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A plugin for reading and annotating PDFs and EPUBs in obsidian.

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Quick Overview

The obsidian-annotator is a plugin for Obsidian, a knowledge management application. It allows users to annotate PDF files directly within Obsidian, integrating seamlessly with the app's note-taking and knowledge management features. This plugin enhances the research and study workflow by enabling users to interact with PDFs and take notes in the same environment.

Pros

  • Seamless integration with Obsidian's ecosystem
  • Supports annotation of PDF files directly within the application
  • Allows for easy linking between annotations and other notes
  • Enhances research and study workflows by combining PDF reading and note-taking

Cons

  • Limited to PDF file format for annotations
  • Requires Obsidian to be installed and used as the primary note-taking tool
  • May have a learning curve for users new to Obsidian or PDF annotation
  • Potential performance issues with large PDF files or numerous annotations

Getting Started

To use the obsidian-annotator plugin:

  1. Install Obsidian from https://obsidian.md/
  2. Open Obsidian and go to Settings > Community Plugins
  3. Disable Safe Mode if prompted
  4. Click "Browse" and search for "Annotator"
  5. Install the "Annotator" plugin and enable it
  6. Create a new note and drag a PDF file into it
  7. Use the annotation tools that appear when viewing the PDF

Note: This is not a code library, so code examples are not applicable.

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  • Extensible architecture: Allows for custom data sources and plugins

Cons of Promnesia

  • Steeper learning curve: Requires more setup and configuration compared to Obsidian Annotator
  • Less integrated with Obsidian: May not provide as seamless an experience within the Obsidian ecosystem
  • Potentially overwhelming: The wide range of features and options might be more than some users need

Code Comparison

Promnesia (Python):

from promnesia.common import Visit, Loc
from datetime import datetime
def index() -> Iterable[Visit]:
    yield Visit(url='https://example.com', dt=datetime.now(), locator=Loc.file('example.txt'))

Obsidian Annotator (JavaScript):

export default class AnnotatorPlugin extends Plugin {
  async onload() {
    this.addRibbonIcon('highlighter', 'Annotate', () => {
      // Annotation logic here
    });
  }
}

The code snippets show that Promnesia uses Python and focuses on indexing visits, while Obsidian Annotator uses JavaScript and integrates directly with Obsidian's plugin system.

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pdf-to-markdown

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Pros of pdf-to-markdown

  • Standalone tool for converting PDFs to Markdown, not tied to any specific note-taking app
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Cons of pdf-to-markdown

  • Limited annotation capabilities compared to Obsidian Annotator
  • Lacks integration with a note-taking system for organizing and linking annotations
  • May not preserve complex PDF layouts or formatting as accurately

Code Comparison

pdf-to-markdown:

public class PdfToMarkdown {
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        // Convert text to Markdown
    }
}

Obsidian Annotator:

export default class AnnotatorPlugin extends Plugin {
    async onload() {
        this.addRibbonIcon('highlighter', 'Annotate PDF', () => {
            // Open PDF annotation view
        });
    }
}

The code snippets show that pdf-to-markdown focuses on direct PDF text extraction and conversion, while Obsidian Annotator integrates with the Obsidian interface for annotation functionality.

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Code comparison

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}

obsidian-annotator (TypeScript):

export async function annotateFile(app: App, file: TFile) {
  const fileContent = await app.vault.read(file);
  const annotatedContent = await annotateContent(fileContent);
  await app.vault.modify(file, annotatedContent);
}

While both projects deal with document interaction, sioyek focuses on PDF viewing and navigation, whereas obsidian-annotator is designed for annotation within the Obsidian environment. The code snippets reflect their different purposes, with sioyek handling PDF-specific features and obsidian-annotator working with Obsidian's file system and content manipulation.

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koreader

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  • Cross-platform compatibility (Linux, Android, iOS)
  • Extensive customization options for reading experience

Cons of KOReader

  • Steeper learning curve due to more complex features
  • Not directly integrated with note-taking systems like Obsidian
  • Requires separate installation and setup

Code Comparison

KOReader (Lua):

local ReaderUI = require("apps/reader/readeruimanager")
local ReaderView = require("ui/widget/readerview")
local Screen = require("device").screen

function ReaderUI:init()
    self.view = ReaderView:new()
end

Obsidian Annotator (TypeScript):

import { Plugin } from 'obsidian';
import { AnnotatorView } from './annotator-view';

export default class AnnotatorPlugin extends Plugin {
    async onload() {
        this.registerView('annotator', (leaf) => new AnnotatorView(leaf));
    }
}

While KOReader is a full-featured e-book reader with its own UI and rendering engine, Obsidian Annotator is a plugin that integrates PDF annotation capabilities into the Obsidian note-taking environment. KOReader offers more comprehensive reading features, while Obsidian Annotator focuses on seamless integration with Obsidian's ecosystem for note-taking and knowledge management.

