Provision

[abessiari]

Added docker file and aws provisionning.

See provision/PROVISION_README.md for local testing and PROVISION_AWS_README.md for aws.

[kltm]

@abessiari I've started testing this and it's looking pretty good. One thing I noticed, when working with a larger query, was that I seemed to get timeouts after a few (5?) seconds: java.util.concurrent.ExecutionException: java.util.concurrent.ExecutionException: org.openrdf.query.QueryInterruptedException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: com.bigdata.bop.engine.QueryTimeoutException: Query deadline is expired. We'll probably want to parameterize timeouts. I was looking to see how to do that, but couldn't figure out where the config files were (https://github.com/geneontology/go-graphstore/pull/19/files#r749868678).

[abessiari]

@kltm

conf/readonly_cors.xml there is timeout set to 30 seconds.

queryTimeout 30000

[kltm]

@abessiari Ah, thank you--I'm not sure how I missed that.

[kltm]

@abessiari With the testing that I'm doing and the timeouts I keep hitting, I think it would be useful if we could parameterize the queryTimeout like we do for the RAM. If that's tricky, I'll try and make up an SOP so we can do this at need.

[kltm]

@abessiari Similar to the reported issue with the other provisioning, I'm running into:

sjcarbon@moiraine:~/local/src/git/go-graphstore-abessiari/provision[provision]$:( ansible-playbook -e "stage_dir=$STAGE_DIR" -u ubuntu -i "$HOST," --private-key $PRIVATE_KEY build_image.yaml 

PLAY [build docker image] ******************************************************

TASK [Gathering Facts] *********************************************************
fatal: [52.5.59.113]: FAILED! => {"changed": false, "module_stderr": "/home/sjcarbon/.ssh/config line 3: Unsupported option \"rsaauthentication\"\r\nShared connection to 52.5.59.113 closed.\r\n", "module_stdout": "/bin/sh: 1: /usr/bin/python: not found\r\n", "msg": "MODULE FAILURE", "rc": 127}

fixed with

ssh -i KEY_PATH login@location 'sudo apt-get update && sudo apt-get -y install python'

[kltm]

Similarly, as with AmiGO, replace the unpacking module with a manual tar pigz command and look to use ansible (or something, even automatic) to start the docker images up.

[kltm]

I can confirm that the "dual" CNAME feature seems to work as advertised so far!

[kltm]

Completed testing cycle: looking good! Is it better to merge now before more work goes on here, or do you want to keep this PR open?

[abessiari]

I am working on the timeout .... Let us wait.

[abessiari]

@kltm

done. we can discuss on the meeting.

https://github.com/geneontology/go-graphstore/pull/19/commits/1323c82e6eb8823a628192f323223772d1d1bfc5

[kltm]

Under discussion, merging now.