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Amy Glen edited this page Aug 18, 2022 · 4 revisions

NOTE: This page is out of date. Instead see ARAX Docker Deployment, RTX-KG2 API Docker Deployment, and Operations & deployment info.

ARAX ARA Capacity and technology stack

The production ARAX server (API endpoint) arax.ncats.io is hosted in AWS EC2 on an instance of type m5a.4xlarge with 16 processors, 64 GiB of memory, a 32 GiB root filesystem, and a 1 TiB filesystem mounted as /translator. The host OS is Ubuntu 18.04 and it has the following software stack:

  • Docker version 19.03.12 for containerization
  • Nginx version 1.14.0 (OpenSSL 1.1.1) for TLS termination (proxying 443 to 8080).
  • sudo 1.8.21p2

ARAX runs within a Docker container rtx1 (which maps host TCP port 8080 to within-container TCP port 80) that has Ubuntu 16.04 as the base image within the container, and that uses the following stack within the container (installed using apt-get unless otherwise indicated):

  • Apache version 2.4.18 as the webserver
  • Flask version 1.1.2 as WSGI web application framework
  • OpenSSH version 7.2p2 (with OpenSSL 1.0.2g)
  • python version 3.7.3 (we are using the system python, /usr/bin/python; see the ARAX requirements file for packages)
  • mysql version 14.14 (Distrib 5.7.19)
  • git version 2.7.4
  • Neo4j version 3.2.6, Community Version (within the rtx1 ARAX server container, Neo4j is a legacy dependency ; most Neo4j usage is via a Neo4j server kg2canonicalized.rtx.ai that is hosted separately from arax.ncats.io)
  • For Neo4j, OpenJDK version 1.8.0_131
  • OpenAPI version 3.0.1 for code generation of interface python classes for the API

KG2 KP Capacity and technology stack

The KG2 KP runs in an AWS EC2 instance of type r5a.4xlarge with 100 GiB of storage, with an Ubuntu 18.04 AMI.

ARAX Deployment Recipe - OLD

All but the final step are to be executed within the rtx1 docker container as user rt. From the host OS, logging into the rtx1 container and becoming user rt would entail:

sudo docker exec -it rtx1 bash -c "su - rt"

Database cache area

Outside container is /data/orangeboard/databases/KG2.3.4

Inside container is /mnt/data/orangeboard/databases/KG2.3.4

Setup

INST=test

SRC=/mnt/data/orangeboard/databases/KG2.3.4

DST=/mnt/data/orangeboard/$INST/RTX

Roll out code

cd $DST/code

git pull

Copy config.json

cd $DST/code

cp -p $SRC/config.json .

Link NodeSynonymizer

cd $DST/code/ARAX/NodeSynonymizer

rm node_synonymizer.sqlite

ln -s $SRC/node_synonymizer.sqlite

Link NGD

cd $DST/code/ARAX/ARAXQuery/Overlay/ngd

rm curie_to_pmids.sqlite

ln -s $SRC/curie_to_pmids.sqlite

Copy COHD

cd $DST/code/ARAX/KnowledgeSources/COHD_local/data

rm COHDdatabase_v*.db

ln -s $SRC/COHDdatabase_v*.db

Copy Drug-Treats-Disease

cd $DST/code/ARAX/ARAXQuery/Overlay/predictor/retrain_data

rm GRAPH.sqlite LogModel.pkl

ln -s $SRC/GRAPH.sqlite

ln -s $SRC/LogModel.pkl

Run tests

cd $DST/code/ARAX/test

pytest -v --durations=10

Restart the service as user root inside container

INST=test

service RTX_OpenAPI_$INST restart

sleep 1

tail -f /tmp/RTX_OpenAPI_$INST.elog

Where are error log files?

  • Apache2 logfile: inside the container, /var/log/apache2/error.log
  • Python flask server logfile: inside the container, /tmp/RTX_OpenAPI_XXXXXXXX.elog, where instead of XXXXXXXX, substitute the deployment label like production, test, legacy, etc.
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