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wallabag

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wallabag is a self hostable application for saving web pages: Save and classify articles. Read them later. Freely.

Pros of Wallabag

  • Standalone web application for saving and organizing web articles
  • Supports multiple users and devices with cloud synchronization
  • Offers a variety of integrations and browser extensions

Cons of Wallabag

  • Not integrated with Obsidian or other note-taking applications
  • Requires server setup and maintenance
  • May have a steeper learning curve for non-technical users

Code Comparison

Wallabag (PHP):

public function addEntry(string $url, string $title = null, array $tags = []): Entry
{
    $entry = $this->fetchEntry($url);
    if (null === $entry) {
        $entry = new Entry($this->user);
        $entry->setUrl($url);
    }
    // ... (additional code)
}

Obsidian Annotator (JavaScript):

async annotateFile(file: TFile) {
    const content = await this.app.vault.read(file);
    const annotations = await this.extractAnnotations(content);
    const updatedContent = this.insertAnnotations(content, annotations);
    await this.app.vault.modify(file, updatedContent);
}

The code snippets show different approaches: Wallabag focuses on adding entries to a database, while Obsidian Annotator works with file content and annotations within the Obsidian environment.

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README

GitHub release (latest SemVer) GitHub All Releases

Obsidian Annotator

This is a plugin for Obsidian (https://obsidian.md). It allows you to open and annotate PDF and EPUB files.

The plugin is based on https://web.hypothes.is/, but modified to store the annotations in a local markdown file instead of on the internet.

Demonstration

annotator demo

Warning! In the above gif I use Dataview syntax to specify the annotation-target. If you do not have the dataview plugin installed, you must instead write the annotation-target in the frontmatter, like this:

---
annotation-target: https://arxiv.org/pdf/2104.13478.pdf
---

Known issues

  1. Plugin doesn't work on iOS 16.3 or higher. Follow #289 issue state up to date.
  2. Reader doesn't show annotations if they were changed on different platforms.

Getting Started

Add the property annotation-target to the frontmatter of your obsidian note, with a value corresponding to the location of the EPUB/PDF file. The location can either be a file in the vault (such as Pdfs/mypdf.pdf), or online (such as https://arxiv.org/pdf/2104.13478.pdf)

Then you can, in the open note pane, select "more options" (the three dots in the top right), and a new option "annotate" should be available.

The plugin automatically tries to determine whether the file is an epub or pdf based on the file path, but in case this doesn't work, you can also add the property annotation-target-type and specify whether it is epub or pdf manually.

If you have dataview installed, then you can also specify the annotation target with a dataview attribute. In this case, obsidian-style links can be used instead of a plain-text path.

WARNING! Don't rename an original pdf or epub file! The plugin is going to lose the connection between annotations and file in that case.

Annotating

Annotation is self-explanatory. Select text with your mouse to get started.

In the future, it would be nice to add colored highlights and image/region highlights. These features will have to be added to hypothes.is first, however. See these relevant issues: https://github.com/hypothesis/product-backlog/issues/198, https://github.com/hypothesis/product-backlog/issues/669

The annotations in markdown

To return to the regular obsidian markdown editing mode, you can select more options → Open as MD. Each annotation has an associated quote block with a block reference. Be careful with modifying these blocks. Minor edits to PREFIX, HIGHLIGHT, and POSTFIX are typically ok. But if the edits are too major, hypothesis may no longer be able to identify the corresponding text.

The COMMENT region can be freely edited. (but ensure that it is still part of the quote block.)

The TAGS region should consist of a comma-separated list of obsidian tags. (like #tag1, #tag2, #tag3)

Dark Mode

The plugin has built-in dark mode support. To toggle dark mode, select more options → Toggle Dark Mode while annotating. You can also tweak the dark mode behavior in the settings tab for the plugin.

