KG2.10.2c Build

[sundareswarpullela]

THE BRANCH FOR THIS ROLLOUT IS: kg2.10.2c THE ARAX-DATABASES.RTX.AI DIRECTORY FOR THIS ROLLOUT IS: /home/rtxconfig/KG2.10.2
Sprint changelog link: (Changelog)

Prerequisites

ssh access

To complete this workflow, you will need ssh access to:

• [x] arax-databases.rtx.ai
• [x] the self-hosted ARAX/KG2 instance, arax.ncats.io (see example configuration information below)
• [x] the self-hosted PloverDB instances, kg2cploverN.rtx.ai
• [x] the self-hosted Neo4j instances for KG2c, kg2canoncalizedN.rtx.ai
• [x] the self-hosted CI/CD instance, cicd.rtx.ai
• [x] the webserver for downloading of the KG2c "lite" JSON file, kg2webhost.rtx.ai

GitHub access

• [x] write access to the RTXteam/PloverDB project area
• [x] write access to the RTXteam/RTX project area
• [x] write access to the ncats/translator-lfs-artifacts project area (not critical, but needed for some final archiving steps; Amy Glen and Sundar Pullela have access)

AWS access

You will need:

• [x] access to the AWS Console (you'll need an IAM username; ask Stephen Ramsey about getting one)
• [x] IAM permission to start and stop instances in EC2 via the AWS Console
• [x] access to the S3 bucket s3://rtx-kg2/ (ask Stephen Ramsey for access)

Slack workspaces

You will also need access to the following Slack workspaces:

• [x] ARAXTeam (subscribe to #deployment)
• [x] NCATSTranslator (subscribe to #devops-teamexpanderagent)

Example ssh config for setting up login into arax.ncats.io:

Host arax.ncats.io
    User stephenr
    ProxyCommand ssh -i ~/.ssh/id_rsa_long -W %h:%p [email protected]
    IdentityFile ~/.ssh/id_rsa_long
    Hostname 172.31.53.16

1. Build and load KG2c:

• [x] merge master into the branch being used for this KG2 version (which would typically be named like KG2.X.Yc). Record this issue number in the merge message.

• [x] update the four hardcoded biolink version numbers in the branch (as needed):

  • [x] in code/UI/OpenAPI/python-flask-server/openapi_server/openapi/openapi.yaml (github; local)
  • [x] in code/UI/OpenAPI/python-flask-server/KG2/openapi_server/openapi/openapi.yaml (github; local)
  • [x] in code/UI/OpenAPI/specifications/export/ARAX/1.5.0/openapi.yaml(github)
  • [x] in code/UI/OpenAPI/specifications/export/KG2/1.5.0/openapi.yaml (github)

• [x] build a new KG2c on buildkg2c.rtx.ai from the branch (how-to is here)

  • [x] before starting the build:
    • [x] make sure there is enough disk space available on arax-databases.rtx.ai (need at least 100G, ideally >120G). delete old KG2 database directories as needed (warn the team on Slack in advance).

