update manifest for Gen3 Release 2020.02

[haraprasadj]

No description provided.

[PlanXCyborg]

genomel.bionimbus.org/manifest.json

Deployment changes

• arborist
  • Assuming any commons running Arborist < 2.3 was using user sync only as AuthZ provider (chore(authz): set authz_provider in migration arborist#111)
  • One-off: Update authz_provider to the correct values (Feat/authz provider arborist#109)
  • Database deployment (feat/db: add database persistence arborist#42)
  • See migrations folder for database schema and setup utilities (feat/db: add database persistence arborist#42)
• fence
  • Fence does NOT handle c999 the same as before. If using dbgap sync w/ consent code parsing and indexd records have acls with just phsid to represent objects someone w/ c999 should be able to see, you will need to ensure that the records also have the phsid.consent_code as well or users will lose access (Feat/dbgap options fence#702)
  • Fence has a new configuration to support more dbGaP syncing options: if you require "Common Exchange Area" data access, review the new configuration and supply necessary values (Feat/dbgap options fence#702)
  • Fence config ENABLED_IDENTITY_PROVIDERS section deprecated and replaced by LOGIN_OPTIONS section to allow enabling several login options for the same provider (backwards compatible) (Feat/incommon updates fence#703)
  • Requires manual work in Arborist DB to fill in the empty authz_provider fields (Synapse Integration fence#696)
  • new cloud automation job for database migration feat(jobs): fence db create job cloud-automation#977 (feat(fence-create): new migrate command to migrate the database fence#694)
  • configuration added for requester pays Google Buckets. if this is needed, you'll need to update configuration. default config does not support requester pays bucket access (Feat/requester pays fence#668)
• indexd
  • Add script to run for filling out records' authz fields based on the acl fields. (chore(authz-migration): add migration script indexd#218)
• peregrine
  • ARBORIST_URL environment variable replaces broken default ARBORIST config variable (fix(arborist-url) peregrine#142)
  • Optional configuration variable ARBORIST (arborist base URL) (Feat/arborist peregrine#138)
  • Requires Arborist to be deployed (Feat/arborist peregrine#138)
  • look for INDEX_CLIENT instead of SIGNPOST in app.config (Remove signpost peregrine#135)
  • get INDEX_CLIENT_HOST env var instead of SIGNPOST_HOST (Remove signpost peregrine#135)
• pidgin
  • added required configuration variable "API_HEALTH_URL" for status endpoint (Fix/_status pidgin#31)
  • use the latest version of the python 3 base image (Chore/bump image pidgin#29)
  • The Dockerfile now uses an Alpine image (feat(alpine-docker): use alpine image pidgin#24)
• portal
  • InCommon login needs fence 4.8.0 (uc-cdis/portal#595)
  • Need Guppy 0.3.7+ to handle large file size (uc-cdis/portal#603)
  • if deployed with "useArboristUI": true, needs Arborist's GET /auth/mapping endpoint to be exposed via revproxy. (useArboristUI false by default) (uc-cdis/portal#592)
