Gen3 Monthly Release 2021.07 qa-covid19.planx-pla.net 1625845274 #1493

themarcelor · 2021-07-09T15:41:16Z

Applying version 2021.07 to qa-covid19.planx-pla.net

…_net_1625845274

qa-covid19.planx-pla.net/manifest.json

PlanXCyborg · 2021-07-12T19:35:48Z

qa-covid19.planx-pla.net/manifest.json

Deployment changes

arborist
- Needs Fence later than 4.22.2 or 2020.08 (which introduces the new JWT scopes claim). ((PXP-6617): remove scopes from jwt aud claim arborist#130)
awshelper
- The new version of the audit service will require running gen3 kube-setup-audit-service and gen3 kube-setup-fence again, and updating the audit-service and fence configuration files (PXP-7805 Audit Service SQS cloud-automation#1603)
fence
- For existing deployments with "ENABLE_AUDIT_LOGS" turned ON, to DISABLE pushing audit logs to an AWS SQS, the configuration "PUSH_AUDIT_LOGS_CONFIG.type" must be changed to "api" (default: "aws_sqs"). If audit-service has never been deployed, no action required. (PXP-7805 Push audit logs to an AWS SQS fence#923)
- To ENABLE pushing audit logs to an AWS SQS (REQUIRES audit-service 1.0.0 or more recent), create/update the configuration file's "PUSH_AUDIT_LOGS_CONFIG" field ("type: aws_sqs" (default), and the SQS URL and region can be copied from the audit-service configuration - or run gen3 sqs info $(gen3 api safe-name audit-sqs)), see https://github.com/uc-cdis/fence/blob/fec3dd937d68384e86b2ed6f9b53daf0026c2df9/fence/config-default.yaml#L632-L636. Then run kubectl delete secret fence-config and gen3 kube-setup-fence (PXP-7805 Push audit logs to an AWS SQS fence#923)
- This commit includes patches to allow old style refresh tokens and API keys to pass new style validation, while issuing new style refresh tokens and API keys. Since refresh tokens and API keys have a default TTL of 30 days, stay on this tag for 30 days if possible. (PXP-6617 Remove scopes from aud claim in tokens fence#839)
- Old access tokens will NOT work once this is deployed so active sessions may be temporarily interrupted. (PXP-6617 Remove scopes from aud claim in tokens fence#839)
indexd
- When running gen3authz, backoff package needed separate poetry run pip install (PXP-6824: return 401 errors from Arborist indexd#304)

paulineribeyre · 2021-07-12T19:37:24Z

qa-covid19.planx-pla.net/manifest.json

-    "sheepdog": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sheepdog:2021.04",
-    "portal": "quay.io/cdis/data-portal:feat_WLSmapDataOverlays",
-    "tube": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/tube:0.5.0",
+    "covid19-bayes-model": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/covid19-bayes-model:3.4.3",


