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    Alexey Alekhin
    @laughedelic
    and yes, wish you great holidays!
    alberskib
    @alberskib
    Hello @laughedelic
    I come back from holiday and now I am in Switzerland. I will start my contribution to project. If you have any clues, notes, message (sth like this) do not hesitate to send me. I will start to looking into your changes,
    When it comes to the master thesis I am still working on it. Basically all experiments are finished but I need to spend some time to write text, but you know: person cannot just take a seat and spend several hours on writing text - you need a break for writing some code :wink:
    alberskib
    @alberskib
    Hello @eparejatobes @evdokim @laughedelic. I take a look into cosas (former pointless) and it perfectly fit for dynamograph - It is ready for that? What is more I see that you launch some new projects that seems to be interesting i.e angulillos, I noticed that scarph becoming more and more powerful :smile:
    Alexey Alekhin
    @laughedelic
    Hi @alberskib! We were away with @evdokim for a couple of weeks (attending a workshop in London), so not much things have changed since then.. :smile:
    Now we are back and going to work on all this.. I’m trying currently to bring scarph to the "first-release" state. Also tabula was planed to be reworked (again) and since the decision it was not touched (other priorities). cosas (btw, what do you think about the name?) is in quite a nice state at the moment — a lot of effort was put to split all the abstract parts of other projects into this one and make it consistent..
    And about angulillos, I think only @eparejatobes can tell something meaningful.
    alberskib
    @alberskib
    Hi @laughedelic! cosas (as I remember previous name was pointless) for me name is ok (at first glance it was a little mysterious but after checking the meaning in spanish dictionary it becomes clear for me) - probably better than pointless :smile:
    alberskib
    @alberskib
    Hi @/all How is going with tabula and scarph? Those projects now are using typesets which was replaced by cosas. Is there plan to migrate them to cosas? I tried to update dynamograph to use cosas but without migration tabula and scarph to cosas it will be extremely difficult.
    Alexey Alekhin
    @laughedelic
    Hi! Yes, sure, we’re working on moving everything to cosas. If I remember right, scarph 0.5.0-SNAPSHOT is on cosas already. Maybe I should release that version, it worked I think. I’m just working already on ohnosequences/scarph#22 and forgot about that version..
    About tabula, I don’t know, of course we will move it to cosas, but other plans... I think we should discuss it with @eparejatobes.
    alberskib
    @alberskib
    Ok
    Eduardo Pareja Tobes
    @eparejatobes
    Hi all
    About dynamograph I think we should wait for scarph and tabula, I don't want to have yet another migration etc :)
    Eduardo Pareja Tobes
    @eparejatobes
    @alberskib about angulillos is something similar to scarph in some sense; it is (I think) close to the limit of what you can do in Java. We are polishing a new Java version of the main Bio4j distribution based on it. It would be nice to implement a DynamoDB backend for it. If you are interested we could think a bit about it, it should be pretty easy; we could also use it as an idea for GSoC15
    maybe I could give a presentation on angulillos
    alberskib
    @alberskib
    Hey @eparejatobes. DynamoDb backend for java version is also interesing for me - I'm in. I almost finish first draft of my master thesis so in couple of days I will much more time. Regarding this presentation on anulillos - there will be some streaming or slides? I would like to watch it but probably my time availability is not sufficient (evenings) so I could take a look into presenation or recording.
    Eduardo Pareja Tobes
    @eparejatobes
    streaming and slides :)
    Eduardo Pareja Tobes
    @eparejatobes

    @alberskib I was thinking that it'd be a good idea if you could take a look at the current state of both https://github.com/bio4j/angulillos and https://github.com/bio4j/angulillos-titan, and ask me if there's something that you don't understand there. Overall the library is pretty straightforward if you factor out the java generics noise :)

    I think it should be pretty straightforward to implement bio4j/angulillos-dynamodb, and it would let us experiment with DynamoDB as a backend with real big data. The scarph stuff is really nice but I honestly cannot give you an estimate of when it will be ready; so I want to keep things going regarding DynamoDB and your project.

