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Add usage instructions to README

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Marty Oehme 2022-12-22 21:43:10 +01:00
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Quickly extract annotations from your pdf files with the help of the pubs bibliography manager.
Installation:
## Installation:
Still a bit painful since I have not set up any package management:
Put `extract` folder in your pubs `plugs` directory.
Add extract to your plugin list in pubs configuration file.
Then add `extract` to your plugin list in the pubs configuration file.
Usage:
## Usage:
`pubs extract <citekeys>`
`pubs extract [-h|-w|-e] <citekeys>`
This readme is a stub so far, feel free to extend it and raise a PR if you have the time.
What follows is a not-very-sorted train of though on the plugin and pubs in general,
to keep my thoughts in one place while I work on it.
For example, to extract annotations from two entries, do:
## extractor plugin:
```bash
pubs extract Bayat2015 Peck2004
```
- extracts highlights and annotations from a doc file (e.g. using PyMuPDF)
- puts those in the annotation file of a doc in a customizable format
- option to have it automatically run after a file is updated?
- needs some way to delimit where it puts stuff and user stuff is in note
- one way is to have it look at `> [17] here be extracted annotation from page seventeen` annotations and put it in between
- another, probably simpler first, is to just append missing annotations to the end of the note
- some highlights (or annotations in general) do not contain text as content
- pymupdf can extract the content of the underlying rectangle (mostly)
- issue is that sometimes the highlight contents are in content, sometimes a user comment instead
- we could have a comparison function which estimates how 'close' the two text snippets are and act accordingly
- config option to map colors in annotations to meaning ('read', 'important', 'extra') in pubs
- colors are given in very exact 0.6509979 RGB values, meaning we could once again estimate if a color is 'close enough' in distance to tag it accordingly
- make invoking the command run a query if `-e` option provided (or whatever) in pubs syntax and use resulting papers
- confirm?
This will print the extracted annotations to the commandline through stdout.
# would also be nice in pubs, missing for me
If you invoke the command with the `-w` option, it will write it into your notes instead:
```bash
pubs extract -w Bayat2015 Peck2004
```
Will create notes for the two entries in your pubs note directory and fill them with
the annotations. If a note already exists for any of the entries, it will instead append
the annotations to the end of it, dropping all those that it already finds in the note
(essentially only adding new annotations to the end).
**PLEASE** Be aware that so far, I spent a single afternoon coding this plugin, it
contains no tests and operates on your notes. In my use nothing too bad happened but
only use it with adequate backup in place, or with your library being version controlled.
You can invoke the command with `-e` to instantly edit the notes:
```bash
pubs extract -w -e Bayat2015 Peck2004
```
Will create/append annotations and drop you into the Bayat2015 note, when you close it
directly into the Peck2004 note. Take care that it will be fairly annoying if you use this
option with hundreds of entries being annotated.
To extract the annotations for all your existing entries in one go, you can use:
```bash
pubs extract -w $(pubs list -k)
```
However, the warning for your notes' safety goes doubly for this command since it will touch
*most* or *all* of your notes, depending on how many entries in your library have pdfs attached.
This readme is still a bit messy, feel free to extend it and raise a PR if you have the time.
What follows is a not-very-sorted train of though on where the plugin is at and where I
could see myself taking it one day, provided I find the time.
Pull requests tackling one of these areas of course very welcome.
## Roadmap:
- [x] extracts highlights and annotations from a doc file (e.g. using PyMuPDF)
- [ ] puts those in the annotation file of a doc in a customizable format
- [x] option to have it automatically run after a file is added?
- option to have it run whenever a pdf in the library was updated?
- [ ] needs some way to delimit where it puts stuff and user stuff is in note
- [ ] one way is to have it look at `> [17] here be extracted annotation from page seventeen` annotations and put it in between
- [x] another, probably simpler first, is to just append missing annotations to the end of the note
- [ ] some highlights (or annotations in general) do not contain text as content
- [ ] pymupdf can extract the content of the underlying rectangle (mostly)
- [ ] issue is that sometimes the highlight contents are in content, sometimes a user comment instead
- [ ] we could have a comparison function which estimates how 'close' the two text snippets are and act accordingly
- [ ] config option to map colors in annotations to meaning ('read', 'important', 'extra') in pubs
- [ ] colors are given in very exact 0.6509979 RGB values, meaning we could once again estimate if a color is 'close enough' in distance to tag it accordingly
- [ ] make invoking the command run a query if corresponding option provided (or whatever) in pubs syntax and use resulting papers
- [ ] confirm for many papers?
## Things that would also be nice in pubs in general and don't really belong in this repository
- `show` command which simply displays given entry in a nice way
- could take multiple entries but present them all in the same larger way