#knowledge-base #hypothesis #cli #wiki

bin+lib gooseberry

A command line utility to generate a knowledge base from Hypothesis annotations

15 unstable releases

0.9.3 Apr 30, 2022
0.9.1 Jul 14, 2021
0.7.1 Mar 29, 2021
0.1.1 Nov 28, 2020

#618 in Command line utilities

Download history 2/week @ 2022-11-22 1/week @ 2022-12-06 16/week @ 2022-12-13 2/week @ 2022-12-20 1/week @ 2023-01-03 1/week @ 2023-01-17 6/week @ 2023-01-24 6/week @ 2023-01-31 16/week @ 2023-02-07 39/week @ 2023-02-14 17/week @ 2023-02-21

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MIT and LGPL-3.0-or-later

2.5K SLoC

Gooseberry - a Knowledge Base for the Lazy

Crates.io CI GitHub release dependency status

Gooseberry provides a command-line interface for Hypothesis (a tool to annotate the web) and lets you generate a knowledge-base wiki without you having to actually type your knowledge out.

Obsidian example


made with asciinema, svg-term-cli, and svgembed

This demonstrates the interactive search functionality. Enter adds a new tag, Shift-Left deletes a tag, and Shift-Right deletes an annotation. (TODO: embed keypresses in GIF)

Table of Contents


Installation requirements

  • A Hypothesis account, and a personal API token obtained as described here.
  • bat to display highlighted markdown in the terminal.


See the releases

  • OSX - allow gooseberry via System Preferences (necessary in Catalina at least)
  • Linux - chmod +x gooseberry
  • Currently, doesn't work on Windows (waiting on this issue)

With brew (OSX)

brew tap out-of-cheese-error/gooseberry && brew install gooseberry


gooseberry is now also available on the Arch User Repo here


See CONTRIBUTING.md for an in-depth explanation of how Gooseberry works and what could be improved.


So yes, knowledge-base tools are old hat and a dime a dozen, and we really have no excuse to not have a nice big tangled folder of markdown files filled with our overflowing wisdom. But after spending all day writing code and papers and tasks, it just isn't fair that our reading time also needs to be typing time to get all that knowledge down. And if we don't type things out our fancy knowledge-base is bare, empty, and sad.

In comes Gooseberry - a tool to build a knowledge base from highlighting and annotating passages while reading news articles, blog posts, papers, what have you. Gooseberry combines the ease of annotation offered by Hypothesis, bulk tagging and organization support in the command line, and a customizable plaintext wiki with HandleBars templating.

A typical workflow

  1. Find an article, blog post, paper etc. to read.
  2. Highlight lines and facts you'd like to remember later. You can add comments and tags already if you're up for it but the focus can also be just on reading and highlighting without thinking too much about taking notes.
  3. More often than not, when one gets into a topic it ends in 50 open tabs of subtopics. This is fine, keep reading and highlighting away, we'll get back to this.
  4. Finally, once your thirst for knowledge has been fulfilled, fire up a terminal and run
    • gooseberry sync to download all your latest highlights and annotations.
    • gooseberry tag --from "9a.m." topic to tag everything you've read this morning with the topic you were looking into. This subcommand is super flexible. You can tag something by a website, so that all annotations from subtopic B's wikipedia page are tagged as B for instance. Or just open up search to search your annotations and add tags to everything matching a search query (or remove tags and annotations). Tags are very nestable, definitely make use of this - e.g. all annotations today may be about topic A, five of them are also subtopic B etc.
    • gooseberry make to add all this new tagged information to your knowledge base.

Here's an example. Today I read and annotated three articles about insects: this Nautilus article titled "We need insects more than they need us", this publication about honey bees and pesticides, and an Atlantic article about the "anternet" .

I synced and tagged these annotations:

gooseberry sync and tag

Then ran gooseberry make to make an mdBook style wiki which I could then open in the browser:

Tag page example

Or an Obsidian style wiki, with annotations grouped into folders based on the document/web-page title

Obsidian example

Annotation text is just markdown so text formatting, LaTeX, pictures etc. goes too!

Picture example

The annotation template is configurable, as is the folder and grouping structure. Each annotation can link back to the position in the website that you got it from, if ever you feel like you're missing context.