Linking to annotations

An obsidian link to an annotation block-reference will, when clicked, open the corresponding file and scroll to the associated highlight. If the file is already open in a pane, then the link will cause the existing pane to scroll instead.

Contributing

Visit CONTRIBUTING.md for information on building from source or contribution improvements. To report a bug, ask a question or suggest an improvement for this plugin, you can create an issue.

Changelog

0.2.11 (2024-01-06)

  • Fix issue with rendering annotator in Obsidian 1.5.3 and later (See issue #356)

0.2.10 (2023-01-09)

  • Fix bug #284 Plugin didn't start on iOS

0.2.9 (2023-01-05)

  • Click on annotation link in markdown causes an immediate jump to annotation in PDF (Thanks to @HardwayLinka)
  • Fix broken drag-and-dropped link to highlight caused by line breaks. (See issue #267, Thanks to @HardwayLinka)

0.2.8 (2022-11-27)

  • Fixed issue with "Annotate" button not appearing (See issue #253)
  • Fixed issue with scroll getting stuck after clicking annotation link (See PR #259, Thanks to @HardwayLinka for the contribution)
  • Partially fixed issue with annotation links not working (See PR #231, Thanks to @XSAM for the contribution)

0.2.7 (2022-10-31)

  • Fixed issue with Latex Equations not rendering in annotations (See issue #228)
  • Removed "sign-in/log-in" buttons (See issue #241)
  • CSS Snippets can now be used to style the hypothesis sidebar

0.2.6 (2022-08-19)

  • Fix bug #208 introduced in 0.2.5 It was impossible to open an internal link because of the plugin

  • Internal changes

    • Use dataview package to communicate with dataview plugin

0.2.5 (2022-08-14)

  • Move buttons 'Annotate', 'Toggle Dark Mode', 'Open as Markdown' to top of options menu

  • Video annotation

  • Internal changes

    • CodeMirror updated to v6
    • obsidian-api updated to 0.15.9
    • betterer was installed with strict typing settings to make plugin more stable and reliable in a future

0.2.4 (2022-07-23)

0.2.2 (2022-05-14) Minor improvement

  • hypothes.is updated up to v1.1055.0

0.2.1 (2022-03-06) BRAT release Basic web and video annotation

  • annotation-target-type can now take on the values web and video.
    • With web the annotation target can (in theory) be any website. Some work better than others. Link navigation does not work.
    • With video, only youtube links are supported. In order to use this feature, a link to a zip file with the annotator.tv resources must be provided in the plugin settings. It cannot be bundled with the plugin since that would most likely violate copyright.
    • Other improvements:
      • Some behind-the-scenes changes have been made so that the hypothes.is version can be more easily upgraded in the future.

0.2.0 (2022-01-26) BRAT release Improved markdown rendering, epub reader

  • Markdown in the hypothesis sidebar should now fully support the regular obsidian syntax. (including links, embeds, custom codeblocks etc.)
  • Several Epub improvements, Thanks to @aladmit for these!
    • New option added for font size scaling (See PR #127)
    • New "epub reader mode" setting added. Infinite scrolling is now supported! (See PR #114)
    • Reduced page padding so that maximum available space is used. (See PR #126)

0.1.9 (2022-01-17) Minor fix

  • Removed sentry logging, again, (See issue #97)

0.1.8 (2022-01-16) Minor fixes, added default annotation mode setting

  • Fixed issue with pane loading on startup
  • Fixed some issues with epub highlighting
  • Added setting to choose default annotation mode, Thanks to @aladmit for the PR! (See PR #113)

0.1.7 (2022-01-14) BRAT release chinese file name support

  • Fixed issue with chinese file names, as discussed in issue #53

0.1.6 (2022-01-12) BRAT release Live Preview Drag and Drop fix + chinese character support

  • Drag and drop should now work in live preview (See issue #103)
  • Upgraded pdf.js to a newer version.
    • Improved character support. (Japanese and Chinese letters should now work), (See issue #53)
  • Removed sentry logging (See issue #97)

0.1.5 (2021-12-19) Quick fix

  • Apparently the previous update broke some of the old annotations for some people (See issue #95). This version hopefully fixes that.

0.1.4 (2021-12-18) Fix Issue With Ipad + Windows/Android compatibility.

  • See issue #70, Thanks to @jonasmerlin for the fix!

0.1.3 (2021-09-12) Basic CORS support for desktop

  • Added a basic workaround for CORS issues. This should make more links possible to view. (See issue #15)
    • Note that this workaround only works on the desktop version of obsidian.

