https://github.com/mlcruz/articleformatter

CLI app to help formatting bibTex bibliography files. Abbreviates journal titles in a file/Remove uncited entries/Populates missing fields with a tag for highlighting/ and more
https://github.com/mlcruz/articleformatter

Last synced: 2 months ago
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CLI app to help formatting bibTex bibliography files. Abbreviates journal titles in a file/Remove uncited entries/Populates missing fields with a tag for highlighting/ and more

• Host: GitHub
• URL: https://github.com/mlcruz/articleformatter
• Owner: mlcruz
• Created: 2019-03-23T11:55:03.000Z (about 6 years ago)
• Default Branch: master
• Last Pushed: 2022-12-08T18:53:12.000Z (over 2 years ago)
• Last Synced: 2025-02-02T03:27:41.302Z (4 months ago)
• Language: JavaScript
• Homepage:
• Size: 1.97 MB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 7
• Metadata Files:
  • Readme: README.md

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README

        
# articleFormatter

## CLI app to help formatting bibTex files. 

### Funcionalities:

* Formats and indents file

* Normalizes non-standard characters

* Removes uncited citations from bib file

* Filters unwanted fields from citations (ex: notes and urls)

* Populates missing fields with a tag to make it explicit

* Abbreviates journal titles

* Removes comments

* Deals with common formatation errors

## Instalation and usage

 

### Simple Instalation Guide:

  

  If you are using windows, [chocolatey](https://chocolatey.org/install) is needed for this tutorial.

  

  #### Prerequisites

  

  You can use either yarn or npm to manage your packages. For this tutorial, we are going to use yarn.

  

  This project used Visual Studio Code + extensions (Tslint, prettier) for its development, and has some style rules already    defined. I just opened the project folder with vscode and implemented stuff, so i don't know if the folder structure is going to make it annoying if you are using something else.

  

  ##### Windows:

  

   open the command prompy as admin and follow the steps:

 

  1. install nodejs

  * with chocolatey: `choco install nodejs`

  

  2. install npm or yarn

  * with chocolatey: `choco install yarn`

  

  3. typescript compiler (if you want to compile the project)

   `yarn global add typescript`

  

  

  ##### Unix (Debian/Ubuntu):

  

   1. install nodejs :

   

    curl -sL https://deb.nodesource.com/setup_11.x | sudo -E bash -

    sudo apt-get install -y nodejs

    

   2.  install npm or yarn:

   

     curl -sS https://dl.yarnpkg.com/debian/pubkey.gpg | sudo apt-key add -

     echo "deb https://dl.yarnpkg.com/debian/ stable main" | sudo tee /etc/apt/sources.list.d/yarn.list

     sudo apt update

     sudo apt install yarn

     

   3. typescript compiler (if you want to compile the project)

   `  yarn global add typescript`

#### Instalation

  

  

  1. git clone or download the repository

  2. Initialize and download packages for the project by running `yarn` in the root directory

  

#### Usage:

  

This program assumes that the bibliography is valid bibTeX file and has no syntax errors. 

Most errors are related to some bibTex error (ex: not ending a block with a }, or missing a comma somewhere ). Reading the error msg and using something like notepad++ to go to the error char offset should be able to fix most issues with badly formated input files

  

  Source files can be fount at /src

  

  Built files can be found /build/src

  

  Important files (can be found in root for src/build files):

  1.  tableData.csv (LTWA abreviations data)

  2.  shortwords.txt 

  

  

  Running the formatter (assuming you are at the /build/src folder containing the js files): `node formatBib -t [tex file location] -b [bib file location] `. 

  

   Options:

   *   set tex input file location (required) - `-t [input file location]` 

   *  set bib input file location (required) - `-b [input file location]` 

   *   set output file location (optional, default is outbib.bib) `-o [output file location]`

   *   set LTWA table data location (optional, current folder) `-l [input file location]`

   *   set shortwords data location (optional, current folder) `-l [input file location]`

   *   help: `--help`

    

 You can also install ts-node to run the source typescript files at /src

### Compiling

  run `tsc` at root. 

 

### FAQ:

Some commom errors:

1. Error : `Unexpected token at index $Offset` => Something is badly formated. Use notepad++ or something similar and goto to the reported character offset and fix the error

2. Error: `Syntax Error: Unexpected token at index $Offset : Expected $Token, got % ` => A comment is messing things up somewhere. Probably fixed by now

3. Error : `SyntaxError: Unexpected token at index 0: Expected "@", got "%"` => First line in the file is a comment.

4. SyntaxError: `Escape sequence not recognized: $Sequence` => Some escape sequence is not parseable. To fix, replace or remove the unrecognized sequence

### Implementation:

  * simple pipeline running a list of transformations on a json file representing a bib file

  

  * funcionalities definied by steps, easily expanded

  

  * filters definied @ steps/allowedTypes and steps/filterCamptsStep

  

  * normalization rules @ steps/normalize

  

  * very loosely/badly typed

  

  * Uses [abbrevIso](https://github.com/marcinwrochna/abbrevIso) to abbreviate titles

  

  * Uses [Citation.js](https://citation.js.org/) to convert bibTex to JSON