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  • May 19 13:06

    kyostiebi on Issue97

    tmp commit (compare)

  • May 18 15:27

    garrettjstevens on Issue97

    Add comments about chunk size a… (compare)

  • May 18 14:30

    kyostiebi on Issue97

    tmp commit tmp commit (compare)

  • May 18 03:29
    garrettjstevens commented #97
  • May 18 03:05
    cmdcolin commented #97
  • May 18 02:52
    garrettjstevens milestoned #97
  • May 18 02:52
    garrettjstevens assigned #97
  • May 18 02:52
    garrettjstevens opened #97
  • May 18 02:24

    garrettjstevens on Issue92

    (compare)

  • May 18 02:24

    garrettjstevens on main

    Add assembly from file (#96) *… (compare)

  • May 18 02:24
    garrettjstevens closed #92
  • May 18 02:24
    garrettjstevens closed #96
  • May 18 02:24
    garrettjstevens ready_for_review #96
  • May 18 02:20
    garrettjstevens synchronize #96
  • May 18 02:20

    garrettjstevens on Issue92

    Log all errors at debug level Register new changes Remove temporary testing code and 1 more (compare)

  • May 17 12:02
    kyostiebi synchronize #96
  • May 17 12:02

    kyostiebi on Issue92

    tmp commit Works also with FASTA file. Fix… (compare)

  • May 17 02:42
    garrettjstevens commented #96
  • May 17 02:41
    garrettjstevens synchronize #96
  • May 17 02:41

    garrettjstevens on Issue92

    Add fasta test file (compare)

