Ecosyste.ms: Awesome

An open API service indexing awesome lists of open source software.

Awesome Lists | Featured Topics | Projects

https://github.com/out-of-cheese-error/gooseberry

A command line utility to generate a knowledge base from Hypothesis annotations
https://github.com/out-of-cheese-error/gooseberry

command-line hypothesis hypothesis-annotations knowledge-base mdbook obsidian-md wiki

Last synced: 25 days ago
JSON representation

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

Awesome Lists containing this project

README 

        
# Gooseberry - a Knowledge Base for the Lazy



[![Crates.io](https://img.shields.io/crates/v/gooseberry.svg)](https://crates.io/crates/gooseberry)

[![CI](https://github.com/out-of-cheese-error/gooseberry/workflows/Continuous%20Integration/badge.svg)](https://github.com/out-of-cheese-error/gooseberry/actions)

[![GitHub release](https://img.shields.io/github/release/out-of-cheese-error/gooseberry.svg)](https://GitHub.com/out-of-cheese-error/gooseberry/releases/)

[![dependency status](https://deps.rs/repo/github/out-of-cheese-error/gooseberry/status.svg)](https://deps.rs/repo/github/out-of-cheese-error/gooseberry)



[!["Buy Me A Coffee"](https://www.buymeacoffee.com/assets/img/custom_images/orange_img.png)](https://www.buymeacoffee.com/ninjani)



Gooseberry provides 

- a command-line interface for [Hypothesis](https://web.hypothes.is/) (a tool to annotate the web) 

- lets you generate a knowledge-base wiki without you having to actually type your knowledge out.



![Obsidian example](data/images/obsidian_example.png)



![demo](data/images/gooseberry-embedded.svg)



> made with [asciinema](https://github.com/asciinema/asciinema), [svg-term-cli](https://github.com/marionebl/svg-term-cli), and [svgembed](https://github.com/miraclx/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)



## Install



### Installation requirements



* A Hypothesis account, and a personal API token obtained as described [here](https://h.readthedocs.io/en/latest/api/authorization/).

* [bat](https://github.com/sharkdp/bat) to display highlighted markdown in the terminal.



### Binaries



See the [releases](https://github.com/out-of-cheese-error/gooseberry/releases/latest)



* 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](https://github.com/lotabout/skim/issues/293))



### With brew (OSX)



```bash

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

```

### AUR

gooseberry is [now](https://github.com/out-of-cheese-error/gooseberry/discussions/72) also available on the Arch User Repo [here](https://aur.archlinux.org/packages/gooseberry-bin/) 



## Contributing



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



## Motivation



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](https://web.hypothes.is/), 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"](https://nautil.us/issue/73/play/we-need-insects-more-than-they-need-us),

this [publication about honey bees and pesticides](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0070182),

and [an Atlantic article about the "anternet"](https://www.theatlantic.com/technology/archive/2012/08/lessons-from-the-anternet-what-ants-and-computers-have-in-common/261580/)

.



I synced and tagged these annotations:



![gooseberry sync and tag](data/images/sync_tag.png)



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



![Tag page example](data/images/wiki.png)



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



![Obsidian example](data/images/obsidian_example.png)



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



![Picture example](data/images/md_picture.png)



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.)



## Usage

```

Usage: gooseberry [OPTIONS] 



Commands:

  sync      Sync newly added or updated Hypothesis annotations

  search    Opens a search buffer to filter annotations. Has keyboard shortcuts for deleting annotations, modifying tags, and creating knowledge-base files

  tag       Tag annotations according to topic

  delete    Delete annotations in bulk

  view      View (optionally filtered) annotations

  uri       Get the set of URIs from a list of (optionally filtered) annotations

  make      Create knowledge-base text files using optionally filtered annotations

  index     Create an index file using hierarchy and optionally filtered annotations

  complete  Generate shell completions

  config    Manage configuration

  clear     Clear all gooseberry data

  move      Move (optionally filtered) annotations from a different hypothesis group to Gooseberry's

  help      Print this message or the help of the given subcommand(s)



Options:

  -c, --config   Location of config file (uses default XDG location or environment variable if not given) [env: GOOSEBERRY_CONFIG=]

  -h, --help             Print help

```



The default config TOML file is located in



* Linux: `/home//.config`

* Mac: `/Users//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 ` 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 given Hypothesis group(s) which you can create/set with `gooseberry config group`. This automatically syncs all existing annotations from these groups.



Sync newly added annotations with `gooseberry sync`.



The `search` command provides an interactive search interface to your annotations (optionally pre-filtered using the filtering options below). Each annotation is rendered using the annotation template (configured with `gooseberry config kb annotation` and described below). The interface supports the following keybindings:

Arrow keys to scroll, Tab to toggle selection, Ctrl-A to select all, Esc to abort

Enter to add a tag, Shift-Left to delete a tag, Shift-Right to delete an annotation

Shift-Down to make knowledge-base files, Shift-Up to print the set of URIs.