  • New optional portal config field called adminPreAppliedFilters. Goes in data/config/*.json. (uc-cdis/portal#576)
  • For a "cert" if the required document is a quiz, then hasCorrectAnswers should be true, otherwise false. (uc-cdis/portal#571)
  • Windmill lists unmapped files by checking Indexd. Before centralized auth's deployment, a file was determined to be unmapped by checking if the acl field was null. After centralized auth, we use the authz field instead. The new manifest configuration setting use_indexd_authz in the global block specifies which of the two fields should be used. This field defaults to false. (uc-cdis/portal#570)
  • Deployed in https://qa-canine.planx-pla.net with fence version < 3, index authz field set to false (uc-cdis/portal#570)
  • (by default). (uc-cdis/portal#570)
  • Deployed in https://qa-brain.planx-pla.net with fence version > 3, index authz field set to true. (uc-cdis/portal#570)
  • New portal configuration and images for AnVIL (uc-cdis/portal#569)
  • Requires a url to be specified in dataExplorerConfig called terraExportURL (uc-cdis/portal#568)
  • This should be bvdp-saturn-${env}.appspot.com/#import-data, where ${env} is dev, staging, or prod (uc-cdis/portal#568)
  • Needs a version of cloud-automation that exposes arborist's auth/proxy endpoint (uc-cdis/portal#565)
  • fixed DAT requires Guppy >= 0.3.1 (uc-cdis/portal#563)
  • DAT requires Guppy >= 0.3.0 (uc-cdis/portal#561)
  • This change requires sower version >= 0.3.0. (uc-cdis/portal#562)
  • This PR requires feat/support is not op for filter guppy#45 (0.2.1+) if want to use Guppy for NIAID (uc-cdis/portal#558)
  • require fileExplorerConfig block with buttons (uc-cdis/portal#554)
  • New manifest.json variable: logout_inactive_users. Defaults to true if not provided. (uc-cdis/portal#526)
  • Feat/logout user opt out cloud-automation#818 (uc-cdis/portal#526)
  • enable source map tool so that developers could have better debugging under dev mode (uc-cdis/portal#514)
• sheepdog
  • Fix Travis coverage reports (combine the results of all 3 tests into one coverage report). (PXP-3408 Update Sheepdog to Python3 sheepdog#314)
  • ARBORIST_URL environment variable replaces broken default ARBORIST config variable (fix(arborist-url) sheepdog#304)
  • Optional configuration variable ARBORIST (arborist base URL) (Feat/arborist2 sheepdog#298)
  • Requires Arborist to be deployed (Feat/arborist2 sheepdog#298)
  • look for INDEX_CLIENT instead of SIGNPOST in app.config (remove signpost from sheepdog deps sheepdog#291)
  • get INDEX_CLIENT_HOST env var instead of SIGNPOST_HOST (remove signpost from sheepdog deps sheepdog#291)
  • Sheepdog will now create (or replace) the missing indexes during migration (PXD-2916: implement uniqueKeys sheepdog#259)
  • New unique indexes have been added to all nodes PXD-2916: add unique indexes for uniqueKeys gen3datamodel#12 (PXD-2916: implement uniqueKeys sheepdog#259)