Nathan Dunn
@nathandunn
jar tvf Apoll2.war
Nathan Dunn
@nathandunn
./grailsw run-app
cd apollo-gmod-js
rm -rf pwd/temp-apollo-test-data
cp -r pwd/test-data pwd/temp-apollo-test-data
Robert Buels
@rbuels
What are all these snippets
Nathan Dunn
@nathandunn
oh . . . are pair programming with @peterkxie and @garrettjstevens
I guess we coudl do that offline
Nathan Dunn
@nathandunn
@garrettjstevens / @peterkxie we should probably update the AMI (after reading the Apollo group) for Apollo 2.6.4 . . its pretty easy. Better yet, I’ll send out instructions and you can do it (or I can just do it). Let me know what makes the most sense.
Nathan Dunn
@nathandunn
I may have to fix the AMI memory settings, so we’ll see
Nathan Dunn
@nathandunn
@rbuels / @garrettjstevens / @peterkxie https://upenn.zoom.us/j/92729464470#success
should have at least one of you here
Robert Buels
@rbuels
What meeting is that
Is there a calendar invite
Nathan Dunn
@nathandunn
VeuPathDB . . .
Robert Buels
@rbuels
I have a conflict this morning, can’t make it. maybe I missed the email thread with this date and time? Maybe we can schedule something next week to follow up on this
Garrett Stevens
@garrettjstevens
There is a meeting now? Sorry, I can't make it, either.
Nathan Dunn
@nathandunn
@garrettjstevens / @peterkxie the https://github.com/GMOD/Apollo3Server build works now. bintray was deprecated as a host for jfrog. Let me know if you have any troubles.
Also, there is a meeting next Tuesday at 8 am PT.
invites will go out. Let me know if that time doesn’t work.
Robert Buels
@rbuels
That time works for me
Nathan Dunn
@nathandunn
FYI if you want a pure micronaut / swagger installation, I started this branch: https://github.com/GMOD/Apollo3Server/tree/micronaut-swagger
Garrett Stevens
@garrettjstevens
That time works for me, too. Also, I can confirm ./grailsw test-app -unit in Apollo3Server works for me, now.
Robert Buels
@rbuels
Nice
Nathan Dunn
@nathandunn
:+1:
A little more than what we or most curators want, but definitely worth taking a look at
Nathan Dunn
@nathandunn
./gradlew gwtc
./gradlew devmode
Nathan Dunn
@nathandunn
FYI GMOD/Apollo#2618 ready for review @peterkxie @garrettjstevens
Nathan Dunn
@nathandunn
GMOD/Apollo#2619 ready for review @peterkxie @garrettjstevens
Nathan Dunn
@nathandunn
@peterkxie / @garrettjstevens / @rbuels not sure long-term what you guys are doing, but I’ve been pretty impressed with nestjs + graphql. I like the code-first approach (very similar to running an ORM in some ways, but without the overhead of bound objects). Coupling with neo here: https://medium.com/@faaizhussain/nestjs-graphql-neo4j-1e3e6e552a80 kind of interseting / FYI
Robert Buels
@rbuels
i know garrett was looking at how graphql APIs seemed to play well with neo4j
Garrett Stevens
@garrettjstevens
Yeah, I've looked at neo4j and graphql, although I looked at a different NPM package (neo4j-graphql-js, which is made by the neo4j team). nestjs is new to me, though, and it seems like a really nice node framework.
Robin Haw
@hawrobin
Neo4j has been picked up and well used by a number of Bioinformatics projects, including Reactome. Supported by a number of different languages, tools, etc. GraphQL is also really interesting opportunity. One of our GSoC projects last year was to create GraphQL API for the Reactome Neo4j. Lincoln like this approach!
Nathan Dunn
@nathandunn
yeah, I think there is a plugin for neo4j to automatically generate a graphql schema, but you could also generate classes that you will be writing domains out and the graphql schema gets automatically generated (learning about code-first versus schema first)
@hawrobin agreed, that IS a really nice approach
Curtis Ross
@cross12tamu
Been dabbling with some optimization and overall health inspections of our stack at the CPT. Additionally, some "free-ish" money is around for server upgrades. Are there any recommended "specs" for a production-grade server? I have found some RAM recommendations (https://github.com/GMOD/Apollo/blob/develop/docs/Troubleshooting.md#tomcat-memory), I'm curious if there's anything else in another place that could perhaps help me guide my mouse to an appropriate server for ~100ish of concurrent users. The node we have right now is shared with Galaxy, and things can get pretty clunky during high usage times, especially during the semesters that we teach. Any thoughts on this?
Helena Rasche
@hexylena:matrix.org
[m]
@rbuels: I still have merge permissions on apollo, you ok with me merging PRs? (there's a small one from Anthony Bretaudeau fixing the blastview plugin)
not sure how you want to handle PRs/project maintenance since I'm guessing most work is going to be apollo3 and 2 is just maintenance mode now
Robert Buels
@rbuels
@erasche thank you so much for your help, it’s invaluable. I am fine with you merging PRs, but I just want to make sure that each one is at least read by one of the JB core team before it goes in, so we know what’s happening.
3 replies
Helena Rasche
@hexylena:matrix.org
[m]
ok, then I'll just leave it to y'all then :)
Scott Cain
@scottcain
At the moment, the Dockerfile in the apollo repo, develop branch is failing to build. It looks to me like it is a grails problem, as the first indication of a problem is this line Error Resolve error obtaining dependencies: Could not transfer artifact org.odftoolkit:odfdom-java:jar:0.8.5 from/to repo_grails_org_grails_core (http://repo.grails.org/grails/core): Permanent Redirect (308) (Use --stacktrace to see the full trace) with a simple build (docker build .) but to be honest, I’m not that experienced with apollo builds. Any ideas?
Garrett Stevens
@garrettjstevens
It built just fine 10 days ago, when the last change to develop branch was made, so I'm guessing something changed with the grails website.
Looks like they may have changed the structure of their website and something in the installation tools can't follow the redirect.
Scott Cain
@scottcain
Oh, well that’s a pain. As an aside, one of the things I’d like to do (once I get all the other things off my to do list ) is make a base image for apollo that has all the prereqs installed, so that silly things like this wouldn’t prevent building an apollo container.
Garrett Stevens
@garrettjstevens
That would be nice.
Scott Cain
@scottcain
Oh, heck, and that’s not even that easy a thing for us to fix, since the docker file depends on sdkman, which I know nothing about.
Nathan Dunn
@nathandunn
Gradle and groovy also depend on it so I’m pretty sure it’ll get fixed