You can also accomplish these tasks without the interactive interface using the `tag`, `delete`, `view`, `uri`, `make`, and `index` commands.



**NOTE: tagging and deletions are synced to Hypothesis!**



### Filtering



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



```

      --from 

          Only annotations created after this date and time

          

          Can be colloquial, e.g. "last Friday 8pm"



      --before 

          Only annotations created before this date and time

          

          Can be colloquial, e.g. "last Friday 8pm"



  -i, --include-updated

          Include annotations updated in given time range (instead of just created)



      --uri 

          Only annotations with this pattern in their URL

          

          Doesn't have to be the full URL, e.g. "wikipedia"

          

          [default: ]



      --any 

          Only annotations with this pattern in their `quote`, `tags`, `text`, or `uri`

          

          [default: ]



      --tags 

          Only annotations with ANY of these tags (use --and to match ALL)



      --groups 

          Only annotations from these groups



      --exclude-tags 

          Only annotations without ANY of these tags



      --quote 

          Only annotations that contain this text inside the text that was annotated

          

          [default: ]



      --text 

          Only annotations that contain this text in their textual body

          

          [default: ]



  -n, --not

          Annotations NOT matching the given filter criteria



      --and

          (Use with --tags) Annotations matching ALL of the given tags



  -p, --page

          Only page notes



  -a, --annotation

          Only annotations (i.e exclude page notes)

```



### Knowledge base



The `gooseberry make` command is used to generate knowledge base files using (optionally filtered) annotations. By default, it also generates an index file (configured by the `index`

and `link` configuration options) - this can be disabled with `--no-index`. Use `gooseberry index` to generate just the index file.



Configuration options for the knowledge base are as follows:

```

Usage: gooseberry config kb 



Commands:

  all         Change everything related to the knowledge base

  directory   Change knowledge base directory

  annotation  Change annotation handlebars template

  page        Change page handlebars template

  link        Change index link handlebars template

  index       Change index file name

  extension   Change knowledge base file extension

  hierarchy   Change folder & file hierarchy

  sort        Change sort order of annotations within a page

  ignore      Set which tags to ignore

  nest        Set string defining nested tags (e.g "/" => parent/child)

  help        Print this message or the help of the given subcommand(s)

```



You can set all knowledge base configuration options at once by running `gooseberry config kb all` or changing the corresponding keys in the config file (found at `gooseberry config where`).



**IMPORTANT:** The knowledge base 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



The `annotation` template is used to render a single 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](https://docs.rs/chrono/0.4.19/chrono/format/strftime/index.html) for formatting options)

* `updated` - Date of the last modification. Use with the `date_format` helper (See [here](https://docs.rs/chrono/0.4.19/chrono/format/strftime/index.html) for formatting options)

* `{{ user }}` - User account ID formatted as `acct:@`

* `{{ 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.

    * e.g. https://github.com/rust-lang/cargo?asdf becomes https://github.com/

* `{{ 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,

* `{{ group_name }}` - Name 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](https://handlebarsjs.com/guide/#what-is-handlebars) for more on templating. You can also make use of the helpers from [handlebars_misc_helpers](https://lib.rs/crates/handlebars_misc_helpers).



Some examples for using the list keys

and for formatting dates are shown below for different systems:



* mdBook



```markdown

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



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



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



{{text}}



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

```



Renders as:



```markdown

##### 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



```markdown

### {{id}}



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



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



{{text}}



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

```



Renders as:



```markdown

### 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



The `page` template is used for rendering a single page of annotations (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:



```markdown

# {{name}}



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



```



#### Grouping annotations into folders and pages



The `hierarchy` configuration 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.

* Group - Groups annotations by group ID.

* GroupName - Groups annotations by group name.



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



e.g.



`hierarchy = ["Group", "Tag"]` would make a separate folder for each group. 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



The `sort`configuration 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

* Group

* GroupName

* 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.



#### Index link template



The `link` template controls how each link in the index file is rendered. The available keys are:



* `{{ name }}` - file stem

* `{{ relative_path }}` - path relative to KB directory

* `{{ absolute_path }}` - full path on filesystem



Examples:



* mdBook



```markdown

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



```



* Obsidian



```markdown

- [[{{name}}]]



```



to make internal links, or



```markdown

- ![[{{name}}]]



```



to transclude files



* Org-mode



```org

- [[{{relative_path}}][{{name}}]]



```



#### Other options



- `index` - sets 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.

- `ignore` - sets the list of tags to ignore when creating the knowledge base. *Note: Annotations with ignored tags will still be included in the `search` and `tag` commands*

- `nest` -  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. *Note: Commas (",") and semicolons (";") should not be used inside tags as they are used as separators by Gooseberry.*

- `extension` - sets the file extension for the knowledge base files. e.g. "md", "org", "txt" etc. *Note: Don't include the . in the extension*



## Why "Gooseberry"?



Because Discworld will never let me down when it comes to names:

[Dis-organizer Mark 5, the Gooseberry](https://wiki.lspace.org/mediawiki/Dis-organiser)