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lit-review

v0.1.2

Published

Command line tool for scientists doing lit reviews.

Readme

Lit

Perform systematic literature reviews without loosing your mind and without wasting too much time.

Lit is a simple command line tool written in JavaScript. In the future, Lit will also be available as a GUI application for Linux, Mac OS, and Windows, but for now our focus is on nailing the conceptual data model and workflow.

Lit is under heavy development. Do not use Lit for anything mission critical unless you know what you are doing and/or accept the risks. API changes and bugs should be expected.

Lit is not for novice computer users.

Why?

Lit can help you:

  1. Combine sets of phrases (keywords) into search queries.
  2. Automatically collect results from Google Scholar.
  3. Non-destructively remove duplicate results.
  4. Tag articles.

We're also working on exporting collected references in BibTeX format.

Dependencies

To avoid issues, I humbly remind you to prefer installing software using your platform's package manager rather than manually (unless of course you know what you're doing). Package managers are a convenient way of installing and uninstalling applications. Kind of like the App Store on a Mac. Except that the correct thing to say would be that the App Store is like package managers since they've been around for eons. For Mac OS there's Homebrew and for Windows there's Chocolatey, and if you're on Linux you already know what a package manager is :P

  1. Install Node.js and npm (consider a node version manager like e.g. n).
  2. Install Selenium.
  3. Install Google Chrome (or Chromium).
  4. Install chromedriver (ships with Chromium).
  5. Ensure that chromedriver is available in your system's PATH. This should not be an issue if you installed the driver via your package manager.

Installation

npm install -g lit-review

Usage

Usage: lit <command>

lit init               Initialize new review in current dir.

lit status             Show information about current lit review.

lit feed [file]        Feed current review with phrase sets.
  [file]                 JSON formatted list of list of strings.

lit expand             Expand phrase sets into queries.

lit collect [<flags>]  Execute queries and collect results.
  --limit=N              Number of queries to execute.

lit add <tags>         Add tags to list of available tags.
  <tag>                  Tags to add. Separate with spaces.

lit browse [<flags>]   Browse and tag documents.
  --tag                  Tag mode.
  --save                 Save changes whenever prompted.
  --untagged             Only untagged.
  --tagged               Only tagged.
  --only=<tag>           Matching tag.
  --skip=<tag>           Not matching tag.

lit list [<flags>]     Print list of documents to standard out. Alias: 'ls'.
  --untagged             Only untagged.
  --tagged               Only tagged.
  --only=<tag>           Matching tag.
  --skip=<tag>           Not matching tag.

lit show <id>          Show document with id.

Example

This is an example of how a literature review could be carried out. All lit commands used below do yield output (and some are interactive) but for the sake of brevitey output is not shown here.

# Open a clean directory and initialize a lit review.
lit init

# Make a file containing the search phrases you want to use.
# The file should be a JSON formatted list of lists of strings.
echo '[["design principles", "design patterns"], ["oop", "object-oriented programming"]]' > input.json

# Let's feed the search phrases into our lit review.
lit feed input.json

# Let's expand the phrases into search queries.
lit expand

# Collect referenes for as many queries as you'd like.
lit collect --limit=1

# Have a quick look at the references you've collected.
lit ls

# Add whatever tags you'll use in your review.
lit add relevant irrelevant

# Enter the streamlined tagging/reviewing workflow.
lit browse --tag --save

# If you exit the tagging you can resume later using:
lit browse --tag --save --untagged

# Explore the references you've marked as (e.g.) relevant at any time.
lit browse --only=relevant

Contributing

Lit is very specialized tool so while issue reports and pull requests are truly very appreciated, not all proposals will be accepted. Our principles are as follows:

  • Simplicity: For intermediate users and power users.
  • Consistancy: Only allowing safe actions.
  • Respectfulness: No aggressive scraping of search results.

License

This software is released under GNU GPL v3.

Full license text available at: https://www.gnu.org/licenses/gpl-3.0.en.html.