Research Helper

This is a plugin for diagrams.net(drawio) which retrieves the library from your Zotero personal account and organizes your references according to the collection in it. With this plugin, you can add tags for blocks with standard citation format.

The Website

Please use our customized drawio. A third-party plugin is not allowed in the official drawio web app directly.

Quick Start

1. Add the plugin.
   • Visit our customized drawio and go to Extra > Plugins...
   • Click Add and Custom...
   • Enter

     plugins/zotero.js
     

     <!--``` https://sciyen.github.io/ResearchHelper/plugins/zotero.js ```--> and click Add. Finally, apply the change and refresh the site.
     
2. Click Extras > Zotero Tag Selector... to open the tag selector.
3. (Optional) If you are working on writing a thesis using Latex, you can upload the bibliography meta-file (.bbl) of your project. It will try to match the citation number in your thesis by matching the DOI of an item.
4. Enter the personal account information to diagrams.net.
   • Register a private API key from here.
   • Lookup for your userID from here (login first).
   • Enter the UID and keys, and click the Refresh button.
5. Select a block in your diagram, and add a tag by clicking Add button or remove a tag by clicking Remove.
6. And you should see the attached block with standard citation format. The red indicates a journal paper; the blue indicates a conference paper.

Exporting PDFs

You need to install wkhtmltopdf, see the instruction here.

sudo apt-get install wkhtmltopdf
pip install pdfkit

To export pdfs according to the bibliography in your Latex project, you can use the following steps.

1. Click Extras > Zotero Tag Selector... to open the tag selector.
2. Click Export CSV button to download the csv file, which contains the item key, proper citation format, and item title.
3. Excute the script to copy PDF files.

   python3 export_pdf.py <csv_path> <lib_json_path> <zotero_storage_path> [--output_folder=<output_folder>]
   

   Replace
   • <csv_path> with the path of the csv file just downloaded
   • <lib_json_path> is the better biblatex library json file exported from Zotero, which can be obtained by clicking Export Library in the Zotero. Remember to select the BetterBibTex JSON format.
   • <zotero_storage_path> is the path of the storage folder of your Zotero. You can find it by right clicking any item in the Zotero and click Show File. The folder should be the parent folder of the file.

Steps to Load Plugin in Official App Website (Alternative)

Content-Security-Policy

For developing usage, you can install this chrome extension to disable Content-Security-Policy for a web application. And you can use our plugin on the official web app. Additional approval is required after the reloading of the page. Please re-authorize it by clicking the Disable Content-Security button.

Loading External Plugins

After 20.3.0 release, the original author prohibited the load of third party plugin. And therefore, we need extra steps to bypass this checking. If you have a better method to deal with this, please let me know, thanks.

1. Press F12 to open the dev tools, go to the Source tab, and open the file top/app.diagrams.net/js/app.min.js. Click the space left to the line number to add a breakpoint at the beginning.
2. Turn on the disable-content-security extension to disable CSR protection.
3. Refresh the page. You should notice that the page halts during loading.
4. Go to the Console tab in dev tools. Enter

   window.ALLOW_CUSTOM_PLUGINS = true
   

   and execute it.
5. Resume the breakpoint.

Get Involved

We are currently working on the following subjects. Feel free to join us.

• Developing the plugin for diagrams.net, please checkout to feature/drawio_plugin for more details
• Unclassified documents will not shown in the tags. As mentioned in #2.
• The call number may be occupied by some useful information (usually in the literature of the book type) if it is used as a reference number field. As mentioned in #2.
• Enhance user interface.

Recommended Method for Debugging

Preparing the Environment

• This vscode extension allows you to host the files with a local server.
• Since 20.3.0 release, one needs to force the external plugin from different domain available by the following steps. This chrome extension allows you to add plugins from arbitrary sources. So, you can just debug locally without pushing it, which has been tested in Windows 10 WSL 1.0.

Use Our Customized Drawio

1. Our our customized drawio does not have the restriction of loading external plugins. It is recommended to use this version for debugging.
2. Use vscode to open this project. Open /publics/index.html, right click Open in Default Browser at any line. Then, you obtain a local file server, e.g. http://localhost:52330/plugins/zotero.js.
3. Use this link as an experimental plugin. In drawio, click Extra>Plugins>Add>Custom, and paste the url.
4. Turn on the disable-content-security extension to disable CSR protection, and refresh the page. Now, the plugin should be loaded successfully.