  NOTE: For detailed deployment instructions, follow the instructions here

  • [x] to do a standard build of a new synonymizer (expected runtime: 2-4 hours), run:
    • [x] cd RTX/code/kg2c/synonymizer_build
    • [x] python build_synonymizer.py 2.X.Y v1.0 --downloadkg2pre --uploadartifacts
    • [x] after the build, run the Synonymizer pytest regression test suite:
      • [x] pytest -vs test_synonymizer.py --synonymizername node_synonymizer_v1.0_KG2.X.Y.sqlite
    • [x] make sure that node_synonymizer_v1.0_KG2.X.Y.sqlite is about 8-15 GB and its last modified date is today
    • [x] copy node_synonymizer_v1.0_KG2.X.Y.sqlite to the public S3 bucket for RTX-KG2: aws s3 cp node_synonymizer_v1.0_KG2.X.Y.sqlite s3://rtx-kg2-public/
  • [x] to do a standard full build of a new KG2c (expected runtime: 8-10 hours), run:
    • [x] cd RTX/code/kg2c
    • [x] python build_kg2c.py 2.X.Y v1.0 4.2.1 --uploadartifacts
      • NOTE: 4.2.1 is the Biolink version, please use the latest biolink version based on the KG2pre build's biolink version. Add a --test flag to the KG2c build execution to do a test build.
    • [x] after the build is done, make sure kg2c_lite.json.gz's last modified date is today (or whatever day the build was run)
  • [x] the synonymizer and KG2c artifacts should have been auto-uploaded into the proper directory on arax-databases.rtx.ai (/home/rtxconfig/KG2.X.Y) and to kg2webhost.rtx.ai (if --uploadartifacts flag during the KG2c build is set). If not, manually upload the files using scp.
  • [x] Upload the JSON-lines files (kg2c-2.X.Y-v1.0-nodes.jsonl.gz and kg2c-2.X.y-v1.0-edges.jsonl.gz) to the public S3 bucket, s3://rtx-kg2-public

• [x] load the new KG2c into neo4j at http://kg2-X-Yc.rtx.ai:7474/browser/ (how to is here)

  • [x] verify the correct KG2 version was uploaded by running this query: match (n {id:"RTX:KG2c"}) return n

• [x] update RTX/code/config_dbs.json in the branch:

  • [x] update the synonymizer version number/path
  • [x] update the fda_approved_drugs version number/path
  • [x] update the autocomplete version number/path
  • [x] update the meta_kg version number/path
  • [x] update the kg2c sqlite version number/path
  • [x] update the KG2pre and KG2c Neo4j endpoints

• [x] load the new KG2c into Plover (how-to is here)

  • [x] update config_kg2c.json in the kg2.X.Yc branch of the Plover repo to point to the new KG2.X.Yc json lines nodes and edges files on kg2webhost.rtx.ai (push this change)
  • [x] ssh [email protected]
  • [x] cd PloverDB && git pull origin kg2.X.Yc
  • [x] if you have not yet built the 2.X.Y docker image/container on this instance, run:
    • [x] bash -x run.sh (takes about an hour)
  • [x] otherwise, simply run:
    • [x] sudo docker start plovercontainer (takes about ten minutes)

• [x] verify that Plover's regression tests pass, and fix any broken tests; from any instance/computer, run:

  • [x] cd PloverDB/test
  • [x] pytest -v --endpoint https://kg2cploverN.rtx.ai:9990

• [x] update config_dbs.json in the branch for this KG2 version in the RTX repo to point to the new Plover in the plover_url_override slot

2. Rebuild downstream databases:

The following databases should be rebuilt and copies of them should be put in /home/rtxconfig/KG2.X.Y on arax-databases.rtx.ai. Please use this kind of naming format: mydatabase_v1.0_KG2.X.Y.sqlite.

• [x] NGD database (how-to is here)
  • [x] Upload the file curie_to_pmids_v1.0_KG2.X.Y.sqlite to the public S3 bucket s3://rtx-kg2-public.
• [x] Build CURIE NGD database @mohsenht
• [x] refreshed XDTD database @chunyuma
• [x] XDTD database @chunyuma (may be skipped - depends on the changes in this KG2 version)
• [x] refreshed XCRG database @chunyuma
• [x] XCRG database @chunyuma (may be skipped - depends on the changes in this KG2 version)

NOTE: As databases are rebuilt, RTX/code/config_dbs.json will need to be updated to point to their new paths! Push these changes to the branch for this KG2 version, unless the rollout of this KG2 version has already occurred, in which case you should push to master (but first follow the steps described here).

3. Update the ARAX codebase:

All code changes should go in the branch for this KG2 version!

