:56:08

2
-----
Text: Biocatalysts, including enzymes, which are functional proteins known for their outstanding catalytic efficiency, specificity, and selectivity, ha
ve been greatly studied for both research purposes and industrial applications
Color: #a28ae5
Relative Page: 2
Doc Page: 2
Creation Date: 2024-09-08 05:54:42
Modification Date: 2024-09-08 05:54:42

3
-----
Text: well-defined 3D structure of enzyme@ZIF-90 crystals during ultrafast milling reactions. We further demonstrated
Color: #5fb236
Relative Page: 2
Doc Page: 2
Creation Date: 2024-09-08 05:54:35
Modification Date: 2024-09-08 05:54:35

Print Annotation Text

-p --print-annotation-text

water-based conditions to maintain enzymatic activity due to the inherent fragility

Biocatalysts, including enzymes, which are functional proteins known for their outstanding catalytic efficiency, specificity, and selectivity, have been greatly studied for both research purposes and industrial applications

well-defined 3D structure of enzyme@ZIF-90 crystals during ultrafast milling reactions. We further demonstrate

Zotero Tags

-T --zotero-tags

zot2sioyek -T "/home/eduardotc/Zotero/storage/E5M6X2IH/green ultrafast one-pot mechanochemical bio catalyst encapsulation in MO.pdf"

Biological, Catalysis, Encapsulating, MOF, Mechanochemistry, Synthesis, Unread, ⭐️⭐️

Add Zotero Tag

-A --add-zotero-tag

zot2sioyek -A "/home/eduardotc/Zotero/storage/E5M6X2IH/green ultrafast one-pot mechanochemical bio catalyst encapsulation in MO.pdf" Testing

Tag Testing added to PDF parent item.

Remove Zotero Tag

-R --remove-zotero-tag

zot2sioyek -R "/home/eduardotc/Zotero/storage/E5M6X2IH/green ultrafast one-pot mechanochemical bio catalyst encapsulation in MO.pdf" Testing

Tag Testing removed from item.

Sioyek

List Sioyek Files

-f --list-sioyek-files

zot2sioyek -f

f607f555da6ff4f2beb80653e9b07723 : /home/eduardotc/Zotero/storage/HN3SF8WA/Quiroz et al. - 2018 - Controlling Reaction Selectivity over Hybrid Plasmonic Nanocatalysts.pdf
304ca2c74cdfdc66e70098442fb5f75c : /home/eduardotc/Zotero/storage/L9PG5ZKI/Kolemen et al. - 2016 - Remote-Controlled Release of Singlet Oxygen by the.pdf
8b2479fdeaf3261f6de4804c4c2995bc : /home/eduardotc/Zotero/storage/R9RLP4UW/Supporting_MOF_anthracene_singlet.pdf
bfc2bac356c35a457f660a63e8d1ae77 : /home/eduardotc/Zotero/storage/9HAKQCTN/Vijayakumar - 2023 - Cancer targeted contrast studies and photothermal therapy using engineered gold nanoparticles.pdf
303185f111afbd8452b5194b58d00244 : /home/eduardotc/output.pdf

[!WARNING] This Command prits all present files in your sioyek database, so be aware for the possibillity of being a realy long output.

List Sioyek Hash

-H --list-sioyek-hash

zot2sioyek -H "/home/eduardotc/Zotero/storage/HN3SF8WA/Quiroz et al. - 2018 - Controlling Reaction Selectivity over Hybrid Plasmonic Nanocatalysts.pdf"

f607f555da6ff4f2beb80653e9b07723 

[!NOTE] In reality, this command only gets an already stored file hash value from the sioyek database, upon a file path matching. That being so, if the passed file has never being opened in sioyek, the hash won't be part of the database and won't be returned.

📝 TODO

• Embed all zotero database highlights starting from a specified date.

• Create import from sioyek database to zotero database highlights.

  • Currently, I couldn't find a way of adding zotero highlights through pyzotero, or through zotero api/sql. If anyone knows how to do it, please message or email me so that I can update this script, or feel free to implement the needed updates and send a pull request, I'll be very thankful.

🤝 Contributing

Feel free to make pending or other optimizations and pull requests, this script is still under development and any contribution is very much appreciated.

• Clone the repo to your local environment:

💓 Aknowledgements

• Ahrm for developing Sioyek PDF reader.

• Urschrei for Pyzotero

• Blob42 for Koreader-sioyek-import, which parts of this script was based from.

• The Zotero team.