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  • Aug 01 2016 00:35

    bmpvieira on master

    Add bionode talks and organise (compare)

  • Jul 10 2016 23:28

    bmpvieira on master

    Create output_example.js Merge pull request #1 from adri… (compare)

  • Jul 10 2016 23:28
    bmpvieira closed #1
  • Jul 10 2016 23:26

    bmpvieira on master

    Fix link in README.md (compare)

  • Jul 10 2016 23:23

    bmpvieira on master

    Add 1st edition BioHackers to R… (compare)

  • Jul 09 2016 11:21

    adrianalexa on master

    Plan for the day - bionodehack (compare)

  • Jul 09 2016 11:20

    adrianalexa on master

    Data landscape by Repositive (compare)

  • Jul 09 2016 11:19

    adrianalexa on master

    Plan for the day slide deck (compare)

  • Jul 09 2016 10:20
    adrianalexa opened #1
  • Jul 09 2016 08:48

    Istar-Eldritch on master

    Add Programe Merge branch 'master' of github… (compare)

  • Jul 08 2016 15:03

    bmpvieira on master

    Add presentation about Streams … (compare)

  • Jul 08 2016 14:37

    Istar-Eldritch on master

    Add Streams Handbook tutorial b… (compare)

Clarkie
@clarkie
in particular is a streams tutorial
Giovanni
@giovannic
@DennisSchwartz Thanks, I'll have a look
Louis Maddox
@biochemistries_twitter
Claudiu Creanga
@ClaudiuCreanga
can you share the ebi url for the data please
Marc Rivelles
@fsdevlondon

var url = require('url');
var request = require('request');

var urlObject = {
protocol: 'http',
host: 'www.ebi.ac.uk',
pathname: '/eva/webservices/rest/v1/meta/studies/list',
search: '?species=hsapiens_grch37'
}
var urlString = url.format(urlObject);

request(urlString).pipe(process.stdout);

Dennis Schwartz
@DennisSchwartz
Here is the link to the slides again:
This is the current talk with the code.
Giovanni
@giovannic
@DennisSchwartz cheers, miss.from and miss.to look really cool
Adrian Alexa
@adrianalexa
The slides presented by Charlotte on Genomic data landscape will be available on the https://github.com/bionode-hack/discussions/ repository after the lunch break
Clarkie
@clarkie
for documentation on all these modules you can go to https://www.npmjs.com/ (e.g. https://www.npmjs.com/package/jsonstream)
Clarkie
@clarkie
'use strict';

const url = require('url');
const request = require('request');
const JSONStream = require('jsonstream');
const split = require('split');
const through = require('through2');

const urlObject = {
  protocol: 'http',
  host: 'www.ebi.ac.uk',
  pathname: '/eva/webservices/rest/v1/meta/studies/list',
  search: '?species=hsapiens_grch37'
};


var urlString = url.format(urlObject);

const filter = function (object, encoding, callback) {
  this.push(JSON.stringify(object) + '\n');
  return callback();
}

const myFilter = through.obj(filter);

request(urlString)
  .pipe(split())
  .pipe(JSONStream.parse())
  .pipe(myFilter)
  .pipe(process.stdout);
if you get bored of re-running node index.js you can install nodemon globally (npm install -g nodemon). nodemon watches your files for changes and restarts the process (nodemon index.js) https://www.npmjs.com/package/nodemon
Adrian Alexa
@adrianalexa
The slide decks are up on github - bionode-hack/discussions
James Tindal
@james-tindal
Team Billy Gene has claimed blonde-pgp!
Clarkie
@clarkie
:+1:
Jessica Jordan
@jessica-jordan
top top top!
James Tindal
@james-tindal
bionode-pgp *
Shun Liang
@shun-liang
Team Eva has claimed bionode-eva
Shyam Rallapalli
@shyamrallapalli
:thumbsup:
julns
@julns
:thumbsup:
Erce Kalabalikoglu
@ercekal
:thumbsup:
MCarmen Jimenez Campos
@mcarmenjc
:thumbsup:
Bruno Vieira
@bmpvieira
Shyam Rallapalli
@shyamrallapalli
MCarmen Jimenez Campos
@mcarmenjc
teamevagroup.slack.com
Achilleas Tsoumitas
@Knorcedger
Shun Liang
@shun-liang
Marc Rivelles
@fsdevlondon
team the-v-team has claimed bionode-ncbi-dbvar
Florian Rathgeber
@kynan
FYI: if you leave out the db field for NCBI esearch it defaults to pubmed
Julian Mazzitelli
@thejmazz
@giovannic for "streamifying" promises/callbacks there are also modules like stream-from-promise - read the source! essentially it just doesthis.push(resolvedValue); this.push(null). for callbacks, you can see how I did it here - but that is for a "curried callback" - i.e. something like
function(options) {
  return function(callback) {
      // do stuff
      callback()
 }
}
Giovanni
@giovannic
@thejmazz thanks, but I've already been corrupted by highland http://highlandjs.org/#streamifyAll
Julian Mazzitelli
@thejmazz
aha yes highland is awesome. good call, I should refactor to use some of these functions!
Bruno Vieira
@bmpvieira
David Ross
@bunnybooboo
This message was deleted
Ismail Moghul
@IsmailM
Clarkie
@clarkie
also, if anyone is into node we have a user group here in London that meets once a month: http://lnug.org/
Bruno Vieira
@bmpvieira
Feedback form: campus.co/thx1q
Florian Rathgeber
@kynan
our fork of bionode-ncbi with some additions: https://github.com/bionode-hack/bionode-ncbi