[PlanXCyborg]

genomel.bionimbus.org/manifest.json

Deployment changes

• arborist
  • Assuming any commons running Arborist < 2.3 was using user sync only as AuthZ provider (chore(authz): set authz_provider in migration arborist#111)
  • One-off: Update authz_provider to the correct values (Feat/authz provider arborist#109)
  • Database deployment (feat/db: add database persistence arborist#42)
  • See migrations folder for database schema and setup utilities (feat/db: add database persistence arborist#42)
• fence
  • Fence does NOT handle c999 the same as before. If using dbgap sync w/ consent code parsing and indexd records have acls with just phsid to represent objects someone w/ c999 should be able to see, you will need to ensure that the records also have the phsid.consent_code as well or users will lose access (Feat/dbgap options fence#702)
  • Fence has a new configuration to support more dbGaP syncing options: if you require "Common Exchange Area" data access, review the new configuration and supply necessary values (Feat/dbgap options fence#702)
  • Fence config ENABLED_IDENTITY_PROVIDERS section deprecated and replaced by LOGIN_OPTIONS section to allow enabling several login options for the same provider (backwards compatible) (Feat/incommon updates fence#703)
  • Requires manual work in Arborist DB to fill in the empty authz_provider fields (Synapse Integration fence#696)
  • new cloud automation job for database migration feat(jobs): fence db create job cloud-automation#977 (feat(fence-create): new migrate command to migrate the database fence#694)
  • configuration added for requester pays Google Buckets. if this is needed, you'll need to update configuration. default config does not support requester pays bucket access (Feat/requester pays fence#668)
• indexd
  • Add script to run for filling out records' authz fields based on the acl fields. (chore(authz-migration): add migration script indexd#218)
• peregrine
  • ARBORIST_URL environment variable replaces broken default ARBORIST config variable (fix(arborist-url) peregrine#142)
  • Optional configuration variable ARBORIST (arborist base URL) (Feat/arborist peregrine#138)
  • Requires Arborist to be deployed (Feat/arborist peregrine#138)
  • look for INDEX_CLIENT instead of SIGNPOST in app.config (Remove signpost peregrine#135)
  • get INDEX_CLIENT_HOST env var instead of SIGNPOST_HOST (Remove signpost peregrine#135)
• pidgin
  • added required configuration variable "API_HEALTH_URL" for status endpoint (Fix/_status pidgin#31)
  • use the latest version of the python 3 base image (Chore/bump image pidgin#29)
  • The Dockerfile now uses an Alpine image (feat(alpine-docker): use alpine image pidgin#24)
• portal
  • InCommon login needs fence 4.8.0 (uc-cdis/portal#595)
  • Need Guppy 0.3.7+ to handle large file size (uc-cdis/portal#603)
  • if deployed with "useArboristUI": true, needs Arborist's GET /auth/mapping endpoint to be exposed via revproxy. (useArboristUI false by default) (uc-cdis/portal#592)
  • New optional portal config field called adminPreAppliedFilters. Goes in data/config/*.json. (uc-cdis/portal#576)
  • For a "cert" if the required document is a quiz, then hasCorrectAnswers should be true, otherwise false. (uc-cdis/portal#571)
  • Windmill lists unmapped files by checking Indexd. Before centralized auth's deployment, a file was determined to be unmapped by checking if the acl field was null. After centralized auth, we use the authz field instead. The new manifest configuration setting use_indexd_authz in the global block specifies which of the two fields should be used. This field defaults to false. (uc-cdis/portal#570)
  • Deployed in https://qa-canine.planx-pla.net with fence version < 3, index authz field set to false (uc-cdis/portal#570)
  • (by default). (uc-cdis/portal#570)
  • Deployed in https://qa-brain.planx-pla.net with fence version > 3, index authz field set to true. (uc-cdis/portal#570)
  • New portal configuration and images for AnVIL (uc-cdis/portal#569)
  • Requires a url to be specified in dataExplorerConfig called terraExportURL (uc-cdis/portal#568)
  • This should be bvdp-saturn-${env}.appspot.com/#import-data, where ${env} is dev, staging, or prod (uc-cdis/portal#568)
  • Needs a version of cloud-automation that exposes arborist's auth/proxy endpoint (uc-cdis/portal#565)
  • fixed DAT requires Guppy >= 0.3.1 (uc-cdis/portal#563)
  • DAT requires Guppy >= 0.3.0 (uc-cdis/portal#561)
  • This change requires sower version >= 0.3.0. (uc-cdis/portal#562)
  • This PR requires feat/support is not op for filter guppy#45 (0.2.1+) if want to use Guppy for NIAID (uc-cdis/portal#558)
  • require fileExplorerConfig block with buttons (uc-cdis/portal#554)
  • New manifest.json variable: logout_inactive_users. Defaults to true if not provided. (uc-cdis/portal#526)
  • Feat/logout user opt out cloud-automation#818 (uc-cdis/portal#526)
  • enable source map tool so that developers could have better debugging under dev mode (uc-cdis/portal#514)
• sheepdog
  • Fix Travis coverage reports (combine the results of all 3 tests into one coverage report). (PXP-3408 Update Sheepdog to Python3 sheepdog#314)
  • ARBORIST_URL environment variable replaces broken default ARBORIST config variable (fix(arborist-url) sheepdog#304)
  • Optional configuration variable ARBORIST (arborist base URL) (Feat/arborist2 sheepdog#298)
  • Requires Arborist to be deployed (Feat/arborist2 sheepdog#298)
  • look for INDEX_CLIENT instead of SIGNPOST in app.config (remove signpost from sheepdog deps sheepdog#291)
  • get INDEX_CLIENT_HOST env var instead of SIGNPOST_HOST (remove signpost from sheepdog deps sheepdog#291)
  • Sheepdog will now create (or replace) the missing indexes during migration (PXD-2916: implement uniqueKeys sheepdog#259)
  • New unique indexes have been added to all nodes PXD-2916: add unique indexes for uniqueKeys gen3datamodel#12 (PXD-2916: implement uniqueKeys sheepdog#259)

[fauzigo]

LGTM

[trevars]

lgtm, too