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protocolsioapi

0.0.8 • Public • Published

What is this?

protocolsioapi is an NPM module that allows you easy access to the protocols.io REST api for searching protocols, retrieving metadata in JSON format, and downloading a PDF specification.

If you enjoy using protocolsioapi, please check us out on github or follow me on twitter.

How do I use it?

First add it to your project with:

$ npm install protocolsioapi

Then import it into your code using:

var ProtocolsIO = require('protocolsioapi');
var protocolsioapi = new ProtocolsIO('<your api key here>');

To get a listing of all protocols matching a the keyword 'foo', use:

protocolsioapi.getProtocols('foo', null, function(error, result) {
    if(error) {
        console.log(error);
    } else {
        /// do something with result here
    }
});

An example of output from this would be:

{
    "request": "OK",
    "protocols": [{
        "protocol_name": "Transformation of Skeletonema marinoi using Multipulse Electroporation",
        "protocol_id": "5038",
        "version_class": "5038",
        "activity": "1486591925",
        "is_owner": "0"
    }, {
        "protocol_name": "Modeling ecological drivers in marine viral communities using comparative metagenomics and network analyses",
        "protocol_id": "2248",
        "version_class": "2248",
        "activity": "1486591923",
        "is_owner": "0"
    }, {
        "protocol_name": "Enumerating algal viruses by flow cytometry",
        "protocol_id": "4714",
        "version_class": "3172",
        "activity": "1486591921",
        "is_owner": "0"
    }, {
        "protocol_name": "Transient genetic transformation of Bodo caudatus using square wave electroporation system and pUB-GFP plasmid",
        "protocol_id": "5016",
        "version_class": "5016",
        "activity": "1484604721",
        "is_owner": "0"
    }, {
        "protocol_name": "Electroporation of COS-7 cells and functionalization of QDs",
        "protocol_id": "4909",
        "version_class": "4909",
        "activity": "1484604721",
        "is_owner": "0"
    }, {
        "protocol_name": "Preparation of 1.5 mg\/mL Sera-mag carbolylate modified magnetic particles",
        "protocol_id": "4898",
        "version_class": "4898",
        "activity": "1484604721",
        "is_owner": "0"
    }, {
        "protocol_name": "Library Preparation for Sequencing of Assembled Gene Clusters",
        "protocol_id": "4896",
        "version_class": "4896",
        "activity": "1484604721",
        "is_owner": "0"
    }, {
        "protocol_name": "Protein renaturation from pellet samples",
        "protocol_id": "4876",
        "version_class": "4876",
        "activity": "1484604721",
        "is_owner": "0"
    }, {
        "protocol_name": "Microcystinase (MlrA) sample preparation for enzymatic activity assay",
        "protocol_id": "4874",
        "version_class": "4874",
        "activity": "1484604721",
        "is_owner": "0"
    }, {
        "protocol_name": "Microsome preparation",
        "protocol_id": "4872",
        "version_class": "4872",
        "activity": "1484604721",
        "is_owner": "0"
    }],
    "total_results": "108",
    "total_pages": 11,
    "page_served": 0,
    "extras": {
        "2": [{
            "group_name": "VERVE Net",
            "group_logo": "https:\/\/s3.amazonaws.com\/pr-journal\/cdqcwwe.png",
            "uri": "verve-net",
            "total": 122
        }, {
            "group_name": "Sullivan Lab",
            "group_logo": "https:\/\/s3.amazonaws.com\/pr-journal\/fxc3an.jpg",
            "uri": "sullivan-lab",
            "total": 37
        }, {
            "group_name": "BioLegend",
            "group_logo": "https:\/\/s3.amazonaws.com\/pr-journal\/djiecje.png",
            "uri": "biolegend",
            "total": 31
        }, {
            "group_name": "Hurwitz Lab",
            "group_logo": "https:\/\/s3.amazonaws.com\/pr-journal\/iscwwe.png",
            "uri": "hurwitz-lab",
            "total": 22
        }, {
            "group_name": "G-Biosciences",
            "group_logo": "https:\/\/s3.amazonaws.com\/pr-journal\/d6heeee.png",
            "uri": "gbiosciences",
            "total": 20
        }, {
            "group_name": "MetaFunc Course",
            "group_logo": "https:\/\/s3.amazonaws.com\/pr-journal\/emybvtw.jpg",
            "uri": "metafunc-course",
            "total": 19
        }, {
            "group_name": "OpenPlant Project",
            "group_logo": "https:\/\/s3.amazonaws.com\/pr-journal\/d73eiee.png",
            "uri": "openplant-project",
            "total": 14
        }, {
            "group_name": "Bioline",
            "group_logo": "https:\/\/s3.amazonaws.com\/pr-journal\/ftxe5pn.png",
            "uri": "bioline",
            "total": 12
        }, {
            "group_name": "Genetics",
            "group_logo": "https:\/\/s3.amazonaws.com\/pr-journal\/55wpd.png",
            "uri": "genetics",
            "total": 12
        }, {
            "group_name": "Upton-Lab",
            "group_logo": "https:\/\/s3.amazonaws.com\/pr-journal\/6xbf8w.jpg",
            "uri": "uptonlab",
            "total": 9
        }]
    },
    "author_details": null,
    "host": 1,
    "status_code": 0
}

You can get individual pages of results using the pageid argument:

protocolsioapi.getProtocols('foo', '3', function(error, result) {
    if(error){
        console.log(error);
    } else {
        /// do something with result here
    }
});

Getting JSON metadata works similarly but requires a protocol id number:

protocolsioapi.getProtocolJSON('5308', function(error, result) {
    if(error) {
        console.log(error);
    } else {
        // do something with the result
    }
});

You can retrieve multiple protocols' JSON at once using getProtocolJSONArray:

protocolsioapi.getProtocolJSONArray(['5308', '4714', '2248'], function(error, result) {
    if(error) {
        console.log(error);
    } else {
        // result contains the JSON for each of the protocols, and the protocol ids are the keys
        // for example, print the JSON for protocol 4714
        console.log(result['4714']);
    }
});

And to get the PDF specification of the protocol:

protocolsioapi.getProtocolPDF('5308', function(error, result) {
    if(error) {
        console.log(error);
    } else {
        // do something with the result (perhaps save it to the disk?)
    }
});

You can even get multiple PDFs at once using getProtocolPDFArray:

protocolsioapi.getProtocolPDFArray(['5308', '4714', '2248'], function(error, result) {
    if(error) {
        console.log(error);
    } else {
        // result contains the PDFs for each of the protocols, and the protocol ids are the keys
        // for example, write the PDF for protocol 5308
        fs.writeFile('5308.pdf', result['5308'], function(err) {
            if(err) {
                return console.log(err);
            }
            console.log('File 5308.pdf successfully written to disk.');
        });
    }
});

install

npm i protocolsioapi

Downloadsweekly downloads

16

version

0.0.8

license

ISC

homepage

github.com

repository

Gitgithub

last publish

collaborators

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