These are chat archives for biojs/biojs

28th
Feb 2015
Sebastian Wilzbach
@wilzbach
Feb 28 2015 07:28

we have to make a d3.js snippets in package.json but in source code repo there is no d3.js snippets

Well this snipspector tutorial is a bit outdated (that is why I want move forward to a new tutorial series). Now we normally require everything:

npm install d3 --save

and then in the file

var d3 = require("d3");

So can I add d3 snippets to the package.json in source code repo or make a PR ??

As mentioned above you don't need to add the d3 dependency to the "js" section of the sniper when you have defined it as a npm dependency.

I am getting error "d3 is not defined" but I have added the d3 snippets in package.json. How to solve it ?

  • Did you wrap your code into a module.exports?
  • Does it download the d3 library (see the network section of chrome)?
tyreek
@tyreek
Feb 28 2015 07:42
(biojs-registry via irc) BioJS package update: slush-biojs to 0.7.11 by BioJS
David Dao
@daviddao
Feb 28 2015 07:42
@ayusharma thanks for bug finding. Just fixed the vis tutorial
Ayush Sharma
@ayusharma
Feb 28 2015 07:47
@daviddao I am doing the changes.. :)
Ayush Sharma
@ayusharma
Feb 28 2015 08:22
@greenify @daviddao I have made some changes.. Please take a look whether it is correct ? I have created the PR
Can I update the tutorial link also ?
Sebastian Wilzbach
@wilzbach
Feb 28 2015 08:25

I have made some changes..

Thx. Already done :)

Can I update the tutorial link also ?

Sure - to which link are you referring to?

Ayush Sharma
@ayusharma
Feb 28 2015 08:26

http://edu.biojs.net/snipspector_adv/vis_d3/

I want to update these changes in this doc

Sebastian Wilzbach
@wilzbach
Feb 28 2015 08:26
yeah sure - go ahead :)
Ayush Sharma
@ayusharma
Feb 28 2015 08:51
@greenify can we also add the npm install d3 --save to the readme.md of biojs-vis-snipspector ?
Sebastian Wilzbach
@wilzbach
Feb 28 2015 08:55
There is no need - is is already stored in the package.json ;-)
Ayush Sharma
@ayusharma
Feb 28 2015 10:46

Hi all , I am going through the D3 Visualization tutorial link http://edu.biojs.net/snipspector_adv/vis_d3/

and found incorrect tilde markup . Image attached http://pasteboard.co/1s8RFHDp.png

@greenify is this a issue ? Should I go to correct it ?

tyreek
@tyreek
Feb 28 2015 10:49
(ashutoshsaboo via irc) Hello, Sir/Madam, Let me take the the pleasure of introducting myself -:
(ashutoshsaboo via irc) I am Ashutosh Saboo, a first year college student in BITS Pilani, K.K. Birla Goa Campus. I read about your organization, and found some of your projects really interesting!
(ashutoshsaboo via irc) I would like to contribute to the company in any way possible.
(ashutoshsaboo via irc) Please do let me know if there is any way, in which I could contribute to this organization!
(ashutoshsaboo via irc) I would definitely like to contribute to your projects
Sebastian Wilzbach
@wilzbach
Feb 28 2015 19:25
@ayusharma: Yes I know, I already corrected it - should be updated very soon
Prasun Anand
@prasunanand
Feb 28 2015 19:27
https://github.com/biojs/biojs/wiki/BioJS-parser defines the standards for a generic-parser.
Should I be defining the basic methods like 'parse' and 'write' in the generic parser , and then use these methods in the other parsers (that use generic parser as dependency)
Sebastian Wilzbach
@wilzbach
Feb 28 2015 19:27
ashutoshsaboo: we are very happy about anyone who likes to contribute to use, but we are not a company - we are an open source community! Have you read this guide already?
ashutoshsaboo: There are many ways to contribute to BioJS - just pick sth. you like! If the contribution guide doesn't help you, let us know ;-)
Sebastian Wilzbach
@wilzbach
Feb 28 2015 19:38

Should I be defining the basic methods like 'parse' and 'write' in the generic parser

Well currently there is no generic parser package, I guess your question is more whether we should have a generic parser package which you can require?

Prasun Anand
@prasunanand
Feb 28 2015 19:39
yes
I tried to create it. The generic parser would have a parse and write method. But different file formats need a lot of methods that would return different sets of values. How to take care of that.
By set of value I mean 'meta' 'refrences' 'sequences'
Sebastian Wilzbach
@wilzbach
Feb 28 2015 19:43
Okay the advantage would be that we can add some generic functionality like a read method which downloads a file from the web, or maybe later other helpers for interaction with streams

But different file formats need a lot of methods that would return different sets of values.

Yes nearly every parser would return a different model, but the methods would still be the same?

One disadvantage that comes to my mind is that if someone requires the generic parser modules it will automatically add some (maybe unneeded) dependencies like xhr or others (e.g. stream modules)
Prasun Anand
@prasunanand
Feb 28 2015 19:50
But that would not be a big issue, i think
Sebastian Wilzbach
@wilzbach
Feb 28 2015 19:51
We force people to require stuff they don't need or want?
Prasun Anand
@prasunanand
Feb 28 2015 19:54
:worried:
Prasun Anand
@prasunanand
Feb 28 2015 20:07
what should be done then?
Sebastian Wilzbach
@wilzbach
Feb 28 2015 20:10
Hmm I would vote in favor of creating a very, very lightweight generic parser module
Prasun Anand
@prasunanand
Feb 28 2015 20:19
sure, Will try to come up with something ;)
Sebastian Wilzbach
@wilzbach
Feb 28 2015 21:28
@prasunanand: how about using biojs-io-parser? :)
Prasun Anand
@prasunanand
Feb 28 2015 21:30
nice :D
:+1: