These are chat archives for bio4j/bio4j

31st
Aug 2015
Eduardo Pareja Tobes
@eparejatobes
Aug 31 2015 08:21
yep true. As for the size it's just a tar archive, so extracted size should be the same. I will make a note about it.
Anyway, in the next few days we will simplify things a bit. We allso want to have all Titan binary files there as S3 objects, not in a .tar file. That would let you use cheaper machines without the need to attach volumes etc.
Pablo Pareja Tobes
@pablopareja
Aug 31 2015 10:25
mmm I see I'm a bit late here :smiley:
Anyway, cool that you managed to get things working :+1:
Alexey Alekhin
@laughedelic
Aug 31 2015 12:43
This message was deleted
nlakhani
@nlakhani
Aug 31 2015 16:19
working is a strong term (I'm new to titan completely) :)
As far as I can understand, I will download titan, modify the rexster-cassandra-es.xml to point to /storage/bio4j and then launch titan.sh and rexster.sh?
then i can go to address:8182/ and the doghouse
i just feel that i'm missing something in terms of loading the extracted tar 'into' titan
Eduardo Pareja Tobes
@eparejatobes
Aug 31 2015 16:46
Honestly I never used rexster
Depends on what you want
if you want a REST endpoint based on Bio4j, I guess you can use that
nlakhani
@nlakhani
Aug 31 2015 16:47
i guess firstly my question is, what do i do now
the value i saw in rexster was visualizing the graph
but even prior to that, just loading the db into gremlin would be a good start
Eduardo Pareja Tobes
@eparejatobes
Aug 31 2015 16:47
yup, but the graph is kinda big :)
It would be great to have a really restricted subset of everything imported
it's just that it is hard to maintain integrity in that case
nlakhani
@nlakhani
Aug 31 2015 16:49
yes i understand
Eduardo Pareja Tobes
@eparejatobes
Aug 31 2015 16:49
anyway, back to what you can do now
you already have a big Titan db there
nlakhani
@nlakhani
Aug 31 2015 16:49
so i have an instance, i have the extracted db in /storage/bio4j
Eduardo Pareja Tobes
@eparejatobes
Aug 31 2015 16:50
yes, that's it
now, from a Java program (for example)
you can create a Titan instance
and from that a Bio4j API instance
and run queries on it
nlakhani
@nlakhani
Aug 31 2015 16:52
so do i need to download titan and run titan.sh at all?
on my instance
Eduardo Pareja Tobes
@eparejatobes
Aug 31 2015 16:53
no, you don't need to
you can just write normal Java code
nlakhani
@nlakhani
Aug 31 2015 16:54
ok
Eduardo Pareja Tobes
@eparejatobes
Aug 31 2015 16:54
to which you pass the location of the Titan db
and that's all
I normally use this through Scala or using bio4j/angulillos, so I'm not up to the full details
probably @pablopareja can give you a hand here
nlakhani
@nlakhani
Aug 31 2015 16:56
no worries, i work with scala in my world tho a quite different stack, and my devops knowledge is very weak ;)
Eduardo Pareja Tobes
@eparejatobes
Aug 31 2015 16:56
I think there are simple Java-based examples somewhere
nlakhani
@nlakhani
Aug 31 2015 16:57
i will hack around with some scala on the db but will continue to explore rexster, i think a graphical view would be really cool, and it also has a gremlin console there
Eduardo Pareja Tobes
@eparejatobes
Aug 31 2015 16:57
sure, if you can get it working that's cool
nlakhani
@nlakhani
Aug 31 2015 16:58
which is my other question, can i use gremlin REPL for some basic queries to see how things work
Eduardo Pareja Tobes
@eparejatobes
Aug 31 2015 16:58
yes sure
in the end is just a Titan DB like any other else
nlakhani
@nlakhani
Aug 31 2015 16:58
is it just TitanFactory.open(/path/)
Eduardo Pareja Tobes
@eparejatobes
Aug 31 2015 16:58
yes
nlakhani
@nlakhani
Aug 31 2015 16:59
and then i could do something like graph.v.out.groupCount.cap
or maybe that is too much, i guess we will see
Eduardo Pareja Tobes
@eparejatobes
Aug 31 2015 16:59
We will be opening a Scala API in the next few weeks, working on it right now
nlakhani
@nlakhani
Aug 31 2015 16:59
nice
Eduardo Pareja Tobes
@eparejatobes
Aug 31 2015 17:00
Things are in a state of flux right now :) sorry about it
nlakhani
@nlakhani
Aug 31 2015 17:00
not a problem
as i mentioned, once i get to a point where i can do 1 unit of value, i'd love to write an extension to the docs for people coming from different fields
Alexey Alekhin
@laughedelic
Aug 31 2015 17:01

Scala API in the next few weeks, working on it right now

it's optimistic (like any forecasts from @eparejatobes :trollface:), but yes, we are working on it

Eduardo Pareja Tobes
@eparejatobes
Aug 31 2015 17:01
that would be great
nlakhani
@nlakhani
Aug 31 2015 17:01
are you all mostly from spain?
Alexey Alekhin
@laughedelic
Aug 31 2015 17:02
we work in Spain (Granada), but I'm from Russia :ru: :smile:
Eduardo Pareja Tobes
@eparejatobes
Aug 31 2015 17:02
based there, yes
nlakhani
@nlakhani
Aug 31 2015 17:02
cool, better weather than Russia is my guess ;)
Alexey Alekhin
@laughedelic
Aug 31 2015 17:03
haha :smile: that's true. but a bit too hot this year...
Eduardo Pareja Tobes
@eparejatobes
Aug 31 2015 17:09
there's something in bio4j/bio4j-examples
anyway as I said, pinging @pablopareja
Eduardo Pareja Tobes
@eparejatobes
Aug 31 2015 17:19
If you're used to Scala this could appear less Java-ish
you can run that overriding graph() with a TitanUniProtGraph, from bio4j-titan
gotta leave now
nlakhani
@nlakhani
Aug 31 2015 17:22
thanks for all the help, i will continue to mess around and hopefully not ask too many bad quesitons