• [x] update Expand code as needed
• [x] update any other modules as needed
• [x] test everything together:
  • [x] check out the branch and pull to get the latest changes
  • [x] then run the entire ARAX pytest suite (i.e., pytest -v)
  • [x] address any failing tests
• [x] update the KG2 and ARAX version numbers in the appropriate places (in the branch for this KG2 version)
  • [x] Bump version on line 12 in RTX/code/UI/OpenAPI/python-flask-server/openapi_server/openapi/openapi.yaml (github; local); the major and minor release numbers are kept synchronous with the TRAPI version; just bump the patch release version (least significant digit)
  • [x] Bump version on line 12 in RTX/code/UI/OpenAPI/specifications/export/ARAX/1.5.0/openapi.yaml (github; local); the first three digits are kept synchronous with the KG2 release version
  • [x] Bump version on line 4 in RTX/code/UI/OpenAPI/specifications/working/RTX_OA3_TRAPI1.4_KG2.yaml (github; local); same as for the ARAX openapi.yaml file
  • [x] Bump version on line 4 in RTX/code/UI/OpenAPI/specifications/working/RTX_OA3_TRAPI1.4_ARAX.yaml (github; local); same as for the KG2 openapi.yaml file

4. Pre-upload databases:

Before rolling out, we need to pre-upload the new databases (referenced in config_dbs.json) to arax.ncats.io and the ITRB SFTP server. These steps can be done well in advance of the rollout; it doesn't hurt anything to do them early.

• [x] make sure arax.ncats.io has at least 100G of disk space free; delete old KG2 databases to free up space as needed (before doing this, warn the team on the #deployment Slack channel on the ARAXTeam workspace)
• [x] copy the new databases from arax-databases.rtx.ai to arax.ncats.io:/translator/data/orangeboard/databases/KG2.X.Y; example for KG2.8.0:
  • [x] ssh [email protected]
  • [x] cd /translator/data/orangeboard/databases/
  • [x] mkdir -m 777 KG2.X.Y
  • [x] scp [email protected]:/home/rtxconfig/KG2.X.Y/*2.X.Y* KG2.X.Y/
• [x] upload the new databases and their md5 checksums to ITRB's SFTP server using the steps detailed here

5. Rollout new KG2c version to arax.ncats.io development endpoints

• [ ] Notify the #deployment channel in the ARAXTeam Slack workspace that you are rolling out a new version of KG2c to the various arax.ncats.io development endpoints. Provide the KG2c version number in this notification.
• [ ] for the RTXteam/RTX project, merge the master branch into the branch for this KG2 version. Record the RTX issue number (for the KG2c rollout checklist issue) in the merge message.
• [ ] for the RTXteam/RTX project, merge this KG2 version's branch back into the master branch. Record this issue number in the merge message.
• [ ] to roll master out to a specific ARAX or KG2 endpoint named /EEE, you would do the following steps:
  • [ ] If you are offsite, log into your office VPN (there are strict IP address block restrictions on client IPs that can ssh into arax.ncats.io)
  • [ ] Log in to arax.ncats.io: ssh arax.ncats.io (you previously need to have set up your username, etc. in ~/.ssh/config; see the top of this issue template for an example)
  • [ ] Enter the rtx1 container: sudo docker exec -it rtx1 bash
  • [ ] Become user rt: su - rt
  • [ ] Go to the directory of the code repo for the EEE endpoint: cd /mnt/data/orangeboard/EEE/RTX
  • [ ] Make sure it is on the master branch: git branch (should show * master)
  • [ ] Stash any updated files (this is IMPORTANT): git stash
  • [ ] Update the code: git pull origin master
  • [ ] Restore updated files: git stash pop
  • [ ] If there have been changes to requirements.txt, make sure to do pip3 install -r code/requirements.txt
  • [ ] Become superuser: exit (exiting out of your shell session as user rt should return you to a root user session)
  • [ ] Restart the service: service RTX_OpenAPI_EEE restart
  • [ ] View the STDERR logfile as the service starts up: tail -f /tmp/RTX_OpenAPI_EEE.elog
  • [ ] Test the endpoint via the web browser interface to make sure it is working
  • [ ] Query the KG2c version by entering this TRAPI query JSON into the browser UI: {"nodes": {"n00": {"ids": ["RTX:KG2c"]}}, "edges": {}} (it should return 1 result and the name of that node gives the KG2c version that is installed in the PloverDB that is being queried by the endpoint)
  • [ ] look up RTX:KG2 in the Synonyms tab in the UI
• [ ] roll master out to the various arax.ncats.io development endpoints. Usually in this order:
  • [ ] devED
  • [ ] beta
  • [ ] test
  • [ ] devLM
• [ ] inside the Docker rtx1 container, run the pytest suite on the various ARAX development endpoints (that means devED, devLM, test, and beta):
  • [ ] cd /mnt/data/orangeboard/EEE/RTX/code/ARAX/test && pytest -v
• [ ] update our CI/CD testing instance with the new databases:
  • [ ] ssh [email protected]
  • [ ] cd RTX
  • [ ] git pull origin master
  • [ ] If there have been changes to requirements.txt, make sure to do ~/venv3.9/bin/pip3 install -r requirements.txt
  • [ ] sudo bash
  • [ ] mkdir -m 777 /mnt/data/orangeboard/databases/KG2.X.Y
  • [ ] exit
  • [ ] ~/venv3.9/bin/python3 code/ARAX/ARAXQuery/ARAX_database_manager.py --mnt --skip-if-exists --remove_unused
  • [ ] run a Test Build through GitHub Actions, to ensure that the CI/CD is working with the updated databases; all of the pytest tests that are not skipped, should pass

