PXP-7947 KidsFirst prod 2021.06 + fence:5.2.1

[paulineribeyre]

Link to Jira ticket if there is one: https://ctds-planx.atlassian.net/browse/PXP-7947

in staging: #3219

Environments

KidsFirst prod

Description of changes

2021.06 + fence:5.2.1 + deploy audit-service

[PlanXCyborg]

data.kidsfirstdrc.org/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)
• 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)
  • Audit logs for user logins and data downloads can be enabled by deploying the audit-service and adding setting ENABLE_AUDIT_LOGS to the fence config (see https://github.com/uc-cdis/fence/blob/1c850d07e54f8527dbde182fdd9dd593d18f660e/fence/config-default.yaml#L586-L588) (PXP-7447 audit-service integration fence#885)
  • REQUIRES A FENCE DB MIGRATION, since with this update there is now an additional column in the authorization_code table "refresh_token_expires_in" (Feat/refresh expires in fence#848)
• indexd
  • When running gen3authz, backoff package needed separate poetry run pip install (PXP-6824: return 401 errors from Arborist indexd#304)
• portal
  • envs with customized color schemes no longer need to overwrite dictionary button color in their gitops.css ((PXP-6570): refactor/dictionaryBtnColor: change dictionary btn to use defined global colors data-portal#822)
  • New optional config property, tierAccessLevel, in each tab of the explorerConfig block in the portal config. Used to enable index-scoped tiered-access, which is only available starting with Guppy server version 0.11.0. See README for more information. (Feat/index scoped tiered access data-portal#802)
  • To deploy Discovery page: ((PXP-7402) Discovery page data-portal#803)
  • "featureFlags": { "discovery": true } must be set in the portal config. ((PXP-7402) Discovery page data-portal#803)
  • If discoveryConfig.features.authorization.enabled: true, "useArboristUI": true must be set in the portal config. ((PXP-7402) Discovery page data-portal#803)
  • "discoveryConfig": <DiscoveryConfig> must be set in the portal config. DiscoveryConfig documentation can be found at https://github.com/uc-cdis/data-portal/blob/master/docs/portal_config.md ((PXP-7402) Discovery page data-portal#803)
  • To upload data to Discovery page, data must be uploaded to environment's metadata-service instance with guid_type: "discovery_metadata". The metadata must all be under the top-level property gen3_discovery. (No documentation on this process yet, see this gist for right now https://gist.github.com/Avantol13/a53593837503fede2881f315198247c4) ((PXP-7402) Discovery page data-portal#803)
  • Added new entry GWASApp for analysisTools for this new GWAS app for VA. Beaware not to confuse with the old "GWAS PoC" app, which bears the entry vaGWAS (PXP-7296 PXP-7180 Feat/va gwas app data-portal#777)
  • antd modal now by default will use g3-color__base-blue as header background color, this is consistant with our color schemes for other UI components. If an env has customized color scheme, please override .ant-modal-header in gitops.css (PXP-7296 PXP-7180 Feat/va gwas app data-portal#777)
  • The new feature of Portal requires Guppy v0.10.0 ((PXP-6540): Feat/explorer download formats data-portal#780)
  • Added new button types in the Portal config. See portal_config.md for an example. ((PXP-6540): Feat/explorer download formats data-portal#780)