    alberskib
    @alberskib
    Hello @eparejatobes. Today i just took a quick look and at the begining I had one question. I was diving into code and after some time I think that I found answer for my question but maybe it will be better if you answer it - just to be sure: Could you tell me why i.e. TypedEdge have parameter SourceGraph (SG)/TargetGraph (TG) ? In a weekend I spend some more time.
    Alexey Alekhin
    @laughedelic
    It’s better if @eparejatobes answer this, but I have a quick guess :wink:
    I think it’s because it was developed with bio4j in mind, so bio4j has different parts/modules/subgraphs (like GO, Uniprot, etc.) and we want to have each such graph independent, while being able to connect them — so an edge can go from a (source-)type in one graph to a (target-)type in another graph.
    alberskib
    @alberskib
    Ok - it makes sense, I forget about it.
    Alexey Alekhin
    @laughedelic
    cool “) but remember, it’s my speculation, because I don’t know much about angulillos...
    Eduardo Pareja Tobes
    @eparejatobes
    yup, that's it. It's not that I love it, but I couldn't think of any other way of doing it in Java
    alberskib
    @alberskib
    Hello. I think that I can start working on bio4j/angulillos-dynamodb - for now I do not have other questions. Could you create this project on github or give me privilleges that enables me doing it on myself?
    alberskib
    @alberskib
    I forgot to use gitter notification @eparejatobes
    Eduardo Pareja Tobes
    @eparejatobes
    Hey @alberskib sorry I've been on the road this past few days. Let me try to do this from my phone
    Eduardo Pareja Tobes
    @eparejatobes
    Done, do g8 era7bio/scala -b java for a project template
    Eduardo Pareja Tobes
    @eparejatobes
    hey @alberskib tell me if you have any questions about this
    At first I'd be more interested in doing the writing part; reading is easy
    alberskib
    @alberskib
    Ok - I will concentrate on writing part - I have really busy this weekend so probaby some progress will be done from start of next week.
    Eduardo Pareja Tobes
    @eparejatobes
    nice!
    Alexey Alekhin
    @laughedelic
    @alberskib :wink: Happy birthday, Bart! :tada::confetti_ball::tada:
    alberskib
    @alberskib
    @laughedelic Thank you very much :smile:. It is really nice!
    Alexey Alekhin
    @laughedelic
    :blush:
    alberskib
    @alberskib
    Hey. I just want to inform that for two weeks I must suspend work(master thesis). I will start from 29.12
    Eduardo Pareja Tobes
    @eparejatobes
    @alberskib fine, good luck with it!
    alberskib
    @alberskib
    @/all Hey guys!
    First of all I would like to tell you that I am feeling terrible that I was constantly saying that I am starting but I did not produce any progress. Sorry for that!
    Today I come back and I will do everything(I have job so I will be working mostly on evenings and weekends) to deliver first version as soon as possible. From now I am starting work on that (regularly) to deliver systematicly product increments. I think that at some point I will need little help from you.
    One more time sorry for that.
    alberskib
    @alberskib
    Hey. I think that I am missing part of big picture - as a result I have next questions:
    1. Do I need to override TypedEdge, TypedVertex in order to provide specific versions for DynamoDb backend or just implement some kind of DynamoDbRawVertex, DynamoDbRawEdge. I am not sure: I think that yes I need to, but when I look into titan or neo4j implementation of angulillos there is no such files.
    2. I in TypedEdge and TypedVertex is just for identifying used backend and offer possibility to communicate graphs from different backends?
    Eduardo Pareja Tobes
    @eparejatobes
    hey @alberskib sorry missed this
    gitter notifications are pretty buggy
    Eduardo Pareja Tobes
    @eparejatobes
    You don't need to override anything
    First, all the actual interaction happens at the UntypedGraph level
    You do need to define classes like DynamoDBRawVertex, DynamoDBRawVertexType, etc
    Eduardo Pareja Tobes
    @eparejatobes
    In the case of Titan, they're already provided by Titan; we're just reusing TitanVertex, VertexLabelMaker, etc.
    As here we're free to implement all those things as we please, we can take a more reasonable approach.
    Eduardo Pareja Tobes
    @eparejatobes
    DynamoDBRawVertexType for example should have a link to the corresponding DynamoDB tables used to store the vertices; DynamoDBRawEdgeType should have refs to the corresponding source and target raw types, together will all the edge-specific tables
    Tables means just table names, of course
    All the XXXType classes should be completely decoupled from any resource management, auth etc.
    That should be at the untyped graph level
    About raw edges and vertices, they should have just a link to the corresponding type together with something identifying them (the property id used in the corresponding table , for example)
    You could implement everything then at the untyped graph level
    retrieving things from DynamoDB etc
    also, any stuff like caching of properties etc should go there I think