0.1.2 (2021-09-11) Quick Fix

  • Fixed critical bug that prevented any annotations from being saved. (See issue #61)

0.1.1 (2021-09-10) Drag & Drop Fixes, Open links in new pane, Multi-Line Comments Fix

  • Drag and drop has been improved. The drop handlers are now unloaded when the plugin is unloaded. The issues regarding interferrence with other Drag and Drop functionality are hopefully also resolved. (See Issue #50)
  • Using an array format for the annotation target should now work. This improves compatibility with MetaEdit (See Issue #51)
  • Holding ctrl and clicking links (or clicking with the mouse-wheel) now opens annotations in a new pane. (See Issue #54)
  • Issue with multi-line comments should be resolved. (See Issue #47)
  • A new command (`Toggle Annotation/Markdown mode) has been added. This can be bound to a hotkey in obsidian, enabling more efficient switching between the two modes. (See issue #39)
  • Other things
    • A basic unit-test for annotation loading has also been added. More tests will be added as issues arise. This will guarantee that the plugin becomes increasingly stable over time.

0.1.0 (2021-09-03) Added annotation highlight drag and drop

  • By holding the shift key you can now drag highlights from the epub/pdf into a separate Obsidian note, and a link to the highlight will be inserted. highlight drag and drop

0.0.9 (2021-09-03) Quick fix for annotation id bug

  • See #37

0.0.8 (2021-09-03) Added Pre/Postfix setting toggles, Fixed scrolling issue, More size reductions.

  • The plugin is now available in the community plugins list!
  • The Pre- and Postfix parts of the annotation markdown can now be disabled in the settings. (See #30)
  • Clicking a PDF annotation link now causes an immediate jump to the annotation. No more glitchy scrolling. (See #21)
  • Potential fix to the memory leak mentioned in #28 added.
  • Added core-js. Will hopefully mean that the plugin works with older versions of node (see #34)
  • Disabled global WebSocket override. Should resolve issues with Obsidian Sync (see #36)
  • Further size reductions of the plugin
    • React is now built in 'production' mode.
    • All the embedded resources now use the highest zip compression ratio.

0.0.7 (2021-09-01) Added Custom Default Path setting, Page notes fix, Slight JSON size reduction, etc.

  • Added a new setting called Custom Default Path. See this comment on #19 for more info.
  • Top-level values in the annotation JSON will now be ommited if their values are "unsurprising". See #24
  • Fixed page notes breaking the loading of annotations.
  • Made the Post to... button always say Post to Only Me to reduce privacy confusion.
  • Further reduced plugin size
    • Switched from base64 to full unicode encoding
    • Added minimization of resources before zip generation
    • Added minimization of final rollup output
  • Minor fixes
    • Removed warning about websocket userid mismatch
    • Added possible fix to #13

0.0.6 (2021-08-30) file: protocol support, various url fixes, privacy improvements, minor fixes

  • Fixed so that no initial http request is made to the hypothes.is servers.
  • Hypothes.is performance trackers removed.
  • No more error messages from the websocket api.
  • The stored annotations no longer reference the sample pdf url, since that confused some users. (See issue #7)
  • Initial support for file: protocol links added. (Has not been tested much yet.)
  • The placeholder staus bar text has been removed (See issue #17)

0.0.5 (2021-08-26) Fixed EPUB bug, minor file restructuring

  • The files necessary for the epub reader were .gitignored, which prevented it from working in the previous releases. (See issue #6)
  • The code files has been moved to the src directiory so that the repo looks a bit less messy.

0.0.4 (2021-08-26) Chinese File name support

  • Added support for chinese file names. (See issue #4)

0.0.3 (2021-08-26) Plugin Size Reduction

  • Removed some unnecessary files to reduce plugin size.

0.0.2 (2021-08-26) Minor fixes

  • Removed logging,
  • Simplified link handling
  • viewer height is now 100% instead of fixed to 1000px.

0.0.1 (2021-08-25) First Release

  • Basic functionality of the plugin implemented

License

Note: The files under the resources folder are scraped from the web. Each website has its licence file attached in the associated folder.

Obsidian Annotator is licensed under the GNU AGPLv3 license. Refer to LICENSE for more information.

Support

If you want to support me and my work, you can sponsor me on Github (preferred method) or donate something on Paypal.