6. Final items/clean up:

• [ ] update the current RTX GitHub changelog issue (add the rollout of this KG2 version as a changelog item)
• [ ] delete the kg2.X.Yc branch in the RTX repo (since it has been merged into master at this point)
• [ ] turn off the old KG2c version's neo4j instance (if it has not already been turned off; it is likely to have been turned off when the old KG2c was rolled out)
  • [ ] determine what is the DNS A record hostname for kg2-X-Zc.rtx.ai (where Z is one less than the new minor release version): run nslookup kg2-X-Zc.rtx.ai (it will return either kg2canonicalized.rtx.ai or kg2canonicalized2.rtx.ai; we'll call it kg2canonicalizedN.rtx.ai).
  • [ ] message the #deployment channel in the ARAXTeam Slack workspace that you will be stopping the kg2canonicalizedN.rtx.ai Neo4j endpoint
  • [ ] ssh [email protected]
  • [ ] sudo service neo4j stop
  • [ ] In the AWS console, stop the instance kg2canonicalizedN.rtx.ai
• [ ] turn off the old KG2c version's plover instance (if it has not already been turned off during the previous KG2c roll-out; under normal circumstances, we turn off the self-hosted PloverDB for the new KG2c, during clean-up)
  • [ ] Determine what is the DNS A record hostname for kg2-X-Zcplover.rtx.ai (where Z is one less than the new minor release version): run nslookup kg2-X-Zploverc.rtx.ai (it will return either kg2cplover.rtx.ai or kg2cplover3.rtx.ai; we'll call it kg2cploverN.rtx.ai).
  • [ ] message the #deployment channel in the ARAXTeam Slack workspace that you will be stopping the kg2-X-Zcplover.rtx.ai PloverDB service
  • [ ] Log into kg2cploverN.rtx.ai: ssh [email protected]
  • [ ] Stop the PloverDB container: sudo docker stop plovercontainer2.X.Z (if you are not sure of the container name, use sudo docker container ls -a to get the container name).
• [ ] turn off the new KG2pre version's Neo4j instance (Coordinate with the KG2pre team before doing this)
• [ ] deploy new PloverDB service into ITRB CI that is backed by the new KG2c database:
  • [ ] merge PloverDB main branch into kg2.X.Yc branch (if main has any commits ahead of kg2.X.Yc). Reference this issue (via its full GitHub URL) in the merge message.
  • [ ] merge PloverDB kg2.X.Yc branch into main branch. Reference this issue (via its full GitHub URL) in the merge message.
  • [ ] wait about 70 minutes for Jenkins to build the PloverDB project and deploy it to kg2cploverdb.ci.transltr.io
  • [ ] verify that the CI Plover is running the new KG2 version by:
    • [ ] going to https://kg2cploverdb.ci.transltr.io/code_version and verifying that the correct nodes and edges jsonlines files were used
    • [ ] running the following test and inspecting the command line output: cd PloverDB/test && pytest -vsk test_version --endpoint https://kg2cploverdb.ci.transltr.io
  • [ ] run the full Plover test suite to verify everything is working: cd PloverDB/test && pytest -v --endpoint https://kg2cploverdb.ci.transltr.io
  • [ ] run the ARAX pytest suite using the CI KG2 Plover (locally remove the plover_url_override in RTX/code/config_dbs.json by setting it to null)
  • [ ] if all tests pass, update RTX/code/config_dbs.json in the master branch with your local change: (plover_url_override: null)
  • [ ] push the latest master branch code commit to the various endpoints on arax.ncats.io that you previously updated (this is in order to get the changed config_dbs.json file) and restart ARAX services
  • [ ] check the Test Build (CI/CD tests) to make sure all non-skipped pytest tests have passed
  • [ ] turn off the self-hosted plover endpoint for the new version of KG2c
    • [ ] message the #deployment channel to notify people what you are about to do
    • [ ] ssh [email protected]
    • [ ] sudo docker container ls -a (gives you the name of the container; assume it is plovercontainer)
    • [ ] sudo docker stop plovercontainer
  • [ ] verify once more that ARAX is still working properly, even with the self-hosted new-KG2c-version PloverDB service turned off
  • [ ] delete the kg2.X.Yc branch in the PloverDB repo (since it has been merged into main at this point)
• [ ] upload the new kg2c_lite_2.X.Y.json.gz file to the translator-lfs-artifacts repo (ask Amy Glen or Sundar Pullela, who have permission to do this)
• [ ] Download, update, and re-upload to s3://rtx-kg2-public the index file index.html to add a new section with four hyperlinks for the four information artifacts from the new build (KG2c nodes, KG2c edges, node synonymizer, and curie-to-pmids).

