sparqling/spang repository overview

⁠SPANG

spang2 is a commmand-line SPARQL client implemented in JavaScript.

⁠Installation

spang2 requires node (version >= 14).

node -v

If you have installed it, skip installation of node.

⁠Installation of node on Linux

If you do not have npm, install it.

sudo apt -y install npm

on Ubuntu, or

sudo yum -y install npm

on CentOS.

The defualt directories for installation of npm modules are under /usr/local/, which requires sudo.

You can change the directories as follows.

npm set prefix ~/.npm-global

The configuration is saved in ~/.npmrc, so you can also configure by editing it.

Install n to manage node version.

npm install -g n
n stable
node -v

⁠Installation of node on Mac

If you do not have brew, install it.

brew -v

/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"

Install nodebrew using brew.

brew install nodebrew
mkdir -p ~/.nodebrew/src
export PATH=$HOME/.nodebrew/current/bin:$PATH

Now you can use node. Check the version.

node -v

⁠Installation of spang

Download the source code from GitHub.

git clone https://github.com/sparqling/spang

Install by using npm command.

cd spang
npm install
npm link

⁠Using SPARQL client

For the help message, just type the command

spang2

⁠Test examples

npm test

⁠Using SPARQL formatter

⁠Usage in command line

$ cat messy.rq 
SELECT * WHERE         {         ?s ?p ?o }

$ spfmt messy.rq 
SELECT *
WHERE {
    ?s ?p ?o .
}

⁠Usage on a web site

See: https://github.com/sparqling/sparql-formatter⁠

An example web site:
https://spang.dbcls.jp/example_fmt.html⁠

• Download spfmt.js and use it in your HTML.

<script src="/js/spfmt.js"></script>

• Then you can use spfmt.

spfmt("SELECT * WHERE {?s ?p ?o}");
/*
SELECT *
WHERE {
  ?s ?p ?o .
}
*/

• You can also call spfmt.js through the jsDelivr service.

    <textarea id="sparql-text" rows=5></textarea>
    <button id="reformat-button">Reformat</button>
    <textarea id="sparql-text-after" rows=5></textarea>
    
    <script src="https://cdn.jsdelivr.net/gh/sparqling/spang@master/js/spfmt.js"></script>
    <script type="text/javascript">
     window.onload = () => {
         var textArea = 
             document.querySelector("#reformat-button").addEventListener('click', (event) => {
                 document.querySelector("#sparql-text-after").value =
                     spfmt(document.querySelector("#sparql-text").value);
             });
     };
    </script>

⁠For maintainers

js/*.js should be updated for those who call spang functions through their Web applications.

• js/spang.js should be updated after modifying codes.
• js/spfmt.js should be updated after modifying parser or formatter codes.

Update the js/*.js by converting codes using browserify as follows.

npm run browserify

⁠Requirements

• npm (>= 6.12.0)

⁠SPARQL specifications

⁠Syntax

The EBNF notation of SPARQL is extracted from:
https://www.w3.org/TR/sparql11-query/#sparqlGrammar⁠

The PEG expression of SPARQL grammer was originally provided by:
https://github.com/antoniogarrote/rdfstore-js/⁠

PEG can be tested at:
https://pegjs.org/online⁠

⁠Medadata

sparql-doc⁠

# @title Get orthololog from MBGD
# @author Hirokazu Chiba
# @tag ortholog
# @endpoint http://sparql.nibb.ac.jp/sparql

extension

# @prefixes https://
# @input_class id:Taxon
# @output_class up:Protein
# @param gene=