doc_manage

Some bash shell scripts helping managing documents and research references on local disk

Overview

I'm trying to do some management work on my collection of research papers, current model I'm using:

• Create a folder at ~/Papers, everything happens inside this.
• Save all the PDF files or doc files in one sub-folder: ~/Papers/collection.
• Create a number of sub-folders under ~/Papers, using topic names as folder names, e.g. ~/Papers/global_warming.
• Create relative symlinks from the document files into topic subfolders, e.g. ln -sr ~/Papers/collection/file1.pdf ../global_warming/. This way, a paper can appear in multiple topic folder without taking up multiples of disk space, and any changes (highlights, notes) made to it applies to all symlinks.

Scripts

1. find_links.sh

Given an input document file, find all topic folder names by following symlinks E.g.

./find_links.sh ~/Papers/collection/file1.pdf

outputs

global_warming
global_warming_too_fast
global_warming_too_fast_too_bad

2. find_orphans.sh

Scan through the collection folder and list all files with no symlinks, i.e. papers you haven't assign any topics to.

E.g.

./find_orphans.sh

3. add_links.sh

Given an input document file and a topic name, search (case insensitively) folders with name of the topic within the library folder (~/Papers). If none exists, ask to create a new folder under the library folder. Then (ask to) copy the file to the collection folder, and (ask to) create a symlink(s) from the new location iside collection folder to all subfolders with name "topic".

Use this to add new paper to the collection and assign topic tags.

4. add_links_folder.sh

Call add_links.sh on each doc in a folder, using the folder name as tag.

Use this to batch-add a folder of new documents.

5. getBib.sh

Search string in a .bib file containing multiple entries, and return all entries containing the search string.

E.g.

./getBib.sh 'Osborn2000' ./my_bib.bib

It will first call grep -i 'Osborn2000' ./my_bib.bib to get all matching line numbers, and from each matching, look up and down to get the whole bib entry (enclosed by @article{ and }). After remoivng duplicates, it returns all entries.

6. recoll_query.sh

This is me playing around with the rofi launcher with the recoll search engine.

After launching ./recoll_query.sh, rofi pops up an input box for you to type in the search string. After pressing enter, recoll does a full text search (according to your setup of indexing), and return returns via rofi again. Select (by moving up/down) and hit enter on one or more than one entries, PDFs (or docs or whatever) opens in external programs.

config_oneliner, config_recoll, Arc-Dark.rasi, arthur_modified.rasi are the relevant rofi config files used in this. Typically you put them in ~/.config/rofi/.

Notices

I learned quite some bash scripting when making these, and they certainly contain some issues/bugs. If you found any please don't hesitate to fire up an issue. And new ideas are welcome too.

When packing up the library folder (e.g. do a back up or transfer to another machine), in order to preserve the relative symlinks, the easiest way is to tar up the entire folder and unpack in the new location.