GMOD/Apollo

Genome annotation editor, with a Java servlet backend and a Javascript client that runs in a web browser as a JBrowse plugin

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

Scott Cain

@scottcain

OK, still working on getting the Apollo container to build. I switched to pulling from the develop branch for Apollo, and it felt like it was working, because the build ran longer, but it ended up dying at the same place as above, trying to get odfdom-java. I thought the problem was a failure to gracefully redirect (since there is a 308 error thrown), and that may still be the most current problem, but when I go in a browser to http://repo.grails.org/grails/core and get redirected to https://repo.grails.org/artifactory/core/, I see that there is no listing for odfdom-java there, so even if the redirect were successful, I don’t think the build would complete successfully. So, I’m left wondering if we can/should try to get odfdom-java from somewhere else, or I am misinterpreting what’s going on? @garrettjstevens @nathandunn

(or can we pitch odfdom for the AGR build of apollo? No clue)

Nathan Dunn

@nathandunn

@garrettjstevens I would push to dev and see if its fixed there

its in maven central, so it should be getting picked up: https://mvnrepository.com/artifact/org.odftoolkit/odfdom-java

Garrett Stevens

@garrettjstevens

@scottcain looks like it's a problem with grails: grails/grails-core#11825. I realized it wasn't just docker, I couldn't build Apollo locally, either. Hopefully I'll have a fix in develop soon: GMOD/Apollo#2624.

Scott Cain

@scottcain

I figured it was something like that (ie, updating a repo url) but I didn’t know where to do it.

Garrett Stevens

@garrettjstevens

Just merged. Should be able to try again now.

Scott Cain

@scottcain

Yep, worked on my local apollo docker file; now I’ll try with the AGR container. Thanks!

Nathan Dunn

@nathandunn

Sorry, just put this on the twitters. Building a genome browser from neo4j: https://twitter.com/precogincog/status/1405612735077908481 . Not sure if the title is misleading, but its still kind of interesting.

childers

@childers

Hey all, is there any thought on adding two factor auth for apollo?

Robert Buels

@rbuels

Not the current one, no. Next gen one that we are currently working on might support external authn that could provide that

childers

@childers

@rbuels Cool. Thanks for the update

Nathan Dunn

@nathandunn

@childers for now (sorry for a very late response), you can use apache + https://genomearchitect.readthedocs.io/en/latest/OpenIDConnectAuthentication.html?highlight=REMOTE#apollo-configuration

childers

@childers

@nathandunn Thanks! I'll check that out.

Does Apollo support java 17? I know the docs say 8+ but that is a pretty big jump

Curtis Ross

@cross12tamu

Hello, is there an easy way to prune/delete organisms (as an admin?)

Helena Rasche

@hexylena:matrix.org

[m]

If you've got a list of of organism common names or so, use arrow

https://github.com/galaxy-genome-annotation/python-apollo you can pretty quickly write a loop in bash to call the delete organism function

Curtis Ross

@cross12tamu

Thanks

Scott Cain

@scottcain

When I’m running the apollo container that we use at AGR, I see several sql errors when running the launch script and then the message Not using chado!. Given that the container isn’t working (tomcat is returning 500 errors), is this likely the problem, and what should I do.

(and of course, our devops guy says to me again: “ you should really create a base container that has a chado database already in it”. yeah, yeah, I know.)

2 replies

Nathan Dunn

@nathandunn

@scottcain the base docker container of Apollo has docker in it

so, just need to merge that in

https://https://github.com/GMOD/Apollo/blob/develop/Dockerfile#L37github.com/GMOD/Apollo/blob/develop/Dockerfile#L37

https://github.com/GMOD/Apollo/blob/develop/docker-files/launch.sh#L41-L44

probably a few other places as well

Helena Rasche

@hexylena:matrix.org

[m]

Oh yeah no worries, didn't know if you knew, and yeah new moving parts is always more work, totally get it.

Hour and a half to rebuild

Oof yeah that's a mood.

Scott Cain

@scottcain

It was something stupid (isn’t it always): I changed a set of urls and forgot to tell apollo

Where communities thrive

People

Repo info

Activity