Some advantages

  • You barely have to type while reading unless you're in the mood for taking notes.
  • If you're in the mood, the note-taking won't involve window switching.
  • Even without using the wiki functionality you end up with a CLI to quickly tag your Hypothesis annotations.
  • Even without using the tagging functionality you end up with a pretty cool wiki listing all your annotations.
  • Since it's just plaintext, and the template can be customized, you can integrate it with any knowledge base system accepting plaintext files (like Obsidian, mdBook, org-mode, vim-wiki, etc.)


You can filter the annotations you want to modify or export using the following options in most gooseberry commands:

    -i, --include-updated
            Include annotations updated in given time range (instead of just created)

    -n, --not
            Annotations NOT matching the given filter criteria

    -o, --or
            (Use with --tags) Annotations matching ANY of the given tags

    -p, --page
            Only page notes

    -a, --annotation
            Only annotations (i.e exclude page notes)

        --from <from>
            Only annotations created after this date and time

            Can be colloquial, e.g. "last Friday 8pm"
        --before <before>
            Only annotations created before this date and time

            Can be colloquial, e.g. "last Friday 8pm"
        --uri <uri>
            Only annotations with this pattern in their URL

            Doesn't have to be the full URL, e.g. "wikipedia" [default: ]
        --any <any>
            Only annotations with this pattern in their `quote`, `tags`, `text`, or `uri` [default: ]

        --tags <tags>...
            Only annotations with ALL of these tags (use --or to match ANY)

        --exclude-tags <exclude-tags>...
            Only annotations without ANY of these tags

        --quote <quote>
            Only annotations that contain this text inside the text that was annotated [default: ]

        --text <text>
            Only annotations that contain this text in their textual body [default: ]


The default config TOML file is located in

  • Linux: /home/<username>/.config
  • Mac: /Users/<username>/Library/Preferences

Change this by creating a config file with gooseberry config default > config.toml and modifying the contents. You can then use this as your configuration with gooseberry -c path/to/config.toml <subcommand> or by setting the environment variable $GOOSEBERRY_CONFIG to point to the file.


Authorize Hypothesis either by setting the $HYPOTHESIS_NAME and $HYPOTHESIS_KEY environment variables to your username and developer API token or by running gooseberry config authorize.

Gooseberry takes annotations from a given Hypothesis group which you can create/set with gooseberry config group.

Knowledge base

You can set all the below options at once by running gooseberry config kb all or changing the corresponding keys in the config file (found at gooseberry config location)

Generate knowledge base files using gooseberry make - this command has options to filter annotations, and to clear the directory before generating (-c or --clear). By default, it also generates an index file (configured by the index and link configuration options below) using the filtered annotations - this can be disabled with --no-index. Use gooseberry index to generate just the index file, this command also has annotation filtering options.

Knowledge base directory

gooseberry config kb directory

The directory to save the generated knowledge base files.

IMPORTANT: This directory is cleared at every sync so if you're storing Hypothesis annotations alongside other notes, make sure to make a separate folder.

Annotation template

gooseberry config kb annotation

Change the template used for rendering the annotation.

The following keys can be used inside the template

  • {{ id }} - Annotation ID
  • created - Date of creation. Use with the date_format helper (See here for formatting options)
  • updated - Date of the last modification. Use with the date_format helper (See here for formatting options)
  • {{ user }} - User account ID formatted as acct:<username>@<authority>
  • {{ uri }} - URI of page being annotated (this can be a website URL or a PDF URN)
  • {{ base_uri }} - Base website of URI, i.e just the protocol and domain.
  • {{ title }} - Title of webpage/article/document
  • {{ incontext }} - Link to annotation in context (opens the Hypothesis sidebar and focuses on the annotation)
  • highlight - List of selected/highlighted lines from document (split by newline)
  • {{ text }} - The text content of the annotation body
  • tags - A list of tags associated with the annotation.
  • {{ group }} - ID of Hypothesis group,
  • references - List of annotation IDs for any annotations this annotation references (e.g. is a reply to)
  • {{ display_name }} - Display name of annotation creator. This may not be set.

See the Handlebars Language Guide for more on templating. You can also make use of the helpers from handlebars_misc_helpers.