just making sure this was pushed to ECR

Yes it is pushed to ECR

PlanXCyborg · 2021-07-12T21:56:33Z

qa-covid19.planx-pla.net/manifest.json

Deployment changes

arborist
- Needs Fence later than 4.22.2 or 2020.08 (which introduces the new JWT scopes claim). ((PXP-6617): remove scopes from jwt aud claim arborist#130)
awshelper
- The new version of the audit service will require running gen3 kube-setup-audit-service and gen3 kube-setup-fence again, and updating the audit-service and fence configuration files (PXP-7805 Audit Service SQS cloud-automation#1603)
fence
- By default Fence will allow only visas issued by RAS staging, RAS prod, and itself; if a different set of allowed visa issuers is needed, edit the GA4GH_VISA_ISSUER_ALLOWLIST config value. Otherwise, no action needed. ((PXP-6339): RAS visa validation fence#933)
- /link/google will DENY requests with "redirect" param values that aren't in the "allowed redirects" for OAuth2/OIDC Clients in Fence (You have to add any valid redirects to the client before deploying this) ((PXP-8286): fix(google): add redirect validation to /link/google fence#927)
- For existing deployments with "ENABLE_AUDIT_LOGS" turned ON, to DISABLE pushing audit logs to an AWS SQS, the configuration "PUSH_AUDIT_LOGS_CONFIG.type" must be changed to "api" (default: "aws_sqs"). If audit-service has never been deployed, no action required. (PXP-7805 Push audit logs to an AWS SQS fence#923)
- To ENABLE pushing audit logs to an AWS SQS (REQUIRES audit-service 1.0.0 or more recent), create/update the configuration file's "PUSH_AUDIT_LOGS_CONFIG" field ("type: aws_sqs" (default), and the SQS URL and region can be copied from the audit-service configuration - or run gen3 sqs info $(gen3 api safe-name audit-sqs)), see https://github.com/uc-cdis/fence/blob/fec3dd937d68384e86b2ed6f9b53daf0026c2df9/fence/config-default.yaml#L632-L636. Then run kubectl delete secret fence-config and gen3 kube-setup-fence (PXP-7805 Push audit logs to an AWS SQS fence#923)
- This commit includes patches to allow old style refresh tokens and API keys to pass new style validation, while issuing new style refresh tokens and API keys. Since refresh tokens and API keys have a default TTL of 30 days, stay on this tag for 30 days if possible. (PXP-6617 Remove scopes from aud claim in tokens fence#839)
- Old access tokens will NOT work once this is deployed so active sessions may be temporarily interrupted. (PXP-6617 Remove scopes from aud claim in tokens fence#839)
indexd
- When running gen3authz, backoff package needed separate poetry run pip install (PXP-6824: return 401 errors from Arborist indexd#304)

themarcelor added 2 commits July 9, 2021 10:41

apply version 2021.07 to qa-covid19.planx-pla.net

fd89b5f

apply version 2021.07 to qa-covid19.planx-pla.net

618ab63

themarcelor requested a review from atharvar28 as a code owner July 9, 2021 15:41

themarcelor added the automerge label Jul 9, 2021

Merge branch 'master' into chore/apply_202107_to_qa-covid19_planx-pla…

5955de3

…_net_1625845274

atharvar28 removed the automerge label Jul 12, 2021

atharvar28 requested a review from paulineribeyre July 12, 2021 17:56

paulineribeyre requested changes Jul 12, 2021

View reviewed changes

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fixing the versions and urls

059be4f

atharvar28 requested a review from paulineribeyre July 12, 2021 19:32

paulineribeyre reviewed Jul 12, 2021

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paulineribeyre approved these changes Jul 12, 2021

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change the fence version

10a160c

atharvar28 merged commit ee5c0c0 into master Jul 13, 2021

atharvar28 deleted the chore/apply_202107_to_qa-covid19_planx-pla_net_1625845274 branch July 13, 2021 20:03

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Gen3 Monthly Release 2021.07 qa-covid19.planx-pla.net 1625845274 #1493

Gen3 Monthly Release 2021.07 qa-covid19.planx-pla.net 1625845274 #1493

themarcelor commented Jul 9, 2021

PlanXCyborg commented Jul 12, 2021

paulineribeyre Jul 12, 2021

atharvar28 Jul 12, 2021

PlanXCyborg commented Jul 12, 2021

Gen3 Monthly Release 2021.07 qa-covid19.planx-pla.net 1625845274 #1493

Gen3 Monthly Release 2021.07 qa-covid19.planx-pla.net 1625845274 #1493

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themarcelor commented Jul 9, 2021

PlanXCyborg commented Jul 12, 2021

qa-covid19.planx-pla.net/manifest.json

Deployment changes

paulineribeyre Jul 12, 2021

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atharvar28 Jul 12, 2021

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PlanXCyborg commented Jul 12, 2021

qa-covid19.planx-pla.net/manifest.json

Deployment changes