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Tony Bargnesi
@abargnesi
I remember OpenBEL/rest-api was deployed there, right?
Nick Bargnesi
@nbargnesi
yes
juliakozlovsky
@juliakozlovsky
Hi Everybody! (looks a lot like Slack in here ;-)) We have a question about one of the open issues in GitHub: OpenBEL/bel.rb#65 - about changing URIs in bel2rdf to follow identifiers.org conventions. First of all, since this impacts more than just bel2rdf (it also impacts the resource-generator and so on), I think it would be useful for us to get together with you briefly to make sure that we coordinate - perhaps, rather than just modifying bel2rdf, or modifying the resource-generator, it would be better to encapsulate the URI generation somehow, so it can be used by multiple other modules. And/or if you are already doing that, it would be good for us to know and not repeat the work. In addition, we would like to discuss how to handle the URIs that are not in miriam, as well as any custom namespaces. It would be good to create and follow some sort of a convention - perhaps we can make that a configurable functionality. Do you have some time in the next few days? We could set up a Skype chat (or something similar).
Tony Bargnesi
@abargnesi
Yes, can we get together tomorrow over skype?
juliakozlovsky
@juliakozlovsky
We are open between 9am and 11am or so - any time during that interval work for you?
Tony Bargnesi
@abargnesi
9-10 works
juliakozlovsky
@juliakozlovsky
thank you, see you then!
Tony Bargnesi
@abargnesi
np looking forward to it
Tony Bargnesi
@abargnesi
@juliakozlovsky I created a google doc to track our discussion. https://docs.google.com/document/d/1QJtRJQ0XhiecRorT5NK8WiocArJl3O61MmaRuN125lA/edit?usp=sharing
Tony Bargnesi
@abargnesi
@juliakozlovsky closed OpenBEL/bel.rb#65 in favor of OpenBEL/bel.rb#92, you should be able to see activity on the right of the chat.
Dexter Pratt
@dexterpratt
Hi Julia, we heard from Jan at Roche that they now have the BEL version of metabase and he would like to load it to their NDEx server. We are in the process of adding a path for I/O of .bel files (currently we just do .xbel) and will want to test to make sure he is successful. Are there some of your files converted to BEL that you could share with us that we could use for testing purposes?
juliakozlovsky
@juliakozlovsky
@abargnesi Thank you!
Tony Bargnesi
@abargnesi
@dexterpratt Is the CX format document generally available? I have the google doc, but I'm wondering if I can link to it in the meeting notes.
Dexter Pratt
@dexterpratt
@abargnesi - No, it will be available with the v1.3 NDEx release - which could be as early as next week
We are wrapping things up for that release but we are running a bit behind on testing. But very soon.
Tony Bargnesi
@abargnesi
thanks dexter, good luck with it, can't wait to try it out.
Tony Bargnesi
@abargnesi
Released version 0.5.0 of bel.rb, https://github.com/OpenBEL/bel.rb/releases/tag/0.5.0
Tony Bargnesi
@abargnesi
@dexterpratt Completed a rough tutorial on creating a bel.rb translator. Would love some input. https://github.com/OpenBEL/bel.rb/wiki/Creating-a-translator-plugin
Tony Bargnesi
@abargnesi
@kellymccann91 Take a look at the tutorial as well, I'm interested in your thoughts on the flow of the tutorial.
Tony Bargnesi
@abargnesi
@nbargnesi @wshayes opened OpenBEL/belmgr#50 regarding configurable pubmedBaseUrl
Nick Bargnesi
@nbargnesi
commented and merged
William Hayes
@wshayes
I’d prefer to handle configuration in a different way. I’ll probably back this out after deploying an updated configuration system.
Tony Bargnesi
@abargnesi
sounds good
Nick Bargnesi
@nbargnesi
no need to back it out once we have something better in place (i.e., git revert?)
Tony Bargnesi
@abargnesi
I had the sense BASE_URL/PUBMED_URL would be obsolete and removed after a new configuration system is in place
William Hayes
@wshayes
@abargnesi Yes - I prefer to put a new system in place first :)
William Hayes
@wshayes
Or not - can’t pull Env variables from a Javascript app. Duh! and aarrrgghhh!!!
Nick Bargnesi
@nbargnesi
@abargnesi opened PR 101
Tony Bargnesi
@abargnesi
@nbargnesi Commented on the "secret" configuration. Otherwise looks great.
Nick Bargnesi
@nbargnesi
@abargnesi updated PR with comments for each setting, thanks for the :star:
Tony Bargnesi
@abargnesi
Thanks. Totally missed the auth middleware regarding secret.
Tony Bargnesi
@abargnesi
@juliakozlovsky Fix for OpenBEL/bel.rb#111 dropped on the next branch. This includes the work I mentioned in our earlier skype conversation with Alexandr. The commit is OpenBEL/bel.rb@d9ce98c.
We're planning to push this out in a bel 0.6.0 version today. We should then be able to integrate Alexandr's work on OpenBEL/bel.rb#92 on 0.6.0 when he's ready.
Tony Bargnesi
@abargnesi
@/all bel.rb 0.6.0 is released (https://github.com/OpenBEL/bel.rb/releases/tag/0.6.0).
sbagewadi
@sbagewadi
Tony: could you please send me the links we discussed about last week. This should include the tutorial for adding new annotations. Also, could you point me to the latest BEL tutorial documentation. http://wiki.openbel.org/display/BLD/BEL+Information+PDFs this is 2011 version. Do you have a latest one?
Tony Bargnesi
@abargnesi
@sbagewadi Sure, the links were added to the 2016-03-08 meeting notes.
I don't think we have much of a tutorial at the moment though @kellymccann91 is working on it. You can refer to the BEL 1.0 reference on the wiki or the official specification.
Tony Bargnesi
@abargnesi
@all Anyone know who manages the OpenBEL linkedin community page?
William Hayes
@wshayes
I will check when I get back to the office.
Tony Bargnesi
@abargnesi
thanks!
Tony Bargnesi
@abargnesi
@all Added a changelog for belmgr in preparation for the 0.2.0 release.
These are a must! Just checkout bel.rb changelog.
Nick Bargnesi
@nbargnesi
Definitely a must, +1 there
A dozen IPAs :beer: to whoever comes up with a good lightweight automation for changelog generation too. To be fair, IPAs are gross so this isn't a significant incentive.
Tony Bargnesi
@abargnesi
:)
I think automation can be part of it, but I like interpreting the changes for the users of the project.
It can be a pain though, and it's usually after the fact.
I've seen some uses of structured git commits to that end.