Some examples for using the list keys and for formatting dates are shown below for different systems:

  • mdBook
##### {{date_format "%c" created}} - *{{id}}*

{{#each tags}}| [{{this}}]({{this}}.md) {{#if @last}}|{{/if}}{{/each}}

{{#each highlight}}> {{this}}{{/each}}


[See in context]({{incontext}})

Renders as:

##### Sat Jan 16 11:12:49 2021 - *test*

| [tag1](tag1.md) | [tag2](tag2.md) |

> exact text highlighted in website

testing annotation

[See in context](https://incontext_link.com)

This makes each tag a link to a dedicated page consisting of annotations with that tag - you can set this up by configuring the hierarchy (hierarchy = ["tag"]).

  • Obsidian
### {{id}}

Created: {{date_format "%c" created}} Tags: {{#each tags}}#{{this}}{{#unless @last}}, {{/unless}}{{/each}}

{{#each highlight}}> {{this}}{{/each}}


[See in context]({{incontext}})

Renders as:

### test

Created: Sat Jan 16 10:22:20 2021 Tags: #tag1, #tag2

> exact text highlighted in website

testing annotation

This uses #tags b/c Obsidian likes those.

TODO add org-mode example

Page template

gooseberry config kb page

Change the template used for rendering a single page (NOT the Index page).

The following keys can be used inside the template:

  • {{ name }} - file stem
  • {{ relative_path }} - path relative to KB directory
  • {{ absolute_path }} - full path on filesystem
  • annotations - a list of rendered annotations (according to the annotation template)
  • raw_annotations - a list of annotations (in case you need info for the page about the annotations - e.g. {{raw_annotations.0.title}})

The default template is:

# {{name}}

{{#each annotations}}{{this}}{{/each}}

Grouping annotations into folders and pages

gooseberry config kb hierarchy

The hierarchy defines how the folder and file structure of the knowledge base looks and which annotations are on what pages.

The available options are:

  • Empty - Set hierarchy = [] to have all annotations rendered on the index page.
  • Tag - Groups annotations by tag
  • URI - Groups annotations by their URI
  • BaseURI - Groups annotations by their base URI
  • Title - Group annotations by the title of their webpage/article/document
  • ID - Groups annotations by annotation ID.

Multiple hierarchies combined make folders and sub-folders, with the last entry defining pages.


hierarchy = ["BaseURI", "Tag"] would make a separate folder for each base_uri. Within each folder would be a page for each tag consisting of annotations marked with that tag.

hierarchy = ["Tag"] gives the structure in the mdbook figure above, i.e. no folders, a page for each tag.

Sorting annotations within a page

gooseberry config kb sort

This defines how annotations are sorted within each page.

The available options are:

  • Tag - Sorts by tag (multiple tags are considered as "tag1,tag2,tag3" for sorting)
  • URI
  • BaseURI
  • Title
  • ID
  • Created
  • Updated

Multiple sort options can be combined in order of priority e.g. sort = ["Tag", "Created"] sorts by tags, then by the date of creation.

Tags and nesting

gooseberry config kb nested

This defines the pattern to use for nesting tags. e.g. if nested_tag = "/" then a tag of "parent/child" combined with hierarchy = ["Tag"] would create a "parent" folder with a "child" file inside it.

Commas (",") and semicolons (";") should not be used inside tags as they are used as separators by Gooseberry.

gooseberry config kb link

This configures the index file, which generally contains links to all other pages in the generated knowledge base (unless hierarchy=[] in which case all annotations are rendered on the index page). The template controls how each of these links are rendered.

Available keys:

  • {{ name }} - file stem
  • {{ relative_path }} - path relative to KB directory
  • {{ absolute_path }} - full path on filesystem


  • mdBook
- [{{name}}]({{relative_path}})

  • Obsidian
- [[{{name}}]]

to make internal links, or

- ![[{{name}}]]

to transclude files

  • Org-mode
- [[{{relative_path}}][{{name}}]]

Index filename

gooseberry config kb index

The name of the Index file, e.g. mdbook needs this to be called "SUMMARY" and in Obisidan you could use "00INDEX" to make it show up first in the file explorer.

Ignoring tags

gooseberry config kb ignore

Some annotations maybe aren't meant for the knowledge base. You can exclude these by tagging them with a specific tag, and then adding this tag to the ignore_tags configuration option (manually in the config file or with the above command). Note: Annotations with ignored tags will still be included in the search and tag commands.

File extensions

gooseberry config kb extension

e.g. "md", "org", "txt" etc. (Don't include the .)

Why "Gooseberry"?

Because Discworld will never let me down when it comes to names: Dis-organizer Mark 5, the Gooseberry


~769K SLoC