[sundareswarpullela]

The clinical trials edges in the KG2.10.2pre, are missing the knowledge_level and agent_type information due to a mismatch in the infores identifier in the kg2-provided-by-curie-to-infores-curie.yaml and the knowledge-level-agent-type-map.yaml. This has since been fixed on the kg2.10.2 branch of RTXTeam/RTX-KG2 repo.

[sundareswarpullela]

The above issue has been fixed and verified that KLAT info is now present on clinical trials edges. KG2.10.2c synonymizer build has been triggered.

[sundareswarpullela]

node_synonymizer_v1.0_KG2.10.2.sqlite successfully built and uploaded to arax-databases.rtx.ai

[sundareswarpullela]

@mohsenht to build curies_ngd database for KG2.10.2c @chunyuma to build refreshed xDTD and xCRG databases for KG2.10.2c

[chunyuma]

Thanks @sundareswarpullela. I have refreshed xDTD and xCRG data and uploaded them to KG2.10.2c folder on arax-databases.rtx.ai.

[bazarkua]

I've created issue #2468 summarizing our investigations with @saramsey and @sundareswarpullela regrading NGD build and specifically curie_to_pmids.sqlite file so far. To help us keep track of this issue.

[bazarkua]

@mohsenht curie_to_pmids_v1.0_KG2.10.2.sqlite was uploaded on s3 bucket rtx-kg2-public.

[mohsenht]

Thanks @bazarkua for letting me know

[mohsenht]

Hi @bazarkua,

I have uploaded curie_ngd_v1.0_KG2.10.2 to rtxconfig server

[sundareswarpullela]

Since Erica mentioned on Slack that she uses the KG2.10.2pre endpoint regularly, we are choosing not to shut down the kg2endpoint3.rtx.ai for the time being.

[saramsey]

Well done, @sundareswarpullela and @bazarkua and the whole KG2.10.2 team!